Updated coffeescript, svg export working fine, interval mapping zoom working

75 files changed, 6654 insertions, 12366 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 843862aa..2a79dc9c 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -162,14 +162,15 @@ class Markers(object):
         for marker in markers:
             if (marker['chr'] != "X") and (marker['chr'] != "Y"):
                 marker['chr'] = int(marker['chr'])
-            else:
-                marker['chr'] = 19
+            #else:
+            #    marker['chr'] = 20
             print("Mb:", marker['Mb'])
             marker['Mb'] = float(marker['Mb'])
             
         self.markers = markers
         #print("self.markers:", self.markers)
     
+    
     def add_pvalues(self, p_values):
         print("length of self.markers:", len(self.markers))
         print("length of p_values:", len(p_values))
diff --git a/wqflask/other_config/nginx_conf/penguin.conf b/wqflask/other_config/nginx_conf/penguin.conf
index 5c380da8..0a89072e 100755
--- a/wqflask/other_config/nginx_conf/penguin.conf
+++ b/wqflask/other_config/nginx_conf/penguin.conf
@@ -1,5 +1,7 @@
 server {
     # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/
+
+    client_max_body_size 20M;
     listen 80;
 
     server_name gn2python.genenetwork.org;
diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py
index a81a62b4..4ac7bde2 100755
--- a/wqflask/wqflask/interval_mapping/interval_mapping.py
+++ b/wqflask/wqflask/interval_mapping/interval_mapping.py
@@ -58,18 +58,18 @@ class IntervalMapping(object):
  
         self.json_data = {}
  
-        if self.method == "qtl_reaper":
-            self.json_data['lodnames'] = ['lod.hk']
-            self.gen_reaper_results(tempdata)
-        else:
-            self.gen_pylmm_results(tempdata)
+        #if self.method == "qtl_reaper":
+        self.json_data['lodnames'] = ['lod.hk']
+        self.gen_reaper_results(tempdata)
+        #else:
+        #    self.gen_pylmm_results(tempdata)
         #self.gen_qtl_results(tempdata)
 
         #Get chromosome lengths for drawing the interval map plot
         chromosome_mb_lengths = {}
         self.json_data['chrnames'] = []
         for key in self.species.chromosomes.chromosomes.keys():
-            self.json_data['chrnames'].append(self.species.chromosomes.chromosomes[key].name)
+            self.json_data['chrnames'].append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length])
             
             chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length
         
@@ -94,10 +94,10 @@ class IntervalMapping(object):
         #self.plot_scale = start_vars['scale']
         #if self.plotScale == 'physic' and not fd.genotype.Mbmap:
         #    self.plotScale = 'morgan'
-        self.method = start_vars['mapping_method']
+        #self.method = start_vars['mapping_method']
         self.num_permutations = int(start_vars['num_permutations'])
         #self.do_bootstrap = start_vars['do_bootstrap']
-        self.selected_chr = start_vars['chromosome']
+        #self.selected_chr = start_vars['chromosome']
         if start_vars['display_additive'] == "yes":
             self.additive = True
         else:
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index d43fe37c..30c6453c 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -1,585 +1,599 @@
-from __future__ import absolute_import, print_function, division
-
-from base.trait import GeneralTrait
-from base import data_set  #import create_dataset
-
-from pprint import pformat as pf
-
-import string
-import sys
-import datetime
-import os
-import collections
-import uuid
-
-import numpy as np
-from scipy import linalg
-
-import cPickle as pickle
-
-import simplejson as json
-
-from redis import Redis
-Redis = Redis()
-
-from flask import Flask, g
-
-from base.trait import GeneralTrait
-from base import data_set
-from base import species
-from base import webqtlConfig
-from utility import webqtlUtil
-from wqflask.my_pylmm.data import prep_data
-from wqflask.my_pylmm.pyLMM import lmm
-from wqflask.my_pylmm.pyLMM import input
-from utility import helper_functions
-from utility import Plot, Bunch
-from utility import temp_data
-
-from utility.benchmark import Bench
-
-
-class MarkerRegression(object):
-
-    def __init__(self, start_vars, temp_uuid):
-
-        helper_functions.get_species_dataset_trait(self, start_vars)
-
-        #tempdata = temp_data.TempData(temp_uuid)
-        
-        self.samples = [] # Want only ones with values
-        self.vals = []
-
-        for sample in self.dataset.group.samplelist:
-            value = start_vars['value:' + sample]
-            self.samples.append(str(sample))
-            self.vals.append(value)
- 
-        self.mapping_method = start_vars['method']
-        self.maf = start_vars['maf'] # Minor allele frequency
-        print("self.maf:", self.maf)
- 
-        if self.mapping_method == "gemma":
-            qtl_results = self.run_gemma()
-        elif self.mapping_method == "plink":
-            qtl_results = self.run_plink()
-            #print("qtl_results:", pf(qtl_results))
-        elif self.mapping_method == "pylmm":
-            print("RUNNING PYLMM")
-            #self.qtl_results = self.gen_data(tempdata)
-            qtl_results = self.gen_data(str(temp_uuid))
-        else:
-            print("RUNNING NOTHING")
-            
-        self.lod_cutoff = 2
-        self.filtered_markers = []
-        for marker in qtl_results:
-            if marker['chr'] > 0:
-                self.filtered_markers.append(marker)
-            #if marker['lod_score'] > self.lod_cutoff:
-
-                
-        #print("filtered_markers:", self.filtered_markers)
-
-        #Get chromosome lengths for drawing the manhattan plot
-        chromosome_mb_lengths = {}
-        for key in self.species.chromosomes.chromosomes.keys():
-            chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length
-        
-        self.js_data = dict(
-            this_trait = self.this_trait.name,
-            data_set = self.dataset.name,
-            maf = self.maf,
-            chromosomes = chromosome_mb_lengths,
-            qtl_results = self.filtered_markers,
-        )
-
-    def run_gemma(self):
-        """Generates p-values for each marker using GEMMA"""
-        
-        self.dataset.group.get_markers()
-        
-        #filename = webqtlUtil.genRandStr("{}_{}_".format(self.dataset.group.name, self.this_trait.name))
-        self.gen_pheno_txt_file()
-
-        os.chdir("/home/zas1024/gene/web/gemma")
-
-        gemma_command = './gemma -bfile %s -k output_%s.cXX.txt -lmm 1 -o %s_output' % (
-                                                                                                 self.dataset.group.name,
-                                                                                                 self.dataset.group.name,
-                                                                                                 self.dataset.group.name)
-        print("gemma_command:" + gemma_command)
-        
-        os.system(gemma_command)
-        
-        included_markers, p_values = self.parse_gemma_output()
-        
-        self.dataset.group.get_specified_markers(markers = included_markers)
-        
-        #for marker in self.dataset.group.markers.markers:
-        #    if marker['name'] not in included_markers:
-        #        print("marker:", marker)
-        #        self.dataset.group.markers.markers.remove(marker)
-        #        #del self.dataset.group.markers.markers[marker]
-        
-        self.dataset.group.markers.add_pvalues(p_values)
-
-        return self.dataset.group.markers.markers
-
-
-    def parse_gemma_output(self):
-        included_markers = []
-        p_values = []
-        with open("/home/zas1024/gene/web/gemma/output/{}_output.assoc.txt".format(self.dataset.group.name)) as output_file:
-            for line in output_file:
-                if line.startswith("chr"):
-                    continue
-                else:
-                    included_markers.append(line.split("\t")[1])
-                    p_values.append(float(line.split("\t")[10]))
-                    #p_values[line.split("\t")[1]] = float(line.split("\t")[10])
-        print("p_values: ", p_values)
-        return included_markers, p_values
-
-    def gen_pheno_txt_file(self):
-        """Generates phenotype file for GEMMA"""
-        
-        #with open("/home/zas1024/gene/web/gemma/tmp_pheno/{}.txt".format(filename), "w") as outfile:
-        #    for sample, i in enumerate(self.samples):
-        #        print("sample:" + str(i))
-        #        print("self.vals[i]:" + str(self.vals[sample]))
-        #        outfile.write(str(i) + "\t" + str(self.vals[sample]) + "\n")
-                
-        with open("/home/zas1024/gene/web/gemma/{}.fam".format(self.dataset.group.name), "w") as outfile:
-            for i, sample in enumerate(self.samples):
-                outfile.write(str(sample) + " " + str(sample) + " 0 0 0 " + str(self.vals[i]) + "\n")
-
-    #def gen_plink_for_gemma(self, filename):
-    #    
-    #    make_bed = "/home/zas1024/plink/plink --file /home/zas1024/plink/%s --noweb --no-fid --no-parents --no-sex --no-pheno --pheno %s%s.txt --out %s%s --make-bed" % (webqtlConfig.HTMLPATH,
-    #                                                                                                                                             webqtlConfig.HTMLPATH,
-    #                                                                                                                                             self.dataset.group.name,
-    #                                                                                                                                             webqtlConfig.TMPDIR,
-    #                                                                                                                                             filename,
-    #                                                                                                                                             webqtlConfig.TMPDIR,
-    #                                                                                                                                             filename)
-    #
-    #
-    
-    def run_plink(self):
-    
-        os.chdir("/home/zas1024/plink")
-        
-        self.dataset.group.get_markers()
-        
-        plink_output_filename = webqtlUtil.genRandStr("%s_%s_"%(self.dataset.group.name, self.this_trait.name))
-        
-        self.gen_pheno_txt_file_plink(pheno_filename = plink_output_filename)
-        
-        plink_command = './plink --noweb --ped %s.ped --no-fid --no-parents --no-sex --no-pheno --map %s.map --pheno %s/%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (self.dataset.group.name, self.dataset.group.name, webqtlConfig.TMPDIR, plink_output_filename, self.this_trait.name, self.maf, webqtlConfig.TMPDIR, plink_output_filename)
-        
-        os.system(plink_command)
-
-        count, p_values = self.parse_plink_output(plink_output_filename)
-        #gemma_command = './gemma -bfile %s -k output_%s.cXX.txt -lmm 1 -o %s_output' % (
-        #                                                                                         self.dataset.group.name,
-        #                                                                                         self.dataset.group.name,
-        #                                                                                         self.dataset.group.name)
-        #print("gemma_command:" + gemma_command)
-        #
-        #os.system(gemma_command)
-        #
-        #included_markers, p_values = self.parse_gemma_output()
-        #
-        #self.dataset.group.get_specified_markers(markers = included_markers)
-        
-        #for marker in self.dataset.group.markers.markers:
-        #    if marker['name'] not in included_markers:
-        #        print("marker:", marker)
-        #        self.dataset.group.markers.markers.remove(marker)
-        #        #del self.dataset.group.markers.markers[marker]
-        
-        print("p_values:", pf(p_values))
-        
-        self.dataset.group.markers.add_pvalues(p_values)
-
-        return self.dataset.group.markers.markers
-    
-    
-    def gen_pheno_txt_file_plink(self, pheno_filename = ''):
-        ped_sample_list = self.get_samples_from_ped_file()	
-        output_file = open("%s%s.txt" % (webqtlConfig.TMPDIR, pheno_filename), "wb")
-        header = 'FID\tIID\t%s\n' % self.this_trait.name
-        output_file.write(header)
-    
-        new_value_list = []
-        
-        #if valueDict does not include some strain, value will be set to -9999 as missing value
-        for i, sample in enumerate(ped_sample_list):
-            try:
-                value = self.vals[i]
-                value = str(value).replace('value=','')
-                value = value.strip()
-            except:
-                value = -9999
-    
-            new_value_list.append(value)
-            
-            
-        new_line = ''
-        for i, sample in enumerate(ped_sample_list):
-            j = i+1
-            value = new_value_list[i]
-            new_line += '%s\t%s\t%s\n'%(sample, sample, value)
-            
-            if j%1000 == 0:
-                output_file.write(newLine)
-                new_line = ''
-        
-        if new_line:
-            output_file.write(new_line)
-            
-        output_file.close()
-    
-    # get strain name from ped file in order
-    def get_samples_from_ped_file(self):
-        
-        os.chdir("/home/zas1024/plink")
-        
-        ped_file= open("{}.ped".format(self.dataset.group.name),"r")
-        line = ped_file.readline()
-        sample_list=[]
-        
-        while line:
-            lineList = string.split(string.strip(line), '\t')
-            lineList = map(string.strip, lineList)
-            
-            sample_name = lineList[0]
-            sample_list.append(sample_name)
-            
-            line = ped_file.readline()
-        
-        return sample_list
-    
-    ################################################################
-    # Generate Chr list, Chr OrderId and Retrieve Length Information 
-    ################################################################		
-    #def getChrNameOrderIdLength(self,RISet=''):
-    #    try:
-    #        query = """
-    #            Select
-    #                Chr_Length.Name,Chr_Length.OrderId,Length from Chr_Length, InbredSet
-    #            where
-    #                Chr_Length.SpeciesId = InbredSet.SpeciesId AND
-    #                InbredSet.Name = '%s' 
-    #            Order by OrderId
-    #            """ % (self.dataset.group.name)
-    #        results =g.db.execute(query).fetchall()
-    #        ChrList=[]
-    #        ChrLengthMbList=[]
-    #        ChrNameOrderIdDict={}
-    #        ChrOrderIdNameDict={}
-    #        
-    #        for item in results:
-    #            ChrList.append(item[0])
-    #            ChrNameOrderIdDict[item[0]]=item[1] # key is chr name, value is orderId
-    #            ChrOrderIdNameDict[item[1]]=item[0] # key is orderId, value is chr name
-    #            ChrLengthMbList.append(item[2])				
-    #            
-    #    except:
-    #        ChrList=[]
-    #        ChrNameOrderIdDict={}
-    #        ChrLengthMbList=[]
-    #        
-    #    return ChrList,ChrNameOrderIdDict,ChrOrderIdNameDict,ChrLengthMbList
-    
-    
-    def parse_plink_output(self, output_filename):
-        plink_results={}
-    
-        threshold_p_value = 0.01
-    
-        result_fp = open("%s%s.qassoc"% (webqtlConfig.TMPDIR, output_filename), "rb")
-        
-        header_line = result_fp.readline()# read header line
-        line = result_fp.readline()
-        
-        value_list = [] # initialize value list, this list will include snp, bp and pvalue info
-        p_value_dict = {}
-        count = 0
-        
-        while line:
-            #convert line from str to list
-            line_list = self.build_line_list(line=line)
-    
-            # only keep the records whose chromosome name is in db
-            if self.species.chromosomes.chromosomes.has_key(int(line_list[0])) and line_list[-1] and line_list[-1].strip()!='NA':
-    
-                chr_name = self.species.chromosomes.chromosomes[int(line_list[0])]
-                snp = line_list[1]
-                BP = line_list[2]
-                p_value = float(line_list[-1])
-                if threshold_p_value >= 0 and threshold_p_value <= 1:
-                    if p_value < threshold_p_value:
-                        p_value_dict[snp] = p_value
-                
-                if plink_results.has_key(chr_name):
-                    value_list = plink_results[chr_name]
-                    
-                    # pvalue range is [0,1]
-                    if threshold_p_value >=0 and threshold_p_value <= 1:
-                        if p_value < threshold_p_value:
-                            value_list.append((snp, BP, p_value))
-                            count += 1
-                    
-                    plink_results[chr_name] = value_list
-                    value_list = []
-                else:
-                    if threshold_p_value >= 0 and threshold_p_value <= 1:
-                        if p_value < threshold_p_value:
-                            value_list.append((snp, BP, p_value))
-                            count += 1
-
-                    if value_list:
-                        plink_results[chr_name] = value_list
-
-                    value_list=[]
-
-                line = result_fp.readline()
-            else:
-                line = result_fp.readline()
-
-        #if p_value_list:
-        #    min_p_value = min(p_value_list)
-        #else:
-        #    min_p_value = 0
-            
-        return count, p_value_dict
-    
-    ######################################################
-    # input: line: str,one line read from file
-    # function: convert line from str to list; 
-    # output: lineList list
-    #######################################################
-    def build_line_list(self, line=None):
-        
-        line_list = string.split(string.strip(line),' ')# irregular number of whitespaces between columns
-        line_list = [item for item in line_list if item <>'']
-        line_list = map(string.strip, line_list)
-    
-        return line_list
-    
-    #def gen_data(self, tempdata):
-    def gen_data(self, temp_uuid):
-        """Generates p-values for each marker"""
-
-        self.dataset.group.get_markers()
-
-        pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals])
-
-        #lmm_uuid = str(uuid.uuid4())
-
-        key = "pylmm:input:" + temp_uuid
-        print("key is:", pf(key))
-        #with Bench("Loading cache"):
-        #    result = Redis.get(key)
-
-        if self.dataset.group.species == "human":
-            p_values, t_stats = self.gen_human_results(pheno_vector, key, temp_uuid)
-            #p_values = self.trim_results(p_values)
-            
-        else:
-            print("NOW CWD IS:", os.getcwd())
-            genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers]
-            
-            no_val_samples = self.identify_empty_samples()
-            trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)
-            
-            genotype_matrix = np.array(trimmed_genotype_data).T
-
-            #print("pheno_vector: ", pf(pheno_vector))
-            #print("genotype_matrix: ", pf(genotype_matrix))
-            #print("genotype_matrix.shape: ", pf(genotype_matrix.shape))
-
-            #params = {"pheno_vector": pheno_vector,
-            #            "genotype_matrix": genotype_matrix,
-            #            "restricted_max_likelihood": True,
-            #            "refit": False,
-            #            "temp_data": tempdata}
-            
-            params = dict(pheno_vector = pheno_vector.tolist(),
-                        genotype_matrix = genotype_matrix.tolist(),
-                        restricted_max_likelihood = True,
-                        refit = False,
-                        temp_uuid = temp_uuid,
-                        
-                        # meta data
-                        timestamp = datetime.datetime.now().isoformat(),
-                        )
-            
-            json_params = json.dumps(params)
-            #print("json_params:", json_params)
-            Redis.set(key, json_params)
-            Redis.expire(key, 60*60)
-            print("before printing command")
-
-            command = 'python /home/zas1024/gene/wqflask/wqflask/my_pylmm/pyLMM/lmm.py --key {} --species {}'.format(key,
-                                                                                                                    "other")
-            print("command is:", command)
-            print("after printing command")
-
-            os.system(command)
-
-            #t_stats, p_values = lmm.run(key)
-            #lmm.run(key)
-            
-            json_results = Redis.blpop("pylmm:results:" + temp_uuid, 45*60)
-            results = json.loads(json_results[1])
-            p_values = [float(result) for result in results['p_values']]
-            print("p_values:", p_values)
-            #p_values = self.trim_results(p_values)
-            t_stats = results['t_stats']
-            
-            #t_stats, p_values = lmm.run(
-            #    pheno_vector,
-            #    genotype_matrix,
-            #    restricted_max_likelihood=True,
-            #    refit=False,
-            #    temp_data=tempdata
-            #)
-            #print("p_values:", p_values)
-
-        self.dataset.group.markers.add_pvalues(p_values)
-        
-        #self.get_lod_score_cutoff()
-        
-        return self.dataset.group.markers.markers
-
-    def trim_results(self, p_values):
-        print("len_p_values:", len(p_values))
-        if len(p_values) > 500:
-            p_values.sort(reverse=True)
-            trimmed_values = p_values[:500]
-        
-        return trimmed_values
-
-    #def gen_human_results(self, pheno_vector, tempdata):
-    def gen_human_results(self, pheno_vector, key, temp_uuid):
-        file_base = os.path.join(webqtlConfig.PYLMM_PATH, self.dataset.group.name)
-
-        plink_input = input.plink(file_base, type='b')
-        input_file_name = os.path.join(webqtlConfig.SNP_PATH, self.dataset.group.name + ".snps.gz")
-
-        pheno_vector = pheno_vector.reshape((len(pheno_vector), 1))
-        covariate_matrix = np.ones((pheno_vector.shape[0],1))
-        kinship_matrix = np.fromfile(open(file_base + '.kin','r'),sep=" ")
-        kinship_matrix.resize((len(plink_input.indivs),len(plink_input.indivs)))
-
-        print("Before creating params")
-
-        params = dict(pheno_vector = pheno_vector.tolist(),
-                    covariate_matrix = covariate_matrix.tolist(),
-                    input_file_name = input_file_name,
-                    kinship_matrix = kinship_matrix.tolist(),
-                    refit = False,
-                    temp_uuid = temp_uuid,
-                        
-                    # meta data
-                    timestamp = datetime.datetime.now().isoformat(),
-                    )
-        
-        print("After creating params")
-        
-        json_params = json.dumps(params)
-        Redis.set(key, json_params)
-        Redis.expire(key, 60*60)
-
-        print("Before creating the command")
-
-        command = 'python /home/zas1024/gene/wqflask/wqflask/my_pylmm/pyLMM/lmm.py --key {} --species {}'.format(key,
-                                                                                                                "human")
-        
-        print("command is:", command)
-        
-        os.system(command)
-        
-        json_results = Redis.blpop("pylmm:results:" + temp_uuid, 45*60)
-        results = json.loads(json_results[1])
-        t_stats = results['t_stats']
-        p_values = results['p_values']
-        
-
-        #p_values, t_stats = lmm.run_human(key)
-
-        #p_values, t_stats = lmm.run_human(
-        #        pheno_vector,
-        #        covariate_matrix,
-        #        input_file_name,
-        #        kinship_matrix,
-        #        loading_progress=tempdata
-        #    )
-
-        return p_values, t_stats
-
-    def get_lod_score_cutoff(self):
-        print("INSIDE GET LOD CUTOFF")
-        high_qtl_count = 0
-        for marker in self.dataset.group.markers.markers:
-            if marker['lod_score'] > 1:
-                high_qtl_count += 1
-
-        if high_qtl_count > 1000:
-            return 1
-        else:
-            return 0
-
-    def identify_empty_samples(self):
-        no_val_samples = []
-        for sample_count, val in enumerate(self.vals):
-            if val == "x":
-                no_val_samples.append(sample_count)
-        return no_val_samples
-        
-    def trim_genotypes(self, genotype_data, no_value_samples):
-        trimmed_genotype_data = []
-        for marker in genotype_data:
-            new_genotypes = []
-            for item_count, genotype in enumerate(marker):
-                if item_count in no_value_samples:
-                    continue
-                try:
-                    genotype = float(genotype)
-                except ValueError:
-                    genotype = np.nan
-                    pass
-                new_genotypes.append(genotype)
-            trimmed_genotype_data.append(new_genotypes)
-        return trimmed_genotype_data
-    
-def create_snp_iterator_file(group):
-    plink_file_base = os.path.join(webqtlConfig.PYLMM_PATH, group)
-    plink_input = input.plink(plink_file_base, type='b')
-    
-    data = dict(plink_input = list(plink_input),
-                numSNPs = plink_input.numSNPs)
-    
-    #input_dict = {}
-    #
-    #input_dict['plink_input'] = list(plink_input)
-    #input_dict['numSNPs'] = plink_input.numSNPs
-    #
-    
-    snp_file_base = os.path.join(webqtlConfig.SNP_PATH, group + ".snps.gz")
-    
-    with gzip.open(snp_file_base, "wb") as fh:
-        pickle.dump(data, fh, pickle.HIGHEST_PROTOCOL)
-
-#if __name__ == '__main__':
-#    import cPickle as pickle
-#    import gzip
-#    create_snp_iterator_file("HLC")
-    
-if __name__ == '__main__':
-    import cPickle as pickle
-    import gzip
-    create_snp_iterator_file("HLC")
+from __future__ import absolute_import, print_function, division

+

+from base.trait import GeneralTrait

+from base import data_set  #import create_dataset

+

+from pprint import pformat as pf

+

+import string

+import sys

+import datetime

+import os

+import collections

+import uuid

+

+import numpy as np

+from scipy import linalg

+

+import cPickle as pickle

+

+import simplejson as json

+

+from redis import Redis

+Redis = Redis()

+

+from flask import Flask, g

+

+from base.trait import GeneralTrait

+from base import data_set

+from base import species

+from base import webqtlConfig

+from utility import webqtlUtil

+from wqflask.my_pylmm.data import prep_data

+from wqflask.my_pylmm.pyLMM import lmm

+from wqflask.my_pylmm.pyLMM import input

+from utility import helper_functions

+from utility import Plot, Bunch

+from utility import temp_data

+

+from utility.benchmark import Bench

+

+

+class MarkerRegression(object):

+

+    def __init__(self, start_vars, temp_uuid):

+

+        helper_functions.get_species_dataset_trait(self, start_vars)

+

+        #tempdata = temp_data.TempData(temp_uuid)

+        

+        self.json_data = {}

+        self.json_data['lodnames'] = ['lod.hk']

+        

+        self.samples = [] # Want only ones with values

+        self.vals = []

+

+        for sample in self.dataset.group.samplelist:

+            value = start_vars['value:' + sample]

+            self.samples.append(str(sample))

+            self.vals.append(value)

+ 

+        self.mapping_method = start_vars['method']

+        self.maf = start_vars['maf'] # Minor allele frequency

+        print("self.maf:", self.maf)

+ 

+        self.dataset.group.get_markers()

+        if self.mapping_method == "gemma":

+            qtl_results = self.run_gemma()

+        elif self.mapping_method == "plink":

+            qtl_results = self.run_plink()

+            #print("qtl_results:", pf(qtl_results))

+        elif self.mapping_method == "pylmm":

+            print("RUNNING PYLMM")

+            #self.qtl_results = self.gen_data(tempdata)

+            qtl_results = self.gen_data(str(temp_uuid))

+        else:

+            print("RUNNING NOTHING")

+            

+        self.lod_cutoff = 2    

+        self.filtered_markers = []

+        for marker in qtl_results:

+            if marker['chr'] > 0 or marker['chr'] == "X" or marker['chr'] == "X/Y":

+                if 'lod_score' in marker:

+                    self.filtered_markers.append(marker)

+

+

+        self.json_data['chr'] = []

+        self.json_data['pos'] = []

+        self.json_data['lod.hk'] = []

+        self.json_data['markernames'] = []

+

+        #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary

+        self.qtl_results = []

+        for qtl in self.filtered_markers:

+            print("lod score is:", qtl['lod_score'])

+            self.json_data['chr'].append(str(qtl['chr']))

+            self.json_data['pos'].append(qtl['Mb'])

+            self.json_data['lod.hk'].append(str(qtl['lod_score']))

+            self.json_data['markernames'].append(qtl['name'])

+

+        #Get chromosome lengths for drawing the interval map plot

+        chromosome_mb_lengths = {}

+        self.json_data['chrnames'] = []

+        for key in self.species.chromosomes.chromosomes.keys():

+            self.json_data['chrnames'].append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length])

+            

+            chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length

+        

+        self.js_data = dict(

+            json_data = self.json_data,

+            this_trait = self.this_trait.name,

+            data_set = self.dataset.name,

+            maf = self.maf,

+            chromosomes = chromosome_mb_lengths,

+            qtl_results = self.filtered_markers,

+        )

+

+    def run_gemma(self):

+        """Generates p-values for each marker using GEMMA"""

+        

+        #filename = webqtlUtil.genRandStr("{}_{}_".format(self.dataset.group.name, self.this_trait.name))

+        self.gen_pheno_txt_file()

+

+        os.chdir("/home/zas1024/gene/web/gemma")

+

+        gemma_command = './gemma -bfile %s -k output_%s.cXX.txt -lmm 1 -o %s_output' % (

+                                                                                                 self.dataset.group.name,

+                                                                                                 self.dataset.group.name,

+                                                                                                 self.dataset.group.name)

+        print("gemma_command:" + gemma_command)

+        

+        os.system(gemma_command)

+        

+        included_markers, p_values = self.parse_gemma_output()

+        

+        self.dataset.group.get_specified_markers(markers = included_markers)

+        

+        #for marker in self.dataset.group.markers.markers:

+        #    if marker['name'] not in included_markers:

+        #        print("marker:", marker)

+        #        self.dataset.group.markers.markers.remove(marker)

+        #        #del self.dataset.group.markers.markers[marker]

+        

+        self.dataset.group.markers.add_pvalues(p_values)

+

+        return self.dataset.group.markers.markers

+

+

+    def parse_gemma_output(self):

+        included_markers = []

+        p_values = []

+        with open("/home/zas1024/gene/web/gemma/output/{}_output.assoc.txt".format(self.dataset.group.name)) as output_file:

+            for line in output_file:

+                if line.startswith("chr"):

+                    continue

+                else:

+                    included_markers.append(line.split("\t")[1])

+                    p_values.append(float(line.split("\t")[10]))

+                    #p_values[line.split("\t")[1]] = float(line.split("\t")[10])

+        print("p_values: ", p_values)

+        return included_markers, p_values

+

+    def gen_pheno_txt_file(self):

+        """Generates phenotype file for GEMMA"""

+        

+        #with open("/home/zas1024/gene/web/gemma/tmp_pheno/{}.txt".format(filename), "w") as outfile:

+        #    for sample, i in enumerate(self.samples):

+        #        print("sample:" + str(i))

+        #        print("self.vals[i]:" + str(self.vals[sample]))

+        #        outfile.write(str(i) + "\t" + str(self.vals[sample]) + "\n")

+                

+        with open("/home/zas1024/gene/web/gemma/{}.fam".format(self.dataset.group.name), "w") as outfile:

+            for i, sample in enumerate(self.samples):

+                outfile.write(str(sample) + " " + str(sample) + " 0 0 0 " + str(self.vals[i]) + "\n")

+

+    #def gen_plink_for_gemma(self, filename):

+    #    

+    #    make_bed = "/home/zas1024/plink/plink --file /home/zas1024/plink/%s --noweb --no-fid --no-parents --no-sex --no-pheno --pheno %s%s.txt --out %s%s --make-bed" % (webqtlConfig.HTMLPATH,

+    #                                                                                                                                             webqtlConfig.HTMLPATH,

+    #                                                                                                                                             self.dataset.group.name,

+    #                                                                                                                                             webqtlConfig.TMPDIR,

+    #                                                                                                                                             filename,

+    #                                                                                                                                             webqtlConfig.TMPDIR,

+    #                                                                                                                                             filename)

+    #

+    #

+    

+    def run_plink(self):

+    

+        os.chdir("/home/zas1024/plink")

+        

+        plink_output_filename = webqtlUtil.genRandStr("%s_%s_"%(self.dataset.group.name, self.this_trait.name))

+        

+        self.gen_pheno_txt_file_plink(pheno_filename = plink_output_filename)

+        

+        plink_command = './plink --noweb --ped %s.ped --no-fid --no-parents --no-sex --no-pheno --map %s.map --pheno %s/%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (self.dataset.group.name, self.dataset.group.name, webqtlConfig.TMPDIR, plink_output_filename, self.this_trait.name, self.maf, webqtlConfig.TMPDIR, plink_output_filename)

+        

+        os.system(plink_command)

+

+        count, p_values = self.parse_plink_output(plink_output_filename)

+        #gemma_command = './gemma -bfile %s -k output_%s.cXX.txt -lmm 1 -o %s_output' % (

+        #                                                                                         self.dataset.group.name,

+        #                                                                                         self.dataset.group.name,

+        #                                                                                         self.dataset.group.name)

+        #print("gemma_command:" + gemma_command)

+        #

+        #os.system(gemma_command)

+        #

+        #included_markers, p_values = self.parse_gemma_output()

+        #

+        #self.dataset.group.get_specified_markers(markers = included_markers)

+        

+        #for marker in self.dataset.group.markers.markers:

+        #    if marker['name'] not in included_markers:

+        #        print("marker:", marker)

+        #        self.dataset.group.markers.markers.remove(marker)

+        #        #del self.dataset.group.markers.markers[marker]

+        

+        print("p_values:", pf(p_values))

+        

+        self.dataset.group.markers.add_pvalues(p_values)

+

+        return self.dataset.group.markers.markers

+    

+    

+    def gen_pheno_txt_file_plink(self, pheno_filename = ''):

+        ped_sample_list = self.get_samples_from_ped_file()	

+        output_file = open("%s%s.txt" % (webqtlConfig.TMPDIR, pheno_filename), "wb")

+        header = 'FID\tIID\t%s\n' % self.this_trait.name

+        output_file.write(header)

+    

+        new_value_list = []

+        

+        #if valueDict does not include some strain, value will be set to -9999 as missing value

+        for i, sample in enumerate(ped_sample_list):

+            try:

+                value = self.vals[i]

+                value = str(value).replace('value=','')

+                value = value.strip()

+            except:

+                value = -9999

+    

+            new_value_list.append(value)

+            

+            

+        new_line = ''

+        for i, sample in enumerate(ped_sample_list):

+            j = i+1

+            value = new_value_list[i]

+            new_line += '%s\t%s\t%s\n'%(sample, sample, value)

+            

+            if j%1000 == 0:

+                output_file.write(newLine)

+                new_line = ''

+        

+        if new_line:

+            output_file.write(new_line)

+            

+        output_file.close()

+    

+    # get strain name from ped file in order

+    def get_samples_from_ped_file(self):

+        

+        os.chdir("/home/zas1024/plink")

+        

+        ped_file= open("{}.ped".format(self.dataset.group.name),"r")

+        line = ped_file.readline()

+        sample_list=[]

+        

+        while line:

+            lineList = string.split(string.strip(line), '\t')

+            lineList = map(string.strip, lineList)

+            

+            sample_name = lineList[0]

+            sample_list.append(sample_name)

+            

+            line = ped_file.readline()

+        

+        return sample_list

+    

+    ################################################################

+    # Generate Chr list, Chr OrderId and Retrieve Length Information 

+    ################################################################		

+    #def getChrNameOrderIdLength(self,RISet=''):

+    #    try:

+    #        query = """

+    #            Select

+    #                Chr_Length.Name,Chr_Length.OrderId,Length from Chr_Length, InbredSet

+    #            where

+    #                Chr_Length.SpeciesId = InbredSet.SpeciesId AND

+    #                InbredSet.Name = '%s' 

+    #            Order by OrderId

+    #            """ % (self.dataset.group.name)

+    #        results =g.db.execute(query).fetchall()

+    #        ChrList=[]

+    #        ChrLengthMbList=[]

+    #        ChrNameOrderIdDict={}

+    #        ChrOrderIdNameDict={}

+    #        

+    #        for item in results:

+    #            ChrList.append(item[0])

+    #            ChrNameOrderIdDict[item[0]]=item[1] # key is chr name, value is orderId

+    #            ChrOrderIdNameDict[item[1]]=item[0] # key is orderId, value is chr name

+    #            ChrLengthMbList.append(item[2])				

+    #            

+    #    except:

+    #        ChrList=[]

+    #        ChrNameOrderIdDict={}

+    #        ChrLengthMbList=[]

+    #        

+    #    return ChrList,ChrNameOrderIdDict,ChrOrderIdNameDict,ChrLengthMbList

+    

+    

+    def parse_plink_output(self, output_filename):

+        plink_results={}

+    

+        threshold_p_value = 0.01

+    

+        result_fp = open("%s%s.qassoc"% (webqtlConfig.TMPDIR, output_filename), "rb")

+        

+        header_line = result_fp.readline()# read header line

+        line = result_fp.readline()

+        

+        value_list = [] # initialize value list, this list will include snp, bp and pvalue info

+        p_value_dict = {}

+        count = 0

+        

+        while line:

+            #convert line from str to list

+            line_list = self.build_line_list(line=line)

+    

+            # only keep the records whose chromosome name is in db

+            if self.species.chromosomes.chromosomes.has_key(int(line_list[0])) and line_list[-1] and line_list[-1].strip()!='NA':

+    

+                chr_name = self.species.chromosomes.chromosomes[int(line_list[0])]

+                snp = line_list[1]

+                BP = line_list[2]

+                p_value = float(line_list[-1])

+                if threshold_p_value >= 0 and threshold_p_value <= 1:

+                    if p_value < threshold_p_value:

+                        p_value_dict[snp] = p_value

+                

+                if plink_results.has_key(chr_name):

+                    value_list = plink_results[chr_name]

+                    

+                    # pvalue range is [0,1]

+                    if threshold_p_value >=0 and threshold_p_value <= 1:

+                        if p_value < threshold_p_value:

+                            value_list.append((snp, BP, p_value))

+                            count += 1

+                    

+                    plink_results[chr_name] = value_list

+                    value_list = []

+                else:

+                    if threshold_p_value >= 0 and threshold_p_value <= 1:

+                        if p_value < threshold_p_value:

+                            value_list.append((snp, BP, p_value))

+                            count += 1

+

+                    if value_list:

+                        plink_results[chr_name] = value_list

+

+                    value_list=[]

+

+                line = result_fp.readline()

+            else:

+                line = result_fp.readline()

+

+        #if p_value_list:

+        #    min_p_value = min(p_value_list)

+        #else:

+        #    min_p_value = 0

+            

+        return count, p_value_dict

+    

+    ######################################################

+    # input: line: str,one line read from file

+    # function: convert line from str to list; 

+    # output: lineList list

+    #######################################################

+    def build_line_list(self, line=None):

+        

+        line_list = string.split(string.strip(line),' ')# irregular number of whitespaces between columns

+        line_list = [item for item in line_list if item <>'']

+        line_list = map(string.strip, line_list)

+    

+        return line_list

+    

+    #def gen_data(self, tempdata):

+    def gen_data(self, temp_uuid):

+        """Generates p-values for each marker"""

+

+        pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals])

+

+        #lmm_uuid = str(uuid.uuid4())

+

+        key = "pylmm:input:" + temp_uuid

+        print("key is:", pf(key))

+        #with Bench("Loading cache"):

+        #    result = Redis.get(key)

+

+        if self.dataset.group.species == "human":

+            p_values, t_stats = self.gen_human_results(pheno_vector, key, temp_uuid)

+            #p_values = self.trim_results(p_values)

+            

+        else:

+            print("NOW CWD IS:", os.getcwd())

+            genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers]

+            

+            no_val_samples = self.identify_empty_samples()

+            trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)

+            

+            genotype_matrix = np.array(trimmed_genotype_data).T

+

+            #print("pheno_vector: ", pf(pheno_vector))

+            #print("genotype_matrix: ", pf(genotype_matrix))

+            #print("genotype_matrix.shape: ", pf(genotype_matrix.shape))

+

+            #params = {"pheno_vector": pheno_vector,

+            #            "genotype_matrix": genotype_matrix,

+            #            "restricted_max_likelihood": True,

+            #            "refit": False,

+            #            "temp_data": tempdata}

+            

+            params = dict(pheno_vector = pheno_vector.tolist(),

+                        genotype_matrix = genotype_matrix.tolist(),

+                        restricted_max_likelihood = True,

+                        refit = False,

+                        temp_uuid = temp_uuid,

+                        

+                        # meta data

+                        timestamp = datetime.datetime.now().isoformat(),

+                        )

+            

+            json_params = json.dumps(params)

+            #print("json_params:", json_params)

+            Redis.set(key, json_params)

+            Redis.expire(key, 60*60)

+            print("before printing command")

+

+            command = 'python /home/zas1024/gene/wqflask/wqflask/my_pylmm/pyLMM/lmm.py --key {} --species {}'.format(key,

+                                                                                                                    "other")

+            print("command is:", command)

+            print("after printing command")

+

+            os.system(command)

+

+            #t_stats, p_values = lmm.run(key)

+            #lmm.run(key)

+            

+            json_results = Redis.blpop("pylmm:results:" + temp_uuid, 45*60)

+            results = json.loads(json_results[1])

+            p_values = [float(result) for result in results['p_values']]

+            print("p_values:", p_values)

+            #p_values = self.trim_results(p_values)

+            t_stats = results['t_stats']

+            

+            #t_stats, p_values = lmm.run(

+            #    pheno_vector,

+            #    genotype_matrix,

+            #    restricted_max_likelihood=True,

+            #    refit=False,

+            #    temp_data=tempdata

+            #)

+            #print("p_values:", p_values)

+

+        self.dataset.group.markers.add_pvalues(p_values)

+        

+        #self.get_lod_score_cutoff()

+        

+        return self.dataset.group.markers.markers

+

+    def trim_results(self, p_values):

+        print("len_p_values:", len(p_values))

+        if len(p_values) > 500:

+            p_values.sort(reverse=True)

+            trimmed_values = p_values[:500]

+        

+        return trimmed_values

+

+    #def gen_human_results(self, pheno_vector, tempdata):

+    def gen_human_results(self, pheno_vector, key, temp_uuid):

+        file_base = os.path.join(webqtlConfig.PYLMM_PATH, self.dataset.group.name)

+

+        plink_input = input.plink(file_base, type='b')

+        input_file_name = os.path.join(webqtlConfig.SNP_PATH, self.dataset.group.name + ".snps.gz")

+

+        pheno_vector = pheno_vector.reshape((len(pheno_vector), 1))

+        covariate_matrix = np.ones((pheno_vector.shape[0],1))

+        kinship_matrix = np.fromfile(open(file_base + '.kin','r'),sep=" ")

+        kinship_matrix.resize((len(plink_input.indivs),len(plink_input.indivs)))

+

+        print("Before creating params")

+

+        params = dict(pheno_vector = pheno_vector.tolist(),

+                    covariate_matrix = covariate_matrix.tolist(),

+                    input_file_name = input_file_name,

+                    kinship_matrix = kinship_matrix.tolist(),

+                    refit = False,

+                    temp_uuid = temp_uuid,

+                        

+                    # meta data

+                    timestamp = datetime.datetime.now().isoformat(),

+                    )

+        

+        print("After creating params")

+        

+        json_params = json.dumps(params)

+        Redis.set(key, json_params)

+        Redis.expire(key, 60*60)

+

+        print("Before creating the command")

+

+        command = 'python /home/zas1024/gene/wqflask/wqflask/my_pylmm/pyLMM/lmm.py --key {} --species {}'.format(key,

+                                                                                                                "human")

+        

+        print("command is:", command)

+        

+        os.system(command)

+        

+        json_results = Redis.blpop("pylmm:results:" + temp_uuid, 45*60)

+        results = json.loads(json_results[1])

+        t_stats = results['t_stats']

+        p_values = results['p_values']

+        

+

+        #p_values, t_stats = lmm.run_human(key)

+

+        #p_values, t_stats = lmm.run_human(

+        #        pheno_vector,

+        #        covariate_matrix,

+        #        input_file_name,

+        #        kinship_matrix,

+        #        loading_progress=tempdata

+        #    )

+

+        return p_values, t_stats

+

+    def get_lod_score_cutoff(self):

+        print("INSIDE GET LOD CUTOFF")

+        high_qtl_count = 0

+        for marker in self.dataset.group.markers.markers:

+            if marker['lod_score'] > 1:

+                high_qtl_count += 1

+

+        if high_qtl_count > 1000:

+            return 1

+        else:

+            return 0

+

+    def identify_empty_samples(self):

+        no_val_samples = []

+        for sample_count, val in enumerate(self.vals):

+            if val == "x":

+                no_val_samples.append(sample_count)

+        return no_val_samples

+        

+    def trim_genotypes(self, genotype_data, no_value_samples):

+        trimmed_genotype_data = []

+        for marker in genotype_data:

+            new_genotypes = []

+            for item_count, genotype in enumerate(marker):

+                if item_count in no_value_samples:

+                    continue

+                try:

+                    genotype = float(genotype)

+                except ValueError:

+                    genotype = np.nan

+                    pass

+                new_genotypes.append(genotype)

+            trimmed_genotype_data.append(new_genotypes)

+        return trimmed_genotype_data

+    

+def create_snp_iterator_file(group):

+    plink_file_base = os.path.join(webqtlConfig.PYLMM_PATH, group)

+    plink_input = input.plink(plink_file_base, type='b')

+    

+    data = dict(plink_input = list(plink_input),

+                numSNPs = plink_input.numSNPs)

+    

+    #input_dict = {}

+    #

+    #input_dict['plink_input'] = list(plink_input)

+    #input_dict['numSNPs'] = plink_input.numSNPs

+    #

+    

+    snp_file_base = os.path.join(webqtlConfig.SNP_PATH, group + ".snps.gz")

+    

+    with gzip.open(snp_file_base, "wb") as fh:

+        pickle.dump(data, fh, pickle.HIGHEST_PROTOCOL)

+

+#if __name__ == '__main__':

+#    import cPickle as pickle

+#    import gzip

+#    create_snp_iterator_file("HLC")

+    

+if __name__ == '__main__':

+    import cPickle as pickle

+    import gzip

+    create_snp_iterator_file("HLC")

diff --git a/wqflask/wqflask/my_pylmm/data/genofile_parser.py b/wqflask/wqflask/my_pylmm/data/genofile_parser.py
index baf6aee4..1f4760a9 100755
--- a/wqflask/wqflask/my_pylmm/data/genofile_parser.py
+++ b/wqflask/wqflask/my_pylmm/data/genofile_parser.py
@@ -96,8 +96,9 @@ class ConvertGenoFile(object):
             this_marker.chr = row_items[0]
             #this_marker.cM = row_items[2]
             if self.cm_exists and self.mb_exists:
-                this_marker.Mb = row_items[3]
-                genotypes = row_items[4:]
+                #print("cm and mb exists")
+                this_marker.Mb = row_items[2]
+                genotypes = row_items[3:]
             elif self.mb_exists:
                 this_marker.Mb = row_items[2]
                 genotypes = row_items[3:]
@@ -193,7 +194,7 @@ if __name__=="__main__":
     New_Geno_Directory = """/home/zas1024/gene/web/new_genotypes/"""
     #Input_File = """/home/zas1024/gene/web/genotypes/BXD.geno"""
     #Output_File = """/home/zas1024/gene/wqflask/wqflask/pylmm/data/bxd.snps"""
-    convertob = ConvertGenoFile("/home/zas1024/gene/web/genotypes/Linsenbardt-Boehm.geno", "/home/zas1024/gene/web/new_genotypes/Linsenbardt-Boehm.json")
+    convertob = ConvertGenoFile("/home/zas1024/gene/web/genotypes/HSNIH.geno", "/home/zas1024/gene/web/new_genotypes/HSNIH.json")
     convertob.convert()
     #ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory)
     #ConvertGenoFiles(Geno_Directory)
diff --git a/wqflask/wqflask/static/new/css/.corr_matrix.css.swp b/wqflask/wqflask/static/new/css/.corr_matrix.css.swp
deleted file mode 100755
index 24d852dc..00000000
--- a/wqflask/wqflask/static/new/css/.corr_matrix.css.swp
+++ /dev/null
Binary files differdiff --git a/wqflask/wqflask/static/new/css/interval_mapping.css b/wqflask/wqflask/static/new/css/interval_mapping.css
index 5ebf7742..4a55d2e3 100755
--- a/wqflask/wqflask/static/new/css/interval_mapping.css
+++ b/wqflask/wqflask/static/new/css/interval_mapping.css
@@ -1,26 +1,26 @@
-.interval_map .y_axis path,

-.interval_map .y_axis line {

+.chr_interval_map .y_axis path,

+.chr_interval_map .y_axis line {

     fill: none;

     stroke: black;

     shape-rendering: crispEdges;

 }

-.interval_map .y_axis text {

+.chr_interval_map .y_axis text {

     font-family: sans-serif;

     font-size: 14px;

 }

 

-.interval_map .x_axis path,

-.interval_map .x_axis line {

+.chr_interval_map .x_axis path,

+.chr_interval_map .x_axis line {

     fill: none;

     stroke: black;

     shape-rendering: crispEdges;

 }

-.interval_map .x_axis text {

+.chr_interval_map .x_axis text {

     text-anchor: end;

     font-family: sans-serif;

     font-size: 8px;

 }

-

+/*

 interval_map rect {

     stroke: WhiteSmoke;

     fill: white;

@@ -29,4 +29,4 @@ interval_map rect {
 interval_map path {

     stroke: steelblue;

     stroke-width: 1;

-}
\ No newline at end of file
+}*/
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/css/marker_regression.css b/wqflask/wqflask/static/new/css/marker_regression.css
index 56980026..d81b5021 100755
--- a/wqflask/wqflask/static/new/css/marker_regression.css
+++ b/wqflask/wqflask/static/new/css/marker_regression.css
@@ -1,22 +1,22 @@
-.manhattan_plot .y_axis path,
-.manhattan_plot .y_axis line {
+.chr_manhattan_plot .y_axis path,
+.chr_manhattan_plot .y_axis line {
     fill: none;
     stroke: black;
     shape-rendering: crispEdges;
 }
-.manhattan_plot .y_axis text {
+.chr_manhattan_plot .y_axis text {
     font-family: sans-serif;
     font-size: 14px;
 }
 
-.manhattan_plot .x_axis path,
-.manhattan_plot .x_axis line {
+.chr_manhattan_plot .x_axis path,
+.chr_manhattan_plot .x_axis line {
     fill: none;
     stroke: black;
     shape-rendering: crispEdges;
 }
 
-.manhattan_plot .x_axis text {
+.chr_manhattan_plot .x_axis text {
     text-anchor: end;
     font-family: sans-serif;
     font-size: 10px;
diff --git a/wqflask/wqflask/static/new/javascript/bar_chart.js b/wqflask/wqflask/static/new/javascript/bar_chart.js
index 6f9b27e0..6b484232 100755
--- a/wqflask/wqflask/static/new/javascript/bar_chart.js
+++ b/wqflask/wqflask/static/new/javascript/bar_chart.js
@@ -1,52 +1,50 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var Bar_Chart, root,
-    __hasProp = {}.hasOwnProperty,
-    __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; };
+// Generated by CoffeeScript 1.7.1
+var Bar_Chart, root,
+  __hasProp = {}.hasOwnProperty,
+  __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; };
 
-  root = typeof exports !== "undefined" && exports !== null ? exports : this;
+root = typeof exports !== "undefined" && exports !== null ? exports : this;
 
-  Bar_Chart = (function() {
-
-    function Bar_Chart(sample_list) {
-      var longest_sample_name, sample,
-        _this = this;
-      this.sample_list = sample_list;
-      this.sort_by = "name";
-      this.get_samples();
-      console.log("sample names:", this.sample_names);
-      if (this.sample_attr_vals.length > 0) {
-        this.get_distinct_attr_vals();
-        this.get_attr_color_dict(this.distinct_attr_vals);
+Bar_Chart = (function() {
+  function Bar_Chart(sample_list) {
+    var longest_sample_name, sample;
+    this.sample_list = sample_list;
+    this.sort_by = "name";
+    this.get_samples();
+    console.log("sample names:", this.sample_names);
+    if (this.sample_attr_vals.length > 0) {
+      this.get_distinct_attr_vals();
+      this.get_attr_color_dict(this.distinct_attr_vals);
+    }
+    longest_sample_name = d3.max((function() {
+      var _i, _len, _ref, _results;
+      _ref = this.sample_names;
+      _results = [];
+      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+        sample = _ref[_i];
+        _results.push(sample.length);
       }
-      longest_sample_name = d3.max((function() {
-        var _i, _len, _ref, _results;
-        _ref = this.sample_names;
-        _results = [];
-        for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-          sample = _ref[_i];
-          _results.push(sample.length);
-        }
-        return _results;
-      }).call(this));
-      this.margin = {
-        top: 20,
-        right: 20,
-        bottom: longest_sample_name * 7,
-        left: 40
-      };
-      this.plot_width = this.sample_vals.length * 20 - this.margin.left - this.margin.right;
-      this.range = this.sample_vals.length * 20;
-      this.plot_height = 500 - this.margin.top - this.margin.bottom;
-      this.x_buffer = this.plot_width / 20;
-      this.y_buffer = this.plot_height / 20;
-      this.y_min = d3.min(this.sample_vals);
-      this.y_max = d3.max(this.sample_vals) * 1.1;
-      this.svg = this.create_svg();
-      this.plot_height -= this.y_buffer;
-      this.create_scales();
-      this.create_graph();
-      d3.select("#color_attribute").on("change", function() {
+      return _results;
+    }).call(this));
+    this.margin = {
+      top: 20,
+      right: 20,
+      bottom: longest_sample_name * 7,
+      left: 40
+    };
+    this.plot_width = this.sample_vals.length * 20 - this.margin.left - this.margin.right;
+    this.range = this.sample_vals.length * 20;
+    this.plot_height = 500 - this.margin.top - this.margin.bottom;
+    this.x_buffer = this.plot_width / 20;
+    this.y_buffer = this.plot_height / 20;
+    this.y_min = d3.min(this.sample_vals);
+    this.y_max = d3.max(this.sample_vals) * 1.1;
+    this.svg = this.create_svg();
+    this.plot_height -= this.y_buffer;
+    this.create_scales();
+    this.create_graph();
+    d3.select("#color_attribute").on("change", (function(_this) {
+      return function() {
         _this.attribute = $("#color_attribute").val();
         console.log("attr_color_dict:", _this.attr_color_dict);
         if (_this.sort_by = "name") {
@@ -69,33 +67,40 @@
           });
         }
         return _this.add_legend(_this.attribute, _this.distinct_attr_vals[_this.attribute]);
-      });
-      $(".sort_by_value").on("click", function() {
+      };
+    })(this));
+    $(".sort_by_value").on("click", (function(_this) {
+      return function() {
         console.log("sorting by value");
         _this.sort_by = "value";
         if (_this.attributes.length > 0) {
           _this.attribute = $("#color_attribute").val();
         }
         return _this.rebuild_bar_graph(_this.sorted_samples());
-      });
-      $(".sort_by_name").on("click", function() {
+      };
+    })(this));
+    $(".sort_by_name").on("click", (function(_this) {
+      return function() {
         console.log("sorting by name");
         _this.sort_by = "name";
         if (_this.attributes.length > 0) {
           _this.attribute = $("#color_attribute").val();
         }
         return _this.rebuild_bar_graph(_this.samples);
-      });
-      d3.select("#color_by_trait").on("click", function() {
+      };
+    })(this));
+    d3.select("#color_by_trait").on("click", (function(_this) {
+      return function() {
         return _this.open_trait_selection();
-      });
-    }
+      };
+    })(this));
+  }
 
-    Bar_Chart.prototype.rebuild_bar_graph = function(samples) {
-      var sample, sample_names, x_scale,
-        _this = this;
-      console.log("samples:", samples);
-      this.svg.selectAll(".bar").data(samples).transition().duration(1000).style("fill", function(d) {
+  Bar_Chart.prototype.rebuild_bar_graph = function(samples) {
+    var sample, sample_names, x_scale;
+    console.log("samples:", samples);
+    this.svg.selectAll(".bar").data(samples).transition().duration(1000).style("fill", (function(_this) {
+      return function(d) {
         if (_this.attributes.length === 0 && (_this.trait_color_dict != null)) {
           console.log("SAMPLE:", d[0]);
           console.log("CHECKING:", _this.trait_color_dict[d[0]]);
@@ -108,335 +113,366 @@
         } else {
           return "steelblue";
         }
-      }).attr("y", function(d) {
+      };
+    })(this)).attr("y", (function(_this) {
+      return function(d) {
         return _this.y_scale(d[1]);
-      }).attr("height", function(d) {
+      };
+    })(this)).attr("height", (function(_this) {
+      return function(d) {
         return _this.plot_height - _this.y_scale(d[1]);
-      }).select("title").text(function(d) {
+      };
+    })(this)).select("title").text((function(_this) {
+      return function(d) {
         return d[1];
-      });
-      sample_names = (function() {
-        var _i, _len, _results;
-        _results = [];
-        for (_i = 0, _len = samples.length; _i < _len; _i++) {
-          sample = samples[_i];
-          _results.push(sample[0]);
-        }
-        return _results;
-      })();
-      console.log("sample_names2:", sample_names);
-      x_scale = d3.scale.ordinal().domain(sample_names).rangeRoundBands([0, this.range], 0.1, 0);
-      $('.bar_chart').find('.x.axis').remove();
-      return this.add_x_axis(x_scale);
-    };
-
-    Bar_Chart.prototype.get_attr_color_dict = function(vals) {
-      var color, color_range, distinct_vals, i, key, this_color_dict, value, _i, _j, _len, _len1, _results,
-        _this = this;
-      this.attr_color_dict = {};
-      console.log("vals:", vals);
+      };
+    })(this));
+    sample_names = (function() {
+      var _i, _len, _results;
       _results = [];
-      for (key in vals) {
-        if (!__hasProp.call(vals, key)) continue;
-        distinct_vals = vals[key];
-        this_color_dict = {};
-        if (distinct_vals.length < 10) {
-          color = d3.scale.category10();
-          for (i = _i = 0, _len = distinct_vals.length; _i < _len; i = ++_i) {
-            value = distinct_vals[i];
-            this_color_dict[value] = color(i);
-          }
-        } else {
-          console.log("distinct_values:", distinct_vals);
-          if (_.every(distinct_vals, function(d) {
+      for (_i = 0, _len = samples.length; _i < _len; _i++) {
+        sample = samples[_i];
+        _results.push(sample[0]);
+      }
+      return _results;
+    })();
+    console.log("sample_names2:", sample_names);
+    x_scale = d3.scale.ordinal().domain(sample_names).rangeRoundBands([0, this.range], 0.1, 0);
+    $('.bar_chart').find('.x.axis').remove();
+    return this.add_x_axis(x_scale);
+  };
+
+  Bar_Chart.prototype.get_attr_color_dict = function(vals) {
+    var color, color_range, distinct_vals, i, key, this_color_dict, value, _i, _j, _len, _len1, _results;
+    this.attr_color_dict = {};
+    console.log("vals:", vals);
+    _results = [];
+    for (key in vals) {
+      if (!__hasProp.call(vals, key)) continue;
+      distinct_vals = vals[key];
+      this_color_dict = {};
+      if (distinct_vals.length < 10) {
+        color = d3.scale.category10();
+        for (i = _i = 0, _len = distinct_vals.length; _i < _len; i = ++_i) {
+          value = distinct_vals[i];
+          this_color_dict[value] = color(i);
+        }
+      } else {
+        console.log("distinct_values:", distinct_vals);
+        if (_.every(distinct_vals, (function(_this) {
+          return function(d) {
             if (isNaN(d)) {
               return false;
             } else {
               return true;
             }
-          })) {
-            color_range = d3.scale.linear().domain([d3.min(distinct_vals), d3.max(distinct_vals)]).range([0, 255]);
-            for (i = _j = 0, _len1 = distinct_vals.length; _j < _len1; i = ++_j) {
-              value = distinct_vals[i];
-              console.log("color_range(value):", parseInt(color_range(value)));
-              this_color_dict[value] = d3.rgb(parseInt(color_range(value)), 0, 0);
-            }
+          };
+        })(this))) {
+          color_range = d3.scale.linear().domain([d3.min(distinct_vals), d3.max(distinct_vals)]).range([0, 255]);
+          for (i = _j = 0, _len1 = distinct_vals.length; _j < _len1; i = ++_j) {
+            value = distinct_vals[i];
+            console.log("color_range(value):", parseInt(color_range(value)));
+            this_color_dict[value] = d3.rgb(parseInt(color_range(value)), 0, 0);
           }
         }
-        _results.push(this.attr_color_dict[key] = this_color_dict);
       }
-      return _results;
-    };
+      _results.push(this.attr_color_dict[key] = this_color_dict);
+    }
+    return _results;
+  };
 
-    Bar_Chart.prototype.get_trait_color_dict = function(samples, vals) {
-      var color, color_range, distinct_vals, i, key, sample, this_color_dict, value, _i, _j, _len, _len1, _results,
-        _this = this;
-      this.trait_color_dict = {};
-      console.log("vals:", vals);
-      for (key in vals) {
-        if (!__hasProp.call(vals, key)) continue;
-        distinct_vals = vals[key];
-        this_color_dict = {};
-        if (distinct_vals.length < 10) {
-          color = d3.scale.category10();
-          for (i = _i = 0, _len = distinct_vals.length; _i < _len; i = ++_i) {
-            value = distinct_vals[i];
-            this_color_dict[value] = color(i);
-          }
-        } else {
-          console.log("distinct_values:", distinct_vals);
-          if (_.every(distinct_vals, function(d) {
+  Bar_Chart.prototype.get_trait_color_dict = function(samples, vals) {
+    var color, color_range, distinct_vals, i, key, sample, this_color_dict, value, _i, _j, _len, _len1, _results;
+    this.trait_color_dict = {};
+    console.log("vals:", vals);
+    for (key in vals) {
+      if (!__hasProp.call(vals, key)) continue;
+      distinct_vals = vals[key];
+      this_color_dict = {};
+      if (distinct_vals.length < 10) {
+        color = d3.scale.category10();
+        for (i = _i = 0, _len = distinct_vals.length; _i < _len; i = ++_i) {
+          value = distinct_vals[i];
+          this_color_dict[value] = color(i);
+        }
+      } else {
+        console.log("distinct_values:", distinct_vals);
+        if (_.every(distinct_vals, (function(_this) {
+          return function(d) {
             if (isNaN(d)) {
               return false;
             } else {
               return true;
             }
-          })) {
-            color_range = d3.scale.linear().domain([d3.min(distinct_vals), d3.max(distinct_vals)]).range([0, 255]);
-            for (i = _j = 0, _len1 = distinct_vals.length; _j < _len1; i = ++_j) {
-              value = distinct_vals[i];
-              console.log("color_range(value):", parseInt(color_range(value)));
-              this_color_dict[value] = d3.rgb(parseInt(color_range(value)), 0, 0);
-            }
+          };
+        })(this))) {
+          color_range = d3.scale.linear().domain([d3.min(distinct_vals), d3.max(distinct_vals)]).range([0, 255]);
+          for (i = _j = 0, _len1 = distinct_vals.length; _j < _len1; i = ++_j) {
+            value = distinct_vals[i];
+            console.log("color_range(value):", parseInt(color_range(value)));
+            this_color_dict[value] = d3.rgb(parseInt(color_range(value)), 0, 0);
           }
         }
       }
-      _results = [];
-      for (sample in samples) {
-        if (!__hasProp.call(samples, sample)) continue;
-        value = samples[sample];
-        _results.push(this.trait_color_dict[sample] = this_color_dict[value]);
-      }
-      return _results;
-    };
+    }
+    _results = [];
+    for (sample in samples) {
+      if (!__hasProp.call(samples, sample)) continue;
+      value = samples[sample];
+      _results.push(this.trait_color_dict[sample] = this_color_dict[value]);
+    }
+    return _results;
+  };
 
-    Bar_Chart.prototype.convert_into_colors = function(values) {
-      var color_range, i, value, _i, _len, _results;
-      color_range = d3.scale.linear().domain([d3.min(values), d3.max(values)]).range([0, 255]);
+  Bar_Chart.prototype.convert_into_colors = function(values) {
+    var color_range, i, value, _i, _len, _results;
+    color_range = d3.scale.linear().domain([d3.min(values), d3.max(values)]).range([0, 255]);
+    _results = [];
+    for (i = _i = 0, _len = values.length; _i < _len; i = ++_i) {
+      value = values[i];
+      console.log("color_range(value):", color_range(parseInt(value)));
+      _results.push(this_color_dict[value] = d3.rgb(color_range(parseInt(value)), 0, 0));
+    }
+    return _results;
+  };
+
+  Bar_Chart.prototype.get_samples = function() {
+    var attr_vals, attribute, key, sample, _i, _j, _len, _len1, _ref, _ref1;
+    this.sample_names = (function() {
+      var _i, _len, _ref, _results;
+      _ref = this.sample_list;
       _results = [];
-      for (i = _i = 0, _len = values.length; _i < _len; i = ++_i) {
-        value = values[i];
-        console.log("color_range(value):", color_range(parseInt(value)));
-        _results.push(this_color_dict[value] = d3.rgb(color_range(parseInt(value)), 0, 0));
+      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+        sample = _ref[_i];
+        if (sample.value !== null) {
+          _results.push(sample.name);
+        }
       }
       return _results;
-    };
-
-    Bar_Chart.prototype.get_samples = function() {
-      var attr_vals, attribute, key, sample, _i, _j, _len, _len1, _ref, _ref1;
-      this.sample_names = (function() {
-        var _i, _len, _ref, _results;
-        _ref = this.sample_list;
-        _results = [];
-        for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-          sample = _ref[_i];
-          if (sample.value !== null) {
-            _results.push(sample.name);
-          }
-        }
-        return _results;
-      }).call(this);
-      this.sample_vals = (function() {
-        var _i, _len, _ref, _results;
-        _ref = this.sample_list;
-        _results = [];
-        for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-          sample = _ref[_i];
-          if (sample.value !== null) {
-            _results.push(sample.value);
-          }
-        }
-        return _results;
-      }).call(this);
-      this.attributes = (function() {
-        var _results;
-        _results = [];
-        for (key in this.sample_list[0]["extra_attributes"]) {
-          _results.push(key);
-        }
-        return _results;
-      }).call(this);
-      console.log("attributes:", this.attributes);
-      this.sample_attr_vals = [];
-      if (this.attributes.length > 0) {
-        _ref = this.sample_list;
-        for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-          sample = _ref[_i];
-          attr_vals = {};
-          _ref1 = this.attributes;
-          for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) {
-            attribute = _ref1[_j];
-            attr_vals[attribute] = sample["extra_attributes"][attribute];
-          }
-          this.sample_attr_vals.push(attr_vals);
+    }).call(this);
+    this.sample_vals = (function() {
+      var _i, _len, _ref, _results;
+      _ref = this.sample_list;
+      _results = [];
+      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+        sample = _ref[_i];
+        if (sample.value !== null) {
+          _results.push(sample.value);
         }
       }
-      return this.samples = _.zip(this.sample_names, this.sample_vals, this.sample_attr_vals);
-    };
-
-    Bar_Chart.prototype.get_distinct_attr_vals = function() {
-      var attribute, sample, _i, _len, _ref, _results;
-      this.distinct_attr_vals = {};
-      _ref = this.sample_attr_vals;
+      return _results;
+    }).call(this);
+    this.attributes = (function() {
+      var _results;
       _results = [];
+      for (key in this.sample_list[0]["extra_attributes"]) {
+        _results.push(key);
+      }
+      return _results;
+    }).call(this);
+    console.log("attributes:", this.attributes);
+    this.sample_attr_vals = [];
+    if (this.attributes.length > 0) {
+      _ref = this.sample_list;
       for (_i = 0, _len = _ref.length; _i < _len; _i++) {
         sample = _ref[_i];
-        _results.push((function() {
-          var _ref1, _results1;
-          _results1 = [];
-          for (attribute in sample) {
-            if (!this.distinct_attr_vals[attribute]) {
-              this.distinct_attr_vals[attribute] = [];
-            }
-            if (_ref1 = sample[attribute], __indexOf.call(this.distinct_attr_vals[attribute], _ref1) < 0) {
-              _results1.push(this.distinct_attr_vals[attribute].push(sample[attribute]));
-            } else {
-              _results1.push(void 0);
-            }
-          }
-          return _results1;
-        }).call(this));
+        attr_vals = {};
+        _ref1 = this.attributes;
+        for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) {
+          attribute = _ref1[_j];
+          attr_vals[attribute] = sample["extra_attributes"][attribute];
+        }
+        this.sample_attr_vals.push(attr_vals);
       }
-      return _results;
-    };
+    }
+    return this.samples = _.zip(this.sample_names, this.sample_vals, this.sample_attr_vals);
+  };
 
-    Bar_Chart.prototype.create_svg = function() {
-      var svg;
-      svg = d3.select("#bar_chart").append("svg").attr("class", "bar_chart").attr("width", this.plot_width + this.margin.left + this.margin.right).attr("height", this.plot_height + this.margin.top + this.margin.bottom).append("g").attr("transform", "translate(" + this.margin.left + "," + this.margin.top + ")");
-      return svg;
-    };
+  Bar_Chart.prototype.get_distinct_attr_vals = function() {
+    var attribute, sample, _i, _len, _ref, _results;
+    this.distinct_attr_vals = {};
+    _ref = this.sample_attr_vals;
+    _results = [];
+    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+      sample = _ref[_i];
+      _results.push((function() {
+        var _ref1, _results1;
+        _results1 = [];
+        for (attribute in sample) {
+          if (!this.distinct_attr_vals[attribute]) {
+            this.distinct_attr_vals[attribute] = [];
+          }
+          if (_ref1 = sample[attribute], __indexOf.call(this.distinct_attr_vals[attribute], _ref1) < 0) {
+            _results1.push(this.distinct_attr_vals[attribute].push(sample[attribute]));
+          } else {
+            _results1.push(void 0);
+          }
+        }
+        return _results1;
+      }).call(this));
+    }
+    return _results;
+  };
 
-    Bar_Chart.prototype.create_scales = function() {
-      this.x_scale = d3.scale.ordinal().domain(this.sample_names).rangeRoundBands([0, this.range], 0.1, 0);
-      return this.y_scale = d3.scale.linear().domain([this.y_min * 0.75, this.y_max]).range([this.plot_height, this.y_buffer]);
-    };
+  Bar_Chart.prototype.create_svg = function() {
+    var svg;
+    svg = d3.select("#bar_chart").append("svg").attr("class", "bar_chart").attr("width", this.plot_width + this.margin.left + this.margin.right).attr("height", this.plot_height + this.margin.top + this.margin.bottom).append("g").attr("transform", "translate(" + this.margin.left + "," + this.margin.top + ")");
+    return svg;
+  };
 
-    Bar_Chart.prototype.create_graph = function() {
-      this.add_x_axis(this.x_scale);
-      this.add_y_axis();
-      return this.add_bars();
-    };
+  Bar_Chart.prototype.create_scales = function() {
+    this.x_scale = d3.scale.ordinal().domain(this.sample_names).rangeRoundBands([0, this.range], 0.1, 0);
+    return this.y_scale = d3.scale.linear().domain([this.y_min * 0.75, this.y_max]).range([this.plot_height, this.y_buffer]);
+  };
 
-    Bar_Chart.prototype.add_x_axis = function(scale) {
-      var xAxis,
-        _this = this;
-      xAxis = d3.svg.axis().scale(scale).orient("bottom");
-      return this.svg.append("g").attr("class", "x axis").attr("transform", "translate(0," + this.plot_height + ")").call(xAxis).selectAll("text").style("text-anchor", "end").style("font-size", "12px").attr("dx", "-.8em").attr("dy", "-.3em").attr("transform", function(d) {
+  Bar_Chart.prototype.create_graph = function() {
+    this.add_x_axis(this.x_scale);
+    this.add_y_axis();
+    return this.add_bars();
+  };
+
+  Bar_Chart.prototype.add_x_axis = function(scale) {
+    var xAxis;
+    xAxis = d3.svg.axis().scale(scale).orient("bottom");
+    return this.svg.append("g").attr("class", "x axis").attr("transform", "translate(0," + this.plot_height + ")").call(xAxis).selectAll("text").style("text-anchor", "end").style("font-size", "12px").attr("dx", "-.8em").attr("dy", "-.3em").attr("transform", (function(_this) {
+      return function(d) {
         return "rotate(-90)";
-      });
-    };
+      };
+    })(this));
+  };
 
-    Bar_Chart.prototype.add_y_axis = function() {
-      var yAxis;
-      yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
-      return this.svg.append("g").attr("class", "y axis").call(yAxis).append("text").attr("transform", "rotate(-90)").attr("y", 6).attr("dy", ".71em").style("text-anchor", "end");
-    };
+  Bar_Chart.prototype.add_y_axis = function() {
+    var yAxis;
+    yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
+    return this.svg.append("g").attr("class", "y axis").call(yAxis).append("text").attr("transform", "rotate(-90)").attr("y", 6).attr("dy", ".71em").style("text-anchor", "end");
+  };
 
-    Bar_Chart.prototype.add_bars = function() {
-      var _this = this;
-      return this.svg.selectAll(".bar").data(this.samples).enter().append("rect").style("fill", "steelblue").attr("class", "bar").attr("x", function(d) {
+  Bar_Chart.prototype.add_bars = function() {
+    return this.svg.selectAll(".bar").data(this.samples).enter().append("rect").style("fill", "steelblue").attr("class", "bar").attr("x", (function(_this) {
+      return function(d) {
         return _this.x_scale(d[0]);
-      }).attr("width", this.x_scale.rangeBand()).attr("y", function(d) {
+      };
+    })(this)).attr("width", this.x_scale.rangeBand()).attr("y", (function(_this) {
+      return function(d) {
         return _this.y_scale(d[1]);
-      }).attr("height", function(d) {
+      };
+    })(this)).attr("height", (function(_this) {
+      return function(d) {
         return _this.plot_height - _this.y_scale(d[1]);
-      }).append("svg:title").text(function(d) {
+      };
+    })(this)).append("svg:title").text((function(_this) {
+      return function(d) {
         return d[1];
-      });
-    };
+      };
+    })(this));
+  };
 
-    Bar_Chart.prototype.sorted_samples = function() {
-      var sample_list, sorted,
-        _this = this;
-      sample_list = _.zip(this.sample_names, this.sample_vals, this.sample_attr_vals);
-      sorted = _.sortBy(sample_list, function(sample) {
+  Bar_Chart.prototype.sorted_samples = function() {
+    var sample_list, sorted;
+    sample_list = _.zip(this.sample_names, this.sample_vals, this.sample_attr_vals);
+    sorted = _.sortBy(sample_list, (function(_this) {
+      return function(sample) {
         return sample[1];
-      });
-      console.log("sorted:", sorted);
-      return sorted;
-    };
+      };
+    })(this));
+    console.log("sorted:", sorted);
+    return sorted;
+  };
 
-    Bar_Chart.prototype.add_legend = function(attribute, distinct_vals) {
-      var legend, legend_rect, legend_text,
-        _this = this;
-      legend = this.svg.append("g").attr("class", "legend").attr("height", 100).attr("width", 100).attr('transform', 'translate(-20,50)');
-      legend_rect = legend.selectAll('rect').data(distinct_vals).enter().append("rect").attr("x", this.plot_width - 65).attr("width", 10).attr("height", 10).attr("y", function(d, i) {
+  Bar_Chart.prototype.add_legend = function(attribute, distinct_vals) {
+    var legend, legend_rect, legend_text;
+    legend = this.svg.append("g").attr("class", "legend").attr("height", 100).attr("width", 100).attr('transform', 'translate(-20,50)');
+    legend_rect = legend.selectAll('rect').data(distinct_vals).enter().append("rect").attr("x", this.plot_width - 65).attr("width", 10).attr("height", 10).attr("y", (function(_this) {
+      return function(d, i) {
         return i * 20;
-      }).style("fill", function(d) {
+      };
+    })(this)).style("fill", (function(_this) {
+      return function(d) {
         console.log("TEST:", _this.attr_color_dict[attribute][d]);
         return _this.attr_color_dict[attribute][d];
-      });
-      return legend_text = legend.selectAll('text').data(distinct_vals).enter().append("text").attr("x", this.plot_width - 52).attr("y", function(d, i) {
+      };
+    })(this));
+    return legend_text = legend.selectAll('text').data(distinct_vals).enter().append("text").attr("x", this.plot_width - 52).attr("y", (function(_this) {
+      return function(d, i) {
         return i * 20 + 9;
-      }).text(function(d) {
+      };
+    })(this)).text((function(_this) {
+      return function(d) {
         return d;
-      });
-    };
+      };
+    })(this));
+  };
 
-    Bar_Chart.prototype.open_trait_selection = function() {
-      var _this = this;
-      return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', function() {
+  Bar_Chart.prototype.open_trait_selection = function() {
+    return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', (function(_this) {
+      return function() {
         $.colorbox({
           inline: true,
           href: "#collections_holder"
         });
         return $('a.collection_name').attr('onClick', 'return false');
-      });
-    };
+      };
+    })(this));
+  };
 
-    Bar_Chart.prototype.color_by_trait = function(trait_sample_data) {
-      var distinct_values, trimmed_samples,
-        _this = this;
-      console.log("BXD1:", trait_sample_data["BXD1"]);
-      console.log("trait_sample_data:", trait_sample_data);
-      trimmed_samples = this.trim_values(trait_sample_data);
-      distinct_values = {};
-      distinct_values["collection_trait"] = this.get_distinct_values(trimmed_samples);
-      this.get_trait_color_dict(trimmed_samples, distinct_values);
-      console.log("TRAIT_COLOR_DICT:", this.trait_color_dict);
-      console.log("SAMPLES:", this.samples);
-      if (this.sort_by = "value") {
-        return this.svg.selectAll(".bar").data(this.samples).transition().duration(1000).style("fill", function(d) {
+  Bar_Chart.prototype.color_by_trait = function(trait_sample_data) {
+    var distinct_values, trimmed_samples;
+    console.log("BXD1:", trait_sample_data["BXD1"]);
+    console.log("trait_sample_data:", trait_sample_data);
+    trimmed_samples = this.trim_values(trait_sample_data);
+    distinct_values = {};
+    distinct_values["collection_trait"] = this.get_distinct_values(trimmed_samples);
+    this.get_trait_color_dict(trimmed_samples, distinct_values);
+    console.log("TRAIT_COLOR_DICT:", this.trait_color_dict);
+    console.log("SAMPLES:", this.samples);
+    if (this.sort_by = "value") {
+      return this.svg.selectAll(".bar").data(this.samples).transition().duration(1000).style("fill", (function(_this) {
+        return function(d) {
           console.log("this color:", _this.trait_color_dict[d[0]]);
           return _this.trait_color_dict[d[0]];
-        }).select("title").text(function(d) {
+        };
+      })(this)).select("title").text((function(_this) {
+        return function(d) {
           return d[1];
-        });
-      } else {
-        return this.svg.selectAll(".bar").data(this.sorted_samples()).transition().duration(1000).style("fill", function(d) {
+        };
+      })(this));
+    } else {
+      return this.svg.selectAll(".bar").data(this.sorted_samples()).transition().duration(1000).style("fill", (function(_this) {
+        return function(d) {
           console.log("this color:", _this.trait_color_dict[d[0]]);
           return _this.trait_color_dict[d[0]];
-        }).select("title").text(function(d) {
+        };
+      })(this)).select("title").text((function(_this) {
+        return function(d) {
           return d[1];
-        });
-      }
-    };
+        };
+      })(this));
+    }
+  };
 
-    Bar_Chart.prototype.trim_values = function(trait_sample_data) {
-      var sample, trimmed_samples, _i, _len, _ref;
-      trimmed_samples = {};
-      _ref = this.sample_names;
-      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-        sample = _ref[_i];
-        if (sample in trait_sample_data) {
-          trimmed_samples[sample] = trait_sample_data[sample];
-        }
+  Bar_Chart.prototype.trim_values = function(trait_sample_data) {
+    var sample, trimmed_samples, _i, _len, _ref;
+    trimmed_samples = {};
+    _ref = this.sample_names;
+    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+      sample = _ref[_i];
+      if (sample in trait_sample_data) {
+        trimmed_samples[sample] = trait_sample_data[sample];
       }
-      console.log("trimmed_samples:", trimmed_samples);
-      return trimmed_samples;
-    };
-
-    Bar_Chart.prototype.get_distinct_values = function(samples) {
-      var distinct_values;
-      distinct_values = _.uniq(_.values(samples));
-      console.log("distinct_values:", distinct_values);
-      return distinct_values;
-    };
+    }
+    console.log("trimmed_samples:", trimmed_samples);
+    return trimmed_samples;
+  };
 
-    return Bar_Chart;
+  Bar_Chart.prototype.get_distinct_values = function(samples) {
+    var distinct_values;
+    distinct_values = _.uniq(_.values(samples));
+    console.log("distinct_values:", distinct_values);
+    return distinct_values;
+  };
 
-  })();
+  return Bar_Chart;
 
-  root.Bar_Chart = Bar_Chart;
+})();
 
-}).call(this);
+root.Bar_Chart = Bar_Chart;
diff --git a/wqflask/wqflask/static/new/javascript/box_plot.js b/wqflask/wqflask/static/new/javascript/box_plot.js
index 736df9c9..4b80956f 100755
--- a/wqflask/wqflask/static/new/javascript/box_plot.js
+++ b/wqflask/wqflask/static/new/javascript/box_plot.js
@@ -1,57 +1,55 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var Box_Plot, root;
+// Generated by CoffeeScript 1.7.1
+var Box_Plot, root;
 
-  root = typeof exports !== "undefined" && exports !== null ? exports : this;
+root = typeof exports !== "undefined" && exports !== null ? exports : this;
 
-  Box_Plot = (function() {
-
-    function Box_Plot(sample_list, sample_group) {
-      this.sample_list = sample_list;
-      this.sample_group = sample_group;
-      this.get_samples();
-      this.margin = {
-        top: 10,
-        right: 50,
-        bottom: 20,
-        left: 50
-      };
-      this.plot_width = 200 - this.margin.left - this.margin.right;
-      this.plot_height = 500 - this.margin.top - this.margin.bottom;
-      this.min = d3.min(this.sample_vals);
-      this.max = d3.max(this.sample_vals);
-      this.svg = this.create_svg();
-      this.enter_data();
-    }
+Box_Plot = (function() {
+  function Box_Plot(sample_list, sample_group) {
+    this.sample_list = sample_list;
+    this.sample_group = sample_group;
+    this.get_samples();
+    this.margin = {
+      top: 10,
+      right: 50,
+      bottom: 20,
+      left: 50
+    };
+    this.plot_width = 200 - this.margin.left - this.margin.right;
+    this.plot_height = 500 - this.margin.top - this.margin.bottom;
+    this.min = d3.min(this.sample_vals);
+    this.max = d3.max(this.sample_vals);
+    this.svg = this.create_svg();
+    this.enter_data();
+  }
 
-    Box_Plot.prototype.get_samples = function() {
-      var sample;
-      return this.sample_vals = (function() {
-        var _i, _len, _ref, _results;
-        _ref = this.sample_list;
-        _results = [];
-        for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-          sample = _ref[_i];
-          if (sample.value !== null) {
-            _results.push(sample.value);
-          }
+  Box_Plot.prototype.get_samples = function() {
+    var sample;
+    return this.sample_vals = (function() {
+      var _i, _len, _ref, _results;
+      _ref = this.sample_list;
+      _results = [];
+      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+        sample = _ref[_i];
+        if (sample.value !== null) {
+          _results.push(sample.value);
         }
-        return _results;
-      }).call(this);
-    };
+      }
+      return _results;
+    }).call(this);
+  };
 
-    Box_Plot.prototype.create_svg = function() {
-      var svg;
-      svg = d3.box().whiskers(this.inter_quartile_range(1.5)).width(this.plot_width - 30).height(this.plot_height - 30).domain([this.min, this.max]);
-      return svg;
-    };
+  Box_Plot.prototype.create_svg = function() {
+    var svg;
+    svg = d3.box().whiskers(this.inter_quartile_range(1.5)).width(this.plot_width - 30).height(this.plot_height - 30).domain([this.min, this.max]);
+    return svg;
+  };
 
-    Box_Plot.prototype.enter_data = function() {
-      return d3.select("#box_plot").selectAll("svg").data([this.sample_vals]).enter().append("svg:svg").attr("class", "box").attr("width", this.plot_width).attr("height", this.plot_height).append("svg:g").call(this.svg);
-    };
+  Box_Plot.prototype.enter_data = function() {
+    return d3.select("#box_plot").selectAll("svg").data([this.sample_vals]).enter().append("svg:svg").attr("class", "box").attr("width", this.plot_width).attr("height", this.plot_height).append("svg:g").call(this.svg);
+  };
 
-    Box_Plot.prototype.inter_quartile_range = function(k) {
-      var _this = this;
+  Box_Plot.prototype.inter_quartile_range = function(k) {
+    return (function(_this) {
       return function(d, i) {
         var inter_quartile_range, j, q1, q3;
         console.log("iqr d:", d);
@@ -72,12 +70,11 @@
         console.log("[i, j]", [i, j]);
         return [i, j];
       };
-    };
-
-    return Box_Plot;
+    })(this);
+  };
 
-  })();
+  return Box_Plot;
 
-  root.Box_Plot = Box_Plot;
+})();
 
-}).call(this);
+root.Box_Plot = Box_Plot;
diff --git a/wqflask/wqflask/static/new/javascript/chr_interval_map.coffee b/wqflask/wqflask/static/new/javascript/chr_interval_map.coffee
new file mode 100644
index 00000000..62ce4d3d
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/chr_interval_map.coffee
@@ -0,0 +1,293 @@
+class Chr_Interval_Map

+    constructor: (@plot_height, @plot_width, @chr) ->

+        @qtl_results = js_data.qtl_results

+        console.log("qtl_results are:", @qtl_results)

+        console.log("chr is:", @chr)

+        

+        @get_max_chr()

+

+        @filter_qtl_results()

+        console.log("filtered results:", @these_results)

+        @get_qtl_count()

+

+        @x_coords = []

+        @y_coords = []

+        @marker_names = []

+

+        console.time('Create coordinates')

+        @create_coordinates()

+        console.log("@x_coords: ", @x_coords)

+        console.log("@y_coords: ", @y_coords)

+        console.timeEnd('Create coordinates')

+        

+        # Buffer to allow for the ticks/labels to be drawn

+        @x_buffer = @plot_width/30

+        @y_buffer = @plot_height/20

+        

+        @x_max = d3.max(@x_coords)

+        @y_max = d3.max(@y_coords) * 1.2

+    

+        @y_threshold = @get_lod_threshold()

+    

+        @svg = @create_svg()

+

+        @plot_coordinates = _.zip(@x_coords, @y_coords, @marker_names)

+        console.log("coordinates:", @plot_coordinates)

+

+        @plot_height -= @y_buffer

+

+        @create_scales()

+

+        console.time('Create graph')

+        @create_graph()

+        console.timeEnd('Create graph')

+       

+    get_max_chr: () ->

+        @max_chr = 0

+        for key of js_data.chromosomes

+            console.log("key is:", key)

+            if parseInt(key) > @max_chr

+                @max_chr = parseInt(key)

+        

+    filter_qtl_results: () ->

+        @these_results = []

+        this_chr = 100

+        for result in @qtl_results

+            if result.chr == "X"

+                this_chr = @max_chr

+            else

+                this_chr = result.chr

+            console.log("this_chr is:", this_chr)

+            console.log("@chr[0] is:", parseInt(@chr[0]))

+            if this_chr > parseInt(@chr[0])

+                break

+            if parseInt(this_chr) == parseInt(@chr[0])

+                @these_results.push(result)

+

+    get_qtl_count: () ->

+        high_qtl_count = 0

+        for result in @these_results

+            if result.lrs_value > 1

+                high_qtl_count += 1

+        console.log("high_qtl_count:", high_qtl_count)

+        

+        #if high_qtl_count > 10000

+        @y_axis_filter = 2

+        #else if high_qtl_count > 1000

+        #    @y_axis_filter = 1

+        #else

+        #    @y_axis_filter = 0

+

+    create_coordinates: () ->

+        for result in @these_results

+            @x_coords.push(parseFloat(result.Mb))

+            @y_coords.push(result.lrs_value)

+            @marker_names.push(result.name)

+            

+    create_svg: () ->

+        svg = d3.select("#topchart")

+            .append("svg")

+            .attr("class", "chr_interval_map")

+            .attr("width", @plot_width+@x_buffer)

+            .attr("height", @plot_height+@y_buffer)

+            .append("g")

+        return svg

+

+    create_scales: () ->

+        console.log("chr[1] is:", @chr[1])

+        @x_scale = d3.scale.linear()

+            .domain([0, @chr[1]])

+            .range([@x_buffer, @plot_width])

+        @y_scale = d3.scale.linear()

+            .domain([0, @y_max])

+            .range([@plot_height, @y_buffer])

+            

+    get_lod_threshold: () ->

+        if @y_max/2 > 2

+            return @y_max/2

+        else

+            return 2

+

+    create_graph: () ->

+        @add_border()

+        @add_x_axis()

+        @add_y_axis()

+        @add_title()

+        @add_back_button()

+        @add_path()

+

+    add_border: () ->

+        border_coords = [[@y_buffer, @plot_height, @x_buffer, @x_buffer],

+                         [@y_buffer, @plot_height, @plot_width, @plot_width],

+                         [@y_buffer, @y_buffer, @x_buffer, @plot_width],

+                         [@plot_height, @plot_height, @x_buffer, @plot_width]]

+            

+        @svg.selectAll("line")

+            .data(border_coords)

+            .enter()

+            .append("line")

+            .attr("y1", (d) =>

+                return d[0]

+            )

+            .attr("y2", (d) =>

+                return d[1]

+            )

+            .attr("x1", (d) =>

+                return d[2]

+            )

+            .attr("x2", (d) =>

+                return d[3]

+            )             

+            .style("stroke", "#000")

+

+    add_x_axis: () ->

+        @xAxis = d3.svg.axis()

+                .scale(@x_scale)

+                .orient("bottom")

+                .ticks(20)

+

+        @xAxis.tickFormat((d) =>

+            d3.format("d") #format as integer

+            return (d)

+        )

+

+        @svg.append("g")

+            .attr("class", "x_axis")

+            .attr("transform", "translate(0," + @plot_height + ")")

+            .call(@xAxis)

+            .selectAll("text")

+                .attr("text-anchor", "right")

+                .attr("font-size", "12px")

+                .attr("dx", "-1.6em")

+                .attr("transform", (d) =>

+                    return "translate(-12,0) rotate(-90)"

+                )

+                

+    add_y_axis: () ->

+        @yAxis = d3.svg.axis()

+                .scale(@y_scale)

+                .orient("left")

+                .ticks(5)

+        

+        @svg.append("g")

+            .attr("class", "y_axis")

+            .attr("transform", "translate(" + @x_buffer + ",0)")

+            .call(@yAxis)

+

+    add_title: () ->

+        @svg.append("text")

+            .attr("class", "title")

+            .text("Chr " + @chr[0])

+            .attr("x", (d) =>

+                return (@plot_width + @x_buffer)/2

+            )

+            .attr("y", @y_buffer + 20)

+            .attr("dx", "0em")

+            .attr("text-anchor", "middle")

+            .attr("font-family", "sans-serif")

+            .attr("font-size", "18px")

+            .attr("fill", "black")

+

+    add_back_button: () ->

+        @svg.append("text")

+            .attr("class", "back")

+            .text("Return to full view")

+            .attr("x", @x_buffer*2)

+            .attr("y", @y_buffer/2)

+            .attr("dx", "0em")

+            .attr("text-anchor", "middle")

+            .attr("font-family", "sans-serif")

+            .attr("font-size", "18px")

+            .attr("cursor", "pointer")

+            .attr("fill", "black")

+            .on("click", @return_to_full_view)

+

+    add_path: () ->

+        line_function = d3.svg.line()

+                            .x( (d) => return @x_scale(d[0]))

+                            .y( (d) => return @y_scale(d[1]))

+                            .interpolate("linear")

+                            

+        line_graph = @svg.append("path")

+                        .attr("d", line_function(@plot_coordinates))

+                        .attr("stroke", "blue")

+                        .attr("stroke-width", 1)

+                        .attr("fill", "none")

+

+

+    #add_plot_points: () ->

+    #    @plot_point = @svg.selectAll("circle")

+    #        .data(@plot_coordinates)

+    #        .enter()

+    #        .append("circle")

+    #        .attr("cx", (d) =>

+    #            return @x_scale(d[0])

+    #        )

+    #        .attr("cy", (d) =>

+    #            return @y_scale(d[1])

+    #        )

+    #        .attr("r", (d) =>

+    #            #if d[1] > 2

+    #            #    return 3

+    #            #else

+    #            return 2

+    #        )

+    #        .attr("fill", (d) =>

+    #            #if d[1] > 2

+    #            #    return "white"

+    #            #else

+    #            return "black"

+    #        )

+    #        .attr("stroke", "black")

+    #        .attr("stroke-width", "1")

+    #        .attr("id", (d) =>

+    #            return "point_" + String(d[2])

+    #        )

+    #        .classed("circle", true)

+    #        .on("mouseover", (d) =>

+    #            console.log("d3.event is:", d3.event)

+    #            console.log("d is:", d)

+    #            this_id = "point_" + String(d[2])

+    #            d3.select("#" + this_id).classed("d3_highlight", true)

+    #                .attr("r", 5)

+    #                .attr("stroke", "none")

+    #                .attr("fill", "blue")

+    #                .call(@show_marker_in_table(d))

+    #        )

+    #        .on("mouseout", (d) =>

+    #            this_id = "point_" + String(d[2])

+    #            d3.select("#" + this_id).classed("d3_highlight", false)

+    #                .attr("r", (d) =>

+    #                    #if d[1] > 2

+    #                    #    return 3

+    #                    #else

+    #                    return 2

+    #                )

+    #                .attr("fill", (d) =>

+    #                    #if d[1] > 2

+    #                    #    return "white"

+    #                    #else

+    #                    return "black"

+    #                )

+    #                .attr("stroke", "black")

+    #                .attr("stroke-width", "1")

+    #        )

+    #        .append("svg:title")

+    #            .text((d) =>

+    #                return d[2]

+    #            )

+

+    return_to_full_view: () ->

+        $('#topchart').remove()

+        $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>')

+        create_interval_map()

+

+    show_marker_in_table: (marker_info) ->

+        console.log("in show_marker_in_table")

+        ### Searches for the select marker in the results table below ###

+        if marker_info

+            marker_name = marker_info[2]

+            $("#qtl_results_filter").find("input:first").val(marker_name).change()

+        #else

+        #    marker_name = ""

+        #$("#qtl_results_filter").find("input:first").val(marker_name).change()

diff --git a/wqflask/wqflask/static/new/javascript/chr_interval_map.js b/wqflask/wqflask/static/new/javascript/chr_interval_map.js
new file mode 100644
index 00000000..a4752a12
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/chr_interval_map.js
@@ -0,0 +1,224 @@
+// Generated by CoffeeScript 1.7.1
+var Chr_Interval_Map;
+
+Chr_Interval_Map = (function() {
+  function Chr_Interval_Map(plot_height, plot_width, chr) {
+    this.plot_height = plot_height;
+    this.plot_width = plot_width;
+    this.chr = chr;
+    this.qtl_results = js_data.qtl_results;
+    console.log("qtl_results are:", this.qtl_results);
+    console.log("chr is:", this.chr);
+    this.get_max_chr();
+    this.filter_qtl_results();
+    console.log("filtered results:", this.these_results);
+    this.get_qtl_count();
+    this.x_coords = [];
+    this.y_coords = [];
+    this.marker_names = [];
+    console.time('Create coordinates');
+    this.create_coordinates();
+    console.log("@x_coords: ", this.x_coords);
+    console.log("@y_coords: ", this.y_coords);
+    console.timeEnd('Create coordinates');
+    this.x_buffer = this.plot_width / 30;
+    this.y_buffer = this.plot_height / 20;
+    this.x_max = d3.max(this.x_coords);
+    this.y_max = d3.max(this.y_coords) * 1.2;
+    this.y_threshold = this.get_lod_threshold();
+    this.svg = this.create_svg();
+    this.plot_coordinates = _.zip(this.x_coords, this.y_coords, this.marker_names);
+    console.log("coordinates:", this.plot_coordinates);
+    this.plot_height -= this.y_buffer;
+    this.create_scales();
+    console.time('Create graph');
+    this.create_graph();
+    console.timeEnd('Create graph');
+  }
+
+  Chr_Interval_Map.prototype.get_max_chr = function() {
+    var key, _results;
+    this.max_chr = 0;
+    _results = [];
+    for (key in js_data.chromosomes) {
+      console.log("key is:", key);
+      if (parseInt(key) > this.max_chr) {
+        _results.push(this.max_chr = parseInt(key));
+      } else {
+        _results.push(void 0);
+      }
+    }
+    return _results;
+  };
+
+  Chr_Interval_Map.prototype.filter_qtl_results = function() {
+    var result, this_chr, _i, _len, _ref, _results;
+    this.these_results = [];
+    this_chr = 100;
+    _ref = this.qtl_results;
+    _results = [];
+    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+      result = _ref[_i];
+      if (result.chr === "X") {
+        this_chr = this.max_chr;
+      } else {
+        this_chr = result.chr;
+      }
+      console.log("this_chr is:", this_chr);
+      console.log("@chr[0] is:", parseInt(this.chr[0]));
+      if (this_chr > parseInt(this.chr[0])) {
+        break;
+      }
+      if (parseInt(this_chr) === parseInt(this.chr[0])) {
+        _results.push(this.these_results.push(result));
+      } else {
+        _results.push(void 0);
+      }
+    }
+    return _results;
+  };
+
+  Chr_Interval_Map.prototype.get_qtl_count = function() {
+    var high_qtl_count, result, _i, _len, _ref;
+    high_qtl_count = 0;
+    _ref = this.these_results;
+    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+      result = _ref[_i];
+      if (result.lrs_value > 1) {
+        high_qtl_count += 1;
+      }
+    }
+    console.log("high_qtl_count:", high_qtl_count);
+    return this.y_axis_filter = 2;
+  };
+
+  Chr_Interval_Map.prototype.create_coordinates = function() {
+    var result, _i, _len, _ref, _results;
+    _ref = this.these_results;
+    _results = [];
+    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+      result = _ref[_i];
+      this.x_coords.push(parseFloat(result.Mb));
+      this.y_coords.push(result.lrs_value);
+      _results.push(this.marker_names.push(result.name));
+    }
+    return _results;
+  };
+
+  Chr_Interval_Map.prototype.create_svg = function() {
+    var svg;
+    svg = d3.select("#topchart").append("svg").attr("class", "chr_interval_map").attr("width", this.plot_width + this.x_buffer).attr("height", this.plot_height + this.y_buffer).append("g");
+    return svg;
+  };
+
+  Chr_Interval_Map.prototype.create_scales = function() {
+    console.log("chr[1] is:", this.chr[1]);
+    this.x_scale = d3.scale.linear().domain([0, this.chr[1]]).range([this.x_buffer, this.plot_width]);
+    return this.y_scale = d3.scale.linear().domain([0, this.y_max]).range([this.plot_height, this.y_buffer]);
+  };
+
+  Chr_Interval_Map.prototype.get_lod_threshold = function() {
+    if (this.y_max / 2 > 2) {
+      return this.y_max / 2;
+    } else {
+      return 2;
+    }
+  };
+
+  Chr_Interval_Map.prototype.create_graph = function() {
+    this.add_border();
+    this.add_x_axis();
+    this.add_y_axis();
+    this.add_title();
+    this.add_back_button();
+    return this.add_path();
+  };
+
+  Chr_Interval_Map.prototype.add_border = function() {
+    var border_coords;
+    border_coords = [[this.y_buffer, this.plot_height, this.x_buffer, this.x_buffer], [this.y_buffer, this.plot_height, this.plot_width, this.plot_width], [this.y_buffer, this.y_buffer, this.x_buffer, this.plot_width], [this.plot_height, this.plot_height, this.x_buffer, this.plot_width]];
+    return this.svg.selectAll("line").data(border_coords).enter().append("line").attr("y1", (function(_this) {
+      return function(d) {
+        return d[0];
+      };
+    })(this)).attr("y2", (function(_this) {
+      return function(d) {
+        return d[1];
+      };
+    })(this)).attr("x1", (function(_this) {
+      return function(d) {
+        return d[2];
+      };
+    })(this)).attr("x2", (function(_this) {
+      return function(d) {
+        return d[3];
+      };
+    })(this)).style("stroke", "#000");
+  };
+
+  Chr_Interval_Map.prototype.add_x_axis = function() {
+    this.xAxis = d3.svg.axis().scale(this.x_scale).orient("bottom").ticks(20);
+    this.xAxis.tickFormat((function(_this) {
+      return function(d) {
+        d3.format("d");
+        return d;
+      };
+    })(this));
+    return this.svg.append("g").attr("class", "x_axis").attr("transform", "translate(0," + this.plot_height + ")").call(this.xAxis).selectAll("text").attr("text-anchor", "right").attr("font-size", "12px").attr("dx", "-1.6em").attr("transform", (function(_this) {
+      return function(d) {
+        return "translate(-12,0) rotate(-90)";
+      };
+    })(this));
+  };
+
+  Chr_Interval_Map.prototype.add_y_axis = function() {
+    this.yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
+    return this.svg.append("g").attr("class", "y_axis").attr("transform", "translate(" + this.x_buffer + ",0)").call(this.yAxis);
+  };
+
+  Chr_Interval_Map.prototype.add_title = function() {
+    return this.svg.append("text").attr("class", "title").text("Chr " + this.chr[0]).attr("x", (function(_this) {
+      return function(d) {
+        return (_this.plot_width + _this.x_buffer) / 2;
+      };
+    })(this)).attr("y", this.y_buffer + 20).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("fill", "black");
+  };
+
+  Chr_Interval_Map.prototype.add_back_button = function() {
+    return this.svg.append("text").attr("class", "back").text("Return to full view").attr("x", this.x_buffer * 2).attr("y", this.y_buffer / 2).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("cursor", "pointer").attr("fill", "black").on("click", this.return_to_full_view);
+  };
+
+  Chr_Interval_Map.prototype.add_path = function() {
+    var line_function, line_graph;
+    line_function = d3.svg.line().x((function(_this) {
+      return function(d) {
+        return _this.x_scale(d[0]);
+      };
+    })(this)).y((function(_this) {
+      return function(d) {
+        return _this.y_scale(d[1]);
+      };
+    })(this)).interpolate("linear");
+    return line_graph = this.svg.append("path").attr("d", line_function(this.plot_coordinates)).attr("stroke", "blue").attr("stroke-width", 1).attr("fill", "none");
+  };
+
+  Chr_Interval_Map.prototype.return_to_full_view = function() {
+    $('#topchart').remove();
+    $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>');
+    return create_interval_map();
+  };
+
+  Chr_Interval_Map.prototype.show_marker_in_table = function(marker_info) {
+    var marker_name;
+    console.log("in show_marker_in_table");
+
+    /* Searches for the select marker in the results table below */
+    if (marker_info) {
+      marker_name = marker_info[2];
+      return $("#qtl_results_filter").find("input:first").val(marker_name).change();
+    }
+  };
+
+  return Chr_Interval_Map;
+
+})();
diff --git a/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.coffee b/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.coffee
index 8b27caa1..8b62d58a 100755
--- a/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.coffee
+++ b/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.coffee
@@ -1,5 +1,3 @@
-root = exports ? this

-    

 class Chr_Manhattan_Plot

     constructor: (@plot_height, @plot_width, @chr) ->

         @qtl_results = js_data.qtl_results

@@ -87,9 +85,9 @@ class Chr_Manhattan_Plot
             @marker_names.push(result.name)

             

     create_svg: () ->

-        svg = d3.select("#manhattan_plot")

+        svg = d3.select("#topchart")

             .append("svg")

-            .attr("class", "manhattan_plot")

+            .attr("class", "chr_manhattan_plot")

             .attr("width", @plot_width+@x_buffer)

             .attr("height", @plot_height+@y_buffer)

             .append("g")

@@ -100,7 +98,7 @@ class Chr_Manhattan_Plot
             .domain([0, @chr[1]])

             .range([@x_buffer, @plot_width])

         @y_scale = d3.scale.linear()

-            .domain([@y_axis_filter, @y_max])

+            .domain([0, @y_max])

             .range([@plot_height, @y_buffer])

             

     get_lod_threshold: () ->

@@ -203,6 +201,7 @@ class Chr_Manhattan_Plot
             .attr("fill", "black")

             .on("click", @return_to_full_view)

 

+

     add_plot_points: () ->

         @plot_point = @svg.selectAll("circle")

             .data(@plot_coordinates)

@@ -266,9 +265,9 @@ class Chr_Manhattan_Plot
                 )

 

     return_to_full_view: () ->

-        $('#manhattan_plot').remove()

-        $('#manhattan_plot_container').append('<div id="manhattan_plot"></div>')

-        root.manhattan_plot = new root.Manhattan_Plot

+        $('#topchart').remove()

+        $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>')

+        create_manhattan_plot()

 

     show_marker_in_table: (marker_info) ->

         console.log("in show_marker_in_table")

@@ -279,5 +278,3 @@ class Chr_Manhattan_Plot
         #else

         #    marker_name = ""

         #$("#qtl_results_filter").find("input:first").val(marker_name).change()

-

-root.Chr_Manhattan_Plot = Chr_Manhattan_Plot
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.js b/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.js
index b7f64094..24d8b962 100755
--- a/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.js
+++ b/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.js
@@ -1,204 +1,223 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var Chr_Manhattan_Plot, root;
-
-  root = typeof exports !== "undefined" && exports !== null ? exports : this;
-
-  Chr_Manhattan_Plot = (function() {
-
-    function Chr_Manhattan_Plot(plot_height, plot_width, chr) {
-      this.plot_height = plot_height;
-      this.plot_width = plot_width;
-      this.chr = chr;
-      this.qtl_results = js_data.qtl_results;
-      console.log("qtl_results are:", this.qtl_results);
-      console.log("chr is:", this.chr);
-      this.get_max_chr();
-      this.filter_qtl_results();
-      console.log("filtered results:", this.these_results);
-      this.get_qtl_count();
-      this.x_coords = [];
-      this.y_coords = [];
-      this.marker_names = [];
-      console.time('Create coordinates');
-      this.create_coordinates();
-      console.log("@x_coords: ", this.x_coords);
-      console.log("@y_coords: ", this.y_coords);
-      console.timeEnd('Create coordinates');
-      this.x_buffer = this.plot_width / 30;
-      this.y_buffer = this.plot_height / 20;
-      this.x_max = d3.max(this.x_coords);
-      this.y_max = d3.max(this.y_coords) * 1.2;
-      this.y_threshold = this.get_lod_threshold();
-      this.svg = this.create_svg();
-      this.plot_coordinates = _.zip(this.x_coords, this.y_coords, this.marker_names);
-      console.log("coordinates:", this.plot_coordinates);
-      this.plot_height -= this.y_buffer;
-      this.create_scales();
-      console.time('Create graph');
-      this.create_graph();
-      console.timeEnd('Create graph');
-    }
-
-    Chr_Manhattan_Plot.prototype.get_max_chr = function() {
-      var key, _results;
-      this.max_chr = 0;
-      _results = [];
-      for (key in js_data.chromosomes) {
-        console.log("key is:", key);
-        if (parseInt(key) > this.max_chr) {
-          _results.push(this.max_chr = parseInt(key));
-        } else {
-          _results.push(void 0);
-        }
-      }
-      return _results;
-    };
-
-    Chr_Manhattan_Plot.prototype.filter_qtl_results = function() {
-      var result, this_chr, _i, _len, _ref, _results;
-      this.these_results = [];
-      this_chr = 100;
-      _ref = this.qtl_results;
-      _results = [];
-      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-        result = _ref[_i];
-        if (result.chr === "X") {
-          this_chr = this.max_chr;
-        } else {
-          this_chr = result.chr;
-        }
-        console.log("this_chr is:", this_chr);
-        console.log("@chr[0] is:", parseInt(this.chr[0]));
-        if (this_chr > parseInt(this.chr[0])) {
-          break;
-        }
-        if (parseInt(this_chr) === parseInt(this.chr[0])) {
-          _results.push(this.these_results.push(result));
-        } else {
-          _results.push(void 0);
-        }
+// Generated by CoffeeScript 1.7.1
+var Chr_Manhattan_Plot;
+
+Chr_Manhattan_Plot = (function() {
+  function Chr_Manhattan_Plot(plot_height, plot_width, chr) {
+    this.plot_height = plot_height;
+    this.plot_width = plot_width;
+    this.chr = chr;
+    this.qtl_results = js_data.qtl_results;
+    console.log("qtl_results are:", this.qtl_results);
+    console.log("chr is:", this.chr);
+    this.get_max_chr();
+    this.filter_qtl_results();
+    console.log("filtered results:", this.these_results);
+    this.get_qtl_count();
+    this.x_coords = [];
+    this.y_coords = [];
+    this.marker_names = [];
+    console.time('Create coordinates');
+    this.create_coordinates();
+    console.log("@x_coords: ", this.x_coords);
+    console.log("@y_coords: ", this.y_coords);
+    console.timeEnd('Create coordinates');
+    this.x_buffer = this.plot_width / 30;
+    this.y_buffer = this.plot_height / 20;
+    this.x_max = d3.max(this.x_coords);
+    this.y_max = d3.max(this.y_coords) * 1.2;
+    this.y_threshold = this.get_lod_threshold();
+    this.svg = this.create_svg();
+    this.plot_coordinates = _.zip(this.x_coords, this.y_coords, this.marker_names);
+    console.log("coordinates:", this.plot_coordinates);
+    this.plot_height -= this.y_buffer;
+    this.create_scales();
+    console.time('Create graph');
+    this.create_graph();
+    console.timeEnd('Create graph');
+  }
+
+  Chr_Manhattan_Plot.prototype.get_max_chr = function() {
+    var key, _results;
+    this.max_chr = 0;
+    _results = [];
+    for (key in js_data.chromosomes) {
+      console.log("key is:", key);
+      if (parseInt(key) > this.max_chr) {
+        _results.push(this.max_chr = parseInt(key));
+      } else {
+        _results.push(void 0);
       }
-      return _results;
-    };
-
-    Chr_Manhattan_Plot.prototype.get_qtl_count = function() {
-      var high_qtl_count, result, _i, _len, _ref;
-      high_qtl_count = 0;
-      _ref = this.these_results;
-      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-        result = _ref[_i];
-        if (result.lod_score > 1) {
-          high_qtl_count += 1;
-        }
+    }
+    return _results;
+  };
+
+  Chr_Manhattan_Plot.prototype.filter_qtl_results = function() {
+    var result, this_chr, _i, _len, _ref, _results;
+    this.these_results = [];
+    this_chr = 100;
+    _ref = this.qtl_results;
+    _results = [];
+    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+      result = _ref[_i];
+      if (result.chr === "X") {
+        this_chr = this.max_chr;
+      } else {
+        this_chr = result.chr;
       }
-      console.log("high_qtl_count:", high_qtl_count);
-      return this.y_axis_filter = 2;
-    };
-
-    Chr_Manhattan_Plot.prototype.create_coordinates = function() {
-      var result, _i, _len, _ref, _results;
-      _ref = this.these_results;
-      _results = [];
-      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-        result = _ref[_i];
-        this.x_coords.push(parseFloat(result.Mb));
-        this.y_coords.push(result.lod_score);
-        _results.push(this.marker_names.push(result.name));
+      console.log("this_chr is:", this_chr);
+      console.log("@chr[0] is:", parseInt(this.chr[0]));
+      if (this_chr > parseInt(this.chr[0])) {
+        break;
       }
-      return _results;
-    };
-
-    Chr_Manhattan_Plot.prototype.create_svg = function() {
-      var svg;
-      svg = d3.select("#manhattan_plot").append("svg").attr("class", "manhattan_plot").attr("width", this.plot_width + this.x_buffer).attr("height", this.plot_height + this.y_buffer).append("g");
-      return svg;
-    };
-
-    Chr_Manhattan_Plot.prototype.create_scales = function() {
-      this.x_scale = d3.scale.linear().domain([0, this.chr[1]]).range([this.x_buffer, this.plot_width]);
-      return this.y_scale = d3.scale.linear().domain([this.y_axis_filter, this.y_max]).range([this.plot_height, this.y_buffer]);
-    };
-
-    Chr_Manhattan_Plot.prototype.get_lod_threshold = function() {
-      if (this.y_max / 2 > 2) {
-        return this.y_max / 2;
+      if (parseInt(this_chr) === parseInt(this.chr[0])) {
+        _results.push(this.these_results.push(result));
       } else {
-        return 2;
+        _results.push(void 0);
       }
-    };
-
-    Chr_Manhattan_Plot.prototype.create_graph = function() {
-      this.add_border();
-      this.add_x_axis();
-      this.add_y_axis();
-      this.add_title();
-      this.add_back_button();
-      return this.add_plot_points();
-    };
-
-    Chr_Manhattan_Plot.prototype.add_border = function() {
-      var border_coords,
-        _this = this;
-      border_coords = [[this.y_buffer, this.plot_height, this.x_buffer, this.x_buffer], [this.y_buffer, this.plot_height, this.plot_width, this.plot_width], [this.y_buffer, this.y_buffer, this.x_buffer, this.plot_width], [this.plot_height, this.plot_height, this.x_buffer, this.plot_width]];
-      return this.svg.selectAll("line").data(border_coords).enter().append("line").attr("y1", function(d) {
+    }
+    return _results;
+  };
+
+  Chr_Manhattan_Plot.prototype.get_qtl_count = function() {
+    var high_qtl_count, result, _i, _len, _ref;
+    high_qtl_count = 0;
+    _ref = this.these_results;
+    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+      result = _ref[_i];
+      if (result.lod_score > 1) {
+        high_qtl_count += 1;
+      }
+    }
+    console.log("high_qtl_count:", high_qtl_count);
+    return this.y_axis_filter = 2;
+  };
+
+  Chr_Manhattan_Plot.prototype.create_coordinates = function() {
+    var result, _i, _len, _ref, _results;
+    _ref = this.these_results;
+    _results = [];
+    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+      result = _ref[_i];
+      this.x_coords.push(parseFloat(result.Mb));
+      this.y_coords.push(result.lod_score);
+      _results.push(this.marker_names.push(result.name));
+    }
+    return _results;
+  };
+
+  Chr_Manhattan_Plot.prototype.create_svg = function() {
+    var svg;
+    svg = d3.select("#topchart").append("svg").attr("class", "chr_manhattan_plot").attr("width", this.plot_width + this.x_buffer).attr("height", this.plot_height + this.y_buffer).append("g");
+    return svg;
+  };
+
+  Chr_Manhattan_Plot.prototype.create_scales = function() {
+    this.x_scale = d3.scale.linear().domain([0, this.chr[1]]).range([this.x_buffer, this.plot_width]);
+    return this.y_scale = d3.scale.linear().domain([0, this.y_max]).range([this.plot_height, this.y_buffer]);
+  };
+
+  Chr_Manhattan_Plot.prototype.get_lod_threshold = function() {
+    if (this.y_max / 2 > 2) {
+      return this.y_max / 2;
+    } else {
+      return 2;
+    }
+  };
+
+  Chr_Manhattan_Plot.prototype.create_graph = function() {
+    this.add_border();
+    this.add_x_axis();
+    this.add_y_axis();
+    this.add_title();
+    this.add_back_button();
+    return this.add_plot_points();
+  };
+
+  Chr_Manhattan_Plot.prototype.add_border = function() {
+    var border_coords;
+    border_coords = [[this.y_buffer, this.plot_height, this.x_buffer, this.x_buffer], [this.y_buffer, this.plot_height, this.plot_width, this.plot_width], [this.y_buffer, this.y_buffer, this.x_buffer, this.plot_width], [this.plot_height, this.plot_height, this.x_buffer, this.plot_width]];
+    return this.svg.selectAll("line").data(border_coords).enter().append("line").attr("y1", (function(_this) {
+      return function(d) {
         return d[0];
-      }).attr("y2", function(d) {
+      };
+    })(this)).attr("y2", (function(_this) {
+      return function(d) {
         return d[1];
-      }).attr("x1", function(d) {
+      };
+    })(this)).attr("x1", (function(_this) {
+      return function(d) {
         return d[2];
-      }).attr("x2", function(d) {
+      };
+    })(this)).attr("x2", (function(_this) {
+      return function(d) {
         return d[3];
-      }).style("stroke", "#000");
-    };
-
-    Chr_Manhattan_Plot.prototype.add_x_axis = function() {
-      var _this = this;
-      this.xAxis = d3.svg.axis().scale(this.x_scale).orient("bottom").ticks(20);
-      this.xAxis.tickFormat(function(d) {
+      };
+    })(this)).style("stroke", "#000");
+  };
+
+  Chr_Manhattan_Plot.prototype.add_x_axis = function() {
+    this.xAxis = d3.svg.axis().scale(this.x_scale).orient("bottom").ticks(20);
+    this.xAxis.tickFormat((function(_this) {
+      return function(d) {
         d3.format("d");
         return d;
-      });
-      return this.svg.append("g").attr("class", "x_axis").attr("transform", "translate(0," + this.plot_height + ")").call(this.xAxis).selectAll("text").attr("text-anchor", "right").attr("font-size", "12px").attr("dx", "-1.6em").attr("transform", function(d) {
+      };
+    })(this));
+    return this.svg.append("g").attr("class", "x_axis").attr("transform", "translate(0," + this.plot_height + ")").call(this.xAxis).selectAll("text").attr("text-anchor", "right").attr("font-size", "12px").attr("dx", "-1.6em").attr("transform", (function(_this) {
+      return function(d) {
         return "translate(-12,0) rotate(-90)";
-      });
-    };
-
-    Chr_Manhattan_Plot.prototype.add_y_axis = function() {
-      this.yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
-      return this.svg.append("g").attr("class", "y_axis").attr("transform", "translate(" + this.x_buffer + ",0)").call(this.yAxis);
-    };
-
-    Chr_Manhattan_Plot.prototype.add_title = function() {
-      var _this = this;
-      return this.svg.append("text").attr("class", "title").text("Chr " + this.chr[0]).attr("x", function(d) {
+      };
+    })(this));
+  };
+
+  Chr_Manhattan_Plot.prototype.add_y_axis = function() {
+    this.yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
+    return this.svg.append("g").attr("class", "y_axis").attr("transform", "translate(" + this.x_buffer + ",0)").call(this.yAxis);
+  };
+
+  Chr_Manhattan_Plot.prototype.add_title = function() {
+    return this.svg.append("text").attr("class", "title").text("Chr " + this.chr[0]).attr("x", (function(_this) {
+      return function(d) {
         return (_this.plot_width + _this.x_buffer) / 2;
-      }).attr("y", this.y_buffer + 20).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("fill", "black");
-    };
+      };
+    })(this)).attr("y", this.y_buffer + 20).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("fill", "black");
+  };
 
-    Chr_Manhattan_Plot.prototype.add_back_button = function() {
-      return this.svg.append("text").attr("class", "back").text("Return to full view").attr("x", this.x_buffer * 2).attr("y", this.y_buffer / 2).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("cursor", "pointer").attr("fill", "black").on("click", this.return_to_full_view);
-    };
+  Chr_Manhattan_Plot.prototype.add_back_button = function() {
+    return this.svg.append("text").attr("class", "back").text("Return to full view").attr("x", this.x_buffer * 2).attr("y", this.y_buffer / 2).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("cursor", "pointer").attr("fill", "black").on("click", this.return_to_full_view);
+  };
 
-    Chr_Manhattan_Plot.prototype.add_plot_points = function() {
-      var _this = this;
-      return this.plot_point = this.svg.selectAll("circle").data(this.plot_coordinates).enter().append("circle").attr("cx", function(d) {
+  Chr_Manhattan_Plot.prototype.add_plot_points = function() {
+    return this.plot_point = this.svg.selectAll("circle").data(this.plot_coordinates).enter().append("circle").attr("cx", (function(_this) {
+      return function(d) {
         return _this.x_scale(d[0]);
-      }).attr("cy", function(d) {
+      };
+    })(this)).attr("cy", (function(_this) {
+      return function(d) {
         return _this.y_scale(d[1]);
-      }).attr("r", function(d) {
+      };
+    })(this)).attr("r", (function(_this) {
+      return function(d) {
         return 2;
-      }).attr("fill", function(d) {
+      };
+    })(this)).attr("fill", (function(_this) {
+      return function(d) {
         return "black";
-      }).attr("stroke", "black").attr("stroke-width", "1").attr("id", function(d) {
+      };
+    })(this)).attr("stroke", "black").attr("stroke-width", "1").attr("id", (function(_this) {
+      return function(d) {
         return "point_" + String(d[2]);
-      }).classed("circle", true).on("mouseover", function(d) {
+      };
+    })(this)).classed("circle", true).on("mouseover", (function(_this) {
+      return function(d) {
         var this_id;
         console.log("d3.event is:", d3.event);
         console.log("d is:", d);
         this_id = "point_" + String(d[2]);
         return d3.select("#" + this_id).classed("d3_highlight", true).attr("r", 5).attr("stroke", "none").attr("fill", "blue").call(_this.show_marker_in_table(d));
-      }).on("mouseout", function(d) {
+      };
+    })(this)).on("mouseout", (function(_this) {
+      return function(d) {
         var this_id;
         this_id = "point_" + String(d[2]);
         return d3.select("#" + this_id).classed("d3_highlight", false).attr("r", function(d) {
@@ -206,33 +225,31 @@
         }).attr("fill", function(d) {
           return "black";
         }).attr("stroke", "black").attr("stroke-width", "1");
-      }).append("svg:title").text(function(d) {
+      };
+    })(this)).append("svg:title").text((function(_this) {
+      return function(d) {
         return d[2];
-      });
-    };
-
-    Chr_Manhattan_Plot.prototype.return_to_full_view = function() {
-      $('#manhattan_plot').remove();
-      $('#manhattan_plot_container').append('<div id="manhattan_plot"></div>');
-      return root.manhattan_plot = new root.Manhattan_Plot;
-    };
-
-    Chr_Manhattan_Plot.prototype.show_marker_in_table = function(marker_info) {
-      var marker_name;
-      console.log("in show_marker_in_table");
-      /* Searches for the select marker in the results table below
-      */
-
-      if (marker_info) {
-        marker_name = marker_info[2];
-        return $("#qtl_results_filter").find("input:first").val(marker_name).change();
-      }
-    };
-
-    return Chr_Manhattan_Plot;
-
-  })();
+      };
+    })(this));
+  };
+
+  Chr_Manhattan_Plot.prototype.return_to_full_view = function() {
+    $('#topchart').remove();
+    $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>');
+    return create_manhattan_plot();
+  };
+
+  Chr_Manhattan_Plot.prototype.show_marker_in_table = function(marker_info) {
+    var marker_name;
+    console.log("in show_marker_in_table");
+
+    /* Searches for the select marker in the results table below */
+    if (marker_info) {
+      marker_name = marker_info[2];
+      return $("#qtl_results_filter").find("input:first").val(marker_name).change();
+    }
+  };
 
-  root.Chr_Manhattan_Plot = Chr_Manhattan_Plot;
+  return Chr_Manhattan_Plot;
 
-}).call(this);
+})();
diff --git a/wqflask/wqflask/static/new/javascript/compare_traits_scatterplot.js b/wqflask/wqflask/static/new/javascript/compare_traits_scatterplot.js
index a45eb3c0..34977878 100644
--- a/wqflask/wqflask/static/new/javascript/compare_traits_scatterplot.js
+++ b/wqflask/wqflask/static/new/javascript/compare_traits_scatterplot.js
@@ -1,124 +1,121 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var root;
+// Generated by CoffeeScript 1.7.1
+var root;
 
-  root = typeof exports !== "undefined" && exports !== null ? exports : this;
+root = typeof exports !== "undefined" && exports !== null ? exports : this;
 
-  root.create_scatterplot = function(json_ids, json_data) {
-    var data, h, halfh, halfw, indID, margin, mychart, totalh, totalw, w;
-    console.log("TESTING2");
-    h = 400;
-    w = 500;
-    margin = {
-      left: 60,
-      top: 40,
-      right: 40,
-      bottom: 40,
-      inner: 5
-    };
-    halfh = h + margin.top + margin.bottom;
-    totalh = halfh * 2;
-    halfw = w + margin.left + margin.right;
-    totalw = halfw * 2;
-    mychart = scatterplot().xvar(0).yvar(1).xlab("X").ylab("Y").height(h).width(w).margin(margin);
+root.create_scatterplot = function(json_ids, json_data) {
+  var data, h, halfh, halfw, indID, margin, mychart, totalh, totalw, w;
+  console.log("TESTING2");
+  h = 400;
+  w = 500;
+  margin = {
+    left: 60,
+    top: 40,
+    right: 40,
+    bottom: 40,
+    inner: 5
+  };
+  halfh = h + margin.top + margin.bottom;
+  totalh = halfh * 2;
+  halfw = w + margin.left + margin.right;
+  totalw = halfw * 2;
+  mychart = scatterplot().xvar(0).yvar(1).xlab("X").ylab("Y").height(h).width(w).margin(margin);
+  data = json_data;
+  indID = json_ids;
+  d3.select("div#comparison_scatterplot").datum({
+    data: data,
+    indID: indID
+  }).call(mychart);
+  return mychart.pointsSelect().on("mouseover", function(d) {
+    return d3.select(this).attr("r", mychart.pointsize() * 3);
+  }).on("mouseout", function(d) {
+    return d3.select(this).attr("r", mychart.pointsize());
+  });
+};
+
+root.create_scatterplots = function(trait_names, json_ids, json_data) {
+  var brush, brushend, brushmove, brushstart, chart, data, h, halfh, halfw, i, indID, margin, mychart, num_traits, svg, totalh, totalw, w, xscale, xshift, xvar, yscale, yshift, yvar, _i, _j, _k, _ref, _ref1, _ref2, _results;
+  console.log("json_data:", json_data);
+  console.log("trait_names:", trait_names);
+  num_traits = json_data.length;
+  console.log("num_traits:", num_traits);
+  h = 300;
+  w = 400;
+  margin = {
+    left: 60,
+    top: 40,
+    right: 40,
+    bottom: 40,
+    inner: 5
+  };
+  halfh = h + margin.top + margin.bottom;
+  totalh = halfh * (num_traits - 1);
+  halfw = w + margin.left + margin.right;
+  totalw = halfw;
+  xvar = [];
+  yvar = [];
+  xshift = [];
+  yshift = [];
+  for (i = _i = 0, _ref = num_traits - 1; 0 <= _ref ? _i <= _ref : _i >= _ref; i = 0 <= _ref ? ++_i : --_i) {
+    xvar.push(i);
+    yvar.push(0);
+    xshift.push(0);
+    yshift.push(halfh * i);
+  }
+  console.log("xvar:", xvar);
+  console.log("yvar:", yvar);
+  svg = d3.select("div#comparison_scatterplot").append("svg").attr("height", totalh).attr("width", totalw);
+  mychart = [];
+  chart = [];
+  for (i = _j = 1, _ref1 = num_traits - 1; 1 <= _ref1 ? _j <= _ref1 : _j >= _ref1; i = 1 <= _ref1 ? ++_j : --_j) {
+    mychart[i - 1] = scatterplot().xvar(xvar[i]).yvar(yvar[i]).nxticks(6).height(h).width(w).margin(margin).pointsize(4).xlab("" + trait_names[i - 1]).ylab("" + trait_names[0]).title("" + trait_names[0] + " vs. " + trait_names[i - 1]);
     data = json_data;
     indID = json_ids;
-    d3.select("div#comparison_scatterplot").datum({
+    chart[i - 1] = svg.append("g").attr("id", "chart" + (i - 1)).attr("transform", "translate(" + xshift[i] + "," + yshift[i - 1] + ")");
+    chart[i - 1].datum({
       data: data,
       indID: indID
-    }).call(mychart);
-    return mychart.pointsSelect().on("mouseover", function(d) {
-      return d3.select(this).attr("r", mychart.pointsize() * 3);
-    }).on("mouseout", function(d) {
-      return d3.select(this).attr("r", mychart.pointsize());
-    });
-  };
-
-  root.create_scatterplots = function(trait_names, json_ids, json_data) {
-    var brush, brushend, brushmove, brushstart, chart, data, h, halfh, halfw, i, indID, margin, mychart, num_traits, svg, totalh, totalw, w, xscale, xshift, xvar, yscale, yshift, yvar, _i, _j, _k, _ref, _ref1, _ref2, _results;
-    console.log("json_data:", json_data);
-    console.log("trait_names:", trait_names);
-    num_traits = json_data.length;
-    console.log("num_traits:", num_traits);
-    h = 300;
-    w = 400;
-    margin = {
-      left: 60,
-      top: 40,
-      right: 40,
-      bottom: 40,
-      inner: 5
-    };
-    halfh = h + margin.top + margin.bottom;
-    totalh = halfh * (num_traits - 1);
-    halfw = w + margin.left + margin.right;
-    totalw = halfw;
-    xvar = [];
-    yvar = [];
-    xshift = [];
-    yshift = [];
-    for (i = _i = 0, _ref = num_traits - 1; 0 <= _ref ? _i <= _ref : _i >= _ref; i = 0 <= _ref ? ++_i : --_i) {
-      xvar.push(i);
-      yvar.push(0);
-      xshift.push(0);
-      yshift.push(halfh * i);
-    }
-    console.log("xvar:", xvar);
-    console.log("yvar:", yvar);
-    svg = d3.select("div#comparison_scatterplot").append("svg").attr("height", totalh).attr("width", totalw);
-    mychart = [];
-    chart = [];
-    for (i = _j = 1, _ref1 = num_traits - 1; 1 <= _ref1 ? _j <= _ref1 : _j >= _ref1; i = 1 <= _ref1 ? ++_j : --_j) {
-      mychart[i - 1] = scatterplot().xvar(xvar[i]).yvar(yvar[i]).nxticks(6).height(h).width(w).margin(margin).pointsize(4).xlab("" + trait_names[i - 1]).ylab("" + trait_names[0]).title("" + trait_names[0] + " vs. " + trait_names[i - 1]);
-      data = json_data;
-      indID = json_ids;
-      chart[i - 1] = svg.append("g").attr("id", "chart" + (i - 1)).attr("transform", "translate(" + xshift[i] + "," + yshift[i - 1] + ")");
-      chart[i - 1].datum({
-        data: data,
-        indID: indID
-      }).call(mychart[i - 1]);
-    }
-    brush = [];
-    brushstart = function(i) {
-      return function() {
-        var j, _k, _ref2;
-        for (j = _k = 0, _ref2 = num_traits - 2; 0 <= _ref2 ? _k <= _ref2 : _k >= _ref2; j = 0 <= _ref2 ? ++_k : --_k) {
-          if (j !== i) {
-            chart[j].call(brush[j].clear());
-          }
+    }).call(mychart[i - 1]);
+  }
+  brush = [];
+  brushstart = function(i) {
+    return function() {
+      var j, _k, _ref2;
+      for (j = _k = 0, _ref2 = num_traits - 2; 0 <= _ref2 ? _k <= _ref2 : _k >= _ref2; j = 0 <= _ref2 ? ++_k : --_k) {
+        if (j !== i) {
+          chart[j].call(brush[j].clear());
         }
-        return svg.selectAll("circle").attr("opacity", 0.6).classed("selected", false);
-      };
-    };
-    brushmove = function(i) {
-      return function() {
-        var e;
-        svg.selectAll("circle").classed("selected", false);
-        e = brush[i].extent();
-        return chart[i].selectAll("circle").classed("selected", function(d, j) {
-          var circ, cx, cy, selected;
-          circ = d3.select(this);
-          cx = circ.attr("cx");
-          cy = circ.attr("cy");
-          selected = e[0][0] <= cx && cx <= e[1][0] && e[0][1] <= cy && cy <= e[1][1];
-          if (selected) {
-            svg.selectAll("circle.pt" + j).classed("selected", true);
-          }
-          return selected;
-        });
-      };
+      }
+      return svg.selectAll("circle").attr("opacity", 0.6).classed("selected", false);
     };
-    brushend = function() {
-      return svg.selectAll("circle").attr("opacity", 1);
+  };
+  brushmove = function(i) {
+    return function() {
+      var e;
+      svg.selectAll("circle").classed("selected", false);
+      e = brush[i].extent();
+      return chart[i].selectAll("circle").classed("selected", function(d, j) {
+        var circ, cx, cy, selected;
+        circ = d3.select(this);
+        cx = circ.attr("cx");
+        cy = circ.attr("cy");
+        selected = e[0][0] <= cx && cx <= e[1][0] && e[0][1] <= cy && cy <= e[1][1];
+        if (selected) {
+          svg.selectAll("circle.pt" + j).classed("selected", true);
+        }
+        return selected;
+      });
     };
-    xscale = d3.scale.linear().domain([margin.left, margin.left + w]).range([margin.left, margin.left + w]);
-    yscale = d3.scale.linear().domain([margin.top, margin.top + h]).range([margin.top, margin.top + h]);
-    _results = [];
-    for (i = _k = 0, _ref2 = num_traits - 2; 0 <= _ref2 ? _k <= _ref2 : _k >= _ref2; i = 0 <= _ref2 ? ++_k : --_k) {
-      brush[i] = d3.svg.brush().x(xscale).y(yscale).on("brushstart", brushstart(i)).on("brush", brushmove(i)).on("brushend", brushend);
-      _results.push(chart[i].call(brush[i]));
-    }
-    return _results;
   };
-
-}).call(this);
+  brushend = function() {
+    return svg.selectAll("circle").attr("opacity", 1);
+  };
+  xscale = d3.scale.linear().domain([margin.left, margin.left + w]).range([margin.left, margin.left + w]);
+  yscale = d3.scale.linear().domain([margin.top, margin.top + h]).range([margin.top, margin.top + h]);
+  _results = [];
+  for (i = _k = 0, _ref2 = num_traits - 2; 0 <= _ref2 ? _k <= _ref2 : _k >= _ref2; i = 0 <= _ref2 ? ++_k : --_k) {
+    brush[i] = d3.svg.brush().x(xscale).y(yscale).on("brushstart", brushstart(i)).on("brush", brushmove(i)).on("brushend", brushend);
+    _results.push(chart[i].call(brush[i]));
+  }
+  return _results;
+};
diff --git a/wqflask/wqflask/static/new/javascript/corr_matrix.js b/wqflask/wqflask/static/new/javascript/corr_matrix.js
index 17625f99..cfe2159e 100644
--- a/wqflask/wqflask/static/new/javascript/corr_matrix.js
+++ b/wqflask/wqflask/static/new/javascript/corr_matrix.js
@@ -1,157 +1,154 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var iplotCorr, root;
+// Generated by CoffeeScript 1.7.1
+var iplotCorr, root;
 
-  root = typeof exports !== "undefined" && exports !== null ? exports : this;
+root = typeof exports !== "undefined" && exports !== null ? exports : this;
 
-  iplotCorr = function(data, chartOpts) {
-    var cells, chartdivid, colorScale, corXscale, corYscale, corZscale, corcolors, corr, corr_tip, corrplot, cortitle, drawScatter, height, i, j, margin, nGroup, ncorrX, ncorrY, nind, nvar, pixel_height, pixel_width, rectcolor, scat_tip, scatcolors, scatterplot, scattitle, svg, totalh, totalw, width, zlim, _ref, _ref1, _ref2, _ref3, _ref4, _ref5, _ref6, _ref7, _ref8, _ref9;
-    height = (_ref = chartOpts != null ? chartOpts.height : void 0) != null ? _ref : 450;
-    width = (_ref1 = chartOpts != null ? chartOpts.width : void 0) != null ? _ref1 : height;
-    margin = (_ref2 = chartOpts != null ? chartOpts.margin : void 0) != null ? _ref2 : {
-      left: 70,
-      top: 40,
-      right: 5,
-      bottom: 70,
-      inner: 5
-    };
-    corcolors = (_ref3 = chartOpts != null ? chartOpts.corcolors : void 0) != null ? _ref3 : ["darkslateblue", "white", "crimson"];
-    zlim = (_ref4 = chartOpts != null ? chartOpts.zlim : void 0) != null ? _ref4 : [-1, 0, 1];
-    rectcolor = (_ref5 = chartOpts != null ? chartOpts.rectcolor : void 0) != null ? _ref5 : d3.rgb(230, 230, 230);
-    cortitle = (_ref6 = chartOpts != null ? chartOpts.cortitle : void 0) != null ? _ref6 : "";
-    scattitle = (_ref7 = chartOpts != null ? chartOpts.scattitle : void 0) != null ? _ref7 : "";
-    scatcolors = (_ref8 = chartOpts != null ? chartOpts.scatcolors : void 0) != null ? _ref8 : null;
-    chartdivid = (_ref9 = chartOpts != null ? chartOpts.chartdivid : void 0) != null ? _ref9 : 'chart';
-    totalh = height + margin.top + margin.bottom;
-    totalw = (width + margin.left + margin.right) * 2;
-    svg = d3.select("div#" + chartdivid).append("svg").attr("height", totalh).attr("width", totalw);
-    corrplot = svg.append("g").attr("id", "corplot").attr("transform", "translate(" + margin.left + "," + margin.top + ")");
-    scatterplot = svg.append("g").attr("id", "scatterplot").attr("transform", "translate(" + (margin.left * 2 + margin.right + width) + "," + margin.top + ")");
-    nind = data.indID.length;
-    nvar = data["var"].length;
-    ncorrX = data.cols.length;
-    ncorrY = data.rows.length;
-    corXscale = d3.scale.ordinal().domain(d3.range(ncorrX)).rangeBands([0, width]);
-    corYscale = d3.scale.ordinal().domain(d3.range(ncorrY)).rangeBands([height, 0]);
-    corZscale = d3.scale.linear().domain(zlim).range(corcolors);
-    pixel_width = corXscale(1) - corXscale(0);
-    pixel_height = corYscale(0) - corYscale(1);
-    corr = [];
-    for (i in data.corr) {
-      for (j in data.corr[i]) {
-        corr.push({
-          row: i,
-          col: j,
-          value: data.corr[i][j]
-        });
-      }
+iplotCorr = function(data, chartOpts) {
+  var cells, chartdivid, colorScale, corXscale, corYscale, corZscale, corcolors, corr, corr_tip, corrplot, cortitle, drawScatter, height, i, j, margin, nGroup, ncorrX, ncorrY, nind, nvar, pixel_height, pixel_width, rectcolor, scat_tip, scatcolors, scatterplot, scattitle, svg, totalh, totalw, width, zlim, _ref, _ref1, _ref2, _ref3, _ref4, _ref5, _ref6, _ref7, _ref8, _ref9;
+  height = (_ref = chartOpts != null ? chartOpts.height : void 0) != null ? _ref : 450;
+  width = (_ref1 = chartOpts != null ? chartOpts.width : void 0) != null ? _ref1 : height;
+  margin = (_ref2 = chartOpts != null ? chartOpts.margin : void 0) != null ? _ref2 : {
+    left: 70,
+    top: 40,
+    right: 5,
+    bottom: 70,
+    inner: 5
+  };
+  corcolors = (_ref3 = chartOpts != null ? chartOpts.corcolors : void 0) != null ? _ref3 : ["darkslateblue", "white", "crimson"];
+  zlim = (_ref4 = chartOpts != null ? chartOpts.zlim : void 0) != null ? _ref4 : [-1, 0, 1];
+  rectcolor = (_ref5 = chartOpts != null ? chartOpts.rectcolor : void 0) != null ? _ref5 : d3.rgb(230, 230, 230);
+  cortitle = (_ref6 = chartOpts != null ? chartOpts.cortitle : void 0) != null ? _ref6 : "";
+  scattitle = (_ref7 = chartOpts != null ? chartOpts.scattitle : void 0) != null ? _ref7 : "";
+  scatcolors = (_ref8 = chartOpts != null ? chartOpts.scatcolors : void 0) != null ? _ref8 : null;
+  chartdivid = (_ref9 = chartOpts != null ? chartOpts.chartdivid : void 0) != null ? _ref9 : 'chart';
+  totalh = height + margin.top + margin.bottom;
+  totalw = (width + margin.left + margin.right) * 2;
+  svg = d3.select("div#" + chartdivid).append("svg").attr("height", totalh).attr("width", totalw);
+  corrplot = svg.append("g").attr("id", "corplot").attr("transform", "translate(" + margin.left + "," + margin.top + ")");
+  scatterplot = svg.append("g").attr("id", "scatterplot").attr("transform", "translate(" + (margin.left * 2 + margin.right + width) + "," + margin.top + ")");
+  nind = data.indID.length;
+  nvar = data["var"].length;
+  ncorrX = data.cols.length;
+  ncorrY = data.rows.length;
+  corXscale = d3.scale.ordinal().domain(d3.range(ncorrX)).rangeBands([0, width]);
+  corYscale = d3.scale.ordinal().domain(d3.range(ncorrY)).rangeBands([height, 0]);
+  corZscale = d3.scale.linear().domain(zlim).range(corcolors);
+  pixel_width = corXscale(1) - corXscale(0);
+  pixel_height = corYscale(0) - corYscale(1);
+  corr = [];
+  for (i in data.corr) {
+    for (j in data.corr[i]) {
+      corr.push({
+        row: i,
+        col: j,
+        value: data.corr[i][j]
+      });
     }
-    scatterplot.append("rect").attr("height", height).attr("width", width).attr("fill", rectcolor).attr("stroke", "black").attr("stroke-width", 1).attr("pointer-events", "none");
-    corr_tip = d3.tip().attr('class', 'd3-tip').html(function(d) {
-      return d3.format(".2f")(d.value);
-    }).direction('e').offset([0, 10]);
-    corrplot.call(corr_tip);
-    cells = corrplot.selectAll("empty").data(corr).enter().append("rect").attr("class", "cell").attr("x", function(d) {
-      return corXscale(d.col);
-    }).attr("y", function(d) {
-      return corYscale(d.row);
-    }).attr("width", corXscale.rangeBand()).attr("height", corYscale.rangeBand()).attr("fill", function(d) {
-      return corZscale(d.value);
-    }).attr("stroke", "none").attr("stroke-width", 2).on("mouseover", function(d) {
-      d3.select(this).attr("stroke", "black");
-      corr_tip.show(d);
-      corrplot.append("text").attr("class", "corrlabel").attr("x", corXscale(d.col) + pixel_width / 2).attr("y", height + margin.bottom * 0.2).text(data["var"][data.cols[d.col]]).attr("dominant-baseline", "middle").attr("text-anchor", "middle");
-      return corrplot.append("text").attr("class", "corrlabel").attr("y", corYscale(d.row) + pixel_height / 2).attr("x", -margin.left * 0.1).text(data["var"][data.rows[d.row]]).attr("dominant-baseline", "middle").attr("text-anchor", "end");
-    }).on("mouseout", function(d) {
-      corr_tip.hide(d);
-      d3.selectAll("text.corrlabel").remove();
-      return d3.select(this).attr("stroke", "none");
-    }).on("click", function(d) {
-      return drawScatter(d.col, d.row);
-    });
-    nGroup = d3.max(data.group);
-    if (!(scatcolors != null) || scatcolors.length < nGroup) {
-      if (nGroup === 1) {
-        scatcolors = [d3.rgb(150, 150, 150)];
-      } else if (nGroup <= 3) {
-        scatcolors = ["crimson", "green", "darkslateblue"];
+  }
+  scatterplot.append("rect").attr("height", height).attr("width", width).attr("fill", rectcolor).attr("stroke", "black").attr("stroke-width", 1).attr("pointer-events", "none");
+  corr_tip = d3.tip().attr('class', 'd3-tip').html(function(d) {
+    return d3.format(".2f")(d.value);
+  }).direction('e').offset([0, 10]);
+  corrplot.call(corr_tip);
+  cells = corrplot.selectAll("empty").data(corr).enter().append("rect").attr("class", "cell").attr("x", function(d) {
+    return corXscale(d.col);
+  }).attr("y", function(d) {
+    return corYscale(d.row);
+  }).attr("width", corXscale.rangeBand()).attr("height", corYscale.rangeBand()).attr("fill", function(d) {
+    return corZscale(d.value);
+  }).attr("stroke", "none").attr("stroke-width", 2).on("mouseover", function(d) {
+    d3.select(this).attr("stroke", "black");
+    corr_tip.show(d);
+    corrplot.append("text").attr("class", "corrlabel").attr("x", corXscale(d.col) + pixel_width / 2).attr("y", height + margin.bottom * 0.2).text(data["var"][data.cols[d.col]]).attr("dominant-baseline", "middle").attr("text-anchor", "middle");
+    return corrplot.append("text").attr("class", "corrlabel").attr("y", corYscale(d.row) + pixel_height / 2).attr("x", -margin.left * 0.1).text(data["var"][data.rows[d.row]]).attr("dominant-baseline", "middle").attr("text-anchor", "end");
+  }).on("mouseout", function(d) {
+    corr_tip.hide(d);
+    d3.selectAll("text.corrlabel").remove();
+    return d3.select(this).attr("stroke", "none");
+  }).on("click", function(d) {
+    return drawScatter(d.col, d.row);
+  });
+  nGroup = d3.max(data.group);
+  if (!(scatcolors != null) || scatcolors.length < nGroup) {
+    if (nGroup === 1) {
+      scatcolors = [d3.rgb(150, 150, 150)];
+    } else if (nGroup <= 3) {
+      scatcolors = ["crimson", "green", "darkslateblue"];
+    } else {
+      if (nGroup <= 10) {
+        colorScale = d3.scale.category10();
       } else {
-        if (nGroup <= 10) {
-          colorScale = d3.scale.category10();
-        } else {
-          colorScale = d3.scale.category20();
-        }
-        scatcolors = (function() {
-          var _results;
-          _results = [];
-          for (i in d3.range(nGroup)) {
-            _results.push(colorScale(i));
-          }
-          return _results;
-        })();
+        colorScale = d3.scale.category20();
       }
-    }
-    scat_tip = d3.tip().attr('class', 'd3-tip').html(function(d, i) {
-      return data.indID[i];
-    }).direction('e').offset([0, 10]);
-    scatterplot.call(scat_tip);
-    drawScatter = function(i, j) {
-      var xScale, xticks, yScale, yticks;
-      d3.selectAll("circle.points").remove();
-      d3.selectAll("text.axes").remove();
-      d3.selectAll("line.axes").remove();
-      console.log("data.dat:", data.dat);
-      console.log("data.cols:", data.cols);
-      xScale = d3.scale.linear().domain(d3.extent(data.dat[data.cols[i]])).range([margin.inner, width - margin.inner]);
-      yScale = d3.scale.linear().domain(d3.extent(data.dat[data.rows[j]])).range([height - margin.inner, margin.inner]);
-      scatterplot.append("text").attr("id", "xaxis").attr("class", "axes").attr("x", width / 2).attr("y", height + margin.bottom * 0.7).text(data["var"][data.cols[i]]).attr("dominant-baseline", "middle").attr("text-anchor", "middle").attr("fill", "slateblue");
-      scatterplot.append("text").attr("id", "yaxis").attr("class", "axes").attr("x", -margin.left * 0.8).attr("y", height / 2).text(data["var"][data.rows[j]]).attr("dominant-baseline", "middle").attr("text-anchor", "middle").attr("transform", "rotate(270," + (-margin.left * 0.8) + "," + (height / 2) + ")").attr("fill", "slateblue");
-      xticks = xScale.ticks(5);
-      yticks = yScale.ticks(5);
-      scatterplot.selectAll("empty").data(xticks).enter().append("text").attr("class", "axes").text(function(d) {
-        return formatAxis(xticks)(d);
-      }).attr("x", function(d) {
-        return xScale(d);
-      }).attr("y", height + margin.bottom * 0.3).attr("dominant-baseline", "middle").attr("text-anchor", "middle");
-      scatterplot.selectAll("empty").data(yticks).enter().append("text").attr("class", "axes").text(function(d) {
-        return formatAxis(yticks)(d);
-      }).attr("x", -margin.left * 0.1).attr("y", function(d) {
-        return yScale(d);
-      }).attr("dominant-baseline", "middle").attr("text-anchor", "end");
-      scatterplot.selectAll("empty").data(xticks).enter().append("line").attr("class", "axes").attr("x1", function(d) {
-        return xScale(d);
-      }).attr("x2", function(d) {
-        return xScale(d);
-      }).attr("y1", 0).attr("y2", height).attr("stroke", "white").attr("stroke-width", 1);
-      scatterplot.selectAll("empty").data(yticks).enter().append("line").attr("class", "axes").attr("y1", function(d) {
-        return yScale(d);
-      }).attr("y2", function(d) {
-        return yScale(d);
-      }).attr("x1", 0).attr("x2", width).attr("stroke", "white").attr("stroke-width", 1);
-      return scatterplot.selectAll("empty").data(d3.range(nind)).enter().append("circle").attr("class", "points").attr("cx", function(d) {
-        return xScale(data.dat[data.cols[i]][d]);
-      }).attr("cy", function(d) {
-        return yScale(data.dat[data.rows[j]][d]);
-      }).attr("r", function(d) {
-        var x, y;
-        x = data.dat[data.cols[i]][d];
-        y = data.dat[data.rows[j]][d];
-        if ((x != null) && (y != null)) {
-          return 3;
-        } else {
-          return null;
+      scatcolors = (function() {
+        var _results;
+        _results = [];
+        for (i in d3.range(nGroup)) {
+          _results.push(colorScale(i));
         }
-      }).attr("stroke", "black").attr("stroke-width", 1).attr("fill", function(d) {
-        return scatcolors[data.group[d] - 1];
-      }).on("mouseover", scat_tip.show).on("mouseout", scat_tip.hide);
-    };
-    corrplot.append("rect").attr("height", height).attr("width", width).attr("fill", "none").attr("stroke", "black").attr("stroke-width", 1).attr("pointer-events", "none");
-    scatterplot.append("rect").attr("height", height).attr("width", width).attr("fill", "none").attr("stroke", "black").attr("stroke-width", 1).attr("pointer-events", "none");
-    corrplot.append("text").text(cortitle).attr("id", "corrtitle").attr("x", width / 2).attr("y", -margin.top / 2).attr("dominant-baseline", "middle").attr("text-anchor", "middle");
-    scatterplot.append("text").text(scattitle).attr("id", "scattitle").attr("x", width / 2).attr("y", -margin.top / 2).attr("dominant-baseline", "middle").attr("text-anchor", "middle");
-    return d3.select("div#caption").style("opacity", 1);
+        return _results;
+      })();
+    }
+  }
+  scat_tip = d3.tip().attr('class', 'd3-tip').html(function(d, i) {
+    return data.indID[i];
+  }).direction('e').offset([0, 10]);
+  scatterplot.call(scat_tip);
+  drawScatter = function(i, j) {
+    var xScale, xticks, yScale, yticks;
+    d3.selectAll("circle.points").remove();
+    d3.selectAll("text.axes").remove();
+    d3.selectAll("line.axes").remove();
+    console.log("data.dat:", data.dat);
+    console.log("data.cols:", data.cols);
+    xScale = d3.scale.linear().domain(d3.extent(data.dat[data.cols[i]])).range([margin.inner, width - margin.inner]);
+    yScale = d3.scale.linear().domain(d3.extent(data.dat[data.rows[j]])).range([height - margin.inner, margin.inner]);
+    scatterplot.append("text").attr("id", "xaxis").attr("class", "axes").attr("x", width / 2).attr("y", height + margin.bottom * 0.7).text(data["var"][data.cols[i]]).attr("dominant-baseline", "middle").attr("text-anchor", "middle").attr("fill", "slateblue");
+    scatterplot.append("text").attr("id", "yaxis").attr("class", "axes").attr("x", -margin.left * 0.8).attr("y", height / 2).text(data["var"][data.rows[j]]).attr("dominant-baseline", "middle").attr("text-anchor", "middle").attr("transform", "rotate(270," + (-margin.left * 0.8) + "," + (height / 2) + ")").attr("fill", "slateblue");
+    xticks = xScale.ticks(5);
+    yticks = yScale.ticks(5);
+    scatterplot.selectAll("empty").data(xticks).enter().append("text").attr("class", "axes").text(function(d) {
+      return formatAxis(xticks)(d);
+    }).attr("x", function(d) {
+      return xScale(d);
+    }).attr("y", height + margin.bottom * 0.3).attr("dominant-baseline", "middle").attr("text-anchor", "middle");
+    scatterplot.selectAll("empty").data(yticks).enter().append("text").attr("class", "axes").text(function(d) {
+      return formatAxis(yticks)(d);
+    }).attr("x", -margin.left * 0.1).attr("y", function(d) {
+      return yScale(d);
+    }).attr("dominant-baseline", "middle").attr("text-anchor", "end");
+    scatterplot.selectAll("empty").data(xticks).enter().append("line").attr("class", "axes").attr("x1", function(d) {
+      return xScale(d);
+    }).attr("x2", function(d) {
+      return xScale(d);
+    }).attr("y1", 0).attr("y2", height).attr("stroke", "white").attr("stroke-width", 1);
+    scatterplot.selectAll("empty").data(yticks).enter().append("line").attr("class", "axes").attr("y1", function(d) {
+      return yScale(d);
+    }).attr("y2", function(d) {
+      return yScale(d);
+    }).attr("x1", 0).attr("x2", width).attr("stroke", "white").attr("stroke-width", 1);
+    return scatterplot.selectAll("empty").data(d3.range(nind)).enter().append("circle").attr("class", "points").attr("cx", function(d) {
+      return xScale(data.dat[data.cols[i]][d]);
+    }).attr("cy", function(d) {
+      return yScale(data.dat[data.rows[j]][d]);
+    }).attr("r", function(d) {
+      var x, y;
+      x = data.dat[data.cols[i]][d];
+      y = data.dat[data.rows[j]][d];
+      if ((x != null) && (y != null)) {
+        return 3;
+      } else {
+        return null;
+      }
+    }).attr("stroke", "black").attr("stroke-width", 1).attr("fill", function(d) {
+      return scatcolors[data.group[d] - 1];
+    }).on("mouseover", scat_tip.show).on("mouseout", scat_tip.hide);
   };
+  corrplot.append("rect").attr("height", height).attr("width", width).attr("fill", "none").attr("stroke", "black").attr("stroke-width", 1).attr("pointer-events", "none");
+  scatterplot.append("rect").attr("height", height).attr("width", width).attr("fill", "none").attr("stroke", "black").attr("stroke-width", 1).attr("pointer-events", "none");
+  corrplot.append("text").text(cortitle).attr("id", "corrtitle").attr("x", width / 2).attr("y", -margin.top / 2).attr("dominant-baseline", "middle").attr("text-anchor", "middle");
+  scatterplot.append("text").text(scattitle).attr("id", "scattitle").attr("x", width / 2).attr("y", -margin.top / 2).attr("dominant-baseline", "middle").attr("text-anchor", "middle");
+  return d3.select("div#caption").style("opacity", 1);
+};
 
-  root.corr_matrix = iplotCorr;
-
-}).call(this);
+root.corr_matrix = iplotCorr;
diff --git a/wqflask/wqflask/static/new/javascript/create_corr_matrix.js b/wqflask/wqflask/static/new/javascript/create_corr_matrix.js
index 64dc834d..ca5962f4 100644
--- a/wqflask/wqflask/static/new/javascript/create_corr_matrix.js
+++ b/wqflask/wqflask/static/new/javascript/create_corr_matrix.js
@@ -1,47 +1,44 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var get_data, get_options, root;
+// Generated by CoffeeScript 1.7.1
+var get_data, get_options, root;
 
-  root = typeof exports !== "undefined" && exports !== null ? exports : this;
+root = typeof exports !== "undefined" && exports !== null ? exports : this;
 
-  $(function() {
-    var chartOpts, data, mychart;
-    console.log("js_data:", js_data);
-    chartOpts = get_options();
-    data = get_data();
-    console.log(data);
-    return mychart = corr_matrix(data, chartOpts);
-  });
+$(function() {
+  var chartOpts, data, mychart;
+  console.log("js_data:", js_data);
+  chartOpts = get_options();
+  data = get_data();
+  console.log(data);
+  return mychart = corr_matrix(data, chartOpts);
+});
 
-  get_options = function() {
-    var chartOpts;
-    chartOpts = {
-      cortitle: "Correlation Matrix",
-      scattitle: "Scatterplot",
-      h: 450,
-      w: 450,
-      margin: {
-        left: 100,
-        top: 40,
-        right: 5,
-        bottom: 70,
-        inner: 5
-      }
-    };
-    return chartOpts;
+get_options = function() {
+  var chartOpts;
+  chartOpts = {
+    cortitle: "Correlation Matrix",
+    scattitle: "Scatterplot",
+    h: 450,
+    w: 450,
+    margin: {
+      left: 100,
+      top: 40,
+      right: 5,
+      bottom: 70,
+      inner: 5
+    }
   };
+  return chartOpts;
+};
 
-  get_data = function() {
-    var data;
-    data = {};
-    data["var"] = js_data.traits;
-    data.group = js_data.groups;
-    data.indID = js_data.samples;
-    data.dat = js_data.sample_data;
-    data.corr = js_data.corr_results;
-    data.cols = js_data.cols;
-    data.rows = js_data.rows;
-    return data;
-  };
-
-}).call(this);
+get_data = function() {
+  var data;
+  data = {};
+  data["var"] = js_data.traits;
+  data.group = js_data.groups;
+  data.indID = js_data.samples;
+  data.dat = js_data.sample_data;
+  data.corr = js_data.corr_results;
+  data.cols = js_data.cols;
+  data.rows = js_data.rows;
+  return data;
+};
diff --git a/wqflask/wqflask/static/new/javascript/create_interval_map.coffee b/wqflask/wqflask/static/new/javascript/create_interval_map.coffee
new file mode 100644
index 00000000..cacba03e
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/create_interval_map.coffee
@@ -0,0 +1,91 @@
+create_interval_map = ->

+    h = 500

+    w = 1200

+    margin = {left:60, top:40, right:40, bottom: 40, inner:5}

+    halfh = (h+margin.top+margin.bottom)

+    totalh = halfh*2

+    totalw = (w+margin.left+margin.right)

+    

+    # simplest use

+    #d3.json "data.json", (data) ->

+    mychart = lodchart().lodvarname("lod.hk")

+                        .height(h)

+                        .width(w)

+                        .margin(margin)

+    

+    data = js_data.json_data

+    

+    d3.select("div#topchart")

+      .datum(data)

+      .call(mychart)

+    

+    # grab chromosome rectangles; color pink on hover

+    chrrect = mychart.chrSelect()

+    chrrect.on "mouseover", ->

+                d3.select(this).attr("fill", "#E9CFEC")

+           .on "mouseout", (d,i) ->

+                d3.select(this).attr("fill", ->

+                      return "#F1F1F9"  if i % 2

+                      "#FBFBFF")

+    

+    # animate points at markers on click

+    mychart.markerSelect()

+              .on "click", (d) ->

+                    r = d3.select(this).attr("r")

+                    d3.select(this)

+                      .transition().duration(500).attr("r", r*3)

+                      .transition().duration(500).attr("r", r)

+

+create_interval_map()

+

+$("#export").click =>

+    #Get d3 SVG element

+    svg = $("#topchart").find("svg")[0]

+    

+    #Extract SVG text string

+    svg_xml = (new XMLSerializer).serializeToString(svg)

+    console.log("svg_xml:", svg_xml)

+        

+    #Set filename

+    filename = "interval_map_" + js_data.this_trait

+

+    #Make a form with the SVG data

+    form = $("#exportform")

+    form.find("#data").val(svg_xml)

+    form.find("#filename").val(filename)

+    form.submit()

+

+# two LOD charts within one SVG

+#d3.json "data.json", (data) ->

+#  mychart_em = lodchart().lodvarname("lod.em")

+#                         .height(h)

+#                         .width(w)

+#                         .margin(margin)

+#                         .ylab("LOD score (by EM)")

+#                         .pointsize(1)

+#                         .nyticks(9)

+#                         .title("Standard interval mapping")

+#  mychart_hk = lodchart().lodvarname("lod.hk")

+#                         .height(h)

+#                         .width(w)

+#                         .margin(margin)

+#                         .ylab("LOD score (by H-K)")

+#                         .linecolor("Crimson")

+#                         .yticks([0, 1, 2, 4, 6, 8])

+#                         .title("Haley-Knott regression")

+#

+#  svg = d3.select("div#bottomchart")

+#          .append("svg")

+#          .attr("height", totalh)

+#          .attr("width", totalw)

+#

+#  chart1 = svg.append("g").attr("id", "chart1")

+#

+#  chart2 = svg.append("g").attr("id", "chart2")

+#              .attr("transform", "translate(0, #{halfh})")

+#

+#  chart1.datum(data)

+#    .call(mychart_em)

+#

+#  chart2.datum(data)

+#    .call(mychart_hk)
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/create_interval_map.js b/wqflask/wqflask/static/new/javascript/create_interval_map.js
new file mode 100644
index 00000000..5041cfea
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/create_interval_map.js
@@ -0,0 +1,53 @@
+// Generated by CoffeeScript 1.7.1
+var create_interval_map;
+
+create_interval_map = function() {
+  var chrrect, data, h, halfh, margin, mychart, totalh, totalw, w;
+  h = 500;
+  w = 1200;
+  margin = {
+    left: 60,
+    top: 40,
+    right: 40,
+    bottom: 40,
+    inner: 5
+  };
+  halfh = h + margin.top + margin.bottom;
+  totalh = halfh * 2;
+  totalw = w + margin.left + margin.right;
+  mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin);
+  data = js_data.json_data;
+  d3.select("div#topchart").datum(data).call(mychart);
+  chrrect = mychart.chrSelect();
+  chrrect.on("mouseover", function() {
+    return d3.select(this).attr("fill", "#E9CFEC");
+  }).on("mouseout", function(d, i) {
+    return d3.select(this).attr("fill", function() {
+      if (i % 2) {
+        return "#F1F1F9";
+      }
+      return "#FBFBFF";
+    });
+  });
+  return mychart.markerSelect().on("click", function(d) {
+    var r;
+    r = d3.select(this).attr("r");
+    return d3.select(this).transition().duration(500).attr("r", r * 3).transition().duration(500).attr("r", r);
+  });
+};
+
+create_interval_map();
+
+$("#export").click((function(_this) {
+  return function() {
+    var filename, form, svg, svg_xml;
+    svg = $("#topchart").find("svg")[0];
+    svg_xml = (new XMLSerializer).serializeToString(svg);
+    console.log("svg_xml:", svg_xml);
+    filename = "interval_map_" + js_data.this_trait;
+    form = $("#exportform");
+    form.find("#data").val(svg_xml);
+    form.find("#filename").val(filename);
+    return form.submit();
+  };
+})(this));
diff --git a/wqflask/wqflask/static/new/javascript/create_manhattan_plot.coffee b/wqflask/wqflask/static/new/javascript/create_manhattan_plot.coffee
new file mode 100644
index 00000000..258d5c01
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/create_manhattan_plot.coffee
@@ -0,0 +1,57 @@
+create_manhattan_plot = ->

+    h = 500

+    w = 1200

+    margin = {left:60, top:40, right:40, bottom: 40, inner:5}

+    halfh = (h+margin.top+margin.bottom)

+    totalh = halfh*2

+    totalw = (w+margin.left+margin.right)

+    

+    # simplest use

+    #d3.json "data.json", (data) ->

+    mychart = lodchart().lodvarname("lod.hk")

+                        .height(h)

+                        .width(w)

+                        .margin(margin)

+    

+    data = js_data.json_data

+    

+    d3.select("div#topchart")

+      .datum(data)

+      .call(mychart)

+    

+    # grab chromosome rectangles; color pink on hover

+    chrrect = mychart.chrSelect()

+    chrrect.on "mouseover", ->

+                d3.select(this).attr("fill", "#E9CFEC")

+           .on "mouseout", (d,i) ->

+                d3.select(this).attr("fill", ->

+                      return "#F1F1F9"  if i % 2

+                      "#FBFBFF")

+    

+    # animate points at markers on click

+    mychart.markerSelect()

+              .on "click", (d) ->

+                    r = d3.select(this).attr("r")

+                    d3.select(this)

+                      .transition().duration(500).attr("r", r*3)

+                      .transition().duration(500).attr("r", r)

+                  

+create_manhattan_plot()

+

+$("#export").click =>

+    #Get d3 SVG element

+    svg = $("#topchart").find("svg")[0]

+    

+    #Extract SVG text string

+    svg_xml = (new XMLSerializer).serializeToString(svg)

+    console.log("svg_xml:", svg_xml)

+        

+    #Set filename

+    filename = "manhattan_plot_" + js_data.this_trait

+

+    #Make a form with the SVG data

+    form = $("#exportform")

+    form.find("#data").val(svg_xml)

+    form.find("#filename").val(filename)

+    form.submit()

+

diff --git a/wqflask/wqflask/static/new/javascript/create_manhattan_plot.js b/wqflask/wqflask/static/new/javascript/create_manhattan_plot.js
new file mode 100644
index 00000000..7daaa921
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/create_manhattan_plot.js
@@ -0,0 +1,53 @@
+// Generated by CoffeeScript 1.7.1
+var create_manhattan_plot;
+
+create_manhattan_plot = function() {
+  var chrrect, data, h, halfh, margin, mychart, totalh, totalw, w;
+  h = 500;
+  w = 1200;
+  margin = {
+    left: 60,
+    top: 40,
+    right: 40,
+    bottom: 40,
+    inner: 5
+  };
+  halfh = h + margin.top + margin.bottom;
+  totalh = halfh * 2;
+  totalw = w + margin.left + margin.right;
+  mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin);
+  data = js_data.json_data;
+  d3.select("div#topchart").datum(data).call(mychart);
+  chrrect = mychart.chrSelect();
+  chrrect.on("mouseover", function() {
+    return d3.select(this).attr("fill", "#E9CFEC");
+  }).on("mouseout", function(d, i) {
+    return d3.select(this).attr("fill", function() {
+      if (i % 2) {
+        return "#F1F1F9";
+      }
+      return "#FBFBFF";
+    });
+  });
+  return mychart.markerSelect().on("click", function(d) {
+    var r;
+    r = d3.select(this).attr("r");
+    return d3.select(this).transition().duration(500).attr("r", r * 3).transition().duration(500).attr("r", r);
+  });
+};
+
+create_manhattan_plot();
+
+$("#export").click((function(_this) {
+  return function() {
+    var filename, form, svg, svg_xml;
+    svg = $("#topchart").find("svg")[0];
+    svg_xml = (new XMLSerializer).serializeToString(svg);
+    console.log("svg_xml:", svg_xml);
+    filename = "manhattan_plot_" + js_data.this_trait;
+    form = $("#exportform");
+    form.find("#data").val(svg_xml);
+    form.find("#filename").val(filename);
+    return form.submit();
+  };
+})(this));
diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
index 3a2f044f..f4ca2c37 100755
--- a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
+++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
@@ -1,136 +1,137 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-
-  $(function() {
-    var apply_default, dataset_info, group_info, make_default, open_window, populate_dataset, populate_group, populate_species, populate_type, process_json, redo_dropdown,
-      _this = this;
-    process_json = function(data) {
-      window.jdata = data;
-      populate_species();
-      return apply_default();
-    };
-    $.ajax('/static/new/javascript/dataset_menu_structure.json', {
-      dataType: 'json',
-      success: process_json
-    });
-    populate_species = function() {
-      var species_list;
-      species_list = this.jdata.species;
-      redo_dropdown($('#species'), species_list);
+// Generated by CoffeeScript 1.7.1
+$(function() {
+  var apply_default, dataset_info, group_info, make_default, open_window, populate_dataset, populate_group, populate_species, populate_type, process_json, redo_dropdown;
+  process_json = function(data) {
+    window.jdata = data;
+    populate_species();
+    return apply_default();
+  };
+  $.ajax('/static/new/javascript/dataset_menu_structure.json', {
+    dataType: 'json',
+    success: process_json
+  });
+  populate_species = function() {
+    var species_list;
+    species_list = this.jdata.species;
+    redo_dropdown($('#species'), species_list);
+    return populate_group();
+  };
+  window.populate_species = populate_species;
+  populate_group = function() {
+    var group_list, species;
+    console.log("in populate group");
+    species = $('#species').val();
+    group_list = this.jdata.groups[species];
+    redo_dropdown($('#group'), group_list);
+    return populate_type();
+  };
+  window.populate_group = populate_group;
+  populate_type = function() {
+    var group, species, type_list;
+    species = $('#species').val();
+    group = $('#group').val();
+    type_list = this.jdata.types[species][group];
+    redo_dropdown($('#type'), type_list);
+    return populate_dataset();
+  };
+  window.populate_type = populate_type;
+  populate_dataset = function() {
+    var dataset_list, group, species, type;
+    species = $('#species').val();
+    group = $('#group').val();
+    type = $('#type').val();
+    console.log("sgt:", species, group, type);
+    dataset_list = this.jdata.datasets[species][group][type];
+    console.log("pop_dataset:", dataset_list);
+    return redo_dropdown($('#dataset'), dataset_list);
+  };
+  window.populate_dataset = populate_dataset;
+  redo_dropdown = function(dropdown, items) {
+    var item, _i, _len, _results;
+    console.log("in redo:", dropdown, items);
+    dropdown.empty();
+    _results = [];
+    for (_i = 0, _len = items.length; _i < _len; _i++) {
+      item = items[_i];
+      _results.push(dropdown.append($("<option />").val(item[0]).text(item[1])));
+    }
+    return _results;
+  };
+  $('#species').change((function(_this) {
+    return function() {
       return populate_group();
     };
-    window.populate_species = populate_species;
-    populate_group = function() {
-      var group_list, species;
-      console.log("in populate group");
-      species = $('#species').val();
-      group_list = this.jdata.groups[species];
-      redo_dropdown($('#group'), group_list);
+  })(this));
+  $('#group').change((function(_this) {
+    return function() {
       return populate_type();
     };
-    window.populate_group = populate_group;
-    populate_type = function() {
-      var group, species, type_list;
-      species = $('#species').val();
-      group = $('#group').val();
-      type_list = this.jdata.types[species][group];
-      redo_dropdown($('#type'), type_list);
+  })(this));
+  $('#type').change((function(_this) {
+    return function() {
       return populate_dataset();
     };
-    window.populate_type = populate_type;
-    populate_dataset = function() {
-      var dataset_list, group, species, type;
-      species = $('#species').val();
-      group = $('#group').val();
-      type = $('#type').val();
-      console.log("sgt:", species, group, type);
-      dataset_list = this.jdata.datasets[species][group][type];
-      console.log("pop_dataset:", dataset_list);
-      return redo_dropdown($('#dataset'), dataset_list);
-    };
-    window.populate_dataset = populate_dataset;
-    redo_dropdown = function(dropdown, items) {
-      var item, _i, _len, _results;
-      console.log("in redo:", dropdown, items);
-      dropdown.empty();
-      _results = [];
-      for (_i = 0, _len = items.length; _i < _len; _i++) {
-        item = items[_i];
-        _results.push(dropdown.append($("<option />").val(item[0]).text(item[1])));
-      }
-      return _results;
-    };
-    $('#species').change(function() {
-      return populate_group();
+  })(this));
+  open_window = function(url, name) {
+    var options;
+    options = "menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900";
+    return open(url, name, options).focus();
+  };
+  group_info = function() {
+    var group, species, url;
+    species = $('#species').val();
+    group = $('#group').val();
+    url = "/" + species + "Cross.html#" + group;
+    return open_window(url, "Group Info");
+  };
+  $('#group_info').click(group_info);
+  dataset_info = function() {
+    var dataset, url;
+    dataset = $('#dataset').val();
+    url = "/webqtl/main.py?FormID=sharinginfo&InfoPageName=" + dataset;
+    return open_window(url, "Dataset Info");
+  };
+  $('#dataset_info').click(dataset_info);
+  make_default = function() {
+    var holder, item, jholder, _i, _len, _ref;
+    holder = {};
+    _ref = ['species', 'group', 'type', 'dataset'];
+    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+      item = _ref[_i];
+      holder[item] = $("#" + item).val();
+    }
+    jholder = JSON.stringify(holder);
+    return $.cookie('search_defaults', jholder, {
+      expires: 365
     });
-    $('#group').change(function() {
-      return populate_type();
-    });
-    $('#type').change(function() {
-      return populate_dataset();
-    });
-    open_window = function(url, name) {
-      var options;
-      options = "menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900";
-      return open(url, name, options).focus();
-    };
-    group_info = function() {
-      var group, species, url;
-      species = $('#species').val();
-      group = $('#group').val();
-      url = "/" + species + "Cross.html#" + group;
-      return open_window(url, "Group Info");
-    };
-    $('#group_info').click(group_info);
-    dataset_info = function() {
-      var dataset, url;
-      dataset = $('#dataset').val();
-      url = "/webqtl/main.py?FormID=sharinginfo&InfoPageName=" + dataset;
-      return open_window(url, "Dataset Info");
-    };
-    $('#dataset_info').click(dataset_info);
-    make_default = function() {
-      var holder, item, jholder, _i, _len, _ref;
-      holder = {};
-      _ref = ['species', 'group', 'type', 'dataset'];
-      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-        item = _ref[_i];
-        holder[item] = $("#" + item).val();
-      }
-      jholder = JSON.stringify(holder);
-      return $.cookie('search_defaults', jholder, {
-        expires: 365
-      });
-    };
-    apply_default = function() {
-      var defaults, item, populate_function, _i, _len, _ref, _results;
-      defaults = $.cookie('search_defaults');
-      if (defaults) {
-        defaults = $.parseJSON(defaults);
+  };
+  apply_default = function() {
+    var defaults, item, populate_function, _i, _len, _ref, _results;
+    defaults = $.cookie('search_defaults');
+    if (defaults) {
+      defaults = $.parseJSON(defaults);
+    } else {
+      defaults = {
+        species: "mouse",
+        group: "BXD",
+        type: "Hippocampus mRNA",
+        dataset: "HC_M2_0606_P"
+      };
+    }
+    _ref = [['species', 'group'], ['group', 'type'], ['type', 'dataset'], ['dataset', null]];
+    _results = [];
+    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+      item = _ref[_i];
+      $("#" + item[0]).val(defaults[item[0]]);
+      if (item[1]) {
+        populate_function = "populate_" + item[1];
+        console.log("Calling:", populate_function);
+        _results.push(window[populate_function]());
       } else {
-        defaults = {
-          species: "mouse",
-          group: "BXD",
-          type: "Hippocampus mRNA",
-          dataset: "HC_M2_0606_P"
-        };
-      }
-      _ref = [['species', 'group'], ['group', 'type'], ['type', 'dataset'], ['dataset', null]];
-      _results = [];
-      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-        item = _ref[_i];
-        $("#" + item[0]).val(defaults[item[0]]);
-        if (item[1]) {
-          populate_function = "populate_" + item[1];
-          console.log("Calling:", populate_function);
-          _results.push(window[populate_function]());
-        } else {
-          _results.push(void 0);
-        }
+        _results.push(void 0);
       }
-      return _results;
-    };
-    return $("#make_default").click(make_default);
-  });
-
-}).call(this);
+    }
+    return _results;
+  };
+  return $("#make_default").click(make_default);
+});
diff --git a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
index 396f4bbe..10cefcd7 100644
--- a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
+++ b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
@@ -1,50 +1,47 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var data, h, halfh, halfw, indID, intercept, margin, mychart, slope, totalh, totalw, w;
+// Generated by CoffeeScript 1.7.1
+var data, h, halfh, halfw, indID, intercept, margin, mychart, slope, totalh, totalw, w;
 
-  h = 400;
+h = 400;
 
-  w = 500;
+w = 500;
 
-  margin = {
-    left: 60,
-    top: 40,
-    right: 40,
-    bottom: 40,
-    inner: 5
-  };
+margin = {
+  left: 60,
+  top: 40,
+  right: 40,
+  bottom: 40,
+  inner: 5
+};
 
-  halfh = h + margin.top + margin.bottom;
+halfh = h + margin.top + margin.bottom;
 
-  totalh = halfh * 2;
+totalh = halfh * 2;
 
-  halfw = w + margin.left + margin.right;
+halfw = w + margin.left + margin.right;
 
-  totalw = halfw * 2;
+totalw = halfw * 2;
 
-  mychart = scatterplot().xvar(0).yvar(1).xlab(js_data.trait_1).ylab(js_data.trait_2).height(h).width(w).margin(margin);
+mychart = scatterplot().xvar(0).yvar(1).xlab(js_data.trait_1).ylab(js_data.trait_2).height(h).width(w).margin(margin);
 
-  data = js_data.data;
+data = js_data.data;
 
-  indID = js_data.indIDs;
+indID = js_data.indIDs;
 
-  slope = js_data.slope;
+slope = js_data.slope;
 
-  intercept = js_data.intercept;
+intercept = js_data.intercept;
 
-  console.log("THE DATA IS:", data);
+console.log("THE DATA IS:", data);
 
-  d3.select("div#chart1").datum({
-    data: data,
-    indID: indID,
-    slope: slope,
-    intercept: intercept
-  }).call(mychart);
+d3.select("div#chart1").datum({
+  data: data,
+  indID: indID,
+  slope: slope,
+  intercept: intercept
+}).call(mychart);
 
-  mychart.pointsSelect().on("mouseover", function(d) {
-    return d3.select(this).attr("r", mychart.pointsize() * 3);
-  }).on("mouseout", function(d) {
-    return d3.select(this).attr("r", mychart.pointsize());
-  });
-
-}).call(this);
+mychart.pointsSelect().on("mouseover", function(d) {
+  return d3.select(this).attr("r", mychart.pointsize() * 3);
+}).on("mouseout", function(d) {
+  return d3.select(this).attr("r", mychart.pointsize());
+});
diff --git a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
index df3eacf3..402d62f4 100755
--- a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
+++ b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
@@ -1,195 +1,192 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var add_trait_data, assemble_into_json, back_to_collections, collection_click, collection_list, color_by_trait, get_this_trait_vals, get_trait_data, process_traits, selected_traits, submit_click, this_trait_data, trait_click,
-    __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; };
+// Generated by CoffeeScript 1.7.1
+var add_trait_data, assemble_into_json, back_to_collections, collection_click, collection_list, color_by_trait, get_this_trait_vals, get_trait_data, process_traits, selected_traits, submit_click, this_trait_data, trait_click,
+  __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; };
 
-  console.log("before get_traits_from_collection");
+console.log("before get_traits_from_collection");
 
-  collection_list = null;
+collection_list = null;
 
-  this_trait_data = null;
+this_trait_data = null;
 
-  selected_traits = {};
-
-  collection_click = function() {
-    var this_collection_url;
-    console.log("Clicking on:", $(this));
-    this_collection_url = $(this).find('.collection_name').prop("href");
-    this_collection_url += "&json";
-    console.log("this_collection_url", this_collection_url);
-    collection_list = $("#collections_holder").html();
-    return $.ajax({
-      dataType: "json",
-      url: this_collection_url,
-      success: process_traits
-    });
-  };
+selected_traits = {};
 
-  submit_click = function() {
-    var all_vals, sample, samples, this_trait_vals, trait, trait_names, traits, _i, _j, _len, _len1, _ref;
-    selected_traits = {};
-    traits = [];
-    $('#collections_holder').find('input[type=checkbox]:checked').each(function() {
-      var this_dataset, this_trait, this_trait_url;
-      this_trait = $(this).parents('tr').find('.trait').text();
-      console.log("this_trait is:", this_trait);
-      this_dataset = $(this).parents('tr').find('.dataset').text();
-      console.log("this_dataset is:", this_dataset);
-      this_trait_url = "/trait/get_sample_data?trait=" + this_trait + "&dataset=" + this_dataset;
-      return $.ajax({
-        dataType: "json",
-        url: this_trait_url,
-        async: false,
-        success: add_trait_data
-      });
-    });
-    console.log("SELECTED_TRAITS IS:", selected_traits);
-    trait_names = [];
-    samples = $('input[name=allsamples]').val().split(" ");
-    all_vals = [];
-    this_trait_vals = get_this_trait_vals(samples);
-    all_vals.push(this_trait_vals);
-    _ref = Object.keys(selected_traits);
-    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-      trait = _ref[_i];
-      trait_names.push(trait);
-      this_trait_vals = [];
-      for (_j = 0, _len1 = samples.length; _j < _len1; _j++) {
-        sample = samples[_j];
-        if (__indexOf.call(Object.keys(selected_traits[trait]), sample) >= 0) {
-          this_trait_vals.push(parseFloat(selected_traits[trait][sample]));
-        } else {
-          this_trait_vals.push(null);
-        }
-      }
-      all_vals.push(this_trait_vals);
-    }
-    create_scatterplots(trait_names, samples, all_vals);
-    return $.colorbox.close();
-  };
+collection_click = function() {
+  var this_collection_url;
+  console.log("Clicking on:", $(this));
+  this_collection_url = $(this).find('.collection_name').prop("href");
+  this_collection_url += "&json";
+  console.log("this_collection_url", this_collection_url);
+  collection_list = $("#collections_holder").html();
+  return $.ajax({
+    dataType: "json",
+    url: this_collection_url,
+    success: process_traits
+  });
+};
 
-  trait_click = function() {
-    var dataset, this_trait_url, trait;
-    console.log("Clicking on:", $(this));
-    trait = $(this).parent().find('.trait').text();
-    dataset = $(this).parent().find('.dataset').text();
-    this_trait_url = "/trait/get_sample_data?trait=" + trait + "&dataset=" + dataset;
-    console.log("this_trait_url", this_trait_url);
+submit_click = function() {
+  var all_vals, sample, samples, this_trait_vals, trait, trait_names, traits, _i, _j, _len, _len1, _ref;
+  selected_traits = {};
+  traits = [];
+  $('#collections_holder').find('input[type=checkbox]:checked').each(function() {
+    var this_dataset, this_trait, this_trait_url;
+    this_trait = $(this).parents('tr').find('.trait').text();
+    console.log("this_trait is:", this_trait);
+    this_dataset = $(this).parents('tr').find('.dataset').text();
+    console.log("this_dataset is:", this_dataset);
+    this_trait_url = "/trait/get_sample_data?trait=" + this_trait + "&dataset=" + this_dataset;
     return $.ajax({
       dataType: "json",
       url: this_trait_url,
-      success: get_trait_data
+      async: false,
+      success: add_trait_data
     });
-  };
-
-  $.colorbox.close();
-
-  add_trait_data = function(trait_data, textStatus, jqXHR) {
-    var trait_name, trait_sample_data;
-    trait_name = trait_data[0];
-    trait_sample_data = trait_data[1];
-    selected_traits[trait_name] = trait_sample_data;
-    return console.log("selected_traits:", selected_traits);
-  };
-
-  get_trait_data = function(trait_data, textStatus, jqXHR) {
-    var sample, samples, this_trait_vals, trait_sample_data, vals, _i, _len;
-    console.log("trait:", trait_data[0]);
-    trait_sample_data = trait_data[1];
-    console.log("trait_sample_data:", trait_sample_data);
-    samples = $('input[name=allsamples]').val().split(" ");
-    vals = [];
-    for (_i = 0, _len = samples.length; _i < _len; _i++) {
-      sample = samples[_i];
-      if (__indexOf.call(Object.keys(trait_sample_data), sample) >= 0) {
-        vals.push(parseFloat(trait_sample_data[sample]));
-      } else {
-        vals.push(null);
-      }
-    }
-    if ($('input[name=samples]').length < 1) {
-      $('#hidden_inputs').append('<input type="hidden" name="samples" value="[' + samples.toString() + ']" />');
-    }
-    $('#hidden_inputs').append('<input type="hidden" name="vals" value="[' + vals.toString() + ']" />');
-    this_trait_vals = get_this_trait_vals(samples);
-    console.log("THE LENGTH IS:", $('input[name=vals]').length);
-    if ($('input[name=vals]').length === 1) {
-      return create_scatterplot(samples, [this_trait_vals, vals]);
-    }
-  };
-
-  get_this_trait_vals = function(samples) {
-    var sample, this_trait_vals, this_val, this_vals_json, _i, _len;
+  });
+  console.log("SELECTED_TRAITS IS:", selected_traits);
+  trait_names = [];
+  samples = $('input[name=allsamples]').val().split(" ");
+  all_vals = [];
+  this_trait_vals = get_this_trait_vals(samples);
+  all_vals.push(this_trait_vals);
+  _ref = Object.keys(selected_traits);
+  for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+    trait = _ref[_i];
+    trait_names.push(trait);
     this_trait_vals = [];
-    for (_i = 0, _len = samples.length; _i < _len; _i++) {
-      sample = samples[_i];
-      this_val = parseFloat($("input[name='value:" + sample + "']").val());
-      if (!isNaN(this_val)) {
-        this_trait_vals.push(this_val);
+    for (_j = 0, _len1 = samples.length; _j < _len1; _j++) {
+      sample = samples[_j];
+      if (__indexOf.call(Object.keys(selected_traits[trait]), sample) >= 0) {
+        this_trait_vals.push(parseFloat(selected_traits[trait][sample]));
       } else {
         this_trait_vals.push(null);
       }
     }
-    console.log("this_trait_vals:", this_trait_vals);
-    this_vals_json = '[' + this_trait_vals.toString() + ']';
-    return this_trait_vals;
-  };
-
-  assemble_into_json = function(this_trait_vals) {
-    var json_data, json_ids, num_traits, samples,
-      _this = this;
-    num_traits = $('input[name=vals]').length;
-    samples = $('input[name=samples]').val();
-    json_ids = samples;
-    json_data = '[' + this_trait_vals;
-    $('input[name=vals]').each(function(index, element) {
-      return json_data += ',' + $(element).val();
-    });
-    json_data += ']';
-    return [json_ids, json_data];
-  };
-
-  color_by_trait = function(trait_sample_data, textStatus, jqXHR) {
-    return root.bar_chart.color_by_trait(trait_sample_data);
-  };
-
-  process_traits = function(trait_data, textStatus, jqXHR) {
-    var the_html, trait, _i, _len;
-    console.log('in process_traits with trait_data:', trait_data);
-    the_html = "<button id='back_to_collections' class='btn btn-inverse btn-small'>";
-    the_html += "<i class='icon-white icon-arrow-left'></i> Back </button>";
-    the_html += "    <button id='submit' class='btn btn-primary btn-small'> Submit </button>";
-    the_html += "<table class='table table-hover'>";
-    the_html += "<thead><tr><th></th><th>Record</th><th>Data Set</th><th>Description</th><th>Mean</th></tr></thead>";
-    the_html += "<tbody>";
-    for (_i = 0, _len = trait_data.length; _i < _len; _i++) {
-      trait = trait_data[_i];
-      the_html += "<tr class='trait_line'>";
-      the_html += "<td class='select_trait'><input type='checkbox' name='selectCheck' class='checkbox edit_sample_checkbox'></td>";
-      the_html += "<td class='trait'>" + trait.name + "</td>";
-      the_html += "<td class='dataset'>" + trait.dataset + "</td>";
-      the_html += "<td>" + trait.description + "</td>";
-      the_html += "<td>" + (trait.mean || '&nbsp;') + "</td></tr>";
-    }
-    the_html += "</tbody>";
-    the_html += "</table>";
-    $("#collections_holder").html(the_html);
-    return $('#collections_holder').colorbox.resize();
-  };
-
-  back_to_collections = function() {
-    console.log("collection_list:", collection_list);
-    $("#collections_holder").html(collection_list);
-    $(document).on("click", ".collection_line", collection_click);
-    return $('#collections_holder').colorbox.resize();
-  };
-
-  $(function() {
-    console.log("inside get_traits_from_collection");
-    $(document).on("click", ".collection_line", collection_click);
-    $(document).on("click", "#submit", submit_click);
-    $(document).on("click", ".trait", trait_click);
-    return $(document).on("click", "#back_to_collections", back_to_collections);
+    all_vals.push(this_trait_vals);
+  }
+  create_scatterplots(trait_names, samples, all_vals);
+  return $.colorbox.close();
+};
+
+trait_click = function() {
+  var dataset, this_trait_url, trait;
+  console.log("Clicking on:", $(this));
+  trait = $(this).parent().find('.trait').text();
+  dataset = $(this).parent().find('.dataset').text();
+  this_trait_url = "/trait/get_sample_data?trait=" + trait + "&dataset=" + dataset;
+  console.log("this_trait_url", this_trait_url);
+  $.ajax({
+    dataType: "json",
+    url: this_trait_url,
+    success: get_trait_data
   });
-
-}).call(this);
+  return $.colorbox.close();
+};
+
+add_trait_data = function(trait_data, textStatus, jqXHR) {
+  var trait_name, trait_sample_data;
+  trait_name = trait_data[0];
+  trait_sample_data = trait_data[1];
+  selected_traits[trait_name] = trait_sample_data;
+  return console.log("selected_traits:", selected_traits);
+};
+
+get_trait_data = function(trait_data, textStatus, jqXHR) {
+  var sample, samples, this_trait_vals, trait_sample_data, vals, _i, _len;
+  console.log("trait:", trait_data[0]);
+  trait_sample_data = trait_data[1];
+  console.log("trait_sample_data:", trait_sample_data);
+  samples = $('input[name=allsamples]').val().split(" ");
+  vals = [];
+  for (_i = 0, _len = samples.length; _i < _len; _i++) {
+    sample = samples[_i];
+    if (__indexOf.call(Object.keys(trait_sample_data), sample) >= 0) {
+      vals.push(parseFloat(trait_sample_data[sample]));
+    } else {
+      vals.push(null);
+    }
+  }
+  if ($('input[name=samples]').length < 1) {
+    $('#hidden_inputs').append('<input type="hidden" name="samples" value="[' + samples.toString() + ']" />');
+  }
+  $('#hidden_inputs').append('<input type="hidden" name="vals" value="[' + vals.toString() + ']" />');
+  this_trait_vals = get_this_trait_vals(samples);
+  console.log("THE LENGTH IS:", $('input[name=vals]').length);
+  if ($('input[name=vals]').length === 1) {
+    return create_scatterplot(samples, [this_trait_vals, vals]);
+  }
+};
+
+get_this_trait_vals = function(samples) {
+  var sample, this_trait_vals, this_val, this_vals_json, _i, _len;
+  this_trait_vals = [];
+  for (_i = 0, _len = samples.length; _i < _len; _i++) {
+    sample = samples[_i];
+    this_val = parseFloat($("input[name='value:" + sample + "']").val());
+    if (!isNaN(this_val)) {
+      this_trait_vals.push(this_val);
+    } else {
+      this_trait_vals.push(null);
+    }
+  }
+  console.log("this_trait_vals:", this_trait_vals);
+  this_vals_json = '[' + this_trait_vals.toString() + ']';
+  return this_trait_vals;
+};
+
+assemble_into_json = function(this_trait_vals) {
+  var json_data, json_ids, num_traits, samples;
+  num_traits = $('input[name=vals]').length;
+  samples = $('input[name=samples]').val();
+  json_ids = samples;
+  json_data = '[' + this_trait_vals;
+  $('input[name=vals]').each((function(_this) {
+    return function(index, element) {
+      return json_data += ',' + $(element).val();
+    };
+  })(this));
+  json_data += ']';
+  return [json_ids, json_data];
+};
+
+color_by_trait = function(trait_sample_data, textStatus, jqXHR) {
+  return root.bar_chart.color_by_trait(trait_sample_data);
+};
+
+process_traits = function(trait_data, textStatus, jqXHR) {
+  var the_html, trait, _i, _len;
+  console.log('in process_traits with trait_data:', trait_data);
+  the_html = "<button id='back_to_collections' class='btn btn-inverse btn-small'>";
+  the_html += "<i class='icon-white icon-arrow-left'></i> Back </button>";
+  the_html += "    <button id='submit' class='btn btn-primary btn-small'> Submit </button>";
+  the_html += "<table class='table table-hover'>";
+  the_html += "<thead><tr><th></th><th>Record</th><th>Data Set</th><th>Description</th><th>Mean</th></tr></thead>";
+  the_html += "<tbody>";
+  for (_i = 0, _len = trait_data.length; _i < _len; _i++) {
+    trait = trait_data[_i];
+    the_html += "<tr class='trait_line'>";
+    the_html += "<td class='select_trait'><input type='checkbox' name='selectCheck' class='checkbox edit_sample_checkbox'></td>";
+    the_html += "<td class='trait'>" + trait.name + "</td>";
+    the_html += "<td class='dataset'>" + trait.dataset + "</td>";
+    the_html += "<td>" + trait.description + "</td>";
+    the_html += "<td>" + (trait.mean || '&nbsp;') + "</td></tr>";
+  }
+  the_html += "</tbody>";
+  the_html += "</table>";
+  $("#collections_holder").html(the_html);
+  return $('#collections_holder').colorbox.resize();
+};
+
+back_to_collections = function() {
+  console.log("collection_list:", collection_list);
+  $("#collections_holder").html(collection_list);
+  $(document).on("click", ".collection_line", collection_click);
+  return $('#collections_holder').colorbox.resize();
+};
+
+$(function() {
+  console.log("inside get_traits_from_collection");
+  $(document).on("click", ".collection_line", collection_click);
+  $(document).on("click", "#submit", submit_click);
+  $(document).on("click", ".trait", trait_click);
+  return $(document).on("click", "#back_to_collections", back_to_collections);
+});
diff --git a/wqflask/wqflask/static/new/javascript/histogram.js b/wqflask/wqflask/static/new/javascript/histogram.js
index d8067ced..207a00c4 100755
--- a/wqflask/wqflask/static/new/javascript/histogram.js
+++ b/wqflask/wqflask/static/new/javascript/histogram.js
@@ -1,122 +1,124 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var Histogram, root;
-
-  root = typeof exports !== "undefined" && exports !== null ? exports : this;
-
-  Histogram = (function() {
-
-    function Histogram(sample_list, sample_group) {
-      this.sample_list = sample_list;
-      this.sample_group = sample_group;
-      this.sort_by = "name";
-      this.format_count = d3.format(",.0f");
-      this.get_sample_vals();
-      this.margin = {
-        top: 10,
-        right: 30,
-        bottom: 30,
-        left: 30
-      };
-      this.plot_width = 960 - this.margin.left - this.margin.right;
-      this.plot_height = 500 - this.margin.top - this.margin.bottom;
-      this.x_buffer = this.plot_width / 20;
-      this.y_buffer = this.plot_height / 20;
-      this.y_min = d3.min(this.sample_vals);
-      this.y_max = d3.max(this.sample_vals) * 1.1;
-      this.plot_height -= this.y_buffer;
-      this.create_x_scale();
-      this.get_histogram_data();
-      this.create_y_scale();
-      this.svg = this.create_svg();
-      this.create_graph();
-    }
-
-    Histogram.prototype.get_sample_vals = function() {
-      var sample;
-      return this.sample_vals = (function() {
-        var _i, _len, _ref, _results;
-        _ref = this.sample_list;
-        _results = [];
-        for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-          sample = _ref[_i];
-          if (sample.value !== null) {
-            _results.push(sample.value);
-          }
-        }
-        return _results;
-      }).call(this);
-    };
-
-    Histogram.prototype.create_svg = function() {
-      var svg;
-      svg = d3.select("#histogram").append("svg").attr("class", "histogram").attr("width", this.plot_width + this.margin.left + this.margin.right).attr("height", this.plot_height + this.margin.top + this.margin.bottom).append("g").attr("transform", "translate(" + this.margin.left + "," + this.margin.top + ")");
-      return svg;
-    };
-
-    Histogram.prototype.create_x_scale = function() {
-      var x0;
-      console.log("min/max:", d3.min(this.sample_vals) + "," + d3.max(this.sample_vals));
-      x0 = Math.max(-d3.min(this.sample_vals), d3.max(this.sample_vals));
-      return this.x_scale = d3.scale.linear().domain([d3.min(this.sample_vals), d3.max(this.sample_vals)]).range([0, this.plot_width]).nice();
+// Generated by CoffeeScript 1.7.1
+var Histogram, root;
+
+root = typeof exports !== "undefined" && exports !== null ? exports : this;
+
+Histogram = (function() {
+  function Histogram(sample_list, sample_group) {
+    this.sample_list = sample_list;
+    this.sample_group = sample_group;
+    this.sort_by = "name";
+    this.format_count = d3.format(",.0f");
+    this.get_sample_vals();
+    this.margin = {
+      top: 10,
+      right: 30,
+      bottom: 30,
+      left: 30
     };
-
-    Histogram.prototype.get_histogram_data = function() {
-      console.log("sample_vals:", this.sample_vals);
-      this.histogram_data = d3.layout.histogram().bins(this.x_scale.ticks(20))(this.sample_vals);
-      return console.log("histogram_data:", this.histogram_data[0]);
-    };
-
-    Histogram.prototype.create_y_scale = function() {
-      var _this = this;
-      return this.y_scale = d3.scale.linear().domain([
-        0, d3.max(this.histogram_data, function(d) {
+    this.plot_width = 960 - this.margin.left - this.margin.right;
+    this.plot_height = 500 - this.margin.top - this.margin.bottom;
+    this.x_buffer = this.plot_width / 20;
+    this.y_buffer = this.plot_height / 20;
+    this.y_min = d3.min(this.sample_vals);
+    this.y_max = d3.max(this.sample_vals) * 1.1;
+    this.plot_height -= this.y_buffer;
+    this.create_x_scale();
+    this.get_histogram_data();
+    this.create_y_scale();
+    this.svg = this.create_svg();
+    this.create_graph();
+  }
+
+  Histogram.prototype.get_sample_vals = function() {
+    var sample;
+    return this.sample_vals = (function() {
+      var _i, _len, _ref, _results;
+      _ref = this.sample_list;
+      _results = [];
+      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+        sample = _ref[_i];
+        if (sample.value !== null) {
+          _results.push(sample.value);
+        }
+      }
+      return _results;
+    }).call(this);
+  };
+
+  Histogram.prototype.create_svg = function() {
+    var svg;
+    svg = d3.select("#histogram").append("svg").attr("class", "histogram").attr("width", this.plot_width + this.margin.left + this.margin.right).attr("height", this.plot_height + this.margin.top + this.margin.bottom).append("g").attr("transform", "translate(" + this.margin.left + "," + this.margin.top + ")");
+    return svg;
+  };
+
+  Histogram.prototype.create_x_scale = function() {
+    var x0;
+    console.log("min/max:", d3.min(this.sample_vals) + "," + d3.max(this.sample_vals));
+    x0 = Math.max(-d3.min(this.sample_vals), d3.max(this.sample_vals));
+    return this.x_scale = d3.scale.linear().domain([d3.min(this.sample_vals), d3.max(this.sample_vals)]).range([0, this.plot_width]).nice();
+  };
+
+  Histogram.prototype.get_histogram_data = function() {
+    console.log("sample_vals:", this.sample_vals);
+    this.histogram_data = d3.layout.histogram().bins(this.x_scale.ticks(20))(this.sample_vals);
+    return console.log("histogram_data:", this.histogram_data[0]);
+  };
+
+  Histogram.prototype.create_y_scale = function() {
+    return this.y_scale = d3.scale.linear().domain([
+      0, d3.max(this.histogram_data, (function(_this) {
+        return function(d) {
           return d.y;
-        })
-      ]).range([this.plot_height, 0]);
-    };
-
-    Histogram.prototype.create_graph = function() {
-      this.add_x_axis();
-      this.add_y_axis();
-      return this.add_bars();
-    };
-
-    Histogram.prototype.add_x_axis = function() {
-      var x_axis;
-      x_axis = d3.svg.axis().scale(this.x_scale).orient("bottom");
-      return this.svg.append("g").attr("class", "x axis").attr("transform", "translate(0," + this.plot_height + ")").call(x_axis);
-    };
-
-    Histogram.prototype.add_y_axis = function() {
-      var yAxis;
-      yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
-      return this.svg.append("g").attr("class", "y axis").call(yAxis).append("text").attr("transform", "rotate(-90)").attr("y", 6).attr("dy", ".71em").style("text-anchor", "end");
-    };
-
-    Histogram.prototype.add_bars = function() {
-      var bar,
-        _this = this;
-      console.log("bar_width:", this.x_scale(this.histogram_data[0].dx));
-      bar = this.svg.selectAll(".bar").data(this.histogram_data).enter().append("g").attr("class", "bar").attr("transform", function(d) {
+        };
+      })(this))
+    ]).range([this.plot_height, 0]);
+  };
+
+  Histogram.prototype.create_graph = function() {
+    this.add_x_axis();
+    this.add_y_axis();
+    return this.add_bars();
+  };
+
+  Histogram.prototype.add_x_axis = function() {
+    var x_axis;
+    x_axis = d3.svg.axis().scale(this.x_scale).orient("bottom");
+    return this.svg.append("g").attr("class", "x axis").attr("transform", "translate(0," + this.plot_height + ")").call(x_axis);
+  };
+
+  Histogram.prototype.add_y_axis = function() {
+    var yAxis;
+    yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
+    return this.svg.append("g").attr("class", "y axis").call(yAxis).append("text").attr("transform", "rotate(-90)").attr("y", 6).attr("dy", ".71em").style("text-anchor", "end");
+  };
+
+  Histogram.prototype.add_bars = function() {
+    var bar;
+    console.log("bar_width:", this.x_scale(this.histogram_data[0].dx));
+    bar = this.svg.selectAll(".bar").data(this.histogram_data).enter().append("g").attr("class", "bar").attr("transform", (function(_this) {
+      return function(d) {
         return "translate(" + _this.x_scale(d.x) + "," + _this.y_scale(d.y) + ")";
-      });
-      bar.append("rect").attr("x", 1).attr("width", this.x_scale(this.histogram_data[0].x + this.histogram_data[0].dx) - 1).attr("height", function(d) {
+      };
+    })(this));
+    bar.append("rect").attr("x", 1).attr("width", this.x_scale(this.histogram_data[0].x + this.histogram_data[0].dx) - 1).attr("height", (function(_this) {
+      return function(d) {
         return _this.plot_height - _this.y_scale(d.y);
-      });
-      return bar.append("text").attr("dy", ".75em").attr("y", 6).attr("x", this.x_scale(this.histogram_data[0].dx) / 2).attr("text-anchor", "middle").style("fill", "#fff").text(function(d) {
+      };
+    })(this));
+    return bar.append("text").attr("dy", ".75em").attr("y", 6).attr("x", this.x_scale(this.histogram_data[0].dx) / 2).attr("text-anchor", "middle").style("fill", "#fff").text((function(_this) {
+      return function(d) {
         var bar_height;
         bar_height = _this.plot_height - _this.y_scale(d.y);
         if (bar_height > 20) {
           return _this.format_count(d.y);
         }
-      });
-    };
-
-    return Histogram;
+      };
+    })(this));
+  };
 
-  })();
+  return Histogram;
 
-  root.Histogram = Histogram;
+})();
 
-}).call(this);
+root.Histogram = Histogram;
diff --git a/wqflask/wqflask/static/new/javascript/interval_map_new.coffee b/wqflask/wqflask/static/new/javascript/interval_map_new.coffee
index 898df6d1..d60b900d 100644
--- a/wqflask/wqflask/static/new/javascript/interval_map_new.coffee
+++ b/wqflask/wqflask/static/new/javascript/interval_map_new.coffee
@@ -1,39 +1,59 @@
-h = 500

-w = 1200

-margin = {left:60, top:40, right:40, bottom: 40, inner:5}

-halfh = (h+margin.top+margin.bottom)

-totalh = halfh*2

-totalw = (w+margin.left+margin.right)

+create_interval_map = ->

+    h = 500

+    w = 1200

+    margin = {left:60, top:40, right:40, bottom: 40, inner:5}

+    halfh = (h+margin.top+margin.bottom)

+    totalh = halfh*2

+    totalw = (w+margin.left+margin.right)

+    

+    # simplest use

+    #d3.json "data.json", (data) ->

+    mychart = lodchart().lodvarname("lod.hk")

+                        .height(h)

+                        .width(w)

+                        .margin(margin)

+    

+    data = js_data.json_data

+    

+    d3.select("div#topchart")

+      .datum(data)

+      .call(mychart)

+    

+    # grab chromosome rectangles; color pink on hover

+    chrrect = mychart.chrSelect()

+    chrrect.on "mouseover", ->

+                d3.select(this).attr("fill", "#E9CFEC")

+           .on "mouseout", (d,i) ->

+                d3.select(this).attr("fill", ->

+                      return "#F1F1F9"  if i % 2

+                      "#FBFBFF")

+    

+    # animate points at markers on click

+    mychart.markerSelect()

+              .on "click", (d) ->

+                    r = d3.select(this).attr("r")

+                    d3.select(this)

+                      .transition().duration(500).attr("r", r*3)

+                      .transition().duration(500).attr("r", r)

 

-# simplest use

-#d3.json "data.json", (data) ->

-mychart = lodchart().lodvarname("lod.hk")

-                    .height(h)

-                    .width(w)

-                    .margin(margin)

-

-data = js_data.json_data

-

-d3.select("div#topchart")

-  .datum(data)

-  .call(mychart)

+create_interval_map()

 

-# grab chromosome rectangles; color pink on hover

-chrrect = mychart.chrSelect()

-chrrect.on "mouseover", ->

-            d3.select(this).attr("fill", "#E9CFEC")

-       .on "mouseout", (d,i) ->

-            d3.select(this).attr("fill", ->

-                  return "#F1F1F9"  if i % 2

-                  "#FBFBFF")

+$("#export").click =>

+    #Get d3 SVG element

+    svg = $("#topchart").find("svg")[0]

+    

+    #Extract SVG text string

+    svg_xml = (new XMLSerializer).serializeToString(svg)

+    console.log("svg_xml:", svg_xml)

+        

+    #Set filename

+    filename = "manhattan_plot_" + js_data.this_trait

 

-# animate points at markers on click

-mychart.markerSelect()

-          .on "click", (d) ->

-                r = d3.select(this).attr("r")

-                d3.select(this)

-                  .transition().duration(500).attr("r", r*3)

-                  .transition().duration(500).attr("r", r)

+    #Make a form with the SVG data

+    form = $("#exportform")

+    form.find("#data").val(svg_xml)

+    form.find("#filename").val(filename)

+    form.submit()

 

 # two LOD charts within one SVG

 #d3.json "data.json", (data) ->

diff --git a/wqflask/wqflask/static/new/javascript/interval_map_new.js b/wqflask/wqflask/static/new/javascript/interval_map_new.js
index 8861419c..6515ac0d 100644
--- a/wqflask/wqflask/static/new/javascript/interval_map_new.js
+++ b/wqflask/wqflask/static/new/javascript/interval_map_new.js
@@ -1,11 +1,10 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var chrrect, data, h, halfh, margin, mychart, totalh, totalw, w;
+// Generated by CoffeeScript 1.7.1
+var create_interval_map;
 
+create_interval_map = function() {
+  var chrrect, data, h, halfh, margin, mychart, totalh, totalw, w;
   h = 500;
-
   w = 1200;
-
   margin = {
     left: 60,
     top: 40,
@@ -13,21 +12,13 @@
     bottom: 40,
     inner: 5
   };
-
   halfh = h + margin.top + margin.bottom;
-
   totalh = halfh * 2;
-
   totalw = w + margin.left + margin.right;
-
   mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin);
-
   data = js_data.json_data;
-
   d3.select("div#topchart").datum(data).call(mychart);
-
   chrrect = mychart.chrSelect();
-
   chrrect.on("mouseover", function() {
     return d3.select(this).attr("fill", "#E9CFEC");
   }).on("mouseout", function(d, i) {
@@ -38,11 +29,25 @@
       return "#FBFBFF";
     });
   });
-
-  mychart.markerSelect().on("click", function(d) {
+  return mychart.markerSelect().on("click", function(d) {
     var r;
     r = d3.select(this).attr("r");
     return d3.select(this).transition().duration(500).attr("r", r * 3).transition().duration(500).attr("r", r);
   });
-
-}).call(this);
+};
+
+create_interval_map();
+
+$("#export").click((function(_this) {
+  return function() {
+    var filename, form, svg, svg_xml;
+    svg = $("#topchart").find("svg")[0];
+    svg_xml = (new XMLSerializer).serializeToString(svg);
+    console.log("svg_xml:", svg_xml);
+    filename = "manhattan_plot_" + js_data.this_trait;
+    form = $("#exportform");
+    form.find("#data").val(svg_xml);
+    form.find("#filename").val(filename);
+    return form.submit();
+  };
+})(this));
diff --git a/wqflask/wqflask/static/new/javascript/interval_mapping.js b/wqflask/wqflask/static/new/javascript/interval_mapping.js
index 3a2ce6d7..3544f75c 100755
--- a/wqflask/wqflask/static/new/javascript/interval_mapping.js
+++ b/wqflask/wqflask/static/new/javascript/interval_mapping.js
@@ -1,178 +1,183 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; };
+// Generated by CoffeeScript 1.7.1
+var __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; };
 
-  $(function() {
-    var Interval_Map;
-    Interval_Map = (function() {
+$(function() {
+  var Interval_Map;
+  Interval_Map = (function() {
+    function Interval_Map(plot_height, plot_width) {
+      var _ref;
+      this.plot_height = plot_height;
+      this.plot_width = plot_width;
+      this.qtl_results = js_data.qtl_results;
+      console.log("qtl_results are:", this.qtl_results);
+      this.chromosomes = js_data.chromosomes;
+      this.total_length = 0;
+      this.max_chr = this.get_max_chr();
+      this.x_coords = [];
+      this.y_coords = [];
+      this.marker_names = [];
+      console.time('Create coordinates');
+      this.create_coordinates();
+      console.log("@x_coords: ", this.x_coords);
+      console.log("@y_coords: ", this.y_coords);
+      console.timeEnd('Create coordinates');
+      _ref = this.get_chr_lengths(), this.chr_lengths = _ref[0], this.cumulative_chr_lengths = _ref[1];
+      this.x_buffer = this.plot_width / 30;
+      this.y_buffer = this.plot_height / 20;
+      this.x_max = this.total_length;
+      console.log("@x_max: ", this.x_max);
+      console.log("@x_buffer: ", this.x_buffer);
+      this.y_max = d3.max(this.y_coords) * 1.2;
+      this.svg = this.create_svg();
+      this.plot_coordinates = _.zip(this.x_coords, this.y_coords, this.marker_names);
+      this.plot_height -= this.y_buffer;
+      this.create_scales();
+      console.time('Create graph');
+      this.create_graph();
+      console.timeEnd('Create graph');
+    }
 
-      function Interval_Map(plot_height, plot_width) {
-        var _ref;
-        this.plot_height = plot_height;
-        this.plot_width = plot_width;
-        this.qtl_results = js_data.qtl_results;
-        console.log("qtl_results are:", this.qtl_results);
-        this.chromosomes = js_data.chromosomes;
-        this.total_length = 0;
-        this.max_chr = this.get_max_chr();
-        this.x_coords = [];
-        this.y_coords = [];
-        this.marker_names = [];
-        console.time('Create coordinates');
-        this.create_coordinates();
-        console.log("@x_coords: ", this.x_coords);
-        console.log("@y_coords: ", this.y_coords);
-        console.timeEnd('Create coordinates');
-        _ref = this.get_chr_lengths(), this.chr_lengths = _ref[0], this.cumulative_chr_lengths = _ref[1];
-        this.x_buffer = this.plot_width / 30;
-        this.y_buffer = this.plot_height / 20;
-        this.x_max = this.total_length;
-        console.log("@x_max: ", this.x_max);
-        console.log("@x_buffer: ", this.x_buffer);
-        this.y_max = d3.max(this.y_coords) * 1.2;
-        this.svg = this.create_svg();
-        this.plot_coordinates = _.zip(this.x_coords, this.y_coords, this.marker_names);
-        this.plot_height -= this.y_buffer;
-        this.create_scales();
-        console.time('Create graph');
-        this.create_graph();
-        console.timeEnd('Create graph');
-      }
-
-      Interval_Map.prototype.get_max_chr = function() {
-        var chr, max_chr, result, _i, _len, _ref;
-        max_chr = 0;
-        _ref = this.qtl_results;
-        for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-          result = _ref[_i];
-          chr = parseInt(result.chr);
-          if (!_.isNaN(chr)) {
-            if (chr > max_chr) {
-              max_chr = chr;
-            }
+    Interval_Map.prototype.get_max_chr = function() {
+      var chr, max_chr, result, _i, _len, _ref;
+      max_chr = 0;
+      _ref = this.qtl_results;
+      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+        result = _ref[_i];
+        chr = parseInt(result.chr);
+        if (!_.isNaN(chr)) {
+          if (chr > max_chr) {
+            max_chr = chr;
           }
         }
-        return max_chr;
-      };
+      }
+      return max_chr;
+    };
 
-      Interval_Map.prototype.get_chr_lengths = function() {
-        /*
-        #Gets a list of both individual and cumulative (the position of one on the graph
-        #is its own length plus the lengths of all preceding chromosomes) lengths in order
-        #to draw the vertical lines separating chromosomes and the chromosome labels
-        #
-        */
+    Interval_Map.prototype.get_chr_lengths = function() {
 
-        var chr_lengths, cumulative_chr_lengths, key, this_length, total_length;
-        console.log("@chromosomes: ", this.chromosomes);
-        cumulative_chr_lengths = [];
-        chr_lengths = [];
-        total_length = 0;
-        for (key in this.chromosomes) {
-          this_length = this.chromosomes[key];
-          chr_lengths.push(this_length);
-          cumulative_chr_lengths.push(total_length + this_length);
-          total_length += this_length;
-        }
-        console.log("chr_lengths: ", chr_lengths);
-        return [chr_lengths, cumulative_chr_lengths];
-      };
+      /*
+       *Gets a list of both individual and cumulative (the position of one on the graph
+       *is its own length plus the lengths of all preceding chromosomes) lengths in order
+       *to draw the vertical lines separating chromosomes and the chromosome labels
+       *
+       */
+      var chr_lengths, cumulative_chr_lengths, key, this_length, total_length;
+      console.log("@chromosomes: ", this.chromosomes);
+      cumulative_chr_lengths = [];
+      chr_lengths = [];
+      total_length = 0;
+      for (key in this.chromosomes) {
+        this_length = this.chromosomes[key];
+        chr_lengths.push(this_length);
+        cumulative_chr_lengths.push(total_length + this_length);
+        total_length += this_length;
+      }
+      console.log("chr_lengths: ", chr_lengths);
+      return [chr_lengths, cumulative_chr_lengths];
+    };
 
-      Interval_Map.prototype.create_coordinates = function() {
-        var chr_length, chr_lengths, chr_seen, result, _i, _len, _ref, _ref1;
-        chr_lengths = [];
-        chr_seen = [];
-        _ref = js_data.qtl_results;
-        for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-          result = _ref[_i];
-          if (result.chr === "X") {
-            chr_length = parseFloat(this.chromosomes[20]);
-          } else {
-            chr_length = parseFloat(this.chromosomes[result.chr]);
-          }
-          if (!(_ref1 = result.chr, __indexOf.call(chr_seen, _ref1) >= 0)) {
-            chr_seen.push(result.chr);
-            chr_lengths.push(chr_length);
-            if (result.chr !== "1") {
-              this.total_length += parseFloat(chr_lengths[chr_lengths.length - 2]);
-            }
+    Interval_Map.prototype.create_coordinates = function() {
+      var chr_length, chr_lengths, chr_seen, result, _i, _len, _ref, _ref1;
+      chr_lengths = [];
+      chr_seen = [];
+      _ref = js_data.qtl_results;
+      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+        result = _ref[_i];
+        if (result.chr === "X") {
+          chr_length = parseFloat(this.chromosomes[20]);
+        } else {
+          chr_length = parseFloat(this.chromosomes[result.chr]);
+        }
+        if (!(_ref1 = result.chr, __indexOf.call(chr_seen, _ref1) >= 0)) {
+          chr_seen.push(result.chr);
+          chr_lengths.push(chr_length);
+          if (result.chr !== "1") {
+            this.total_length += parseFloat(chr_lengths[chr_lengths.length - 2]);
           }
-          this.x_coords.push(this.total_length + parseFloat(result.Mb));
-          this.y_coords.push(result.lrs_value);
-          this.marker_names.push(result.name);
         }
-        return this.total_length += parseFloat(chr_lengths[chr_lengths.length - 1]);
-      };
+        this.x_coords.push(this.total_length + parseFloat(result.Mb));
+        this.y_coords.push(result.lrs_value);
+        this.marker_names.push(result.name);
+      }
+      return this.total_length += parseFloat(chr_lengths[chr_lengths.length - 1]);
+    };
 
-      Interval_Map.prototype.create_svg = function() {
-        var svg;
-        svg = d3.select("#interval_map").append("svg").attr("class", "interval_map").attr("width", this.plot_width + this.x_buffer).attr("height", this.plot_height + this.y_buffer);
-        return svg;
-      };
+    Interval_Map.prototype.create_svg = function() {
+      var svg;
+      svg = d3.select("#interval_map").append("svg").attr("class", "interval_map").attr("width", this.plot_width + this.x_buffer).attr("height", this.plot_height + this.y_buffer);
+      return svg;
+    };
 
-      Interval_Map.prototype.create_graph = function() {
-        this.add_border();
-        this.add_x_axis();
-        this.add_y_axis();
-        this.add_chr_lines();
-        this.fill_chr_areas();
-        this.add_chr_labels();
-        return this.connect_markers();
-      };
+    Interval_Map.prototype.create_graph = function() {
+      this.add_border();
+      this.add_x_axis();
+      this.add_y_axis();
+      this.add_chr_lines();
+      this.fill_chr_areas();
+      this.add_chr_labels();
+      return this.connect_markers();
+    };
 
-      Interval_Map.prototype.add_border = function() {
-        var border_coords,
-          _this = this;
-        border_coords = [[this.y_buffer, this.plot_height, this.x_buffer, this.x_buffer], [this.y_buffer, this.plot_height, this.plot_width, this.plot_width], [this.y_buffer, this.y_buffer, this.x_buffer, this.plot_width], [this.plot_height, this.plot_height, this.x_buffer, this.plot_width]];
-        return this.svg.selectAll("line").data(border_coords).enter().append("line").attr("y1", function(d) {
+    Interval_Map.prototype.add_border = function() {
+      var border_coords;
+      border_coords = [[this.y_buffer, this.plot_height, this.x_buffer, this.x_buffer], [this.y_buffer, this.plot_height, this.plot_width, this.plot_width], [this.y_buffer, this.y_buffer, this.x_buffer, this.plot_width], [this.plot_height, this.plot_height, this.x_buffer, this.plot_width]];
+      return this.svg.selectAll("line").data(border_coords).enter().append("line").attr("y1", (function(_this) {
+        return function(d) {
           return d[0];
-        }).attr("y2", function(d) {
+        };
+      })(this)).attr("y2", (function(_this) {
+        return function(d) {
           return d[1];
-        }).attr("x1", function(d) {
+        };
+      })(this)).attr("x1", (function(_this) {
+        return function(d) {
           return d[2];
-        }).attr("x2", function(d) {
+        };
+      })(this)).attr("x2", (function(_this) {
+        return function(d) {
           return d[3];
-        }).style("stroke", "#000");
-      };
+        };
+      })(this)).style("stroke", "#000");
+    };
 
-      Interval_Map.prototype.create_scales = function() {
-        this.x_scale = d3.scale.linear().domain([0, d3.max(this.x_coords)]).range([this.x_buffer, this.plot_width]);
-        return this.y_scale = d3.scale.linear().domain([0, this.y_max]).range([this.plot_height, this.y_buffer]);
-      };
+    Interval_Map.prototype.create_scales = function() {
+      this.x_scale = d3.scale.linear().domain([0, d3.max(this.x_coords)]).range([this.x_buffer, this.plot_width]);
+      return this.y_scale = d3.scale.linear().domain([0, this.y_max]).range([this.plot_height, this.y_buffer]);
+    };
 
-      Interval_Map.prototype.create_x_axis_tick_values = function() {
-        var chr_ticks, i, length, tick, tick_count, tick_val, tick_vals, val, _i, _j, _k, _len, _ref, _ref1, _ref2;
-        tick_vals = [];
-        for (val = _i = 25, _ref = this.cumulative_chr_lengths[0]; 25 <= _ref ? _i <= _ref : _i >= _ref; val = 25 <= _ref ? ++_i : --_i) {
-          if (val % 25 === 0) {
-            tick_vals.push(val);
-          }
+    Interval_Map.prototype.create_x_axis_tick_values = function() {
+      var chr_ticks, i, length, tick, tick_count, tick_val, tick_vals, val, _i, _j, _k, _len, _ref, _ref1, _ref2;
+      tick_vals = [];
+      for (val = _i = 25, _ref = this.cumulative_chr_lengths[0]; 25 <= _ref ? _i <= _ref : _i >= _ref; val = 25 <= _ref ? ++_i : --_i) {
+        if (val % 25 === 0) {
+          tick_vals.push(val);
         }
-        _ref1 = this.cumulative_chr_lengths;
-        for (i = _j = 0, _len = _ref1.length; _j < _len; i = ++_j) {
-          length = _ref1[i];
-          if (i === 0) {
-            continue;
-          }
-          chr_ticks = [];
-          tick_count = Math.floor(this.chr_lengths[i] / 25);
-          tick_val = parseInt(this.cumulative_chr_lengths[i - 1]);
-          for (tick = _k = 0, _ref2 = tick_count - 1; 0 <= _ref2 ? _k <= _ref2 : _k >= _ref2; tick = 0 <= _ref2 ? ++_k : --_k) {
-            tick_val += 25;
-            chr_ticks.push(tick_val);
-          }
-          Array.prototype.push.apply(tick_vals, chr_ticks);
+      }
+      _ref1 = this.cumulative_chr_lengths;
+      for (i = _j = 0, _len = _ref1.length; _j < _len; i = ++_j) {
+        length = _ref1[i];
+        if (i === 0) {
+          continue;
         }
-        return tick_vals;
-      };
+        chr_ticks = [];
+        tick_count = Math.floor(this.chr_lengths[i] / 25);
+        tick_val = parseInt(this.cumulative_chr_lengths[i - 1]);
+        for (tick = _k = 0, _ref2 = tick_count - 1; 0 <= _ref2 ? _k <= _ref2 : _k >= _ref2; tick = 0 <= _ref2 ? ++_k : --_k) {
+          tick_val += 25;
+          chr_ticks.push(tick_val);
+        }
+        Array.prototype.push.apply(tick_vals, chr_ticks);
+      }
+      return tick_vals;
+    };
 
-      Interval_Map.prototype.add_x_axis = function() {
-        var next_chr, tmp_tick_val, xAxis,
-          _this = this;
-        xAxis = d3.svg.axis().scale(this.x_scale).orient("bottom").tickValues(this.create_x_axis_tick_values());
-        next_chr = 1;
-        tmp_tick_val = 0;
-        xAxis.tickFormat(function(d) {
+    Interval_Map.prototype.add_x_axis = function() {
+      var next_chr, tmp_tick_val, xAxis;
+      xAxis = d3.svg.axis().scale(this.x_scale).orient("bottom").tickValues(this.create_x_axis_tick_values());
+      next_chr = 1;
+      tmp_tick_val = 0;
+      xAxis.tickFormat((function(_this) {
+        return function(d) {
           var next_chr_length, tick_val;
           d3.format("d");
           if (d < _this.cumulative_chr_lengths[0]) {
@@ -189,85 +194,104 @@
             }
           }
           return tick_val;
-        });
-        return this.svg.append("g").attr("class", "x_axis").attr("transform", "translate(0," + this.plot_height + ")").call(xAxis).selectAll("text").attr("text-anchor", "right").attr("dx", "-1.6em").attr("transform", function(d) {
+        };
+      })(this));
+      return this.svg.append("g").attr("class", "x_axis").attr("transform", "translate(0," + this.plot_height + ")").call(xAxis).selectAll("text").attr("text-anchor", "right").attr("dx", "-1.6em").attr("transform", (function(_this) {
+        return function(d) {
           return "translate(-12,0) rotate(-90)";
-        });
-      };
+        };
+      })(this));
+    };
 
-      Interval_Map.prototype.add_y_axis = function() {
-        var yAxis;
-        yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
-        return this.svg.append("g").attr("class", "y_axis").attr("transform", "translate(" + this.x_buffer + ",0)").call(yAxis);
-      };
+    Interval_Map.prototype.add_y_axis = function() {
+      var yAxis;
+      yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
+      return this.svg.append("g").attr("class", "y_axis").attr("transform", "translate(" + this.x_buffer + ",0)").call(yAxis);
+    };
 
-      Interval_Map.prototype.add_chr_lines = function() {
-        var _this = this;
-        return this.svg.selectAll("line").data(this.cumulative_chr_lengths, function(d) {
+    Interval_Map.prototype.add_chr_lines = function() {
+      return this.svg.selectAll("line").data(this.cumulative_chr_lengths, (function(_this) {
+        return function(d) {
           return d;
-        }).enter().append("line").attr("y1", this.y_buffer).attr("y2", this.plot_height).attr("x1", this.x_scale).attr("x2", this.x_scale).style("stroke", "#ccc");
-      };
+        };
+      })(this)).enter().append("line").attr("y1", this.y_buffer).attr("y2", this.plot_height).attr("x1", this.x_scale).attr("x2", this.x_scale).style("stroke", "#ccc");
+    };
 
-      Interval_Map.prototype.fill_chr_areas = function() {
-        var _this = this;
-        return this.svg.selectAll("rect.chr_fill_area_1").data(_.zip(this.chr_lengths, this.cumulative_chr_lengths), function(d) {
+    Interval_Map.prototype.fill_chr_areas = function() {
+      return this.svg.selectAll("rect.chr_fill_area_1").data(_.zip(this.chr_lengths, this.cumulative_chr_lengths), (function(_this) {
+        return function(d) {
           return d;
-        }).enter().append("rect").attr("class", "chr_fill_area_1").attr("x", function(d, i) {
+        };
+      })(this)).enter().append("rect").attr("class", "chr_fill_area_1").attr("x", (function(_this) {
+        return function(d, i) {
           if (i === 0) {
             return _this.x_scale(0);
           } else {
             return _this.x_scale(_this.cumulative_chr_lengths[i - 1]);
           }
-        }).attr("y", this.y_buffer).attr("width", function(d) {
+        };
+      })(this)).attr("y", this.y_buffer).attr("width", (function(_this) {
+        return function(d) {
           return _this.x_scale(d[0]);
-        }).attr("height", this.plot_height - this.y_buffer).attr("fill", "white");
-      };
+        };
+      })(this)).attr("height", this.plot_height - this.y_buffer).attr("fill", "white");
+    };
 
-      Interval_Map.prototype.add_chr_labels = function() {
-        var chr_info, chr_names, key,
-          _this = this;
-        chr_names = [];
-        for (key in this.chromosomes) {
-          chr_names.push(key);
-        }
-        chr_info = _.zip(chr_names, this.chr_lengths, this.cumulative_chr_lengths);
-        return this.svg.selectAll("text").data(chr_info, function(d) {
+    Interval_Map.prototype.add_chr_labels = function() {
+      var chr_info, chr_names, key;
+      chr_names = [];
+      for (key in this.chromosomes) {
+        chr_names.push(key);
+      }
+      chr_info = _.zip(chr_names, this.chr_lengths, this.cumulative_chr_lengths);
+      return this.svg.selectAll("text").data(chr_info, (function(_this) {
+        return function(d) {
           return d;
-        }).enter().append("text").text(function(d) {
+        };
+      })(this)).enter().append("text").text((function(_this) {
+        return function(d) {
           return d[0];
-        }).attr("x", function(d) {
+        };
+      })(this)).attr("x", (function(_this) {
+        return function(d) {
           return _this.x_scale(d[2] - d[1] / 2);
-        }).attr("y", this.plot_height * 0.1).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px");
-      };
+        };
+      })(this)).attr("y", this.plot_height * 0.1).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px");
+    };
 
-      Interval_Map.prototype.connect_markers = function() {
-        var _this = this;
-        return this.svg.selectAll("line").data(this.plot_coordinates).enter().append("line").attr("x1", function(d, i) {
+    Interval_Map.prototype.connect_markers = function() {
+      return this.svg.selectAll("line").data(this.plot_coordinates).enter().append("line").attr("x1", (function(_this) {
+        return function(d, i) {
           if (i === 0) {
             return _this.x_buffer;
           } else {
             return parseFloat(_this.x_buffer) + ((parseFloat(_this.plot_width) - parseFloat(_this.x_buffer)) * _this.plot_coordinates[i - 1][0] / parseFloat(_this.x_max));
           }
-        }).attr("y1", function(d, i) {
+        };
+      })(this)).attr("y1", (function(_this) {
+        return function(d, i) {
           if (i === 0) {
             return _this.plot_height;
           } else {
             return _this.plot_height - ((_this.plot_height - _this.y_buffer) * _this.plot_coordinates[i - 1][1] / _this.y_max);
           }
-        }).attr("x2", function(d) {
+        };
+      })(this)).attr("x2", (function(_this) {
+        return function(d) {
           return parseFloat(_this.x_buffer) + ((parseFloat(_this.plot_width) - parseFloat(_this.x_buffer)) * d[0] / parseFloat(_this.x_max));
-        }).attr("y2", function(d) {
+        };
+      })(this)).attr("y2", (function(_this) {
+        return function(d) {
           return _this.plot_height - ((_this.plot_height - _this.y_buffer) * d[1] / _this.y_max);
-        }).style("stroke", "black");
-      };
-
-      return Interval_Map;
+        };
+      })(this)).style("stroke", "black");
+    };
 
-    })();
-    console.time('Create interval map');
-    console.log("TESTING");
-    new Interval_Map(600, 1200);
-    return console.timeEnd('Create interval map');
-  });
+    return Interval_Map;
 
-}).call(this);
+  })();
+  console.time('Create interval map');
+  console.log("TESTING");
+  new Interval_Map(600, 1200);
+  return console.timeEnd('Create interval map');
+});
diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.coffee b/wqflask/wqflask/static/new/javascript/lod_chart.coffee
index 38325e60..777aac2a 100644
--- a/wqflask/wqflask/static/new/javascript/lod_chart.coffee
+++ b/wqflask/wqflask/static/new/javascript/lod_chart.coffee
@@ -1,5 +1,3 @@
-root = exports ? this

-

 lodchart = () ->

     width = 800

     height = 500

@@ -40,6 +38,9 @@ lodchart = () ->
     ## the main function

     chart = (selection) ->

       selection.each (data) ->

+        

+        console.log("data:", data)

+        

         lodvarname = lodvarname ? data.lodnames[0]

         data[lodvarname] = (Math.abs(x) for x in data[lodvarname]) # take absolute values

         data['additive'] = (Math.abs(x) for x in data['additive'])

@@ -96,7 +97,7 @@ lodchart = () ->
                    .data(data.chrnames)

                    .enter()

                    .append("rect")

-                   .attr("id", (d) -> "chrrect#{d}")

+                   .attr("id", (d) -> "chrrect#{d[0]}")

                    .attr("x", (d,i) ->

                      return data.chrStart[i] if i==0 and pad4heatmap

                      data.chrStart[i]-chrGap/2)

@@ -109,6 +110,9 @@ lodchart = () ->
                       return darkrect if i % 2

                       lightrect)

                    .attr("stroke", "none")

+                   .on("click", (d) ->

+                      redraw_plot(d)

+                    )   

   

         # x-axis labels

         xaxis = g.append("g").attr("class", "x axis")

@@ -116,13 +120,26 @@ lodchart = () ->
              .data(data.chrnames)

              .enter()

              .append("text")

-             .text((d) -> d)

+             .text((d) -> d[0])

              .attr("x", (d,i) -> (data.chrStart[i]+data.chrEnd[i])/2)

              .attr("y", margin.top+height+axispos.xlabel)

+             .attr("cursor", "pointer")

+             .on("click", (d) ->

+                 redraw_plot(d)

+              )   

+             

         xaxis.append("text").attr("class", "title")

              .attr("y", margin.top+height+axispos.xtitle)

              .attr("x", margin.left+width/2)

              .text(xlab)

+

+  

+        redraw_plot = (chr_ob) ->

+             console.log("chr_name is:", chr_ob[0])

+             console.log("chr_length is:", chr_ob[1])

+             $('#topchart').remove()

+             $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>')

+             chr_plot = new Chr_Interval_Map(600, 1200, chr_ob)

   

         # y-axis

         rotate_ylab = rotate_ylab ? (ylab.length > 1)

@@ -231,21 +248,22 @@ lodchart = () ->
   

         for chr in data.chrnames

           curves.append("path")

-                .datum(data.posByChr[chr])

-                .attr("d", lodcurve(chr, lodvarnum))

+                .datum(data.posByChr[chr[0]])

+                .attr("d", lodcurve(chr[0], lodvarnum))

                 .attr("stroke", lodlinecolor)

                 .attr("fill", "none")

                 .attr("stroke-width", linewidth)

                 .style("pointer-events", "none")

-                

-        for chr in data.chrnames

-          curves.append("path")

-                .datum(data.posByChr[chr])

-                .attr("d", additivecurve(chr, lodvarnum))

-                .attr("stroke", additivelinecolor)

-                .attr("fill", "none")

-                .attr("stroke-width", 1)

-                .style("pointer-events", "none")

+        

+        if data['additive'].length > 0

+            for chr in data.chrnames

+                curves.append("path")

+                      .datum(data.posByChr[chr[0]])

+                      .attr("d", additivecurve(chr[0], lodvarnum))

+                      .attr("stroke", additivelinecolor)

+                      .attr("fill", "none")

+                      .attr("stroke-width", 1)

+                      .style("pointer-events", "none")

   

         # points at markers

         if pointsize > 0

@@ -261,6 +279,25 @@ lodchart = () ->
                       .attr("stroke", pointstroke)

                       .attr("pointer-events", "hidden")

   

+        # title

+        titlegrp = g.append("g").attr("class", "title")

+         .append("text")

+         .attr("x", margin.left+width/2)

+         .attr("y", margin.top-titlepos)

+         .text(title)

+  

+        # another box around edge

+        g.append("rect")

+         .attr("x", margin.left)

+         .attr("y", margin.top)

+         .attr("height", height)

+         .attr("width", () ->

+            return(data.chrEnd[-1..][0]-margin.left) if pad4heatmap

+            data.chrEnd[-1..][0]-margin.left+chrGap/2)

+         .attr("fill", "none")

+         .attr("stroke", "black")

+         .attr("stroke-width", "none")

+  

         if pointsAtMarkers

           # these hidden points are what gets selected...a bit larger

           hiddenpoints = g.append("g").attr("id", "markerpoints_hidden")

@@ -293,24 +330,7 @@ lodchart = () ->
                            d3.select(this).attr("opacity", 0)

                                           .call(markertip.hide)

   

-        # title

-        titlegrp = g.append("g").attr("class", "title")

-         .append("text")

-         .attr("x", margin.left+width/2)

-         .attr("y", margin.top-titlepos)

-         .text(title)

-  

-        # another box around edge

-        g.append("rect")

-         .attr("x", margin.left)

-         .attr("y", margin.top)

-         .attr("height", height)

-         .attr("width", () ->

-            return(data.chrEnd[-1..][0]-margin.left) if pad4heatmap

-            data.chrEnd[-1..][0]-margin.left+chrGap/2)

-         .attr("fill", "none")

-         .attr("stroke", "black")

-         .attr("stroke-width", "none")

+

   

     ## configuration parameters

     chart.width = (value) ->

@@ -460,8 +480,6 @@ lodchart = () ->
     # return the chart function

     chart

 

-root.lodchart = lodchart

-

 # reorganize lod/pos by chromosome

 # lodvarname==null    -> case for multiple LOD columns (lodheatmap)

 # lodvarname provided -> case for one LOD column (lodchart)

@@ -471,18 +489,18 @@ reorgLodData = (data, lodvarname=null) ->
     data.additiveByChr = {}

     

     for chr,i in data.chrnames

-      data.posByChr[chr] = []

-      data.lodByChr[chr] = []

-      data.additiveByChr[chr] = []

+      data.posByChr[chr[0]] = []

+      data.lodByChr[chr[0]] = []

+      data.additiveByChr[chr[0]] = []

       for pos, j in data.pos

-        if data.chr[j] == chr

-          data.posByChr[chr].push(pos)

+        if data.chr[j] == chr[0]

+          data.posByChr[chr[0]].push(pos)

           data.lodnames = [data.lodnames] unless Array.isArray(data.lodnames)

           if data['additive'].length > 0

             additiveval = (data['additive'][j] for lodcolumn in data.lodnames)

           lodval = (data[lodcolumn][j] for lodcolumn in data.lodnames)

-          data.additiveByChr[chr].push(additiveval)

-          data.lodByChr[chr].push(lodval)

+          data.additiveByChr[chr[0]].push(additiveval)

+          data.lodByChr[chr[0]].push(lodval)

 

     

     if lodvarname?

@@ -503,10 +521,10 @@ chrscales = (data, width, chrGap, leftMargin, pad4heatmap) ->
     totalChrLength = 0

     maxd = 0

     for chr in data.chrnames

-      d = maxdiff(data.posByChr[chr])

+      d = maxdiff(data.posByChr[chr[0]])

       maxd = d if d > maxd

   

-      rng = d3.extent(data.posByChr[chr])

+      rng = d3.extent(data.posByChr[chr[0]])

       chrStart.push(rng[0])

       chrEnd.push(rng[1])

       L = rng[1] - rng[0]

@@ -533,7 +551,7 @@ chrscales = (data, width, chrGap, leftMargin, pad4heatmap) ->
       data.chrEnd.push(cur + w)

       cur = data.chrEnd[i] + chrGap

       # x-axis scales, by chromosome

-      data.xscale[chr] = d3.scale.linear()

+      data.xscale[chr[0]] = d3.scale.linear()

                            .domain([chrStart[i], chrEnd[i]])

                            .range([data.chrStart[i], data.chrEnd[i]])

   

diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.js b/wqflask/wqflask/static/new/javascript/lod_chart.js
index 0938cf06..c974c9d2 100644
--- a/wqflask/wqflask/static/new/javascript/lod_chart.js
+++ b/wqflask/wqflask/static/new/javascript/lod_chart.js
@@ -1,574 +1,582 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var chrscales, formatAxis, lodchart, maxdiff, reorgLodData, root;
+// Generated by CoffeeScript 1.7.1
+var chrscales, formatAxis, lodchart, maxdiff, reorgLodData;
 
-  root = typeof exports !== "undefined" && exports !== null ? exports : this;
-
-  lodchart = function() {
-    var additive_ylab, additive_ylim, additive_yscale, additive_yticks, additivelinecolor, axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, significantcolor, suggestivecolor, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks;
-    width = 800;
-    height = 500;
-    margin = {
-      left: 60,
-      top: 40,
-      right: 40,
-      bottom: 40,
-      inner: 5
-    };
-    axispos = {
-      xtitle: 25,
-      ytitle: 30,
-      xlabel: 5,
-      ylabel: 5
-    };
-    titlepos = 20;
-    ylim = null;
-    additive_ylim = null;
-    nyticks = 5;
-    yticks = null;
-    additive_yticks = null;
-    chrGap = 8;
-    darkrect = "#F1F1F9";
-    lightrect = "#FBFBFF";
-    lodlinecolor = "darkslateblue";
-    additivelinecolor = "red";
-    linewidth = 2;
-    suggestivecolor = "gainsboro";
-    significantcolor = "#EBC7C7";
-    pointcolor = "#E9CFEC";
-    pointsize = 0;
-    pointstroke = "black";
-    title = "";
-    xlab = "Chromosome";
-    ylab = "LRS score";
-    additive_ylab = "Additive Effect";
-    rotate_ylab = null;
-    yscale = d3.scale.linear();
-    additive_yscale = d3.scale.linear();
-    xscale = null;
-    pad4heatmap = false;
-    lodcurve = null;
-    lodvarname = null;
-    markerSelect = null;
-    chrSelect = null;
-    pointsAtMarkers = true;
-    chart = function(selection) {
-      return selection.each(function(data) {
-        var additive_yaxis, additivecurve, chr, curves, g, gEnter, hiddenpoints, lodvarnum, markerpoints, markertip, rotate_additive_ylab, suggestive_bar, svg, titlegrp, x, xaxis, yaxis, _i, _j, _len, _len1, _ref, _ref1;
-        lodvarname = lodvarname != null ? lodvarname : data.lodnames[0];
-        data[lodvarname] = (function() {
-          var _i, _len, _ref, _results;
-          _ref = data[lodvarname];
-          _results = [];
-          for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-            x = _ref[_i];
-            _results.push(Math.abs(x));
-          }
-          return _results;
-        })();
-        data['additive'] = (function() {
-          var _i, _len, _ref, _results;
-          _ref = data['additive'];
-          _results = [];
-          for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-            x = _ref[_i];
-            _results.push(Math.abs(x));
-          }
-          return _results;
-        })();
-        ylim = ylim != null ? ylim : [0, d3.max(data[lodvarname])];
-        if (data['additive'].length > 0) {
-          additive_ylim = additive_ylim != null ? additive_ylim : [0, d3.max(data['additive'])];
+lodchart = function() {
+  var additive_ylab, additive_ylim, additive_yscale, additive_yticks, additivelinecolor, axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, significantcolor, suggestivecolor, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks;
+  width = 800;
+  height = 500;
+  margin = {
+    left: 60,
+    top: 40,
+    right: 40,
+    bottom: 40,
+    inner: 5
+  };
+  axispos = {
+    xtitle: 25,
+    ytitle: 30,
+    xlabel: 5,
+    ylabel: 5
+  };
+  titlepos = 20;
+  ylim = null;
+  additive_ylim = null;
+  nyticks = 5;
+  yticks = null;
+  additive_yticks = null;
+  chrGap = 8;
+  darkrect = "#F1F1F9";
+  lightrect = "#FBFBFF";
+  lodlinecolor = "darkslateblue";
+  additivelinecolor = "red";
+  linewidth = 2;
+  suggestivecolor = "gainsboro";
+  significantcolor = "#EBC7C7";
+  pointcolor = "#E9CFEC";
+  pointsize = 0;
+  pointstroke = "black";
+  title = "";
+  xlab = "Chromosome";
+  ylab = "LRS score";
+  additive_ylab = "Additive Effect";
+  rotate_ylab = null;
+  yscale = d3.scale.linear();
+  additive_yscale = d3.scale.linear();
+  xscale = null;
+  pad4heatmap = false;
+  lodcurve = null;
+  lodvarname = null;
+  markerSelect = null;
+  chrSelect = null;
+  pointsAtMarkers = true;
+  chart = function(selection) {
+    return selection.each(function(data) {
+      var additive_yaxis, additivecurve, chr, curves, g, gEnter, hiddenpoints, lodvarnum, markerpoints, markertip, redraw_plot, rotate_additive_ylab, suggestive_bar, svg, titlegrp, x, xaxis, yaxis, _i, _j, _len, _len1, _ref, _ref1;
+      console.log("data:", data);
+      lodvarname = lodvarname != null ? lodvarname : data.lodnames[0];
+      data[lodvarname] = (function() {
+        var _i, _len, _ref, _results;
+        _ref = data[lodvarname];
+        _results = [];
+        for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+          x = _ref[_i];
+          _results.push(Math.abs(x));
         }
-        lodvarnum = data.lodnames.indexOf(lodvarname);
-        svg = d3.select(this).selectAll("svg").data([data]);
-        gEnter = svg.enter().append("svg").append("g");
-        svg.attr("width", width + margin.left + margin.right).attr("height", height + margin.top + margin.bottom);
-        g = svg.select("g");
-        g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", width).attr("fill", darkrect).attr("stroke", "none");
-        yscale.domain(ylim).range([height + margin.top, margin.top + margin.inner]);
-        if (data['additive'].length > 0) {
-          additive_yscale.domain(additive_ylim).range([height + margin.top, margin.top + margin.inner + height / 2]);
+        return _results;
+      })();
+      data['additive'] = (function() {
+        var _i, _len, _ref, _results;
+        _ref = data['additive'];
+        _results = [];
+        for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+          x = _ref[_i];
+          _results.push(Math.abs(x));
         }
-        yticks = yticks != null ? yticks : yscale.ticks(nyticks);
-        if (data['additive'].length > 0) {
-          additive_yticks = additive_yticks != null ? additive_yticks : additive_yscale.ticks(nyticks);
+        return _results;
+      })();
+      ylim = ylim != null ? ylim : [0, d3.max(data[lodvarname])];
+      if (data['additive'].length > 0) {
+        additive_ylim = additive_ylim != null ? additive_ylim : [0, d3.max(data['additive'])];
+      }
+      lodvarnum = data.lodnames.indexOf(lodvarname);
+      svg = d3.select(this).selectAll("svg").data([data]);
+      gEnter = svg.enter().append("svg").append("g");
+      svg.attr("width", width + margin.left + margin.right).attr("height", height + margin.top + margin.bottom);
+      g = svg.select("g");
+      g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", width).attr("fill", darkrect).attr("stroke", "none");
+      yscale.domain(ylim).range([height + margin.top, margin.top + margin.inner]);
+      if (data['additive'].length > 0) {
+        additive_yscale.domain(additive_ylim).range([height + margin.top, margin.top + margin.inner + height / 2]);
+      }
+      yticks = yticks != null ? yticks : yscale.ticks(nyticks);
+      if (data['additive'].length > 0) {
+        additive_yticks = additive_yticks != null ? additive_yticks : additive_yscale.ticks(nyticks);
+      }
+      data = reorgLodData(data, lodvarname);
+      data = chrscales(data, width, chrGap, margin.left, pad4heatmap);
+      xscale = data.xscale;
+      chrSelect = g.append("g").attr("class", "chrRect").selectAll("empty").data(data.chrnames).enter().append("rect").attr("id", function(d) {
+        return "chrrect" + d[0];
+      }).attr("x", function(d, i) {
+        if (i === 0 && pad4heatmap) {
+          return data.chrStart[i];
         }
-        data = reorgLodData(data, lodvarname);
-        data = chrscales(data, width, chrGap, margin.left, pad4heatmap);
-        xscale = data.xscale;
-        chrSelect = g.append("g").attr("class", "chrRect").selectAll("empty").data(data.chrnames).enter().append("rect").attr("id", function(d) {
-          return "chrrect" + d;
-        }).attr("x", function(d, i) {
-          if (i === 0 && pad4heatmap) {
-            return data.chrStart[i];
-          }
-          return data.chrStart[i] - chrGap / 2;
-        }).attr("width", function(d, i) {
-          if ((i === 0 || i + 1 === data.chrnames.length) && pad4heatmap) {
-            return data.chrEnd[i] - data.chrStart[i] + chrGap / 2;
-          }
-          return data.chrEnd[i] - data.chrStart[i] + chrGap;
-        }).attr("y", margin.top).attr("height", height).attr("fill", function(d, i) {
-          if (i % 2) {
-            return darkrect;
-          }
-          return lightrect;
-        }).attr("stroke", "none");
-        xaxis = g.append("g").attr("class", "x axis");
-        xaxis.selectAll("empty").data(data.chrnames).enter().append("text").text(function(d) {
-          return d;
-        }).attr("x", function(d, i) {
-          return (data.chrStart[i] + data.chrEnd[i]) / 2;
-        }).attr("y", margin.top + height + axispos.xlabel);
-        xaxis.append("text").attr("class", "title").attr("y", margin.top + height + axispos.xtitle).attr("x", margin.left + width / 2).text(xlab);
-        rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1;
-        yaxis = g.append("g").attr("class", "y axis");
-        yaxis.selectAll("empty").data(yticks).enter().append("line").attr("y1", function(d) {
-          return yscale(d);
-        }).attr("y2", function(d) {
-          return yscale(d);
-        }).attr("x1", margin.left).attr("x2", margin.left + 7).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none");
-        yaxis.selectAll("empty").data(yticks).enter().append("text").attr("y", function(d) {
-          return yscale(d);
-        }).attr("x", margin.left - axispos.ylabel).attr("fill", "blue").text(function(d) {
-          return formatAxis(yticks)(d);
-        });
-        yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : "");
-        if (data['additive'].length > 0) {
-          rotate_additive_ylab = rotate_additive_ylab != null ? rotate_additive_ylab : additive_ylab.length > 1;
-          additive_yaxis = g.append("g").attr("class", "y axis");
-          additive_yaxis.selectAll("empty").data(additive_yticks).enter().append("line").attr("y1", function(d) {
-            return additive_yscale(d);
-          }).attr("y2", function(d) {
-            return additive_yscale(d);
-          }).attr("x1", margin.left + width).attr("x2", margin.left + width - 7).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none");
-          additive_yaxis.selectAll("empty").data(additive_yticks).enter().append("text").attr("y", function(d) {
-            return additive_yscale(d);
-          }).attr("x", function(d) {
-            return margin.left + width + axispos.ylabel + 20;
-          }).attr("fill", "green").text(function(d) {
-            return formatAxis(additive_yticks)(d);
-          });
-          additive_yaxis.append("text").attr("class", "title").attr("y", margin.top + 1.5 * height).attr("x", margin.left + width + axispos.ytitle).text(additive_ylab).attr("transform", rotate_additive_ylab ? "rotate(270," + (margin.left + width + axispos.ytitle) + ", " + (margin.top + height * 1.5) + ")" : "");
+        return data.chrStart[i] - chrGap / 2;
+      }).attr("width", function(d, i) {
+        if ((i === 0 || i + 1 === data.chrnames.length) && pad4heatmap) {
+          return data.chrEnd[i] - data.chrStart[i] + chrGap / 2;
         }
-        suggestive_bar = g.append("g").attr("class", "suggestive");
-        suggestive_bar.selectAll("empty").data([data.suggestive]).enter().append("line").attr("y1", function(d) {
-          return yscale(d);
-        }).attr("y2", function(d) {
-          return yscale(d);
-        }).attr("x1", margin.left).attr("x2", margin.left + width).attr("fill", "none").attr("stroke", suggestivecolor).attr("stroke-width", 5).style("pointer-events", "none");
-        suggestive_bar = g.append("g").attr("class", "significant");
-        suggestive_bar.selectAll("empty").data([data.significant]).enter().append("line").attr("y1", function(d) {
-          return yscale(d);
+        return data.chrEnd[i] - data.chrStart[i] + chrGap;
+      }).attr("y", margin.top).attr("height", height).attr("fill", function(d, i) {
+        if (i % 2) {
+          return darkrect;
+        }
+        return lightrect;
+      }).attr("stroke", "none").on("click", function(d) {
+        return redraw_plot(d);
+      });
+      xaxis = g.append("g").attr("class", "x axis");
+      xaxis.selectAll("empty").data(data.chrnames).enter().append("text").text(function(d) {
+        return d[0];
+      }).attr("x", function(d, i) {
+        return (data.chrStart[i] + data.chrEnd[i]) / 2;
+      }).attr("y", margin.top + height + axispos.xlabel).attr("cursor", "pointer").on("click", function(d) {
+        return redraw_plot(d);
+      });
+      xaxis.append("text").attr("class", "title").attr("y", margin.top + height + axispos.xtitle).attr("x", margin.left + width / 2).text(xlab);
+      redraw_plot = function(chr_ob) {
+        var chr_plot;
+        console.log("chr_name is:", chr_ob[0]);
+        console.log("chr_length is:", chr_ob[1]);
+        $('#topchart').remove();
+        $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>');
+        return chr_plot = new Chr_Interval_Map(600, 1200, chr_ob);
+      };
+      rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1;
+      yaxis = g.append("g").attr("class", "y axis");
+      yaxis.selectAll("empty").data(yticks).enter().append("line").attr("y1", function(d) {
+        return yscale(d);
+      }).attr("y2", function(d) {
+        return yscale(d);
+      }).attr("x1", margin.left).attr("x2", margin.left + 7).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none");
+      yaxis.selectAll("empty").data(yticks).enter().append("text").attr("y", function(d) {
+        return yscale(d);
+      }).attr("x", margin.left - axispos.ylabel).attr("fill", "blue").text(function(d) {
+        return formatAxis(yticks)(d);
+      });
+      yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : "");
+      if (data['additive'].length > 0) {
+        rotate_additive_ylab = rotate_additive_ylab != null ? rotate_additive_ylab : additive_ylab.length > 1;
+        additive_yaxis = g.append("g").attr("class", "y axis");
+        additive_yaxis.selectAll("empty").data(additive_yticks).enter().append("line").attr("y1", function(d) {
+          return additive_yscale(d);
         }).attr("y2", function(d) {
-          return yscale(d);
-        }).attr("x1", margin.left).attr("x2", margin.left + width).attr("fill", "none").attr("stroke", significantcolor).attr("stroke-width", 5).style("pointer-events", "none");
-        lodcurve = function(chr, lodcolumn) {
+          return additive_yscale(d);
+        }).attr("x1", margin.left + width).attr("x2", margin.left + width - 7).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none");
+        additive_yaxis.selectAll("empty").data(additive_yticks).enter().append("text").attr("y", function(d) {
+          return additive_yscale(d);
+        }).attr("x", function(d) {
+          return margin.left + width + axispos.ylabel + 20;
+        }).attr("fill", "green").text(function(d) {
+          return formatAxis(additive_yticks)(d);
+        });
+        additive_yaxis.append("text").attr("class", "title").attr("y", margin.top + 1.5 * height).attr("x", margin.left + width + axispos.ytitle).text(additive_ylab).attr("transform", rotate_additive_ylab ? "rotate(270," + (margin.left + width + axispos.ytitle) + ", " + (margin.top + height * 1.5) + ")" : "");
+      }
+      suggestive_bar = g.append("g").attr("class", "suggestive");
+      suggestive_bar.selectAll("empty").data([data.suggestive]).enter().append("line").attr("y1", function(d) {
+        return yscale(d);
+      }).attr("y2", function(d) {
+        return yscale(d);
+      }).attr("x1", margin.left).attr("x2", margin.left + width).attr("fill", "none").attr("stroke", suggestivecolor).attr("stroke-width", 5).style("pointer-events", "none");
+      suggestive_bar = g.append("g").attr("class", "significant");
+      suggestive_bar.selectAll("empty").data([data.significant]).enter().append("line").attr("y1", function(d) {
+        return yscale(d);
+      }).attr("y2", function(d) {
+        return yscale(d);
+      }).attr("x1", margin.left).attr("x2", margin.left + width).attr("fill", "none").attr("stroke", significantcolor).attr("stroke-width", 5).style("pointer-events", "none");
+      lodcurve = function(chr, lodcolumn) {
+        return d3.svg.line().x(function(d) {
+          return xscale[chr](d);
+        }).y(function(d, i) {
+          return yscale(data.lodByChr[chr][i][lodcolumn]);
+        });
+      };
+      if (data['additive'].length > 0) {
+        additivecurve = function(chr, lodcolumn) {
           return d3.svg.line().x(function(d) {
             return xscale[chr](d);
           }).y(function(d, i) {
-            return yscale(data.lodByChr[chr][i][lodcolumn]);
+            return additive_yscale(data.additiveByChr[chr][i][lodcolumn]);
           });
         };
-        if (data['additive'].length > 0) {
-          additivecurve = function(chr, lodcolumn) {
-            return d3.svg.line().x(function(d) {
-              return xscale[chr](d);
-            }).y(function(d, i) {
-              return additive_yscale(data.additiveByChr[chr][i][lodcolumn]);
-            });
-          };
-        }
-        curves = g.append("g").attr("id", "curves");
-        _ref = data.chrnames;
-        for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-          chr = _ref[_i];
-          curves.append("path").datum(data.posByChr[chr]).attr("d", lodcurve(chr, lodvarnum)).attr("stroke", lodlinecolor).attr("fill", "none").attr("stroke-width", linewidth).style("pointer-events", "none");
-        }
+      }
+      curves = g.append("g").attr("id", "curves");
+      _ref = data.chrnames;
+      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+        chr = _ref[_i];
+        curves.append("path").datum(data.posByChr[chr[0]]).attr("d", lodcurve(chr[0], lodvarnum)).attr("stroke", lodlinecolor).attr("fill", "none").attr("stroke-width", linewidth).style("pointer-events", "none");
+      }
+      if (data['additive'].length > 0) {
         _ref1 = data.chrnames;
         for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) {
           chr = _ref1[_j];
-          curves.append("path").datum(data.posByChr[chr]).attr("d", additivecurve(chr, lodvarnum)).attr("stroke", additivelinecolor).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none");
-        }
-        if (pointsize > 0) {
-          markerpoints = g.append("g").attr("id", "markerpoints_visible");
-          markerpoints.selectAll("empty").data(data.markers).enter().append("circle").attr("cx", function(d) {
-            return xscale[d.chr](d.pos);
-          }).attr("cy", function(d) {
-            return yscale(d.lod);
-          }).attr("r", pointsize).attr("fill", pointcolor).attr("stroke", pointstroke).attr("pointer-events", "hidden");
-        }
-        if (pointsAtMarkers) {
-          hiddenpoints = g.append("g").attr("id", "markerpoints_hidden");
-          markertip = d3.tip().attr('class', 'd3-tip').html(function(d) {
-            return [d.name, " LRS = " + (d3.format('.2f')(d.lod))];
-          }).direction("e").offset([0, 10]);
-          svg.call(markertip);
-          markerSelect = hiddenpoints.selectAll("empty").data(data.markers).enter().append("circle").attr("cx", function(d) {
-            return xscale[d.chr](d.pos);
-          }).attr("cy", function(d) {
-            return yscale(d.lod);
-          }).attr("id", function(d) {
-            return d.name;
-          }).attr("r", d3.max([pointsize * 2, 3])).attr("opacity", 0).attr("fill", pointcolor).attr("stroke", pointstroke).attr("stroke-width", "1").on("mouseover.paneltip", function(d) {
-            d3.select(this).attr("opacity", 1);
-            return markertip.show(d);
-          }).on("mouseout.paneltip", function() {
-            return d3.select(this).attr("opacity", 0).call(markertip.hide);
-          });
+          curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)).attr("stroke", additivelinecolor).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none");
         }
-        titlegrp = g.append("g").attr("class", "title").append("text").attr("x", margin.left + width / 2).attr("y", margin.top - titlepos).text(title);
-        return g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", function() {
-          if (pad4heatmap) {
-            return data.chrEnd.slice(-1)[0] - margin.left;
-          }
-          return data.chrEnd.slice(-1)[0] - margin.left + chrGap / 2;
-        }).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none");
-      });
-    };
-    chart.width = function(value) {
-      if (!arguments.length) {
-        return width;
-      }
-      width = value;
-      return chart;
-    };
-    chart.height = function(value) {
-      if (!arguments.length) {
-        return height;
-      }
-      height = value;
-      return chart;
-    };
-    chart.margin = function(value) {
-      if (!arguments.length) {
-        return margin;
-      }
-      margin = value;
-      return chart;
-    };
-    chart.titlepos = function(value) {
-      if (!arguments.length) {
-        return titlepos;
-      }
-      titlepos;
-      return chart;
-    };
-    chart.axispos = function(value) {
-      if (!arguments.length) {
-        return axispos;
-      }
-      axispos = value;
-      return chart;
-    };
-    chart.ylim = function(value) {
-      if (!arguments.length) {
-        return ylim;
-      }
-      ylim = value;
-      return chart;
-    };
-    chart.additive_ylim = function(value) {
-      if (!arguments.length) {
-        return additive_ylim;
-      }
-      additive_ylim = value;
-      return chart;
-    };
-    chart.nyticks = function(value) {
-      if (!arguments.length) {
-        return nyticks;
-      }
-      nyticks = value;
-      return chart;
-    };
-    chart.yticks = function(value) {
-      if (!arguments.length) {
-        return yticks;
-      }
-      yticks = value;
-      return chart;
-    };
-    chart.chrGap = function(value) {
-      if (!arguments.length) {
-        return chrGap;
-      }
-      chrGap = value;
-      return chart;
-    };
-    chart.darkrect = function(value) {
-      if (!arguments.length) {
-        return darkrect;
-      }
-      darkrect = value;
-      return chart;
-    };
-    chart.lightrect = function(value) {
-      if (!arguments.length) {
-        return lightrect;
-      }
-      lightrect = value;
-      return chart;
-    };
-    chart.linecolor = function(value) {
-      var linecolor;
-      if (!arguments.length) {
-        return linecolor;
-      }
-      linecolor = value;
-      return chart;
-    };
-    chart.linewidth = function(value) {
-      if (!arguments.length) {
-        return linewidth;
-      }
-      linewidth = value;
-      return chart;
-    };
-    chart.pointcolor = function(value) {
-      if (!arguments.length) {
-        return pointcolor;
-      }
-      pointcolor = value;
-      return chart;
-    };
-    chart.pointsize = function(value) {
-      if (!arguments.length) {
-        return pointsize;
-      }
-      pointsize = value;
-      return chart;
-    };
-    chart.pointstroke = function(value) {
-      if (!arguments.length) {
-        return pointstroke;
-      }
-      pointstroke = value;
-      return chart;
-    };
-    chart.title = function(value) {
-      if (!arguments.length) {
-        return title;
-      }
-      title = value;
-      return chart;
-    };
-    chart.xlab = function(value) {
-      if (!arguments.length) {
-        return xlab;
-      }
-      xlab = value;
-      return chart;
-    };
-    chart.ylab = function(value) {
-      if (!arguments.length) {
-        return ylab;
-      }
-      ylab = value;
-      return chart;
-    };
-    chart.rotate_ylab = function(value) {
-      if (!arguments.length) {
-        return rotate_ylab;
       }
-      rotate_ylab = value;
-      return chart;
-    };
-    chart.lodvarname = function(value) {
-      if (!arguments.length) {
-        return lodvarname;
+      if (pointsize > 0) {
+        markerpoints = g.append("g").attr("id", "markerpoints_visible");
+        markerpoints.selectAll("empty").data(data.markers).enter().append("circle").attr("cx", function(d) {
+          return xscale[d.chr](d.pos);
+        }).attr("cy", function(d) {
+          return yscale(d.lod);
+        }).attr("r", pointsize).attr("fill", pointcolor).attr("stroke", pointstroke).attr("pointer-events", "hidden");
       }
-      lodvarname = value;
-      return chart;
-    };
-    chart.pad4heatmap = function(value) {
-      if (!arguments.length) {
-        return pad4heatmap;
-      }
-      pad4heatmap = value;
-      return chart;
-    };
-    chart.pointsAtMarkers = function(value) {
-      if (!arguments.length) {
-        return pointsAtMarkers;
+      titlegrp = g.append("g").attr("class", "title").append("text").attr("x", margin.left + width / 2).attr("y", margin.top - titlepos).text(title);
+      g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", function() {
+        if (pad4heatmap) {
+          return data.chrEnd.slice(-1)[0] - margin.left;
+        }
+        return data.chrEnd.slice(-1)[0] - margin.left + chrGap / 2;
+      }).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none");
+      if (pointsAtMarkers) {
+        hiddenpoints = g.append("g").attr("id", "markerpoints_hidden");
+        markertip = d3.tip().attr('class', 'd3-tip').html(function(d) {
+          return [d.name, " LRS = " + (d3.format('.2f')(d.lod))];
+        }).direction("e").offset([0, 10]);
+        svg.call(markertip);
+        return markerSelect = hiddenpoints.selectAll("empty").data(data.markers).enter().append("circle").attr("cx", function(d) {
+          return xscale[d.chr](d.pos);
+        }).attr("cy", function(d) {
+          return yscale(d.lod);
+        }).attr("id", function(d) {
+          return d.name;
+        }).attr("r", d3.max([pointsize * 2, 3])).attr("opacity", 0).attr("fill", pointcolor).attr("stroke", pointstroke).attr("stroke-width", "1").on("mouseover.paneltip", function(d) {
+          d3.select(this).attr("opacity", 1);
+          return markertip.show(d);
+        }).on("mouseout.paneltip", function() {
+          return d3.select(this).attr("opacity", 0).call(markertip.hide);
+        });
       }
-      pointsAtMarkers = value;
-      return chart;
-    };
-    chart.yscale = function() {
-      return yscale;
-    };
-    chart.additive_yscale = function() {
-      return additive_yscale;
-    };
-    chart.xscale = function() {
-      return xscale;
-    };
-    chart.lodcurve = function() {
-      return lodcurve;
-    };
-    chart.additivecurve = function() {
-      return additivecurve;
-    };
-    chart.markerSelect = function() {
-      return markerSelect;
-    };
-    chart.chrSelect = function() {
-      return chrSelect;
-    };
+    });
+  };
+  chart.width = function(value) {
+    if (!arguments.length) {
+      return width;
+    }
+    width = value;
     return chart;
   };
-
-  root.lodchart = lodchart;
-
-  reorgLodData = function(data, lodvarname) {
-    var additiveval, chr, i, j, lodcolumn, lodval, marker, pos, _i, _j, _k, _len, _len1, _len2, _ref, _ref1, _ref2;
-    if (lodvarname == null) {
-      lodvarname = null;
+  chart.height = function(value) {
+    if (!arguments.length) {
+      return height;
     }
-    data.posByChr = {};
-    data.lodByChr = {};
-    data.additiveByChr = {};
-    _ref = data.chrnames;
-    for (i = _i = 0, _len = _ref.length; _i < _len; i = ++_i) {
-      chr = _ref[i];
-      data.posByChr[chr] = [];
-      data.lodByChr[chr] = [];
-      data.additiveByChr[chr] = [];
-      _ref1 = data.pos;
-      for (j = _j = 0, _len1 = _ref1.length; _j < _len1; j = ++_j) {
-        pos = _ref1[j];
-        if (data.chr[j] === chr) {
-          data.posByChr[chr].push(pos);
-          if (!Array.isArray(data.lodnames)) {
-            data.lodnames = [data.lodnames];
-          }
-          if (data['additive'].length > 0) {
-            additiveval = (function() {
-              var _k, _len2, _ref2, _results;
-              _ref2 = data.lodnames;
-              _results = [];
-              for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) {
-                lodcolumn = _ref2[_k];
-                _results.push(data['additive'][j]);
-              }
-              return _results;
-            })();
-          }
-          lodval = (function() {
+    height = value;
+    return chart;
+  };
+  chart.margin = function(value) {
+    if (!arguments.length) {
+      return margin;
+    }
+    margin = value;
+    return chart;
+  };
+  chart.titlepos = function(value) {
+    if (!arguments.length) {
+      return titlepos;
+    }
+    titlepos;
+    return chart;
+  };
+  chart.axispos = function(value) {
+    if (!arguments.length) {
+      return axispos;
+    }
+    axispos = value;
+    return chart;
+  };
+  chart.ylim = function(value) {
+    if (!arguments.length) {
+      return ylim;
+    }
+    ylim = value;
+    return chart;
+  };
+  chart.additive_ylim = function(value) {
+    if (!arguments.length) {
+      return additive_ylim;
+    }
+    additive_ylim = value;
+    return chart;
+  };
+  chart.nyticks = function(value) {
+    if (!arguments.length) {
+      return nyticks;
+    }
+    nyticks = value;
+    return chart;
+  };
+  chart.yticks = function(value) {
+    if (!arguments.length) {
+      return yticks;
+    }
+    yticks = value;
+    return chart;
+  };
+  chart.chrGap = function(value) {
+    if (!arguments.length) {
+      return chrGap;
+    }
+    chrGap = value;
+    return chart;
+  };
+  chart.darkrect = function(value) {
+    if (!arguments.length) {
+      return darkrect;
+    }
+    darkrect = value;
+    return chart;
+  };
+  chart.lightrect = function(value) {
+    if (!arguments.length) {
+      return lightrect;
+    }
+    lightrect = value;
+    return chart;
+  };
+  chart.linecolor = function(value) {
+    var linecolor;
+    if (!arguments.length) {
+      return linecolor;
+    }
+    linecolor = value;
+    return chart;
+  };
+  chart.linewidth = function(value) {
+    if (!arguments.length) {
+      return linewidth;
+    }
+    linewidth = value;
+    return chart;
+  };
+  chart.pointcolor = function(value) {
+    if (!arguments.length) {
+      return pointcolor;
+    }
+    pointcolor = value;
+    return chart;
+  };
+  chart.pointsize = function(value) {
+    if (!arguments.length) {
+      return pointsize;
+    }
+    pointsize = value;
+    return chart;
+  };
+  chart.pointstroke = function(value) {
+    if (!arguments.length) {
+      return pointstroke;
+    }
+    pointstroke = value;
+    return chart;
+  };
+  chart.title = function(value) {
+    if (!arguments.length) {
+      return title;
+    }
+    title = value;
+    return chart;
+  };
+  chart.xlab = function(value) {
+    if (!arguments.length) {
+      return xlab;
+    }
+    xlab = value;
+    return chart;
+  };
+  chart.ylab = function(value) {
+    if (!arguments.length) {
+      return ylab;
+    }
+    ylab = value;
+    return chart;
+  };
+  chart.rotate_ylab = function(value) {
+    if (!arguments.length) {
+      return rotate_ylab;
+    }
+    rotate_ylab = value;
+    return chart;
+  };
+  chart.lodvarname = function(value) {
+    if (!arguments.length) {
+      return lodvarname;
+    }
+    lodvarname = value;
+    return chart;
+  };
+  chart.pad4heatmap = function(value) {
+    if (!arguments.length) {
+      return pad4heatmap;
+    }
+    pad4heatmap = value;
+    return chart;
+  };
+  chart.pointsAtMarkers = function(value) {
+    if (!arguments.length) {
+      return pointsAtMarkers;
+    }
+    pointsAtMarkers = value;
+    return chart;
+  };
+  chart.yscale = function() {
+    return yscale;
+  };
+  chart.additive_yscale = function() {
+    return additive_yscale;
+  };
+  chart.xscale = function() {
+    return xscale;
+  };
+  chart.lodcurve = function() {
+    return lodcurve;
+  };
+  chart.additivecurve = function() {
+    return additivecurve;
+  };
+  chart.markerSelect = function() {
+    return markerSelect;
+  };
+  chart.chrSelect = function() {
+    return chrSelect;
+  };
+  return chart;
+};
+
+reorgLodData = function(data, lodvarname) {
+  var additiveval, chr, i, j, lodcolumn, lodval, marker, pos, _i, _j, _k, _len, _len1, _len2, _ref, _ref1, _ref2;
+  if (lodvarname == null) {
+    lodvarname = null;
+  }
+  data.posByChr = {};
+  data.lodByChr = {};
+  data.additiveByChr = {};
+  _ref = data.chrnames;
+  for (i = _i = 0, _len = _ref.length; _i < _len; i = ++_i) {
+    chr = _ref[i];
+    data.posByChr[chr[0]] = [];
+    data.lodByChr[chr[0]] = [];
+    data.additiveByChr[chr[0]] = [];
+    _ref1 = data.pos;
+    for (j = _j = 0, _len1 = _ref1.length; _j < _len1; j = ++_j) {
+      pos = _ref1[j];
+      if (data.chr[j] === chr[0]) {
+        data.posByChr[chr[0]].push(pos);
+        if (!Array.isArray(data.lodnames)) {
+          data.lodnames = [data.lodnames];
+        }
+        if (data['additive'].length > 0) {
+          additiveval = (function() {
             var _k, _len2, _ref2, _results;
             _ref2 = data.lodnames;
             _results = [];
             for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) {
               lodcolumn = _ref2[_k];
-              _results.push(data[lodcolumn][j]);
+              _results.push(data['additive'][j]);
             }
             return _results;
           })();
-          data.additiveByChr[chr].push(additiveval);
-          data.lodByChr[chr].push(lodval);
         }
+        lodval = (function() {
+          var _k, _len2, _ref2, _results;
+          _ref2 = data.lodnames;
+          _results = [];
+          for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) {
+            lodcolumn = _ref2[_k];
+            _results.push(data[lodcolumn][j]);
+          }
+          return _results;
+        })();
+        data.additiveByChr[chr[0]].push(additiveval);
+        data.lodByChr[chr[0]].push(lodval);
       }
     }
-    if (lodvarname != null) {
-      data.markers = [];
-      _ref2 = data.markernames;
-      for (i = _k = 0, _len2 = _ref2.length; _k < _len2; i = ++_k) {
-        marker = _ref2[i];
-        if (marker !== "") {
-          data.markers.push({
-            name: marker,
-            chr: data.chr[i],
-            pos: data.pos[i],
-            lod: data[lodvarname][i]
-          });
-        }
+  }
+  if (lodvarname != null) {
+    data.markers = [];
+    _ref2 = data.markernames;
+    for (i = _k = 0, _len2 = _ref2.length; _k < _len2; i = ++_k) {
+      marker = _ref2[i];
+      if (marker !== "") {
+        data.markers.push({
+          name: marker,
+          chr: data.chr[i],
+          pos: data.pos[i],
+          lod: data[lodvarname][i]
+        });
       }
     }
-    return data;
-  };
+  }
+  return data;
+};
 
-  chrscales = function(data, width, chrGap, leftMargin, pad4heatmap) {
-    var L, chr, chrEnd, chrLength, chrStart, cur, d, i, maxd, rng, totalChrLength, w, _i, _j, _len, _len1, _ref, _ref1;
-    chrStart = [];
-    chrEnd = [];
-    chrLength = [];
-    totalChrLength = 0;
-    maxd = 0;
-    _ref = data.chrnames;
-    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-      chr = _ref[_i];
-      d = maxdiff(data.posByChr[chr]);
-      if (d > maxd) {
-        maxd = d;
-      }
-      rng = d3.extent(data.posByChr[chr]);
-      chrStart.push(rng[0]);
-      chrEnd.push(rng[1]);
-      L = rng[1] - rng[0];
-      chrLength.push(L);
-      totalChrLength += L;
-    }
-    if (pad4heatmap) {
-      data.recwidth = maxd;
-      chrStart = chrStart.map(function(x) {
-        return x - maxd / 2;
-      });
-      chrEnd = chrEnd.map(function(x) {
-        return x + maxd / 2;
-      });
-      chrLength = chrLength.map(function(x) {
-        return x + maxd;
-      });
-      totalChrLength += chrLength.length * maxd;
-    }
-    data.chrStart = [];
-    data.chrEnd = [];
-    cur = leftMargin;
-    if (!pad4heatmap) {
-      cur += chrGap / 2;
-    }
-    data.xscale = {};
-    _ref1 = data.chrnames;
-    for (i = _j = 0, _len1 = _ref1.length; _j < _len1; i = ++_j) {
-      chr = _ref1[i];
-      data.chrStart.push(cur);
-      w = Math.round((width - chrGap * (data.chrnames.length - pad4heatmap)) / totalChrLength * chrLength[i]);
-      data.chrEnd.push(cur + w);
-      cur = data.chrEnd[i] + chrGap;
-      data.xscale[chr] = d3.scale.linear().domain([chrStart[i], chrEnd[i]]).range([data.chrStart[i], data.chrEnd[i]]);
+chrscales = function(data, width, chrGap, leftMargin, pad4heatmap) {
+  var L, chr, chrEnd, chrLength, chrStart, cur, d, i, maxd, rng, totalChrLength, w, _i, _j, _len, _len1, _ref, _ref1;
+  chrStart = [];
+  chrEnd = [];
+  chrLength = [];
+  totalChrLength = 0;
+  maxd = 0;
+  _ref = data.chrnames;
+  for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+    chr = _ref[_i];
+    d = maxdiff(data.posByChr[chr[0]]);
+    if (d > maxd) {
+      maxd = d;
     }
-    return data;
-  };
+    rng = d3.extent(data.posByChr[chr[0]]);
+    chrStart.push(rng[0]);
+    chrEnd.push(rng[1]);
+    L = rng[1] - rng[0];
+    chrLength.push(L);
+    totalChrLength += L;
+  }
+  if (pad4heatmap) {
+    data.recwidth = maxd;
+    chrStart = chrStart.map(function(x) {
+      return x - maxd / 2;
+    });
+    chrEnd = chrEnd.map(function(x) {
+      return x + maxd / 2;
+    });
+    chrLength = chrLength.map(function(x) {
+      return x + maxd;
+    });
+    totalChrLength += chrLength.length * maxd;
+  }
+  data.chrStart = [];
+  data.chrEnd = [];
+  cur = leftMargin;
+  if (!pad4heatmap) {
+    cur += chrGap / 2;
+  }
+  data.xscale = {};
+  _ref1 = data.chrnames;
+  for (i = _j = 0, _len1 = _ref1.length; _j < _len1; i = ++_j) {
+    chr = _ref1[i];
+    data.chrStart.push(cur);
+    w = Math.round((width - chrGap * (data.chrnames.length - pad4heatmap)) / totalChrLength * chrLength[i]);
+    data.chrEnd.push(cur + w);
+    cur = data.chrEnd[i] + chrGap;
+    data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], chrEnd[i]]).range([data.chrStart[i], data.chrEnd[i]]);
+  }
+  return data;
+};
 
-  maxdiff = function(x) {
-    var d, i, result, _i, _ref;
-    if (x.length < 2) {
-      return null;
-    }
-    result = x[1] - x[0];
-    if (x.length < 3) {
-      return result;
-    }
-    for (i = _i = 2, _ref = x.length; 2 <= _ref ? _i < _ref : _i > _ref; i = 2 <= _ref ? ++_i : --_i) {
-      d = x[i] - x[i - 1];
-      if (d > result) {
-        result = d;
-      }
-    }
+maxdiff = function(x) {
+  var d, i, result, _i, _ref;
+  if (x.length < 2) {
+    return null;
+  }
+  result = x[1] - x[0];
+  if (x.length < 3) {
     return result;
-  };
-
-  formatAxis = function(d) {
-    var ndig;
-    d = d[1] - d[0];
-    ndig = Math.floor(Math.log(d % 10) / Math.log(10));
-    if (ndig > 0) {
-      ndig = 0;
+  }
+  for (i = _i = 2, _ref = x.length; 2 <= _ref ? _i < _ref : _i > _ref; i = 2 <= _ref ? ++_i : --_i) {
+    d = x[i] - x[i - 1];
+    if (d > result) {
+      result = d;
     }
-    ndig = Math.abs(ndig);
-    return d3.format("." + ndig + "f");
-  };
+  }
+  return result;
+};
 
-}).call(this);
+formatAxis = function(d) {
+  var ndig;
+  d = d[1] - d[0];
+  ndig = Math.floor(Math.log(d % 10) / Math.log(10));
+  if (ndig > 0) {
+    ndig = 0;
+  }
+  ndig = Math.abs(ndig);
+  return d3.format("." + ndig + "f");
+};
diff --git a/wqflask/wqflask/static/new/javascript/login.js b/wqflask/wqflask/static/new/javascript/login.js
index f6fd1b2e..a64d1b2d 100755
--- a/wqflask/wqflask/static/new/javascript/login.js
+++ b/wqflask/wqflask/static/new/javascript/login.js
@@ -1,45 +1,41 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-
-  $(function() {
-    var form_success, modalize, submit_form;
-    modalize = function(event) {
-      event.preventDefault();
-      console.log("in modal_replace:", $(this).attr("href"));
-      return $.colorbox({
-        open: true,
-        href: this.href,
-        onComplete: function() {
-          return $(".focused").focus();
-        }
-      });
-    };
-    $(document).one("click", ".modalize", modalize);
-    console.log("Modalized click!!!");
-    form_success = function(data) {
-      return $.colorbox({
-        open: true,
-        html: data,
-        onComplete: function() {
-          return $("form").on("submit", submit_form);
-        }
-      });
-    };
-    submit_form = function(event) {
-      var data, submit_to;
-      event.preventDefault();
-      submit_to = $(this).attr('action');
-      data = $(this).serialize();
-      console.log("submit_to is:", submit_to);
-      return $.ajax({
-        type: "POST",
-        url: submit_to,
-        data: data,
-        dataType: "html",
-        success: form_success
-      });
-    };
-    return $("#colorbox form").on("submit", submit_form);
-  });
-
-}).call(this);
+// Generated by CoffeeScript 1.7.1
+$(function() {
+  var form_success, modalize, submit_form;
+  modalize = function(event) {
+    event.preventDefault();
+    console.log("in modal_replace:", $(this).attr("href"));
+    return $.colorbox({
+      open: true,
+      href: this.href,
+      onComplete: function() {
+        return $(".focused").focus();
+      }
+    });
+  };
+  $(document).one("click", ".modalize", modalize);
+  console.log("Modalized click!!!");
+  form_success = function(data) {
+    return $.colorbox({
+      open: true,
+      html: data,
+      onComplete: function() {
+        return $("form").on("submit", submit_form);
+      }
+    });
+  };
+  submit_form = function(event) {
+    var data, submit_to;
+    event.preventDefault();
+    submit_to = $(this).attr('action');
+    data = $(this).serialize();
+    console.log("submit_to is:", submit_to);
+    return $.ajax({
+      type: "POST",
+      url: submit_to,
+      data: data,
+      dataType: "html",
+      success: form_success
+    });
+  };
+  return $("#colorbox form").on("submit", submit_form);
+});
diff --git a/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee b/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee
new file mode 100644
index 00000000..492c2f3f
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee
@@ -0,0 +1,534 @@
+lodchart = () ->

+    width = 800

+    height = 500

+    margin = {left:60, top:40, right:40, bottom: 40, inner:5}

+    axispos = {xtitle:25, ytitle:30, xlabel:5, ylabel:5}

+    titlepos = 20

+    ylim = null

+    nyticks = 5

+    yticks = null

+    chrGap = 8

+    darkrect = "#F1F1F9"

+    lightrect = "#FBFBFF" 

+    lodlinecolor = "darkslateblue"

+    linewidth = 2

+    pointcolor = "darkslateblue" # pink

+    pointhover = "#E9CFEC" # pink

+    pointsize = 2 # default = no visible points at markers

+    pointstroke = "black"

+    title = ""

+    xlab = "Chromosome"

+    ylab = "LOD score"

+    rotate_ylab = null

+    yscale = d3.scale.linear()

+    xscale = null

+    pad4heatmap = false

+    lodcurve = null

+    lodvarname = null

+    markerSelect = null

+    chrSelect = null

+    pointsAtMarkers = true

+  

+    ## the main function

+    chart = (selection) ->

+      selection.each (data) ->

+          

+        console.log("data:", data)

+          

+        lodvarname = lodvarname ? data.lodnames[0]

+        data[lodvarname] = (Math.abs(x) for x in data[lodvarname]) # take absolute values

+        ylim = ylim ? [0, d3.max(data[lodvarname])]

+        lodvarnum = data.lodnames.indexOf(lodvarname)

+  

+        # Select the svg element, if it exists.

+        svg = d3.select(this).selectAll("svg").data([data])

+  

+        # Otherwise, create the skeletal chart.

+        gEnter = svg.enter().append("svg").append("g")

+  

+        # Update the outer dimensions.

+        svg.attr("width", width+margin.left+margin.right)

+           .attr("height", height+margin.top+margin.bottom)

+  

+        # Update the inner dimensions.

+        g = svg.select("g")

+  

+        # box

+        g.append("rect")

+         .attr("x", margin.left)

+         .attr("y", margin.top)

+         .attr("height", height)

+         .attr("width", width)

+         .attr("fill", darkrect)

+         .attr("stroke", "none")

+  

+        yscale.domain(ylim)

+              .range([height+margin.top, margin.top+margin.inner])

+  

+        # if yticks not provided, use nyticks to choose pretty ones

+        yticks = yticks ? yscale.ticks(nyticks)

+  

+        # reorganize lod,pos by chromosomes

+        data = reorgLodData(data, lodvarname)

+  

+        # add chromosome scales (for x-axis)

+        data = chrscales(data, width, chrGap, margin.left, pad4heatmap)

+        xscale = data.xscale

+  

+        # chr rectangles

+        chrSelect =

+                  g.append("g").attr("class", "chrRect")

+                   .selectAll("empty")

+                   .data(data.chrnames)

+                   .enter()

+                   .append("rect")

+                   .attr("id", (d) -> "chrrect#{d[0]}")

+                   .attr("x", (d,i) ->

+                     return data.chrStart[i] if i==0 and pad4heatmap

+                     data.chrStart[i]-chrGap/2)

+                   .attr("width", (d,i) ->

+                      return data.chrEnd[i] - data.chrStart[i]+chrGap/2 if (i==0 or i+1 == data.chrnames.length) and pad4heatmap

+                      data.chrEnd[i] - data.chrStart[i]+chrGap)

+                   .attr("y", margin.top)

+                   .attr("height", height)

+                   .attr("fill", (d,i) ->

+                      return darkrect if i % 2

+                      lightrect)

+                   .attr("stroke", "none")

+                   .on("click", (d) ->

+                      redraw_plot(d)

+                    )   

+  

+        # x-axis labels

+        xaxis = g.append("g").attr("class", "x axis")

+        xaxis.selectAll("empty")

+             .data(data.chrnames)

+             .enter()

+             .append("text")

+             .attr("class", "chr_label")

+             .text((d) -> d[0])

+             .attr("x", (d,i) -> (data.chrStart[i]+data.chrEnd[i])/2)

+             .attr("y", margin.top+height+axispos.xlabel)

+             .attr("cursor", "pointer")

+             .on("click", (d) ->

+                 redraw_plot(d)

+              )   

+

+        xaxis.append("text").attr("class", "title")

+             .attr("y", margin.top+height+axispos.xtitle)

+             .attr("x", margin.left+width/2)

+             .text(xlab)

+  

+        redraw_plot = (chr_ob) ->

+             console.log("chr_name is:", chr_ob[0])

+             console.log("chr_length is:", chr_ob[1])

+             $('#topchart').remove()

+             $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>')

+             chr_plot = new Chr_Manhattan_Plot(600, 1200, chr_ob)

+        

+  

+        # y-axis

+        rotate_ylab = rotate_ylab ? (ylab.length > 1)

+        yaxis = g.append("g").attr("class", "y axis")

+        yaxis.selectAll("empty")

+             .data(yticks)

+             .enter()

+             .append("line")

+             .attr("y1", (d) -> yscale(d))

+             .attr("y2", (d) -> yscale(d))

+             .attr("x1", margin.left)

+             .attr("x2", margin.left+7)

+             .attr("fill", "none")

+             .attr("stroke", "white")

+             .attr("stroke-width", 1)

+             .style("pointer-events", "none")

+             

+        yaxis.selectAll("empty")

+             .data(yticks)

+             .enter()

+             .append("text")

+             .attr("y", (d) -> yscale(d))

+             .attr("x", margin.left-axispos.ylabel)

+             .attr("fill", "blue")

+             .text((d) -> formatAxis(yticks)(d))

+             

+        yaxis.append("text").attr("class", "title")

+             .attr("y", margin.top+height/2)

+             .attr("x", margin.left-axispos.ytitle)

+             .text(ylab)

+             .attr("transform", if rotate_ylab then "rotate(270,#{margin.left-axispos.ytitle},#{margin.top+height/2})" else "")

+  

+        # lod curves by chr

+        #lodcurve = (chr, lodcolumn) ->

+        #    d3.svg.line()

+        #      .x((d) -> xscale[chr](d))

+        #      .y((d,i) -> yscale(data.lodByChr[chr][i][lodcolumn]))

+              

+          #add_plot_points: () ->

+          #    @plot_point = @svg.selectAll("circle")

+          #        .data(@plot_coordinates)

+          #        .enter()

+          #        .append("circle")

+          #        .attr("cx", (d) =>

+          #            return @x_scale(d[0])

+          #        )

+          #        .attr("cy", (d) =>

+          #            return @y_scale(d[1])

+          #        )

+          #        .attr("r", (d) =>

+          #            #if d[1] > 3

+          #            #    return 3

+          #            #else

+          #            return 2

+          #        )

+          #        .attr("fill", (d) =>

+          #            #if d[1] > 3

+          #            #    return "white"

+          #            #else

+          #            return "black"

+          #        )

+          #        .attr("stroke", "black")

+          #        .attr("stroke-width", "1")

+          #        .attr("id", (d) =>

+          #            return "point_" + String(d[2])

+          #        )

+          #        .classed("circle", true)

+          #        .on("mouseover", (d) =>

+          #            console.log("d3.event is:", d3.event)

+          #            console.log("d is:", d)

+          #            this_id = "point_" + String(d[2])

+          #            d3.select("#" + this_id).classed("d3_highlight", true)

+          #                .attr("r", 5)

+          #                .attr("stroke", "none")

+          #                .attr("fill", "blue")

+          #                .call(@show_marker_in_table(d))

+          #        )

+          #        .on("mouseout", (d) =>

+          #            this_id = "point_" + String(d[2])

+          #            d3.select("#" + this_id).classed("d3_highlight", false)

+          #                .attr("r", (d) =>

+          #                    #if d[1] > 2

+          #                    #    return 3

+          #                    #else

+          #                    return 2

+          #                )

+          #                .attr("fill", (d) =>

+          #                    #if d[1] > 2

+          #                    #    return "white"

+          #                    #else

+          #                    return "black"

+          #                )

+          #                .attr("stroke", "black")

+          #                .attr("stroke-width", "1")

+          #        )

+          #        .append("svg:title")

+          #            .text((d) =>

+          #                return d[2]

+          #            )

+  

+        #curves = g.append("g").attr("id", "curves")

+  

+        #for chr in data.chrnames

+        #  curves.append("path")

+        #        .datum(data.posByChr[chr])

+        #        .attr("d", lodcurve(chr, lodvarnum))

+        #        .attr("stroke", lodlinecolor)

+        #        .attr("fill", "none")

+        #        .attr("stroke-width", linewidth)

+        #        .style("pointer-events", "none")

+  

+        # points at markers

+        if pointsize > 0

+          markerpoints = g.append("g").attr("id", "markerpoints_visible")

+          markerpoints.selectAll("empty")

+                      .data(data.markers)

+                      .enter()

+                      .append("circle")

+                      .attr("cx", (d) -> xscale[d.chr](d.pos))

+                      .attr("cy", (d) -> yscale(d.lod))

+                      .attr("r", pointsize)

+                      .attr("fill", pointcolor)

+                      .attr("stroke", pointstroke)

+                      .attr("pointer-events", "hidden")

+  

+        # title

+        titlegrp = g.append("g").attr("class", "title")

+         .append("text")

+         .attr("x", margin.left+width/2)

+         .attr("y", margin.top-titlepos)

+         .text(title)

+  

+        # another box around edge

+        g.append("rect")

+         .attr("x", margin.left)

+         .attr("y", margin.top)

+         .attr("height", height)

+         .attr("width", () ->

+            return(data.chrEnd[-1..][0]-margin.left) if pad4heatmap

+            data.chrEnd[-1..][0]-margin.left+chrGap/2)

+         .attr("fill", "none")

+         .attr("stroke", "black")

+         .attr("stroke-width", "none")

+         

+        if pointsAtMarkers

+          # these hidden points are what gets selected...a bit larger

+          hiddenpoints = g.append("g").attr("id", "markerpoints_hidden")

+  

+          markertip = d3.tip()

+                        .attr('class', 'd3-tip')

+                        .html((d) ->

+                          [d.name, " LRS = #{d3.format('.2f')(d.lod)}"])

+                        .direction("e")

+                        .offset([0,10])

+          svg.call(markertip)

+  

+          markerSelect =

+            hiddenpoints.selectAll("empty")

+                        .data(data.markers)

+                        .enter()

+                        .append("circle")

+                        .attr("cx", (d) -> xscale[d.chr](d.pos))

+                        .attr("cy", (d) -> yscale(d.lod))

+                        .attr("id", (d) -> d.name)

+                        .attr("r", d3.max([pointsize*2, 3]))

+                        .attr("opacity", 0)

+                        .attr("fill", pointhover)

+                        .attr("stroke", pointstroke)

+                        .attr("stroke-width", "1")

+                        .on "mouseover.paneltip", (d) ->

+                           d3.select(this).attr("opacity", 1)

+                           markertip.show(d)

+                        .on "mouseout.paneltip", ->

+                           d3.select(this).attr("opacity", 0)

+                                          .call(markertip.hide)

+  

+    ## configuration parameters

+    chart.width = (value) ->

+      return width unless arguments.length

+      width = value

+      chart

+  

+    chart.height = (value) ->

+      return height unless arguments.length

+      height = value

+      chart

+  

+    chart.margin = (value) ->

+      return margin unless arguments.length

+      margin = value

+      chart

+  

+    chart.titlepos = (value) ->

+      return titlepos unless arguments.length

+      titlepos

+      chart

+  

+    chart.axispos = (value) ->

+      return axispos unless arguments.length

+      axispos = value

+      chart

+  

+    chart.ylim = (value) ->

+      return ylim unless arguments.length

+      ylim = value

+      chart

+      

+    chart.nyticks = (value) ->

+      return nyticks unless arguments.length

+      nyticks = value

+      chart

+  

+    chart.yticks = (value) ->

+      return yticks unless arguments.length

+      yticks = value

+      chart

+  

+    chart.chrGap = (value) ->

+      return chrGap unless arguments.length

+      chrGap = value

+      chart

+  

+    chart.darkrect = (value) ->

+      return darkrect unless arguments.length

+      darkrect = value

+      chart

+  

+    chart.lightrect = (value) ->

+      return lightrect unless arguments.length

+      lightrect = value

+      chart

+  

+    chart.linecolor = (value) ->

+      return linecolor unless arguments.length

+      linecolor = value

+      chart

+  

+    chart.linewidth = (value) ->

+      return linewidth unless arguments.length

+      linewidth = value

+      chart

+  

+    chart.pointcolor = (value) ->

+      return pointcolor unless arguments.length

+      pointcolor = value

+      chart

+  

+    chart.pointhover = (value) ->

+      return pointhover unless arguments.length

+      pointhover = value

+      chart

+  

+    chart.pointsize = (value) ->

+      return pointsize unless arguments.length

+      pointsize = value

+      chart

+  

+    chart.pointstroke = (value) ->

+      return pointstroke unless arguments.length

+      pointstroke = value

+      chart

+  

+    chart.title = (value) ->

+      return title unless arguments.length

+      title = value

+      chart

+  

+    chart.xlab = (value) ->

+      return xlab unless arguments.length

+      xlab = value

+      chart

+  

+    chart.ylab = (value) ->

+      return ylab unless arguments.length

+      ylab = value

+      chart

+  

+    chart.rotate_ylab = (value) ->

+      return rotate_ylab if !arguments.length

+      rotate_ylab = value

+      chart

+  

+    chart.lodvarname = (value) ->

+      return lodvarname unless arguments.length

+      lodvarname = value

+      chart

+  

+    chart.pad4heatmap = (value) ->

+      return pad4heatmap unless arguments.length

+      pad4heatmap = value

+      chart

+  

+    chart.pointsAtMarkers = (value) ->

+      return pointsAtMarkers unless arguments.length

+      pointsAtMarkers = value

+      chart

+  

+    chart.yscale = () ->

+      return yscale

+  

+    chart.xscale = () ->

+      return xscale

+  

+    #chart.lodcurve = () ->

+    #  return lodcurve

+  

+    chart.markerSelect = () ->

+      return markerSelect

+  

+    chart.chrSelect = () ->

+      return chrSelect

+  

+    # return the chart function

+    chart

+

+

+# reorganize lod/pos by chromosome

+# lodvarname==null    -> case for multiple LOD columns (lodheatmap)

+# lodvarname provided -> case for one LOD column (lodchart)

+reorgLodData = (data, lodvarname=null) ->

+    data.posByChr = {}

+    data.lodByChr = {}

+    

+    for chr,i in data.chrnames

+      data.posByChr[chr[0]] = []

+      data.lodByChr[chr[0]] = []

+      for pos, j in data.pos

+        if data.chr[j] == chr[0]

+          data.posByChr[chr[0]].push(pos)

+          data.lodnames = [data.lodnames] unless Array.isArray(data.lodnames)

+          lodval = (data[lodcolumn][j] for lodcolumn in data.lodnames)

+          data.lodByChr[chr[0]].push(lodval)

+

+    

+    if lodvarname?

+      data.markers = []

+      for marker,i in data.markernames

+        if marker != ""

+          data.markers.push({name:marker, chr:data.chr[i], pos:data.pos[i], lod:data[lodvarname][i]})

+    

+    data

+

+

+# calculate chromosome start/end + scales, for heat map

+chrscales = (data, width, chrGap, leftMargin, pad4heatmap) ->

+    # start and end of chromosome positions

+    chrStart = []

+    chrEnd = []

+    chrLength = []

+    totalChrLength = 0

+    maxd = 0

+    for chr in data.chrnames

+      d = maxdiff(data.posByChr[chr[0]])

+      maxd = d if d > maxd

+  

+      rng = d3.extent(data.posByChr[chr[0]])

+      chrStart.push(rng[0])

+      chrEnd.push(rng[1])

+      L = rng[1] - rng[0]

+      chrLength.push(L)

+      totalChrLength += L

+  

+    # adjust lengths for heatmap

+    if pad4heatmap

+      data.recwidth = maxd

+      chrStart = chrStart.map (x) -> x-maxd/2

+      chrEnd = chrEnd.map (x) -> x+maxd/2

+      chrLength = chrLength.map (x) -> x+maxd

+      totalChrLength += (chrLength.length*maxd)

+  

+    # break up x axis into chromosomes by length, with gaps

+    data.chrStart = []

+    data.chrEnd = []

+    cur = leftMargin

+    cur += chrGap/2 unless pad4heatmap

+    data.xscale = {}

+    for chr,i in data.chrnames

+      data.chrStart.push(cur)

+      w = Math.round((width-chrGap*(data.chrnames.length-pad4heatmap))/totalChrLength*chrLength[i])

+      data.chrEnd.push(cur + w)

+      cur = data.chrEnd[i] + chrGap

+      # x-axis scales, by chromosome

+      data.xscale[chr[0]] = d3.scale.linear()

+                           .domain([chrStart[i], chrEnd[i]])

+                           .range([data.chrStart[i], data.chrEnd[i]])

+  

+    # return data with new stuff added

+    data

+    

+# maximum difference between adjacent values in a vector

+maxdiff = (x) ->

+    return null if x.length < 2

+    result = x[1] - x[0]

+    return result if x.length < 3

+    for i in [2...x.length]

+      d = x[i] - x[i-1]

+      result = d if d > result

+    result

+    

+# determine rounding of axis labels

+formatAxis = (d) ->

+    d = d[1] - d[0]

+    ndig = Math.floor( Math.log(d % 10) / Math.log(10) )

+    ndig = 0 if ndig > 0

+    ndig = Math.abs(ndig)

+    d3.format(".#{ndig}f")

diff --git a/wqflask/wqflask/static/new/javascript/manhattan_plot.js b/wqflask/wqflask/static/new/javascript/manhattan_plot.js
new file mode 100644
index 00000000..546cf9a9
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/manhattan_plot.js
@@ -0,0 +1,475 @@
+// Generated by CoffeeScript 1.7.1
+var chrscales, formatAxis, lodchart, maxdiff, reorgLodData;
+
+lodchart = function() {
+  var axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointhover, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks;
+  width = 800;
+  height = 500;
+  margin = {
+    left: 60,
+    top: 40,
+    right: 40,
+    bottom: 40,
+    inner: 5
+  };
+  axispos = {
+    xtitle: 25,
+    ytitle: 30,
+    xlabel: 5,
+    ylabel: 5
+  };
+  titlepos = 20;
+  ylim = null;
+  nyticks = 5;
+  yticks = null;
+  chrGap = 8;
+  darkrect = "#F1F1F9";
+  lightrect = "#FBFBFF";
+  lodlinecolor = "darkslateblue";
+  linewidth = 2;
+  pointcolor = "darkslateblue";
+  pointhover = "#E9CFEC";
+  pointsize = 2;
+  pointstroke = "black";
+  title = "";
+  xlab = "Chromosome";
+  ylab = "LOD score";
+  rotate_ylab = null;
+  yscale = d3.scale.linear();
+  xscale = null;
+  pad4heatmap = false;
+  lodcurve = null;
+  lodvarname = null;
+  markerSelect = null;
+  chrSelect = null;
+  pointsAtMarkers = true;
+  chart = function(selection) {
+    return selection.each(function(data) {
+      var g, gEnter, hiddenpoints, lodvarnum, markerpoints, markertip, redraw_plot, svg, titlegrp, x, xaxis, yaxis;
+      console.log("data:", data);
+      lodvarname = lodvarname != null ? lodvarname : data.lodnames[0];
+      data[lodvarname] = (function() {
+        var _i, _len, _ref, _results;
+        _ref = data[lodvarname];
+        _results = [];
+        for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+          x = _ref[_i];
+          _results.push(Math.abs(x));
+        }
+        return _results;
+      })();
+      ylim = ylim != null ? ylim : [0, d3.max(data[lodvarname])];
+      lodvarnum = data.lodnames.indexOf(lodvarname);
+      svg = d3.select(this).selectAll("svg").data([data]);
+      gEnter = svg.enter().append("svg").append("g");
+      svg.attr("width", width + margin.left + margin.right).attr("height", height + margin.top + margin.bottom);
+      g = svg.select("g");
+      g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", width).attr("fill", darkrect).attr("stroke", "none");
+      yscale.domain(ylim).range([height + margin.top, margin.top + margin.inner]);
+      yticks = yticks != null ? yticks : yscale.ticks(nyticks);
+      data = reorgLodData(data, lodvarname);
+      data = chrscales(data, width, chrGap, margin.left, pad4heatmap);
+      xscale = data.xscale;
+      chrSelect = g.append("g").attr("class", "chrRect").selectAll("empty").data(data.chrnames).enter().append("rect").attr("id", function(d) {
+        return "chrrect" + d[0];
+      }).attr("x", function(d, i) {
+        if (i === 0 && pad4heatmap) {
+          return data.chrStart[i];
+        }
+        return data.chrStart[i] - chrGap / 2;
+      }).attr("width", function(d, i) {
+        if ((i === 0 || i + 1 === data.chrnames.length) && pad4heatmap) {
+          return data.chrEnd[i] - data.chrStart[i] + chrGap / 2;
+        }
+        return data.chrEnd[i] - data.chrStart[i] + chrGap;
+      }).attr("y", margin.top).attr("height", height).attr("fill", function(d, i) {
+        if (i % 2) {
+          return darkrect;
+        }
+        return lightrect;
+      }).attr("stroke", "none").on("click", function(d) {
+        return redraw_plot(d);
+      });
+      xaxis = g.append("g").attr("class", "x axis");
+      xaxis.selectAll("empty").data(data.chrnames).enter().append("text").attr("class", "chr_label").text(function(d) {
+        return d[0];
+      }).attr("x", function(d, i) {
+        return (data.chrStart[i] + data.chrEnd[i]) / 2;
+      }).attr("y", margin.top + height + axispos.xlabel).attr("cursor", "pointer").on("click", function(d) {
+        return redraw_plot(d);
+      });
+      xaxis.append("text").attr("class", "title").attr("y", margin.top + height + axispos.xtitle).attr("x", margin.left + width / 2).text(xlab);
+      redraw_plot = function(chr_ob) {
+        var chr_plot;
+        console.log("chr_name is:", chr_ob[0]);
+        console.log("chr_length is:", chr_ob[1]);
+        $('#topchart').remove();
+        $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>');
+        return chr_plot = new Chr_Manhattan_Plot(600, 1200, chr_ob);
+      };
+      rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1;
+      yaxis = g.append("g").attr("class", "y axis");
+      yaxis.selectAll("empty").data(yticks).enter().append("line").attr("y1", function(d) {
+        return yscale(d);
+      }).attr("y2", function(d) {
+        return yscale(d);
+      }).attr("x1", margin.left).attr("x2", margin.left + 7).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none");
+      yaxis.selectAll("empty").data(yticks).enter().append("text").attr("y", function(d) {
+        return yscale(d);
+      }).attr("x", margin.left - axispos.ylabel).attr("fill", "blue").text(function(d) {
+        return formatAxis(yticks)(d);
+      });
+      yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : "");
+      if (pointsize > 0) {
+        markerpoints = g.append("g").attr("id", "markerpoints_visible");
+        markerpoints.selectAll("empty").data(data.markers).enter().append("circle").attr("cx", function(d) {
+          return xscale[d.chr](d.pos);
+        }).attr("cy", function(d) {
+          return yscale(d.lod);
+        }).attr("r", pointsize).attr("fill", pointcolor).attr("stroke", pointstroke).attr("pointer-events", "hidden");
+      }
+      titlegrp = g.append("g").attr("class", "title").append("text").attr("x", margin.left + width / 2).attr("y", margin.top - titlepos).text(title);
+      g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", function() {
+        if (pad4heatmap) {
+          return data.chrEnd.slice(-1)[0] - margin.left;
+        }
+        return data.chrEnd.slice(-1)[0] - margin.left + chrGap / 2;
+      }).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none");
+      if (pointsAtMarkers) {
+        hiddenpoints = g.append("g").attr("id", "markerpoints_hidden");
+        markertip = d3.tip().attr('class', 'd3-tip').html(function(d) {
+          return [d.name, " LRS = " + (d3.format('.2f')(d.lod))];
+        }).direction("e").offset([0, 10]);
+        svg.call(markertip);
+        return markerSelect = hiddenpoints.selectAll("empty").data(data.markers).enter().append("circle").attr("cx", function(d) {
+          return xscale[d.chr](d.pos);
+        }).attr("cy", function(d) {
+          return yscale(d.lod);
+        }).attr("id", function(d) {
+          return d.name;
+        }).attr("r", d3.max([pointsize * 2, 3])).attr("opacity", 0).attr("fill", pointhover).attr("stroke", pointstroke).attr("stroke-width", "1").on("mouseover.paneltip", function(d) {
+          d3.select(this).attr("opacity", 1);
+          return markertip.show(d);
+        }).on("mouseout.paneltip", function() {
+          return d3.select(this).attr("opacity", 0).call(markertip.hide);
+        });
+      }
+    });
+  };
+  chart.width = function(value) {
+    if (!arguments.length) {
+      return width;
+    }
+    width = value;
+    return chart;
+  };
+  chart.height = function(value) {
+    if (!arguments.length) {
+      return height;
+    }
+    height = value;
+    return chart;
+  };
+  chart.margin = function(value) {
+    if (!arguments.length) {
+      return margin;
+    }
+    margin = value;
+    return chart;
+  };
+  chart.titlepos = function(value) {
+    if (!arguments.length) {
+      return titlepos;
+    }
+    titlepos;
+    return chart;
+  };
+  chart.axispos = function(value) {
+    if (!arguments.length) {
+      return axispos;
+    }
+    axispos = value;
+    return chart;
+  };
+  chart.ylim = function(value) {
+    if (!arguments.length) {
+      return ylim;
+    }
+    ylim = value;
+    return chart;
+  };
+  chart.nyticks = function(value) {
+    if (!arguments.length) {
+      return nyticks;
+    }
+    nyticks = value;
+    return chart;
+  };
+  chart.yticks = function(value) {
+    if (!arguments.length) {
+      return yticks;
+    }
+    yticks = value;
+    return chart;
+  };
+  chart.chrGap = function(value) {
+    if (!arguments.length) {
+      return chrGap;
+    }
+    chrGap = value;
+    return chart;
+  };
+  chart.darkrect = function(value) {
+    if (!arguments.length) {
+      return darkrect;
+    }
+    darkrect = value;
+    return chart;
+  };
+  chart.lightrect = function(value) {
+    if (!arguments.length) {
+      return lightrect;
+    }
+    lightrect = value;
+    return chart;
+  };
+  chart.linecolor = function(value) {
+    var linecolor;
+    if (!arguments.length) {
+      return linecolor;
+    }
+    linecolor = value;
+    return chart;
+  };
+  chart.linewidth = function(value) {
+    if (!arguments.length) {
+      return linewidth;
+    }
+    linewidth = value;
+    return chart;
+  };
+  chart.pointcolor = function(value) {
+    if (!arguments.length) {
+      return pointcolor;
+    }
+    pointcolor = value;
+    return chart;
+  };
+  chart.pointhover = function(value) {
+    if (!arguments.length) {
+      return pointhover;
+    }
+    pointhover = value;
+    return chart;
+  };
+  chart.pointsize = function(value) {
+    if (!arguments.length) {
+      return pointsize;
+    }
+    pointsize = value;
+    return chart;
+  };
+  chart.pointstroke = function(value) {
+    if (!arguments.length) {
+      return pointstroke;
+    }
+    pointstroke = value;
+    return chart;
+  };
+  chart.title = function(value) {
+    if (!arguments.length) {
+      return title;
+    }
+    title = value;
+    return chart;
+  };
+  chart.xlab = function(value) {
+    if (!arguments.length) {
+      return xlab;
+    }
+    xlab = value;
+    return chart;
+  };
+  chart.ylab = function(value) {
+    if (!arguments.length) {
+      return ylab;
+    }
+    ylab = value;
+    return chart;
+  };
+  chart.rotate_ylab = function(value) {
+    if (!arguments.length) {
+      return rotate_ylab;
+    }
+    rotate_ylab = value;
+    return chart;
+  };
+  chart.lodvarname = function(value) {
+    if (!arguments.length) {
+      return lodvarname;
+    }
+    lodvarname = value;
+    return chart;
+  };
+  chart.pad4heatmap = function(value) {
+    if (!arguments.length) {
+      return pad4heatmap;
+    }
+    pad4heatmap = value;
+    return chart;
+  };
+  chart.pointsAtMarkers = function(value) {
+    if (!arguments.length) {
+      return pointsAtMarkers;
+    }
+    pointsAtMarkers = value;
+    return chart;
+  };
+  chart.yscale = function() {
+    return yscale;
+  };
+  chart.xscale = function() {
+    return xscale;
+  };
+  chart.markerSelect = function() {
+    return markerSelect;
+  };
+  chart.chrSelect = function() {
+    return chrSelect;
+  };
+  return chart;
+};
+
+reorgLodData = function(data, lodvarname) {
+  var chr, i, j, lodcolumn, lodval, marker, pos, _i, _j, _k, _len, _len1, _len2, _ref, _ref1, _ref2;
+  if (lodvarname == null) {
+    lodvarname = null;
+  }
+  data.posByChr = {};
+  data.lodByChr = {};
+  _ref = data.chrnames;
+  for (i = _i = 0, _len = _ref.length; _i < _len; i = ++_i) {
+    chr = _ref[i];
+    data.posByChr[chr[0]] = [];
+    data.lodByChr[chr[0]] = [];
+    _ref1 = data.pos;
+    for (j = _j = 0, _len1 = _ref1.length; _j < _len1; j = ++_j) {
+      pos = _ref1[j];
+      if (data.chr[j] === chr[0]) {
+        data.posByChr[chr[0]].push(pos);
+        if (!Array.isArray(data.lodnames)) {
+          data.lodnames = [data.lodnames];
+        }
+        lodval = (function() {
+          var _k, _len2, _ref2, _results;
+          _ref2 = data.lodnames;
+          _results = [];
+          for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) {
+            lodcolumn = _ref2[_k];
+            _results.push(data[lodcolumn][j]);
+          }
+          return _results;
+        })();
+        data.lodByChr[chr[0]].push(lodval);
+      }
+    }
+  }
+  if (lodvarname != null) {
+    data.markers = [];
+    _ref2 = data.markernames;
+    for (i = _k = 0, _len2 = _ref2.length; _k < _len2; i = ++_k) {
+      marker = _ref2[i];
+      if (marker !== "") {
+        data.markers.push({
+          name: marker,
+          chr: data.chr[i],
+          pos: data.pos[i],
+          lod: data[lodvarname][i]
+        });
+      }
+    }
+  }
+  return data;
+};
+
+chrscales = function(data, width, chrGap, leftMargin, pad4heatmap) {
+  var L, chr, chrEnd, chrLength, chrStart, cur, d, i, maxd, rng, totalChrLength, w, _i, _j, _len, _len1, _ref, _ref1;
+  chrStart = [];
+  chrEnd = [];
+  chrLength = [];
+  totalChrLength = 0;
+  maxd = 0;
+  _ref = data.chrnames;
+  for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+    chr = _ref[_i];
+    d = maxdiff(data.posByChr[chr[0]]);
+    if (d > maxd) {
+      maxd = d;
+    }
+    rng = d3.extent(data.posByChr[chr[0]]);
+    chrStart.push(rng[0]);
+    chrEnd.push(rng[1]);
+    L = rng[1] - rng[0];
+    chrLength.push(L);
+    totalChrLength += L;
+  }
+  if (pad4heatmap) {
+    data.recwidth = maxd;
+    chrStart = chrStart.map(function(x) {
+      return x - maxd / 2;
+    });
+    chrEnd = chrEnd.map(function(x) {
+      return x + maxd / 2;
+    });
+    chrLength = chrLength.map(function(x) {
+      return x + maxd;
+    });
+    totalChrLength += chrLength.length * maxd;
+  }
+  data.chrStart = [];
+  data.chrEnd = [];
+  cur = leftMargin;
+  if (!pad4heatmap) {
+    cur += chrGap / 2;
+  }
+  data.xscale = {};
+  _ref1 = data.chrnames;
+  for (i = _j = 0, _len1 = _ref1.length; _j < _len1; i = ++_j) {
+    chr = _ref1[i];
+    data.chrStart.push(cur);
+    w = Math.round((width - chrGap * (data.chrnames.length - pad4heatmap)) / totalChrLength * chrLength[i]);
+    data.chrEnd.push(cur + w);
+    cur = data.chrEnd[i] + chrGap;
+    data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], chrEnd[i]]).range([data.chrStart[i], data.chrEnd[i]]);
+  }
+  return data;
+};
+
+maxdiff = function(x) {
+  var d, i, result, _i, _ref;
+  if (x.length < 2) {
+    return null;
+  }
+  result = x[1] - x[0];
+  if (x.length < 3) {
+    return result;
+  }
+  for (i = _i = 2, _ref = x.length; 2 <= _ref ? _i < _ref : _i > _ref; i = 2 <= _ref ? ++_i : --_i) {
+    d = x[i] - x[i - 1];
+    if (d > result) {
+      result = d;
+    }
+  }
+  return result;
+};
+
+formatAxis = function(d) {
+  var ndig;
+  d = d[1] - d[0];
+  ndig = Math.floor(Math.log(d % 10) / Math.log(10));
+  if (ndig > 0) {
+    ndig = 0;
+  }
+  ndig = Math.abs(ndig);
+  return d3.format("." + ndig + "f");
+};
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
index 403ee52a..203c174c 100755
--- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
@@ -1,6 +1,11 @@
 root = exports ? this
 
-class Manhattan_Plot
+class Manhattan_Plot

+

+    darkrect = "#F1F1F9"

+    lightrect = "#FBFBFF"

+    hoverrect = "#E9CFEC"

+
     constructor: (@height = 800, @width = 1200) ->
         @qtl_results = js_data.qtl_results
         console.log("qtl_results are:", @qtl_results)
@@ -100,7 +105,7 @@ class Manhattan_Plot
         #else
         #    @y_axis_filter = 0
 
-            
+
     create_coordinates: () -> 
         chr_lengths = []
         chr_seen = []
@@ -334,7 +339,9 @@ class Manhattan_Plot
                 return d
             )
             .enter()
-            .append("rect")
+            .append("rect")

+            .attr("id", (d, i) =>

+                return "chr_fill_area_" + i)
             .attr("x", (d, i) =>
                 return @x_scale(d[1] - d[0])
             )
@@ -349,10 +356,27 @@ class Manhattan_Plot
             .attr("height", @height-@y_buffer - @legend_buffer-3)
             .attr("fill", (d, i) =>
                 if (i+1)%2
-                    return "none"
+                    return darkrect
                 else
-                    return "whitesmoke"
-            )
+                    return lightrect
+            )

+            .on("mouseover", (d, i) =>

+                this_id = "chr_fill_area_" + i

+                console.log("this_id:", this_id)

+                d3.select("#" + this_id)

+                    .attr("fill", hoverrect)

+            )

+            .on("mouseout", (d, i) =>

+                this_id = "chr_fill_area_" + i

+                d3.select("#" + this_id)

+                    .attr("fill", () =>

+                        if (i+1)%2

+                            return darkrect

+                        else

+                            return lightrect

+                    )

+            )

+            
             
     #fill_chr_areas2: () ->
     #    console.log("cumu_chr_lengths:", @cumulative_chr_lengths)
@@ -419,7 +443,6 @@ class Manhattan_Plot
             .attr("cursor", "pointer")
             .attr("fill", "black")
             .on("click", (d) =>
-                this_chr = d
                 @redraw_plot(d)
             )
 
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js
index 8c235189..1fcee9fd 100755
--- a/wqflask/wqflask/static/new/javascript/marker_regression.js
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.js
@@ -1,235 +1,247 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var Manhattan_Plot, root,
-    __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; };
-
-  root = typeof exports !== "undefined" && exports !== null ? exports : this;
-
-  Manhattan_Plot = (function() {
-
-    function Manhattan_Plot(height, width) {
-      var _ref;
-      this.height = height != null ? height : 800;
-      this.width = width != null ? width : 1200;
-      this.qtl_results = js_data.qtl_results;
-      console.log("qtl_results are:", this.qtl_results);
-      this.chromosomes = js_data.chromosomes;
-      console.log("chromosomes are:", this.chromosomes);
-      this.this_trait = js_data.this_trait;
-      this.data_set = js_data.data_set;
-      this.maf = js_data.maf;
-      this.total_length = 0;
-      this.max_chr = this.get_max_chr();
-      this.x_coords = [];
-      this.y_coords = [];
-      this.marker_names = [];
-      console.time('Create coordinates');
-      this.get_qtl_count();
-      this.create_coordinates();
-      console.log("@x_coords: ", this.x_coords);
-      console.log("@y_coords: ", this.y_coords);
-      console.timeEnd('Create coordinates');
-      _ref = this.get_chr_lengths(), this.chr_lengths = _ref[0], this.cumulative_chr_lengths = _ref[1];
-      this.x_buffer = this.width / 30;
-      this.y_buffer = this.height / 20;
-      this.legend_buffer = 30;
-      this.x_max = this.total_length;
-      console.log("@x_max: ", this.x_max);
-      console.log("@x_buffer: ", this.x_buffer);
-      this.y_max = d3.max(this.y_coords) * 1.2;
-      this.svg = this.create_svg();
-      console.log("svg created");
-      this.plot_coordinates = _.zip(this.x_coords, this.y_coords, this.marker_names);
-      console.log("coordinates:", this.plot_coordinates);
-      this.height -= this.y_buffer;
-      this.create_scales();
-      console.time('Create graph');
-      this.create_graph();
-      console.timeEnd('Create graph');
-    }
+// Generated by CoffeeScript 1.7.1
+var Manhattan_Plot, root,
+  __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; };
 
-    Manhattan_Plot.prototype.get_max_chr = function() {
-      var chr, max_chr, result, _i, _len, _ref;
-      max_chr = 0;
-      _ref = this.qtl_results;
-      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-        result = _ref[_i];
-        chr = parseInt(result.chr);
-        if (!_.isNaN(chr)) {
-          if (chr > max_chr) {
-            max_chr = chr;
-          }
+root = typeof exports !== "undefined" && exports !== null ? exports : this;
+
+Manhattan_Plot = (function() {
+  var darkrect, hoverrect, lightrect;
+
+  darkrect = "#F1F1F9";
+
+  lightrect = "#FBFBFF";
+
+  hoverrect = "#E9CFEC";
+
+  function Manhattan_Plot(height, width) {
+    var _ref;
+    this.height = height != null ? height : 800;
+    this.width = width != null ? width : 1200;
+    this.qtl_results = js_data.qtl_results;
+    console.log("qtl_results are:", this.qtl_results);
+    this.chromosomes = js_data.chromosomes;
+    console.log("chromosomes are:", this.chromosomes);
+    this.this_trait = js_data.this_trait;
+    this.data_set = js_data.data_set;
+    this.maf = js_data.maf;
+    this.total_length = 0;
+    this.max_chr = this.get_max_chr();
+    this.x_coords = [];
+    this.y_coords = [];
+    this.marker_names = [];
+    console.time('Create coordinates');
+    this.get_qtl_count();
+    this.create_coordinates();
+    console.log("@x_coords: ", this.x_coords);
+    console.log("@y_coords: ", this.y_coords);
+    console.timeEnd('Create coordinates');
+    _ref = this.get_chr_lengths(), this.chr_lengths = _ref[0], this.cumulative_chr_lengths = _ref[1];
+    this.x_buffer = this.width / 30;
+    this.y_buffer = this.height / 20;
+    this.legend_buffer = 30;
+    this.x_max = this.total_length;
+    console.log("@x_max: ", this.x_max);
+    console.log("@x_buffer: ", this.x_buffer);
+    this.y_max = d3.max(this.y_coords) * 1.2;
+    this.svg = this.create_svg();
+    console.log("svg created");
+    this.plot_coordinates = _.zip(this.x_coords, this.y_coords, this.marker_names);
+    console.log("coordinates:", this.plot_coordinates);
+    this.height -= this.y_buffer;
+    this.create_scales();
+    console.time('Create graph');
+    this.create_graph();
+    console.timeEnd('Create graph');
+  }
+
+  Manhattan_Plot.prototype.get_max_chr = function() {
+    var chr, max_chr, result, _i, _len, _ref;
+    max_chr = 0;
+    _ref = this.qtl_results;
+    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+      result = _ref[_i];
+      chr = parseInt(result.chr);
+      if (!_.isNaN(chr)) {
+        if (chr > max_chr) {
+          max_chr = chr;
         }
       }
-      console.log("max_chr", max_chr);
-      return max_chr;
-    };
-
-    Manhattan_Plot.prototype.get_chr_lengths = function() {
-      /*
-      #Gets a list of both individual and cumulative (the position of one on the graph
-      #is its own length plus the lengths of all preceding chromosomes) lengths in order
-      #to draw the vertical lines separating chromosomes and the chromosome labels
-      #
-      */
-
-      var chr_lengths, cumulative_chr_lengths, key, this_length, total_length;
-      cumulative_chr_lengths = [];
-      chr_lengths = [];
-      total_length = 0;
-      for (key in this.chromosomes) {
-        this_length = this.chromosomes[key];
-        chr_lengths.push(this_length);
-        cumulative_chr_lengths.push(total_length + this_length);
-        total_length += this_length;
+    }
+    console.log("max_chr", max_chr);
+    return max_chr;
+  };
+
+  Manhattan_Plot.prototype.get_chr_lengths = function() {
+
+    /*
+     *Gets a list of both individual and cumulative (the position of one on the graph
+     *is its own length plus the lengths of all preceding chromosomes) lengths in order
+     *to draw the vertical lines separating chromosomes and the chromosome labels
+     *
+     */
+    var chr_lengths, cumulative_chr_lengths, key, this_length, total_length;
+    cumulative_chr_lengths = [];
+    chr_lengths = [];
+    total_length = 0;
+    for (key in this.chromosomes) {
+      this_length = this.chromosomes[key];
+      chr_lengths.push(this_length);
+      cumulative_chr_lengths.push(total_length + this_length);
+      total_length += this_length;
+    }
+    console.log("chr_lengths: ", chr_lengths);
+    return [chr_lengths, cumulative_chr_lengths];
+  };
+
+  Manhattan_Plot.prototype.get_qtl_count = function() {
+    var high_qtl_count, result, _i, _len, _ref;
+    high_qtl_count = 0;
+    _ref = js_data.qtl_results;
+    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+      result = _ref[_i];
+      if (result.lod_score > 1) {
+        high_qtl_count += 1;
       }
-      console.log("chr_lengths: ", chr_lengths);
-      return [chr_lengths, cumulative_chr_lengths];
-    };
-
-    Manhattan_Plot.prototype.get_qtl_count = function() {
-      var high_qtl_count, result, _i, _len, _ref;
-      high_qtl_count = 0;
-      _ref = js_data.qtl_results;
-      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-        result = _ref[_i];
-        if (result.lod_score > 1) {
-          high_qtl_count += 1;
-        }
+    }
+    console.log("high_qtl_count:", high_qtl_count);
+    return this.y_axis_filter = 0;
+  };
+
+  Manhattan_Plot.prototype.create_coordinates = function() {
+    var chr_length, chr_lengths, chr_seen, result, _i, _len, _ref, _ref1;
+    chr_lengths = [];
+    chr_seen = [];
+    _ref = js_data.qtl_results;
+    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+      result = _ref[_i];
+      if (result.chr === "X") {
+        chr_length = parseFloat(this.chromosomes[13]);
+      } else {
+        chr_length = parseFloat(this.chromosomes[result.chr]);
       }
-      console.log("high_qtl_count:", high_qtl_count);
-      return this.y_axis_filter = 0;
-    };
-
-    Manhattan_Plot.prototype.create_coordinates = function() {
-      var chr_length, chr_lengths, chr_seen, result, _i, _len, _ref, _ref1;
-      chr_lengths = [];
-      chr_seen = [];
-      _ref = js_data.qtl_results;
-      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-        result = _ref[_i];
-        if (result.chr === "X") {
-          chr_length = parseFloat(this.chromosomes[13]);
-        } else {
-          chr_length = parseFloat(this.chromosomes[result.chr]);
-        }
-        if (!(_ref1 = result.chr, __indexOf.call(chr_seen, _ref1) >= 0)) {
-          chr_seen.push(result.chr);
-          chr_lengths.push(chr_length);
-          console.log("result.chr:", result.chr);
-          console.log("total_length:", this.total_length);
-          if (parseInt(result.chr) !== 1) {
-            console.log("plus:", chr_lengths.length - 2);
-            console.log("chr_lengths.length", chr_lengths.length);
-            this.total_length += parseFloat(chr_lengths[chr_lengths.length - 2]);
-          }
-        }
-        if (result.lod_score > this.y_axis_filter) {
-          this.x_coords.push(this.total_length + parseFloat(result.Mb));
-          this.y_coords.push(result.lod_score);
-          this.marker_names.push(result.name);
+      if (!(_ref1 = result.chr, __indexOf.call(chr_seen, _ref1) >= 0)) {
+        chr_seen.push(result.chr);
+        chr_lengths.push(chr_length);
+        console.log("result.chr:", result.chr);
+        console.log("total_length:", this.total_length);
+        if (parseInt(result.chr) !== 1) {
+          console.log("plus:", chr_lengths.length - 2);
+          console.log("chr_lengths.length", chr_lengths.length);
+          this.total_length += parseFloat(chr_lengths[chr_lengths.length - 2]);
         }
       }
-      return this.total_length += parseFloat(chr_lengths[chr_lengths.length - 1]);
-    };
-
-    Manhattan_Plot.prototype.show_marker_in_table = function(marker_info) {
-      var marker_name;
-      console.log("in show_marker_in_table");
-      /* Searches for the select marker in the results table below
-      */
-
-      if (marker_info) {
-        marker_name = marker_info[2];
-        return $("#qtl_results_filter").find("input:first").val(marker_name).trigger('change');
+      if (result.lod_score > this.y_axis_filter) {
+        this.x_coords.push(this.total_length + parseFloat(result.Mb));
+        this.y_coords.push(result.lod_score);
+        this.marker_names.push(result.name);
       }
-    };
-
-    Manhattan_Plot.prototype.create_svg = function() {
-      var svg;
-      svg = d3.select("#manhattan_plot").append("svg").attr("class", "manhattan_plot").attr("width", this.width + this.x_buffer).attr("height", this.height + this.y_buffer).append("g");
-      return svg;
-    };
-
-    Manhattan_Plot.prototype.create_graph = function() {
-      this.create_legend();
-      this.add_border();
-      this.add_x_axis();
-      this.add_y_axis();
-      this.add_axis_labels();
-      this.add_chr_lines();
-      this.fill_chr_areas();
-      this.add_chr_labels();
-      return this.add_plot_points();
-    };
-
-    Manhattan_Plot.prototype.create_legend = function() {
-      this.svg.append("text").attr("class", "legend").text("Trait: " + this.this_trait + " : " + this.data_set).attr("x", this.x_buffer).attr("y", 20).attr("dx", "0em").attr("text-anchor", "left").attr("font-family", "sans-serif").attr("font-size", "16px").attr("fill", "black");
-      return this.svg.append("text").attr("class", "legend").text("MAF: " + this.maf).attr("x", this.x_buffer).attr("y", 38).attr("dx", "0em").attr("text-anchor", "left").attr("font-family", "sans-serif").attr("font-size", "16px").attr("fill", "black");
-    };
-
-    Manhattan_Plot.prototype.add_border = function() {
-      var border_coords,
-        _this = this;
-      border_coords = [[this.y_buffer + this.legend_buffer, this.height, this.x_buffer, this.x_buffer], [this.y_buffer + this.legend_buffer, this.height, this.width, this.width], [this.y_buffer + this.legend_buffer, this.y_buffer + this.legend_buffer, this.x_buffer, this.width], [this.height, this.height, this.x_buffer, this.width]];
-      return this.svg.selectAll("line").data(border_coords).enter().append("line").attr("y1", function(d) {
+    }
+    return this.total_length += parseFloat(chr_lengths[chr_lengths.length - 1]);
+  };
+
+  Manhattan_Plot.prototype.show_marker_in_table = function(marker_info) {
+    var marker_name;
+    console.log("in show_marker_in_table");
+
+    /* Searches for the select marker in the results table below */
+    if (marker_info) {
+      marker_name = marker_info[2];
+      return $("#qtl_results_filter").find("input:first").val(marker_name).trigger('change');
+    }
+  };
+
+  Manhattan_Plot.prototype.create_svg = function() {
+    var svg;
+    svg = d3.select("#manhattan_plot").append("svg").attr("class", "manhattan_plot").attr("width", this.width + this.x_buffer).attr("height", this.height + this.y_buffer).append("g");
+    return svg;
+  };
+
+  Manhattan_Plot.prototype.create_graph = function() {
+    this.create_legend();
+    this.add_border();
+    this.add_x_axis();
+    this.add_y_axis();
+    this.add_axis_labels();
+    this.add_chr_lines();
+    this.fill_chr_areas();
+    this.add_chr_labels();
+    return this.add_plot_points();
+  };
+
+  Manhattan_Plot.prototype.create_legend = function() {
+    this.svg.append("text").attr("class", "legend").text("Trait: " + this.this_trait + " : " + this.data_set).attr("x", this.x_buffer).attr("y", 20).attr("dx", "0em").attr("text-anchor", "left").attr("font-family", "sans-serif").attr("font-size", "16px").attr("fill", "black");
+    return this.svg.append("text").attr("class", "legend").text("MAF: " + this.maf).attr("x", this.x_buffer).attr("y", 38).attr("dx", "0em").attr("text-anchor", "left").attr("font-family", "sans-serif").attr("font-size", "16px").attr("fill", "black");
+  };
+
+  Manhattan_Plot.prototype.add_border = function() {
+    var border_coords;
+    border_coords = [[this.y_buffer + this.legend_buffer, this.height, this.x_buffer, this.x_buffer], [this.y_buffer + this.legend_buffer, this.height, this.width, this.width], [this.y_buffer + this.legend_buffer, this.y_buffer + this.legend_buffer, this.x_buffer, this.width], [this.height, this.height, this.x_buffer, this.width]];
+    return this.svg.selectAll("line").data(border_coords).enter().append("line").attr("y1", (function(_this) {
+      return function(d) {
         return d[0];
-      }).attr("y2", function(d) {
+      };
+    })(this)).attr("y2", (function(_this) {
+      return function(d) {
         return d[1];
-      }).attr("x1", function(d) {
+      };
+    })(this)).attr("x1", (function(_this) {
+      return function(d) {
         return d[2];
-      }).attr("x2", function(d) {
+      };
+    })(this)).attr("x2", (function(_this) {
+      return function(d) {
         return d[3];
-      }).style("stroke", "#000");
-    };
-
-    Manhattan_Plot.prototype.create_scales = function() {
-      console.log("y_axis_filter:", this.y_axis_filter);
-      if ('24' in this.chromosomes) {
-        console.log("@chromosomes[24]:", this.chromosomes['24']);
-        console.log("@chromosomes[23]:", this.chromosomes['23']);
-        console.log("@total_length:", this.total_length);
-        console.log("d3.max(@xcoords):", d3.max(this.x_coords));
-        this.x_scale = d3.scale.linear().domain([0, this.total_length + this.chromosomes['24']]).range([this.x_buffer, this.width]);
-      } else {
-        this.x_scale = d3.scale.linear().domain([0, this.total_length + this.chromosomes['20']]).range([this.x_buffer, this.width]);
+      };
+    })(this)).style("stroke", "#000");
+  };
+
+  Manhattan_Plot.prototype.create_scales = function() {
+    console.log("y_axis_filter:", this.y_axis_filter);
+    if ('24' in this.chromosomes) {
+      console.log("@chromosomes[24]:", this.chromosomes['24']);
+      console.log("@chromosomes[23]:", this.chromosomes['23']);
+      console.log("@total_length:", this.total_length);
+      console.log("d3.max(@xcoords):", d3.max(this.x_coords));
+      this.x_scale = d3.scale.linear().domain([0, this.total_length + this.chromosomes['24']]).range([this.x_buffer, this.width]);
+    } else {
+      this.x_scale = d3.scale.linear().domain([0, this.total_length + this.chromosomes['20']]).range([this.x_buffer, this.width]);
+    }
+    return this.y_scale = d3.scale.linear().domain([this.y_axis_filter, this.y_max]).range([this.height, this.y_buffer + this.legend_buffer]);
+  };
+
+  Manhattan_Plot.prototype.create_x_axis_tick_values = function() {
+    var chr_ticks, i, length, tick, tick_count, tick_val, tick_vals, val, _i, _j, _k, _len, _ref, _ref1, _ref2;
+    tick_vals = [];
+    for (val = _i = 25, _ref = this.cumulative_chr_lengths[0]; 25 <= _ref ? _i <= _ref : _i >= _ref; val = 25 <= _ref ? ++_i : --_i) {
+      if (val % 25 === 0) {
+        tick_vals.push(val);
       }
-      return this.y_scale = d3.scale.linear().domain([this.y_axis_filter, this.y_max]).range([this.height, this.y_buffer + this.legend_buffer]);
-    };
-
-    Manhattan_Plot.prototype.create_x_axis_tick_values = function() {
-      var chr_ticks, i, length, tick, tick_count, tick_val, tick_vals, val, _i, _j, _k, _len, _ref, _ref1, _ref2;
-      tick_vals = [];
-      for (val = _i = 25, _ref = this.cumulative_chr_lengths[0]; 25 <= _ref ? _i <= _ref : _i >= _ref; val = 25 <= _ref ? ++_i : --_i) {
-        if (val % 25 === 0) {
-          tick_vals.push(val);
-        }
+    }
+    _ref1 = this.cumulative_chr_lengths;
+    for (i = _j = 0, _len = _ref1.length; _j < _len; i = ++_j) {
+      length = _ref1[i];
+      if (i === 0) {
+        continue;
       }
-      _ref1 = this.cumulative_chr_lengths;
-      for (i = _j = 0, _len = _ref1.length; _j < _len; i = ++_j) {
-        length = _ref1[i];
-        if (i === 0) {
-          continue;
-        }
-        chr_ticks = [];
-        tick_count = Math.floor(this.chr_lengths[i] / 25);
-        tick_val = parseInt(this.cumulative_chr_lengths[i - 1]);
-        for (tick = _k = 0, _ref2 = tick_count - 1; 0 <= _ref2 ? _k <= _ref2 : _k >= _ref2; tick = 0 <= _ref2 ? ++_k : --_k) {
-          tick_val += 25;
-          chr_ticks.push(tick_val);
-        }
-        Array.prototype.push.apply(tick_vals, chr_ticks);
+      chr_ticks = [];
+      tick_count = Math.floor(this.chr_lengths[i] / 25);
+      tick_val = parseInt(this.cumulative_chr_lengths[i - 1]);
+      for (tick = _k = 0, _ref2 = tick_count - 1; 0 <= _ref2 ? _k <= _ref2 : _k >= _ref2; tick = 0 <= _ref2 ? ++_k : --_k) {
+        tick_val += 25;
+        chr_ticks.push(tick_val);
       }
-      return tick_vals;
-    };
-
-    Manhattan_Plot.prototype.add_x_axis = function() {
-      var next_chr, tmp_tick_val,
-        _this = this;
-      this.xAxis = d3.svg.axis().scale(this.x_scale).orient("bottom").tickValues(this.create_x_axis_tick_values());
-      next_chr = 1;
-      tmp_tick_val = 0;
-      this.xAxis.tickFormat(function(d) {
+      Array.prototype.push.apply(tick_vals, chr_ticks);
+    }
+    return tick_vals;
+  };
+
+  Manhattan_Plot.prototype.add_x_axis = function() {
+    var next_chr, tmp_tick_val;
+    this.xAxis = d3.svg.axis().scale(this.x_scale).orient("bottom").tickValues(this.create_x_axis_tick_values());
+    next_chr = 1;
+    tmp_tick_val = 0;
+    this.xAxis.tickFormat((function(_this) {
+      return function(d) {
         var next_chr_length, tick_val;
         d3.format("d");
         if (d < _this.cumulative_chr_lengths[0]) {
@@ -246,63 +258,99 @@
           }
         }
         return tick_val;
-      });
-      return this.svg.append("g").attr("class", "x_axis").attr("transform", "translate(0," + this.height + ")").call(this.xAxis).selectAll("text").attr("text-anchor", "right").attr("dx", "-1.6em").attr("transform", function(d) {
+      };
+    })(this));
+    return this.svg.append("g").attr("class", "x_axis").attr("transform", "translate(0," + this.height + ")").call(this.xAxis).selectAll("text").attr("text-anchor", "right").attr("dx", "-1.6em").attr("transform", (function(_this) {
+      return function(d) {
         return "translate(-12,0) rotate(-90)";
-      });
-    };
+      };
+    })(this));
+  };
 
-    Manhattan_Plot.prototype.add_y_axis = function() {
-      this.yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
-      return this.svg.append("g").attr("class", "y_axis").attr("transform", "translate(" + this.x_buffer + ",0)").call(this.yAxis);
-    };
+  Manhattan_Plot.prototype.add_y_axis = function() {
+    this.yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
+    return this.svg.append("g").attr("class", "y_axis").attr("transform", "translate(" + this.x_buffer + ",0)").call(this.yAxis);
+  };
 
-    Manhattan_Plot.prototype.add_axis_labels = function() {
-      return this.svg.append("text").attr("transform", "rotate(-90)").attr("y", 0 - (this.height / 2)).attr("x", this.x_buffer).attr("dy", "1em").style("text-anchor", "middle").text("LOD Score");
-    };
+  Manhattan_Plot.prototype.add_axis_labels = function() {
+    return this.svg.append("text").attr("transform", "rotate(-90)").attr("y", 0 - (this.height / 2)).attr("x", this.x_buffer).attr("dy", "1em").style("text-anchor", "middle").text("LOD Score");
+  };
 
-    Manhattan_Plot.prototype.add_chr_lines = function() {
-      var _this = this;
-      return this.svg.selectAll("line").data(this.cumulative_chr_lengths, function(d) {
+  Manhattan_Plot.prototype.add_chr_lines = function() {
+    return this.svg.selectAll("line").data(this.cumulative_chr_lengths, (function(_this) {
+      return function(d) {
         return d;
-      }).enter().append("line").attr("x1", this.x_scale).attr("x2", this.x_scale).attr("y1", this.y_buffer + this.legend_buffer).attr("y2", this.height).style("stroke", "#ccc");
-    };
-
-    Manhattan_Plot.prototype.fill_chr_areas = function() {
-      var _this = this;
-      console.log("cumu_chr_lengths:", this.cumulative_chr_lengths);
-      console.log("example:", this.x_scale(this.cumulative_chr_lengths[0]));
-      return this.svg.selectAll("rect.chr_fill_area").data(_.zip(this.chr_lengths, this.cumulative_chr_lengths), function(d) {
+      };
+    })(this)).enter().append("line").attr("x1", this.x_scale).attr("x2", this.x_scale).attr("y1", this.y_buffer + this.legend_buffer).attr("y2", this.height).style("stroke", "#ccc");
+  };
+
+  Manhattan_Plot.prototype.fill_chr_areas = function() {
+    console.log("cumu_chr_lengths:", this.cumulative_chr_lengths);
+    console.log("example:", this.x_scale(this.cumulative_chr_lengths[0]));
+    return this.svg.selectAll("rect.chr_fill_area").data(_.zip(this.chr_lengths, this.cumulative_chr_lengths), (function(_this) {
+      return function(d) {
         return d;
-      }).enter().append("rect").attr("x", function(d, i) {
+      };
+    })(this)).enter().append("rect").attr("id", (function(_this) {
+      return function(d, i) {
+        return "chr_fill_area_" + i;
+      };
+    })(this)).attr("x", (function(_this) {
+      return function(d, i) {
         return _this.x_scale(d[1] - d[0]);
-      }).attr("y", this.y_buffer + this.legend_buffer + 2).attr("width", function(d, i) {
+      };
+    })(this)).attr("y", this.y_buffer + this.legend_buffer + 2).attr("width", (function(_this) {
+      return function(d, i) {
         var ending, starting, width;
         starting = _this.x_scale(d[1] - d[0]);
         ending = _this.x_scale(_this.cumulative_chr_lengths[i]);
         width = ending - starting;
         console.log("width:", d[0]);
         return width;
-      }).attr("height", this.height - this.y_buffer - this.legend_buffer - 3).attr("fill", function(d, i) {
+      };
+    })(this)).attr("height", this.height - this.y_buffer - this.legend_buffer - 3).attr("fill", (function(_this) {
+      return function(d, i) {
         if ((i + 1) % 2) {
-          return "none";
+          return darkrect;
         } else {
-          return "whitesmoke";
+          return lightrect;
         }
-      });
-    };
-
-    Manhattan_Plot.prototype.add_chr_labels = function() {
-      var chr_info, chr_names, key,
-        _this = this;
-      chr_names = [];
-      for (key in this.chromosomes) {
-        chr_names.push(key);
-      }
-      chr_info = _.zip(chr_names, this.chr_lengths, this.cumulative_chr_lengths);
-      return this.svg.selectAll("text").data(chr_info, function(d) {
+      };
+    })(this)).on("mouseover", (function(_this) {
+      return function(d, i) {
+        var this_id;
+        this_id = "chr_fill_area_" + i;
+        console.log("this_id:", this_id);
+        return d3.select("#" + this_id).attr("fill", hoverrect);
+      };
+    })(this)).on("mouseout", (function(_this) {
+      return function(d, i) {
+        var this_id;
+        this_id = "chr_fill_area_" + i;
+        return d3.select("#" + this_id).attr("fill", function() {
+          if ((i + 1) % 2) {
+            return darkrect;
+          } else {
+            return lightrect;
+          }
+        });
+      };
+    })(this));
+  };
+
+  Manhattan_Plot.prototype.add_chr_labels = function() {
+    var chr_info, chr_names, key;
+    chr_names = [];
+    for (key in this.chromosomes) {
+      chr_names.push(key);
+    }
+    chr_info = _.zip(chr_names, this.chr_lengths, this.cumulative_chr_lengths);
+    return this.svg.selectAll("text").data(chr_info, (function(_this) {
+      return function(d) {
         return d;
-      }).enter().append("text").attr("class", "chr_label").text(function(d) {
+      };
+    })(this)).enter().append("text").attr("class", "chr_label").text((function(_this) {
+      return function(d) {
         if (_this.max_chr === 23) {
           if (d[0] === "23") {
             return "X";
@@ -318,34 +366,49 @@
             return d[0];
           }
         }
-      }).attr("x", function(d) {
+      };
+    })(this)).attr("x", (function(_this) {
+      return function(d) {
         return _this.x_scale(d[2] - d[1] / 2);
-      }).attr("y", this.height * 0.1 + this.legend_buffer).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("cursor", "pointer").attr("fill", "black").on("click", function(d) {
-        var this_chr;
-        this_chr = d;
+      };
+    })(this)).attr("y", this.height * 0.1 + this.legend_buffer).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("cursor", "pointer").attr("fill", "black").on("click", (function(_this) {
+      return function(d) {
         return _this.redraw_plot(d);
-      });
-    };
+      };
+    })(this));
+  };
 
-    Manhattan_Plot.prototype.add_plot_points = function() {
-      var _this = this;
-      return this.plot_point = this.svg.selectAll("circle").data(this.plot_coordinates).enter().append("circle").attr("cx", function(d) {
+  Manhattan_Plot.prototype.add_plot_points = function() {
+    return this.plot_point = this.svg.selectAll("circle").data(this.plot_coordinates).enter().append("circle").attr("cx", (function(_this) {
+      return function(d) {
         return _this.x_scale(d[0]);
-      }).attr("cy", function(d) {
+      };
+    })(this)).attr("cy", (function(_this) {
+      return function(d) {
         return _this.y_scale(d[1]);
-      }).attr("r", function(d) {
+      };
+    })(this)).attr("r", (function(_this) {
+      return function(d) {
         return 2;
-      }).attr("fill", function(d) {
+      };
+    })(this)).attr("fill", (function(_this) {
+      return function(d) {
         return "black";
-      }).attr("stroke", "black").attr("stroke-width", "1").attr("id", function(d) {
+      };
+    })(this)).attr("stroke", "black").attr("stroke-width", "1").attr("id", (function(_this) {
+      return function(d) {
         return "point_" + String(d[2]);
-      }).classed("circle", true).on("mouseover", function(d) {
+      };
+    })(this)).classed("circle", true).on("mouseover", (function(_this) {
+      return function(d) {
         var this_id;
         console.log("d3.event is:", d3.event);
         console.log("d is:", d);
         this_id = "point_" + String(d[2]);
         return d3.select("#" + this_id).classed("d3_highlight", true).attr("r", 5).attr("stroke", "none").attr("fill", "blue").call(_this.show_marker_in_table(d));
-      }).on("mouseout", function(d) {
+      };
+    })(this)).on("mouseout", (function(_this) {
+      return function(d) {
         var this_id;
         this_id = "point_" + String(d[2]);
         return d3.select("#" + this_id).classed("d3_highlight", false).attr("r", function(d) {
@@ -353,38 +416,39 @@
         }).attr("fill", function(d) {
           return "black";
         }).attr("stroke", "black").attr("stroke-width", "1");
-      }).append("svg:title").text(function(d) {
+      };
+    })(this)).append("svg:title").text((function(_this) {
+      return function(d) {
         return d[2];
-      });
-    };
-
-    Manhattan_Plot.prototype.redraw_plot = function(chr_ob) {
-      console.log("chr_name is:", chr_ob[0]);
-      console.log("chr_length is:", chr_ob[1]);
-      $('#manhattan_plot').remove();
-      $('#manhattan_plot_container').append('<div id="manhattan_plot"></div>');
-      return root.chr_plot = new Chr_Manhattan_Plot(600, 1200, chr_ob);
-    };
+      };
+    })(this));
+  };
 
-    Manhattan_Plot.prototype.create_zoom_pane = function() {
-      var zoom;
-      zoom = d3.behavior.zoom().on("zoom", draw);
-      return this.svg.append("rect").attr("class", "pane").attr("width", this.width).attr("height", this.height).call(zoom);
-    };
+  Manhattan_Plot.prototype.redraw_plot = function(chr_ob) {
+    console.log("chr_name is:", chr_ob[0]);
+    console.log("chr_length is:", chr_ob[1]);
+    $('#manhattan_plot').remove();
+    $('#manhattan_plot_container').append('<div id="manhattan_plot"></div>');
+    return root.chr_plot = new Chr_Manhattan_Plot(600, 1200, chr_ob);
+  };
 
-    Manhattan_Plot.prototype.draw = function() {
-      this.svg.select("g.x_axis").call(this.xAxis);
-      this.svg.select("g.y_axis").call(this.yAxis);
-      this.svg.select("path.area").attr("d", area);
-      return this.svg.select("path.line").attr("d", line);
-    };
+  Manhattan_Plot.prototype.create_zoom_pane = function() {
+    var zoom;
+    zoom = d3.behavior.zoom().on("zoom", draw);
+    return this.svg.append("rect").attr("class", "pane").attr("width", this.width).attr("height", this.height).call(zoom);
+  };
 
-    return Manhattan_Plot;
+  Manhattan_Plot.prototype.draw = function() {
+    this.svg.select("g.x_axis").call(this.xAxis);
+    this.svg.select("g.y_axis").call(this.yAxis);
+    this.svg.select("path.area").attr("d", area);
+    return this.svg.select("path.line").attr("d", line);
+  };
 
-  })();
+  return Manhattan_Plot;
 
-  root.Manhattan_Plot = Manhattan_Plot;
+})();
 
-  new Manhattan_Plot(600, 1200);
+root.Manhattan_Plot = Manhattan_Plot;
 
-}).call(this);
+new Manhattan_Plot(600, 1200);
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression_old.js b/wqflask/wqflask/static/new/javascript/marker_regression_old.js
index 5dd5b508..9a618e80 100755
--- a/wqflask/wqflask/static/new/javascript/marker_regression_old.js
+++ b/wqflask/wqflask/static/new/javascript/marker_regression_old.js
@@ -1,226 +1,218 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-
-  $(function() {
-    var Chromosome, Manhattan_Plot, Permutation_Histogram, sort_number;
-    sort_number = function(a, b) {
-      return a - b;
-    };
-    Permutation_Histogram = (function() {
-
-      function Permutation_Histogram() {
-        this.process_data();
-        this.display_graph();
-      }
-
-      Permutation_Histogram.prototype.process_data = function() {
-        var bars, floored, key, keys, lrs, lrs_array, _i, _j, _len, _len1;
-        lrs_array = js_data.lrs_array;
-        bars = {};
-        for (_i = 0, _len = lrs_array.length; _i < _len; _i++) {
-          lrs = lrs_array[_i];
-          floored = Math.floor(lrs);
-          if (!(floored in bars)) {
-            bars[floored] = 0;
-          }
-          bars[floored] += 1;
-        }
-        keys = [];
-        for (key in bars) {
-          keys.push(key);
-        }
-        keys.sort(sort_number);
-        this.bars_ordered = [];
-        for (_j = 0, _len1 = keys.length; _j < _len1; _j++) {
-          key = keys[_j];
-          this.bars_ordered.push([parseInt(key), bars[key]]);
+// Generated by CoffeeScript 1.7.1
+$(function() {
+  var Chromosome, Manhattan_Plot, Permutation_Histogram, sort_number;
+  sort_number = function(a, b) {
+    return a - b;
+  };
+  Permutation_Histogram = (function() {
+    function Permutation_Histogram() {
+      this.process_data();
+      this.display_graph();
+    }
+
+    Permutation_Histogram.prototype.process_data = function() {
+      var bars, floored, key, keys, lrs, lrs_array, _i, _j, _len, _len1;
+      lrs_array = js_data.lrs_array;
+      bars = {};
+      for (_i = 0, _len = lrs_array.length; _i < _len; _i++) {
+        lrs = lrs_array[_i];
+        floored = Math.floor(lrs);
+        if (!(floored in bars)) {
+          bars[floored] = 0;
         }
-        console.log("bars is:", bars);
-        console.log("keys are:", keys);
-        return console.log("bars_ordered are:", this.bars_ordered);
-      };
-
-      Permutation_Histogram.prototype.display_graph = function() {
-        return $.jqplot('permutation_histogram', [this.bars_ordered], {
-          title: 'Permutation Histogram',
-          seriesDefaults: {
-            renderer: $.jqplot.BarRenderer,
-            rendererOptions: {
-              barWidth: 15
-            },
-            pointLabels: {
-              show: true
-            }
-          },
-          axesDefaults: {
-            labelRenderer: $.jqplot.CanvasAxisLabelRenderer
-          },
-          axes: {
-            xaxis: {
-              min: 0,
-              label: "LRS",
-              pad: 1.1
-            },
-            yaxis: {
-              min: 0,
-              label: "Frequency"
-            }
-          }
-        });
-      };
-
-      return Permutation_Histogram;
-
-    })();
-    Chromosome = (function() {
-
-      function Chromosome(name) {
-        this.name = name;
-        this.max_mb = 0;
-        this.plot_points = [];
+        bars[floored] += 1;
       }
+      keys = [];
+      for (key in bars) {
+        keys.push(key);
+      }
+      keys.sort(sort_number);
+      this.bars_ordered = [];
+      for (_j = 0, _len1 = keys.length; _j < _len1; _j++) {
+        key = keys[_j];
+        this.bars_ordered.push([parseInt(key), bars[key]]);
+      }
+      console.log("bars is:", bars);
+      console.log("keys are:", keys);
+      return console.log("bars_ordered are:", this.bars_ordered);
+    };
 
-      Chromosome.prototype.process_point = function(mb, lrs) {
-        if (mb > this.max_mb) {
-          this.max_mb = mb;
-        }
-        return this.plot_points.push([mb, lrs]);
-      };
-
-      Chromosome.prototype.display_graph = function(max_lrs) {
-        var div_name, plot_options, x_axis_max, x_axis_ticks, x_tick;
-        div_name = 'manhattan_plot_' + this.name;
-        console.log("div_name:", div_name);
-        x_axis_max = Math.ceil(this.max_mb / 25) * 25;
-        x_axis_ticks = [];
-        x_tick = 0;
-        while (x_tick <= x_axis_max) {
-          x_axis_ticks.push(x_tick);
-          x_tick += 25;
-        }
-        plot_options = {
-          title: this.name,
-          seriesDefaults: {
-            showLine: false,
-            markerRenderer: $.jqplot.MarkerRenderer,
-            markerOptions: {
-              style: "filledCircle",
-              size: 3
-            }
-          },
-          axesDefaults: {
-            tickRenderer: $.jqplot.CanvasAxisTickRenderer,
-            labelRenderer: $.jqplot.CanvasAxisLabelRenderer
+    Permutation_Histogram.prototype.display_graph = function() {
+      return $.jqplot('permutation_histogram', [this.bars_ordered], {
+        title: 'Permutation Histogram',
+        seriesDefaults: {
+          renderer: $.jqplot.BarRenderer,
+          rendererOptions: {
+            barWidth: 15
           },
-          axes: {
-            xaxis: {
-              min: 0,
-              max: x_axis_max,
-              ticks: x_axis_ticks,
-              tickOptions: {
-                angle: 90,
-                showGridline: false,
-                formatString: '%d'
-              },
-              label: "Megabases"
-            }
+          pointLabels: {
+            show: true
           }
-        };
-        if (this.name === "1") {
-          plot_options.axes.yaxis = {
+        },
+        axesDefaults: {
+          labelRenderer: $.jqplot.CanvasAxisLabelRenderer
+        },
+        axes: {
+          xaxis: {
             min: 0,
-            max: Math.floor(max_lrs + 0.1 * max_lrs),
-            tickInterval: 1,
             label: "LRS",
-            tickOptions: {
-              formatString: '%d',
-              showGridline: false
-            }
-          };
-        } else {
-          plot_options.axes.yaxis = {
-            show: false,
+            pad: 1.1
+          },
+          yaxis: {
             min: 0,
-            max: Math.floor(max_lrs + 0.1 * max_lrs),
-            tickInterval: 1,
-            tickOptions: {
-              formatString: '%d',
-              showGridline: false
-            }
-          };
+            label: "Frequency"
+          }
         }
-        return $.jqplot(div_name, [this.plot_points], plot_options);
-      };
+      });
+    };
 
-      return Chromosome;
+    return Permutation_Histogram;
 
-    })();
-    Manhattan_Plot = (function() {
+  })();
+  Chromosome = (function() {
+    function Chromosome(name) {
+      this.name = name;
+      this.max_mb = 0;
+      this.plot_points = [];
+    }
 
-      function Manhattan_Plot() {
-        this.max_lrs = 0;
-        this.chromosomes = {};
-        this.build_chromosomes();
-        this.display_graphs();
+    Chromosome.prototype.process_point = function(mb, lrs) {
+      if (mb > this.max_mb) {
+        this.max_mb = mb;
       }
+      return this.plot_points.push([mb, lrs]);
+    };
 
-      Manhattan_Plot.prototype.build_chromosomes = function() {
-        var chromosome, mb, result, _i, _len, _ref, _results;
-        _ref = js_data.qtl_results;
-        _results = [];
-        for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-          result = _ref[_i];
-          chromosome = result.locus.chromosome;
-          if (!(chromosome in this.chromosomes)) {
-            this.chromosomes[chromosome] = new Chromosome(chromosome);
+    Chromosome.prototype.display_graph = function(max_lrs) {
+      var div_name, plot_options, x_axis_max, x_axis_ticks, x_tick;
+      div_name = 'manhattan_plot_' + this.name;
+      console.log("div_name:", div_name);
+      x_axis_max = Math.ceil(this.max_mb / 25) * 25;
+      x_axis_ticks = [];
+      x_tick = 0;
+      while (x_tick <= x_axis_max) {
+        x_axis_ticks.push(x_tick);
+        x_tick += 25;
+      }
+      plot_options = {
+        title: this.name,
+        seriesDefaults: {
+          showLine: false,
+          markerRenderer: $.jqplot.MarkerRenderer,
+          markerOptions: {
+            style: "filledCircle",
+            size: 3
           }
-          mb = parseInt(result.locus.mb);
-          if (result.lrs > this.max_lrs) {
-            this.max_lrs = result.lrs;
+        },
+        axesDefaults: {
+          tickRenderer: $.jqplot.CanvasAxisTickRenderer,
+          labelRenderer: $.jqplot.CanvasAxisLabelRenderer
+        },
+        axes: {
+          xaxis: {
+            min: 0,
+            max: x_axis_max,
+            ticks: x_axis_ticks,
+            tickOptions: {
+              angle: 90,
+              showGridline: false,
+              formatString: '%d'
+            },
+            label: "Megabases"
           }
-          _results.push(this.chromosomes[chromosome].process_point(mb, result.lrs));
         }
-        return _results;
       };
-
-      Manhattan_Plot.prototype.display_graphs = function() {
-        /* Call display_graph for each chromosome
-        */
-
-        var extra_keys, html, key, keys, numbered_keys, this_class, _i, _len;
-        numbered_keys = [];
-        extra_keys = [];
-        for (key in this.chromosomes) {
-          if (isNaN(key)) {
-            extra_keys.push(key);
-          } else {
-            numbered_keys.push(key);
+      if (this.name === "1") {
+        plot_options.axes.yaxis = {
+          min: 0,
+          max: Math.floor(max_lrs + 0.1 * max_lrs),
+          tickInterval: 1,
+          label: "LRS",
+          tickOptions: {
+            formatString: '%d',
+            showGridline: false
           }
-        }
-        numbered_keys.sort(sort_number);
-        extra_keys.sort();
-        keys = numbered_keys.concat(extra_keys);
-        console.log("keys are:", keys);
-        for (_i = 0, _len = keys.length; _i < _len; _i++) {
-          key = keys[_i];
-          this_class = "manhattan_plot_segment";
-          if (key !== "1") {
-            this_class += " no_y_axis";
+        };
+      } else {
+        plot_options.axes.yaxis = {
+          show: false,
+          min: 0,
+          max: Math.floor(max_lrs + 0.1 * max_lrs),
+          tickInterval: 1,
+          tickOptions: {
+            formatString: '%d',
+            showGridline: false
           }
-          html = "<div id=\"manhattan_plot_" + key + "\" class=" + this_class + "></div>";
-          console.log("html is:", html);
-          $("#manhattan_plots").append(html);
-          this.chromosomes[key].display_graph(this.max_lrs);
+        };
+      }
+      return $.jqplot(div_name, [this.plot_points], plot_options);
+    };
+
+    return Chromosome;
+
+  })();
+  Manhattan_Plot = (function() {
+    function Manhattan_Plot() {
+      this.max_lrs = 0;
+      this.chromosomes = {};
+      this.build_chromosomes();
+      this.display_graphs();
+    }
+
+    Manhattan_Plot.prototype.build_chromosomes = function() {
+      var chromosome, mb, result, _i, _len, _ref, _results;
+      _ref = js_data.qtl_results;
+      _results = [];
+      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+        result = _ref[_i];
+        chromosome = result.locus.chromosome;
+        if (!(chromosome in this.chromosomes)) {
+          this.chromosomes[chromosome] = new Chromosome(chromosome);
         }
-        $('.jqplot-yaxis').hide();
-        return $('#manhattan_plot_1').find('.jqplot-yaxis').show();
-      };
+        mb = parseInt(result.locus.mb);
+        if (result.lrs > this.max_lrs) {
+          this.max_lrs = result.lrs;
+        }
+        _results.push(this.chromosomes[chromosome].process_point(mb, result.lrs));
+      }
+      return _results;
+    };
 
-      return Manhattan_Plot;
+    Manhattan_Plot.prototype.display_graphs = function() {
+
+      /* Call display_graph for each chromosome */
+      var extra_keys, html, key, keys, numbered_keys, this_class, _i, _len;
+      numbered_keys = [];
+      extra_keys = [];
+      for (key in this.chromosomes) {
+        if (isNaN(key)) {
+          extra_keys.push(key);
+        } else {
+          numbered_keys.push(key);
+        }
+      }
+      numbered_keys.sort(sort_number);
+      extra_keys.sort();
+      keys = numbered_keys.concat(extra_keys);
+      console.log("keys are:", keys);
+      for (_i = 0, _len = keys.length; _i < _len; _i++) {
+        key = keys[_i];
+        this_class = "manhattan_plot_segment";
+        if (key !== "1") {
+          this_class += " no_y_axis";
+        }
+        html = "<div id=\"manhattan_plot_" + key + "\" class=" + this_class + "></div>";
+        console.log("html is:", html);
+        $("#manhattan_plots").append(html);
+        this.chromosomes[key].display_graph(this.max_lrs);
+      }
+      $('.jqplot-yaxis').hide();
+      return $('#manhattan_plot_1').find('.jqplot-yaxis').show();
+    };
 
-    })();
-    new Permutation_Histogram;
-    return new Manhattan_Plot;
-  });
+    return Manhattan_Plot;
 
-}).call(this);
+  })();
+  new Permutation_Histogram;
+  return new Manhattan_Plot;
+});
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/.npmignore b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/.npmignore
deleted file mode 100755
index 21e430d2..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/.npmignore
+++ /dev/null
@@ -1,11 +0,0 @@
-*.coffee
-*.html
-.DS_Store
-.git*
-Cakefile
-documentation/
-examples/
-extras/coffee-script.js
-raw/
-src/
-test/
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/CNAME b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/CNAME
deleted file mode 100755
index faadabe5..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/CNAME
+++ /dev/null
@@ -1 +0,0 @@
-coffeescript.org
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/CONTRIBUTING.md b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/CONTRIBUTING.md
deleted file mode 100755
index 6390c68b..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/CONTRIBUTING.md
+++ /dev/null
@@ -1,9 +0,0 @@
-## How to contribute to CoffeeScript
-
-* Before you open a ticket or send a pull request, [search](https://github.com/jashkenas/coffee-script/issues) for previous discussions about the same feature or issue. Add to the earlier ticket if you find one.
-
-* Before sending a pull request for a feature, be sure to have [tests](https://github.com/jashkenas/coffee-script/tree/master/test).
-
-* Use the same coding style as the rest of the [codebase](https://github.com/jashkenas/coffee-script/tree/master/src). If you're just getting started with CoffeeScript, there's a nice [style guide](https://github.com/polarmobile/coffeescript-style-guide).
-
-* In your pull request, do not add documentation to `index.html` or re-build the minified `coffee-script.js` file. We'll do those things before cutting a new release.
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/LICENSE b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/LICENSE
deleted file mode 100755
index dbe6b4e3..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/LICENSE
+++ /dev/null
@@ -1,22 +0,0 @@
-Copyright (c) 2009-2012 Jeremy Ashkenas
-
-Permission is hereby granted, free of charge, to any person
-obtaining a copy of this software and associated documentation
-files (the "Software"), to deal in the Software without
-restriction, including without limitation the rights to use,
-copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the
-Software is furnished to do so, subject to the following
-conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-OTHER DEALINGS IN THE SOFTWARE.
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/README b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/README
deleted file mode 100755
index 69ee6f43..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/README
+++ /dev/null
@@ -1,51 +0,0 @@
-
-            {
-         }   }   {
-        {   {  }  }
-         }   }{  {
-        {  }{  }  }                    _____       __  __
-       ( }{ }{  { )                   / ____|     / _|/ _|
-     .- { { }  { }} -.               | |     ___ | |_| |_ ___  ___
-    (  ( } { } { } }  )              | |    / _ \|  _|  _/ _ \/ _ \
-    |`-..________ ..-'|              | |___| (_) | | | ||  __/  __/
-    |                 |               \_____\___/|_| |_| \___|\___|
-    |                 ;--.
-    |                (__  \            _____           _       _
-    |                 | )  )          / ____|         (_)     | |
-    |                 |/  /          | (___   ___ _ __ _ _ __ | |_
-    |                 (  /            \___ \ / __| '__| | '_ \| __|
-    |                 |/              ____) | (__| |  | | |_) | |_
-    |                 |              |_____/ \___|_|  |_| .__/ \__|
-     `-.._________..-'                                  | |
-                                                        |_|
-
-
-  CoffeeScript is a little language that compiles into JavaScript.
-
-  Install Node.js, and then the CoffeeScript compiler:
-  sudo bin/cake install
-
-  Or, if you have the Node Package Manager installed:
-  npm install -g coffee-script
-  (Leave off the -g if you don't wish to install globally.)
-
-  Execute a script:
-  coffee /path/to/script.coffee
-
-  Compile a script:
-  coffee -c /path/to/script.coffee
-
-  For documentation, usage, and examples, see:
-  http://coffeescript.org/
-
-  To suggest a feature, report a bug, or general discussion:
-  http://github.com/jashkenas/coffee-script/issues/
-
-  If you'd like to chat, drop by #coffeescript on Freenode IRC,
-  or on webchat.freenode.net.
-
-  The source repository:
-  git://github.com/jashkenas/coffee-script.git
-
-  All contributors are listed here:
-  http://github.com/jashkenas/coffee-script/contributors
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/Rakefile b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/Rakefile
deleted file mode 100755
index d90cce36..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/Rakefile
+++ /dev/null
@@ -1,79 +0,0 @@
-require 'rubygems'
-require 'erb'
-require 'fileutils'
-require 'rake/testtask'
-require 'json'
-
-desc "Build the documentation page"
-task :doc do
-  source = 'documentation/index.html.erb'
-  child = fork { exec "bin/coffee -bcw -o documentation/js documentation/coffee/*.coffee" }
-  at_exit { Process.kill("INT", child) }
-  Signal.trap("INT") { exit }
-  loop do
-    mtime = File.stat(source).mtime
-    if !@mtime || mtime > @mtime
-      rendered = ERB.new(File.read(source)).result(binding)
-      File.open('index.html', 'w+') {|f| f.write(rendered) }
-    end
-    @mtime = mtime
-    sleep 1
-  end
-end
-
-desc "Build coffee-script-source gem"
-task :gem do
-  require 'rubygems'
-  require 'rubygems/package'
-
-  gemspec = Gem::Specification.new do |s|
-    s.name      = 'coffee-script-source'
-    s.version   = JSON.parse(File.read('package.json'))["version"]
-    s.date      = Time.now.strftime("%Y-%m-%d")
-
-    s.homepage    = "http://jashkenas.github.com/coffee-script/"
-    s.summary     = "The CoffeeScript Compiler"
-    s.description = <<-EOS
-      CoffeeScript is a little language that compiles into JavaScript.
-      Underneath all of those embarrassing braces and semicolons,
-      JavaScript has always had a gorgeous object model at its heart.
-      CoffeeScript is an attempt to expose the good parts of JavaScript
-      in a simple way.
-    EOS
-
-    s.files = [
-      'lib/coffee_script/coffee-script.js',
-      'lib/coffee_script/source.rb'
-    ]
-
-    s.authors           = ['Jeremy Ashkenas']
-    s.email             = 'jashkenas@gmail.com'
-    s.rubyforge_project = 'coffee-script-source'
-    s.license           = "MIT"
-  end
-
-  file = File.open("coffee-script-source.gem", "w")
-  Gem::Package.open(file, 'w') do |pkg|
-    pkg.metadata = gemspec.to_yaml
-
-    path = "lib/coffee_script/source.rb"
-    contents = <<-ERUBY
-module CoffeeScript
-  module Source
-    def self.bundled_path
-      File.expand_path("../coffee-script.js", __FILE__)
-    end
-  end
-end
-    ERUBY
-    pkg.add_file_simple(path, 0644, contents.size) do |tar_io|
-      tar_io.write(contents)
-    end
-
-    contents = File.read("extras/coffee-script.js")
-    path = "lib/coffee_script/coffee-script.js"
-    pkg.add_file_simple(path, 0644, contents.size) do |tar_io|
-      tar_io.write(contents)
-    end
-  end
-end
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/bin/cake b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/bin/cake
deleted file mode 100755
index 5965f4ee..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/bin/cake
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/usr/bin/env node
-
-var path = require('path');
-var fs   = require('fs');
-var lib  = path.join(path.dirname(fs.realpathSync(__filename)), '../lib');
-
-require(lib + '/coffee-script/cake').run();
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/bin/coffee b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/bin/coffee
deleted file mode 100755
index 3d1d71c8..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/bin/coffee
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/usr/bin/env node
-
-var path = require('path');
-var fs   = require('fs');
-var lib  = path.join(path.dirname(fs.realpathSync(__filename)), '../lib');
-
-require(lib + '/coffee-script/command').run();
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/extras/jsl.conf b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/extras/jsl.conf
deleted file mode 100755
index 1190da52..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/extras/jsl.conf
+++ /dev/null
@@ -1,44 +0,0 @@
-# JavaScriptLint configuration file for CoffeeScript.
-
-+no_return_value              # function {0} does not always return a value
-+duplicate_formal             # duplicate formal argument {0}
--equal_as_assign              # test for equality (==) mistyped as assignment (=)?{0}
-+var_hides_arg                # variable {0} hides argument
-+redeclared_var               # redeclaration of {0} {1}
--anon_no_return_value         # anonymous function does not always return a value
-+missing_semicolon            # missing semicolon
-+meaningless_block            # meaningless block; curly braces have no impact
--comma_separated_stmts        # multiple statements separated by commas (use semicolons?)
-+unreachable_code             # unreachable code
-+missing_break                # missing break statement
--missing_break_for_last_case  # missing break statement for last case in switch
--comparison_type_conv         # comparisons against null, 0, true, false, or an empty string allowing implicit type conversion (use === or !==)
--inc_dec_within_stmt          # increment (++) and decrement (--) operators used as part of greater statement
--useless_void                 # use of the void type may be unnecessary (void is always undefined)
-+multiple_plus_minus          # unknown order of operations for successive plus (e.g. x+++y) or minus (e.g. x---y) signs
-+use_of_label                 # use of label
--block_without_braces         # block statement without curly braces
-+leading_decimal_point        # leading decimal point may indicate a number or an object member
-+trailing_decimal_point       # trailing decimal point may indicate a number or an object member
-+octal_number                 # leading zeros make an octal number
-+nested_comment               # nested comment
-+misplaced_regex              # regular expressions should be preceded by a left parenthesis, assignment, colon, or comma
-+ambiguous_newline            # unexpected end of line; it is ambiguous whether these lines are part of the same statement
-+empty_statement              # empty statement or extra semicolon
--missing_option_explicit      # the "option explicit" control comment is missing
-+partial_option_explicit      # the "option explicit" control comment, if used, must be in the first script tag
-+dup_option_explicit          # duplicate "option explicit" control comment
-+useless_assign               # useless assignment
-+ambiguous_nested_stmt        # block statements containing block statements should use curly braces to resolve ambiguity
-+ambiguous_else_stmt          # the else statement could be matched with one of multiple if statements (use curly braces to indicate intent)
--missing_default_case         # missing default case in switch statement
-+duplicate_case_in_switch     # duplicate case in switch statements
-+default_not_at_end           # the default case is not at the end of the switch statement
-+legacy_cc_not_understood     # couldn't understand control comment using /*@keyword@*/ syntax
-+jsl_cc_not_understood        # couldn't understand control comment using /*jsl:keyword*/ syntax
-+useless_comparison           # useless comparison; comparing identical expressions
-+with_statement               # with statement hides undeclared variables; use temporary variable instead
-+trailing_comma_in_array      # extra comma is not recommended in array initializers
-+assign_to_function_call      # assignment to a function call
-+parseint_missing_radix       # parseInt missing radix parameter
-+lambda_assign_requires_semicolon
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/browser.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/browser.js
deleted file mode 100755
index fec8e690..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/browser.js
+++ /dev/null
@@ -1,101 +0,0 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var CoffeeScript, runScripts,
-    __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; };
-
-  CoffeeScript = require('./coffee-script');
-
-  CoffeeScript.require = require;
-
-  CoffeeScript["eval"] = function(code, options) {
-    var _ref;
-    if (options == null) {
-      options = {};
-    }
-    if ((_ref = options.bare) == null) {
-      options.bare = true;
-    }
-    return eval(CoffeeScript.compile(code, options));
-  };
-
-  CoffeeScript.run = function(code, options) {
-    if (options == null) {
-      options = {};
-    }
-    options.bare = true;
-    return Function(CoffeeScript.compile(code, options))();
-  };
-
-  if (typeof window === "undefined" || window === null) {
-    return;
-  }
-
-  CoffeeScript.load = function(url, callback, options) {
-    var xhr;
-    if (options == null) {
-      options = {};
-    }
-    xhr = window.ActiveXObject ? new window.ActiveXObject('Microsoft.XMLHTTP') : new XMLHttpRequest();
-    xhr.open('GET', url, true);
-    if ('overrideMimeType' in xhr) {
-      xhr.overrideMimeType('text/plain');
-    }
-    xhr.onreadystatechange = function() {
-      var _ref;
-      if (xhr.readyState === 4) {
-        if ((_ref = xhr.status) === 0 || _ref === 200) {
-          CoffeeScript.run(xhr.responseText, options);
-        } else {
-          throw new Error("Could not load " + url);
-        }
-        if (callback) {
-          return callback();
-        }
-      }
-    };
-    return xhr.send(null);
-  };
-
-  runScripts = function() {
-    var coffees, coffeetypes, execute, index, length, s, scripts;
-    scripts = document.getElementsByTagName('script');
-    coffeetypes = ['text/coffeescript', 'text/literate-coffeescript'];
-    coffees = (function() {
-      var _i, _len, _ref, _results;
-      _results = [];
-      for (_i = 0, _len = scripts.length; _i < _len; _i++) {
-        s = scripts[_i];
-        if (_ref = s.type, __indexOf.call(coffeetypes, _ref) >= 0) {
-          _results.push(s);
-        }
-      }
-      return _results;
-    })();
-    index = 0;
-    length = coffees.length;
-    (execute = function() {
-      var mediatype, options, script;
-      script = coffees[index++];
-      mediatype = script != null ? script.type : void 0;
-      if (__indexOf.call(coffeetypes, mediatype) >= 0) {
-        options = {
-          literate: mediatype === 'text/literate-coffeescript'
-        };
-        if (script.src) {
-          return CoffeeScript.load(script.src, execute, options);
-        } else {
-          CoffeeScript.run(script.innerHTML, options);
-          return execute();
-        }
-      }
-    })();
-    return null;
-  };
-
-  if (window.addEventListener) {
-    addEventListener('DOMContentLoaded', runScripts, false);
-  } else {
-    attachEvent('onload', runScripts);
-  }
-
-}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/cake.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/cake.js
deleted file mode 100755
index a0b643f6..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/cake.js
+++ /dev/null
@@ -1,113 +0,0 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var CoffeeScript, cakefileDirectory, existsSync, fatalError, fs, helpers, missingTask, oparse, options, optparse, path, printTasks, switches, tasks;
-
-  fs = require('fs');
-
-  path = require('path');
-
-  helpers = require('./helpers');
-
-  optparse = require('./optparse');
-
-  CoffeeScript = require('./coffee-script');
-
-  existsSync = fs.existsSync || path.existsSync;
-
-  tasks = {};
-
-  options = {};
-
-  switches = [];
-
-  oparse = null;
-
-  helpers.extend(global, {
-    task: function(name, description, action) {
-      var _ref;
-      if (!action) {
-        _ref = [description, action], action = _ref[0], description = _ref[1];
-      }
-      return tasks[name] = {
-        name: name,
-        description: description,
-        action: action
-      };
-    },
-    option: function(letter, flag, description) {
-      return switches.push([letter, flag, description]);
-    },
-    invoke: function(name) {
-      if (!tasks[name]) {
-        missingTask(name);
-      }
-      return tasks[name].action(options);
-    }
-  });
-
-  exports.run = function() {
-    var arg, args, _i, _len, _ref, _results;
-    global.__originalDirname = fs.realpathSync('.');
-    process.chdir(cakefileDirectory(__originalDirname));
-    args = process.argv.slice(2);
-    CoffeeScript.run(fs.readFileSync('Cakefile').toString(), {
-      filename: 'Cakefile'
-    });
-    oparse = new optparse.OptionParser(switches);
-    if (!args.length) {
-      return printTasks();
-    }
-    try {
-      options = oparse.parse(args);
-    } catch (e) {
-      return fatalError("" + e);
-    }
-    _ref = options["arguments"];
-    _results = [];
-    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-      arg = _ref[_i];
-      _results.push(invoke(arg));
-    }
-    return _results;
-  };
-
-  printTasks = function() {
-    var cakefilePath, desc, name, relative, spaces, task;
-    relative = path.relative || path.resolve;
-    cakefilePath = path.join(relative(__originalDirname, process.cwd()), 'Cakefile');
-    console.log("" + cakefilePath + " defines the following tasks:\n");
-    for (name in tasks) {
-      task = tasks[name];
-      spaces = 20 - name.length;
-      spaces = spaces > 0 ? Array(spaces + 1).join(' ') : '';
-      desc = task.description ? "# " + task.description : '';
-      console.log("cake " + name + spaces + " " + desc);
-    }
-    if (switches.length) {
-      return console.log(oparse.help());
-    }
-  };
-
-  fatalError = function(message) {
-    console.error(message + '\n');
-    console.log('To see a list of all tasks/options, run "cake"');
-    return process.exit(1);
-  };
-
-  missingTask = function(task) {
-    return fatalError("No such task: " + task);
-  };
-
-  cakefileDirectory = function(dir) {
-    var parent;
-    if (existsSync(path.join(dir, 'Cakefile'))) {
-      return dir;
-    }
-    parent = path.normalize(path.join(dir, '..'));
-    if (parent !== dir) {
-      return cakefileDirectory(parent);
-    }
-    throw new Error("Cakefile not found in " + (process.cwd()));
-  };
-
-}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/coffee-script.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/coffee-script.js
deleted file mode 100755
index d791035d..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/coffee-script.js
+++ /dev/null
@@ -1,218 +0,0 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var Lexer, compile, ext, fs, helpers, lexer, loadFile, parser, path, sourcemap, vm, _i, _len, _ref,
-    __hasProp = {}.hasOwnProperty;
-
-  fs = require('fs');
-
-  path = require('path');
-
-  Lexer = require('./lexer').Lexer;
-
-  parser = require('./parser').parser;
-
-  helpers = require('./helpers');
-
-  vm = require('vm');
-
-  sourcemap = require('./sourcemap');
-
-  loadFile = function(module, filename) {
-    var raw, stripped;
-    raw = fs.readFileSync(filename, 'utf8');
-    stripped = raw.charCodeAt(0) === 0xFEFF ? raw.substring(1) : raw;
-    return module._compile(compile(stripped, {
-      filename: filename,
-      literate: helpers.isLiterate(filename)
-    }), filename);
-  };
-
-  if (require.extensions) {
-    _ref = ['.coffee', '.litcoffee', '.md', '.coffee.md'];
-    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-      ext = _ref[_i];
-      require.extensions[ext] = loadFile;
-    }
-  }
-
-  exports.VERSION = '1.6.1';
-
-  exports.helpers = helpers;
-
-  exports.compile = compile = function(code, options) {
-    var answer, coffeeFile, currentColumn, currentLine, fragment, fragments, header, js, jsFile, merge, newLines, sourceMap, _j, _len1;
-    if (options == null) {
-      options = {};
-    }
-    merge = exports.helpers.merge;
-    try {
-      if (options.sourceMap) {
-        coffeeFile = helpers.baseFileName(options.filename);
-        jsFile = helpers.baseFileName(options.filename, true) + ".js";
-        sourceMap = new sourcemap.SourceMap();
-      }
-      fragments = (parser.parse(lexer.tokenize(code, options))).compileToFragments(options);
-      currentLine = 0;
-      if (options.header) {
-        currentLine += 1;
-      }
-      if (options.sourceMap) {
-        currentLine += 1;
-      }
-      currentColumn = 0;
-      js = "";
-      for (_j = 0, _len1 = fragments.length; _j < _len1; _j++) {
-        fragment = fragments[_j];
-        if (sourceMap) {
-          if (fragment.locationData) {
-            sourceMap.addMapping([fragment.locationData.first_line, fragment.locationData.first_column], [currentLine, currentColumn], {
-              noReplace: true
-            });
-          }
-          newLines = helpers.count(fragment.code, "\n");
-          currentLine += newLines;
-          currentColumn = fragment.code.length - (newLines ? fragment.code.lastIndexOf("\n") : 0);
-        }
-        js += fragment.code;
-      }
-    } catch (err) {
-      if (options.filename) {
-        err.message = "In " + options.filename + ", " + err.message;
-      }
-      throw err;
-    }
-    if (options.header) {
-      header = "Generated by CoffeeScript " + this.VERSION;
-      js = "// " + header + "\n" + js;
-    }
-    if (options.sourceMap) {
-      answer = {
-        js: js
-      };
-      if (sourceMap) {
-        answer.sourceMap = sourceMap;
-        answer.v3SourceMap = sourcemap.generateV3SourceMap(sourceMap, coffeeFile, jsFile);
-      }
-      return answer;
-    } else {
-      return js;
-    }
-  };
-
-  exports.tokens = function(code, options) {
-    return lexer.tokenize(code, options);
-  };
-
-  exports.nodes = function(source, options) {
-    if (typeof source === 'string') {
-      return parser.parse(lexer.tokenize(source, options));
-    } else {
-      return parser.parse(source);
-    }
-  };
-
-  exports.run = function(code, options) {
-    var mainModule;
-    if (options == null) {
-      options = {};
-    }
-    mainModule = require.main;
-    mainModule.filename = process.argv[1] = options.filename ? fs.realpathSync(options.filename) : '.';
-    mainModule.moduleCache && (mainModule.moduleCache = {});
-    mainModule.paths = require('module')._nodeModulePaths(path.dirname(fs.realpathSync(options.filename)));
-    if (!helpers.isCoffee(mainModule.filename) || require.extensions) {
-      return mainModule._compile(compile(code, options), mainModule.filename);
-    } else {
-      return mainModule._compile(code, mainModule.filename);
-    }
-  };
-
-  exports["eval"] = function(code, options) {
-    var Module, Script, js, k, o, r, sandbox, v, _j, _len1, _module, _ref1, _ref2, _require;
-    if (options == null) {
-      options = {};
-    }
-    if (!(code = code.trim())) {
-      return;
-    }
-    Script = vm.Script;
-    if (Script) {
-      if (options.sandbox != null) {
-        if (options.sandbox instanceof Script.createContext().constructor) {
-          sandbox = options.sandbox;
-        } else {
-          sandbox = Script.createContext();
-          _ref1 = options.sandbox;
-          for (k in _ref1) {
-            if (!__hasProp.call(_ref1, k)) continue;
-            v = _ref1[k];
-            sandbox[k] = v;
-          }
-        }
-        sandbox.global = sandbox.root = sandbox.GLOBAL = sandbox;
-      } else {
-        sandbox = global;
-      }
-      sandbox.__filename = options.filename || 'eval';
-      sandbox.__dirname = path.dirname(sandbox.__filename);
-      if (!(sandbox !== global || sandbox.module || sandbox.require)) {
-        Module = require('module');
-        sandbox.module = _module = new Module(options.modulename || 'eval');
-        sandbox.require = _require = function(path) {
-          return Module._load(path, _module, true);
-        };
-        _module.filename = sandbox.__filename;
-        _ref2 = Object.getOwnPropertyNames(require);
-        for (_j = 0, _len1 = _ref2.length; _j < _len1; _j++) {
-          r = _ref2[_j];
-          if (r !== 'paths') {
-            _require[r] = require[r];
-          }
-        }
-        _require.paths = _module.paths = Module._nodeModulePaths(process.cwd());
-        _require.resolve = function(request) {
-          return Module._resolveFilename(request, _module);
-        };
-      }
-    }
-    o = {};
-    for (k in options) {
-      if (!__hasProp.call(options, k)) continue;
-      v = options[k];
-      o[k] = v;
-    }
-    o.bare = true;
-    js = compile(code, o);
-    if (sandbox === global) {
-      return vm.runInThisContext(js);
-    } else {
-      return vm.runInContext(js, sandbox);
-    }
-  };
-
-  lexer = new Lexer;
-
-  parser.lexer = {
-    lex: function() {
-      var tag, token;
-      token = this.tokens[this.pos++];
-      if (token) {
-        tag = token[0], this.yytext = token[1], this.yylloc = token[2];
-        this.yylineno = this.yylloc.first_line;
-      } else {
-        tag = '';
-      }
-      return tag;
-    },
-    setInput: function(tokens) {
-      this.tokens = tokens;
-      return this.pos = 0;
-    },
-    upcomingInput: function() {
-      return "";
-    }
-  };
-
-  parser.yy = require('./nodes');
-
-}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/command.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/command.js
deleted file mode 100755
index 4077577e..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/command.js
+++ /dev/null
@@ -1,506 +0,0 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var BANNER, CoffeeScript, EventEmitter, SWITCHES, compileJoin, compileOptions, compilePath, compileScript, compileStdio, exec, exists, forkNode, fs, helpers, hidden, joinTimeout, lint, notSources, optionParser, optparse, opts, outputPath, parseOptions, path, printLine, printTokens, printWarn, removeSource, sourceCode, sources, spawn, timeLog, unwatchDir, usage, version, wait, watch, watchDir, watchers, writeJs, _ref;
-
-  fs = require('fs');
-
-  path = require('path');
-
-  helpers = require('./helpers');
-
-  optparse = require('./optparse');
-
-  CoffeeScript = require('./coffee-script');
-
-  _ref = require('child_process'), spawn = _ref.spawn, exec = _ref.exec;
-
-  EventEmitter = require('events').EventEmitter;
-
-  exists = fs.exists || path.exists;
-
-  helpers.extend(CoffeeScript, new EventEmitter);
-
-  printLine = function(line) {
-    return process.stdout.write(line + '\n');
-  };
-
-  printWarn = function(line) {
-    return process.stderr.write(line + '\n');
-  };
-
-  hidden = function(file) {
-    return /^\.|~$/.test(file);
-  };
-
-  BANNER = 'Usage: coffee [options] path/to/script.coffee -- [args]\n\nIf called without options, `coffee` will run your script.';
-
-  SWITCHES = [['-b', '--bare', 'compile without a top-level function wrapper'], ['-c', '--compile', 'compile to JavaScript and save as .js files'], ['-e', '--eval', 'pass a string from the command line as input'], ['-h', '--help', 'display this help message'], ['-i', '--interactive', 'run an interactive CoffeeScript REPL'], ['-j', '--join [FILE]', 'concatenate the source CoffeeScript before compiling'], ['-l', '--lint', 'pipe the compiled JavaScript through JavaScript Lint'], ['-m', '--map', 'generate source map and save as .map files'], ['-n', '--nodes', 'print out the parse tree that the parser produces'], ['--nodejs [ARGS]', 'pass options directly to the "node" binary'], ['-o', '--output [DIR]', 'set the output directory for compiled JavaScript'], ['-p', '--print', 'print out the compiled JavaScript'], ['-s', '--stdio', 'listen for and compile scripts over stdio'], ['-t', '--tokens', 'print out the tokens that the lexer/rewriter produce'], ['-v', '--version', 'display the version number'], ['-w', '--watch', 'watch scripts for changes and rerun commands']];
-
-  opts = {};
-
-  sources = [];
-
-  sourceCode = [];
-
-  notSources = {};
-
-  watchers = {};
-
-  optionParser = null;
-
-  exports.run = function() {
-    var literals, source, _i, _len, _results;
-    parseOptions();
-    if (opts.nodejs) {
-      return forkNode();
-    }
-    if (opts.help) {
-      return usage();
-    }
-    if (opts.version) {
-      return version();
-    }
-    if (opts.interactive) {
-      return require('./repl').start();
-    }
-    if (opts.watch && !fs.watch) {
-      return printWarn("The --watch feature depends on Node v0.6.0+. You are running " + process.version + ".");
-    }
-    if (opts.stdio) {
-      return compileStdio();
-    }
-    if (opts["eval"]) {
-      return compileScript(null, sources[0]);
-    }
-    if (!sources.length) {
-      return require('./repl').start();
-    }
-    literals = opts.run ? sources.splice(1) : [];
-    process.argv = process.argv.slice(0, 2).concat(literals);
-    process.argv[0] = 'coffee';
-    _results = [];
-    for (_i = 0, _len = sources.length; _i < _len; _i++) {
-      source = sources[_i];
-      _results.push(compilePath(source, true, path.normalize(source)));
-    }
-    return _results;
-  };
-
-  compilePath = function(source, topLevel, base) {
-    return fs.stat(source, function(err, stats) {
-      if (err && err.code !== 'ENOENT') {
-        throw err;
-      }
-      if ((err != null ? err.code : void 0) === 'ENOENT') {
-        console.error("File not found: " + source);
-        process.exit(1);
-      }
-      if (stats.isDirectory() && path.dirname(source) !== 'node_modules') {
-        if (opts.watch) {
-          watchDir(source, base);
-        }
-        return fs.readdir(source, function(err, files) {
-          var file, index, _ref1, _ref2;
-          if (err && err.code !== 'ENOENT') {
-            throw err;
-          }
-          if ((err != null ? err.code : void 0) === 'ENOENT') {
-            return;
-          }
-          index = sources.indexOf(source);
-          files = files.filter(function(file) {
-            return !hidden(file);
-          });
-          [].splice.apply(sources, [index, index - index + 1].concat(_ref1 = (function() {
-            var _i, _len, _results;
-            _results = [];
-            for (_i = 0, _len = files.length; _i < _len; _i++) {
-              file = files[_i];
-              _results.push(path.join(source, file));
-            }
-            return _results;
-          })())), _ref1;
-          [].splice.apply(sourceCode, [index, index - index + 1].concat(_ref2 = files.map(function() {
-            return null;
-          }))), _ref2;
-          return files.forEach(function(file) {
-            return compilePath(path.join(source, file), false, base);
-          });
-        });
-      } else if (topLevel || helpers.isCoffee(source)) {
-        if (opts.watch) {
-          watch(source, base);
-        }
-        return fs.readFile(source, function(err, code) {
-          if (err && err.code !== 'ENOENT') {
-            throw err;
-          }
-          if ((err != null ? err.code : void 0) === 'ENOENT') {
-            return;
-          }
-          return compileScript(source, code.toString(), base);
-        });
-      } else {
-        notSources[source] = true;
-        return removeSource(source, base);
-      }
-    });
-  };
-
-  compileScript = function(file, input, base) {
-    var compiled, o, options, t, task;
-    o = opts;
-    options = compileOptions(file);
-    try {
-      t = task = {
-        file: file,
-        input: input,
-        options: options
-      };
-      CoffeeScript.emit('compile', task);
-      if (o.tokens) {
-        return printTokens(CoffeeScript.tokens(t.input, t.options));
-      } else if (o.nodes) {
-        return printLine(CoffeeScript.nodes(t.input, t.options).toString().trim());
-      } else if (o.run) {
-        return CoffeeScript.run(t.input, t.options);
-      } else if (o.join && t.file !== o.join) {
-        sourceCode[sources.indexOf(t.file)] = t.input;
-        return compileJoin();
-      } else {
-        compiled = CoffeeScript.compile(t.input, t.options);
-        t.output = compiled;
-        if (o.map) {
-          t.output = compiled.js;
-          t.sourceMap = compiled.v3SourceMap;
-        }
-        CoffeeScript.emit('success', task);
-        if (o.print) {
-          return printLine(t.output.trim());
-        } else if (o.compile || o.map) {
-          return writeJs(base, t.file, t.output, t.sourceMap);
-        } else if (o.lint) {
-          return lint(t.file, t.output);
-        }
-      }
-    } catch (err) {
-      CoffeeScript.emit('failure', err, task);
-      if (CoffeeScript.listeners('failure').length) {
-        return;
-      }
-      if (o.watch) {
-        return printLine(err.message + '\x07');
-      }
-      printWarn(err instanceof Error && err.stack || ("ERROR: " + err));
-      return process.exit(1);
-    }
-  };
-
-  compileStdio = function() {
-    var code, stdin;
-    code = '';
-    stdin = process.openStdin();
-    stdin.on('data', function(buffer) {
-      if (buffer) {
-        return code += buffer.toString();
-      }
-    });
-    return stdin.on('end', function() {
-      return compileScript(null, code);
-    });
-  };
-
-  joinTimeout = null;
-
-  compileJoin = function() {
-    if (!opts.join) {
-      return;
-    }
-    if (!sourceCode.some(function(code) {
-      return code === null;
-    })) {
-      clearTimeout(joinTimeout);
-      return joinTimeout = wait(100, function() {
-        return compileScript(opts.join, sourceCode.join('\n'), opts.join);
-      });
-    }
-  };
-
-  watch = function(source, base) {
-    var compile, compileTimeout, prevStats, rewatch, watchErr, watcher;
-    prevStats = null;
-    compileTimeout = null;
-    watchErr = function(e) {
-      if (e.code === 'ENOENT') {
-        if (sources.indexOf(source) === -1) {
-          return;
-        }
-        try {
-          rewatch();
-          return compile();
-        } catch (e) {
-          removeSource(source, base, true);
-          return compileJoin();
-        }
-      } else {
-        throw e;
-      }
-    };
-    compile = function() {
-      clearTimeout(compileTimeout);
-      return compileTimeout = wait(25, function() {
-        return fs.stat(source, function(err, stats) {
-          if (err) {
-            return watchErr(err);
-          }
-          if (prevStats && stats.size === prevStats.size && stats.mtime.getTime() === prevStats.mtime.getTime()) {
-            return rewatch();
-          }
-          prevStats = stats;
-          return fs.readFile(source, function(err, code) {
-            if (err) {
-              return watchErr(err);
-            }
-            compileScript(source, code.toString(), base);
-            return rewatch();
-          });
-        });
-      });
-    };
-    try {
-      watcher = fs.watch(source, compile);
-    } catch (e) {
-      watchErr(e);
-    }
-    return rewatch = function() {
-      if (watcher != null) {
-        watcher.close();
-      }
-      return watcher = fs.watch(source, compile);
-    };
-  };
-
-  watchDir = function(source, base) {
-    var readdirTimeout, watcher;
-    readdirTimeout = null;
-    try {
-      return watcher = fs.watch(source, function() {
-        clearTimeout(readdirTimeout);
-        return readdirTimeout = wait(25, function() {
-          return fs.readdir(source, function(err, files) {
-            var file, _i, _len, _results;
-            if (err) {
-              if (err.code !== 'ENOENT') {
-                throw err;
-              }
-              watcher.close();
-              return unwatchDir(source, base);
-            }
-            _results = [];
-            for (_i = 0, _len = files.length; _i < _len; _i++) {
-              file = files[_i];
-              if (!(!hidden(file) && !notSources[file])) {
-                continue;
-              }
-              file = path.join(source, file);
-              if (sources.some(function(s) {
-                return s.indexOf(file) >= 0;
-              })) {
-                continue;
-              }
-              sources.push(file);
-              sourceCode.push(null);
-              _results.push(compilePath(file, false, base));
-            }
-            return _results;
-          });
-        });
-      });
-    } catch (e) {
-      if (e.code !== 'ENOENT') {
-        throw e;
-      }
-    }
-  };
-
-  unwatchDir = function(source, base) {
-    var file, prevSources, toRemove, _i, _len;
-    prevSources = sources.slice(0);
-    toRemove = (function() {
-      var _i, _len, _results;
-      _results = [];
-      for (_i = 0, _len = sources.length; _i < _len; _i++) {
-        file = sources[_i];
-        if (file.indexOf(source) >= 0) {
-          _results.push(file);
-        }
-      }
-      return _results;
-    })();
-    for (_i = 0, _len = toRemove.length; _i < _len; _i++) {
-      file = toRemove[_i];
-      removeSource(file, base, true);
-    }
-    if (!sources.some(function(s, i) {
-      return prevSources[i] !== s;
-    })) {
-      return;
-    }
-    return compileJoin();
-  };
-
-  removeSource = function(source, base, removeJs) {
-    var index, jsPath;
-    index = sources.indexOf(source);
-    sources.splice(index, 1);
-    sourceCode.splice(index, 1);
-    if (removeJs && !opts.join) {
-      jsPath = outputPath(source, base);
-      return exists(jsPath, function(itExists) {
-        if (itExists) {
-          return fs.unlink(jsPath, function(err) {
-            if (err && err.code !== 'ENOENT') {
-              throw err;
-            }
-            return timeLog("removed " + source);
-          });
-        }
-      });
-    }
-  };
-
-  outputPath = function(source, base, extension) {
-    var baseDir, basename, dir, srcDir;
-    if (extension == null) {
-      extension = ".js";
-    }
-    basename = helpers.baseFileName(source, true);
-    srcDir = path.dirname(source);
-    baseDir = base === '.' ? srcDir : srcDir.substring(base.length);
-    dir = opts.output ? path.join(opts.output, baseDir) : srcDir;
-    return path.join(dir, basename + extension);
-  };
-
-  writeJs = function(base, sourcePath, js, generatedSourceMap) {
-    var compile, jsDir, jsPath, sourceMapPath;
-    if (generatedSourceMap == null) {
-      generatedSourceMap = null;
-    }
-    jsPath = outputPath(sourcePath, base);
-    sourceMapPath = outputPath(sourcePath, base, ".map");
-    jsDir = path.dirname(jsPath);
-    compile = function() {
-      if (opts.compile) {
-        if (js.length <= 0) {
-          js = ' ';
-        }
-        if (generatedSourceMap) {
-          js = "//@ sourceMappingURL=" + (helpers.baseFileName(sourceMapPath)) + "\n" + js;
-        }
-        fs.writeFile(jsPath, js, function(err) {
-          if (err) {
-            return printLine(err.message);
-          } else if (opts.compile && opts.watch) {
-            return timeLog("compiled " + sourcePath);
-          }
-        });
-      }
-      if (generatedSourceMap) {
-        return fs.writeFile(sourceMapPath, generatedSourceMap, function(err) {
-          if (err) {
-            return printLine("Could not write source map: " + err.message);
-          }
-        });
-      }
-    };
-    return exists(jsDir, function(itExists) {
-      if (itExists) {
-        return compile();
-      } else {
-        return exec("mkdir -p " + jsDir, compile);
-      }
-    });
-  };
-
-  wait = function(milliseconds, func) {
-    return setTimeout(func, milliseconds);
-  };
-
-  timeLog = function(message) {
-    return console.log("" + ((new Date).toLocaleTimeString()) + " - " + message);
-  };
-
-  lint = function(file, js) {
-    var conf, jsl, printIt;
-    printIt = function(buffer) {
-      return printLine(file + ':\t' + buffer.toString().trim());
-    };
-    conf = __dirname + '/../../extras/jsl.conf';
-    jsl = spawn('jsl', ['-nologo', '-stdin', '-conf', conf]);
-    jsl.stdout.on('data', printIt);
-    jsl.stderr.on('data', printIt);
-    jsl.stdin.write(js);
-    return jsl.stdin.end();
-  };
-
-  printTokens = function(tokens) {
-    var strings, tag, token, value;
-    strings = (function() {
-      var _i, _len, _results;
-      _results = [];
-      for (_i = 0, _len = tokens.length; _i < _len; _i++) {
-        token = tokens[_i];
-        tag = token[0];
-        value = token[1].toString().replace(/\n/, '\\n');
-        _results.push("[" + tag + " " + value + "]");
-      }
-      return _results;
-    })();
-    return printLine(strings.join(' '));
-  };
-
-  parseOptions = function() {
-    var i, o, source, _i, _len;
-    optionParser = new optparse.OptionParser(SWITCHES, BANNER);
-    o = opts = optionParser.parse(process.argv.slice(2));
-    o.compile || (o.compile = !!o.output);
-    o.run = !(o.compile || o.print || o.lint || o.map);
-    o.print = !!(o.print || (o["eval"] || o.stdio && o.compile));
-    sources = o["arguments"];
-    for (i = _i = 0, _len = sources.length; _i < _len; i = ++_i) {
-      source = sources[i];
-      sourceCode[i] = null;
-    }
-  };
-
-  compileOptions = function(filename) {
-    return {
-      filename: filename,
-      literate: helpers.isLiterate(filename),
-      bare: opts.bare,
-      header: opts.compile,
-      sourceMap: opts.map
-    };
-  };
-
-  forkNode = function() {
-    var args, nodeArgs;
-    nodeArgs = opts.nodejs.split(/\s+/);
-    args = process.argv.slice(1);
-    args.splice(args.indexOf('--nodejs'), 2);
-    return spawn(process.execPath, nodeArgs.concat(args), {
-      cwd: process.cwd(),
-      env: process.env,
-      customFds: [0, 1, 2]
-    });
-  };
-
-  usage = function() {
-    return printLine((new optparse.OptionParser(SWITCHES, BANNER)).help());
-  };
-
-  version = function() {
-    return printLine("CoffeeScript version " + CoffeeScript.VERSION);
-  };
-
-}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/grammar.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/grammar.js
deleted file mode 100755
index 4a767433..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/grammar.js
+++ /dev/null
@@ -1,623 +0,0 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var Parser, alt, alternatives, grammar, name, o, operators, token, tokens, unwrap;
-
-  Parser = require('jison').Parser;
-
-  unwrap = /^function\s*\(\)\s*\{\s*return\s*([\s\S]*);\s*\}/;
-
-  o = function(patternString, action, options) {
-    var addLocationDataFn, match, patternCount;
-    patternString = patternString.replace(/\s{2,}/g, ' ');
-    patternCount = patternString.split(' ').length;
-    if (!action) {
-      return [patternString, '$$ = $1;', options];
-    }
-    action = (match = unwrap.exec(action)) ? match[1] : "(" + action + "())";
-    action = action.replace(/\bnew /g, '$&yy.');
-    action = action.replace(/\b(?:Block\.wrap|extend)\b/g, 'yy.$&');
-    addLocationDataFn = function(first, last) {
-      if (!last) {
-        return "yy.addLocationDataFn(@" + first + ")";
-      } else {
-        return "yy.addLocationDataFn(@" + first + ", @" + last + ")";
-      }
-    };
-    action = action.replace(/LOC\(([0-9]*)\)/g, addLocationDataFn('$1'));
-    action = action.replace(/LOC\(([0-9]*),\s*([0-9]*)\)/g, addLocationDataFn('$1', '$2'));
-    return [patternString, "$$ = " + (addLocationDataFn(1, patternCount)) + "(" + action + ");", options];
-  };
-
-  grammar = {
-    Root: [
-      o('', function() {
-        return new Block;
-      }), o('Body'), o('Block TERMINATOR')
-    ],
-    Body: [
-      o('Line', function() {
-        return Block.wrap([$1]);
-      }), o('Body TERMINATOR Line', function() {
-        return $1.push($3);
-      }), o('Body TERMINATOR')
-    ],
-    Line: [o('Expression'), o('Statement')],
-    Statement: [
-      o('Return'), o('Comment'), o('STATEMENT', function() {
-        return new Literal($1);
-      })
-    ],
-    Expression: [o('Value'), o('Invocation'), o('Code'), o('Operation'), o('Assign'), o('If'), o('Try'), o('While'), o('For'), o('Switch'), o('Class'), o('Throw')],
-    Block: [
-      o('INDENT OUTDENT', function() {
-        return new Block;
-      }), o('INDENT Body OUTDENT', function() {
-        return $2;
-      })
-    ],
-    Identifier: [
-      o('IDENTIFIER', function() {
-        return new Literal($1);
-      })
-    ],
-    AlphaNumeric: [
-      o('NUMBER', function() {
-        return new Literal($1);
-      }), o('STRING', function() {
-        return new Literal($1);
-      })
-    ],
-    Literal: [
-      o('AlphaNumeric'), o('JS', function() {
-        return new Literal($1);
-      }), o('REGEX', function() {
-        return new Literal($1);
-      }), o('DEBUGGER', function() {
-        return new Literal($1);
-      }), o('UNDEFINED', function() {
-        return new Undefined;
-      }), o('NULL', function() {
-        return new Null;
-      }), o('BOOL', function() {
-        return new Bool($1);
-      })
-    ],
-    Assign: [
-      o('Assignable = Expression', function() {
-        return new Assign($1, $3);
-      }), o('Assignable = TERMINATOR Expression', function() {
-        return new Assign($1, $4);
-      }), o('Assignable = INDENT Expression OUTDENT', function() {
-        return new Assign($1, $4);
-      })
-    ],
-    AssignObj: [
-      o('ObjAssignable', function() {
-        return new Value($1);
-      }), o('ObjAssignable : Expression', function() {
-        return new Assign(LOC(1)(new Value($1)), $3, 'object');
-      }), o('ObjAssignable :\
-       INDENT Expression OUTDENT', function() {
-        return new Assign(LOC(1)(new Value($1)), $4, 'object');
-      }), o('Comment')
-    ],
-    ObjAssignable: [o('Identifier'), o('AlphaNumeric'), o('ThisProperty')],
-    Return: [
-      o('RETURN Expression', function() {
-        return new Return($2);
-      }), o('RETURN', function() {
-        return new Return;
-      })
-    ],
-    Comment: [
-      o('HERECOMMENT', function() {
-        return new Comment($1);
-      })
-    ],
-    Code: [
-      o('PARAM_START ParamList PARAM_END FuncGlyph Block', function() {
-        return new Code($2, $5, $4);
-      }), o('FuncGlyph Block', function() {
-        return new Code([], $2, $1);
-      })
-    ],
-    FuncGlyph: [
-      o('->', function() {
-        return 'func';
-      }), o('=>', function() {
-        return 'boundfunc';
-      })
-    ],
-    OptComma: [o(''), o(',')],
-    ParamList: [
-      o('', function() {
-        return [];
-      }), o('Param', function() {
-        return [$1];
-      }), o('ParamList , Param', function() {
-        return $1.concat($3);
-      }), o('ParamList OptComma TERMINATOR Param', function() {
-        return $1.concat($4);
-      }), o('ParamList OptComma INDENT ParamList OptComma OUTDENT', function() {
-        return $1.concat($4);
-      })
-    ],
-    Param: [
-      o('ParamVar', function() {
-        return new Param($1);
-      }), o('ParamVar ...', function() {
-        return new Param($1, null, true);
-      }), o('ParamVar = Expression', function() {
-        return new Param($1, $3);
-      })
-    ],
-    ParamVar: [o('Identifier'), o('ThisProperty'), o('Array'), o('Object')],
-    Splat: [
-      o('Expression ...', function() {
-        return new Splat($1);
-      })
-    ],
-    SimpleAssignable: [
-      o('Identifier', function() {
-        return new Value($1);
-      }), o('Value Accessor', function() {
-        return $1.add($2);
-      }), o('Invocation Accessor', function() {
-        return new Value($1, [].concat($2));
-      }), o('ThisProperty')
-    ],
-    Assignable: [
-      o('SimpleAssignable'), o('Array', function() {
-        return new Value($1);
-      }), o('Object', function() {
-        return new Value($1);
-      })
-    ],
-    Value: [
-      o('Assignable'), o('Literal', function() {
-        return new Value($1);
-      }), o('Parenthetical', function() {
-        return new Value($1);
-      }), o('Range', function() {
-        return new Value($1);
-      }), o('This')
-    ],
-    Accessor: [
-      o('.  Identifier', function() {
-        return new Access($2);
-      }), o('?. Identifier', function() {
-        return new Access($2, 'soak');
-      }), o(':: Identifier', function() {
-        return [LOC(1)(new Access(new Literal('prototype'))), LOC(2)(new Access($2))];
-      }), o('?:: Identifier', function() {
-        return [LOC(1)(new Access(new Literal('prototype'), 'soak')), LOC(2)(new Access($2))];
-      }), o('::', function() {
-        return new Access(new Literal('prototype'));
-      }), o('Index')
-    ],
-    Index: [
-      o('INDEX_START IndexValue INDEX_END', function() {
-        return $2;
-      }), o('INDEX_SOAK  Index', function() {
-        return extend($2, {
-          soak: true
-        });
-      })
-    ],
-    IndexValue: [
-      o('Expression', function() {
-        return new Index($1);
-      }), o('Slice', function() {
-        return new Slice($1);
-      })
-    ],
-    Object: [
-      o('{ AssignList OptComma }', function() {
-        return new Obj($2, $1.generated);
-      })
-    ],
-    AssignList: [
-      o('', function() {
-        return [];
-      }), o('AssignObj', function() {
-        return [$1];
-      }), o('AssignList , AssignObj', function() {
-        return $1.concat($3);
-      }), o('AssignList OptComma TERMINATOR AssignObj', function() {
-        return $1.concat($4);
-      }), o('AssignList OptComma INDENT AssignList OptComma OUTDENT', function() {
-        return $1.concat($4);
-      })
-    ],
-    Class: [
-      o('CLASS', function() {
-        return new Class;
-      }), o('CLASS Block', function() {
-        return new Class(null, null, $2);
-      }), o('CLASS EXTENDS Expression', function() {
-        return new Class(null, $3);
-      }), o('CLASS EXTENDS Expression Block', function() {
-        return new Class(null, $3, $4);
-      }), o('CLASS SimpleAssignable', function() {
-        return new Class($2);
-      }), o('CLASS SimpleAssignable Block', function() {
-        return new Class($2, null, $3);
-      }), o('CLASS SimpleAssignable EXTENDS Expression', function() {
-        return new Class($2, $4);
-      }), o('CLASS SimpleAssignable EXTENDS Expression Block', function() {
-        return new Class($2, $4, $5);
-      })
-    ],
-    Invocation: [
-      o('Value OptFuncExist Arguments', function() {
-        return new Call($1, $3, $2);
-      }), o('Invocation OptFuncExist Arguments', function() {
-        return new Call($1, $3, $2);
-      }), o('SUPER', function() {
-        return new Call('super', [new Splat(new Literal('arguments'))]);
-      }), o('SUPER Arguments', function() {
-        return new Call('super', $2);
-      })
-    ],
-    OptFuncExist: [
-      o('', function() {
-        return false;
-      }), o('FUNC_EXIST', function() {
-        return true;
-      })
-    ],
-    Arguments: [
-      o('CALL_START CALL_END', function() {
-        return [];
-      }), o('CALL_START ArgList OptComma CALL_END', function() {
-        return $2;
-      })
-    ],
-    This: [
-      o('THIS', function() {
-        return new Value(new Literal('this'));
-      }), o('@', function() {
-        return new Value(new Literal('this'));
-      })
-    ],
-    ThisProperty: [
-      o('@ Identifier', function() {
-        return new Value(LOC(1)(new Literal('this')), [LOC(2)(new Access($2))], 'this');
-      })
-    ],
-    Array: [
-      o('[ ]', function() {
-        return new Arr([]);
-      }), o('[ ArgList OptComma ]', function() {
-        return new Arr($2);
-      })
-    ],
-    RangeDots: [
-      o('..', function() {
-        return 'inclusive';
-      }), o('...', function() {
-        return 'exclusive';
-      })
-    ],
-    Range: [
-      o('[ Expression RangeDots Expression ]', function() {
-        return new Range($2, $4, $3);
-      })
-    ],
-    Slice: [
-      o('Expression RangeDots Expression', function() {
-        return new Range($1, $3, $2);
-      }), o('Expression RangeDots', function() {
-        return new Range($1, null, $2);
-      }), o('RangeDots Expression', function() {
-        return new Range(null, $2, $1);
-      }), o('RangeDots', function() {
-        return new Range(null, null, $1);
-      })
-    ],
-    ArgList: [
-      o('Arg', function() {
-        return [$1];
-      }), o('ArgList , Arg', function() {
-        return $1.concat($3);
-      }), o('ArgList OptComma TERMINATOR Arg', function() {
-        return $1.concat($4);
-      }), o('INDENT ArgList OptComma OUTDENT', function() {
-        return $2;
-      }), o('ArgList OptComma INDENT ArgList OptComma OUTDENT', function() {
-        return $1.concat($4);
-      })
-    ],
-    Arg: [o('Expression'), o('Splat')],
-    SimpleArgs: [
-      o('Expression'), o('SimpleArgs , Expression', function() {
-        return [].concat($1, $3);
-      })
-    ],
-    Try: [
-      o('TRY Block', function() {
-        return new Try($2);
-      }), o('TRY Block Catch', function() {
-        return new Try($2, $3[0], $3[1]);
-      }), o('TRY Block FINALLY Block', function() {
-        return new Try($2, null, null, $4);
-      }), o('TRY Block Catch FINALLY Block', function() {
-        return new Try($2, $3[0], $3[1], $5);
-      })
-    ],
-    Catch: [
-      o('CATCH Identifier Block', function() {
-        return [$2, $3];
-      }), o('CATCH Object Block', function() {
-        return [LOC(2)(new Value($2)), $3];
-      })
-    ],
-    Throw: [
-      o('THROW Expression', function() {
-        return new Throw($2);
-      })
-    ],
-    Parenthetical: [
-      o('( Body )', function() {
-        return new Parens($2);
-      }), o('( INDENT Body OUTDENT )', function() {
-        return new Parens($3);
-      })
-    ],
-    WhileSource: [
-      o('WHILE Expression', function() {
-        return new While($2);
-      }), o('WHILE Expression WHEN Expression', function() {
-        return new While($2, {
-          guard: $4
-        });
-      }), o('UNTIL Expression', function() {
-        return new While($2, {
-          invert: true
-        });
-      }), o('UNTIL Expression WHEN Expression', function() {
-        return new While($2, {
-          invert: true,
-          guard: $4
-        });
-      })
-    ],
-    While: [
-      o('WhileSource Block', function() {
-        return $1.addBody($2);
-      }), o('Statement  WhileSource', function() {
-        return $2.addBody(LOC(1)(Block.wrap([$1])));
-      }), o('Expression WhileSource', function() {
-        return $2.addBody(LOC(1)(Block.wrap([$1])));
-      }), o('Loop', function() {
-        return $1;
-      })
-    ],
-    Loop: [
-      o('LOOP Block', function() {
-        return new While(LOC(1)(new Literal('true'))).addBody($2);
-      }), o('LOOP Expression', function() {
-        return new While(LOC(1)(new Literal('true'))).addBody(LOC(2)(Block.wrap([$2])));
-      })
-    ],
-    For: [
-      o('Statement  ForBody', function() {
-        return new For($1, $2);
-      }), o('Expression ForBody', function() {
-        return new For($1, $2);
-      }), o('ForBody    Block', function() {
-        return new For($2, $1);
-      })
-    ],
-    ForBody: [
-      o('FOR Range', function() {
-        return {
-          source: LOC(2)(new Value($2))
-        };
-      }), o('ForStart ForSource', function() {
-        $2.own = $1.own;
-        $2.name = $1[0];
-        $2.index = $1[1];
-        return $2;
-      })
-    ],
-    ForStart: [
-      o('FOR ForVariables', function() {
-        return $2;
-      }), o('FOR OWN ForVariables', function() {
-        $3.own = true;
-        return $3;
-      })
-    ],
-    ForValue: [
-      o('Identifier'), o('ThisProperty'), o('Array', function() {
-        return new Value($1);
-      }), o('Object', function() {
-        return new Value($1);
-      })
-    ],
-    ForVariables: [
-      o('ForValue', function() {
-        return [$1];
-      }), o('ForValue , ForValue', function() {
-        return [$1, $3];
-      })
-    ],
-    ForSource: [
-      o('FORIN Expression', function() {
-        return {
-          source: $2
-        };
-      }), o('FOROF Expression', function() {
-        return {
-          source: $2,
-          object: true
-        };
-      }), o('FORIN Expression WHEN Expression', function() {
-        return {
-          source: $2,
-          guard: $4
-        };
-      }), o('FOROF Expression WHEN Expression', function() {
-        return {
-          source: $2,
-          guard: $4,
-          object: true
-        };
-      }), o('FORIN Expression BY Expression', function() {
-        return {
-          source: $2,
-          step: $4
-        };
-      }), o('FORIN Expression WHEN Expression BY Expression', function() {
-        return {
-          source: $2,
-          guard: $4,
-          step: $6
-        };
-      }), o('FORIN Expression BY Expression WHEN Expression', function() {
-        return {
-          source: $2,
-          step: $4,
-          guard: $6
-        };
-      })
-    ],
-    Switch: [
-      o('SWITCH Expression INDENT Whens OUTDENT', function() {
-        return new Switch($2, $4);
-      }), o('SWITCH Expression INDENT Whens ELSE Block OUTDENT', function() {
-        return new Switch($2, $4, $6);
-      }), o('SWITCH INDENT Whens OUTDENT', function() {
-        return new Switch(null, $3);
-      }), o('SWITCH INDENT Whens ELSE Block OUTDENT', function() {
-        return new Switch(null, $3, $5);
-      })
-    ],
-    Whens: [
-      o('When'), o('Whens When', function() {
-        return $1.concat($2);
-      })
-    ],
-    When: [
-      o('LEADING_WHEN SimpleArgs Block', function() {
-        return [[$2, $3]];
-      }), o('LEADING_WHEN SimpleArgs Block TERMINATOR', function() {
-        return [[$2, $3]];
-      })
-    ],
-    IfBlock: [
-      o('IF Expression Block', function() {
-        return new If($2, $3, {
-          type: $1
-        });
-      }), o('IfBlock ELSE IF Expression Block', function() {
-        return $1.addElse(new If($4, $5, {
-          type: $3
-        }));
-      })
-    ],
-    If: [
-      o('IfBlock'), o('IfBlock ELSE Block', function() {
-        return $1.addElse($3);
-      }), o('Statement  POST_IF Expression', function() {
-        return new If($3, LOC(1)(Block.wrap([$1])), {
-          type: $2,
-          statement: true
-        });
-      }), o('Expression POST_IF Expression', function() {
-        return new If($3, LOC(1)(Block.wrap([$1])), {
-          type: $2,
-          statement: true
-        });
-      })
-    ],
-    Operation: [
-      o('UNARY Expression', function() {
-        return new Op($1, $2);
-      }), o('-     Expression', (function() {
-        return new Op('-', $2);
-      }), {
-        prec: 'UNARY'
-      }), o('+     Expression', (function() {
-        return new Op('+', $2);
-      }), {
-        prec: 'UNARY'
-      }), o('-- SimpleAssignable', function() {
-        return new Op('--', $2);
-      }), o('++ SimpleAssignable', function() {
-        return new Op('++', $2);
-      }), o('SimpleAssignable --', function() {
-        return new Op('--', $1, null, true);
-      }), o('SimpleAssignable ++', function() {
-        return new Op('++', $1, null, true);
-      }), o('Expression ?', function() {
-        return new Existence($1);
-      }), o('Expression +  Expression', function() {
-        return new Op('+', $1, $3);
-      }), o('Expression -  Expression', function() {
-        return new Op('-', $1, $3);
-      }), o('Expression MATH     Expression', function() {
-        return new Op($2, $1, $3);
-      }), o('Expression SHIFT    Expression', function() {
-        return new Op($2, $1, $3);
-      }), o('Expression COMPARE  Expression', function() {
-        return new Op($2, $1, $3);
-      }), o('Expression LOGIC    Expression', function() {
-        return new Op($2, $1, $3);
-      }), o('Expression RELATION Expression', function() {
-        if ($2.charAt(0) === '!') {
-          return new Op($2.slice(1), $1, $3).invert();
-        } else {
-          return new Op($2, $1, $3);
-        }
-      }), o('SimpleAssignable COMPOUND_ASSIGN\
-       Expression', function() {
-        return new Assign($1, $3, $2);
-      }), o('SimpleAssignable COMPOUND_ASSIGN\
-       INDENT Expression OUTDENT', function() {
-        return new Assign($1, $4, $2);
-      }), o('SimpleAssignable COMPOUND_ASSIGN TERMINATOR\
-       Expression', function() {
-        return new Assign($1, $4, $2);
-      }), o('SimpleAssignable EXTENDS Expression', function() {
-        return new Extends($1, $3);
-      })
-    ]
-  };
-
-  operators = [['left', '.', '?.', '::', '?::'], ['left', 'CALL_START', 'CALL_END'], ['nonassoc', '++', '--'], ['left', '?'], ['right', 'UNARY'], ['left', 'MATH'], ['left', '+', '-'], ['left', 'SHIFT'], ['left', 'RELATION'], ['left', 'COMPARE'], ['left', 'LOGIC'], ['nonassoc', 'INDENT', 'OUTDENT'], ['right', '=', ':', 'COMPOUND_ASSIGN', 'RETURN', 'THROW', 'EXTENDS'], ['right', 'FORIN', 'FOROF', 'BY', 'WHEN'], ['right', 'IF', 'ELSE', 'FOR', 'WHILE', 'UNTIL', 'LOOP', 'SUPER', 'CLASS'], ['right', 'POST_IF']];
-
-  tokens = [];
-
-  for (name in grammar) {
-    alternatives = grammar[name];
-    grammar[name] = (function() {
-      var _i, _j, _len, _len1, _ref, _results;
-      _results = [];
-      for (_i = 0, _len = alternatives.length; _i < _len; _i++) {
-        alt = alternatives[_i];
-        _ref = alt[0].split(' ');
-        for (_j = 0, _len1 = _ref.length; _j < _len1; _j++) {
-          token = _ref[_j];
-          if (!grammar[token]) {
-            tokens.push(token);
-          }
-        }
-        if (name === 'Root') {
-          alt[1] = "return " + alt[1];
-        }
-        _results.push(alt);
-      }
-      return _results;
-    })();
-  }
-
-  exports.parser = new Parser({
-    tokens: tokens.join(' '),
-    bnf: grammar,
-    operators: operators.reverse(),
-    startSymbol: 'Root'
-  });
-
-}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/helpers.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/helpers.js
deleted file mode 100755
index d7bac3b3..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/helpers.js
+++ /dev/null
@@ -1,150 +0,0 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var buildLocationData, extend, flatten, _ref;
-
-  exports.starts = function(string, literal, start) {
-    return literal === string.substr(start, literal.length);
-  };
-
-  exports.ends = function(string, literal, back) {
-    var len;
-    len = literal.length;
-    return literal === string.substr(string.length - len - (back || 0), len);
-  };
-
-  exports.compact = function(array) {
-    var item, _i, _len, _results;
-    _results = [];
-    for (_i = 0, _len = array.length; _i < _len; _i++) {
-      item = array[_i];
-      if (item) {
-        _results.push(item);
-      }
-    }
-    return _results;
-  };
-
-  exports.count = function(string, substr) {
-    var num, pos;
-    num = pos = 0;
-    if (!substr.length) {
-      return 1 / 0;
-    }
-    while (pos = 1 + string.indexOf(substr, pos)) {
-      num++;
-    }
-    return num;
-  };
-
-  exports.merge = function(options, overrides) {
-    return extend(extend({}, options), overrides);
-  };
-
-  extend = exports.extend = function(object, properties) {
-    var key, val;
-    for (key in properties) {
-      val = properties[key];
-      object[key] = val;
-    }
-    return object;
-  };
-
-  exports.flatten = flatten = function(array) {
-    var element, flattened, _i, _len;
-    flattened = [];
-    for (_i = 0, _len = array.length; _i < _len; _i++) {
-      element = array[_i];
-      if (element instanceof Array) {
-        flattened = flattened.concat(flatten(element));
-      } else {
-        flattened.push(element);
-      }
-    }
-    return flattened;
-  };
-
-  exports.del = function(obj, key) {
-    var val;
-    val = obj[key];
-    delete obj[key];
-    return val;
-  };
-
-  exports.last = function(array, back) {
-    return array[array.length - (back || 0) - 1];
-  };
-
-  exports.some = (_ref = Array.prototype.some) != null ? _ref : function(fn) {
-    var e, _i, _len;
-    for (_i = 0, _len = this.length; _i < _len; _i++) {
-      e = this[_i];
-      if (fn(e)) {
-        return true;
-      }
-    }
-    return false;
-  };
-
-  buildLocationData = function(first, last) {
-    if (!last) {
-      return first;
-    } else {
-      return {
-        first_line: first.first_line,
-        first_column: first.first_column,
-        last_line: last.last_line,
-        last_column: last.last_column
-      };
-    }
-  };
-
-  exports.addLocationDataFn = function(first, last) {
-    return function(obj) {
-      if (((typeof obj) === 'object') && (!!obj['updateLocationDataIfMissing'])) {
-        obj.updateLocationDataIfMissing(buildLocationData(first, last));
-      }
-      return obj;
-    };
-  };
-
-  exports.locationDataToString = function(obj) {
-    var locationData;
-    if (("2" in obj) && ("first_line" in obj[2])) {
-      locationData = obj[2];
-    } else if ("first_line" in obj) {
-      locationData = obj;
-    }
-    if (locationData) {
-      return ("" + (locationData.first_line + 1) + ":" + (locationData.first_column + 1) + "-") + ("" + (locationData.last_line + 1) + ":" + (locationData.last_column + 1));
-    } else {
-      return "No location data";
-    }
-  };
-
-  exports.baseFileName = function(file, stripExt) {
-    var parts;
-    if (stripExt == null) {
-      stripExt = false;
-    }
-    parts = file.split('/');
-    file = parts[parts.length - 1];
-    if (!stripExt) {
-      return file;
-    }
-    parts = file.split('.');
-    parts.pop();
-    if (parts[parts.length - 1] === 'coffee') {
-      parts.pop();
-    }
-    return parts.join('.');
-  };
-
-  exports.isCoffee = function(file) {
-    return /\.((lit)?coffee|coffee\.md)$/.test(file);
-  };
-
-  exports.isLiterate = function(file) {
-    return /\.(litcoffee|coffee\.md)$/.test(file);
-  };
-
-}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/index.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/index.js
deleted file mode 100755
index 1452b452..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/index.js
+++ /dev/null
@@ -1,11 +0,0 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var key, val, _ref;
-
-  _ref = require('./coffee-script');
-  for (key in _ref) {
-    val = _ref[key];
-    exports[key] = val;
-  }
-
-}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/lexer.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/lexer.js
deleted file mode 100755
index 5261242e..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/lexer.js
+++ /dev/null
@@ -1,905 +0,0 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var BOM, BOOL, CALLABLE, CODE, COFFEE_ALIASES, COFFEE_ALIAS_MAP, COFFEE_KEYWORDS, COMMENT, COMPARE, COMPOUND_ASSIGN, HEREDOC, HEREDOC_ILLEGAL, HEREDOC_INDENT, HEREGEX, HEREGEX_OMIT, IDENTIFIER, INDEXABLE, INVERSES, JSTOKEN, JS_FORBIDDEN, JS_KEYWORDS, LINE_BREAK, LINE_CONTINUER, LITERATE, LOGIC, Lexer, MATH, MULTILINER, MULTI_DENT, NOT_REGEX, NOT_SPACED_REGEX, NUMBER, OPERATOR, REGEX, RELATION, RESERVED, Rewriter, SHIFT, SIMPLESTR, STRICT_PROSCRIBED, TRAILING_SPACES, UNARY, WHITESPACE, compact, count, key, last, locationDataToString, starts, _ref, _ref1,
-    __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; };
-
-  _ref = require('./rewriter'), Rewriter = _ref.Rewriter, INVERSES = _ref.INVERSES;
-
-  _ref1 = require('./helpers'), count = _ref1.count, starts = _ref1.starts, compact = _ref1.compact, last = _ref1.last, locationDataToString = _ref1.locationDataToString;
-
-  exports.Lexer = Lexer = (function() {
-
-    function Lexer() {}
-
-    Lexer.prototype.tokenize = function(code, opts) {
-      var consumed, i, tag, _ref2;
-      if (opts == null) {
-        opts = {};
-      }
-      this.literate = opts.literate;
-      this.indent = 0;
-      this.indebt = 0;
-      this.outdebt = 0;
-      this.indents = [];
-      this.ends = [];
-      this.tokens = [];
-      this.chunkLine = opts.line || 0;
-      this.chunkColumn = opts.column || 0;
-      code = this.clean(code);
-      i = 0;
-      while (this.chunk = code.slice(i)) {
-        consumed = this.identifierToken() || this.commentToken() || this.whitespaceToken() || this.lineToken() || this.heredocToken() || this.stringToken() || this.numberToken() || this.regexToken() || this.jsToken() || this.literalToken();
-        _ref2 = this.getLineAndColumnFromChunk(consumed), this.chunkLine = _ref2[0], this.chunkColumn = _ref2[1];
-        i += consumed;
-      }
-      this.closeIndentation();
-      if (tag = this.ends.pop()) {
-        this.error("missing " + tag);
-      }
-      if (opts.rewrite === false) {
-        return this.tokens;
-      }
-      return (new Rewriter).rewrite(this.tokens);
-    };
-
-    Lexer.prototype.clean = function(code) {
-      var line, lines, match;
-      if (code.charCodeAt(0) === BOM) {
-        code = code.slice(1);
-      }
-      code = code.replace(/\r/g, '').replace(TRAILING_SPACES, '');
-      if (WHITESPACE.test(code)) {
-        code = "\n" + code;
-        this.chunkLine--;
-      }
-      if (this.literate) {
-        lines = (function() {
-          var _i, _len, _ref2, _results;
-          _ref2 = code.split('\n');
-          _results = [];
-          for (_i = 0, _len = _ref2.length; _i < _len; _i++) {
-            line = _ref2[_i];
-            if (match = LITERATE.exec(line)) {
-              _results.push(line.slice(match[0].length));
-            } else {
-              _results.push('# ' + line);
-            }
-          }
-          return _results;
-        })();
-        code = lines.join('\n');
-      }
-      return code;
-    };
-
-    Lexer.prototype.identifierToken = function() {
-      var colon, colonOffset, forcedIdentifier, id, idLength, input, match, poppedToken, prev, tag, tagToken, _ref2, _ref3, _ref4;
-      if (!(match = IDENTIFIER.exec(this.chunk))) {
-        return 0;
-      }
-      input = match[0], id = match[1], colon = match[2];
-      idLength = id.length;
-      poppedToken = void 0;
-      if (id === 'own' && this.tag() === 'FOR') {
-        this.token('OWN', id);
-        return id.length;
-      }
-      forcedIdentifier = colon || (prev = last(this.tokens)) && (((_ref2 = prev[0]) === '.' || _ref2 === '?.' || _ref2 === '::' || _ref2 === '?::') || !prev.spaced && prev[0] === '@');
-      tag = 'IDENTIFIER';
-      if (!forcedIdentifier && (__indexOf.call(JS_KEYWORDS, id) >= 0 || __indexOf.call(COFFEE_KEYWORDS, id) >= 0)) {
-        tag = id.toUpperCase();
-        if (tag === 'WHEN' && (_ref3 = this.tag(), __indexOf.call(LINE_BREAK, _ref3) >= 0)) {
-          tag = 'LEADING_WHEN';
-        } else if (tag === 'FOR') {
-          this.seenFor = true;
-        } else if (tag === 'UNLESS') {
-          tag = 'IF';
-        } else if (__indexOf.call(UNARY, tag) >= 0) {
-          tag = 'UNARY';
-        } else if (__indexOf.call(RELATION, tag) >= 0) {
-          if (tag !== 'INSTANCEOF' && this.seenFor) {
-            tag = 'FOR' + tag;
-            this.seenFor = false;
-          } else {
-            tag = 'RELATION';
-            if (this.value() === '!') {
-              poppedToken = this.tokens.pop();
-              id = '!' + id;
-            }
-          }
-        }
-      }
-      if (__indexOf.call(JS_FORBIDDEN, id) >= 0) {
-        if (forcedIdentifier) {
-          tag = 'IDENTIFIER';
-          id = new String(id);
-          id.reserved = true;
-        } else if (__indexOf.call(RESERVED, id) >= 0) {
-          this.error("reserved word \"" + id + "\"");
-        }
-      }
-      if (!forcedIdentifier) {
-        if (__indexOf.call(COFFEE_ALIASES, id) >= 0) {
-          id = COFFEE_ALIAS_MAP[id];
-        }
-        tag = (function() {
-          switch (id) {
-            case '!':
-              return 'UNARY';
-            case '==':
-            case '!=':
-              return 'COMPARE';
-            case '&&':
-            case '||':
-              return 'LOGIC';
-            case 'true':
-            case 'false':
-              return 'BOOL';
-            case 'break':
-            case 'continue':
-              return 'STATEMENT';
-            default:
-              return tag;
-          }
-        })();
-      }
-      tagToken = this.token(tag, id, 0, idLength);
-      if (poppedToken) {
-        _ref4 = [poppedToken[2].first_line, poppedToken[2].first_column], tagToken[2].first_line = _ref4[0], tagToken[2].first_column = _ref4[1];
-      }
-      if (colon) {
-        colonOffset = input.lastIndexOf(':');
-        this.token(':', ':', colonOffset, colon.length);
-      }
-      return input.length;
-    };
-
-    Lexer.prototype.numberToken = function() {
-      var binaryLiteral, lexedLength, match, number, octalLiteral;
-      if (!(match = NUMBER.exec(this.chunk))) {
-        return 0;
-      }
-      number = match[0];
-      if (/^0[BOX]/.test(number)) {
-        this.error("radix prefix '" + number + "' must be lowercase");
-      } else if (/E/.test(number) && !/^0x/.test(number)) {
-        this.error("exponential notation '" + number + "' must be indicated with a lowercase 'e'");
-      } else if (/^0\d*[89]/.test(number)) {
-        this.error("decimal literal '" + number + "' must not be prefixed with '0'");
-      } else if (/^0\d+/.test(number)) {
-        this.error("octal literal '" + number + "' must be prefixed with '0o'");
-      }
-      lexedLength = number.length;
-      if (octalLiteral = /^0o([0-7]+)/.exec(number)) {
-        number = '0x' + (parseInt(octalLiteral[1], 8)).toString(16);
-      }
-      if (binaryLiteral = /^0b([01]+)/.exec(number)) {
-        number = '0x' + (parseInt(binaryLiteral[1], 2)).toString(16);
-      }
-      this.token('NUMBER', number, 0, lexedLength);
-      return lexedLength;
-    };
-
-    Lexer.prototype.stringToken = function() {
-      var match, octalEsc, string;
-      switch (this.chunk.charAt(0)) {
-        case "'":
-          if (!(match = SIMPLESTR.exec(this.chunk))) {
-            return 0;
-          }
-          string = match[0];
-          this.token('STRING', string.replace(MULTILINER, '\\\n'), 0, string.length);
-          break;
-        case '"':
-          if (!(string = this.balancedString(this.chunk, '"'))) {
-            return 0;
-          }
-          if (0 < string.indexOf('#{', 1)) {
-            this.interpolateString(string.slice(1, -1), {
-              strOffset: 1,
-              lexedLength: string.length
-            });
-          } else {
-            this.token('STRING', this.escapeLines(string, 0, string.length));
-          }
-          break;
-        default:
-          return 0;
-      }
-      if (octalEsc = /^(?:\\.|[^\\])*\\(?:0[0-7]|[1-7])/.test(string)) {
-        this.error("octal escape sequences " + string + " are not allowed");
-      }
-      return string.length;
-    };
-
-    Lexer.prototype.heredocToken = function() {
-      var doc, heredoc, match, quote;
-      if (!(match = HEREDOC.exec(this.chunk))) {
-        return 0;
-      }
-      heredoc = match[0];
-      quote = heredoc.charAt(0);
-      doc = this.sanitizeHeredoc(match[2], {
-        quote: quote,
-        indent: null
-      });
-      if (quote === '"' && 0 <= doc.indexOf('#{')) {
-        this.interpolateString(doc, {
-          heredoc: true,
-          strOffset: 3,
-          lexedLength: heredoc.length
-        });
-      } else {
-        this.token('STRING', this.makeString(doc, quote, true), 0, heredoc.length);
-      }
-      return heredoc.length;
-    };
-
-    Lexer.prototype.commentToken = function() {
-      var comment, here, match;
-      if (!(match = this.chunk.match(COMMENT))) {
-        return 0;
-      }
-      comment = match[0], here = match[1];
-      if (here) {
-        this.token('HERECOMMENT', this.sanitizeHeredoc(here, {
-          herecomment: true,
-          indent: Array(this.indent + 1).join(' ')
-        }), 0, comment.length);
-      }
-      return comment.length;
-    };
-
-    Lexer.prototype.jsToken = function() {
-      var match, script;
-      if (!(this.chunk.charAt(0) === '`' && (match = JSTOKEN.exec(this.chunk)))) {
-        return 0;
-      }
-      this.token('JS', (script = match[0]).slice(1, -1), 0, script.length);
-      return script.length;
-    };
-
-    Lexer.prototype.regexToken = function() {
-      var flags, length, match, prev, regex, _ref2, _ref3;
-      if (this.chunk.charAt(0) !== '/') {
-        return 0;
-      }
-      if (match = HEREGEX.exec(this.chunk)) {
-        length = this.heregexToken(match);
-        return length;
-      }
-      prev = last(this.tokens);
-      if (prev && (_ref2 = prev[0], __indexOf.call((prev.spaced ? NOT_REGEX : NOT_SPACED_REGEX), _ref2) >= 0)) {
-        return 0;
-      }
-      if (!(match = REGEX.exec(this.chunk))) {
-        return 0;
-      }
-      _ref3 = match, match = _ref3[0], regex = _ref3[1], flags = _ref3[2];
-      if (regex.slice(0, 2) === '/*') {
-        this.error('regular expressions cannot begin with `*`');
-      }
-      if (regex === '//') {
-        regex = '/(?:)/';
-      }
-      this.token('REGEX', "" + regex + flags, 0, match.length);
-      return match.length;
-    };
-
-    Lexer.prototype.heregexToken = function(match) {
-      var body, flags, flagsOffset, heregex, plusToken, prev, re, tag, token, tokens, value, _i, _len, _ref2, _ref3, _ref4;
-      heregex = match[0], body = match[1], flags = match[2];
-      if (0 > body.indexOf('#{')) {
-        re = body.replace(HEREGEX_OMIT, '').replace(/\//g, '\\/');
-        if (re.match(/^\*/)) {
-          this.error('regular expressions cannot begin with `*`');
-        }
-        this.token('REGEX', "/" + (re || '(?:)') + "/" + flags, 0, heregex.length);
-        return heregex.length;
-      }
-      this.token('IDENTIFIER', 'RegExp', 0, 0);
-      this.token('CALL_START', '(', 0, 0);
-      tokens = [];
-      _ref2 = this.interpolateString(body, {
-        regex: true
-      });
-      for (_i = 0, _len = _ref2.length; _i < _len; _i++) {
-        token = _ref2[_i];
-        tag = token[0], value = token[1];
-        if (tag === 'TOKENS') {
-          tokens.push.apply(tokens, value);
-        } else if (tag === 'NEOSTRING') {
-          if (!(value = value.replace(HEREGEX_OMIT, ''))) {
-            continue;
-          }
-          value = value.replace(/\\/g, '\\\\');
-          token[0] = 'STRING';
-          token[1] = this.makeString(value, '"', true);
-          tokens.push(token);
-        } else {
-          this.error("Unexpected " + tag);
-        }
-        prev = last(this.tokens);
-        plusToken = ['+', '+'];
-        plusToken[2] = prev[2];
-        tokens.push(plusToken);
-      }
-      tokens.pop();
-      if (((_ref3 = tokens[0]) != null ? _ref3[0] : void 0) !== 'STRING') {
-        this.token('STRING', '""', 0, 0);
-        this.token('+', '+', 0, 0);
-      }
-      (_ref4 = this.tokens).push.apply(_ref4, tokens);
-      if (flags) {
-        flagsOffset = heregex.lastIndexOf(flags);
-        this.token(',', ',', flagsOffset, 0);
-        this.token('STRING', '"' + flags + '"', flagsOffset, flags.length);
-      }
-      this.token(')', ')', heregex.length - 1, 0);
-      return heregex.length;
-    };
-
-    Lexer.prototype.lineToken = function() {
-      var diff, indent, match, noNewlines, size;
-      if (!(match = MULTI_DENT.exec(this.chunk))) {
-        return 0;
-      }
-      indent = match[0];
-      this.seenFor = false;
-      size = indent.length - 1 - indent.lastIndexOf('\n');
-      noNewlines = this.unfinished();
-      if (size - this.indebt === this.indent) {
-        if (noNewlines) {
-          this.suppressNewlines();
-        } else {
-          this.newlineToken(0);
-        }
-        return indent.length;
-      }
-      if (size > this.indent) {
-        if (noNewlines) {
-          this.indebt = size - this.indent;
-          this.suppressNewlines();
-          return indent.length;
-        }
-        diff = size - this.indent + this.outdebt;
-        this.token('INDENT', diff, 0, indent.length);
-        this.indents.push(diff);
-        this.ends.push('OUTDENT');
-        this.outdebt = this.indebt = 0;
-      } else {
-        this.indebt = 0;
-        this.outdentToken(this.indent - size, noNewlines, indent.length);
-      }
-      this.indent = size;
-      return indent.length;
-    };
-
-    Lexer.prototype.outdentToken = function(moveOut, noNewlines, outdentLength) {
-      var dent, len;
-      while (moveOut > 0) {
-        len = this.indents.length - 1;
-        if (this.indents[len] === void 0) {
-          moveOut = 0;
-        } else if (this.indents[len] === this.outdebt) {
-          moveOut -= this.outdebt;
-          this.outdebt = 0;
-        } else if (this.indents[len] < this.outdebt) {
-          this.outdebt -= this.indents[len];
-          moveOut -= this.indents[len];
-        } else {
-          dent = this.indents.pop() + this.outdebt;
-          moveOut -= dent;
-          this.outdebt = 0;
-          this.pair('OUTDENT');
-          this.token('OUTDENT', dent, 0, outdentLength);
-        }
-      }
-      if (dent) {
-        this.outdebt -= moveOut;
-      }
-      while (this.value() === ';') {
-        this.tokens.pop();
-      }
-      if (!(this.tag() === 'TERMINATOR' || noNewlines)) {
-        this.token('TERMINATOR', '\n', outdentLength, 0);
-      }
-      return this;
-    };
-
-    Lexer.prototype.whitespaceToken = function() {
-      var match, nline, prev;
-      if (!((match = WHITESPACE.exec(this.chunk)) || (nline = this.chunk.charAt(0) === '\n'))) {
-        return 0;
-      }
-      prev = last(this.tokens);
-      if (prev) {
-        prev[match ? 'spaced' : 'newLine'] = true;
-      }
-      if (match) {
-        return match[0].length;
-      } else {
-        return 0;
-      }
-    };
-
-    Lexer.prototype.newlineToken = function(offset) {
-      while (this.value() === ';') {
-        this.tokens.pop();
-      }
-      if (this.tag() !== 'TERMINATOR') {
-        this.token('TERMINATOR', '\n', offset, 0);
-      }
-      return this;
-    };
-
-    Lexer.prototype.suppressNewlines = function() {
-      if (this.value() === '\\') {
-        this.tokens.pop();
-      }
-      return this;
-    };
-
-    Lexer.prototype.literalToken = function() {
-      var match, prev, tag, value, _ref2, _ref3, _ref4, _ref5;
-      if (match = OPERATOR.exec(this.chunk)) {
-        value = match[0];
-        if (CODE.test(value)) {
-          this.tagParameters();
-        }
-      } else {
-        value = this.chunk.charAt(0);
-      }
-      tag = value;
-      prev = last(this.tokens);
-      if (value === '=' && prev) {
-        if (!prev[1].reserved && (_ref2 = prev[1], __indexOf.call(JS_FORBIDDEN, _ref2) >= 0)) {
-          this.error("reserved word \"" + (this.value()) + "\" can't be assigned");
-        }
-        if ((_ref3 = prev[1]) === '||' || _ref3 === '&&') {
-          prev[0] = 'COMPOUND_ASSIGN';
-          prev[1] += '=';
-          return value.length;
-        }
-      }
-      if (value === ';') {
-        this.seenFor = false;
-        tag = 'TERMINATOR';
-      } else if (__indexOf.call(MATH, value) >= 0) {
-        tag = 'MATH';
-      } else if (__indexOf.call(COMPARE, value) >= 0) {
-        tag = 'COMPARE';
-      } else if (__indexOf.call(COMPOUND_ASSIGN, value) >= 0) {
-        tag = 'COMPOUND_ASSIGN';
-      } else if (__indexOf.call(UNARY, value) >= 0) {
-        tag = 'UNARY';
-      } else if (__indexOf.call(SHIFT, value) >= 0) {
-        tag = 'SHIFT';
-      } else if (__indexOf.call(LOGIC, value) >= 0 || value === '?' && (prev != null ? prev.spaced : void 0)) {
-        tag = 'LOGIC';
-      } else if (prev && !prev.spaced) {
-        if (value === '(' && (_ref4 = prev[0], __indexOf.call(CALLABLE, _ref4) >= 0)) {
-          if (prev[0] === '?') {
-            prev[0] = 'FUNC_EXIST';
-          }
-          tag = 'CALL_START';
-        } else if (value === '[' && (_ref5 = prev[0], __indexOf.call(INDEXABLE, _ref5) >= 0)) {
-          tag = 'INDEX_START';
-          switch (prev[0]) {
-            case '?':
-              prev[0] = 'INDEX_SOAK';
-          }
-        }
-      }
-      switch (value) {
-        case '(':
-        case '{':
-        case '[':
-          this.ends.push(INVERSES[value]);
-          break;
-        case ')':
-        case '}':
-        case ']':
-          this.pair(value);
-      }
-      this.token(tag, value);
-      return value.length;
-    };
-
-    Lexer.prototype.sanitizeHeredoc = function(doc, options) {
-      var attempt, herecomment, indent, match, _ref2;
-      indent = options.indent, herecomment = options.herecomment;
-      if (herecomment) {
-        if (HEREDOC_ILLEGAL.test(doc)) {
-          this.error("block comment cannot contain \"*/\", starting");
-        }
-        if (doc.indexOf('\n') < 0) {
-          return doc;
-        }
-      } else {
-        while (match = HEREDOC_INDENT.exec(doc)) {
-          attempt = match[1];
-          if (indent === null || (0 < (_ref2 = attempt.length) && _ref2 < indent.length)) {
-            indent = attempt;
-          }
-        }
-      }
-      if (indent) {
-        doc = doc.replace(RegExp("\\n" + indent, "g"), '\n');
-      }
-      if (this.literate) {
-        doc = doc.replace(/\n# \n/g, '\n\n');
-      }
-      if (!herecomment) {
-        doc = doc.replace(/^\n/, '');
-      }
-      return doc;
-    };
-
-    Lexer.prototype.tagParameters = function() {
-      var i, stack, tok, tokens;
-      if (this.tag() !== ')') {
-        return this;
-      }
-      stack = [];
-      tokens = this.tokens;
-      i = tokens.length;
-      tokens[--i][0] = 'PARAM_END';
-      while (tok = tokens[--i]) {
-        switch (tok[0]) {
-          case ')':
-            stack.push(tok);
-            break;
-          case '(':
-          case 'CALL_START':
-            if (stack.length) {
-              stack.pop();
-            } else if (tok[0] === '(') {
-              tok[0] = 'PARAM_START';
-              return this;
-            } else {
-              return this;
-            }
-        }
-      }
-      return this;
-    };
-
-    Lexer.prototype.closeIndentation = function() {
-      return this.outdentToken(this.indent);
-    };
-
-    Lexer.prototype.balancedString = function(str, end) {
-      var continueCount, i, letter, match, prev, stack, _i, _ref2;
-      continueCount = 0;
-      stack = [end];
-      for (i = _i = 1, _ref2 = str.length; 1 <= _ref2 ? _i < _ref2 : _i > _ref2; i = 1 <= _ref2 ? ++_i : --_i) {
-        if (continueCount) {
-          --continueCount;
-          continue;
-        }
-        switch (letter = str.charAt(i)) {
-          case '\\':
-            ++continueCount;
-            continue;
-          case end:
-            stack.pop();
-            if (!stack.length) {
-              return str.slice(0, +i + 1 || 9e9);
-            }
-            end = stack[stack.length - 1];
-            continue;
-        }
-        if (end === '}' && (letter === '"' || letter === "'")) {
-          stack.push(end = letter);
-        } else if (end === '}' && letter === '/' && (match = HEREGEX.exec(str.slice(i)) || REGEX.exec(str.slice(i)))) {
-          continueCount += match[0].length - 1;
-        } else if (end === '}' && letter === '{') {
-          stack.push(end = '}');
-        } else if (end === '"' && prev === '#' && letter === '{') {
-          stack.push(end = '}');
-        }
-        prev = letter;
-      }
-      return this.error("missing " + (stack.pop()) + ", starting");
-    };
-
-    Lexer.prototype.interpolateString = function(str, options) {
-      var column, expr, heredoc, i, inner, interpolated, len, letter, lexedLength, line, locationToken, nested, offsetInChunk, pi, plusToken, popped, regex, strOffset, tag, token, tokens, value, _i, _len, _ref2, _ref3, _ref4;
-      if (options == null) {
-        options = {};
-      }
-      heredoc = options.heredoc, regex = options.regex, offsetInChunk = options.offsetInChunk, strOffset = options.strOffset, lexedLength = options.lexedLength;
-      offsetInChunk = offsetInChunk || 0;
-      strOffset = strOffset || 0;
-      lexedLength = lexedLength || str.length;
-      if (heredoc && str.length > 0 && str[0] === '\n') {
-        str = str.slice(1);
-        strOffset++;
-      }
-      tokens = [];
-      pi = 0;
-      i = -1;
-      while (letter = str.charAt(i += 1)) {
-        if (letter === '\\') {
-          i += 1;
-          continue;
-        }
-        if (!(letter === '#' && str.charAt(i + 1) === '{' && (expr = this.balancedString(str.slice(i + 1), '}')))) {
-          continue;
-        }
-        if (pi < i) {
-          tokens.push(this.makeToken('NEOSTRING', str.slice(pi, i), strOffset + pi));
-        }
-        inner = expr.slice(1, -1);
-        if (inner.length) {
-          _ref2 = this.getLineAndColumnFromChunk(strOffset + i + 1), line = _ref2[0], column = _ref2[1];
-          nested = new Lexer().tokenize(inner, {
-            line: line,
-            column: column,
-            rewrite: false
-          });
-          popped = nested.pop();
-          if (((_ref3 = nested[0]) != null ? _ref3[0] : void 0) === 'TERMINATOR') {
-            popped = nested.shift();
-          }
-          if (len = nested.length) {
-            if (len > 1) {
-              nested.unshift(this.makeToken('(', '(', strOffset + i + 1, 0));
-              nested.push(this.makeToken(')', ')', strOffset + i + 1 + inner.length, 0));
-            }
-            tokens.push(['TOKENS', nested]);
-          }
-        }
-        i += expr.length;
-        pi = i + 1;
-      }
-      if ((i > pi && pi < str.length)) {
-        tokens.push(this.makeToken('NEOSTRING', str.slice(pi), strOffset + pi));
-      }
-      if (regex) {
-        return tokens;
-      }
-      if (!tokens.length) {
-        return this.token('STRING', '""', offsetInChunk, lexedLength);
-      }
-      if (tokens[0][0] !== 'NEOSTRING') {
-        tokens.unshift(this.makeToken('NEOSTRING', '', offsetInChunk));
-      }
-      if (interpolated = tokens.length > 1) {
-        this.token('(', '(', offsetInChunk, 0);
-      }
-      for (i = _i = 0, _len = tokens.length; _i < _len; i = ++_i) {
-        token = tokens[i];
-        tag = token[0], value = token[1];
-        if (i) {
-          if (i) {
-            plusToken = this.token('+', '+');
-          }
-          locationToken = tag === 'TOKENS' ? value[0] : token;
-          plusToken[2] = {
-            first_line: locationToken[2].first_line,
-            first_column: locationToken[2].first_column,
-            last_line: locationToken[2].first_line,
-            last_column: locationToken[2].first_column
-          };
-        }
-        if (tag === 'TOKENS') {
-          (_ref4 = this.tokens).push.apply(_ref4, value);
-        } else if (tag === 'NEOSTRING') {
-          token[0] = 'STRING';
-          token[1] = this.makeString(value, '"', heredoc);
-          this.tokens.push(token);
-        } else {
-          this.error("Unexpected " + tag);
-        }
-      }
-      if (interpolated) {
-        this.token(')', ')', offsetInChunk + lexedLength, 0);
-      }
-      return tokens;
-    };
-
-    Lexer.prototype.pair = function(tag) {
-      var size, wanted;
-      if (tag !== (wanted = last(this.ends))) {
-        if ('OUTDENT' !== wanted) {
-          this.error("unmatched " + tag);
-        }
-        this.indent -= size = last(this.indents);
-        this.outdentToken(size, true);
-        return this.pair(tag);
-      }
-      return this.ends.pop();
-    };
-
-    Lexer.prototype.getLineAndColumnFromChunk = function(offset) {
-      var column, lineCount, lines, string;
-      if (offset === 0) {
-        return [this.chunkLine, this.chunkColumn];
-      }
-      if (offset >= this.chunk.length) {
-        string = this.chunk;
-      } else {
-        string = this.chunk.slice(0, +(offset - 1) + 1 || 9e9);
-      }
-      lineCount = count(string, '\n');
-      column = this.chunkColumn;
-      if (lineCount > 0) {
-        lines = string.split('\n');
-        column = (last(lines)).length;
-      } else {
-        column += string.length;
-      }
-      return [this.chunkLine + lineCount, column];
-    };
-
-    Lexer.prototype.makeToken = function(tag, value, offsetInChunk, length) {
-      var lastCharacter, locationData, token, _ref2, _ref3;
-      if (offsetInChunk == null) {
-        offsetInChunk = 0;
-      }
-      if (length == null) {
-        length = value.length;
-      }
-      locationData = {};
-      _ref2 = this.getLineAndColumnFromChunk(offsetInChunk), locationData.first_line = _ref2[0], locationData.first_column = _ref2[1];
-      lastCharacter = Math.max(0, length - 1);
-      _ref3 = this.getLineAndColumnFromChunk(offsetInChunk + (length - 1)), locationData.last_line = _ref3[0], locationData.last_column = _ref3[1];
-      token = [tag, value, locationData];
-      return token;
-    };
-
-    Lexer.prototype.token = function(tag, value, offsetInChunk, length) {
-      var token;
-      token = this.makeToken(tag, value, offsetInChunk, length);
-      this.tokens.push(token);
-      return token;
-    };
-
-    Lexer.prototype.tag = function(index, tag) {
-      var tok;
-      return (tok = last(this.tokens, index)) && (tag ? tok[0] = tag : tok[0]);
-    };
-
-    Lexer.prototype.value = function(index, val) {
-      var tok;
-      return (tok = last(this.tokens, index)) && (val ? tok[1] = val : tok[1]);
-    };
-
-    Lexer.prototype.unfinished = function() {
-      var _ref2;
-      return LINE_CONTINUER.test(this.chunk) || ((_ref2 = this.tag()) === '\\' || _ref2 === '.' || _ref2 === '?.' || _ref2 === '?::' || _ref2 === 'UNARY' || _ref2 === 'MATH' || _ref2 === '+' || _ref2 === '-' || _ref2 === 'SHIFT' || _ref2 === 'RELATION' || _ref2 === 'COMPARE' || _ref2 === 'LOGIC' || _ref2 === 'THROW' || _ref2 === 'EXTENDS');
-    };
-
-    Lexer.prototype.escapeLines = function(str, heredoc) {
-      return str.replace(MULTILINER, heredoc ? '\\n' : '');
-    };
-
-    Lexer.prototype.makeString = function(body, quote, heredoc) {
-      if (!body) {
-        return quote + quote;
-      }
-      body = body.replace(/\\([\s\S])/g, function(match, contents) {
-        if (contents === '\n' || contents === quote) {
-          return contents;
-        } else {
-          return match;
-        }
-      });
-      body = body.replace(RegExp("" + quote, "g"), '\\$&');
-      return quote + this.escapeLines(body, heredoc) + quote;
-    };
-
-    Lexer.prototype.error = function(message) {
-      throw SyntaxError("" + message + " on line " + (this.chunkLine + 1));
-    };
-
-    return Lexer;
-
-  })();
-
-  JS_KEYWORDS = ['true', 'false', 'null', 'this', 'new', 'delete', 'typeof', 'in', 'instanceof', 'return', 'throw', 'break', 'continue', 'debugger', 'if', 'else', 'switch', 'for', 'while', 'do', 'try', 'catch', 'finally', 'class', 'extends', 'super'];
-
-  COFFEE_KEYWORDS = ['undefined', 'then', 'unless', 'until', 'loop', 'of', 'by', 'when'];
-
-  COFFEE_ALIAS_MAP = {
-    and: '&&',
-    or: '||',
-    is: '==',
-    isnt: '!=',
-    not: '!',
-    yes: 'true',
-    no: 'false',
-    on: 'true',
-    off: 'false'
-  };
-
-  COFFEE_ALIASES = (function() {
-    var _results;
-    _results = [];
-    for (key in COFFEE_ALIAS_MAP) {
-      _results.push(key);
-    }
-    return _results;
-  })();
-
-  COFFEE_KEYWORDS = COFFEE_KEYWORDS.concat(COFFEE_ALIASES);
-
-  RESERVED = ['case', 'default', 'function', 'var', 'void', 'with', 'const', 'let', 'enum', 'export', 'import', 'native', '__hasProp', '__extends', '__slice', '__bind', '__indexOf', 'implements', 'interface', 'package', 'private', 'protected', 'public', 'static', 'yield'];
-
-  STRICT_PROSCRIBED = ['arguments', 'eval'];
-
-  JS_FORBIDDEN = JS_KEYWORDS.concat(RESERVED).concat(STRICT_PROSCRIBED);
-
-  exports.RESERVED = RESERVED.concat(JS_KEYWORDS).concat(COFFEE_KEYWORDS).concat(STRICT_PROSCRIBED);
-
-  exports.STRICT_PROSCRIBED = STRICT_PROSCRIBED;
-
-  BOM = 65279;
-
-  IDENTIFIER = /^([$A-Za-z_\x7f-\uffff][$\w\x7f-\uffff]*)([^\n\S]*:(?!:))?/;
-
-  NUMBER = /^0b[01]+|^0o[0-7]+|^0x[\da-f]+|^\d*\.?\d+(?:e[+-]?\d+)?/i;
-
-  HEREDOC = /^("""|''')([\s\S]*?)(?:\n[^\n\S]*)?\1/;
-
-  OPERATOR = /^(?:[-=]>|[-+*\/%<>&|^!?=]=|>>>=?|([-+:])\1|([&|<>])\2=?|\?(\.|::)|\.{2,3})/;
-
-  WHITESPACE = /^[^\n\S]+/;
-
-  COMMENT = /^###([^#][\s\S]*?)(?:###[^\n\S]*|(?:###)$)|^(?:\s*#(?!##[^#]).*)+/;
-
-  LITERATE = /^([ ]{4}|\t)/;
-
-  CODE = /^[-=]>/;
-
-  MULTI_DENT = /^(?:\n[^\n\S]*)+/;
-
-  SIMPLESTR = /^'[^\\']*(?:\\.[^\\']*)*'/;
-
-  JSTOKEN = /^`[^\\`]*(?:\\.[^\\`]*)*`/;
-
-  REGEX = /^(\/(?![\s=])[^[\/\n\\]*(?:(?:\\[\s\S]|\[[^\]\n\\]*(?:\\[\s\S][^\]\n\\]*)*])[^[\/\n\\]*)*\/)([imgy]{0,4})(?!\w)/;
-
-  HEREGEX = /^\/{3}([\s\S]+?)\/{3}([imgy]{0,4})(?!\w)/;
-
-  HEREGEX_OMIT = /\s+(?:#.*)?/g;
-
-  MULTILINER = /\n/g;
-
-  HEREDOC_INDENT = /\n+([^\n\S]*)/g;
-
-  HEREDOC_ILLEGAL = /\*\//;
-
-  LINE_CONTINUER = /^\s*(?:,|\??\.(?![.\d])|::)/;
-
-  TRAILING_SPACES = /\s+$/;
-
-  COMPOUND_ASSIGN = ['-=', '+=', '/=', '*=', '%=', '||=', '&&=', '?=', '<<=', '>>=', '>>>=', '&=', '^=', '|='];
-
-  UNARY = ['!', '~', 'NEW', 'TYPEOF', 'DELETE', 'DO'];
-
-  LOGIC = ['&&', '||', '&', '|', '^'];
-
-  SHIFT = ['<<', '>>', '>>>'];
-
-  COMPARE = ['==', '!=', '<', '>', '<=', '>='];
-
-  MATH = ['*', '/', '%'];
-
-  RELATION = ['IN', 'OF', 'INSTANCEOF'];
-
-  BOOL = ['TRUE', 'FALSE'];
-
-  NOT_REGEX = ['NUMBER', 'REGEX', 'BOOL', 'NULL', 'UNDEFINED', '++', '--', ']'];
-
-  NOT_SPACED_REGEX = NOT_REGEX.concat(')', '}', 'THIS', 'IDENTIFIER', 'STRING');
-
-  CALLABLE = ['IDENTIFIER', 'STRING', 'REGEX', ')', ']', '}', '?', '::', '@', 'THIS', 'SUPER'];
-
-  INDEXABLE = CALLABLE.concat('NUMBER', 'BOOL', 'NULL', 'UNDEFINED');
-
-  LINE_BREAK = ['INDENT', 'OUTDENT', 'TERMINATOR'];
-
-}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/nodes.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/nodes.js
deleted file mode 100755
index c274724d..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/nodes.js
+++ /dev/null
@@ -1,3088 +0,0 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var Access, Arr, Assign, Base, Block, Call, Class, Closure, Code, CodeFragment, Comment, Existence, Extends, For, IDENTIFIER, IDENTIFIER_STR, IS_STRING, If, In, Index, LEVEL_ACCESS, LEVEL_COND, LEVEL_LIST, LEVEL_OP, LEVEL_PAREN, LEVEL_TOP, Literal, METHOD_DEF, NEGATE, NO, Obj, Op, Param, Parens, RESERVED, Range, Return, SIMPLENUM, STRICT_PROSCRIBED, Scope, Slice, Splat, Switch, TAB, THIS, Throw, Try, UTILITIES, Value, While, YES, addLocationDataFn, compact, del, ends, extend, flatten, fragmentsToText, last, locationDataToString, merge, multident, some, starts, unfoldSoak, utility, _ref, _ref1,
-    __hasProp = {}.hasOwnProperty,
-    __extends = function(child, parent) { for (var key in parent) { if (__hasProp.call(parent, key)) child[key] = parent[key]; } function ctor() { this.constructor = child; } ctor.prototype = parent.prototype; child.prototype = new ctor(); child.__super__ = parent.prototype; return child; },
-    __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; },
-    __slice = [].slice;
-
-  Error.stackTraceLimit = Infinity;
-
-  Scope = require('./scope').Scope;
-
-  _ref = require('./lexer'), RESERVED = _ref.RESERVED, STRICT_PROSCRIBED = _ref.STRICT_PROSCRIBED;
-
-  _ref1 = require('./helpers'), compact = _ref1.compact, flatten = _ref1.flatten, extend = _ref1.extend, merge = _ref1.merge, del = _ref1.del, starts = _ref1.starts, ends = _ref1.ends, last = _ref1.last, some = _ref1.some, addLocationDataFn = _ref1.addLocationDataFn, locationDataToString = _ref1.locationDataToString;
-
-  exports.extend = extend;
-
-  exports.addLocationDataFn = addLocationDataFn;
-
-  YES = function() {
-    return true;
-  };
-
-  NO = function() {
-    return false;
-  };
-
-  THIS = function() {
-    return this;
-  };
-
-  NEGATE = function() {
-    this.negated = !this.negated;
-    return this;
-  };
-
-  exports.CodeFragment = CodeFragment = (function() {
-
-    function CodeFragment(parent, code) {
-      var _ref2;
-      this.code = "" + code;
-      this.locationData = parent != null ? parent.locationData : void 0;
-      this.type = (parent != null ? (_ref2 = parent.constructor) != null ? _ref2.name : void 0 : void 0) || 'unknown';
-    }
-
-    CodeFragment.prototype.toString = function() {
-      return "" + this.code + [this.locationData ? ": " + locationDataToString(this.locationData) : void 0];
-    };
-
-    return CodeFragment;
-
-  })();
-
-  fragmentsToText = function(fragments) {
-    var fragment;
-    return ((function() {
-      var _i, _len, _results;
-      _results = [];
-      for (_i = 0, _len = fragments.length; _i < _len; _i++) {
-        fragment = fragments[_i];
-        _results.push(fragment.code);
-      }
-      return _results;
-    })()).join('');
-  };
-
-  exports.Base = Base = (function() {
-
-    function Base() {}
-
-    Base.prototype.compile = function(o, lvl) {
-      return fragmentsToText(this.compileToFragments(o, lvl));
-    };
-
-    Base.prototype.compileToFragments = function(o, lvl) {
-      var node;
-      o = extend({}, o);
-      if (lvl) {
-        o.level = lvl;
-      }
-      node = this.unfoldSoak(o) || this;
-      node.tab = o.indent;
-      if (o.level === LEVEL_TOP || !node.isStatement(o)) {
-        return node.compileNode(o);
-      } else {
-        return node.compileClosure(o);
-      }
-    };
-
-    Base.prototype.compileClosure = function(o) {
-      if (this.jumps()) {
-        throw SyntaxError('cannot use a pure statement in an expression.');
-      }
-      o.sharedScope = true;
-      return Closure.wrap(this).compileNode(o);
-    };
-
-    Base.prototype.cache = function(o, level, reused) {
-      var ref, sub;
-      if (!this.isComplex()) {
-        ref = level ? this.compileToFragments(o, level) : this;
-        return [ref, ref];
-      } else {
-        ref = new Literal(reused || o.scope.freeVariable('ref'));
-        sub = new Assign(ref, this);
-        if (level) {
-          return [sub.compileToFragments(o, level), [this.makeCode(ref.value)]];
-        } else {
-          return [sub, ref];
-        }
-      }
-    };
-
-    Base.prototype.cacheToCodeFragments = function(cacheValues) {
-      return [fragmentsToText(cacheValues[0]), fragmentsToText(cacheValues[1])];
-    };
-
-    Base.prototype.makeReturn = function(res) {
-      var me;
-      me = this.unwrapAll();
-      if (res) {
-        return new Call(new Literal("" + res + ".push"), [me]);
-      } else {
-        return new Return(me);
-      }
-    };
-
-    Base.prototype.contains = function(pred) {
-      var contains;
-      contains = false;
-      this.traverseChildren(false, function(node) {
-        if (pred(node)) {
-          contains = true;
-          return false;
-        }
-      });
-      return contains;
-    };
-
-    Base.prototype.containsType = function(type) {
-      return this instanceof type || this.contains(function(node) {
-        return node instanceof type;
-      });
-    };
-
-    Base.prototype.lastNonComment = function(list) {
-      var i;
-      i = list.length;
-      while (i--) {
-        if (!(list[i] instanceof Comment)) {
-          return list[i];
-        }
-      }
-      return null;
-    };
-
-    Base.prototype.toString = function(idt, name) {
-      var location, tree;
-      if (idt == null) {
-        idt = '';
-      }
-      if (name == null) {
-        name = this.constructor.name;
-      }
-      location = this.locationData ? locationDataToString(this.locationData) : "??";
-      tree = '\n' + idt + location + ": " + name;
-      if (this.soak) {
-        tree += '?';
-      }
-      this.eachChild(function(node) {
-        return tree += node.toString(idt + TAB);
-      });
-      return tree;
-    };
-
-    Base.prototype.eachChild = function(func) {
-      var attr, child, _i, _j, _len, _len1, _ref2, _ref3;
-      if (!this.children) {
-        return this;
-      }
-      _ref2 = this.children;
-      for (_i = 0, _len = _ref2.length; _i < _len; _i++) {
-        attr = _ref2[_i];
-        if (this[attr]) {
-          _ref3 = flatten([this[attr]]);
-          for (_j = 0, _len1 = _ref3.length; _j < _len1; _j++) {
-            child = _ref3[_j];
-            if (func(child) === false) {
-              return this;
-            }
-          }
-        }
-      }
-      return this;
-    };
-
-    Base.prototype.traverseChildren = function(crossScope, func) {
-      return this.eachChild(function(child) {
-        if (func(child) === false) {
-          return false;
-        }
-        return child.traverseChildren(crossScope, func);
-      });
-    };
-
-    Base.prototype.invert = function() {
-      return new Op('!', this);
-    };
-
-    Base.prototype.unwrapAll = function() {
-      var node;
-      node = this;
-      while (node !== (node = node.unwrap())) {
-        continue;
-      }
-      return node;
-    };
-
-    Base.prototype.children = [];
-
-    Base.prototype.isStatement = NO;
-
-    Base.prototype.jumps = NO;
-
-    Base.prototype.isComplex = YES;
-
-    Base.prototype.isChainable = NO;
-
-    Base.prototype.isAssignable = NO;
-
-    Base.prototype.unwrap = THIS;
-
-    Base.prototype.unfoldSoak = NO;
-
-    Base.prototype.assigns = NO;
-
-    Base.prototype.updateLocationDataIfMissing = function(locationData) {
-      if (!this.locationData) {
-        this.locationData = {};
-        extend(this.locationData, locationData);
-      }
-      return this.eachChild(function(child) {
-        return child.updateLocationDataIfMissing(locationData);
-      });
-    };
-
-    Base.prototype.makeCode = function(code) {
-      return new CodeFragment(this, code);
-    };
-
-    Base.prototype.wrapInBraces = function(fragments) {
-      return [].concat(this.makeCode('('), fragments, this.makeCode(')'));
-    };
-
-    Base.prototype.joinFragmentArrays = function(fragmentsList, joinStr) {
-      var answer, fragments, i, _i, _len;
-      answer = [];
-      for (i = _i = 0, _len = fragmentsList.length; _i < _len; i = ++_i) {
-        fragments = fragmentsList[i];
-        if (i) {
-          answer.push(this.makeCode(joinStr));
-        }
-        answer = answer.concat(fragments);
-      }
-      return answer;
-    };
-
-    return Base;
-
-  })();
-
-  exports.Block = Block = (function(_super) {
-
-    __extends(Block, _super);
-
-    function Block(nodes) {
-      this.expressions = compact(flatten(nodes || []));
-    }
-
-    Block.prototype.children = ['expressions'];
-
-    Block.prototype.push = function(node) {
-      this.expressions.push(node);
-      return this;
-    };
-
-    Block.prototype.pop = function() {
-      return this.expressions.pop();
-    };
-
-    Block.prototype.unshift = function(node) {
-      this.expressions.unshift(node);
-      return this;
-    };
-
-    Block.prototype.unwrap = function() {
-      if (this.expressions.length === 1) {
-        return this.expressions[0];
-      } else {
-        return this;
-      }
-    };
-
-    Block.prototype.isEmpty = function() {
-      return !this.expressions.length;
-    };
-
-    Block.prototype.isStatement = function(o) {
-      var exp, _i, _len, _ref2;
-      _ref2 = this.expressions;
-      for (_i = 0, _len = _ref2.length; _i < _len; _i++) {
-        exp = _ref2[_i];
-        if (exp.isStatement(o)) {
-          return true;
-        }
-      }
-      return false;
-    };
-
-    Block.prototype.jumps = function(o) {
-      var exp, _i, _len, _ref2;
-      _ref2 = this.expressions;
-      for (_i = 0, _len = _ref2.length; _i < _len; _i++) {
-        exp = _ref2[_i];
-        if (exp.jumps(o)) {
-          return exp;
-        }
-      }
-    };
-
-    Block.prototype.makeReturn = function(res) {
-      var expr, len;
-      len = this.expressions.length;
-      while (len--) {
-        expr = this.expressions[len];
-        if (!(expr instanceof Comment)) {
-          this.expressions[len] = expr.makeReturn(res);
-          if (expr instanceof Return && !expr.expression) {
-            this.expressions.splice(len, 1);
-          }
-          break;
-        }
-      }
-      return this;
-    };
-
-    Block.prototype.compileToFragments = function(o, level) {
-      if (o == null) {
-        o = {};
-      }
-      if (o.scope) {
-        return Block.__super__.compileToFragments.call(this, o, level);
-      } else {
-        return this.compileRoot(o);
-      }
-    };
-
-    Block.prototype.compileNode = function(o) {
-      var answer, compiledNodes, fragments, index, node, top, _i, _len, _ref2;
-      this.tab = o.indent;
-      top = o.level === LEVEL_TOP;
-      compiledNodes = [];
-      _ref2 = this.expressions;
-      for (index = _i = 0, _len = _ref2.length; _i < _len; index = ++_i) {
-        node = _ref2[index];
-        node = node.unwrapAll();
-        node = node.unfoldSoak(o) || node;
-        if (node instanceof Block) {
-          compiledNodes.push(node.compileNode(o));
-        } else if (top) {
-          node.front = true;
-          fragments = node.compileToFragments(o);
-          if (!node.isStatement(o)) {
-            fragments.unshift(this.makeCode("" + this.tab));
-            fragments.push(this.makeCode(";"));
-          }
-          compiledNodes.push(fragments);
-        } else {
-          compiledNodes.push(node.compileToFragments(o, LEVEL_LIST));
-        }
-      }
-      if (top) {
-        if (this.spaced) {
-          return [].concat(this.makeCode("\n"), this.joinFragmentArrays(compiledNodes, '\n\n'), this.makeCode("\n"));
-        } else {
-          return this.joinFragmentArrays(compiledNodes, '\n');
-        }
-      }
-      if (compiledNodes.length) {
-        answer = this.joinFragmentArrays(compiledNodes, ', ');
-      } else {
-        answer = [this.makeCode("void 0")];
-      }
-      if (compiledNodes.length > 1 && o.level >= LEVEL_LIST) {
-        return this.wrapInBraces(answer);
-      } else {
-        return answer;
-      }
-    };
-
-    Block.prototype.compileRoot = function(o) {
-      var exp, fragments, i, prelude, preludeExps, rest;
-      o.indent = o.bare ? '' : TAB;
-      o.scope = new Scope(null, this, null);
-      o.level = LEVEL_TOP;
-      this.spaced = true;
-      prelude = [];
-      if (!o.bare) {
-        preludeExps = (function() {
-          var _i, _len, _ref2, _results;
-          _ref2 = this.expressions;
-          _results = [];
-          for (i = _i = 0, _len = _ref2.length; _i < _len; i = ++_i) {
-            exp = _ref2[i];
-            if (!(exp.unwrap() instanceof Comment)) {
-              break;
-            }
-            _results.push(exp);
-          }
-          return _results;
-        }).call(this);
-        rest = this.expressions.slice(preludeExps.length);
-        this.expressions = preludeExps;
-        if (preludeExps.length) {
-          prelude = this.compileNode(merge(o, {
-            indent: ''
-          }));
-          prelude.push(this.makeCode("\n"));
-        }
-        this.expressions = rest;
-      }
-      fragments = this.compileWithDeclarations(o);
-      if (o.bare) {
-        return fragments;
-      }
-      return [].concat(prelude, this.makeCode("(function() {\n"), fragments, this.makeCode("\n}).call(this);\n"));
-    };
-
-    Block.prototype.compileWithDeclarations = function(o) {
-      var assigns, declars, exp, fragments, i, post, rest, scope, spaced, _i, _len, _ref2, _ref3, _ref4;
-      fragments = [];
-      post = [];
-      _ref2 = this.expressions;
-      for (i = _i = 0, _len = _ref2.length; _i < _len; i = ++_i) {
-        exp = _ref2[i];
-        exp = exp.unwrap();
-        if (!(exp instanceof Comment || exp instanceof Literal)) {
-          break;
-        }
-      }
-      o = merge(o, {
-        level: LEVEL_TOP
-      });
-      if (i) {
-        rest = this.expressions.splice(i, 9e9);
-        _ref3 = [this.spaced, false], spaced = _ref3[0], this.spaced = _ref3[1];
-        _ref4 = [this.compileNode(o), spaced], fragments = _ref4[0], this.spaced = _ref4[1];
-        this.expressions = rest;
-      }
-      post = this.compileNode(o);
-      scope = o.scope;
-      if (scope.expressions === this) {
-        declars = o.scope.hasDeclarations();
-        assigns = scope.hasAssignments;
-        if (declars || assigns) {
-          if (i) {
-            fragments.push(this.makeCode('\n'));
-          }
-          fragments.push(this.makeCode("" + this.tab + "var "));
-          if (declars) {
-            fragments.push(this.makeCode(scope.declaredVariables().join(', ')));
-          }
-          if (assigns) {
-            if (declars) {
-              fragments.push(this.makeCode(",\n" + (this.tab + TAB)));
-            }
-            fragments.push(this.makeCode(scope.assignedVariables().join(",\n" + (this.tab + TAB))));
-          }
-          fragments.push(this.makeCode(';\n'));
-        }
-      }
-      return fragments.concat(post);
-    };
-
-    Block.wrap = function(nodes) {
-      if (nodes.length === 1 && nodes[0] instanceof Block) {
-        return nodes[0];
-      }
-      return new Block(nodes);
-    };
-
-    return Block;
-
-  })(Base);
-
-  exports.Literal = Literal = (function(_super) {
-
-    __extends(Literal, _super);
-
-    function Literal(value) {
-      this.value = value;
-    }
-
-    Literal.prototype.makeReturn = function() {
-      if (this.isStatement()) {
-        return this;
-      } else {
-        return Literal.__super__.makeReturn.apply(this, arguments);
-      }
-    };
-
-    Literal.prototype.isAssignable = function() {
-      return IDENTIFIER.test(this.value);
-    };
-
-    Literal.prototype.isStatement = function() {
-      var _ref2;
-      return (_ref2 = this.value) === 'break' || _ref2 === 'continue' || _ref2 === 'debugger';
-    };
-
-    Literal.prototype.isComplex = NO;
-
-    Literal.prototype.assigns = function(name) {
-      return name === this.value;
-    };
-
-    Literal.prototype.jumps = function(o) {
-      if (this.value === 'break' && !((o != null ? o.loop : void 0) || (o != null ? o.block : void 0))) {
-        return this;
-      }
-      if (this.value === 'continue' && !(o != null ? o.loop : void 0)) {
-        return this;
-      }
-    };
-
-    Literal.prototype.compileNode = function(o) {
-      var answer, code, _ref2;
-      code = this.value === 'this' ? ((_ref2 = o.scope.method) != null ? _ref2.bound : void 0) ? o.scope.method.context : this.value : this.value.reserved ? "\"" + this.value + "\"" : this.value;
-      answer = this.isStatement() ? "" + this.tab + code + ";" : code;
-      return [this.makeCode(answer)];
-    };
-
-    Literal.prototype.toString = function() {
-      return ' "' + this.value + '"';
-    };
-
-    return Literal;
-
-  })(Base);
-
-  exports.Undefined = (function(_super) {
-
-    __extends(Undefined, _super);
-
-    function Undefined() {
-      return Undefined.__super__.constructor.apply(this, arguments);
-    }
-
-    Undefined.prototype.isAssignable = NO;
-
-    Undefined.prototype.isComplex = NO;
-
-    Undefined.prototype.compileNode = function(o) {
-      return [this.makeCode(o.level >= LEVEL_ACCESS ? '(void 0)' : 'void 0')];
-    };
-
-    return Undefined;
-
-  })(Base);
-
-  exports.Null = (function(_super) {
-
-    __extends(Null, _super);
-
-    function Null() {
-      return Null.__super__.constructor.apply(this, arguments);
-    }
-
-    Null.prototype.isAssignable = NO;
-
-    Null.prototype.isComplex = NO;
-
-    Null.prototype.compileNode = function() {
-      return [this.makeCode("null")];
-    };
-
-    return Null;
-
-  })(Base);
-
-  exports.Bool = (function(_super) {
-
-    __extends(Bool, _super);
-
-    Bool.prototype.isAssignable = NO;
-
-    Bool.prototype.isComplex = NO;
-
-    Bool.prototype.compileNode = function() {
-      return [this.makeCode(this.val)];
-    };
-
-    function Bool(val) {
-      this.val = val;
-    }
-
-    return Bool;
-
-  })(Base);
-
-  exports.Return = Return = (function(_super) {
-
-    __extends(Return, _super);
-
-    function Return(expr) {
-      if (expr && !expr.unwrap().isUndefined) {
-        this.expression = expr;
-      }
-    }
-
-    Return.prototype.children = ['expression'];
-
-    Return.prototype.isStatement = YES;
-
-    Return.prototype.makeReturn = THIS;
-
-    Return.prototype.jumps = THIS;
-
-    Return.prototype.compileToFragments = function(o, level) {
-      var expr, _ref2;
-      expr = (_ref2 = this.expression) != null ? _ref2.makeReturn() : void 0;
-      if (expr && !(expr instanceof Return)) {
-        return expr.compileToFragments(o, level);
-      } else {
-        return Return.__super__.compileToFragments.call(this, o, level);
-      }
-    };
-
-    Return.prototype.compileNode = function(o) {
-      var answer;
-      answer = [];
-      answer.push(this.makeCode(this.tab + ("return" + [this.expression ? " " : void 0])));
-      if (this.expression) {
-        answer = answer.concat(this.expression.compileToFragments(o, LEVEL_PAREN));
-      }
-      answer.push(this.makeCode(";"));
-      return answer;
-    };
-
-    return Return;
-
-  })(Base);
-
-  exports.Value = Value = (function(_super) {
-
-    __extends(Value, _super);
-
-    function Value(base, props, tag) {
-      if (!props && base instanceof Value) {
-        return base;
-      }
-      this.base = base;
-      this.properties = props || [];
-      if (tag) {
-        this[tag] = true;
-      }
-      return this;
-    }
-
-    Value.prototype.children = ['base', 'properties'];
-
-    Value.prototype.add = function(props) {
-      this.properties = this.properties.concat(props);
-      return this;
-    };
-
-    Value.prototype.hasProperties = function() {
-      return !!this.properties.length;
-    };
-
-    Value.prototype.isArray = function() {
-      return !this.properties.length && this.base instanceof Arr;
-    };
-
-    Value.prototype.isComplex = function() {
-      return this.hasProperties() || this.base.isComplex();
-    };
-
-    Value.prototype.isAssignable = function() {
-      return this.hasProperties() || this.base.isAssignable();
-    };
-
-    Value.prototype.isSimpleNumber = function() {
-      return this.base instanceof Literal && SIMPLENUM.test(this.base.value);
-    };
-
-    Value.prototype.isString = function() {
-      return this.base instanceof Literal && IS_STRING.test(this.base.value);
-    };
-
-    Value.prototype.isAtomic = function() {
-      var node, _i, _len, _ref2;
-      _ref2 = this.properties.concat(this.base);
-      for (_i = 0, _len = _ref2.length; _i < _len; _i++) {
-        node = _ref2[_i];
-        if (node.soak || node instanceof Call) {
-          return false;
-        }
-      }
-      return true;
-    };
-
-    Value.prototype.isStatement = function(o) {
-      return !this.properties.length && this.base.isStatement(o);
-    };
-
-    Value.prototype.assigns = function(name) {
-      return !this.properties.length && this.base.assigns(name);
-    };
-
-    Value.prototype.jumps = function(o) {
-      return !this.properties.length && this.base.jumps(o);
-    };
-
-    Value.prototype.isObject = function(onlyGenerated) {
-      if (this.properties.length) {
-        return false;
-      }
-      return (this.base instanceof Obj) && (!onlyGenerated || this.base.generated);
-    };
-
-    Value.prototype.isSplice = function() {
-      return last(this.properties) instanceof Slice;
-    };
-
-    Value.prototype.unwrap = function() {
-      if (this.properties.length) {
-        return this;
-      } else {
-        return this.base;
-      }
-    };
-
-    Value.prototype.cacheReference = function(o) {
-      var base, bref, name, nref;
-      name = last(this.properties);
-      if (this.properties.length < 2 && !this.base.isComplex() && !(name != null ? name.isComplex() : void 0)) {
-        return [this, this];
-      }
-      base = new Value(this.base, this.properties.slice(0, -1));
-      if (base.isComplex()) {
-        bref = new Literal(o.scope.freeVariable('base'));
-        base = new Value(new Parens(new Assign(bref, base)));
-      }
-      if (!name) {
-        return [base, bref];
-      }
-      if (name.isComplex()) {
-        nref = new Literal(o.scope.freeVariable('name'));
-        name = new Index(new Assign(nref, name.index));
-        nref = new Index(nref);
-      }
-      return [base.add(name), new Value(bref || base.base, [nref || name])];
-    };
-
-    Value.prototype.compileNode = function(o) {
-      var fragments, prop, props, _i, _len;
-      this.base.front = this.front;
-      props = this.properties;
-      fragments = this.base.compileToFragments(o, (props.length ? LEVEL_ACCESS : null));
-      if ((this.base instanceof Parens || props.length) && SIMPLENUM.test(fragmentsToText(fragments))) {
-        fragments.push(this.makeCode('.'));
-      }
-      for (_i = 0, _len = props.length; _i < _len; _i++) {
-        prop = props[_i];
-        fragments.push.apply(fragments, prop.compileToFragments(o));
-      }
-      return fragments;
-    };
-
-    Value.prototype.unfoldSoak = function(o) {
-      var _ref2,
-        _this = this;
-      return (_ref2 = this.unfoldedSoak) != null ? _ref2 : this.unfoldedSoak = (function() {
-        var fst, i, ifn, prop, ref, snd, _i, _len, _ref3, _ref4;
-        if (ifn = _this.base.unfoldSoak(o)) {
-          (_ref3 = ifn.body.properties).push.apply(_ref3, _this.properties);
-          return ifn;
-        }
-        _ref4 = _this.properties;
-        for (i = _i = 0, _len = _ref4.length; _i < _len; i = ++_i) {
-          prop = _ref4[i];
-          if (!prop.soak) {
-            continue;
-          }
-          prop.soak = false;
-          fst = new Value(_this.base, _this.properties.slice(0, i));
-          snd = new Value(_this.base, _this.properties.slice(i));
-          if (fst.isComplex()) {
-            ref = new Literal(o.scope.freeVariable('ref'));
-            fst = new Parens(new Assign(ref, fst));
-            snd.base = ref;
-          }
-          return new If(new Existence(fst), snd, {
-            soak: true
-          });
-        }
-        return false;
-      })();
-    };
-
-    return Value;
-
-  })(Base);
-
-  exports.Comment = Comment = (function(_super) {
-
-    __extends(Comment, _super);
-
-    function Comment(comment) {
-      this.comment = comment;
-    }
-
-    Comment.prototype.isStatement = YES;
-
-    Comment.prototype.makeReturn = THIS;
-
-    Comment.prototype.compileNode = function(o, level) {
-      var code;
-      code = '/*' + multident(this.comment, this.tab) + ("\n" + this.tab + "*/\n");
-      if ((level || o.level) === LEVEL_TOP) {
-        code = o.indent + code;
-      }
-      return [this.makeCode(code)];
-    };
-
-    return Comment;
-
-  })(Base);
-
-  exports.Call = Call = (function(_super) {
-
-    __extends(Call, _super);
-
-    function Call(variable, args, soak) {
-      this.args = args != null ? args : [];
-      this.soak = soak;
-      this.isNew = false;
-      this.isSuper = variable === 'super';
-      this.variable = this.isSuper ? null : variable;
-    }
-
-    Call.prototype.children = ['variable', 'args'];
-
-    Call.prototype.newInstance = function() {
-      var base, _ref2;
-      base = ((_ref2 = this.variable) != null ? _ref2.base : void 0) || this.variable;
-      if (base instanceof Call && !base.isNew) {
-        base.newInstance();
-      } else {
-        this.isNew = true;
-      }
-      return this;
-    };
-
-    Call.prototype.superReference = function(o) {
-      var accesses, method;
-      method = o.scope.namedMethod();
-      if (method != null ? method.klass : void 0) {
-        accesses = [new Access(new Literal('__super__'))];
-        if (method["static"]) {
-          accesses.push(new Access(new Literal('constructor')));
-        }
-        accesses.push(new Access(new Literal(method.name)));
-        return (new Value(new Literal(method.klass), accesses)).compile(o);
-      } else if (method != null ? method.ctor : void 0) {
-        return "" + method.name + ".__super__.constructor";
-      } else {
-        throw SyntaxError('cannot call super outside of an instance method.');
-      }
-    };
-
-    Call.prototype.superThis = function(o) {
-      var method;
-      method = o.scope.method;
-      return (method && !method.klass && method.context) || "this";
-    };
-
-    Call.prototype.unfoldSoak = function(o) {
-      var call, ifn, left, list, rite, _i, _len, _ref2, _ref3;
-      if (this.soak) {
-        if (this.variable) {
-          if (ifn = unfoldSoak(o, this, 'variable')) {
-            return ifn;
-          }
-          _ref2 = new Value(this.variable).cacheReference(o), left = _ref2[0], rite = _ref2[1];
-        } else {
-          left = new Literal(this.superReference(o));
-          rite = new Value(left);
-        }
-        rite = new Call(rite, this.args);
-        rite.isNew = this.isNew;
-        left = new Literal("typeof " + (left.compile(o)) + " === \"function\"");
-        return new If(left, new Value(rite), {
-          soak: true
-        });
-      }
-      call = this;
-      list = [];
-      while (true) {
-        if (call.variable instanceof Call) {
-          list.push(call);
-          call = call.variable;
-          continue;
-        }
-        if (!(call.variable instanceof Value)) {
-          break;
-        }
-        list.push(call);
-        if (!((call = call.variable.base) instanceof Call)) {
-          break;
-        }
-      }
-      _ref3 = list.reverse();
-      for (_i = 0, _len = _ref3.length; _i < _len; _i++) {
-        call = _ref3[_i];
-        if (ifn) {
-          if (call.variable instanceof Call) {
-            call.variable = ifn;
-          } else {
-            call.variable.base = ifn;
-          }
-        }
-        ifn = unfoldSoak(o, call, 'variable');
-      }
-      return ifn;
-    };
-
-    Call.prototype.compileNode = function(o) {
-      var arg, argIndex, compiledArgs, compiledArray, fragments, preface, _i, _len, _ref2, _ref3;
-      if ((_ref2 = this.variable) != null) {
-        _ref2.front = this.front;
-      }
-      compiledArray = Splat.compileSplattedArray(o, this.args, true);
-      if (compiledArray.length) {
-        return this.compileSplat(o, compiledArray);
-      }
-      compiledArgs = [];
-      _ref3 = this.args;
-      for (argIndex = _i = 0, _len = _ref3.length; _i < _len; argIndex = ++_i) {
-        arg = _ref3[argIndex];
-        if (argIndex) {
-          compiledArgs.push(this.makeCode(", "));
-        }
-        compiledArgs.push.apply(compiledArgs, arg.compileToFragments(o, LEVEL_LIST));
-      }
-      fragments = [];
-      if (this.isSuper) {
-        preface = this.superReference(o) + (".call(" + (this.superThis(o)));
-        if (compiledArgs.length) {
-          preface += ", ";
-        }
-        fragments.push(this.makeCode(preface));
-      } else {
-        if (this.isNew) {
-          fragments.push(this.makeCode('new '));
-        }
-        fragments.push.apply(fragments, this.variable.compileToFragments(o, LEVEL_ACCESS));
-        fragments.push(this.makeCode("("));
-      }
-      fragments.push.apply(fragments, compiledArgs);
-      fragments.push(this.makeCode(")"));
-      return fragments;
-    };
-
-    Call.prototype.compileSplat = function(o, splatArgs) {
-      var answer, base, fun, idt, name, ref;
-      if (this.isSuper) {
-        return [].concat(this.makeCode("" + (this.superReference(o)) + ".apply(" + (this.superThis(o)) + ", "), splatArgs, this.makeCode(")"));
-      }
-      if (this.isNew) {
-        idt = this.tab + TAB;
-        return [].concat(this.makeCode("(function(func, args, ctor) {\n" + idt + "ctor.prototype = func.prototype;\n" + idt + "var child = new ctor, result = func.apply(child, args);\n" + idt + "return Object(result) === result ? result : child;\n" + this.tab + "})("), this.variable.compileToFragments(o, LEVEL_LIST), this.makeCode(", "), splatArgs, this.makeCode(", function(){})"));
-      }
-      answer = [];
-      base = new Value(this.variable);
-      if ((name = base.properties.pop()) && base.isComplex()) {
-        ref = o.scope.freeVariable('ref');
-        answer = answer.concat(this.makeCode("(" + ref + " = "), base.compileToFragments(o, LEVEL_LIST), this.makeCode(")"), name.compileToFragments(o));
-      } else {
-        fun = base.compileToFragments(o, LEVEL_ACCESS);
-        if (SIMPLENUM.test(fragmentsToText(fun))) {
-          fun = this.wrapInBraces(fun);
-        }
-        if (name) {
-          ref = fragmentsToText(fun);
-          fun.push.apply(fun, name.compileToFragments(o));
-        } else {
-          ref = 'null';
-        }
-        answer = answer.concat(fun);
-      }
-      return answer = answer.concat(this.makeCode(".apply(" + ref + ", "), splatArgs, this.makeCode(")"));
-    };
-
-    return Call;
-
-  })(Base);
-
-  exports.Extends = Extends = (function(_super) {
-
-    __extends(Extends, _super);
-
-    function Extends(child, parent) {
-      this.child = child;
-      this.parent = parent;
-    }
-
-    Extends.prototype.children = ['child', 'parent'];
-
-    Extends.prototype.compileToFragments = function(o) {
-      return new Call(new Value(new Literal(utility('extends'))), [this.child, this.parent]).compileToFragments(o);
-    };
-
-    return Extends;
-
-  })(Base);
-
-  exports.Access = Access = (function(_super) {
-
-    __extends(Access, _super);
-
-    function Access(name, tag) {
-      this.name = name;
-      this.name.asKey = true;
-      this.soak = tag === 'soak';
-    }
-
-    Access.prototype.children = ['name'];
-
-    Access.prototype.compileToFragments = function(o) {
-      var name;
-      name = this.name.compileToFragments(o);
-      if (IDENTIFIER.test(fragmentsToText(name))) {
-        name.unshift(this.makeCode("."));
-      } else {
-        name.unshift(this.makeCode("["));
-        name.push(this.makeCode("]"));
-      }
-      return name;
-    };
-
-    Access.prototype.isComplex = NO;
-
-    return Access;
-
-  })(Base);
-
-  exports.Index = Index = (function(_super) {
-
-    __extends(Index, _super);
-
-    function Index(index) {
-      this.index = index;
-    }
-
-    Index.prototype.children = ['index'];
-
-    Index.prototype.compileToFragments = function(o) {
-      return [].concat(this.makeCode("["), this.index.compileToFragments(o, LEVEL_PAREN), this.makeCode("]"));
-    };
-
-    Index.prototype.isComplex = function() {
-      return this.index.isComplex();
-    };
-
-    return Index;
-
-  })(Base);
-
-  exports.Range = Range = (function(_super) {
-
-    __extends(Range, _super);
-
-    Range.prototype.children = ['from', 'to'];
-
-    function Range(from, to, tag) {
-      this.from = from;
-      this.to = to;
-      this.exclusive = tag === 'exclusive';
-      this.equals = this.exclusive ? '' : '=';
-    }
-
-    Range.prototype.compileVariables = function(o) {
-      var step, _ref2, _ref3, _ref4, _ref5;
-      o = merge(o, {
-        top: true
-      });
-      _ref2 = this.cacheToCodeFragments(this.from.cache(o, LEVEL_LIST)), this.fromC = _ref2[0], this.fromVar = _ref2[1];
-      _ref3 = this.cacheToCodeFragments(this.to.cache(o, LEVEL_LIST)), this.toC = _ref3[0], this.toVar = _ref3[1];
-      if (step = del(o, 'step')) {
-        _ref4 = this.cacheToCodeFragments(step.cache(o, LEVEL_LIST)), this.step = _ref4[0], this.stepVar = _ref4[1];
-      }
-      _ref5 = [this.fromVar.match(SIMPLENUM), this.toVar.match(SIMPLENUM)], this.fromNum = _ref5[0], this.toNum = _ref5[1];
-      if (this.stepVar) {
-        return this.stepNum = this.stepVar.match(SIMPLENUM);
-      }
-    };
-
-    Range.prototype.compileNode = function(o) {
-      var cond, condPart, from, gt, idx, idxName, known, lt, namedIndex, stepPart, to, varPart, _ref2, _ref3;
-      if (!this.fromVar) {
-        this.compileVariables(o);
-      }
-      if (!o.index) {
-        return this.compileArray(o);
-      }
-      known = this.fromNum && this.toNum;
-      idx = del(o, 'index');
-      idxName = del(o, 'name');
-      namedIndex = idxName && idxName !== idx;
-      varPart = "" + idx + " = " + this.fromC;
-      if (this.toC !== this.toVar) {
-        varPart += ", " + this.toC;
-      }
-      if (this.step !== this.stepVar) {
-        varPart += ", " + this.step;
-      }
-      _ref2 = ["" + idx + " <" + this.equals, "" + idx + " >" + this.equals], lt = _ref2[0], gt = _ref2[1];
-      condPart = this.stepNum ? +this.stepNum > 0 ? "" + lt + " " + this.toVar : "" + gt + " " + this.toVar : known ? ((_ref3 = [+this.fromNum, +this.toNum], from = _ref3[0], to = _ref3[1], _ref3), from <= to ? "" + lt + " " + to : "" + gt + " " + to) : (cond = this.stepVar ? "" + this.stepVar + " > 0" : "" + this.fromVar + " <= " + this.toVar, "" + cond + " ? " + lt + " " + this.toVar + " : " + gt + " " + this.toVar);
-      stepPart = this.stepVar ? "" + idx + " += " + this.stepVar : known ? namedIndex ? from <= to ? "++" + idx : "--" + idx : from <= to ? "" + idx + "++" : "" + idx + "--" : namedIndex ? "" + cond + " ? ++" + idx + " : --" + idx : "" + cond + " ? " + idx + "++ : " + idx + "--";
-      if (namedIndex) {
-        varPart = "" + idxName + " = " + varPart;
-      }
-      if (namedIndex) {
-        stepPart = "" + idxName + " = " + stepPart;
-      }
-      return [this.makeCode("" + varPart + "; " + condPart + "; " + stepPart)];
-    };
-
-    Range.prototype.compileArray = function(o) {
-      var args, body, cond, hasArgs, i, idt, post, pre, range, result, vars, _i, _ref2, _ref3, _results;
-      if (this.fromNum && this.toNum && Math.abs(this.fromNum - this.toNum) <= 20) {
-        range = (function() {
-          _results = [];
-          for (var _i = _ref2 = +this.fromNum, _ref3 = +this.toNum; _ref2 <= _ref3 ? _i <= _ref3 : _i >= _ref3; _ref2 <= _ref3 ? _i++ : _i--){ _results.push(_i); }
-          return _results;
-        }).apply(this);
-        if (this.exclusive) {
-          range.pop();
-        }
-        return [this.makeCode("[" + (range.join(', ')) + "]")];
-      }
-      idt = this.tab + TAB;
-      i = o.scope.freeVariable('i');
-      result = o.scope.freeVariable('results');
-      pre = "\n" + idt + result + " = [];";
-      if (this.fromNum && this.toNum) {
-        o.index = i;
-        body = fragmentsToText(this.compileNode(o));
-      } else {
-        vars = ("" + i + " = " + this.fromC) + (this.toC !== this.toVar ? ", " + this.toC : '');
-        cond = "" + this.fromVar + " <= " + this.toVar;
-        body = "var " + vars + "; " + cond + " ? " + i + " <" + this.equals + " " + this.toVar + " : " + i + " >" + this.equals + " " + this.toVar + "; " + cond + " ? " + i + "++ : " + i + "--";
-      }
-      post = "{ " + result + ".push(" + i + "); }\n" + idt + "return " + result + ";\n" + o.indent;
-      hasArgs = function(node) {
-        return node != null ? node.contains(function(n) {
-          return n instanceof Literal && n.value === 'arguments' && !n.asKey;
-        }) : void 0;
-      };
-      if (hasArgs(this.from) || hasArgs(this.to)) {
-        args = ', arguments';
-      }
-      return [this.makeCode("(function() {" + pre + "\n" + idt + "for (" + body + ")" + post + "}).apply(this" + (args != null ? args : '') + ")")];
-    };
-
-    return Range;
-
-  })(Base);
-
-  exports.Slice = Slice = (function(_super) {
-
-    __extends(Slice, _super);
-
-    Slice.prototype.children = ['range'];
-
-    function Slice(range) {
-      this.range = range;
-      Slice.__super__.constructor.call(this);
-    }
-
-    Slice.prototype.compileNode = function(o) {
-      var compiled, compiledText, from, fromCompiled, to, toStr, _ref2;
-      _ref2 = this.range, to = _ref2.to, from = _ref2.from;
-      fromCompiled = from && from.compileToFragments(o, LEVEL_PAREN) || [this.makeCode('0')];
-      if (to) {
-        compiled = to.compileToFragments(o, LEVEL_PAREN);
-        compiledText = fragmentsToText(compiled);
-        if (!(!this.range.exclusive && +compiledText === -1)) {
-          toStr = ', ' + (this.range.exclusive ? compiledText : SIMPLENUM.test(compiledText) ? "" + (+compiledText + 1) : (compiled = to.compileToFragments(o, LEVEL_ACCESS), "+" + (fragmentsToText(compiled)) + " + 1 || 9e9"));
-        }
-      }
-      return [this.makeCode(".slice(" + (fragmentsToText(fromCompiled)) + (toStr || '') + ")")];
-    };
-
-    return Slice;
-
-  })(Base);
-
-  exports.Obj = Obj = (function(_super) {
-
-    __extends(Obj, _super);
-
-    function Obj(props, generated) {
-      this.generated = generated != null ? generated : false;
-      this.objects = this.properties = props || [];
-    }
-
-    Obj.prototype.children = ['properties'];
-
-    Obj.prototype.compileNode = function(o) {
-      var answer, i, idt, indent, join, lastNoncom, node, prop, props, _i, _j, _len, _len1;
-      props = this.properties;
-      if (!props.length) {
-        return [this.makeCode(this.front ? '({})' : '{}')];
-      }
-      if (this.generated) {
-        for (_i = 0, _len = props.length; _i < _len; _i++) {
-          node = props[_i];
-          if (node instanceof Value) {
-            throw new Error('cannot have an implicit value in an implicit object');
-          }
-        }
-      }
-      idt = o.indent += TAB;
-      lastNoncom = this.lastNonComment(this.properties);
-      answer = [];
-      for (i = _j = 0, _len1 = props.length; _j < _len1; i = ++_j) {
-        prop = props[i];
-        join = i === props.length - 1 ? '' : prop === lastNoncom || prop instanceof Comment ? '\n' : ',\n';
-        indent = prop instanceof Comment ? '' : idt;
-        if (prop instanceof Value && prop["this"]) {
-          prop = new Assign(prop.properties[0].name, prop, 'object');
-        }
-        if (!(prop instanceof Comment)) {
-          if (!(prop instanceof Assign)) {
-            prop = new Assign(prop, prop, 'object');
-          }
-          (prop.variable.base || prop.variable).asKey = true;
-        }
-        if (indent) {
-          answer.push(this.makeCode(indent));
-        }
-        answer.push.apply(answer, prop.compileToFragments(o, LEVEL_TOP));
-        if (join) {
-          answer.push(this.makeCode(join));
-        }
-      }
-      answer.unshift(this.makeCode("{" + (props.length && '\n')));
-      answer.push(this.makeCode("" + (props.length && '\n' + this.tab) + "}"));
-      if (this.front) {
-        return this.wrapInBraces(answer);
-      } else {
-        return answer;
-      }
-    };
-
-    Obj.prototype.assigns = function(name) {
-      var prop, _i, _len, _ref2;
-      _ref2 = this.properties;
-      for (_i = 0, _len = _ref2.length; _i < _len; _i++) {
-        prop = _ref2[_i];
-        if (prop.assigns(name)) {
-          return true;
-        }
-      }
-      return false;
-    };
-
-    return Obj;
-
-  })(Base);
-
-  exports.Arr = Arr = (function(_super) {
-
-    __extends(Arr, _super);
-
-    function Arr(objs) {
-      this.objects = objs || [];
-    }
-
-    Arr.prototype.children = ['objects'];
-
-    Arr.prototype.compileNode = function(o) {
-      var answer, compiledObjs, fragments, index, obj, _i, _len;
-      if (!this.objects.length) {
-        return [this.makeCode('[]')];
-      }
-      o.indent += TAB;
-      answer = Splat.compileSplattedArray(o, this.objects);
-      if (answer.length) {
-        return answer;
-      }
-      answer = [];
-      compiledObjs = (function() {
-        var _i, _len, _ref2, _results;
-        _ref2 = this.objects;
-        _results = [];
-        for (_i = 0, _len = _ref2.length; _i < _len; _i++) {
-          obj = _ref2[_i];
-          _results.push(obj.compileToFragments(o, LEVEL_LIST));
-        }
-        return _results;
-      }).call(this);
-      for (index = _i = 0, _len = compiledObjs.length; _i < _len; index = ++_i) {
-        fragments = compiledObjs[index];
-        if (index) {
-          answer.push(this.makeCode(", "));
-        }
-        answer.push.apply(answer, fragments);
-      }
-      if ((fragmentsToText(answer)).indexOf('\n') >= 0) {
-        answer.unshift(this.makeCode("[\n" + o.indent));
-        answer.push(this.makeCode("\n" + this.tab + "]"));
-      } else {
-        answer.unshift(this.makeCode("["));
-        answer.push(this.makeCode("]"));
-      }
-      return answer;
-    };
-
-    Arr.prototype.assigns = function(name) {
-      var obj, _i, _len, _ref2;
-      _ref2 = this.objects;
-      for (_i = 0, _len = _ref2.length; _i < _len; _i++) {
-        obj = _ref2[_i];
-        if (obj.assigns(name)) {
-          return true;
-        }
-      }
-      return false;
-    };
-
-    return Arr;
-
-  })(Base);
-
-  exports.Class = Class = (function(_super) {
-
-    __extends(Class, _super);
-
-    function Class(variable, parent, body) {
-      this.variable = variable;
-      this.parent = parent;
-      this.body = body != null ? body : new Block;
-      this.boundFuncs = [];
-      this.body.classBody = true;
-    }
-
-    Class.prototype.children = ['variable', 'parent', 'body'];
-
-    Class.prototype.determineName = function() {
-      var decl, tail;
-      if (!this.variable) {
-        return null;
-      }
-      decl = (tail = last(this.variable.properties)) ? tail instanceof Access && tail.name.value : this.variable.base.value;
-      if (__indexOf.call(STRICT_PROSCRIBED, decl) >= 0) {
-        throw SyntaxError("variable name may not be " + decl);
-      }
-      return decl && (decl = IDENTIFIER.test(decl) && decl);
-    };
-
-    Class.prototype.setContext = function(name) {
-      return this.body.traverseChildren(false, function(node) {
-        if (node.classBody) {
-          return false;
-        }
-        if (node instanceof Literal && node.value === 'this') {
-          return node.value = name;
-        } else if (node instanceof Code) {
-          node.klass = name;
-          if (node.bound) {
-            return node.context = name;
-          }
-        }
-      });
-    };
-
-    Class.prototype.addBoundFunctions = function(o) {
-      var body, bound, func, lhs, name, rhs, _i, _len, _ref2, _ref3;
-      if (this.boundFuncs.length) {
-        o.scope.assign('_this', 'this');
-        _ref2 = this.boundFuncs;
-        for (_i = 0, _len = _ref2.length; _i < _len; _i++) {
-          _ref3 = _ref2[_i], name = _ref3[0], func = _ref3[1];
-          lhs = new Value(new Literal("this"), [new Access(name)]);
-          body = new Block([new Return(new Literal("" + this.ctor.name + ".prototype." + name.value + ".apply(_this, arguments)"))]);
-          rhs = new Code(func.params, body, 'boundfunc');
-          bound = new Assign(lhs, rhs);
-          this.ctor.body.unshift(bound);
-        }
-      }
-    };
-
-    Class.prototype.addProperties = function(node, name, o) {
-      var assign, base, exprs, func, props;
-      props = node.base.properties.slice(0);
-      exprs = (function() {
-        var _results;
-        _results = [];
-        while (assign = props.shift()) {
-          if (assign instanceof Assign) {
-            base = assign.variable.base;
-            delete assign.context;
-            func = assign.value;
-            if (base.value === 'constructor') {
-              if (this.ctor) {
-                throw new Error('cannot define more than one constructor in a class');
-              }
-              if (func.bound) {
-                throw new Error('cannot define a constructor as a bound function');
-              }
-              if (func instanceof Code) {
-                assign = this.ctor = func;
-              } else {
-                this.externalCtor = o.scope.freeVariable('class');
-                assign = new Assign(new Literal(this.externalCtor), func);
-              }
-            } else {
-              if (assign.variable["this"]) {
-                func["static"] = true;
-                if (func.bound) {
-                  func.context = name;
-                }
-              } else {
-                assign.variable = new Value(new Literal(name), [new Access(new Literal('prototype')), new Access(base)]);
-                if (func instanceof Code && func.bound) {
-                  this.boundFuncs.push([base, func]);
-                  func.bound = false;
-                }
-              }
-            }
-          }
-          _results.push(assign);
-        }
-        return _results;
-      }).call(this);
-      return compact(exprs);
-    };
-
-    Class.prototype.walkBody = function(name, o) {
-      var _this = this;
-      return this.traverseChildren(false, function(child) {
-        var cont, exps, i, node, _i, _len, _ref2;
-        cont = true;
-        if (child instanceof Class) {
-          return false;
-        }
-        if (child instanceof Block) {
-          _ref2 = exps = child.expressions;
-          for (i = _i = 0, _len = _ref2.length; _i < _len; i = ++_i) {
-            node = _ref2[i];
-            if (node instanceof Value && node.isObject(true)) {
-              cont = false;
-              exps[i] = _this.addProperties(node, name, o);
-            }
-          }
-          child.expressions = exps = flatten(exps);
-        }
-        return cont && !(child instanceof Class);
-      });
-    };
-
-    Class.prototype.hoistDirectivePrologue = function() {
-      var expressions, index, node;
-      index = 0;
-      expressions = this.body.expressions;
-      while ((node = expressions[index]) && node instanceof Comment || node instanceof Value && node.isString()) {
-        ++index;
-      }
-      return this.directives = expressions.splice(0, index);
-    };
-
-    Class.prototype.ensureConstructor = function(name) {
-      if (!this.ctor) {
-        this.ctor = new Code;
-        if (this.parent) {
-          this.ctor.body.push(new Literal("" + name + ".__super__.constructor.apply(this, arguments)"));
-        }
-        if (this.externalCtor) {
-          this.ctor.body.push(new Literal("" + this.externalCtor + ".apply(this, arguments)"));
-        }
-        this.ctor.body.makeReturn();
-        this.body.expressions.unshift(this.ctor);
-      }
-      this.ctor.ctor = this.ctor.name = name;
-      this.ctor.klass = null;
-      return this.ctor.noReturn = true;
-    };
-
-    Class.prototype.compileNode = function(o) {
-      var call, decl, klass, lname, name, params, _ref2;
-      decl = this.determineName();
-      name = decl || '_Class';
-      if (name.reserved) {
-        name = "_" + name;
-      }
-      lname = new Literal(name);
-      this.hoistDirectivePrologue();
-      this.setContext(name);
-      this.walkBody(name, o);
-      this.ensureConstructor(name);
-      this.body.spaced = true;
-      if (!(this.ctor instanceof Code)) {
-        this.body.expressions.unshift(this.ctor);
-      }
-      this.body.expressions.push(lname);
-      (_ref2 = this.body.expressions).unshift.apply(_ref2, this.directives);
-      this.addBoundFunctions(o);
-      call = Closure.wrap(this.body);
-      if (this.parent) {
-        this.superClass = new Literal(o.scope.freeVariable('super', false));
-        this.body.expressions.unshift(new Extends(lname, this.superClass));
-        call.args.push(this.parent);
-        params = call.variable.params || call.variable.base.params;
-        params.push(new Param(this.superClass));
-      }
-      klass = new Parens(call, true);
-      if (this.variable) {
-        klass = new Assign(this.variable, klass);
-      }
-      return klass.compileToFragments(o);
-    };
-
-    return Class;
-
-  })(Base);
-
-  exports.Assign = Assign = (function(_super) {
-
-    __extends(Assign, _super);
-
-    function Assign(variable, value, context, options) {
-      var forbidden, name, _ref2;
-      this.variable = variable;
-      this.value = value;
-      this.context = context;
-      this.param = options && options.param;
-      this.subpattern = options && options.subpattern;
-      forbidden = (_ref2 = (name = this.variable.unwrapAll().value), __indexOf.call(STRICT_PROSCRIBED, _ref2) >= 0);
-      if (forbidden && this.context !== 'object') {
-        throw SyntaxError("variable name may not be \"" + name + "\"");
-      }
-    }
-
-    Assign.prototype.children = ['variable', 'value'];
-
-    Assign.prototype.isStatement = function(o) {
-      return (o != null ? o.level : void 0) === LEVEL_TOP && (this.context != null) && __indexOf.call(this.context, "?") >= 0;
-    };
-
-    Assign.prototype.assigns = function(name) {
-      return this[this.context === 'object' ? 'value' : 'variable'].assigns(name);
-    };
-
-    Assign.prototype.unfoldSoak = function(o) {
-      return unfoldSoak(o, this, 'variable');
-    };
-
-    Assign.prototype.compileNode = function(o) {
-      var answer, compiledName, isValue, match, name, val, varBase, _ref2, _ref3, _ref4, _ref5;
-      if (isValue = this.variable instanceof Value) {
-        if (this.variable.isArray() || this.variable.isObject()) {
-          return this.compilePatternMatch(o);
-        }
-        if (this.variable.isSplice()) {
-          return this.compileSplice(o);
-        }
-        if ((_ref2 = this.context) === '||=' || _ref2 === '&&=' || _ref2 === '?=') {
-          return this.compileConditional(o);
-        }
-      }
-      compiledName = this.variable.compileToFragments(o, LEVEL_LIST);
-      name = fragmentsToText(compiledName);
-      if (!this.context) {
-        if (!(varBase = this.variable.unwrapAll()).isAssignable()) {
-          throw SyntaxError("\"" + (this.variable.compile(o)) + "\" cannot be assigned.");
-        }
-        if (!(typeof varBase.hasProperties === "function" ? varBase.hasProperties() : void 0)) {
-          if (this.param) {
-            o.scope.add(name, 'var');
-          } else {
-            o.scope.find(name);
-          }
-        }
-      }
-      if (this.value instanceof Code && (match = METHOD_DEF.exec(name))) {
-        if (match[1]) {
-          this.value.klass = match[1];
-        }
-        this.value.name = (_ref3 = (_ref4 = (_ref5 = match[2]) != null ? _ref5 : match[3]) != null ? _ref4 : match[4]) != null ? _ref3 : match[5];
-      }
-      val = this.value.compileToFragments(o, LEVEL_LIST);
-      if (this.context === 'object') {
-        return compiledName.concat(this.makeCode(": "), val);
-      }
-      answer = compiledName.concat(this.makeCode(" " + (this.context || '=') + " "), val);
-      if (o.level <= LEVEL_LIST) {
-        return answer;
-      } else {
-        return this.wrapInBraces(answer);
-      }
-    };
-
-    Assign.prototype.compilePatternMatch = function(o) {
-      var acc, assigns, code, fragments, i, idx, isObject, ivar, name, obj, objects, olen, ref, rest, splat, top, val, value, vvar, vvarText, _i, _len, _ref2, _ref3, _ref4, _ref5, _ref6, _ref7;
-      top = o.level === LEVEL_TOP;
-      value = this.value;
-      objects = this.variable.base.objects;
-      if (!(olen = objects.length)) {
-        code = value.compileToFragments(o);
-        if (o.level >= LEVEL_OP) {
-          return this.wrapInBraces(code);
-        } else {
-          return code;
-        }
-      }
-      isObject = this.variable.isObject();
-      if (top && olen === 1 && !((obj = objects[0]) instanceof Splat)) {
-        if (obj instanceof Assign) {
-          _ref2 = obj, (_ref3 = _ref2.variable, idx = _ref3.base), obj = _ref2.value;
-        } else {
-          idx = isObject ? obj["this"] ? obj.properties[0].name : obj : new Literal(0);
-        }
-        acc = IDENTIFIER.test(idx.unwrap().value || 0);
-        value = new Value(value);
-        value.properties.push(new (acc ? Access : Index)(idx));
-        if (_ref4 = obj.unwrap().value, __indexOf.call(RESERVED, _ref4) >= 0) {
-          throw new SyntaxError("assignment to a reserved word: " + (obj.compile(o)) + " = " + (value.compile(o)));
-        }
-        return new Assign(obj, value, null, {
-          param: this.param
-        }).compileToFragments(o, LEVEL_TOP);
-      }
-      vvar = value.compileToFragments(o, LEVEL_LIST);
-      vvarText = fragmentsToText(vvar);
-      assigns = [];
-      splat = false;
-      if (!IDENTIFIER.test(vvarText) || this.variable.assigns(vvarText)) {
-        assigns.push([this.makeCode("" + (ref = o.scope.freeVariable('ref')) + " = ")].concat(__slice.call(vvar)));
-        vvar = [this.makeCode(ref)];
-        vvarText = ref;
-      }
-      for (i = _i = 0, _len = objects.length; _i < _len; i = ++_i) {
-        obj = objects[i];
-        idx = i;
-        if (isObject) {
-          if (obj instanceof Assign) {
-            _ref5 = obj, (_ref6 = _ref5.variable, idx = _ref6.base), obj = _ref5.value;
-          } else {
-            if (obj.base instanceof Parens) {
-              _ref7 = new Value(obj.unwrapAll()).cacheReference(o), obj = _ref7[0], idx = _ref7[1];
-            } else {
-              idx = obj["this"] ? obj.properties[0].name : obj;
-            }
-          }
-        }
-        if (!splat && obj instanceof Splat) {
-          name = obj.name.unwrap().value;
-          obj = obj.unwrap();
-          val = "" + olen + " <= " + vvarText + ".length ? " + (utility('slice')) + ".call(" + vvarText + ", " + i;
-          if (rest = olen - i - 1) {
-            ivar = o.scope.freeVariable('i');
-            val += ", " + ivar + " = " + vvarText + ".length - " + rest + ") : (" + ivar + " = " + i + ", [])";
-          } else {
-            val += ") : []";
-          }
-          val = new Literal(val);
-          splat = "" + ivar + "++";
-        } else {
-          name = obj.unwrap().value;
-          if (obj instanceof Splat) {
-            obj = obj.name.compileToFragments(o);
-            throw new SyntaxError("multiple splats are disallowed in an assignment: " + obj + "...");
-          }
-          if (typeof idx === 'number') {
-            idx = new Literal(splat || idx);
-            acc = false;
-          } else {
-            acc = isObject && IDENTIFIER.test(idx.unwrap().value || 0);
-          }
-          val = new Value(new Literal(vvarText), [new (acc ? Access : Index)(idx)]);
-        }
-        if ((name != null) && __indexOf.call(RESERVED, name) >= 0) {
-          throw new SyntaxError("assignment to a reserved word: " + (obj.compile(o)) + " = " + (val.compile(o)));
-        }
-        assigns.push(new Assign(obj, val, null, {
-          param: this.param,
-          subpattern: true
-        }).compileToFragments(o, LEVEL_LIST));
-      }
-      if (!(top || this.subpattern)) {
-        assigns.push(vvar);
-      }
-      fragments = this.joinFragmentArrays(assigns, ', ');
-      if (o.level < LEVEL_LIST) {
-        return fragments;
-      } else {
-        return this.wrapInBraces(fragments);
-      }
-    };
-
-    Assign.prototype.compileConditional = function(o) {
-      var left, right, _ref2;
-      _ref2 = this.variable.cacheReference(o), left = _ref2[0], right = _ref2[1];
-      if (!left.properties.length && left.base instanceof Literal && left.base.value !== "this" && !o.scope.check(left.base.value)) {
-        throw new Error("the variable \"" + left.base.value + "\" can't be assigned with " + this.context + " because it has not been defined.");
-      }
-      if (__indexOf.call(this.context, "?") >= 0) {
-        o.isExistentialEquals = true;
-      }
-      return new Op(this.context.slice(0, -1), left, new Assign(right, this.value, '=')).compileToFragments(o);
-    };
-
-    Assign.prototype.compileSplice = function(o) {
-      var answer, exclusive, from, fromDecl, fromRef, name, to, valDef, valRef, _ref2, _ref3, _ref4;
-      _ref2 = this.variable.properties.pop().range, from = _ref2.from, to = _ref2.to, exclusive = _ref2.exclusive;
-      name = this.variable.compile(o);
-      if (from) {
-        _ref3 = this.cacheToCodeFragments(from.cache(o, LEVEL_OP)), fromDecl = _ref3[0], fromRef = _ref3[1];
-      } else {
-        fromDecl = fromRef = '0';
-      }
-      if (to) {
-        if ((from != null ? from.isSimpleNumber() : void 0) && to.isSimpleNumber()) {
-          to = +to.compile(o) - +fromRef;
-          if (!exclusive) {
-            to += 1;
-          }
-        } else {
-          to = to.compile(o, LEVEL_ACCESS) + ' - ' + fromRef;
-          if (!exclusive) {
-            to += ' + 1';
-          }
-        }
-      } else {
-        to = "9e9";
-      }
-      _ref4 = this.value.cache(o, LEVEL_LIST), valDef = _ref4[0], valRef = _ref4[1];
-      answer = [].concat(this.makeCode("[].splice.apply(" + name + ", [" + fromDecl + ", " + to + "].concat("), valDef, this.makeCode(")), "), valRef);
-      if (o.level > LEVEL_TOP) {
-        return this.wrapInBraces(answer);
-      } else {
-        return answer;
-      }
-    };
-
-    return Assign;
-
-  })(Base);
-
-  exports.Code = Code = (function(_super) {
-
-    __extends(Code, _super);
-
-    function Code(params, body, tag) {
-      this.params = params || [];
-      this.body = body || new Block;
-      this.bound = tag === 'boundfunc';
-      if (this.bound) {
-        this.context = '_this';
-      }
-    }
-
-    Code.prototype.children = ['params', 'body'];
-
-    Code.prototype.isStatement = function() {
-      return !!this.ctor;
-    };
-
-    Code.prototype.jumps = NO;
-
-    Code.prototype.compileNode = function(o) {
-      var answer, code, exprs, i, idt, lit, name, p, param, params, ref, splats, uniqs, val, wasEmpty, _i, _j, _k, _l, _len, _len1, _len2, _len3, _len4, _len5, _len6, _m, _n, _o, _ref2, _ref3, _ref4, _ref5, _ref6, _ref7, _ref8;
-      o.scope = new Scope(o.scope, this.body, this);
-      o.scope.shared = del(o, 'sharedScope');
-      o.indent += TAB;
-      delete o.bare;
-      delete o.isExistentialEquals;
-      params = [];
-      exprs = [];
-      _ref2 = this.paramNames();
-      for (_i = 0, _len = _ref2.length; _i < _len; _i++) {
-        name = _ref2[_i];
-        if (!o.scope.check(name)) {
-          o.scope.parameter(name);
-        }
-      }
-      _ref3 = this.params;
-      for (_j = 0, _len1 = _ref3.length; _j < _len1; _j++) {
-        param = _ref3[_j];
-        if (!param.splat) {
-          continue;
-        }
-        _ref4 = this.params;
-        for (_k = 0, _len2 = _ref4.length; _k < _len2; _k++) {
-          p = _ref4[_k].name;
-          if (p["this"]) {
-            p = p.properties[0].name;
-          }
-          if (p.value) {
-            o.scope.add(p.value, 'var', true);
-          }
-        }
-        splats = new Assign(new Value(new Arr((function() {
-          var _l, _len3, _ref5, _results;
-          _ref5 = this.params;
-          _results = [];
-          for (_l = 0, _len3 = _ref5.length; _l < _len3; _l++) {
-            p = _ref5[_l];
-            _results.push(p.asReference(o));
-          }
-          return _results;
-        }).call(this))), new Value(new Literal('arguments')));
-        break;
-      }
-      _ref5 = this.params;
-      for (_l = 0, _len3 = _ref5.length; _l < _len3; _l++) {
-        param = _ref5[_l];
-        if (param.isComplex()) {
-          val = ref = param.asReference(o);
-          if (param.value) {
-            val = new Op('?', ref, param.value);
-          }
-          exprs.push(new Assign(new Value(param.name), val, '=', {
-            param: true
-          }));
-        } else {
-          ref = param;
-          if (param.value) {
-            lit = new Literal(ref.name.value + ' == null');
-            val = new Assign(new Value(param.name), param.value, '=');
-            exprs.push(new If(lit, val));
-          }
-        }
-        if (!splats) {
-          params.push(ref);
-        }
-      }
-      wasEmpty = this.body.isEmpty();
-      if (splats) {
-        exprs.unshift(splats);
-      }
-      if (exprs.length) {
-        (_ref6 = this.body.expressions).unshift.apply(_ref6, exprs);
-      }
-      for (i = _m = 0, _len4 = params.length; _m < _len4; i = ++_m) {
-        p = params[i];
-        params[i] = p.compileToFragments(o);
-        o.scope.parameter(fragmentsToText(params[i]));
-      }
-      uniqs = [];
-      _ref7 = this.paramNames();
-      for (_n = 0, _len5 = _ref7.length; _n < _len5; _n++) {
-        name = _ref7[_n];
-        if (__indexOf.call(uniqs, name) >= 0) {
-          throw SyntaxError("multiple parameters named '" + name + "'");
-        }
-        uniqs.push(name);
-      }
-      if (!(wasEmpty || this.noReturn)) {
-        this.body.makeReturn();
-      }
-      if (this.bound) {
-        if ((_ref8 = o.scope.parent.method) != null ? _ref8.bound : void 0) {
-          this.bound = this.context = o.scope.parent.method.context;
-        } else if (!this["static"]) {
-          o.scope.parent.assign('_this', 'this');
-        }
-      }
-      idt = o.indent;
-      code = 'function';
-      if (this.ctor) {
-        code += ' ' + this.name;
-      }
-      code += '(';
-      answer = [this.makeCode(code)];
-      for (i = _o = 0, _len6 = params.length; _o < _len6; i = ++_o) {
-        p = params[i];
-        if (i) {
-          answer.push(this.makeCode(", "));
-        }
-        answer.push.apply(answer, p);
-      }
-      answer.push(this.makeCode(') {'));
-      if (!this.body.isEmpty()) {
-        answer = answer.concat(this.makeCode("\n"), this.body.compileWithDeclarations(o), this.makeCode("\n" + this.tab));
-      }
-      answer.push(this.makeCode('}'));
-      if (this.ctor) {
-        return [this.makeCode(this.tab)].concat(__slice.call(answer));
-      }
-      if (this.front || (o.level >= LEVEL_ACCESS)) {
-        return this.wrapInBraces(answer);
-      } else {
-        return answer;
-      }
-    };
-
-    Code.prototype.paramNames = function() {
-      var names, param, _i, _len, _ref2;
-      names = [];
-      _ref2 = this.params;
-      for (_i = 0, _len = _ref2.length; _i < _len; _i++) {
-        param = _ref2[_i];
-        names.push.apply(names, param.names());
-      }
-      return names;
-    };
-
-    Code.prototype.traverseChildren = function(crossScope, func) {
-      if (crossScope) {
-        return Code.__super__.traverseChildren.call(this, crossScope, func);
-      }
-    };
-
-    return Code;
-
-  })(Base);
-
-  exports.Param = Param = (function(_super) {
-
-    __extends(Param, _super);
-
-    function Param(name, value, splat) {
-      var _ref2;
-      this.name = name;
-      this.value = value;
-      this.splat = splat;
-      if (_ref2 = (name = this.name.unwrapAll().value), __indexOf.call(STRICT_PROSCRIBED, _ref2) >= 0) {
-        throw SyntaxError("parameter name \"" + name + "\" is not allowed");
-      }
-    }
-
-    Param.prototype.children = ['name', 'value'];
-
-    Param.prototype.compileToFragments = function(o) {
-      return this.name.compileToFragments(o, LEVEL_LIST);
-    };
-
-    Param.prototype.asReference = function(o) {
-      var node;
-      if (this.reference) {
-        return this.reference;
-      }
-      node = this.name;
-      if (node["this"]) {
-        node = node.properties[0].name;
-        if (node.value.reserved) {
-          node = new Literal(o.scope.freeVariable(node.value));
-        }
-      } else if (node.isComplex()) {
-        node = new Literal(o.scope.freeVariable('arg'));
-      }
-      node = new Value(node);
-      if (this.splat) {
-        node = new Splat(node);
-      }
-      return this.reference = node;
-    };
-
-    Param.prototype.isComplex = function() {
-      return this.name.isComplex();
-    };
-
-    Param.prototype.names = function(name) {
-      var atParam, names, obj, _i, _len, _ref2;
-      if (name == null) {
-        name = this.name;
-      }
-      atParam = function(obj) {
-        var value;
-        value = obj.properties[0].name.value;
-        if (value.reserved) {
-          return [];
-        } else {
-          return [value];
-        }
-      };
-      if (name instanceof Literal) {
-        return [name.value];
-      }
-      if (name instanceof Value) {
-        return atParam(name);
-      }
-      names = [];
-      _ref2 = name.objects;
-      for (_i = 0, _len = _ref2.length; _i < _len; _i++) {
-        obj = _ref2[_i];
-        if (obj instanceof Assign) {
-          names.push.apply(names, this.names(obj.value.unwrap()));
-        } else if (obj instanceof Splat) {
-          names.push(obj.name.unwrap().value);
-        } else if (obj instanceof Value) {
-          if (obj.isArray() || obj.isObject()) {
-            names.push.apply(names, this.names(obj.base));
-          } else if (obj["this"]) {
-            names.push.apply(names, atParam(obj));
-          } else {
-            names.push(obj.base.value);
-          }
-        } else {
-          throw SyntaxError("illegal parameter " + (obj.compile()));
-        }
-      }
-      return names;
-    };
-
-    return Param;
-
-  })(Base);
-
-  exports.Splat = Splat = (function(_super) {
-
-    __extends(Splat, _super);
-
-    Splat.prototype.children = ['name'];
-
-    Splat.prototype.isAssignable = YES;
-
-    function Splat(name) {
-      this.name = name.compile ? name : new Literal(name);
-    }
-
-    Splat.prototype.assigns = function(name) {
-      return this.name.assigns(name);
-    };
-
-    Splat.prototype.compileToFragments = function(o) {
-      return this.name.compileToFragments(o);
-    };
-
-    Splat.prototype.unwrap = function() {
-      return this.name;
-    };
-
-    Splat.compileSplattedArray = function(o, list, apply) {
-      var args, base, compiledNode, concatPart, fragments, i, index, node, _i, _len;
-      index = -1;
-      while ((node = list[++index]) && !(node instanceof Splat)) {
-        continue;
-      }
-      if (index >= list.length) {
-        return [];
-      }
-      if (list.length === 1) {
-        node = list[0];
-        fragments = node.compileToFragments(o, LEVEL_LIST);
-        if (apply) {
-          return fragments;
-        }
-        return [].concat(node.makeCode("" + (utility('slice')) + ".call("), fragments, node.makeCode(")"));
-      }
-      args = list.slice(index);
-      for (i = _i = 0, _len = args.length; _i < _len; i = ++_i) {
-        node = args[i];
-        compiledNode = node.compileToFragments(o, LEVEL_LIST);
-        args[i] = node instanceof Splat ? [].concat(node.makeCode("" + (utility('slice')) + ".call("), compiledNode, node.makeCode(")")) : [].concat(node.makeCode("["), compiledNode, node.makeCode("]"));
-      }
-      if (index === 0) {
-        node = list[0];
-        concatPart = node.joinFragmentArrays(args.slice(1), ', ');
-        return args[0].concat(node.makeCode(".concat("), concatPart, node.makeCode(")"));
-      }
-      base = (function() {
-        var _j, _len1, _ref2, _results;
-        _ref2 = list.slice(0, index);
-        _results = [];
-        for (_j = 0, _len1 = _ref2.length; _j < _len1; _j++) {
-          node = _ref2[_j];
-          _results.push(node.compileToFragments(o, LEVEL_LIST));
-        }
-        return _results;
-      })();
-      base = list[0].joinFragmentArrays(base, ', ');
-      concatPart = list[index].joinFragmentArrays(args, ', ');
-      return [].concat(list[0].makeCode("["), base, list[index].makeCode("].concat("), concatPart, (last(list)).makeCode(")"));
-    };
-
-    return Splat;
-
-  })(Base);
-
-  exports.While = While = (function(_super) {
-
-    __extends(While, _super);
-
-    function While(condition, options) {
-      this.condition = (options != null ? options.invert : void 0) ? condition.invert() : condition;
-      this.guard = options != null ? options.guard : void 0;
-    }
-
-    While.prototype.children = ['condition', 'guard', 'body'];
-
-    While.prototype.isStatement = YES;
-
-    While.prototype.makeReturn = function(res) {
-      if (res) {
-        return While.__super__.makeReturn.apply(this, arguments);
-      } else {
-        this.returns = !this.jumps({
-          loop: true
-        });
-        return this;
-      }
-    };
-
-    While.prototype.addBody = function(body) {
-      this.body = body;
-      return this;
-    };
-
-    While.prototype.jumps = function() {
-      var expressions, node, _i, _len;
-      expressions = this.body.expressions;
-      if (!expressions.length) {
-        return false;
-      }
-      for (_i = 0, _len = expressions.length; _i < _len; _i++) {
-        node = expressions[_i];
-        if (node.jumps({
-          loop: true
-        })) {
-          return node;
-        }
-      }
-      return false;
-    };
-
-    While.prototype.compileNode = function(o) {
-      var answer, body, rvar, set;
-      o.indent += TAB;
-      set = '';
-      body = this.body;
-      if (body.isEmpty()) {
-        body = '';
-      } else {
-        if (this.returns) {
-          body.makeReturn(rvar = o.scope.freeVariable('results'));
-          set = "" + this.tab + rvar + " = [];\n";
-        }
-        if (this.guard) {
-          if (body.expressions.length > 1) {
-            body.expressions.unshift(new If((new Parens(this.guard)).invert(), new Literal("continue")));
-          } else {
-            if (this.guard) {
-              body = Block.wrap([new If(this.guard, body)]);
-            }
-          }
-        }
-        body = [].concat(this.makeCode("\n"), body.compileToFragments(o, LEVEL_TOP), this.makeCode("\n" + this.tab));
-      }
-      answer = [].concat(this.makeCode(set + this.tab + "while ("), this.condition.compileToFragments(o, LEVEL_PAREN), this.makeCode(") {"), body, this.makeCode("}"));
-      if (this.returns) {
-        answer.push(this.makeCode("\n" + this.tab + "return " + rvar + ";"));
-      }
-      return answer;
-    };
-
-    return While;
-
-  })(Base);
-
-  exports.Op = Op = (function(_super) {
-    var CONVERSIONS, INVERSIONS;
-
-    __extends(Op, _super);
-
-    function Op(op, first, second, flip) {
-      if (op === 'in') {
-        return new In(first, second);
-      }
-      if (op === 'do') {
-        return this.generateDo(first);
-      }
-      if (op === 'new') {
-        if (first instanceof Call && !first["do"] && !first.isNew) {
-          return first.newInstance();
-        }
-        if (first instanceof Code && first.bound || first["do"]) {
-          first = new Parens(first);
-        }
-      }
-      this.operator = CONVERSIONS[op] || op;
-      this.first = first;
-      this.second = second;
-      this.flip = !!flip;
-      return this;
-    }
-
-    CONVERSIONS = {
-      '==': '===',
-      '!=': '!==',
-      'of': 'in'
-    };
-
-    INVERSIONS = {
-      '!==': '===',
-      '===': '!=='
-    };
-
-    Op.prototype.children = ['first', 'second'];
-
-    Op.prototype.isSimpleNumber = NO;
-
-    Op.prototype.isUnary = function() {
-      return !this.second;
-    };
-
-    Op.prototype.isComplex = function() {
-      var _ref2;
-      return !(this.isUnary() && ((_ref2 = this.operator) === '+' || _ref2 === '-')) || this.first.isComplex();
-    };
-
-    Op.prototype.isChainable = function() {
-      var _ref2;
-      return (_ref2 = this.operator) === '<' || _ref2 === '>' || _ref2 === '>=' || _ref2 === '<=' || _ref2 === '===' || _ref2 === '!==';
-    };
-
-    Op.prototype.invert = function() {
-      var allInvertable, curr, fst, op, _ref2;
-      if (this.isChainable() && this.first.isChainable()) {
-        allInvertable = true;
-        curr = this;
-        while (curr && curr.operator) {
-          allInvertable && (allInvertable = curr.operator in INVERSIONS);
-          curr = curr.first;
-        }
-        if (!allInvertable) {
-          return new Parens(this).invert();
-        }
-        curr = this;
-        while (curr && curr.operator) {
-          curr.invert = !curr.invert;
-          curr.operator = INVERSIONS[curr.operator];
-          curr = curr.first;
-        }
-        return this;
-      } else if (op = INVERSIONS[this.operator]) {
-        this.operator = op;
-        if (this.first.unwrap() instanceof Op) {
-          this.first.invert();
-        }
-        return this;
-      } else if (this.second) {
-        return new Parens(this).invert();
-      } else if (this.operator === '!' && (fst = this.first.unwrap()) instanceof Op && ((_ref2 = fst.operator) === '!' || _ref2 === 'in' || _ref2 === 'instanceof')) {
-        return fst;
-      } else {
-        return new Op('!', this);
-      }
-    };
-
-    Op.prototype.unfoldSoak = function(o) {
-      var _ref2;
-      return ((_ref2 = this.operator) === '++' || _ref2 === '--' || _ref2 === 'delete') && unfoldSoak(o, this, 'first');
-    };
-
-    Op.prototype.generateDo = function(exp) {
-      var call, func, param, passedParams, ref, _i, _len, _ref2;
-      passedParams = [];
-      func = exp instanceof Assign && (ref = exp.value.unwrap()) instanceof Code ? ref : exp;
-      _ref2 = func.params || [];
-      for (_i = 0, _len = _ref2.length; _i < _len; _i++) {
-        param = _ref2[_i];
-        if (param.value) {
-          passedParams.push(param.value);
-          delete param.value;
-        } else {
-          passedParams.push(param);
-        }
-      }
-      call = new Call(exp, passedParams);
-      call["do"] = true;
-      return call;
-    };
-
-    Op.prototype.compileNode = function(o) {
-      var answer, isChain, _ref2, _ref3;
-      isChain = this.isChainable() && this.first.isChainable();
-      if (!isChain) {
-        this.first.front = this.front;
-      }
-      if (this.operator === 'delete' && o.scope.check(this.first.unwrapAll().value)) {
-        throw SyntaxError('delete operand may not be argument or var');
-      }
-      if (((_ref2 = this.operator) === '--' || _ref2 === '++') && (_ref3 = this.first.unwrapAll().value, __indexOf.call(STRICT_PROSCRIBED, _ref3) >= 0)) {
-        throw SyntaxError('prefix increment/decrement may not have eval or arguments operand');
-      }
-      if (this.isUnary()) {
-        return this.compileUnary(o);
-      }
-      if (isChain) {
-        return this.compileChain(o);
-      }
-      if (this.operator === '?') {
-        return this.compileExistence(o);
-      }
-      answer = [].concat(this.first.compileToFragments(o, LEVEL_OP), this.makeCode(' ' + this.operator + ' '), this.second.compileToFragments(o, LEVEL_OP));
-      if (o.level <= LEVEL_OP) {
-        return answer;
-      } else {
-        return this.wrapInBraces(answer);
-      }
-    };
-
-    Op.prototype.compileChain = function(o) {
-      var fragments, fst, shared, _ref2;
-      _ref2 = this.first.second.cache(o), this.first.second = _ref2[0], shared = _ref2[1];
-      fst = this.first.compileToFragments(o, LEVEL_OP);
-      fragments = fst.concat(this.makeCode(" " + (this.invert ? '&&' : '||') + " "), shared.compileToFragments(o), this.makeCode(" " + this.operator + " "), this.second.compileToFragments(o, LEVEL_OP));
-      return this.wrapInBraces(fragments);
-    };
-
-    Op.prototype.compileExistence = function(o) {
-      var fst, ref;
-      if (this.first.isComplex()) {
-        ref = new Literal(o.scope.freeVariable('ref'));
-        fst = new Parens(new Assign(ref, this.first));
-      } else {
-        fst = this.first;
-        ref = fst;
-      }
-      return new If(new Existence(fst), ref, {
-        type: 'if'
-      }).addElse(this.second).compileToFragments(o);
-    };
-
-    Op.prototype.compileUnary = function(o) {
-      var op, parts, plusMinus;
-      parts = [];
-      op = this.operator;
-      parts.push([this.makeCode(op)]);
-      if (op === '!' && this.first instanceof Existence) {
-        this.first.negated = !this.first.negated;
-        return this.first.compileToFragments(o);
-      }
-      if (o.level >= LEVEL_ACCESS) {
-        return (new Parens(this)).compileToFragments(o);
-      }
-      plusMinus = op === '+' || op === '-';
-      if ((op === 'new' || op === 'typeof' || op === 'delete') || plusMinus && this.first instanceof Op && this.first.operator === op) {
-        parts.push([this.makeCode(' ')]);
-      }
-      if ((plusMinus && this.first instanceof Op) || (op === 'new' && this.first.isStatement(o))) {
-        this.first = new Parens(this.first);
-      }
-      parts.push(this.first.compileToFragments(o, LEVEL_OP));
-      if (this.flip) {
-        parts.reverse();
-      }
-      return this.joinFragmentArrays(parts, '');
-    };
-
-    Op.prototype.toString = function(idt) {
-      return Op.__super__.toString.call(this, idt, this.constructor.name + ' ' + this.operator);
-    };
-
-    return Op;
-
-  })(Base);
-
-  exports.In = In = (function(_super) {
-
-    __extends(In, _super);
-
-    function In(object, array) {
-      this.object = object;
-      this.array = array;
-    }
-
-    In.prototype.children = ['object', 'array'];
-
-    In.prototype.invert = NEGATE;
-
-    In.prototype.compileNode = function(o) {
-      var hasSplat, obj, _i, _len, _ref2;
-      if (this.array instanceof Value && this.array.isArray()) {
-        _ref2 = this.array.base.objects;
-        for (_i = 0, _len = _ref2.length; _i < _len; _i++) {
-          obj = _ref2[_i];
-          if (!(obj instanceof Splat)) {
-            continue;
-          }
-          hasSplat = true;
-          break;
-        }
-        if (!hasSplat) {
-          return this.compileOrTest(o);
-        }
-      }
-      return this.compileLoopTest(o);
-    };
-
-    In.prototype.compileOrTest = function(o) {
-      var cmp, cnj, i, item, ref, sub, tests, _i, _len, _ref2, _ref3, _ref4;
-      if (this.array.base.objects.length === 0) {
-        return [this.makeCode("" + (!!this.negated))];
-      }
-      _ref2 = this.object.cache(o, LEVEL_OP), sub = _ref2[0], ref = _ref2[1];
-      _ref3 = this.negated ? [' !== ', ' && '] : [' === ', ' || '], cmp = _ref3[0], cnj = _ref3[1];
-      tests = [];
-      _ref4 = this.array.base.objects;
-      for (i = _i = 0, _len = _ref4.length; _i < _len; i = ++_i) {
-        item = _ref4[i];
-        if (i) {
-          tests.push(this.makeCode(cnj));
-        }
-        tests = tests.concat((i ? ref : sub), this.makeCode(cmp), item.compileToFragments(o, LEVEL_ACCESS));
-      }
-      if (o.level < LEVEL_OP) {
-        return tests;
-      } else {
-        return this.wrapInBraces(tests);
-      }
-    };
-
-    In.prototype.compileLoopTest = function(o) {
-      var fragments, ref, sub, _ref2;
-      _ref2 = this.object.cache(o, LEVEL_LIST), sub = _ref2[0], ref = _ref2[1];
-      fragments = [].concat(this.makeCode(utility('indexOf') + ".call("), this.array.compileToFragments(o, LEVEL_LIST), this.makeCode(", "), ref, this.makeCode(") " + (this.negated ? '< 0' : '>= 0')));
-      if ((fragmentsToText(sub)) === (fragmentsToText(ref))) {
-        return fragments;
-      }
-      fragments = sub.concat(this.makeCode(', '), fragments);
-      if (o.level < LEVEL_LIST) {
-        return fragments;
-      } else {
-        return this.wrapInBraces(fragments);
-      }
-    };
-
-    In.prototype.toString = function(idt) {
-      return In.__super__.toString.call(this, idt, this.constructor.name + (this.negated ? '!' : ''));
-    };
-
-    return In;
-
-  })(Base);
-
-  exports.Try = Try = (function(_super) {
-
-    __extends(Try, _super);
-
-    function Try(attempt, error, recovery, ensure) {
-      this.attempt = attempt;
-      this.error = error;
-      this.recovery = recovery;
-      this.ensure = ensure;
-    }
-
-    Try.prototype.children = ['attempt', 'recovery', 'ensure'];
-
-    Try.prototype.isStatement = YES;
-
-    Try.prototype.jumps = function(o) {
-      var _ref2;
-      return this.attempt.jumps(o) || ((_ref2 = this.recovery) != null ? _ref2.jumps(o) : void 0);
-    };
-
-    Try.prototype.makeReturn = function(res) {
-      if (this.attempt) {
-        this.attempt = this.attempt.makeReturn(res);
-      }
-      if (this.recovery) {
-        this.recovery = this.recovery.makeReturn(res);
-      }
-      return this;
-    };
-
-    Try.prototype.compileNode = function(o) {
-      var catchPart, ensurePart, placeholder, tryPart;
-      o.indent += TAB;
-      tryPart = this.attempt.compileToFragments(o, LEVEL_TOP);
-      catchPart = (function() {
-        var _base, _ref2;
-        if (this.recovery) {
-          if (typeof (_base = this.error).isObject === "function" ? _base.isObject() : void 0) {
-            placeholder = new Literal('_error');
-            this.recovery.unshift(new Assign(this.error, placeholder));
-            this.error = placeholder;
-          }
-          if (_ref2 = this.error.value, __indexOf.call(STRICT_PROSCRIBED, _ref2) >= 0) {
-            throw SyntaxError("catch variable may not be \"" + this.error.value + "\"");
-          }
-          if (!o.scope.check(this.error.value)) {
-            o.scope.add(this.error.value, 'param');
-          }
-          return [].concat(this.makeCode(" catch ("), this.error.compileToFragments(o), this.makeCode(") {\n"), this.recovery.compileToFragments(o, LEVEL_TOP), this.makeCode("\n" + this.tab + "}"));
-        } else if (!(this.ensure || this.recovery)) {
-          return [this.makeCode(' catch (_error) {}')];
-        } else {
-          return [];
-        }
-      }).call(this);
-      ensurePart = this.ensure ? [].concat(this.makeCode(" finally {\n"), this.ensure.compileToFragments(o, LEVEL_TOP), this.makeCode("\n" + this.tab + "}")) : [];
-      return [].concat(this.makeCode("" + this.tab + "try {\n"), tryPart, this.makeCode("\n" + this.tab + "}"), catchPart, ensurePart);
-    };
-
-    return Try;
-
-  })(Base);
-
-  exports.Throw = Throw = (function(_super) {
-
-    __extends(Throw, _super);
-
-    function Throw(expression) {
-      this.expression = expression;
-    }
-
-    Throw.prototype.children = ['expression'];
-
-    Throw.prototype.isStatement = YES;
-
-    Throw.prototype.jumps = NO;
-
-    Throw.prototype.makeReturn = THIS;
-
-    Throw.prototype.compileNode = function(o) {
-      return [].concat(this.makeCode(this.tab + "throw "), this.expression.compileToFragments(o), this.makeCode(";"));
-    };
-
-    return Throw;
-
-  })(Base);
-
-  exports.Existence = Existence = (function(_super) {
-
-    __extends(Existence, _super);
-
-    function Existence(expression) {
-      this.expression = expression;
-    }
-
-    Existence.prototype.children = ['expression'];
-
-    Existence.prototype.invert = NEGATE;
-
-    Existence.prototype.compileNode = function(o) {
-      var cmp, cnj, code, _ref2;
-      this.expression.front = this.front;
-      code = this.expression.compile(o, LEVEL_OP);
-      if (IDENTIFIER.test(code) && !o.scope.check(code)) {
-        _ref2 = this.negated ? ['===', '||'] : ['!==', '&&'], cmp = _ref2[0], cnj = _ref2[1];
-        code = "typeof " + code + " " + cmp + " \"undefined\" " + cnj + " " + code + " " + cmp + " null";
-      } else {
-        code = "" + code + " " + (this.negated ? '==' : '!=') + " null";
-      }
-      return [this.makeCode(o.level <= LEVEL_COND ? code : "(" + code + ")")];
-    };
-
-    return Existence;
-
-  })(Base);
-
-  exports.Parens = Parens = (function(_super) {
-
-    __extends(Parens, _super);
-
-    function Parens(body) {
-      this.body = body;
-    }
-
-    Parens.prototype.children = ['body'];
-
-    Parens.prototype.unwrap = function() {
-      return this.body;
-    };
-
-    Parens.prototype.isComplex = function() {
-      return this.body.isComplex();
-    };
-
-    Parens.prototype.compileNode = function(o) {
-      var bare, expr, fragments;
-      expr = this.body.unwrap();
-      if (expr instanceof Value && expr.isAtomic()) {
-        expr.front = this.front;
-        return expr.compileToFragments(o);
-      }
-      fragments = expr.compileToFragments(o, LEVEL_PAREN);
-      bare = o.level < LEVEL_OP && (expr instanceof Op || expr instanceof Call || (expr instanceof For && expr.returns));
-      if (bare) {
-        return fragments;
-      } else {
-        return this.wrapInBraces(fragments);
-      }
-    };
-
-    return Parens;
-
-  })(Base);
-
-  exports.For = For = (function(_super) {
-
-    __extends(For, _super);
-
-    function For(body, source) {
-      var _ref2;
-      this.source = source.source, this.guard = source.guard, this.step = source.step, this.name = source.name, this.index = source.index;
-      this.body = Block.wrap([body]);
-      this.own = !!source.own;
-      this.object = !!source.object;
-      if (this.object) {
-        _ref2 = [this.index, this.name], this.name = _ref2[0], this.index = _ref2[1];
-      }
-      if (this.index instanceof Value) {
-        throw SyntaxError('index cannot be a pattern matching expression');
-      }
-      this.range = this.source instanceof Value && this.source.base instanceof Range && !this.source.properties.length;
-      this.pattern = this.name instanceof Value;
-      if (this.range && this.index) {
-        throw SyntaxError('indexes do not apply to range loops');
-      }
-      if (this.range && this.pattern) {
-        throw SyntaxError('cannot pattern match over range loops');
-      }
-      this.returns = false;
-    }
-
-    For.prototype.children = ['body', 'source', 'guard', 'step'];
-
-    For.prototype.compileNode = function(o) {
-      var body, bodyFragments, compare, compareDown, declare, declareDown, defPart, defPartFragments, down, forPartFragments, guardPart, idt1, increment, index, ivar, kvar, kvarAssign, lastJumps, lvar, name, namePart, ref, resultPart, returnResult, rvar, scope, source, step, stepNum, stepVar, svar, varPart, _ref2, _ref3;
-      body = Block.wrap([this.body]);
-      lastJumps = (_ref2 = last(body.expressions)) != null ? _ref2.jumps() : void 0;
-      if (lastJumps && lastJumps instanceof Return) {
-        this.returns = false;
-      }
-      source = this.range ? this.source.base : this.source;
-      scope = o.scope;
-      name = this.name && (this.name.compile(o, LEVEL_LIST));
-      index = this.index && (this.index.compile(o, LEVEL_LIST));
-      if (name && !this.pattern) {
-        scope.find(name);
-      }
-      if (index) {
-        scope.find(index);
-      }
-      if (this.returns) {
-        rvar = scope.freeVariable('results');
-      }
-      ivar = (this.object && index) || scope.freeVariable('i');
-      kvar = (this.range && name) || index || ivar;
-      kvarAssign = kvar !== ivar ? "" + kvar + " = " : "";
-      if (this.step && !this.range) {
-        _ref3 = this.cacheToCodeFragments(this.step.cache(o, LEVEL_LIST)), step = _ref3[0], stepVar = _ref3[1];
-        stepNum = stepVar.match(SIMPLENUM);
-      }
-      if (this.pattern) {
-        name = ivar;
-      }
-      varPart = '';
-      guardPart = '';
-      defPart = '';
-      idt1 = this.tab + TAB;
-      if (this.range) {
-        forPartFragments = source.compileToFragments(merge(o, {
-          index: ivar,
-          name: name,
-          step: this.step
-        }));
-      } else {
-        svar = this.source.compile(o, LEVEL_LIST);
-        if ((name || this.own) && !IDENTIFIER.test(svar)) {
-          defPart += "" + this.tab + (ref = scope.freeVariable('ref')) + " = " + svar + ";\n";
-          svar = ref;
-        }
-        if (name && !this.pattern) {
-          namePart = "" + name + " = " + svar + "[" + kvar + "]";
-        }
-        if (!this.object) {
-          if (step !== stepVar) {
-            defPart += "" + this.tab + step + ";\n";
-          }
-          if (!(this.step && stepNum && (down = +stepNum < 0))) {
-            lvar = scope.freeVariable('len');
-          }
-          declare = "" + kvarAssign + ivar + " = 0, " + lvar + " = " + svar + ".length";
-          declareDown = "" + kvarAssign + ivar + " = " + svar + ".length - 1";
-          compare = "" + ivar + " < " + lvar;
-          compareDown = "" + ivar + " >= 0";
-          if (this.step) {
-            if (stepNum) {
-              if (down) {
-                compare = compareDown;
-                declare = declareDown;
-              }
-            } else {
-              compare = "" + stepVar + " > 0 ? " + compare + " : " + compareDown;
-              declare = "(" + stepVar + " > 0 ? (" + declare + ") : " + declareDown + ")";
-            }
-            increment = "" + ivar + " += " + stepVar;
-          } else {
-            increment = "" + (kvar !== ivar ? "++" + ivar : "" + ivar + "++");
-          }
-          forPartFragments = [this.makeCode("" + declare + "; " + compare + "; " + kvarAssign + increment)];
-        }
-      }
-      if (this.returns) {
-        resultPart = "" + this.tab + rvar + " = [];\n";
-        returnResult = "\n" + this.tab + "return " + rvar + ";";
-        body.makeReturn(rvar);
-      }
-      if (this.guard) {
-        if (body.expressions.length > 1) {
-          body.expressions.unshift(new If((new Parens(this.guard)).invert(), new Literal("continue")));
-        } else {
-          if (this.guard) {
-            body = Block.wrap([new If(this.guard, body)]);
-          }
-        }
-      }
-      if (this.pattern) {
-        body.expressions.unshift(new Assign(this.name, new Literal("" + svar + "[" + kvar + "]")));
-      }
-      defPartFragments = [].concat(this.makeCode(defPart), this.pluckDirectCall(o, body));
-      if (namePart) {
-        varPart = "\n" + idt1 + namePart + ";";
-      }
-      if (this.object) {
-        forPartFragments = [this.makeCode("" + kvar + " in " + svar)];
-        if (this.own) {
-          guardPart = "\n" + idt1 + "if (!" + (utility('hasProp')) + ".call(" + svar + ", " + kvar + ")) continue;";
-        }
-      }
-      bodyFragments = body.compileToFragments(merge(o, {
-        indent: idt1
-      }), LEVEL_TOP);
-      if (bodyFragments && (bodyFragments.length > 0)) {
-        bodyFragments = [].concat(this.makeCode("\n"), bodyFragments, this.makeCode("\n"));
-      }
-      return [].concat(defPartFragments, this.makeCode("" + (resultPart || '') + this.tab + "for ("), forPartFragments, this.makeCode(") {" + guardPart + varPart), bodyFragments, this.makeCode("" + this.tab + "}" + (returnResult || '')));
-    };
-
-    For.prototype.pluckDirectCall = function(o, body) {
-      var base, defs, expr, fn, idx, ref, val, _i, _len, _ref2, _ref3, _ref4, _ref5, _ref6, _ref7;
-      defs = [];
-      _ref2 = body.expressions;
-      for (idx = _i = 0, _len = _ref2.length; _i < _len; idx = ++_i) {
-        expr = _ref2[idx];
-        expr = expr.unwrapAll();
-        if (!(expr instanceof Call)) {
-          continue;
-        }
-        val = expr.variable.unwrapAll();
-        if (!((val instanceof Code) || (val instanceof Value && ((_ref3 = val.base) != null ? _ref3.unwrapAll() : void 0) instanceof Code && val.properties.length === 1 && ((_ref4 = (_ref5 = val.properties[0].name) != null ? _ref5.value : void 0) === 'call' || _ref4 === 'apply')))) {
-          continue;
-        }
-        fn = ((_ref6 = val.base) != null ? _ref6.unwrapAll() : void 0) || val;
-        ref = new Literal(o.scope.freeVariable('fn'));
-        base = new Value(ref);
-        if (val.base) {
-          _ref7 = [base, val], val.base = _ref7[0], base = _ref7[1];
-        }
-        body.expressions[idx] = new Call(base, expr.args);
-        defs = defs.concat(this.makeCode(this.tab), new Assign(ref, fn).compileToFragments(o, LEVEL_TOP), this.makeCode(';\n'));
-      }
-      return defs;
-    };
-
-    return For;
-
-  })(While);
-
-  exports.Switch = Switch = (function(_super) {
-
-    __extends(Switch, _super);
-
-    function Switch(subject, cases, otherwise) {
-      this.subject = subject;
-      this.cases = cases;
-      this.otherwise = otherwise;
-    }
-
-    Switch.prototype.children = ['subject', 'cases', 'otherwise'];
-
-    Switch.prototype.isStatement = YES;
-
-    Switch.prototype.jumps = function(o) {
-      var block, conds, _i, _len, _ref2, _ref3, _ref4;
-      if (o == null) {
-        o = {
-          block: true
-        };
-      }
-      _ref2 = this.cases;
-      for (_i = 0, _len = _ref2.length; _i < _len; _i++) {
-        _ref3 = _ref2[_i], conds = _ref3[0], block = _ref3[1];
-        if (block.jumps(o)) {
-          return block;
-        }
-      }
-      return (_ref4 = this.otherwise) != null ? _ref4.jumps(o) : void 0;
-    };
-
-    Switch.prototype.makeReturn = function(res) {
-      var pair, _i, _len, _ref2, _ref3;
-      _ref2 = this.cases;
-      for (_i = 0, _len = _ref2.length; _i < _len; _i++) {
-        pair = _ref2[_i];
-        pair[1].makeReturn(res);
-      }
-      if (res) {
-        this.otherwise || (this.otherwise = new Block([new Literal('void 0')]));
-      }
-      if ((_ref3 = this.otherwise) != null) {
-        _ref3.makeReturn(res);
-      }
-      return this;
-    };
-
-    Switch.prototype.compileNode = function(o) {
-      var block, body, cond, conditions, expr, fragments, i, idt1, idt2, _i, _j, _len, _len1, _ref2, _ref3, _ref4;
-      idt1 = o.indent + TAB;
-      idt2 = o.indent = idt1 + TAB;
-      fragments = [].concat(this.makeCode(this.tab + "switch ("), (this.subject ? this.subject.compileToFragments(o, LEVEL_PAREN) : this.makeCode("false")), this.makeCode(") {\n"));
-      _ref2 = this.cases;
-      for (i = _i = 0, _len = _ref2.length; _i < _len; i = ++_i) {
-        _ref3 = _ref2[i], conditions = _ref3[0], block = _ref3[1];
-        _ref4 = flatten([conditions]);
-        for (_j = 0, _len1 = _ref4.length; _j < _len1; _j++) {
-          cond = _ref4[_j];
-          if (!this.subject) {
-            cond = cond.invert();
-          }
-          fragments = fragments.concat(this.makeCode(idt1 + "case "), cond.compileToFragments(o, LEVEL_PAREN), this.makeCode(":\n"));
-        }
-        if ((body = block.compileToFragments(o, LEVEL_TOP)).length > 0) {
-          fragments = fragments.concat(body, this.makeCode('\n'));
-        }
-        if (i === this.cases.length - 1 && !this.otherwise) {
-          break;
-        }
-        expr = this.lastNonComment(block.expressions);
-        if (expr instanceof Return || (expr instanceof Literal && expr.jumps() && expr.value !== 'debugger')) {
-          continue;
-        }
-        fragments.push(cond.makeCode(idt2 + 'break;\n'));
-      }
-      if (this.otherwise && this.otherwise.expressions.length) {
-        fragments.push.apply(fragments, [this.makeCode(idt1 + "default:\n")].concat(__slice.call(this.otherwise.compileToFragments(o, LEVEL_TOP)), [this.makeCode("\n")]));
-      }
-      fragments.push(this.makeCode(this.tab + '}'));
-      return fragments;
-    };
-
-    return Switch;
-
-  })(Base);
-
-  exports.If = If = (function(_super) {
-
-    __extends(If, _super);
-
-    function If(condition, body, options) {
-      this.body = body;
-      if (options == null) {
-        options = {};
-      }
-      this.condition = options.type === 'unless' ? condition.invert() : condition;
-      this.elseBody = null;
-      this.isChain = false;
-      this.soak = options.soak;
-    }
-
-    If.prototype.children = ['condition', 'body', 'elseBody'];
-
-    If.prototype.bodyNode = function() {
-      var _ref2;
-      return (_ref2 = this.body) != null ? _ref2.unwrap() : void 0;
-    };
-
-    If.prototype.elseBodyNode = function() {
-      var _ref2;
-      return (_ref2 = this.elseBody) != null ? _ref2.unwrap() : void 0;
-    };
-
-    If.prototype.addElse = function(elseBody) {
-      if (this.isChain) {
-        this.elseBodyNode().addElse(elseBody);
-      } else {
-        this.isChain = elseBody instanceof If;
-        this.elseBody = this.ensureBlock(elseBody);
-      }
-      return this;
-    };
-
-    If.prototype.isStatement = function(o) {
-      var _ref2;
-      return (o != null ? o.level : void 0) === LEVEL_TOP || this.bodyNode().isStatement(o) || ((_ref2 = this.elseBodyNode()) != null ? _ref2.isStatement(o) : void 0);
-    };
-
-    If.prototype.jumps = function(o) {
-      var _ref2;
-      return this.body.jumps(o) || ((_ref2 = this.elseBody) != null ? _ref2.jumps(o) : void 0);
-    };
-
-    If.prototype.compileNode = function(o) {
-      if (this.isStatement(o)) {
-        return this.compileStatement(o);
-      } else {
-        return this.compileExpression(o);
-      }
-    };
-
-    If.prototype.makeReturn = function(res) {
-      if (res) {
-        this.elseBody || (this.elseBody = new Block([new Literal('void 0')]));
-      }
-      this.body && (this.body = new Block([this.body.makeReturn(res)]));
-      this.elseBody && (this.elseBody = new Block([this.elseBody.makeReturn(res)]));
-      return this;
-    };
-
-    If.prototype.ensureBlock = function(node) {
-      if (node instanceof Block) {
-        return node;
-      } else {
-        return new Block([node]);
-      }
-    };
-
-    If.prototype.compileStatement = function(o) {
-      var answer, body, child, cond, exeq, ifPart, indent;
-      child = del(o, 'chainChild');
-      exeq = del(o, 'isExistentialEquals');
-      if (exeq) {
-        return new If(this.condition.invert(), this.elseBodyNode(), {
-          type: 'if'
-        }).compileToFragments(o);
-      }
-      indent = o.indent + TAB;
-      cond = this.condition.compileToFragments(o, LEVEL_PAREN);
-      body = this.ensureBlock(this.body).compileToFragments(merge(o, {
-        indent: indent
-      }));
-      ifPart = [].concat(this.makeCode("if ("), cond, this.makeCode(") {\n"), body, this.makeCode("\n" + this.tab + "}"));
-      if (!child) {
-        ifPart.unshift(this.makeCode(this.tab));
-      }
-      if (!this.elseBody) {
-        return ifPart;
-      }
-      answer = ifPart.concat(this.makeCode(' else '));
-      if (this.isChain) {
-        o.chainChild = true;
-        answer = answer.concat(this.elseBody.unwrap().compileToFragments(o, LEVEL_TOP));
-      } else {
-        answer = answer.concat(this.makeCode("{\n"), this.elseBody.compileToFragments(merge(o, {
-          indent: indent
-        }), LEVEL_TOP), this.makeCode("\n" + this.tab + "}"));
-      }
-      return answer;
-    };
-
-    If.prototype.compileExpression = function(o) {
-      var alt, body, cond, fragments;
-      cond = this.condition.compileToFragments(o, LEVEL_COND);
-      body = this.bodyNode().compileToFragments(o, LEVEL_LIST);
-      alt = this.elseBodyNode() ? this.elseBodyNode().compileToFragments(o, LEVEL_LIST) : [this.makeCode('void 0')];
-      fragments = cond.concat(this.makeCode(" ? "), body, this.makeCode(" : "), alt);
-      if (o.level >= LEVEL_COND) {
-        return this.wrapInBraces(fragments);
-      } else {
-        return fragments;
-      }
-    };
-
-    If.prototype.unfoldSoak = function() {
-      return this.soak && this;
-    };
-
-    return If;
-
-  })(Base);
-
-  Closure = {
-    wrap: function(expressions, statement, noReturn) {
-      var args, call, func, mentionsArgs, meth;
-      if (expressions.jumps()) {
-        return expressions;
-      }
-      func = new Code([], Block.wrap([expressions]));
-      args = [];
-      if ((mentionsArgs = expressions.contains(this.literalArgs)) || expressions.contains(this.literalThis)) {
-        if (mentionsArgs && expressions.classBody) {
-          throw SyntaxError("Class bodies shouldn't reference arguments");
-        }
-        meth = new Literal(mentionsArgs ? 'apply' : 'call');
-        args = [new Literal('this')];
-        if (mentionsArgs) {
-          args.push(new Literal('arguments'));
-        }
-        func = new Value(func, [new Access(meth)]);
-      }
-      func.noReturn = noReturn;
-      call = new Call(func, args);
-      if (statement) {
-        return Block.wrap([call]);
-      } else {
-        return call;
-      }
-    },
-    literalArgs: function(node) {
-      return node instanceof Literal && node.value === 'arguments' && !node.asKey;
-    },
-    literalThis: function(node) {
-      return (node instanceof Literal && node.value === 'this' && !node.asKey) || (node instanceof Code && node.bound) || (node instanceof Call && node.isSuper);
-    }
-  };
-
-  unfoldSoak = function(o, parent, name) {
-    var ifn;
-    if (!(ifn = parent[name].unfoldSoak(o))) {
-      return;
-    }
-    parent[name] = ifn.body;
-    ifn.body = new Value(parent);
-    return ifn;
-  };
-
-  UTILITIES = {
-    "extends": function() {
-      return "function(child, parent) { for (var key in parent) { if (" + (utility('hasProp')) + ".call(parent, key)) child[key] = parent[key]; } function ctor() { this.constructor = child; } ctor.prototype = parent.prototype; child.prototype = new ctor(); child.__super__ = parent.prototype; return child; }";
-    },
-    indexOf: function() {
-      return "[].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; }";
-    },
-    hasProp: function() {
-      return '{}.hasOwnProperty';
-    },
-    slice: function() {
-      return '[].slice';
-    }
-  };
-
-  LEVEL_TOP = 1;
-
-  LEVEL_PAREN = 2;
-
-  LEVEL_LIST = 3;
-
-  LEVEL_COND = 4;
-
-  LEVEL_OP = 5;
-
-  LEVEL_ACCESS = 6;
-
-  TAB = '  ';
-
-  IDENTIFIER_STR = "[$A-Za-z_\\x7f-\\uffff][$\\w\\x7f-\\uffff]*";
-
-  IDENTIFIER = RegExp("^" + IDENTIFIER_STR + "$");
-
-  SIMPLENUM = /^[+-]?\d+$/;
-
-  METHOD_DEF = RegExp("^(?:(" + IDENTIFIER_STR + ")\\.prototype(?:\\.(" + IDENTIFIER_STR + ")|\\[(\"(?:[^\\\\\"\\r\\n]|\\\\.)*\"|'(?:[^\\\\'\\r\\n]|\\\\.)*')\\]|\\[(0x[\\da-fA-F]+|\\d*\\.?\\d+(?:[eE][+-]?\\d+)?)\\]))|(" + IDENTIFIER_STR + ")$");
-
-  IS_STRING = /^['"]/;
-
-  utility = function(name) {
-    var ref;
-    ref = "__" + name;
-    Scope.root.assign(ref, UTILITIES[name]());
-    return ref;
-  };
-
-  multident = function(code, tab) {
-    code = code.replace(/\n/g, '$&' + tab);
-    return code.replace(/\s+$/, '');
-  };
-
-}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/optparse.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/optparse.js
deleted file mode 100755
index f650fdd1..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/optparse.js
+++ /dev/null
@@ -1,138 +0,0 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var LONG_FLAG, MULTI_FLAG, OPTIONAL, OptionParser, SHORT_FLAG, buildRule, buildRules, normalizeArguments;
-
-  exports.OptionParser = OptionParser = (function() {
-
-    function OptionParser(rules, banner) {
-      this.banner = banner;
-      this.rules = buildRules(rules);
-    }
-
-    OptionParser.prototype.parse = function(args) {
-      var arg, i, isOption, matchedRule, options, originalArgs, pos, rule, seenNonOptionArg, skippingArgument, value, _i, _j, _len, _len1, _ref;
-      options = {
-        "arguments": []
-      };
-      skippingArgument = false;
-      originalArgs = args;
-      args = normalizeArguments(args);
-      for (i = _i = 0, _len = args.length; _i < _len; i = ++_i) {
-        arg = args[i];
-        if (skippingArgument) {
-          skippingArgument = false;
-          continue;
-        }
-        if (arg === '--') {
-          pos = originalArgs.indexOf('--');
-          options["arguments"] = options["arguments"].concat(originalArgs.slice(pos + 1));
-          break;
-        }
-        isOption = !!(arg.match(LONG_FLAG) || arg.match(SHORT_FLAG));
-        seenNonOptionArg = options["arguments"].length > 0;
-        if (!seenNonOptionArg) {
-          matchedRule = false;
-          _ref = this.rules;
-          for (_j = 0, _len1 = _ref.length; _j < _len1; _j++) {
-            rule = _ref[_j];
-            if (rule.shortFlag === arg || rule.longFlag === arg) {
-              value = true;
-              if (rule.hasArgument) {
-                skippingArgument = true;
-                value = args[i + 1];
-              }
-              options[rule.name] = rule.isList ? (options[rule.name] || []).concat(value) : value;
-              matchedRule = true;
-              break;
-            }
-          }
-          if (isOption && !matchedRule) {
-            throw new Error("unrecognized option: " + arg);
-          }
-        }
-        if (seenNonOptionArg || !isOption) {
-          options["arguments"].push(arg);
-        }
-      }
-      return options;
-    };
-
-    OptionParser.prototype.help = function() {
-      var letPart, lines, rule, spaces, _i, _len, _ref;
-      lines = [];
-      if (this.banner) {
-        lines.unshift("" + this.banner + "\n");
-      }
-      _ref = this.rules;
-      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-        rule = _ref[_i];
-        spaces = 15 - rule.longFlag.length;
-        spaces = spaces > 0 ? Array(spaces + 1).join(' ') : '';
-        letPart = rule.shortFlag ? rule.shortFlag + ', ' : '    ';
-        lines.push('  ' + letPart + rule.longFlag + spaces + rule.description);
-      }
-      return "\n" + (lines.join('\n')) + "\n";
-    };
-
-    return OptionParser;
-
-  })();
-
-  LONG_FLAG = /^(--\w[\w\-]*)/;
-
-  SHORT_FLAG = /^(-\w)$/;
-
-  MULTI_FLAG = /^-(\w{2,})/;
-
-  OPTIONAL = /\[(\w+(\*?))\]/;
-
-  buildRules = function(rules) {
-    var tuple, _i, _len, _results;
-    _results = [];
-    for (_i = 0, _len = rules.length; _i < _len; _i++) {
-      tuple = rules[_i];
-      if (tuple.length < 3) {
-        tuple.unshift(null);
-      }
-      _results.push(buildRule.apply(null, tuple));
-    }
-    return _results;
-  };
-
-  buildRule = function(shortFlag, longFlag, description, options) {
-    var match;
-    if (options == null) {
-      options = {};
-    }
-    match = longFlag.match(OPTIONAL);
-    longFlag = longFlag.match(LONG_FLAG)[1];
-    return {
-      name: longFlag.substr(2),
-      shortFlag: shortFlag,
-      longFlag: longFlag,
-      description: description,
-      hasArgument: !!(match && match[1]),
-      isList: !!(match && match[2])
-    };
-  };
-
-  normalizeArguments = function(args) {
-    var arg, l, match, result, _i, _j, _len, _len1, _ref;
-    args = args.slice(0);
-    result = [];
-    for (_i = 0, _len = args.length; _i < _len; _i++) {
-      arg = args[_i];
-      if (match = arg.match(MULTI_FLAG)) {
-        _ref = match[1].split('');
-        for (_j = 0, _len1 = _ref.length; _j < _len1; _j++) {
-          l = _ref[_j];
-          result.push('-' + l);
-        }
-      } else {
-        result.push(arg);
-      }
-    }
-    return result;
-  };
-
-}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/parser.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/parser.js
deleted file mode 100755
index dde2e61f..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/parser.js
+++ /dev/null
@@ -1,608 +0,0 @@
-/* parser generated by jison 0.4.2 */
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-case 49:this.$ = yy.addLocationDataFn(_$[$0-4], _$[$0])(new yy.Code($$[$0-3], $$[$0], $$[$0-1]));
-break;
-case 50:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Code([], $$[$0], $$[$0-1]));
-break;
-case 51:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])('func');
-break;
-case 52:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])('boundfunc');
-break;
-case 53:this.$ = $$[$0];
-break;
-case 54:this.$ = $$[$0];
-break;
-case 55:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])([]);
-break;
-case 56:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])([$$[$0]]);
-break;
-case 57:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])($$[$0-2].concat($$[$0]));
-break;
-case 58:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])($$[$0-3].concat($$[$0]));
-break;
-case 59:this.$ = yy.addLocationDataFn(_$[$0-5], _$[$0])($$[$0-5].concat($$[$0-2]));
-break;
-case 60:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Param($$[$0]));
-break;
-case 61:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Param($$[$0-1], null, true));
-break;
-case 62:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Param($$[$0-2], $$[$0]));
-break;
-case 63:this.$ = $$[$0];
-break;
-case 64:this.$ = $$[$0];
-break;
-case 65:this.$ = $$[$0];
-break;
-case 66:this.$ = $$[$0];
-break;
-case 67:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Splat($$[$0-1]));
-break;
-case 68:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Value($$[$0]));
-break;
-case 69:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])($$[$0-1].add($$[$0]));
-break;
-case 70:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Value($$[$0-1], [].concat($$[$0])));
-break;
-case 71:this.$ = $$[$0];
-break;
-case 72:this.$ = $$[$0];
-break;
-case 73:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Value($$[$0]));
-break;
-case 74:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Value($$[$0]));
-break;
-case 75:this.$ = $$[$0];
-break;
-case 76:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Value($$[$0]));
-break;
-case 77:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Value($$[$0]));
-break;
-case 78:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Value($$[$0]));
-break;
-case 79:this.$ = $$[$0];
-break;
-case 80:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Access($$[$0]));
-break;
-case 81:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Access($$[$0], 'soak'));
-break;
-case 82:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])([yy.addLocationDataFn(_$[$0-1])(new yy.Access(new yy.Literal('prototype'))), yy.addLocationDataFn(_$[$0])(new yy.Access($$[$0]))]);
-break;
-case 83:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])([yy.addLocationDataFn(_$[$0-1])(new yy.Access(new yy.Literal('prototype'), 'soak')), yy.addLocationDataFn(_$[$0])(new yy.Access($$[$0]))]);
-break;
-case 84:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Access(new yy.Literal('prototype')));
-break;
-case 85:this.$ = $$[$0];
-break;
-case 86:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])($$[$0-1]);
-break;
-case 87:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(yy.extend($$[$0], {
-          soak: true
-        }));
-break;
-case 88:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Index($$[$0]));
-break;
-case 89:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Slice($$[$0]));
-break;
-case 90:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])(new yy.Obj($$[$0-2], $$[$0-3].generated));
-break;
-case 91:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])([]);
-break;
-case 92:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])([$$[$0]]);
-break;
-case 93:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])($$[$0-2].concat($$[$0]));
-break;
-case 94:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])($$[$0-3].concat($$[$0]));
-break;
-case 95:this.$ = yy.addLocationDataFn(_$[$0-5], _$[$0])($$[$0-5].concat($$[$0-2]));
-break;
-case 96:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Class);
-break;
-case 97:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Class(null, null, $$[$0]));
-break;
-case 98:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Class(null, $$[$0]));
-break;
-case 99:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])(new yy.Class(null, $$[$0-1], $$[$0]));
-break;
-case 100:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Class($$[$0]));
-break;
-case 101:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Class($$[$0-1], null, $$[$0]));
-break;
-case 102:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])(new yy.Class($$[$0-2], $$[$0]));
-break;
-case 103:this.$ = yy.addLocationDataFn(_$[$0-4], _$[$0])(new yy.Class($$[$0-3], $$[$0-1], $$[$0]));
-break;
-case 104:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Call($$[$0-2], $$[$0], $$[$0-1]));
-break;
-case 105:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Call($$[$0-2], $$[$0], $$[$0-1]));
-break;
-case 106:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Call('super', [new yy.Splat(new yy.Literal('arguments'))]));
-break;
-case 107:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Call('super', $$[$0]));
-break;
-case 108:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(false);
-break;
-case 109:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(true);
-break;
-case 110:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])([]);
-break;
-case 111:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])($$[$0-2]);
-break;
-case 112:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Value(new yy.Literal('this')));
-break;
-case 113:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Value(new yy.Literal('this')));
-break;
-case 114:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Value(yy.addLocationDataFn(_$[$0-1])(new yy.Literal('this')), [yy.addLocationDataFn(_$[$0])(new yy.Access($$[$0]))], 'this'));
-break;
-case 115:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Arr([]));
-break;
-case 116:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])(new yy.Arr($$[$0-2]));
-break;
-case 117:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])('inclusive');
-break;
-case 118:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])('exclusive');
-break;
-case 119:this.$ = yy.addLocationDataFn(_$[$0-4], _$[$0])(new yy.Range($$[$0-3], $$[$0-1], $$[$0-2]));
-break;
-case 120:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Range($$[$0-2], $$[$0], $$[$0-1]));
-break;
-case 121:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Range($$[$0-1], null, $$[$0]));
-break;
-case 122:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Range(null, $$[$0], $$[$0-1]));
-break;
-case 123:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Range(null, null, $$[$0]));
-break;
-case 124:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])([$$[$0]]);
-break;
-case 125:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])($$[$0-2].concat($$[$0]));
-break;
-case 126:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])($$[$0-3].concat($$[$0]));
-break;
-case 127:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])($$[$0-2]);
-break;
-case 128:this.$ = yy.addLocationDataFn(_$[$0-5], _$[$0])($$[$0-5].concat($$[$0-2]));
-break;
-case 129:this.$ = $$[$0];
-break;
-case 130:this.$ = $$[$0];
-break;
-case 131:this.$ = $$[$0];
-break;
-case 132:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])([].concat($$[$0-2], $$[$0]));
-break;
-case 133:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Try($$[$0]));
-break;
-case 134:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Try($$[$0-1], $$[$0][0], $$[$0][1]));
-break;
-case 135:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])(new yy.Try($$[$0-2], null, null, $$[$0]));
-break;
-case 136:this.$ = yy.addLocationDataFn(_$[$0-4], _$[$0])(new yy.Try($$[$0-3], $$[$0-2][0], $$[$0-2][1], $$[$0]));
-break;
-case 137:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])([$$[$0-1], $$[$0]]);
-break;
-case 138:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])([yy.addLocationDataFn(_$[$0-1])(new yy.Value($$[$0-1])), $$[$0]]);
-break;
-case 139:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Throw($$[$0]));
-break;
-case 140:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Parens($$[$0-1]));
-break;
-case 141:this.$ = yy.addLocationDataFn(_$[$0-4], _$[$0])(new yy.Parens($$[$0-2]));
-break;
-case 142:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.While($$[$0]));
-break;
-case 143:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])(new yy.While($$[$0-2], {
-          guard: $$[$0]
-        }));
-break;
-case 144:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.While($$[$0], {
-          invert: true
-        }));
-break;
-case 145:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])(new yy.While($$[$0-2], {
-          invert: true,
-          guard: $$[$0]
-        }));
-break;
-case 146:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])($$[$0-1].addBody($$[$0]));
-break;
-case 147:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])($$[$0].addBody(yy.addLocationDataFn(_$[$0-1])(yy.Block.wrap([$$[$0-1]]))));
-break;
-case 148:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])($$[$0].addBody(yy.addLocationDataFn(_$[$0-1])(yy.Block.wrap([$$[$0-1]]))));
-break;
-case 149:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])($$[$0]);
-break;
-case 150:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.While(yy.addLocationDataFn(_$[$0-1])(new yy.Literal('true'))).addBody($$[$0]));
-break;
-case 151:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.While(yy.addLocationDataFn(_$[$0-1])(new yy.Literal('true'))).addBody(yy.addLocationDataFn(_$[$0])(yy.Block.wrap([$$[$0]]))));
-break;
-case 152:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.For($$[$0-1], $$[$0]));
-break;
-case 153:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.For($$[$0-1], $$[$0]));
-break;
-case 154:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.For($$[$0], $$[$0-1]));
-break;
-case 155:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])({
-          source: yy.addLocationDataFn(_$[$0])(new yy.Value($$[$0]))
-        });
-break;
-case 156:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])((function () {
-        $$[$0].own = $$[$0-1].own;
-        $$[$0].name = $$[$0-1][0];
-        $$[$0].index = $$[$0-1][1];
-        return $$[$0];
-      }()));
-break;
-case 157:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])($$[$0]);
-break;
-case 158:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])((function () {
-        $$[$0].own = true;
-        return $$[$0];
-      }()));
-break;
-case 159:this.$ = $$[$0];
-break;
-case 160:this.$ = $$[$0];
-break;
-case 161:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Value($$[$0]));
-break;
-case 162:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])(new yy.Value($$[$0]));
-break;
-case 163:this.$ = yy.addLocationDataFn(_$[$0], _$[$0])([$$[$0]]);
-break;
-case 164:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])([$$[$0-2], $$[$0]]);
-break;
-case 165:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])({
-          source: $$[$0]
-        });
-break;
-case 166:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])({
-          source: $$[$0],
-          object: true
-        });
-break;
-case 167:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])({
-          source: $$[$0-2],
-          guard: $$[$0]
-        });
-break;
-case 168:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])({
-          source: $$[$0-2],
-          guard: $$[$0],
-          object: true
-        });
-break;
-case 169:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])({
-          source: $$[$0-2],
-          step: $$[$0]
-        });
-break;
-case 170:this.$ = yy.addLocationDataFn(_$[$0-5], _$[$0])({
-          source: $$[$0-4],
-          guard: $$[$0-2],
-          step: $$[$0]
-        });
-break;
-case 171:this.$ = yy.addLocationDataFn(_$[$0-5], _$[$0])({
-          source: $$[$0-4],
-          step: $$[$0-2],
-          guard: $$[$0]
-        });
-break;
-case 172:this.$ = yy.addLocationDataFn(_$[$0-4], _$[$0])(new yy.Switch($$[$0-3], $$[$0-1]));
-break;
-case 173:this.$ = yy.addLocationDataFn(_$[$0-6], _$[$0])(new yy.Switch($$[$0-5], $$[$0-3], $$[$0-1]));
-break;
-case 174:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])(new yy.Switch(null, $$[$0-1]));
-break;
-case 175:this.$ = yy.addLocationDataFn(_$[$0-5], _$[$0])(new yy.Switch(null, $$[$0-3], $$[$0-1]));
-break;
-case 176:this.$ = $$[$0];
-break;
-case 177:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])($$[$0-1].concat($$[$0]));
-break;
-case 178:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])([[$$[$0-1], $$[$0]]]);
-break;
-case 179:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])([[$$[$0-2], $$[$0-1]]]);
-break;
-case 180:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.If($$[$0-1], $$[$0], {
-          type: $$[$0-2]
-        }));
-break;
-case 181:this.$ = yy.addLocationDataFn(_$[$0-4], _$[$0])($$[$0-4].addElse(new yy.If($$[$0-1], $$[$0], {
-          type: $$[$0-2]
-        })));
-break;
-case 182:this.$ = $$[$0];
-break;
-case 183:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])($$[$0-2].addElse($$[$0]));
-break;
-case 184:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.If($$[$0], yy.addLocationDataFn(_$[$0-2])(yy.Block.wrap([$$[$0-2]])), {
-          type: $$[$0-1],
-          statement: true
-        }));
-break;
-case 185:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.If($$[$0], yy.addLocationDataFn(_$[$0-2])(yy.Block.wrap([$$[$0-2]])), {
-          type: $$[$0-1],
-          statement: true
-        }));
-break;
-case 186:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Op($$[$0-1], $$[$0]));
-break;
-case 187:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Op('-', $$[$0]));
-break;
-case 188:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Op('+', $$[$0]));
-break;
-case 189:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Op('--', $$[$0]));
-break;
-case 190:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Op('++', $$[$0]));
-break;
-case 191:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Op('--', $$[$0-1], null, true));
-break;
-case 192:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Op('++', $$[$0-1], null, true));
-break;
-case 193:this.$ = yy.addLocationDataFn(_$[$0-1], _$[$0])(new yy.Existence($$[$0-1]));
-break;
-case 194:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Op('+', $$[$0-2], $$[$0]));
-break;
-case 195:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Op('-', $$[$0-2], $$[$0]));
-break;
-case 196:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Op($$[$0-1], $$[$0-2], $$[$0]));
-break;
-case 197:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Op($$[$0-1], $$[$0-2], $$[$0]));
-break;
-case 198:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Op($$[$0-1], $$[$0-2], $$[$0]));
-break;
-case 199:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Op($$[$0-1], $$[$0-2], $$[$0]));
-break;
-case 200:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])((function () {
-        if ($$[$0-1].charAt(0) === '!') {
-          return new yy.Op($$[$0-1].slice(1), $$[$0-2], $$[$0]).invert();
-        } else {
-          return new yy.Op($$[$0-1], $$[$0-2], $$[$0]);
-        }
-      }()));
-break;
-case 201:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Assign($$[$0-2], $$[$0], $$[$0-1]));
-break;
-case 202:this.$ = yy.addLocationDataFn(_$[$0-4], _$[$0])(new yy.Assign($$[$0-4], $$[$0-1], $$[$0-3]));
-break;
-case 203:this.$ = yy.addLocationDataFn(_$[$0-3], _$[$0])(new yy.Assign($$[$0-3], $$[$0], $$[$0-2]));
-break;
-case 204:this.$ = yy.addLocationDataFn(_$[$0-2], _$[$0])(new yy.Extends($$[$0-2], $$[$0]));
-break;
-}
-},
-table: 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4:[2,141],105:[2,141],106:[2,141],110:[2,141],118:[2,141],126:[2,141],128:[2,141],129:[2,141],132:[2,141],133:[2,141],134:[2,141],135:[2,141],136:[2,141],137:[2,141]},{1:[2,119],6:[2,119],25:[2,119],26:[2,119],49:[2,119],54:[2,119],57:[2,119],66:[2,119],67:[2,119],68:[2,119],69:[2,119],71:[2,119],73:[2,119],74:[2,119],78:[2,119],84:[2,119],85:[2,119],86:[2,119],91:[2,119],93:[2,119],102:[2,119],104:[2,119],105:[2,119],106:[2,119],110:[2,119],118:[2,119],126:[2,119],128:[2,119],129:[2,119],132:[2,119],133:[2,119],134:[2,119],135:[2,119],136:[2,119],137:[2,119]},{6:[2,126],25:[2,126],26:[2,126],54:[2,126],86:[2,126],91:[2,126]},{6:[2,53],25:[2,53],26:[2,53],53:320,54:[1,229]},{6:[2,127],25:[2,127],26:[2,127],54:[2,127],86:[2,127],91:[2,127]},{1:[2,167],6:[2,167],25:[2,167],26:[2,167],49:[2,167],54:[2,167],57:[2,167],73:[2,167],78:[2,167],86:[2,167],91:[2,167],93:[2,167],102:[2,167],103:87,104:[2,167],105:[2,167],106:[2,167],109:88,110:[2,167],111:69,118:[1,321],126:[2,167],128:[1,80],129:[1,79],132:[1,78],133:[1,81],134:[1,82],135:[1,83],136:[1,84],137:[1,85]},{1:[2,169],6:[2,169],25:[2,169],26:[2,169],49:[2,169],54:[2,169],57:[2,169],73:[2,169],78:[2,169],86:[2,169],91:[2,169],93:[2,169],102:[2,169],103:87,104:[2,169],105:[1,322],106:[2,169],109:88,110:[2,169],111:69,118:[2,169],126:[2,169],128:[1,80],129:[1,79],132:[1,78],133:[1,81],134:[1,82],135:[1,83],136:[1,84],137:[1,85]},{1:[2,168],6:[2,168],25:[2,168],26:[2,168],49:[2,168],54:[2,168],57:[2,168],73:[2,168],78:[2,168],86:[2,168],91:[2,168],93:[2,168],102:[2,168],103:87,104:[2,168],105:[2,168],106:[2,168],109:88,110:[2,168],111:69,118:[2,168],126:[2,168],128:[1,80],129:[1,79],132:[1,78],133:[1,81],134:[1,82],135:[1,83],136:[1,84],137:[1,85]},{6:[2,94],25:[2,94],26:[2,94],54:[2,94],78:[2,94]},{6:[2,53],25:[2,53],26:[2,53],53:323,54:[1,239]},{26:[1,324],103:87,104:[1,65],106:[1,66],109:88,110:[1,68],111:69,126:[1,86],128:[1,80],129:[1,79],132:[1,78],133:[1,81],134:[1,82],135:[1,83],136:[1,84],137:[1,85]},{6:[1,250],25:[1,251],26:[1,325]},{26:[1,326]},{1:[2,175],6:[2,175],25:[2,175],26:[2,175],49:[2,175],54:[2,175],57:[2,175],73:[2,175],78:[2,175],86:[2,175],91:[2,175],93:[2,175],102:[2,175],104:[2,175],105:[2,175],106:[2,175],110:[2,175],118:[2,175],126:[2,175],128:[2,175],129:[2,175],132:[2,175],133:[2,175],134:[2,175],135:[2,175],136:[2,175],137:[2,175]},{26:[2,179],121:[2,179],123:[2,179]},{25:[2,132],54:[2,132],103:87,104:[1,65],106:[1,66],109:88,110:[1,68],111:69,126:[1,86],128:[1,80],129:[1,79],132:[1,78],133:[1,81],134:[1,82],135:[1,83],136:[1,84],137:[1,85]},{6:[1,271],25:[1,272],26:[1,327]},{8:328,9:118,10:20,11:21,12:[1,22],13:8,14:9,15:10,16:11,17:12,18:13,19:14,20:15,21:16,22:17,23:18,24:19,27:62,28:[1,73],29:49,30:[1,71],31:[1,72],32:24,33:[1,50],34:[1,51],35:[1,52],36:[1,53],37:[1,54],38:[1,55],39:23,44:63,45:[1,45],46:[1,46],47:[1,29],50:30,51:[1,60],52:[1,61],58:47,59:48,61:36,63:25,64:26,65:27,76:[1,70],79:[1,43],83:[1,28],88:[1,58],89:[1,59],90:[1,57],96:[1,38],100:[1,44],101:[1,56],103:39,104:[1,65],106:[1,66],107:40,108:[1,67],109:41,110:[1,68],111:69,119:[1,42],124:37,125:[1,64],127:[1,31],128:[1,32],129:[1,33],130:[1,34],131:[1,35]},{8:329,9:118,10:20,11:21,12:[1,22],13:8,14:9,15:10,16:11,17:12,18:13,19:14,20:15,21:16,22:17,23:18,24:19,27:62,28:[1,73],29:49,30:[1,71],31:[1,72],32:24,33:[1,50],34:[1,51],35:[1,52],36:[1,53],37:[1,54],38:[1,55],39:23,44:63,45:[1,45],46:[1,46],47:[1,29],50:30,51:[1,60],52:[1,61],58:47,59:48,61:36,63:25,64:26,65:27,76:[1,70],79:[1,43],83:[1,28],88:[1,58],89:[1,59],90:[1,57],96:[1,38],100:[1,44],101:[1,56],103:39,104:[1,65],106:[1,66],107:40,108:[1,67],109:41,110:[1,68],111:69,119:[1,42],124:37,125:[1,64],127:[1,31],128:[1,32],129:[1,33],130:[1,34],131:[1,35]},{6:[1,282],25:[1,283],26:[1,330]},{6:[2,41],25:[2,41],26:[2,41],54:[2,41],78:[2,41]},{6:[2,59],25:[2,59],26:[2,59],49:[2,59],54:[2,59]},{1:[2,173],6:[2,173],25:[2,173],26:[2,173],49:[2,173],54:[2,173],57:[2,173],73:[2,173],78:[2,173],86:[2,173],91:[2,173],93:[2,173],102:[2,173],104:[2,173],105:[2,173],106:[2,173],110:[2,173],118:[2,173],126:[2,173],128:[2,173],129:[2,173],132:[2,173],133:[2,173],134:[2,173],135:[2,173],136:[2,173],137:[2,173]},{6:[2,128],25:[2,128],26:[2,128],54:[2,128],86:[2,128],91:[2,128]},{1:[2,170],6:[2,170],25:[2,170],26:[2,170],49:[2,170],54:[2,170],57:[2,170],73:[2,170],78:[2,170],86:[2,170],91:[2,170],93:[2,170],102:[2,170],103:87,104:[2,170],105:[2,170],106:[2,170],109:88,110:[2,170],111:69,118:[2,170],126:[2,170],128:[1,80],129:[1,79],132:[1,78],133:[1,81],134:[1,82],135:[1,83],136:[1,84],137:[1,85]},{1:[2,171],6:[2,171],25:[2,171],26:[2,171],49:[2,171],54:[2,171],57:[2,171],73:[2,171],78:[2,171],86:[2,171],91:[2,171],93:[2,171],102:[2,171],103:87,104:[2,171],105:[2,171],106:[2,171],109:88,110:[2,171],111:69,118:[2,171],126:[2,171],128:[1,80],129:[1,79],132:[1,78],133:[1,81],134:[1,82],135:[1,83],136:[1,84],137:[1,85]},{6:[2,95],25:[2,95],26:[2,95],54:[2,95],78:[2,95]}],
-defaultActions: {60:[2,51],61:[2,52],75:[2,3],94:[2,109],191:[2,89]},
-parseError: function parseError(str, hash) {
-    throw new Error(str);
-},
-parse: function parse(input) {
-    var self = this, stack = [0], vstack = [null], lstack = [], table = this.table, yytext = "", yylineno = 0, yyleng = 0, recovering = 0, TERROR = 2, EOF = 1;
-    this.lexer.setInput(input);
-    this.lexer.yy = this.yy;
-    this.yy.lexer = this.lexer;
-    this.yy.parser = this;
-    if (typeof this.lexer.yylloc == "undefined")
-        this.lexer.yylloc = {};
-    var yyloc = this.lexer.yylloc;
-    lstack.push(yyloc);
-    var ranges = this.lexer.options && this.lexer.options.ranges;
-    if (typeof this.yy.parseError === "function")
-        this.parseError = this.yy.parseError;
-    function popStack(n) {
-        stack.length = stack.length - 2 * n;
-        vstack.length = vstack.length - n;
-        lstack.length = lstack.length - n;
-    }
-    function lex() {
-        var token;
-        token = self.lexer.lex() || 1;
-        if (typeof token !== "number") {
-            token = self.symbols_[token] || token;
-        }
-        return token;
-    }
-    var symbol, preErrorSymbol, state, action, a, r, yyval = {}, p, len, newState, expected;
-    while (true) {
-        state = stack[stack.length - 1];
-        if (this.defaultActions[state]) {
-            action = this.defaultActions[state];
-        } else {
-            if (symbol === null || typeof symbol == "undefined") {
-                symbol = lex();
-            }
-            action = table[state] && table[state][symbol];
-        }
-        if (typeof action === "undefined" || !action.length || !action[0]) {
-            var errStr = "";
-            if (!recovering) {
-                expected = [];
-                for (p in table[state])
-                    if (this.terminals_[p] && p > 2) {
-                        expected.push("'" + this.terminals_[p] + "'");
-                    }
-                if (this.lexer.showPosition) {
-                    errStr = "Parse error on line " + (yylineno + 1) + ":\n" + this.lexer.showPosition() + "\nExpecting " + expected.join(", ") + ", got '" + (this.terminals_[symbol] || symbol) + "'";
-                } else {
-                    errStr = "Parse error on line " + (yylineno + 1) + ": Unexpected " + (symbol == 1?"end of input":"'" + (this.terminals_[symbol] || symbol) + "'");
-                }
-                this.parseError(errStr, {text: this.lexer.match, token: this.terminals_[symbol] || symbol, line: this.lexer.yylineno, loc: yyloc, expected: expected});
-            }
-        }
-        if (action[0] instanceof Array && action.length > 1) {
-            throw new Error("Parse Error: multiple actions possible at state: " + state + ", token: " + symbol);
-        }
-        switch (action[0]) {
-        case 1:
-            stack.push(symbol);
-            vstack.push(this.lexer.yytext);
-            lstack.push(this.lexer.yylloc);
-            stack.push(action[1]);
-            symbol = null;
-            if (!preErrorSymbol) {
-                yyleng = this.lexer.yyleng;
-                yytext = this.lexer.yytext;
-                yylineno = this.lexer.yylineno;
-                yyloc = this.lexer.yylloc;
-                if (recovering > 0)
-                    recovering--;
-            } else {
-                symbol = preErrorSymbol;
-                preErrorSymbol = null;
-            }
-            break;
-        case 2:
-            len = this.productions_[action[1]][1];
-            yyval.$ = vstack[vstack.length - len];
-            yyval._$ = {first_line: lstack[lstack.length - (len || 1)].first_line, last_line: lstack[lstack.length - 1].last_line, first_column: lstack[lstack.length - (len || 1)].first_column, last_column: lstack[lstack.length - 1].last_column};
-            if (ranges) {
-                yyval._$.range = [lstack[lstack.length - (len || 1)].range[0], lstack[lstack.length - 1].range[1]];
-            }
-            r = this.performAction.call(yyval, yytext, yyleng, yylineno, this.yy, action[1], vstack, lstack);
-            if (typeof r !== "undefined") {
-                return r;
-            }
-            if (len) {
-                stack = stack.slice(0, -1 * len * 2);
-                vstack = vstack.slice(0, -1 * len);
-                lstack = lstack.slice(0, -1 * len);
-            }
-            stack.push(this.productions_[action[1]][0]);
-            vstack.push(yyval.$);
-            lstack.push(yyval._$);
-            newState = table[stack[stack.length - 2]][stack[stack.length - 1]];
-            stack.push(newState);
-            break;
-        case 3:
-            return true;
-        }
-    }
-    return true;
-}
-};
-undefined
-function Parser () { this.yy = {}; }Parser.prototype = parser;parser.Parser = Parser;
-return new Parser;
-})();
-if (typeof require !== 'undefined' && typeof exports !== 'undefined') {
-exports.parser = parser;
-exports.Parser = parser.Parser;
-exports.parse = function () { return parser.parse.apply(parser, arguments); };
-exports.main = function commonjsMain(args) {
-    if (!args[1]) {
-        console.log('Usage: '+args[0]+' FILE');
-        process.exit(1);
-    }
-    var source = require('fs').readFileSync(require('path').normalize(args[1]), "utf8");
-    return exports.parser.parse(source);
-};
-if (typeof module !== 'undefined' && require.main === module) {
-  exports.main(process.argv.slice(1));
-}
-}
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/repl.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/repl.js
deleted file mode 100755
index 37894a9b..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/repl.js
+++ /dev/null
@@ -1,104 +0,0 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var CoffeeScript, addMultilineHandler, merge, nodeREPL, replDefaults, vm;
-
-  vm = require('vm');
-
-  nodeREPL = require('repl');
-
-  CoffeeScript = require('./coffee-script');
-
-  merge = require('./helpers').merge;
-
-  replDefaults = {
-    prompt: 'coffee> ',
-    "eval": function(input, context, filename, cb) {
-      var js;
-      input = input.replace(/\uFF00/g, '\n');
-      input = input.replace(/(^|[\r\n]+)(\s*)##?(?:[^#\r\n][^\r\n]*|)($|[\r\n])/, '$1$2$3');
-      if (/^(\s*|\(\s*\))$/.test(input)) {
-        return cb(null);
-      }
-      try {
-        js = CoffeeScript.compile("_=(" + input + "\n)", {
-          filename: filename,
-          bare: true
-        });
-        return cb(null, vm.runInContext(js, context, filename));
-      } catch (err) {
-        return cb(err);
-      }
-    }
-  };
-
-  addMultilineHandler = function(repl) {
-    var inputStream, multiline, nodeLineListener, outputStream, rli;
-    rli = repl.rli, inputStream = repl.inputStream, outputStream = repl.outputStream;
-    multiline = {
-      enabled: false,
-      initialPrompt: repl.prompt.replace(/^[^> ]*/, function(x) {
-        return x.replace(/./g, '-');
-      }),
-      prompt: repl.prompt.replace(/^[^> ]*>?/, function(x) {
-        return x.replace(/./g, '.');
-      }),
-      buffer: ''
-    };
-    nodeLineListener = rli.listeners('line')[0];
-    rli.removeListener('line', nodeLineListener);
-    rli.on('line', function(cmd) {
-      if (multiline.enabled) {
-        multiline.buffer += "" + cmd + "\n";
-        rli.setPrompt(multiline.prompt);
-        rli.prompt(true);
-      } else {
-        nodeLineListener(cmd);
-      }
-    });
-    return inputStream.on('keypress', function(char, key) {
-      if (!(key && key.ctrl && !key.meta && !key.shift && key.name === 'v')) {
-        return;
-      }
-      if (multiline.enabled) {
-        if (!multiline.buffer.match(/\n/)) {
-          multiline.enabled = !multiline.enabled;
-          rli.setPrompt(repl.prompt);
-          rli.prompt(true);
-          return;
-        }
-        if ((rli.line != null) && !rli.line.match(/^\s*$/)) {
-          return;
-        }
-        multiline.enabled = !multiline.enabled;
-        rli.line = '';
-        rli.cursor = 0;
-        rli.output.cursorTo(0);
-        rli.output.clearLine(1);
-        multiline.buffer = multiline.buffer.replace(/\n/g, '\uFF00');
-        rli.emit('line', multiline.buffer);
-        multiline.buffer = '';
-      } else {
-        multiline.enabled = !multiline.enabled;
-        rli.setPrompt(multiline.initialPrompt);
-        rli.prompt(true);
-      }
-    });
-  };
-
-  module.exports = {
-    start: function(opts) {
-      var repl;
-      if (opts == null) {
-        opts = {};
-      }
-      opts = merge(replDefaults, opts);
-      repl = nodeREPL.start(opts);
-      repl.on('exit', function() {
-        return repl.outputStream.write('\n');
-      });
-      addMultilineHandler(repl);
-      return repl;
-    }
-  };
-
-}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/rewriter.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/rewriter.js
deleted file mode 100755
index b582bb29..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/rewriter.js
+++ /dev/null
@@ -1,478 +0,0 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var BALANCED_PAIRS, EXPRESSION_CLOSE, EXPRESSION_END, EXPRESSION_START, IMPLICIT_BLOCK, IMPLICIT_CALL, IMPLICIT_END, IMPLICIT_FUNC, IMPLICIT_UNSPACED_CALL, INVERSES, LINEBREAKS, SINGLE_CLOSERS, SINGLE_LINERS, generate, left, rite, _i, _len, _ref,
-    __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; },
-    __slice = [].slice;
-
-  generate = function(tag, value) {
-    var tok;
-    tok = [tag, value];
-    tok.generated = true;
-    return tok;
-  };
-
-  exports.Rewriter = (function() {
-
-    function Rewriter() {}
-
-    Rewriter.prototype.rewrite = function(tokens) {
-      this.tokens = tokens;
-      this.removeLeadingNewlines();
-      this.removeMidExpressionNewlines();
-      this.closeOpenCalls();
-      this.closeOpenIndexes();
-      this.addImplicitIndentation();
-      this.tagPostfixConditionals();
-      this.addImplicitBracesAndParens();
-      this.addLocationDataToGeneratedTokens();
-      return this.tokens;
-    };
-
-    Rewriter.prototype.scanTokens = function(block) {
-      var i, token, tokens;
-      tokens = this.tokens;
-      i = 0;
-      while (token = tokens[i]) {
-        i += block.call(this, token, i, tokens);
-      }
-      return true;
-    };
-
-    Rewriter.prototype.detectEnd = function(i, condition, action) {
-      var levels, token, tokens, _ref, _ref1;
-      tokens = this.tokens;
-      levels = 0;
-      while (token = tokens[i]) {
-        if (levels === 0 && condition.call(this, token, i)) {
-          return action.call(this, token, i);
-        }
-        if (!token || levels < 0) {
-          return action.call(this, token, i - 1);
-        }
-        if (_ref = token[0], __indexOf.call(EXPRESSION_START, _ref) >= 0) {
-          levels += 1;
-        } else if (_ref1 = token[0], __indexOf.call(EXPRESSION_END, _ref1) >= 0) {
-          levels -= 1;
-        }
-        i += 1;
-      }
-      return i - 1;
-    };
-
-    Rewriter.prototype.removeLeadingNewlines = function() {
-      var i, tag, _i, _len, _ref;
-      _ref = this.tokens;
-      for (i = _i = 0, _len = _ref.length; _i < _len; i = ++_i) {
-        tag = _ref[i][0];
-        if (tag !== 'TERMINATOR') {
-          break;
-        }
-      }
-      if (i) {
-        return this.tokens.splice(0, i);
-      }
-    };
-
-    Rewriter.prototype.removeMidExpressionNewlines = function() {
-      return this.scanTokens(function(token, i, tokens) {
-        var _ref;
-        if (!(token[0] === 'TERMINATOR' && (_ref = this.tag(i + 1), __indexOf.call(EXPRESSION_CLOSE, _ref) >= 0))) {
-          return 1;
-        }
-        tokens.splice(i, 1);
-        return 0;
-      });
-    };
-
-    Rewriter.prototype.closeOpenCalls = function() {
-      var action, condition;
-      condition = function(token, i) {
-        var _ref;
-        return ((_ref = token[0]) === ')' || _ref === 'CALL_END') || token[0] === 'OUTDENT' && this.tag(i - 1) === ')';
-      };
-      action = function(token, i) {
-        return this.tokens[token[0] === 'OUTDENT' ? i - 1 : i][0] = 'CALL_END';
-      };
-      return this.scanTokens(function(token, i) {
-        if (token[0] === 'CALL_START') {
-          this.detectEnd(i + 1, condition, action);
-        }
-        return 1;
-      });
-    };
-
-    Rewriter.prototype.closeOpenIndexes = function() {
-      var action, condition;
-      condition = function(token, i) {
-        var _ref;
-        return (_ref = token[0]) === ']' || _ref === 'INDEX_END';
-      };
-      action = function(token, i) {
-        return token[0] = 'INDEX_END';
-      };
-      return this.scanTokens(function(token, i) {
-        if (token[0] === 'INDEX_START') {
-          this.detectEnd(i + 1, condition, action);
-        }
-        return 1;
-      });
-    };
-
-    Rewriter.prototype.matchTags = function() {
-      var fuzz, i, j, pattern, _i, _ref, _ref1;
-      i = arguments[0], pattern = 2 <= arguments.length ? __slice.call(arguments, 1) : [];
-      fuzz = 0;
-      for (j = _i = 0, _ref = pattern.length; 0 <= _ref ? _i < _ref : _i > _ref; j = 0 <= _ref ? ++_i : --_i) {
-        while (this.tag(i + j + fuzz) === 'HERECOMMENT') {
-          fuzz += 2;
-        }
-        if (pattern[j] == null) {
-          continue;
-        }
-        if (typeof pattern[j] === 'string') {
-          pattern[j] = [pattern[j]];
-        }
-        if (_ref1 = this.tag(i + j + fuzz), __indexOf.call(pattern[j], _ref1) < 0) {
-          return false;
-        }
-      }
-      return true;
-    };
-
-    Rewriter.prototype.looksObjectish = function(j) {
-      return this.matchTags(j, '@', null, ':') || this.matchTags(j, null, ':');
-    };
-
-    Rewriter.prototype.findTagsBackwards = function(i, tags) {
-      var backStack, _ref, _ref1, _ref2, _ref3, _ref4, _ref5;
-      backStack = [];
-      while (i >= 0 && (backStack.length || (_ref2 = this.tag(i), __indexOf.call(tags, _ref2) < 0) && ((_ref3 = this.tag(i), __indexOf.call(EXPRESSION_START, _ref3) < 0) || this.tokens[i].generated) && (_ref4 = this.tag(i), __indexOf.call(LINEBREAKS, _ref4) < 0))) {
-        if (_ref = this.tag(i), __indexOf.call(EXPRESSION_END, _ref) >= 0) {
-          backStack.push(this.tag(i));
-        }
-        if ((_ref1 = this.tag(i), __indexOf.call(EXPRESSION_START, _ref1) >= 0) && backStack.length) {
-          backStack.pop();
-        }
-        i -= 1;
-      }
-      return _ref5 = this.tag(i), __indexOf.call(tags, _ref5) >= 0;
-    };
-
-    Rewriter.prototype.addImplicitBracesAndParens = function() {
-      var stack;
-      stack = [];
-      return this.scanTokens(function(token, i, tokens) {
-        var endImplicitCall, endImplicitObject, forward, inImplicit, inImplicitCall, inImplicitControl, inImplicitObject, nextTag, offset, prevTag, s, sameLine, stackIdx, stackTag, stackTop, startIdx, startImplicitCall, startImplicitObject, startsLine, tag, _ref, _ref1, _ref2, _ref3, _ref4, _ref5;
-        tag = token[0];
-        prevTag = (i > 0 ? tokens[i - 1] : [])[0];
-        nextTag = (i < tokens.length - 1 ? tokens[i + 1] : [])[0];
-        stackTop = function() {
-          return stack[stack.length - 1];
-        };
-        startIdx = i;
-        forward = function(n) {
-          return i - startIdx + n;
-        };
-        inImplicit = function() {
-          var _ref, _ref1;
-          return (_ref = stackTop()) != null ? (_ref1 = _ref[2]) != null ? _ref1.ours : void 0 : void 0;
-        };
-        inImplicitCall = function() {
-          var _ref;
-          return inImplicit() && ((_ref = stackTop()) != null ? _ref[0] : void 0) === '(';
-        };
-        inImplicitObject = function() {
-          var _ref;
-          return inImplicit() && ((_ref = stackTop()) != null ? _ref[0] : void 0) === '{';
-        };
-        inImplicitControl = function() {
-          var _ref;
-          return inImplicit && ((_ref = stackTop()) != null ? _ref[0] : void 0) === 'CONTROL';
-        };
-        startImplicitCall = function(j) {
-          var idx;
-          idx = j != null ? j : i;
-          stack.push([
-            '(', idx, {
-              ours: true
-            }
-          ]);
-          tokens.splice(idx, 0, generate('CALL_START', '('));
-          if (j == null) {
-            return i += 1;
-          }
-        };
-        endImplicitCall = function() {
-          stack.pop();
-          tokens.splice(i, 0, generate('CALL_END', ')'));
-          return i += 1;
-        };
-        startImplicitObject = function(j, startsLine) {
-          var idx;
-          if (startsLine == null) {
-            startsLine = true;
-          }
-          idx = j != null ? j : i;
-          stack.push([
-            '{', idx, {
-              sameLine: true,
-              startsLine: startsLine,
-              ours: true
-            }
-          ]);
-          tokens.splice(idx, 0, generate('{', generate(new String('{'))));
-          if (j == null) {
-            return i += 1;
-          }
-        };
-        endImplicitObject = function(j) {
-          j = j != null ? j : i;
-          stack.pop();
-          tokens.splice(j, 0, generate('}', '}'));
-          return i += 1;
-        };
-        if (inImplicitCall() && (tag === 'IF' || tag === 'TRY' || tag === 'FINALLY' || tag === 'CATCH' || tag === 'CLASS' || tag === 'SWITCH')) {
-          stack.push([
-            'CONTROL', i, {
-              ours: true
-            }
-          ]);
-          return forward(1);
-        }
-        if (tag === 'INDENT' && inImplicit()) {
-          if (prevTag !== '=>' && prevTag !== '->' && prevTag !== '[' && prevTag !== '(' && prevTag !== ',' && prevTag !== '{' && prevTag !== 'TRY' && prevTag !== 'ELSE' && prevTag !== '=') {
-            while (inImplicitCall()) {
-              endImplicitCall();
-            }
-          }
-          if (inImplicitControl()) {
-            stack.pop();
-          }
-          stack.push([tag, i]);
-          return forward(1);
-        }
-        if (__indexOf.call(EXPRESSION_START, tag) >= 0) {
-          stack.push([tag, i]);
-          return forward(1);
-        }
-        if (__indexOf.call(EXPRESSION_END, tag) >= 0) {
-          while (inImplicit()) {
-            if (inImplicitCall()) {
-              endImplicitCall();
-            } else if (inImplicitObject()) {
-              endImplicitObject();
-            } else {
-              stack.pop();
-            }
-          }
-          stack.pop();
-        }
-        if ((__indexOf.call(IMPLICIT_FUNC, tag) >= 0 && token.spaced || tag === '?' && i > 0 && !tokens[i - 1].spaced) && (__indexOf.call(IMPLICIT_CALL, nextTag) >= 0 || __indexOf.call(IMPLICIT_UNSPACED_CALL, nextTag) >= 0 && !((_ref = tokens[i + 1]) != null ? _ref.spaced : void 0) && !((_ref1 = tokens[i + 1]) != null ? _ref1.newLine : void 0))) {
-          if (tag === '?') {
-            tag = token[0] = 'FUNC_EXIST';
-          }
-          startImplicitCall(i + 1);
-          return forward(2);
-        }
-        if (this.matchTags(i, IMPLICIT_FUNC, 'INDENT', null, ':') && !this.findTagsBackwards(i, ['CLASS', 'EXTENDS', 'IF', 'CATCH', 'SWITCH', 'LEADING_WHEN', 'FOR', 'WHILE', 'UNTIL'])) {
-          startImplicitCall(i + 1);
-          stack.push(['INDENT', i + 2]);
-          return forward(3);
-        }
-        if (tag === ':') {
-          if (this.tag(i - 2) === '@') {
-            s = i - 2;
-          } else {
-            s = i - 1;
-          }
-          while (this.tag(s - 2) === 'HERECOMMENT') {
-            s -= 2;
-          }
-          startsLine = s === 0 || (_ref2 = this.tag(s - 1), __indexOf.call(LINEBREAKS, _ref2) >= 0) || tokens[s - 1].newLine;
-          if (stackTop()) {
-            _ref3 = stackTop(), stackTag = _ref3[0], stackIdx = _ref3[1];
-            if ((stackTag === '{' || stackTag === 'INDENT' && this.tag(stackIdx - 1) === '{') && (startsLine || this.tag(s - 1) === ',' || this.tag(s - 1) === '{')) {
-              return forward(1);
-            }
-          }
-          startImplicitObject(s, !!startsLine);
-          return forward(2);
-        }
-        if (prevTag === 'OUTDENT' && inImplicitCall() && (tag === '.' || tag === '?.' || tag === '::' || tag === '?::')) {
-          endImplicitCall();
-          return forward(1);
-        }
-        if (inImplicitObject() && __indexOf.call(LINEBREAKS, tag) >= 0) {
-          stackTop()[2].sameLine = false;
-        }
-        if (__indexOf.call(IMPLICIT_END, tag) >= 0) {
-          while (inImplicit()) {
-            _ref4 = stackTop(), stackTag = _ref4[0], stackIdx = _ref4[1], (_ref5 = _ref4[2], sameLine = _ref5.sameLine, startsLine = _ref5.startsLine);
-            if (inImplicitCall() && prevTag !== ',') {
-              endImplicitCall();
-            } else if (inImplicitObject() && sameLine && !startsLine) {
-              endImplicitObject();
-            } else if (inImplicitObject() && tag === 'TERMINATOR' && prevTag !== ',' && !(startsLine && this.looksObjectish(i + 1))) {
-              endImplicitObject();
-            } else {
-              break;
-            }
-          }
-        }
-        if (tag === ',' && !this.looksObjectish(i + 1) && inImplicitObject() && (nextTag !== 'TERMINATOR' || !this.looksObjectish(i + 2))) {
-          offset = nextTag === 'OUTDENT' ? 1 : 0;
-          while (inImplicitObject()) {
-            endImplicitObject(i + offset);
-          }
-        }
-        return forward(1);
-      });
-    };
-
-    Rewriter.prototype.addLocationDataToGeneratedTokens = function() {
-      return this.scanTokens(function(token, i, tokens) {
-        var last_column, last_line, _ref, _ref1, _ref2;
-        if (token[2]) {
-          return 1;
-        }
-        if (!(token.generated || token.explicit)) {
-          return 1;
-        }
-        _ref2 = (_ref = (_ref1 = tokens[i - 1]) != null ? _ref1[2] : void 0) != null ? _ref : {
-          last_line: 0,
-          last_column: 0
-        }, last_line = _ref2.last_line, last_column = _ref2.last_column;
-        token[2] = {
-          first_line: last_line,
-          first_column: last_column,
-          last_line: last_line,
-          last_column: last_column
-        };
-        return 1;
-      });
-    };
-
-    Rewriter.prototype.addImplicitIndentation = function() {
-      var action, condition, indent, outdent, starter;
-      starter = indent = outdent = null;
-      condition = function(token, i) {
-        var _ref;
-        return token[1] !== ';' && (_ref = token[0], __indexOf.call(SINGLE_CLOSERS, _ref) >= 0) && !(token[0] === 'ELSE' && (starter !== 'IF' && starter !== 'THEN'));
-      };
-      action = function(token, i) {
-        return this.tokens.splice((this.tag(i - 1) === ',' ? i - 1 : i), 0, outdent);
-      };
-      return this.scanTokens(function(token, i, tokens) {
-        var tag, _ref, _ref1;
-        tag = token[0];
-        if (tag === 'TERMINATOR' && this.tag(i + 1) === 'THEN') {
-          tokens.splice(i, 1);
-          return 0;
-        }
-        if (tag === 'ELSE' && this.tag(i - 1) !== 'OUTDENT') {
-          tokens.splice.apply(tokens, [i, 0].concat(__slice.call(this.indentation(token))));
-          return 2;
-        }
-        if (tag === 'CATCH' && ((_ref = this.tag(i + 2)) === 'OUTDENT' || _ref === 'TERMINATOR' || _ref === 'FINALLY')) {
-          tokens.splice.apply(tokens, [i + 2, 0].concat(__slice.call(this.indentation(token))));
-          return 4;
-        }
-        if (__indexOf.call(SINGLE_LINERS, tag) >= 0 && this.tag(i + 1) !== 'INDENT' && !(tag === 'ELSE' && this.tag(i + 1) === 'IF')) {
-          starter = tag;
-          _ref1 = this.indentation(token, true), indent = _ref1[0], outdent = _ref1[1];
-          if (starter === 'THEN') {
-            indent.fromThen = true;
-          }
-          tokens.splice(i + 1, 0, indent);
-          this.detectEnd(i + 2, condition, action);
-          if (tag === 'THEN') {
-            tokens.splice(i, 1);
-          }
-          return 1;
-        }
-        return 1;
-      });
-    };
-
-    Rewriter.prototype.tagPostfixConditionals = function() {
-      var action, condition, original;
-      original = null;
-      condition = function(token, i) {
-        var _ref;
-        return (_ref = token[0]) === 'TERMINATOR' || _ref === 'INDENT';
-      };
-      action = function(token, i) {
-        if (token[0] !== 'INDENT' || (token.generated && !token.fromThen)) {
-          return original[0] = 'POST_' + original[0];
-        }
-      };
-      return this.scanTokens(function(token, i) {
-        if (token[0] !== 'IF') {
-          return 1;
-        }
-        original = token;
-        this.detectEnd(i + 1, condition, action);
-        return 1;
-      });
-    };
-
-    Rewriter.prototype.indentation = function(token, implicit) {
-      var indent, outdent;
-      if (implicit == null) {
-        implicit = false;
-      }
-      indent = ['INDENT', 2];
-      outdent = ['OUTDENT', 2];
-      if (implicit) {
-        indent.generated = outdent.generated = true;
-      }
-      if (!implicit) {
-        indent.explicit = outdent.explicit = true;
-      }
-      return [indent, outdent];
-    };
-
-    Rewriter.prototype.generate = generate;
-
-    Rewriter.prototype.tag = function(i) {
-      var _ref;
-      return (_ref = this.tokens[i]) != null ? _ref[0] : void 0;
-    };
-
-    return Rewriter;
-
-  })();
-
-  BALANCED_PAIRS = [['(', ')'], ['[', ']'], ['{', '}'], ['INDENT', 'OUTDENT'], ['CALL_START', 'CALL_END'], ['PARAM_START', 'PARAM_END'], ['INDEX_START', 'INDEX_END']];
-
-  exports.INVERSES = INVERSES = {};
-
-  EXPRESSION_START = [];
-
-  EXPRESSION_END = [];
-
-  for (_i = 0, _len = BALANCED_PAIRS.length; _i < _len; _i++) {
-    _ref = BALANCED_PAIRS[_i], left = _ref[0], rite = _ref[1];
-    EXPRESSION_START.push(INVERSES[rite] = left);
-    EXPRESSION_END.push(INVERSES[left] = rite);
-  }
-
-  EXPRESSION_CLOSE = ['CATCH', 'WHEN', 'ELSE', 'FINALLY'].concat(EXPRESSION_END);
-
-  IMPLICIT_FUNC = ['IDENTIFIER', 'SUPER', ')', 'CALL_END', ']', 'INDEX_END', '@', 'THIS'];
-
-  IMPLICIT_CALL = ['IDENTIFIER', 'NUMBER', 'STRING', 'JS', 'REGEX', 'NEW', 'PARAM_START', 'CLASS', 'IF', 'TRY', 'SWITCH', 'THIS', 'BOOL', 'NULL', 'UNDEFINED', 'UNARY', 'SUPER', '@', '->', '=>', '[', '(', '{', '--', '++'];
-
-  IMPLICIT_UNSPACED_CALL = ['+', '-'];
-
-  IMPLICIT_BLOCK = ['->', '=>', '{', '[', ','];
-
-  IMPLICIT_END = ['POST_IF', 'FOR', 'WHILE', 'UNTIL', 'WHEN', 'BY', 'LOOP', 'TERMINATOR'];
-
-  SINGLE_LINERS = ['ELSE', '->', '=>', 'TRY', 'FINALLY', 'THEN'];
-
-  SINGLE_CLOSERS = ['TERMINATOR', 'CATCH', 'FINALLY', 'ELSE', 'OUTDENT', 'LEADING_WHEN'];
-
-  LINEBREAKS = ['TERMINATOR', 'INDENT', 'OUTDENT'];
-
-}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/scope.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/scope.js
deleted file mode 100755
index 41281734..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/scope.js
+++ /dev/null
@@ -1,147 +0,0 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var Scope, extend, last, _ref;
-
-  _ref = require('./helpers'), extend = _ref.extend, last = _ref.last;
-
-  exports.Scope = Scope = (function() {
-
-    Scope.root = null;
-
-    function Scope(parent, expressions, method) {
-      this.parent = parent;
-      this.expressions = expressions;
-      this.method = method;
-      this.variables = [
-        {
-          name: 'arguments',
-          type: 'arguments'
-        }
-      ];
-      this.positions = {};
-      if (!this.parent) {
-        Scope.root = this;
-      }
-    }
-
-    Scope.prototype.add = function(name, type, immediate) {
-      if (this.shared && !immediate) {
-        return this.parent.add(name, type, immediate);
-      }
-      if (Object.prototype.hasOwnProperty.call(this.positions, name)) {
-        return this.variables[this.positions[name]].type = type;
-      } else {
-        return this.positions[name] = this.variables.push({
-          name: name,
-          type: type
-        }) - 1;
-      }
-    };
-
-    Scope.prototype.namedMethod = function() {
-      var _ref1;
-      if (((_ref1 = this.method) != null ? _ref1.name : void 0) || !this.parent) {
-        return this.method;
-      }
-      return this.parent.namedMethod();
-    };
-
-    Scope.prototype.find = function(name) {
-      if (this.check(name)) {
-        return true;
-      }
-      this.add(name, 'var');
-      return false;
-    };
-
-    Scope.prototype.parameter = function(name) {
-      if (this.shared && this.parent.check(name, true)) {
-        return;
-      }
-      return this.add(name, 'param');
-    };
-
-    Scope.prototype.check = function(name) {
-      var _ref1;
-      return !!(this.type(name) || ((_ref1 = this.parent) != null ? _ref1.check(name) : void 0));
-    };
-
-    Scope.prototype.temporary = function(name, index) {
-      if (name.length > 1) {
-        return '_' + name + (index > 1 ? index - 1 : '');
-      } else {
-        return '_' + (index + parseInt(name, 36)).toString(36).replace(/\d/g, 'a');
-      }
-    };
-
-    Scope.prototype.type = function(name) {
-      var v, _i, _len, _ref1;
-      _ref1 = this.variables;
-      for (_i = 0, _len = _ref1.length; _i < _len; _i++) {
-        v = _ref1[_i];
-        if (v.name === name) {
-          return v.type;
-        }
-      }
-      return null;
-    };
-
-    Scope.prototype.freeVariable = function(name, reserve) {
-      var index, temp;
-      if (reserve == null) {
-        reserve = true;
-      }
-      index = 0;
-      while (this.check((temp = this.temporary(name, index)))) {
-        index++;
-      }
-      if (reserve) {
-        this.add(temp, 'var', true);
-      }
-      return temp;
-    };
-
-    Scope.prototype.assign = function(name, value) {
-      this.add(name, {
-        value: value,
-        assigned: true
-      }, true);
-      return this.hasAssignments = true;
-    };
-
-    Scope.prototype.hasDeclarations = function() {
-      return !!this.declaredVariables().length;
-    };
-
-    Scope.prototype.declaredVariables = function() {
-      var realVars, tempVars, v, _i, _len, _ref1;
-      realVars = [];
-      tempVars = [];
-      _ref1 = this.variables;
-      for (_i = 0, _len = _ref1.length; _i < _len; _i++) {
-        v = _ref1[_i];
-        if (v.type === 'var') {
-          (v.name.charAt(0) === '_' ? tempVars : realVars).push(v.name);
-        }
-      }
-      return realVars.sort().concat(tempVars.sort());
-    };
-
-    Scope.prototype.assignedVariables = function() {
-      var v, _i, _len, _ref1, _results;
-      _ref1 = this.variables;
-      _results = [];
-      for (_i = 0, _len = _ref1.length; _i < _len; _i++) {
-        v = _ref1[_i];
-        if (v.type.assigned) {
-          _results.push("" + v.name + " = " + v.type.value);
-        }
-      }
-      return _results;
-    };
-
-    return Scope;
-
-  })();
-
-}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/sourcemap.js b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/sourcemap.js
deleted file mode 100755
index 245da945..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/lib/coffee-script/sourcemap.js
+++ /dev/null
@@ -1,237 +0,0 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var BASE64_CHARS, LineMapping, MAX_BASE64_VALUE, VLQ_CONTINUATION_BIT, VLQ_SHIFT, VLQ_VALUE_MASK, decodeBase64Char, encodeBase64Char;
-
-  LineMapping = (function() {
-
-    function LineMapping(generatedLine) {
-      this.generatedLine = generatedLine;
-      this.columnMap = {};
-      this.columnMappings = [];
-    }
-
-    LineMapping.prototype.addMapping = function(generatedColumn, _arg, options) {
-      var sourceColumn, sourceLine;
-      sourceLine = _arg[0], sourceColumn = _arg[1];
-      if (options == null) {
-        options = {};
-      }
-      if (this.columnMap[generatedColumn] && options.noReplace) {
-        return;
-      }
-      this.columnMap[generatedColumn] = {
-        generatedLine: this.generatedLine,
-        generatedColumn: generatedColumn,
-        sourceLine: sourceLine,
-        sourceColumn: sourceColumn
-      };
-      this.columnMappings.push(this.columnMap[generatedColumn]);
-      return this.columnMappings.sort(function(a, b) {
-        return a.generatedColumn - b.generatedColumn;
-      });
-    };
-
-    LineMapping.prototype.getSourcePosition = function(generatedColumn) {
-      var answer, columnMapping, lastColumnMapping, _i, _len, _ref;
-      answer = null;
-      lastColumnMapping = null;
-      _ref = this.columnMappings;
-      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-        columnMapping = _ref[_i];
-        if (columnMapping.generatedColumn > generatedColumn) {
-          break;
-        } else {
-          lastColumnMapping = columnMapping;
-        }
-      }
-      if (lastColumnMapping) {
-        return answer = [lastColumnMapping.sourceLine, lastColumnMapping.sourceColumn];
-      }
-    };
-
-    return LineMapping;
-
-  })();
-
-  exports.SourceMap = (function() {
-
-    function SourceMap() {
-      this.generatedLines = [];
-    }
-
-    SourceMap.prototype.addMapping = function(sourceLocation, generatedLocation, options) {
-      var generatedColumn, generatedLine, lineMapping;
-      if (options == null) {
-        options = {};
-      }
-      generatedLine = generatedLocation[0], generatedColumn = generatedLocation[1];
-      lineMapping = this.generatedLines[generatedLine];
-      if (!lineMapping) {
-        lineMapping = this.generatedLines[generatedLine] = new LineMapping(generatedLine);
-      }
-      return lineMapping.addMapping(generatedColumn, sourceLocation, options);
-    };
-
-    SourceMap.prototype.getSourcePosition = function(_arg) {
-      var answer, generatedColumn, generatedLine, lineMapping;
-      generatedLine = _arg[0], generatedColumn = _arg[1];
-      answer = null;
-      lineMapping = this.generatedLines[generatedLine];
-      if (!lineMapping) {
-
-      } else {
-        answer = lineMapping.getSourcePosition(generatedColumn);
-      }
-      return answer;
-    };
-
-    SourceMap.prototype.forEachMapping = function(fn) {
-      var columnMapping, generatedLineNumber, lineMapping, _i, _len, _ref, _results;
-      _ref = this.generatedLines;
-      _results = [];
-      for (generatedLineNumber = _i = 0, _len = _ref.length; _i < _len; generatedLineNumber = ++_i) {
-        lineMapping = _ref[generatedLineNumber];
-        if (lineMapping) {
-          _results.push((function() {
-            var _j, _len1, _ref1, _results1;
-            _ref1 = lineMapping.columnMappings;
-            _results1 = [];
-            for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) {
-              columnMapping = _ref1[_j];
-              _results1.push(fn(columnMapping));
-            }
-            return _results1;
-          })());
-        } else {
-          _results.push(void 0);
-        }
-      }
-      return _results;
-    };
-
-    return SourceMap;
-
-  })();
-
-  exports.generateV3SourceMap = function(sourceMap, sourceFile, generatedFile) {
-    var answer, lastGeneratedColumnWritten, lastSourceColumnWritten, lastSourceLineWritten, mappings, needComma, writingGeneratedLine;
-    if (sourceFile == null) {
-      sourceFile = null;
-    }
-    if (generatedFile == null) {
-      generatedFile = null;
-    }
-    writingGeneratedLine = 0;
-    lastGeneratedColumnWritten = 0;
-    lastSourceLineWritten = 0;
-    lastSourceColumnWritten = 0;
-    needComma = false;
-    mappings = "";
-    sourceMap.forEachMapping(function(mapping) {
-      while (writingGeneratedLine < mapping.generatedLine) {
-        lastGeneratedColumnWritten = 0;
-        needComma = false;
-        mappings += ";";
-        writingGeneratedLine++;
-      }
-      if (needComma) {
-        mappings += ",";
-        needComma = false;
-      }
-      mappings += exports.vlqEncodeValue(mapping.generatedColumn - lastGeneratedColumnWritten);
-      lastGeneratedColumnWritten = mapping.generatedColumn;
-      mappings += exports.vlqEncodeValue(0);
-      mappings += exports.vlqEncodeValue(mapping.sourceLine - lastSourceLineWritten);
-      lastSourceLineWritten = mapping.sourceLine;
-      mappings += exports.vlqEncodeValue(mapping.sourceColumn - lastSourceColumnWritten);
-      lastSourceColumnWritten = mapping.sourceColumn;
-      return needComma = true;
-    });
-    answer = {
-      version: 3,
-      file: generatedFile,
-      sourceRoot: "",
-      sources: sourceFile ? [sourceFile] : [],
-      names: [],
-      mappings: mappings
-    };
-    return JSON.stringify(answer, null, 2);
-  };
-
-  exports.loadV3SourceMap = function(sourceMap) {
-    return todo();
-  };
-
-  BASE64_CHARS = 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/';
-
-  MAX_BASE64_VALUE = BASE64_CHARS.length - 1;
-
-  encodeBase64Char = function(value) {
-    if (value > MAX_BASE64_VALUE) {
-      throw new Error("Cannot encode value " + value + " > " + MAX_BASE64_VALUE);
-    } else if (value < 0) {
-      throw new Error("Cannot encode value " + value + " < 0");
-    }
-    return BASE64_CHARS[value];
-  };
-
-  decodeBase64Char = function(char) {
-    var value;
-    value = BASE64_CHARS.indexOf(char);
-    if (value === -1) {
-      throw new Error("Invalid Base 64 character: " + char);
-    }
-    return value;
-  };
-
-  VLQ_SHIFT = 5;
-
-  VLQ_CONTINUATION_BIT = 1 << VLQ_SHIFT;
-
-  VLQ_VALUE_MASK = VLQ_CONTINUATION_BIT - 1;
-
-  exports.vlqEncodeValue = function(value) {
-    var answer, nextVlqChunk, signBit, valueToEncode;
-    signBit = value < 0 ? 1 : 0;
-    valueToEncode = (Math.abs(value) << 1) + signBit;
-    answer = "";
-    while (valueToEncode || !answer) {
-      nextVlqChunk = valueToEncode & VLQ_VALUE_MASK;
-      valueToEncode = valueToEncode >> VLQ_SHIFT;
-      if (valueToEncode) {
-        nextVlqChunk |= VLQ_CONTINUATION_BIT;
-      }
-      answer += encodeBase64Char(nextVlqChunk);
-    }
-    return answer;
-  };
-
-  exports.vlqDecodeValue = function(str, offset) {
-    var consumed, continuationShift, done, nextChunkValue, nextVlqChunk, position, signBit, value;
-    if (offset == null) {
-      offset = 0;
-    }
-    position = offset;
-    done = false;
-    value = 0;
-    continuationShift = 0;
-    while (!done) {
-      nextVlqChunk = decodeBase64Char(str[position]);
-      position += 1;
-      nextChunkValue = nextVlqChunk & VLQ_VALUE_MASK;
-      value += nextChunkValue << continuationShift;
-      if (!(nextVlqChunk & VLQ_CONTINUATION_BIT)) {
-        done = true;
-      }
-      continuationShift += VLQ_SHIFT;
-    }
-    consumed = position - offset;
-    signBit = value & 1;
-    value = value >> 1;
-    if (signBit) {
-      value = -value;
-    }
-    return [value, consumed];
-  };
-
-}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/package.json b/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/package.json
deleted file mode 100755
index e1aea0c9..00000000
--- a/wqflask/wqflask/static/new/javascript/node_modules/coffee-script/package.json
+++ /dev/null
@@ -1,57 +0,0 @@
-{
-  "name": "coffee-script",
-  "description": "Unfancy JavaScript",
-  "keywords": [
-    "javascript",
-    "language",
-    "coffeescript",
-    "compiler"
-  ],
-  "author": {
-    "name": "Jeremy Ashkenas"
-  },
-  "version": "1.6.1",
-  "licenses": [
-    {
-      "type": "MIT",
-      "url": "https://raw.github.com/jashkenas/coffee-script/master/LICENSE"
-    }
-  ],
-  "engines": {
-    "node": ">=0.4.0"
-  },
-  "directories": {
-    "lib": "./lib/coffee-script"
-  },
-  "main": "./lib/coffee-script/coffee-script",
-  "bin": {
-    "coffee": "./bin/coffee",
-    "cake": "./bin/cake"
-  },
-  "scripts": {
-    "test": "node ./bin/cake test"
-  },
-  "homepage": "http://coffeescript.org",
-  "bugs": {
-    "name": "https://github.com/jashkenas/coffee-script/issues"
-  },
-  "repository": {
-    "type": "git",
-    "url": "git://github.com/jashkenas/coffee-script.git"
-  },
-  "devDependencies": {
-    "uglify-js": "~2.2",
-    "jison": ">=0.2.0"
-  },
-  "_id": "coffee-script@1.6.1",
-  "dependencies": {},
-  "optionalDependencies": {},
-  "_engineSupported": true,
-  "_npmVersion": "1.1.4",
-  "_nodeVersion": "v0.6.12",
-  "_defaultsLoaded": true,
-  "dist": {
-    "shasum": "05d88f953bcd2e72d53bff583c9318a9572a386d"
-  },
-  "_from": "coffee-script"
-}
diff --git a/wqflask/wqflask/static/new/javascript/password_strength.js b/wqflask/wqflask/static/new/javascript/password_strength.js
index 166e1125..a6d90861 100755
--- a/wqflask/wqflask/static/new/javascript/password_strength.js
+++ b/wqflask/wqflask/static/new/javascript/password_strength.js
@@ -1,42 +1,38 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-
-  $(function() {
-    var word_score;
-    $("#password").keyup(function() {
-      var crack_time, display, passtext, result, word;
-      passtext = $(this).val();
-      result = zxcvbn(passtext);
-      if (passtext.length < 6) {
-        $("#password_strength").html('');
-        return $("#password_alert").fadeOut();
-      } else {
-        word = word_score(result.score);
-        crack_time = result.crack_time_display;
-        if (crack_time === "instant") {
-          crack_time = "a second";
-        }
-        display = "This is " + word + " password. It can be cracked in " + crack_time + ".";
-        $("#password_strength").html(display);
-        return $("#password_alert").fadeIn();
+// Generated by CoffeeScript 1.7.1
+$(function() {
+  var word_score;
+  $("#password").keyup(function() {
+    var crack_time, display, passtext, result, word;
+    passtext = $(this).val();
+    result = zxcvbn(passtext);
+    if (passtext.length < 6) {
+      $("#password_strength").html('');
+      return $("#password_alert").fadeOut();
+    } else {
+      word = word_score(result.score);
+      crack_time = result.crack_time_display;
+      if (crack_time === "instant") {
+        crack_time = "a second";
       }
-    });
-    return word_score = function(num_score) {
-      var mapping, result;
-      num_score = parseInt(num_score);
-      console.log("num_score is:", num_score);
-      mapping = {
-        0: "a <strong>terrible</strong>",
-        1: "a <strong>bad</strong>",
-        2: "a <strong>mediocre</strong>",
-        3: "a <strong>good</strong>",
-        4: "an <strong>excellent</strong>"
-      };
-      console.log("mapping is:", mapping);
-      result = mapping[num_score];
-      console.log("result is:", result);
-      return result;
-    };
+      display = "This is " + word + " password. It can be cracked in " + crack_time + ".";
+      $("#password_strength").html(display);
+      return $("#password_alert").fadeIn();
+    }
   });
-
-}).call(this);
+  return word_score = function(num_score) {
+    var mapping, result;
+    num_score = parseInt(num_score);
+    console.log("num_score is:", num_score);
+    mapping = {
+      0: "a <strong>terrible</strong>",
+      1: "a <strong>bad</strong>",
+      2: "a <strong>mediocre</strong>",
+      3: "a <strong>good</strong>",
+      4: "an <strong>excellent</strong>"
+    };
+    console.log("mapping is:", mapping);
+    result = mapping[num_score];
+    console.log("result is:", result);
+    return result;
+  };
+});
diff --git a/wqflask/wqflask/static/new/javascript/scatterplot.js b/wqflask/wqflask/static/new/javascript/scatterplot.js
index ac32301b..96607cbb 100644
--- a/wqflask/wqflask/static/new/javascript/scatterplot.js
+++ b/wqflask/wqflask/static/new/javascript/scatterplot.js
@@ -1,413 +1,410 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var root, scatterplot;
+// Generated by CoffeeScript 1.7.1
+var root, scatterplot;
 
-  root = typeof exports !== "undefined" && exports !== null ? exports : this;
+root = typeof exports !== "undefined" && exports !== null ? exports : this;
 
-  scatterplot = function() {
-    var axispos, chart, dataByInd, height, margin, nxticks, nyticks, pointcolor, pointsSelect, pointsize, pointstroke, rectcolor, rotate_ylab, title, titlepos, width, xNA, xlab, xlim, xscale, xticks, xvar, yNA, ylab, ylim, yscale, yticks, yvar;
-    width = 800;
-    height = 600;
-    margin = {
-      left: 60,
-      top: 40,
-      right: 40,
-      bottom: 40,
-      inner: 5
-    };
-    axispos = {
-      xtitle: 25,
-      ytitle: 45,
-      xlabel: 5,
-      ylabel: 5
-    };
-    titlepos = 20;
-    xNA = {
-      handle: true,
-      force: false,
-      width: 15,
-      gap: 10
-    };
-    yNA = {
-      handle: true,
-      force: false,
-      width: 15,
-      gap: 10
-    };
-    xlim = null;
-    ylim = null;
-    nxticks = 5;
-    xticks = null;
-    nyticks = 5;
-    yticks = null;
-    rectcolor = d3.rgb(230, 230, 230);
-    pointcolor = null;
-    pointstroke = "black";
-    pointsize = 3;
-    title = "Correlation Scatterplot";
-    xlab = "X";
-    ylab = "Y";
-    rotate_ylab = null;
-    yscale = d3.scale.linear();
-    xscale = d3.scale.linear();
-    xvar = 0;
-    yvar = 1;
-    pointsSelect = null;
-    dataByInd = false;
-    chart = function(selection) {
-      return selection.each(function(data) {
-        var g, gEnter, group, i, indID, indtip, na_value, ngroup, panelheight, paneloffset, panelwidth, points, svg, titlegrp, x, xaxis, xrange, xs, y, yaxis, yrange, ys, _i, _ref, _ref1, _ref2, _results;
-        if (dataByInd) {
-          x = data.data.map(function(d) {
-            return d[xvar];
-          });
-          y = data.data.map(function(d) {
-            return d[yvar];
-          });
-        } else {
-          x = data.data[xvar];
-          y = data.data[yvar];
-        }
-        console.log("x:", x);
-        console.log("y:", y);
-        indID = (_ref = data != null ? data.indID : void 0) != null ? _ref : null;
-        indID = indID != null ? indID : (function() {
-          _results = [];
-          for (var _i = 1, _ref1 = x.length; 1 <= _ref1 ? _i <= _ref1 : _i >= _ref1; 1 <= _ref1 ? _i++ : _i--){ _results.push(_i); }
-          return _results;
-        }).apply(this);
-        console.log("indID:", indID);
-        group = (_ref2 = data != null ? data.group : void 0) != null ? _ref2 : (function() {
-          var _j, _len, _results1;
-          _results1 = [];
-          for (_j = 0, _len = x.length; _j < _len; _j++) {
-            i = x[_j];
-            _results1.push(1);
-          }
-          return _results1;
-        })();
-        ngroup = d3.max(group);
-        group = (function() {
-          var _j, _len, _results1;
-          _results1 = [];
-          for (_j = 0, _len = group.length; _j < _len; _j++) {
-            g = group[_j];
-            _results1.push(g - 1);
-          }
-          return _results1;
-        })();
-        pointcolor = pointcolor != null ? pointcolor : selectGroupColors(ngroup, "dark");
-        pointcolor = expand2vector(pointcolor, ngroup);
-        if (x.every(function(v) {
-          return (v != null) && !xNA.force;
-        })) {
-          xNA.handle = false;
-        }
-        if (y.every(function(v) {
-          return (v != null) && !yNA.force;
-        })) {
-          yNA.handle = false;
-        }
-        if (xNA.handle) {
-          paneloffset = xNA.width + xNA.gap;
-          panelwidth = width - paneloffset;
-        } else {
-          paneloffset = 0;
-          panelwidth = width;
-        }
-        if (yNA.handle) {
-          panelheight = height - (yNA.width + yNA.gap);
-        } else {
-          panelheight = height;
-        }
-        xlim = xlim != null ? xlim : d3.extent(x);
-        ylim = ylim != null ? ylim : d3.extent(y);
-        na_value = d3.min(x.concat(y)) - 100;
-        svg = d3.select(this).selectAll("svg").data([data]);
-        gEnter = svg.enter().append("svg").append("g");
-        svg.attr("width", width + margin.left + margin.right).attr("height", height + margin.top + margin.bottom);
-        g = svg.select("g");
-        g.append("rect").attr("x", paneloffset + margin.left).attr("y", margin.top).attr("height", panelheight).attr("width", panelwidth).attr("fill", rectcolor).attr("stroke", "none");
-        if (xNA.handle) {
-          g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", panelheight).attr("width", xNA.width).attr("fill", rectcolor).attr("stroke", "none");
-        }
-        if (xNA.handle && yNA.handle) {
-          g.append("rect").attr("x", margin.left).attr("y", margin.top + height - yNA.width).attr("height", yNA.width).attr("width", xNA.width).attr("fill", rectcolor).attr("stroke", "none");
-        }
-        if (yNA.handle) {
-          g.append("rect").attr("x", margin.left + paneloffset).attr("y", margin.top + height - yNA.width).attr("height", yNA.width).attr("width", panelwidth).attr("fill", rectcolor).attr("stroke", "none");
-        }
-        xrange = [margin.left + paneloffset + margin.inner, margin.left + paneloffset + panelwidth - margin.inner];
-        yrange = [margin.top + panelheight - margin.inner, margin.top + margin.inner];
-        xscale.domain(xlim).range(xrange);
-        yscale.domain(ylim).range(yrange);
-        xs = d3.scale.linear().domain(xlim).range(xrange);
-        ys = d3.scale.linear().domain(ylim).range(yrange);
-        if (xNA.handle) {
-          xscale.domain([na_value].concat(xlim)).range([margin.left + xNA.width / 2].concat(xrange));
-          x = x.map(function(e) {
-            if (e != null) {
-              return e;
-            } else {
-              return na_value;
-            }
-          });
-        }
-        if (yNA.handle) {
-          yscale.domain([na_value].concat(ylim)).range([height + margin.top - yNA.width / 2].concat(yrange));
-          y = y.map(function(e) {
-            if (e != null) {
-              return e;
-            } else {
-              return na_value;
-            }
-          });
-        }
-        yticks = yticks != null ? yticks : ys.ticks(nyticks);
-        xticks = xticks != null ? xticks : xs.ticks(nxticks);
-        titlegrp = g.append("g").attr("class", "title").append("text").attr("x", margin.left + width / 2).attr("y", margin.top - titlepos).text(title);
-        xaxis = g.append("g").attr("class", "x axis");
-        xaxis.selectAll("empty").data(xticks).enter().append("line").attr("x1", function(d) {
-          return xscale(d);
-        }).attr("x2", function(d) {
-          return xscale(d);
-        }).attr("y1", margin.top).attr("y2", margin.top + height).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none");
-        xaxis.selectAll("empty").data(xticks).enter().append("text").attr("x", function(d) {
-          return xscale(d);
-        }).attr("y", margin.top + height + axispos.xlabel).text(function(d) {
-          return formatAxis(xticks)(d);
+scatterplot = function() {
+  var axispos, chart, dataByInd, height, margin, nxticks, nyticks, pointcolor, pointsSelect, pointsize, pointstroke, rectcolor, rotate_ylab, title, titlepos, width, xNA, xlab, xlim, xscale, xticks, xvar, yNA, ylab, ylim, yscale, yticks, yvar;
+  width = 800;
+  height = 600;
+  margin = {
+    left: 60,
+    top: 40,
+    right: 40,
+    bottom: 40,
+    inner: 5
+  };
+  axispos = {
+    xtitle: 25,
+    ytitle: 45,
+    xlabel: 5,
+    ylabel: 5
+  };
+  titlepos = 20;
+  xNA = {
+    handle: true,
+    force: false,
+    width: 15,
+    gap: 10
+  };
+  yNA = {
+    handle: true,
+    force: false,
+    width: 15,
+    gap: 10
+  };
+  xlim = null;
+  ylim = null;
+  nxticks = 5;
+  xticks = null;
+  nyticks = 5;
+  yticks = null;
+  rectcolor = d3.rgb(230, 230, 230);
+  pointcolor = null;
+  pointstroke = "black";
+  pointsize = 3;
+  title = "Correlation Scatterplot";
+  xlab = "X";
+  ylab = "Y";
+  rotate_ylab = null;
+  yscale = d3.scale.linear();
+  xscale = d3.scale.linear();
+  xvar = 0;
+  yvar = 1;
+  pointsSelect = null;
+  dataByInd = false;
+  chart = function(selection) {
+    return selection.each(function(data) {
+      var g, gEnter, group, i, indID, indtip, na_value, ngroup, panelheight, paneloffset, panelwidth, points, svg, titlegrp, x, xaxis, xrange, xs, y, yaxis, yrange, ys, _i, _ref, _ref1, _ref2, _results;
+      if (dataByInd) {
+        x = data.data.map(function(d) {
+          return d[xvar];
         });
-        xaxis.append("text").attr("class", "title").attr("x", margin.left + width / 2).attr("y", margin.top + height + axispos.xtitle).text(xlab);
-        if (xNA.handle) {
-          xaxis.append("text").attr("x", margin.left + xNA.width / 2).attr("y", margin.top + height + axispos.xlabel).text("N/A");
-        }
-        rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1;
-        yaxis = g.append("g").attr("class", "y axis");
-        yaxis.selectAll("empty").data(yticks).enter().append("line").attr("y1", function(d) {
-          return yscale(d);
-        }).attr("y2", function(d) {
-          return yscale(d);
-        }).attr("x1", margin.left).attr("x2", margin.left + width).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none");
-        yaxis.selectAll("empty").data(yticks).enter().append("text").attr("y", function(d) {
-          return yscale(d);
-        }).attr("x", margin.left - axispos.ylabel).text(function(d) {
-          return formatAxis(yticks)(d);
+        y = data.data.map(function(d) {
+          return d[yvar];
         });
-        yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : "");
-        if (yNA.handle) {
-          yaxis.append("text").attr("x", margin.left - axispos.ylabel).attr("y", margin.top + height - yNA.width / 2).text("N/A");
-        }
-        indtip = d3.tip().attr('class', 'd3-tip').html(function(d, i) {
-          return indID[i];
-        }).direction('e').offset([0, 10]);
-        svg.call(indtip);
-        points = g.append("g").attr("id", "points");
-        pointsSelect = points.selectAll("empty").data(d3.range(x.length)).enter().append("circle").attr("cx", function(d, i) {
-          return xscale(x[i]);
-        }).attr("cy", function(d, i) {
-          return yscale(y[i]);
-        }).attr("class", function(d, i) {
-          return "pt" + i;
-        }).attr("r", pointsize).attr("fill", function(d, i) {
-          return pointcolor[group[i]];
-        }).attr("stroke", pointstroke).attr("stroke-width", "1").attr("opacity", function(d, i) {
-          if (((x[i] != null) || xNA.handle) && ((y[i] != null) || yNA.handle)) {
-            return 1;
-          }
-          return 0;
-        }).on("mouseover.paneltip", indtip.show).on("mouseout.paneltip", indtip.hide);
-        g.append("rect").attr("x", margin.left + paneloffset).attr("y", margin.top).attr("height", panelheight).attr("width", panelwidth).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none");
-        if (xNA.handle) {
-          g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", panelheight).attr("width", xNA.width).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none");
-        }
-        if (xNA.handle && yNA.handle) {
-          g.append("rect").attr("x", margin.left).attr("y", margin.top + height - yNA.width).attr("height", yNA.width).attr("width", xNA.width).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none");
+      } else {
+        x = data.data[xvar];
+        y = data.data[yvar];
+      }
+      console.log("x:", x);
+      console.log("y:", y);
+      indID = (_ref = data != null ? data.indID : void 0) != null ? _ref : null;
+      indID = indID != null ? indID : (function() {
+        _results = [];
+        for (var _i = 1, _ref1 = x.length; 1 <= _ref1 ? _i <= _ref1 : _i >= _ref1; 1 <= _ref1 ? _i++ : _i--){ _results.push(_i); }
+        return _results;
+      }).apply(this);
+      console.log("indID:", indID);
+      group = (_ref2 = data != null ? data.group : void 0) != null ? _ref2 : (function() {
+        var _j, _len, _results1;
+        _results1 = [];
+        for (_j = 0, _len = x.length; _j < _len; _j++) {
+          i = x[_j];
+          _results1.push(1);
         }
-        if (yNA.handle) {
-          return g.append("rect").attr("x", margin.left + paneloffset).attr("y", margin.top + height - yNA.width).attr("height", yNA.width).attr("width", panelwidth).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none");
+        return _results1;
+      })();
+      ngroup = d3.max(group);
+      group = (function() {
+        var _j, _len, _results1;
+        _results1 = [];
+        for (_j = 0, _len = group.length; _j < _len; _j++) {
+          g = group[_j];
+          _results1.push(g - 1);
         }
-      });
-    };
-    chart.width = function(value) {
-      if (!arguments.length) {
-        return width;
-      }
-      width = value;
-      return chart;
-    };
-    chart.height = function(value) {
-      if (!arguments.length) {
-        return height;
+        return _results1;
+      })();
+      pointcolor = pointcolor != null ? pointcolor : selectGroupColors(ngroup, "dark");
+      pointcolor = expand2vector(pointcolor, ngroup);
+      if (x.every(function(v) {
+        return (v != null) && !xNA.force;
+      })) {
+        xNA.handle = false;
       }
-      height = value;
-      return chart;
-    };
-    chart.margin = function(value) {
-      if (!arguments.length) {
-        return margin;
+      if (y.every(function(v) {
+        return (v != null) && !yNA.force;
+      })) {
+        yNA.handle = false;
       }
-      margin = value;
-      return chart;
-    };
-    chart.axispos = function(value) {
-      if (!arguments.length) {
-        return axispos;
+      if (xNA.handle) {
+        paneloffset = xNA.width + xNA.gap;
+        panelwidth = width - paneloffset;
+      } else {
+        paneloffset = 0;
+        panelwidth = width;
       }
-      axispos = value;
-      return chart;
-    };
-    chart.titlepos = function(value) {
-      if (!arguments.length) {
-        return titlepos;
+      if (yNA.handle) {
+        panelheight = height - (yNA.width + yNA.gap);
+      } else {
+        panelheight = height;
       }
-      titlepos;
-      return chart;
-    };
-    chart.xlim = function(value) {
-      if (!arguments.length) {
-        return xlim;
+      xlim = xlim != null ? xlim : d3.extent(x);
+      ylim = ylim != null ? ylim : d3.extent(y);
+      na_value = d3.min(x.concat(y)) - 100;
+      svg = d3.select(this).selectAll("svg").data([data]);
+      gEnter = svg.enter().append("svg").append("g");
+      svg.attr("width", width + margin.left + margin.right).attr("height", height + margin.top + margin.bottom);
+      g = svg.select("g");
+      g.append("rect").attr("x", paneloffset + margin.left).attr("y", margin.top).attr("height", panelheight).attr("width", panelwidth).attr("fill", rectcolor).attr("stroke", "none");
+      if (xNA.handle) {
+        g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", panelheight).attr("width", xNA.width).attr("fill", rectcolor).attr("stroke", "none");
       }
-      xlim = value;
-      return chart;
-    };
-    chart.nxticks = function(value) {
-      if (!arguments.length) {
-        return nxticks;
+      if (xNA.handle && yNA.handle) {
+        g.append("rect").attr("x", margin.left).attr("y", margin.top + height - yNA.width).attr("height", yNA.width).attr("width", xNA.width).attr("fill", rectcolor).attr("stroke", "none");
       }
-      nxticks = value;
-      return chart;
-    };
-    chart.xticks = function(value) {
-      if (!arguments.length) {
-        return xticks;
+      if (yNA.handle) {
+        g.append("rect").attr("x", margin.left + paneloffset).attr("y", margin.top + height - yNA.width).attr("height", yNA.width).attr("width", panelwidth).attr("fill", rectcolor).attr("stroke", "none");
       }
-      xticks = value;
-      return chart;
-    };
-    chart.ylim = function(value) {
-      if (!arguments.length) {
-        return ylim;
-      }
-      ylim = value;
-      return chart;
-    };
-    chart.nyticks = function(value) {
-      if (!arguments.length) {
-        return nyticks;
-      }
-      nyticks = value;
-      return chart;
-    };
-    chart.yticks = function(value) {
-      if (!arguments.length) {
-        return yticks;
-      }
-      yticks = value;
-      return chart;
-    };
-    chart.rectcolor = function(value) {
-      if (!arguments.length) {
-        return rectcolor;
-      }
-      rectcolor = value;
-      return chart;
-    };
-    chart.pointcolor = function(value) {
-      if (!arguments.length) {
-        return pointcolor;
-      }
-      pointcolor = value;
-      return chart;
-    };
-    chart.pointsize = function(value) {
-      if (!arguments.length) {
-        return pointsize;
-      }
-      pointsize = value;
-      return chart;
-    };
-    chart.pointstroke = function(value) {
-      if (!arguments.length) {
-        return pointstroke;
-      }
-      pointstroke = value;
-      return chart;
-    };
-    chart.dataByInd = function(value) {
-      if (!arguments.length) {
-        return dataByInd;
-      }
-      dataByInd = value;
-      return chart;
-    };
-    chart.title = function(value) {
-      if (!arguments.length) {
-        return title;
-      }
-      title = value;
-      return chart;
-    };
-    chart.xlab = function(value) {
-      if (!arguments.length) {
-        return xlab;
+      xrange = [margin.left + paneloffset + margin.inner, margin.left + paneloffset + panelwidth - margin.inner];
+      yrange = [margin.top + panelheight - margin.inner, margin.top + margin.inner];
+      xscale.domain(xlim).range(xrange);
+      yscale.domain(ylim).range(yrange);
+      xs = d3.scale.linear().domain(xlim).range(xrange);
+      ys = d3.scale.linear().domain(ylim).range(yrange);
+      if (xNA.handle) {
+        xscale.domain([na_value].concat(xlim)).range([margin.left + xNA.width / 2].concat(xrange));
+        x = x.map(function(e) {
+          if (e != null) {
+            return e;
+          } else {
+            return na_value;
+          }
+        });
       }
-      xlab = value;
-      return chart;
-    };
-    chart.ylab = function(value) {
-      if (!arguments.length) {
-        return ylab;
+      if (yNA.handle) {
+        yscale.domain([na_value].concat(ylim)).range([height + margin.top - yNA.width / 2].concat(yrange));
+        y = y.map(function(e) {
+          if (e != null) {
+            return e;
+          } else {
+            return na_value;
+          }
+        });
       }
-      ylab = value;
-      return chart;
-    };
-    chart.rotate_ylab = function(value) {
-      if (!arguments.length) {
-        return rotate_ylab;
+      yticks = yticks != null ? yticks : ys.ticks(nyticks);
+      xticks = xticks != null ? xticks : xs.ticks(nxticks);
+      titlegrp = g.append("g").attr("class", "title").append("text").attr("x", margin.left + width / 2).attr("y", margin.top - titlepos).text(title);
+      xaxis = g.append("g").attr("class", "x axis");
+      xaxis.selectAll("empty").data(xticks).enter().append("line").attr("x1", function(d) {
+        return xscale(d);
+      }).attr("x2", function(d) {
+        return xscale(d);
+      }).attr("y1", margin.top).attr("y2", margin.top + height).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none");
+      xaxis.selectAll("empty").data(xticks).enter().append("text").attr("x", function(d) {
+        return xscale(d);
+      }).attr("y", margin.top + height + axispos.xlabel).text(function(d) {
+        return formatAxis(xticks)(d);
+      });
+      xaxis.append("text").attr("class", "title").attr("x", margin.left + width / 2).attr("y", margin.top + height + axispos.xtitle).text(xlab);
+      if (xNA.handle) {
+        xaxis.append("text").attr("x", margin.left + xNA.width / 2).attr("y", margin.top + height + axispos.xlabel).text("N/A");
       }
-      rotate_ylab = value;
-      return chart;
-    };
-    chart.xvar = function(value) {
-      if (!arguments.length) {
-        return xvar;
+      rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1;
+      yaxis = g.append("g").attr("class", "y axis");
+      yaxis.selectAll("empty").data(yticks).enter().append("line").attr("y1", function(d) {
+        return yscale(d);
+      }).attr("y2", function(d) {
+        return yscale(d);
+      }).attr("x1", margin.left).attr("x2", margin.left + width).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none");
+      yaxis.selectAll("empty").data(yticks).enter().append("text").attr("y", function(d) {
+        return yscale(d);
+      }).attr("x", margin.left - axispos.ylabel).text(function(d) {
+        return formatAxis(yticks)(d);
+      });
+      yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : "");
+      if (yNA.handle) {
+        yaxis.append("text").attr("x", margin.left - axispos.ylabel).attr("y", margin.top + height - yNA.width / 2).text("N/A");
       }
-      xvar = value;
-      return chart;
-    };
-    chart.yvar = function(value) {
-      if (!arguments.length) {
-        return yvar;
+      indtip = d3.tip().attr('class', 'd3-tip').html(function(d, i) {
+        return indID[i];
+      }).direction('e').offset([0, 10]);
+      svg.call(indtip);
+      points = g.append("g").attr("id", "points");
+      pointsSelect = points.selectAll("empty").data(d3.range(x.length)).enter().append("circle").attr("cx", function(d, i) {
+        return xscale(x[i]);
+      }).attr("cy", function(d, i) {
+        return yscale(y[i]);
+      }).attr("class", function(d, i) {
+        return "pt" + i;
+      }).attr("r", pointsize).attr("fill", function(d, i) {
+        return pointcolor[group[i]];
+      }).attr("stroke", pointstroke).attr("stroke-width", "1").attr("opacity", function(d, i) {
+        if (((x[i] != null) || xNA.handle) && ((y[i] != null) || yNA.handle)) {
+          return 1;
+        }
+        return 0;
+      }).on("mouseover.paneltip", indtip.show).on("mouseout.paneltip", indtip.hide);
+      g.append("rect").attr("x", margin.left + paneloffset).attr("y", margin.top).attr("height", panelheight).attr("width", panelwidth).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none");
+      if (xNA.handle) {
+        g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", panelheight).attr("width", xNA.width).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none");
       }
-      yvar = value;
-      return chart;
-    };
-    chart.xNA = function(value) {
-      if (!arguments.length) {
-        return xNA;
+      if (xNA.handle && yNA.handle) {
+        g.append("rect").attr("x", margin.left).attr("y", margin.top + height - yNA.width).attr("height", yNA.width).attr("width", xNA.width).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none");
       }
-      xNA = value;
-      return chart;
-    };
-    chart.yNA = function(value) {
-      if (!arguments.length) {
-        return yNA;
+      if (yNA.handle) {
+        return g.append("rect").attr("x", margin.left + paneloffset).attr("y", margin.top + height - yNA.width).attr("height", yNA.width).attr("width", panelwidth).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none");
       }
-      yNA = value;
-      return chart;
-    };
-    chart.yscale = function() {
-      return yscale;
-    };
-    chart.xscale = function() {
-      return xscale;
-    };
-    chart.pointsSelect = function() {
-      return pointsSelect;
-    };
+    });
+  };
+  chart.width = function(value) {
+    if (!arguments.length) {
+      return width;
+    }
+    width = value;
     return chart;
   };
+  chart.height = function(value) {
+    if (!arguments.length) {
+      return height;
+    }
+    height = value;
+    return chart;
+  };
+  chart.margin = function(value) {
+    if (!arguments.length) {
+      return margin;
+    }
+    margin = value;
+    return chart;
+  };
+  chart.axispos = function(value) {
+    if (!arguments.length) {
+      return axispos;
+    }
+    axispos = value;
+    return chart;
+  };
+  chart.titlepos = function(value) {
+    if (!arguments.length) {
+      return titlepos;
+    }
+    titlepos;
+    return chart;
+  };
+  chart.xlim = function(value) {
+    if (!arguments.length) {
+      return xlim;
+    }
+    xlim = value;
+    return chart;
+  };
+  chart.nxticks = function(value) {
+    if (!arguments.length) {
+      return nxticks;
+    }
+    nxticks = value;
+    return chart;
+  };
+  chart.xticks = function(value) {
+    if (!arguments.length) {
+      return xticks;
+    }
+    xticks = value;
+    return chart;
+  };
+  chart.ylim = function(value) {
+    if (!arguments.length) {
+      return ylim;
+    }
+    ylim = value;
+    return chart;
+  };
+  chart.nyticks = function(value) {
+    if (!arguments.length) {
+      return nyticks;
+    }
+    nyticks = value;
+    return chart;
+  };
+  chart.yticks = function(value) {
+    if (!arguments.length) {
+      return yticks;
+    }
+    yticks = value;
+    return chart;
+  };
+  chart.rectcolor = function(value) {
+    if (!arguments.length) {
+      return rectcolor;
+    }
+    rectcolor = value;
+    return chart;
+  };
+  chart.pointcolor = function(value) {
+    if (!arguments.length) {
+      return pointcolor;
+    }
+    pointcolor = value;
+    return chart;
+  };
+  chart.pointsize = function(value) {
+    if (!arguments.length) {
+      return pointsize;
+    }
+    pointsize = value;
+    return chart;
+  };
+  chart.pointstroke = function(value) {
+    if (!arguments.length) {
+      return pointstroke;
+    }
+    pointstroke = value;
+    return chart;
+  };
+  chart.dataByInd = function(value) {
+    if (!arguments.length) {
+      return dataByInd;
+    }
+    dataByInd = value;
+    return chart;
+  };
+  chart.title = function(value) {
+    if (!arguments.length) {
+      return title;
+    }
+    title = value;
+    return chart;
+  };
+  chart.xlab = function(value) {
+    if (!arguments.length) {
+      return xlab;
+    }
+    xlab = value;
+    return chart;
+  };
+  chart.ylab = function(value) {
+    if (!arguments.length) {
+      return ylab;
+    }
+    ylab = value;
+    return chart;
+  };
+  chart.rotate_ylab = function(value) {
+    if (!arguments.length) {
+      return rotate_ylab;
+    }
+    rotate_ylab = value;
+    return chart;
+  };
+  chart.xvar = function(value) {
+    if (!arguments.length) {
+      return xvar;
+    }
+    xvar = value;
+    return chart;
+  };
+  chart.yvar = function(value) {
+    if (!arguments.length) {
+      return yvar;
+    }
+    yvar = value;
+    return chart;
+  };
+  chart.xNA = function(value) {
+    if (!arguments.length) {
+      return xNA;
+    }
+    xNA = value;
+    return chart;
+  };
+  chart.yNA = function(value) {
+    if (!arguments.length) {
+      return yNA;
+    }
+    yNA = value;
+    return chart;
+  };
+  chart.yscale = function() {
+    return yscale;
+  };
+  chart.xscale = function() {
+    return xscale;
+  };
+  chart.pointsSelect = function() {
+    return pointsSelect;
+  };
+  return chart;
+};
 
-  root.scatterplot = scatterplot;
-
-}).call(this);
+root.scatterplot = scatterplot;
diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index 477c9b94..e6f55624 100755
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -1,105 +1,101 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-
-  $(function() {
-    var add, change_buttons, checked_traits, deselect_all, invert, remove, removed_traits, select_all;
-    checked_traits = null;
-    select_all = function() {
-      console.log("selected_all");
-      return $(".trait_checkbox").prop('checked', true);
-    };
-    deselect_all = function() {
-      return $(".trait_checkbox").prop('checked', false);
-    };
-    invert = function() {
-      return $(".trait_checkbox").trigger('click');
-    };
-    add = function() {
-      var traits;
-      traits = $("#trait_table input:checked").map(function() {
-        return $(this).val();
-      }).get();
-      console.log("checked length is:", traits.length);
-      console.log("checked is:", traits);
-      return $.colorbox({
-        href: "/collections/add?traits=" + traits
-      });
-    };
-    removed_traits = function() {
-      console.log('in removed_traits with checked_traits:', checked_traits);
-      return checked_traits.closest("tr").fadeOut();
-    };
-    change_buttons = function() {
-      var button, buttons, item, num_checked, text, _i, _j, _k, _l, _len, _len1, _len2, _len3, _results, _results1;
-      buttons = ["#add", "#remove"];
-      num_checked = $('.trait_checkbox:checked').length;
-      console.log("num_checked is:", num_checked);
-      if (num_checked === 0) {
-        for (_i = 0, _len = buttons.length; _i < _len; _i++) {
-          button = buttons[_i];
-          $(button).prop("disabled", true);
-        }
-      } else {
-        for (_j = 0, _len1 = buttons.length; _j < _len1; _j++) {
-          button = buttons[_j];
-          $(button).prop("disabled", false);
-        }
+// Generated by CoffeeScript 1.7.1
+$(function() {
+  var add, change_buttons, checked_traits, deselect_all, invert, remove, removed_traits, select_all;
+  checked_traits = null;
+  select_all = function() {
+    console.log("selected_all");
+    return $(".trait_checkbox").prop('checked', true);
+  };
+  deselect_all = function() {
+    return $(".trait_checkbox").prop('checked', false);
+  };
+  invert = function() {
+    return $(".trait_checkbox").trigger('click');
+  };
+  add = function() {
+    var traits;
+    traits = $("#trait_table input:checked").map(function() {
+      return $(this).val();
+    }).get();
+    console.log("checked length is:", traits.length);
+    console.log("checked is:", traits);
+    return $.colorbox({
+      href: "/collections/add?traits=" + traits
+    });
+  };
+  removed_traits = function() {
+    console.log('in removed_traits with checked_traits:', checked_traits);
+    return checked_traits.closest("tr").fadeOut();
+  };
+  change_buttons = function() {
+    var button, buttons, item, num_checked, text, _i, _j, _k, _l, _len, _len1, _len2, _len3, _results, _results1;
+    buttons = ["#add", "#remove"];
+    num_checked = $('.trait_checkbox:checked').length;
+    console.log("num_checked is:", num_checked);
+    if (num_checked === 0) {
+      for (_i = 0, _len = buttons.length; _i < _len; _i++) {
+        button = buttons[_i];
+        $(button).prop("disabled", true);
       }
-      if (num_checked > 1) {
-        console.log("in loop");
-        _results = [];
-        for (_k = 0, _len2 = buttons.length; _k < _len2; _k++) {
-          item = buttons[_k];
-          console.log("  processing item:", item);
-          text = $(item).html();
-          if (text.indexOf("Records") === -1) {
-            text = text.replace("Record", "Records");
-            _results.push($(item).html(text));
-          } else {
-            _results.push(void 0);
-          }
-        }
-        return _results;
-      } else {
-        console.log("in loop");
-        _results1 = [];
-        for (_l = 0, _len3 = buttons.length; _l < _len3; _l++) {
-          item = buttons[_l];
-          console.log("  processing item:", item);
-          text = $(item).html();
-          text = text.replace("Records", "Record");
-          _results1.push($(item).html(text));
+    } else {
+      for (_j = 0, _len1 = buttons.length; _j < _len1; _j++) {
+        button = buttons[_j];
+        $(button).prop("disabled", false);
+      }
+    }
+    if (num_checked > 1) {
+      console.log("in loop");
+      _results = [];
+      for (_k = 0, _len2 = buttons.length; _k < _len2; _k++) {
+        item = buttons[_k];
+        console.log("  processing item:", item);
+        text = $(item).html();
+        if (text.indexOf("Records") === -1) {
+          text = text.replace("Record", "Records");
+          _results.push($(item).html(text));
+        } else {
+          _results.push(void 0);
         }
-        return _results1;
       }
-    };
-    remove = function() {
-      var traits, uc_id;
-      checked_traits = $("#trait_table input:checked");
-      traits = checked_traits.map(function() {
-        return $(this).val();
-      }).get();
-      console.log("checked length is:", traits.length);
-      console.log("checked is:", traits);
-      uc_id = $("#uc_id").val();
-      console.log("uc.id is:", uc_id);
-      return $.ajax({
-        type: "POST",
-        url: "/collections/remove",
-        data: {
-          uc_id: uc_id,
-          traits: traits
-        },
-        success: removed_traits
-      });
-    };
-    $("#select_all").click(select_all);
-    $("#deselect_all").click(deselect_all);
-    $("#invert").click(invert);
-    $("#add").click(add);
-    $("#remove").click(remove);
-    $('.trait_checkbox').click(change_buttons);
-    return $('.btn').click(change_buttons);
-  });
-
-}).call(this);
+      return _results;
+    } else {
+      console.log("in loop");
+      _results1 = [];
+      for (_l = 0, _len3 = buttons.length; _l < _len3; _l++) {
+        item = buttons[_l];
+        console.log("  processing item:", item);
+        text = $(item).html();
+        text = text.replace("Records", "Record");
+        _results1.push($(item).html(text));
+      }
+      return _results1;
+    }
+  };
+  remove = function() {
+    var traits, uc_id;
+    checked_traits = $("#trait_table input:checked");
+    traits = checked_traits.map(function() {
+      return $(this).val();
+    }).get();
+    console.log("checked length is:", traits.length);
+    console.log("checked is:", traits);
+    uc_id = $("#uc_id").val();
+    console.log("uc.id is:", uc_id);
+    return $.ajax({
+      type: "POST",
+      url: "/collections/remove",
+      data: {
+        uc_id: uc_id,
+        traits: traits
+      },
+      success: removed_traits
+    });
+  };
+  $("#select_all").click(select_all);
+  $("#deselect_all").click(deselect_all);
+  $("#invert").click(invert);
+  $("#add").click(add);
+  $("#remove").click(remove);
+  $('.trait_checkbox').click(change_buttons);
+  return $('.btn').click(change_buttons);
+});
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index e1dc9e76..5f452f32 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -1,417 +1,424 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var Stat_Table_Rows, is_number, root,
-    __hasProp = {}.hasOwnProperty,
-    __slice = [].slice;
+// Generated by CoffeeScript 1.7.1
+var Stat_Table_Rows, is_number, root,
+  __hasProp = {}.hasOwnProperty,
+  __slice = [].slice;
 
-  root = typeof exports !== "undefined" && exports !== null ? exports : this;
+root = typeof exports !== "undefined" && exports !== null ? exports : this;
 
-  console.log("start_b");
+console.log("start_b");
 
-  is_number = function(o) {
-    return !isNaN((o - 0) && o !== null);
-  };
+is_number = function(o) {
+  return !isNaN((o - 0) && o !== null);
+};
 
-  Stat_Table_Rows = [
-    {
-      vn: "n_of_samples",
-      pretty: "N of Samples",
-      digits: 0
-    }, {
-      vn: "mean",
-      pretty: "Mean",
-      digits: 2
-    }, {
-      vn: "median",
-      pretty: "Median",
-      digits: 2
-    }, {
-      vn: "std_error",
-      pretty: "Standard Error (SE)",
-      digits: 2
-    }, {
-      vn: "std_dev",
-      pretty: "Standard Deviation (SD)",
-      digits: 2
-    }, {
-      vn: "min",
-      pretty: "Minimum",
-      digits: 2
-    }, {
-      vn: "max",
-      pretty: "Maximum",
-      digits: 2
-    }, {
-      vn: "range",
-      pretty: "Range (log2)",
-      digits: 2
-    }, {
-      vn: "range_fold",
-      pretty: "Range (fold)",
-      digits: 2
-    }, {
-      vn: "interquartile",
-      pretty: "Interquartile Range",
-      url: "/glossary.html#Interquartile",
-      digits: 2
-    }
-  ];
+Stat_Table_Rows = [
+  {
+    vn: "n_of_samples",
+    pretty: "N of Samples",
+    digits: 0
+  }, {
+    vn: "mean",
+    pretty: "Mean",
+    digits: 2
+  }, {
+    vn: "median",
+    pretty: "Median",
+    digits: 2
+  }, {
+    vn: "std_error",
+    pretty: "Standard Error (SE)",
+    digits: 2
+  }, {
+    vn: "std_dev",
+    pretty: "Standard Deviation (SD)",
+    digits: 2
+  }, {
+    vn: "min",
+    pretty: "Minimum",
+    digits: 2
+  }, {
+    vn: "max",
+    pretty: "Maximum",
+    digits: 2
+  }, {
+    vn: "range",
+    pretty: "Range (log2)",
+    digits: 2
+  }, {
+    vn: "range_fold",
+    pretty: "Range (fold)",
+    digits: 2
+  }, {
+    vn: "interquartile",
+    pretty: "Interquartile Range",
+    url: "/glossary.html#Interquartile",
+    digits: 2
+  }
+];
 
-  $(function() {
-    var block_by_attribute_value, block_by_index, block_outliers, change_stats_value, create_value_dropdown, edit_data_change, export_sample_table_data, get_sample_table_data, hide_no_value, hide_tabs, make_table, on_corr_method_change, open_trait_selection, populate_sample_attributes_values_dropdown, process_id, reset_samples_table, sample_group_types, sample_lists, show_hide_outliers, stats_mdp_change, update_stat_values,
-      _this = this;
-    sample_lists = js_data.sample_lists;
-    sample_group_types = js_data.sample_group_types;
-    root.bar_chart = new Bar_Chart(sample_lists[0]);
-    root.histogram = new Histogram(sample_lists[0]);
-    new Box_Plot(sample_lists[0]);
-    $('.bar_chart_samples_group').change(function() {
-      var all_samples, group;
-      $('#bar_chart').remove();
-      $('#bar_chart_container').append('<div id="bar_chart"></div>');
-      group = $(this).val();
-      if (group === "samples_primary") {
-        return root.bar_chart = new Bar_Chart(sample_lists[0]);
-      } else if (group === "samples_other") {
-        return root.bar_chart = new Bar_Chart(sample_lists[1]);
-      } else if (group === "samples_all") {
-        all_samples = sample_lists[0].concat(sample_lists[1]);
-        return root.bar_chart = new Bar_Chart(all_samples);
-      }
-    });
-    $('.box_plot_samples_group').change(function() {
-      var all_samples, group;
-      $('#box_plot').remove();
-      $('#box_plot_container').append('<div id="box_plot"></div>');
-      group = $(this).val();
-      if (group === "samples_primary") {
-        return new Box_Plot(sample_lists[0]);
-      } else if (group === "samples_other") {
-        return new Box_Plot(sample_lists[1]);
-      } else if (group === "samples_all") {
-        all_samples = sample_lists[0].concat(sample_lists[1]);
-        return new Box_Plot(all_samples);
-      }
-    });
-    d3.select("#select_compare_trait").on("click", function() {
+$(function() {
+  var block_by_attribute_value, block_by_index, block_outliers, change_stats_value, create_value_dropdown, edit_data_change, export_sample_table_data, get_sample_table_data, hide_no_value, hide_tabs, make_table, on_corr_method_change, open_trait_selection, populate_sample_attributes_values_dropdown, process_id, reset_samples_table, sample_group_types, sample_lists, show_hide_outliers, stats_mdp_change, update_stat_values;
+  sample_lists = js_data.sample_lists;
+  sample_group_types = js_data.sample_group_types;
+  root.bar_chart = new Bar_Chart(sample_lists[0]);
+  root.histogram = new Histogram(sample_lists[0]);
+  new Box_Plot(sample_lists[0]);
+  $('.bar_chart_samples_group').change(function() {
+    var all_samples, group;
+    $('#bar_chart').remove();
+    $('#bar_chart_container').append('<div id="bar_chart"></div>');
+    group = $(this).val();
+    if (group === "samples_primary") {
+      return root.bar_chart = new Bar_Chart(sample_lists[0]);
+    } else if (group === "samples_other") {
+      return root.bar_chart = new Bar_Chart(sample_lists[1]);
+    } else if (group === "samples_all") {
+      all_samples = sample_lists[0].concat(sample_lists[1]);
+      return root.bar_chart = new Bar_Chart(all_samples);
+    }
+  });
+  $('.box_plot_samples_group').change(function() {
+    var all_samples, group;
+    $('#box_plot').remove();
+    $('#box_plot_container').append('<div id="box_plot"></div>');
+    group = $(this).val();
+    if (group === "samples_primary") {
+      return new Box_Plot(sample_lists[0]);
+    } else if (group === "samples_other") {
+      return new Box_Plot(sample_lists[1]);
+    } else if (group === "samples_all") {
+      all_samples = sample_lists[0].concat(sample_lists[1]);
+      return new Box_Plot(all_samples);
+    }
+  });
+  d3.select("#select_compare_trait").on("click", (function(_this) {
+    return function() {
       $('.qtlcharts').empty();
       return open_trait_selection();
-    });
-    d3.select("#clear_compare_trait").on("click", function() {
+    };
+  })(this));
+  d3.select("#clear_compare_trait").on("click", (function(_this) {
+    return function() {
       return $('.qtlcharts').empty();
-    });
-    open_trait_selection = function() {
-      var _this = this;
-      return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', function() {
+    };
+  })(this));
+  open_trait_selection = function() {
+    return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', (function(_this) {
+      return function() {
         $.colorbox({
           inline: true,
           href: "#collections_holder"
         });
         return $('a.collection_name').attr('onClick', 'return false');
-      });
-    };
-    hide_tabs = function(start) {
-      var x, _i, _results;
-      _results = [];
-      for (x = _i = start; start <= 10 ? _i <= 10 : _i >= 10; x = start <= 10 ? ++_i : --_i) {
-        _results.push($("#stats_tabs" + x).hide());
-      }
-      return _results;
-    };
-    stats_mdp_change = function() {
-      var selected;
-      selected = $(this).val();
-      hide_tabs(0);
-      return $("#stats_tabs" + selected).show();
-    };
-    change_stats_value = function(sample_sets, category, value_type, decimal_places) {
-      var current_value, id, in_box, the_value, title_value;
-      id = "#" + process_id(category, value_type);
-      console.log("the_id:", id);
-      in_box = $(id).html;
-      current_value = parseFloat($(in_box)).toFixed(decimal_places);
-      the_value = sample_sets[category][value_type]();
-      console.log("After running sample_sets, the_value is:", the_value);
-      if (decimal_places > 0) {
-        title_value = the_value.toFixed(decimal_places * 2);
-        the_value = the_value.toFixed(decimal_places);
+      };
+    })(this));
+  };
+  hide_tabs = function(start) {
+    var x, _i, _results;
+    _results = [];
+    for (x = _i = start; start <= 10 ? _i <= 10 : _i >= 10; x = start <= 10 ? ++_i : --_i) {
+      _results.push($("#stats_tabs" + x).hide());
+    }
+    return _results;
+  };
+  stats_mdp_change = function() {
+    var selected;
+    selected = $(this).val();
+    hide_tabs(0);
+    return $("#stats_tabs" + selected).show();
+  };
+  change_stats_value = function(sample_sets, category, value_type, decimal_places) {
+    var current_value, id, in_box, the_value, title_value;
+    id = "#" + process_id(category, value_type);
+    console.log("the_id:", id);
+    in_box = $(id).html;
+    current_value = parseFloat($(in_box)).toFixed(decimal_places);
+    the_value = sample_sets[category][value_type]();
+    console.log("After running sample_sets, the_value is:", the_value);
+    if (decimal_places > 0) {
+      title_value = the_value.toFixed(decimal_places * 2);
+      the_value = the_value.toFixed(decimal_places);
+    } else {
+      title_value = null;
+    }
+    console.log("*-* the_value:", the_value);
+    console.log("*-* current_value:", current_value);
+    if (the_value !== current_value) {
+      console.log("object:", $(id).html(the_value));
+      $(id).html(the_value).effect("highlight");
+    }
+    if (title_value) {
+      return $(id).attr('title', title_value);
+    }
+  };
+  update_stat_values = function(sample_sets) {
+    var category, row, _i, _len, _ref, _results;
+    _ref = ['samples_primary', 'samples_other', 'samples_all'];
+    _results = [];
+    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+      category = _ref[_i];
+      _results.push((function() {
+        var _j, _len1, _results1;
+        _results1 = [];
+        for (_j = 0, _len1 = Stat_Table_Rows.length; _j < _len1; _j++) {
+          row = Stat_Table_Rows[_j];
+          console.log("Calling change_stats_value");
+          _results1.push(change_stats_value(sample_sets, category, row.vn, row.digits));
+        }
+        return _results1;
+      })());
+    }
+    return _results;
+  };
+  make_table = function() {
+    var header, key, row, row_line, table, the_id, the_rows, value, _i, _len, _ref, _ref1;
+    header = "<thead><tr><th>&nbsp;</th>";
+    console.log("js_data.sample_group_types:", js_data.sample_group_types);
+    _ref = js_data.sample_group_types;
+    for (key in _ref) {
+      if (!__hasProp.call(_ref, key)) continue;
+      value = _ref[key];
+      console.log("aa key:", key);
+      console.log("aa value:", value);
+      the_id = process_id("column", key);
+      header += "<th id=\"" + the_id + "\">" + value + "</th>";
+    }
+    header += "</thead>";
+    console.log("windex header is:", header);
+    the_rows = "<tbody>";
+    for (_i = 0, _len = Stat_Table_Rows.length; _i < _len; _i++) {
+      row = Stat_Table_Rows[_i];
+      console.log("rowing");
+      row_line = "<tr>";
+      if (row.url != null) {
+        row_line += "<td id=\"" + row.vn + "\"><a href=\"" + row.url + "\">" + row.pretty + "</a></td>";
       } else {
-        title_value = null;
-      }
-      console.log("*-* the_value:", the_value);
-      console.log("*-* current_value:", current_value);
-      if (the_value !== current_value) {
-        console.log("object:", $(id).html(the_value));
-        $(id).html(the_value).effect("highlight");
-      }
-      if (title_value) {
-        return $(id).attr('title', title_value);
+        row_line += "<td id=\"" + row.vn + "\">" + row.pretty + "</td>";
       }
-    };
-    update_stat_values = function(sample_sets) {
-      var category, row, _i, _len, _ref, _results;
-      _ref = ['samples_primary', 'samples_other', 'samples_all'];
-      _results = [];
-      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-        category = _ref[_i];
-        _results.push((function() {
-          var _j, _len1, _results1;
-          _results1 = [];
-          for (_j = 0, _len1 = Stat_Table_Rows.length; _j < _len1; _j++) {
-            row = Stat_Table_Rows[_j];
-            console.log("Calling change_stats_value");
-            _results1.push(change_stats_value(sample_sets, category, row.vn, row.digits));
-          }
-          return _results1;
-        })());
-      }
-      return _results;
-    };
-    make_table = function() {
-      var header, key, row, row_line, table, the_id, the_rows, value, _i, _len, _ref, _ref1;
-      header = "<thead><tr><th>&nbsp;</th>";
-      console.log("js_data.sample_group_types:", js_data.sample_group_types);
-      _ref = js_data.sample_group_types;
-      for (key in _ref) {
-        if (!__hasProp.call(_ref, key)) continue;
-        value = _ref[key];
-        console.log("aa key:", key);
-        console.log("aa value:", value);
-        the_id = process_id("column", key);
-        header += "<th id=\"" + the_id + "\">" + value + "</th>";
+      console.log("box - js_data.sample_group_types:", js_data.sample_group_types);
+      _ref1 = js_data.sample_group_types;
+      for (key in _ref1) {
+        if (!__hasProp.call(_ref1, key)) continue;
+        value = _ref1[key];
+        console.log("apple key:", key);
+        the_id = process_id(key, row.vn);
+        console.log("the_id:", the_id);
+        row_line += "<td id=\"" + the_id + "\">foo</td>";
       }
-      header += "</thead>";
-      console.log("windex header is:", header);
-      the_rows = "<tbody>";
-      for (_i = 0, _len = Stat_Table_Rows.length; _i < _len; _i++) {
-        row = Stat_Table_Rows[_i];
-        console.log("rowing");
-        row_line = "<tr>";
-        if (row.url != null) {
-          row_line += "<td id=\"" + row.vn + "\"><a href=\"" + row.url + "\">" + row.pretty + "</a></td>";
-        } else {
-          row_line += "<td id=\"" + row.vn + "\">" + row.pretty + "</td>";
-        }
-        console.log("box - js_data.sample_group_types:", js_data.sample_group_types);
-        _ref1 = js_data.sample_group_types;
-        for (key in _ref1) {
-          if (!__hasProp.call(_ref1, key)) continue;
-          value = _ref1[key];
-          console.log("apple key:", key);
-          the_id = process_id(key, row.vn);
-          console.log("the_id:", the_id);
-          row_line += "<td id=\"" + the_id + "\">foo</td>";
-        }
-        row_line += "</tr>";
-        console.log("row line:", row_line);
-        the_rows += row_line;
-      }
-      the_rows += "</tbody>";
-      table = header + the_rows;
-      console.log("table is:", table);
-      return $("#stats_table").append(table);
-    };
-    process_id = function() {
-      var processed, value, values, _i, _len;
-      values = 1 <= arguments.length ? __slice.call(arguments, 0) : [];
-      /* Make an id or a class valid javascript by, for example, eliminating spaces
-      */
+      row_line += "</tr>";
+      console.log("row line:", row_line);
+      the_rows += row_line;
+    }
+    the_rows += "</tbody>";
+    table = header + the_rows;
+    console.log("table is:", table);
+    return $("#stats_table").append(table);
+  };
+  process_id = function() {
+    var processed, value, values, _i, _len;
+    values = 1 <= arguments.length ? __slice.call(arguments, 0) : [];
 
-      processed = "";
-      for (_i = 0, _len = values.length; _i < _len; _i++) {
-        value = values[_i];
-        console.log("value:", value);
-        value = value.replace(" ", "_");
-        if (processed.length) {
-          processed += "-";
-        }
-        processed += value;
+    /* Make an id or a class valid javascript by, for example, eliminating spaces */
+    processed = "";
+    for (_i = 0, _len = values.length; _i < _len; _i++) {
+      value = values[_i];
+      console.log("value:", value);
+      value = value.replace(" ", "_");
+      if (processed.length) {
+        processed += "-";
       }
-      return processed;
+      processed += value;
+    }
+    return processed;
+  };
+  edit_data_change = function() {
+    var already_seen, checkbox, checked, name, real_value, row, rows, sample_sets, table, tables, _i, _j, _len, _len1;
+    already_seen = {};
+    sample_sets = {
+      samples_primary: new Stats([]),
+      samples_other: new Stats([]),
+      samples_all: new Stats([])
     };
-    edit_data_change = function() {
-      var already_seen, checkbox, checked, name, real_value, row, rows, sample_sets, table, tables, _i, _j, _len, _len1;
-      already_seen = {};
-      sample_sets = {
-        samples_primary: new Stats([]),
-        samples_other: new Stats([]),
-        samples_all: new Stats([])
-      };
-      console.log("at beginning:", sample_sets);
-      tables = ['samples_primary', 'samples_other'];
-      for (_i = 0, _len = tables.length; _i < _len; _i++) {
-        table = tables[_i];
-        rows = $("#" + table).find('tr');
-        for (_j = 0, _len1 = rows.length; _j < _len1; _j++) {
-          row = rows[_j];
-          name = $(row).find('.edit_sample_sample_name').html();
-          name = $.trim(name);
-          real_value = $(row).find('.edit_sample_value').val();
-          console.log("real_value:", real_value);
-          checkbox = $(row).find(".edit_sample_checkbox");
-          checked = $(checkbox).attr('checked');
-          if (checked && is_number(real_value) && real_value !== "") {
-            console.log("in the iffy if");
-            real_value = parseFloat(real_value);
-            sample_sets[table].add_value(real_value);
-            console.log("checking name of:", name);
-            if (!(name in already_seen)) {
-              console.log("haven't seen");
-              sample_sets['samples_all'].add_value(real_value);
-              already_seen[name] = true;
-            }
+    console.log("at beginning:", sample_sets);
+    tables = ['samples_primary', 'samples_other'];
+    for (_i = 0, _len = tables.length; _i < _len; _i++) {
+      table = tables[_i];
+      rows = $("#" + table).find('tr');
+      for (_j = 0, _len1 = rows.length; _j < _len1; _j++) {
+        row = rows[_j];
+        name = $(row).find('.edit_sample_sample_name').html();
+        name = $.trim(name);
+        real_value = $(row).find('.edit_sample_value').val();
+        console.log("real_value:", real_value);
+        checkbox = $(row).find(".edit_sample_checkbox");
+        checked = $(checkbox).attr('checked');
+        if (checked && is_number(real_value) && real_value !== "") {
+          console.log("in the iffy if");
+          real_value = parseFloat(real_value);
+          sample_sets[table].add_value(real_value);
+          console.log("checking name of:", name);
+          if (!(name in already_seen)) {
+            console.log("haven't seen");
+            sample_sets['samples_all'].add_value(real_value);
+            already_seen[name] = true;
           }
         }
       }
-      console.log("towards end:", sample_sets);
-      return update_stat_values(sample_sets);
-    };
-    show_hide_outliers = function() {
-      var label;
-      console.log("FOOBAR in beginning of show_hide_outliers");
-      label = $('#show_hide_outliers').val();
-      console.log("lable is:", label);
-      if (label === "Hide Outliers") {
-        return $('#show_hide_outliers').val("Show Outliers");
-      } else if (label === "Show Outliers") {
-        console.log("Found Show Outliers");
-        $('#show_hide_outliers').val("Hide Outliers");
-        return console.log("Should be now Hide Outliers");
-      }
-    };
-    on_corr_method_change = function() {
-      var corr_method;
-      console.log("in beginning of on_corr_method_change");
-      corr_method = $('select[name=corr_method]').val();
-      console.log("corr_method is:", corr_method);
-      $('.correlation_desc').hide();
-      $('#' + corr_method + "_r_desc").show().effect("highlight");
-      if (corr_method === "lit") {
-        return $("#corr_sample_method_options").hide();
-      } else {
-        return $("#corr_sample_method_options").show();
-      }
-    };
-    $('select[name=corr_method]').change(on_corr_method_change);
-    create_value_dropdown = function(value) {
-      return "<option val=" + value + ">" + value + "</option>";
-    };
-    populate_sample_attributes_values_dropdown = function() {
-      var attribute_info, key, sample_attributes, selected_attribute, value, _i, _len, _ref, _ref1, _results;
-      console.log("in beginning of psavd");
-      $('#attribute_values').empty();
-      sample_attributes = {};
-      _ref = js_data.attribute_names;
-      for (key in _ref) {
-        if (!__hasProp.call(_ref, key)) continue;
-        attribute_info = _ref[key];
-        sample_attributes[attribute_info.name] = attribute_info.distinct_values;
-      }
-      console.log("[visa] attributes is:", sample_attributes);
-      selected_attribute = $('#exclude_menu').val().replace("_", " ");
-      console.log("selected_attribute is:", selected_attribute);
-      _ref1 = sample_attributes[selected_attribute];
-      _results = [];
-      for (_i = 0, _len = _ref1.length; _i < _len; _i++) {
-        value = _ref1[_i];
-        _results.push($(create_value_dropdown(value)).appendTo($('#attribute_values')));
-      }
-      return _results;
-    };
-    if (js_data.attribute_names.length > 0) {
-      populate_sample_attributes_values_dropdown();
     }
-    $('#exclude_menu').change(populate_sample_attributes_values_dropdown);
-    block_by_attribute_value = function() {
-      var attribute_name, cell_class, exclude_by_value,
-        _this = this;
-      attribute_name = $('#exclude_menu').val();
-      exclude_by_value = $('#attribute_values').val();
-      cell_class = ".column_name-" + attribute_name;
-      return $(cell_class).each(function(index, element) {
+    console.log("towards end:", sample_sets);
+    return update_stat_values(sample_sets);
+  };
+  show_hide_outliers = function() {
+    var label;
+    console.log("FOOBAR in beginning of show_hide_outliers");
+    label = $('#show_hide_outliers').val();
+    console.log("lable is:", label);
+    if (label === "Hide Outliers") {
+      return $('#show_hide_outliers').val("Show Outliers");
+    } else if (label === "Show Outliers") {
+      console.log("Found Show Outliers");
+      $('#show_hide_outliers').val("Hide Outliers");
+      return console.log("Should be now Hide Outliers");
+    }
+  };
+  on_corr_method_change = function() {
+    var corr_method;
+    console.log("in beginning of on_corr_method_change");
+    corr_method = $('select[name=corr_method]').val();
+    console.log("corr_method is:", corr_method);
+    $('.correlation_desc').hide();
+    $('#' + corr_method + "_r_desc").show().effect("highlight");
+    if (corr_method === "lit") {
+      return $("#corr_sample_method_options").hide();
+    } else {
+      return $("#corr_sample_method_options").show();
+    }
+  };
+  $('select[name=corr_method]').change(on_corr_method_change);
+  create_value_dropdown = function(value) {
+    return "<option val=" + value + ">" + value + "</option>";
+  };
+  populate_sample_attributes_values_dropdown = function() {
+    var attribute_info, key, sample_attributes, selected_attribute, value, _i, _len, _ref, _ref1, _results;
+    console.log("in beginning of psavd");
+    $('#attribute_values').empty();
+    sample_attributes = {};
+    _ref = js_data.attribute_names;
+    for (key in _ref) {
+      if (!__hasProp.call(_ref, key)) continue;
+      attribute_info = _ref[key];
+      sample_attributes[attribute_info.name] = attribute_info.distinct_values;
+    }
+    console.log("[visa] attributes is:", sample_attributes);
+    selected_attribute = $('#exclude_menu').val().replace("_", " ");
+    console.log("selected_attribute is:", selected_attribute);
+    _ref1 = sample_attributes[selected_attribute];
+    _results = [];
+    for (_i = 0, _len = _ref1.length; _i < _len; _i++) {
+      value = _ref1[_i];
+      _results.push($(create_value_dropdown(value)).appendTo($('#attribute_values')));
+    }
+    return _results;
+  };
+  if (js_data.attribute_names.length > 0) {
+    populate_sample_attributes_values_dropdown();
+  }
+  $('#exclude_menu').change(populate_sample_attributes_values_dropdown);
+  block_by_attribute_value = function() {
+    var attribute_name, cell_class, exclude_by_value;
+    attribute_name = $('#exclude_menu').val();
+    exclude_by_value = $('#attribute_values').val();
+    cell_class = ".column_name-" + attribute_name;
+    return $(cell_class).each((function(_this) {
+      return function(index, element) {
         var row;
         if ($.trim($(element).text()) === exclude_by_value) {
           row = $(element).parent('tr');
           return $(row).find(".trait_value_input").val("x");
         }
-      });
-    };
-    $('#exclude_group').click(block_by_attribute_value);
-    block_by_index = function() {
-      var end_index, index, index_list, index_set, index_string, start_index, _i, _j, _k, _len, _len1, _ref, _results;
-      index_string = $('#remove_samples_field').val();
-      index_list = [];
-      _ref = index_string.split(",");
-      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-        index_set = _ref[_i];
-        if (index_set.indexOf('-') !== -1) {
-          try {
-            start_index = parseInt(index_set.split("-")[0]);
-            end_index = parseInt(index_set.split("-")[1]);
-            for (index = _j = start_index; start_index <= end_index ? _j <= end_index : _j >= end_index; index = start_index <= end_index ? ++_j : --_j) {
-              index_list.push(index);
-            }
-          } catch (error) {
-            alert("Syntax error");
+      };
+    })(this));
+  };
+  $('#exclude_group').click(block_by_attribute_value);
+  block_by_index = function() {
+    var end_index, error, index, index_list, index_set, index_string, start_index, _i, _j, _k, _len, _len1, _ref, _results;
+    index_string = $('#remove_samples_field').val();
+    index_list = [];
+    _ref = index_string.split(",");
+    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+      index_set = _ref[_i];
+      if (index_set.indexOf('-') !== -1) {
+        try {
+          start_index = parseInt(index_set.split("-")[0]);
+          end_index = parseInt(index_set.split("-")[1]);
+          for (index = _j = start_index; start_index <= end_index ? _j <= end_index : _j >= end_index; index = start_index <= end_index ? ++_j : --_j) {
+            index_list.push(index);
           }
-        } else {
-          index = parseInt(index_set);
-          console.log("index:", index);
-          index_list.push(index);
+        } catch (_error) {
+          error = _error;
+          alert("Syntax error");
         }
+      } else {
+        index = parseInt(index_set);
+        console.log("index:", index);
+        index_list.push(index);
       }
-      console.log("index_list:", index_list);
-      _results = [];
-      for (_k = 0, _len1 = index_list.length; _k < _len1; _k++) {
-        index = index_list[_k];
-        if ($('#block_group').val() === "primary") {
-          console.log("block_group:", $('#block_group').val());
-          console.log("row:", $('#Primary_' + index.toString()));
-          _results.push($('#Primary_' + index.toString()).find('.trait_value_input').val("x"));
-        } else if ($('#block_group').val() === "other") {
-          console.log("block_group:", $('#block_group').val());
-          console.log("row:", $('#Other_' + index.toString()));
-          _results.push($('#Other_' + index.toString()).find('.trait_value_input').val("x"));
-        } else {
-          _results.push(void 0);
-        }
+    }
+    console.log("index_list:", index_list);
+    _results = [];
+    for (_k = 0, _len1 = index_list.length; _k < _len1; _k++) {
+      index = index_list[_k];
+      if ($('#block_group').val() === "primary") {
+        console.log("block_group:", $('#block_group').val());
+        console.log("row:", $('#Primary_' + index.toString()));
+        _results.push($('#Primary_' + index.toString()).find('.trait_value_input').val("x"));
+      } else if ($('#block_group').val() === "other") {
+        console.log("block_group:", $('#block_group').val());
+        console.log("row:", $('#Other_' + index.toString()));
+        _results.push($('#Other_' + index.toString()).find('.trait_value_input').val("x"));
+      } else {
+        _results.push(void 0);
       }
-      return _results;
-    };
-    $('#block_by_index').click(block_by_index);
-    hide_no_value = function() {
-      var _this = this;
-      return $('.value_se').each(function(_index, element) {
+    }
+    return _results;
+  };
+  $('#block_by_index').click(block_by_index);
+  hide_no_value = function() {
+    return $('.value_se').each((function(_this) {
+      return function(_index, element) {
         if ($(element).find('.trait_value_input').val() === 'x') {
           return $(element).hide();
         }
-      });
-    };
-    $('#hide_no_value').click(hide_no_value);
-    block_outliers = function() {
-      var _this = this;
-      return $('.outlier').each(function(_index, element) {
+      };
+    })(this));
+  };
+  $('#hide_no_value').click(hide_no_value);
+  block_outliers = function() {
+    return $('.outlier').each((function(_this) {
+      return function(_index, element) {
         return $(element).find('.trait_value_input').val('x');
-      });
-    };
-    $('#block_outliers').click(block_outliers);
-    reset_samples_table = function() {
-      var _this = this;
-      return $('.trait_value_input').each(function(_index, element) {
+      };
+    })(this));
+  };
+  $('#block_outliers').click(block_outliers);
+  reset_samples_table = function() {
+    return $('.trait_value_input').each((function(_this) {
+      return function(_index, element) {
         console.log("value is:", $(element).val());
         $(element).val($(element).data('value'));
         console.log("data-value is:", $(element).data('value'));
         return $(element).parents('.value_se').show();
-      });
-    };
-    $('#reset').click(reset_samples_table);
-    get_sample_table_data = function() {
-      var other_samples, primary_samples, samples,
-        _this = this;
-      samples = {};
-      primary_samples = [];
-      other_samples = [];
-      $('#sortable1').find('.value_se').each(function(_index, element) {
+      };
+    })(this));
+  };
+  $('#reset').click(reset_samples_table);
+  get_sample_table_data = function() {
+    var other_samples, primary_samples, samples;
+    samples = {};
+    primary_samples = [];
+    other_samples = [];
+    $('#sortable1').find('.value_se').each((function(_this) {
+      return function(_index, element) {
         var attribute_info, key, row_data, _ref;
         row_data = {};
         row_data.name = $.trim($(element).find('.column_name-Sample').text());
@@ -427,39 +434,38 @@
         }
         console.log("row_data is:", row_data);
         return primary_samples.push(row_data);
-      });
-      console.log("primary_samples is:", primary_samples);
-      samples.primary_samples = primary_samples;
-      samples.other_samples = other_samples;
-      return samples;
-    };
-    export_sample_table_data = function() {
-      var format, json_sample_data, sample_data;
-      sample_data = get_sample_table_data();
-      console.log("sample_data is:", sample_data);
-      json_sample_data = JSON.stringify(sample_data);
-      console.log("json_sample_data is:", json_sample_data);
-      $('input[name=export_data]').val(json_sample_data);
-      console.log("export_data is", $('input[name=export_data]').val());
-      format = $('#export_format').val();
-      if (format === "excel") {
-        $('#trait_data_form').attr('action', '/export_trait_excel');
-      } else {
-        $('#trait_data_form').attr('action', '/export_trait_csv');
-      }
-      console.log("action is:", $('#trait_data_form').attr('action'));
-      return $('#trait_data_form').submit();
-    };
-    $('#export').click(export_sample_table_data);
-    console.log("before registering block_outliers");
-    $('#block_outliers').click(block_outliers);
-    console.log("after registering block_outliers");
-    _.mixin(_.str.exports());
-    $('#edit_sample_lists').change(edit_data_change);
-    console.log("loaded");
-    make_table();
-    edit_data_change();
-    return console.log("end");
-  });
-
-}).call(this);
+      };
+    })(this));
+    console.log("primary_samples is:", primary_samples);
+    samples.primary_samples = primary_samples;
+    samples.other_samples = other_samples;
+    return samples;
+  };
+  export_sample_table_data = function() {
+    var format, json_sample_data, sample_data;
+    sample_data = get_sample_table_data();
+    console.log("sample_data is:", sample_data);
+    json_sample_data = JSON.stringify(sample_data);
+    console.log("json_sample_data is:", json_sample_data);
+    $('input[name=export_data]').val(json_sample_data);
+    console.log("export_data is", $('input[name=export_data]').val());
+    format = $('#export_format').val();
+    if (format === "excel") {
+      $('#trait_data_form').attr('action', '/export_trait_excel');
+    } else {
+      $('#trait_data_form').attr('action', '/export_trait_csv');
+    }
+    console.log("action is:", $('#trait_data_form').attr('action'));
+    return $('#trait_data_form').submit();
+  };
+  $('#export').click(export_sample_table_data);
+  console.log("before registering block_outliers");
+  $('#block_outliers').click(block_outliers);
+  console.log("after registering block_outliers");
+  _.mixin(_.str.exports());
+  $('#edit_sample_lists').change(edit_data_change);
+  console.log("loaded");
+  make_table();
+  edit_data_change();
+  return console.log("end");
+});
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 9b9070ba..1a2ad637 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -1,52 +1,50 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var root;
+// Generated by CoffeeScript 1.7.1
+var root;
 
-  root = typeof exports !== "undefined" && exports !== null ? exports : this;
+root = typeof exports !== "undefined" && exports !== null ? exports : this;
 
-  $(function() {
-    var composite_mapping_fields, get_progress, mapping_method_fields, submit_special, toggle_enable_disable, update_time_remaining,
-      _this = this;
-    submit_special = function() {
-      var url;
-      console.log("In submit_special");
-      console.log("this is:", this);
-      console.log("$(this) is:", $(this));
-      url = $(this).data("url");
-      console.log("url is:", url);
-      $("#trait_data_form").attr("action", url);
-      return $("#trait_data_form").submit();
-    };
-    update_time_remaining = function(percent_complete) {
-      var minutes_remaining, now, period, total_seconds_remaining;
-      now = new Date();
-      period = now.getTime() - root.start_time;
-      console.log("period is:", period);
-      if (period > 8000) {
-        total_seconds_remaining = (period / percent_complete * (100 - percent_complete)) / 1000;
-        minutes_remaining = Math.round(total_seconds_remaining / 60);
-        if (minutes_remaining < 3) {
-          return $('#time_remaining').text(Math.round(total_seconds_remaining) + " seconds remaining");
-        } else {
-          return $('#time_remaining').text(minutes_remaining + " minutes remaining");
-        }
+$(function() {
+  var composite_mapping_fields, get_progress, mapping_method_fields, submit_special, toggle_enable_disable, update_time_remaining;
+  submit_special = function() {
+    var url;
+    console.log("In submit_special");
+    console.log("this is:", this);
+    console.log("$(this) is:", $(this));
+    url = $(this).data("url");
+    console.log("url is:", url);
+    $("#trait_data_form").attr("action", url);
+    return $("#trait_data_form").submit();
+  };
+  update_time_remaining = function(percent_complete) {
+    var minutes_remaining, now, period, total_seconds_remaining;
+    now = new Date();
+    period = now.getTime() - root.start_time;
+    console.log("period is:", period);
+    if (period > 8000) {
+      total_seconds_remaining = (period / percent_complete * (100 - percent_complete)) / 1000;
+      minutes_remaining = Math.round(total_seconds_remaining / 60);
+      if (minutes_remaining < 3) {
+        return $('#time_remaining').text(Math.round(total_seconds_remaining) + " seconds remaining");
+      } else {
+        return $('#time_remaining').text(minutes_remaining + " minutes remaining");
       }
+    }
+  };
+  get_progress = function() {
+    var params, params_str, temp_uuid, url;
+    console.log("temp_uuid:", $("#temp_uuid").val());
+    temp_uuid = $("#temp_uuid").val();
+    params = {
+      key: temp_uuid
     };
-    get_progress = function() {
-      var params, params_str, temp_uuid, url,
-        _this = this;
-      console.log("temp_uuid:", $("#temp_uuid").val());
-      temp_uuid = $("#temp_uuid").val();
-      params = {
-        key: temp_uuid
-      };
-      params_str = $.param(params);
-      url = "/get_temp_data?" + params_str;
-      console.log("url:", url);
-      $.ajax({
-        type: "GET",
-        url: url,
-        success: function(progress_data) {
+    params_str = $.param(params);
+    url = "/get_temp_data?" + params_str;
+    console.log("url:", url);
+    $.ajax({
+      type: "GET",
+      url: url,
+      success: (function(_this) {
+        return function(progress_data) {
           var percent_complete;
           percent_complete = progress_data['percent_complete'];
           console.log("in get_progress data:", progress_data);
@@ -58,11 +56,13 @@
           } else {
             return root.start_time = new Date().getTime();
           }
-        }
-      });
-      return false;
-    };
-    $("#interval_mapping_compute").click(function() {
+        };
+      })(this)
+    });
+    return false;
+  };
+  $("#interval_mapping_compute").click((function(_this) {
+    return function() {
       var form_data, url;
       console.log("In interval mapping");
       $("#progress_bar_container").modal();
@@ -92,17 +92,21 @@
       console.log("settingInterval");
       _this.my_timer = setInterval(get_progress, 1000);
       return false;
-    });
-    $('#suggestive').hide();
-    $('input[name=display_all]').change(function() {
+    };
+  })(this));
+  $('#suggestive').hide();
+  $('input[name=display_all]').change((function(_this) {
+    return function() {
       console.log("check");
       if ($('input[name=display_all]:checked').val() === "False") {
         return $('#suggestive').show();
       } else {
         return $('#suggestive').hide();
       }
-    });
-    $("#marker_regression_compute").click(function() {
+    };
+  })(this));
+  $("#marker_regression_compute").click((function(_this) {
+    return function() {
       var form_data, url;
       $("#progress_bar_container").modal();
       url = "/marker_regression";
@@ -129,8 +133,10 @@
       console.log("settingInterval");
       _this.my_timer = setInterval(get_progress, 1000);
       return false;
-    });
-    $("#plink_compute").click(function() {
+    };
+  })(this));
+  $("#plink_compute").click((function(_this) {
+    return function() {
       var form_data, url;
       $("#static_progress_bar_container").modal();
       url = "/marker_regression";
@@ -160,8 +166,10 @@
       console.log("settingInterval");
       _this.my_timer = setInterval(get_progress, 1000);
       return false;
-    });
-    $("#gemma_compute").click(function() {
+    };
+  })(this));
+  $("#gemma_compute").click((function(_this) {
+    return function() {
       var form_data, url;
       $("#static_progress_bar_container").modal();
       url = "/marker_regression";
@@ -191,24 +199,23 @@
       console.log("settingInterval");
       _this.my_timer = setInterval(get_progress, 1000);
       return false;
-    });
-    composite_mapping_fields = function() {
-      return $(".composite_fields").toggle();
     };
-    mapping_method_fields = function() {
-      return $(".mapping_method_fields").toggle();
-    };
-    $("#use_composite_choice").change(composite_mapping_fields);
-    $("#mapping_method_choice").change(mapping_method_fields);
-    toggle_enable_disable = function(elem) {
-      return $(elem).prop("disabled", !$(elem).prop("disabled"));
-    };
-    $("#choose_closet_control").change(function() {
-      return toggle_enable_disable("#control_locus");
-    });
-    return $("#display_all_lrs").change(function() {
-      return toggle_enable_disable("#suggestive_lrs");
-    });
+  })(this));
+  composite_mapping_fields = function() {
+    return $(".composite_fields").toggle();
+  };
+  mapping_method_fields = function() {
+    return $(".mapping_method_fields").toggle();
+  };
+  $("#use_composite_choice").change(composite_mapping_fields);
+  $("#mapping_method_choice").change(mapping_method_fields);
+  toggle_enable_disable = function(elem) {
+    return $(elem).prop("disabled", !$(elem).prop("disabled"));
+  };
+  $("#choose_closet_control").change(function() {
+    return toggle_enable_disable("#control_locus");
   });
-
-}).call(this);
+  return $("#display_all_lrs").change(function() {
+    return toggle_enable_disable("#suggestive_lrs");
+  });
+});
diff --git a/wqflask/wqflask/static/new/javascript/stats.js b/wqflask/wqflask/static/new/javascript/stats.js
index d874995f..6f67fcbe 100755
--- a/wqflask/wqflask/static/new/javascript/stats.js
+++ b/wqflask/wqflask/static/new/javascript/stats.js
@@ -1,110 +1,106 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-  var Stats, bxd_only;
+// Generated by CoffeeScript 1.7.1
+var Stats, bxd_only;
+
+Stats = (function() {
+  function Stats(the_values) {
+    this.the_values = the_values;
+  }
+
+  Stats.prototype.add_value = function(value) {
+    return this.the_values.push(value);
+  };
+
+  Stats.prototype.n_of_samples = function() {
+    return this.the_values.length;
+  };
+
+  Stats.prototype.sum = function() {
+    var total, value, _i, _len, _ref;
+    total = 0;
+    _ref = this.the_values;
+    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+      value = _ref[_i];
+      total += value;
+    }
+    return total;
+  };
+
+  Stats.prototype.mean = function() {
+    return this.sum() / this.n_of_samples();
+  };
+
+  Stats.prototype.median = function() {
+    var is_odd, median_position, the_values_sorted;
+    is_odd = this.the_values.length % 2;
+    median_position = Math.floor(this.the_values.length / 2);
+    the_values_sorted = this.the_values.sort(function(a, b) {
+      return a - b;
+    });
+    if (is_odd) {
+      return the_values_sorted[median_position];
+    } else {
+      return (the_values_sorted[median_position] + the_values_sorted[median_position - 1]) / 2;
+    }
+  };
+
+  Stats.prototype.std_dev = function() {
+    var step_a, step_b, sum, value, _i, _len, _ref;
+    sum = 0;
+    _ref = this.the_values;
+    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+      value = _ref[_i];
+      step_a = Math.pow(value - this.mean(), 2);
+      sum += step_a;
+    }
+    step_b = sum / this.the_values.length;
+    return Math.sqrt(step_b);
+  };
 
-  Stats = (function() {
+  Stats.prototype.std_error = function() {
+    return this.std_dev() / Math.sqrt(this.n_of_samples());
+  };
 
-    function Stats(the_values) {
-      this.the_values = the_values;
-    }
+  Stats.prototype.min = function() {
+    return Math.min.apply(Math, this.the_values);
+  };
+
+  Stats.prototype.max = function() {
+    return Math.max.apply(Math, this.the_values);
+  };
+
+  Stats.prototype.range = function() {
+    return this.max() - this.min();
+  };
+
+  Stats.prototype.range_fold = function() {
+    return Math.pow(2, this.range());
+  };
+
+  Stats.prototype.interquartile = function() {
+    var iq, length, q1, q3;
+    length = this.the_values.length;
+    console.log("in interquartile the_values are:", this.the_values);
+    console.log("length is:", length);
+    q1 = this.the_values[Math.floor(length * .25)];
+    q3 = this.the_values[Math.floor(length * .75)];
+    iq = q3 - q1;
+    return Math.pow(2, iq);
+  };
+
+  return Stats;
+
+})();
+
+bxd_only = new Stats([3, 5, 7, 8]);
+
+console.log("[xred] bxd_only mean:", bxd_only.mean());
+
+console.log("[xgreen] bxd_only median:", bxd_only.median());
+
+console.log("[xpurple] bxd_only std_dev:", bxd_only.std_dev());
+
+console.log("[xmagenta] bxd_only std_error:", bxd_only.std_error());
+
+console.log("[xyellow] bxd_only min:", bxd_only.min());
 
-    Stats.prototype.add_value = function(value) {
-      return this.the_values.push(value);
-    };
-
-    Stats.prototype.n_of_samples = function() {
-      return this.the_values.length;
-    };
-
-    Stats.prototype.sum = function() {
-      var total, value, _i, _len, _ref;
-      total = 0;
-      _ref = this.the_values;
-      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-        value = _ref[_i];
-        total += value;
-      }
-      return total;
-    };
-
-    Stats.prototype.mean = function() {
-      return this.sum() / this.n_of_samples();
-    };
-
-    Stats.prototype.median = function() {
-      var is_odd, median_position, the_values_sorted;
-      is_odd = this.the_values.length % 2;
-      median_position = Math.floor(this.the_values.length / 2);
-      the_values_sorted = this.the_values.sort(function(a, b) {
-        return a - b;
-      });
-      if (is_odd) {
-        return the_values_sorted[median_position];
-      } else {
-        return (the_values_sorted[median_position] + the_values_sorted[median_position - 1]) / 2;
-      }
-    };
-
-    Stats.prototype.std_dev = function() {
-      var step_a, step_b, sum, value, _i, _len, _ref;
-      sum = 0;
-      _ref = this.the_values;
-      for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-        value = _ref[_i];
-        step_a = Math.pow(value - this.mean(), 2);
-        sum += step_a;
-      }
-      step_b = sum / this.the_values.length;
-      return Math.sqrt(step_b);
-    };
-
-    Stats.prototype.std_error = function() {
-      return this.std_dev() / Math.sqrt(this.n_of_samples());
-    };
-
-    Stats.prototype.min = function() {
-      return Math.min.apply(Math, this.the_values);
-    };
-
-    Stats.prototype.max = function() {
-      return Math.max.apply(Math, this.the_values);
-    };
-
-    Stats.prototype.range = function() {
-      return this.max() - this.min();
-    };
-
-    Stats.prototype.range_fold = function() {
-      return Math.pow(2, this.range());
-    };
-
-    Stats.prototype.interquartile = function() {
-      var iq, length, q1, q3;
-      length = this.the_values.length;
-      console.log("in interquartile the_values are:", this.the_values);
-      console.log("length is:", length);
-      q1 = this.the_values[Math.floor(length * .25)];
-      q3 = this.the_values[Math.floor(length * .75)];
-      iq = q3 - q1;
-      return Math.pow(2, iq);
-    };
-
-    return Stats;
-
-  })();
-
-  bxd_only = new Stats([3, 5, 7, 8]);
-
-  console.log("[xred] bxd_only mean:", bxd_only.mean());
-
-  console.log("[xgreen] bxd_only median:", bxd_only.median());
-
-  console.log("[xpurple] bxd_only std_dev:", bxd_only.std_dev());
-
-  console.log("[xmagenta] bxd_only std_error:", bxd_only.std_error());
-
-  console.log("[xyellow] bxd_only min:", bxd_only.min());
-
-  window.Stats = Stats;
-
-}).call(this);
+window.Stats = Stats;
diff --git a/wqflask/wqflask/static/new/javascript/thank_you.js b/wqflask/wqflask/static/new/javascript/thank_you.js
index bffff179..c0a4f34b 100755
--- a/wqflask/wqflask/static/new/javascript/thank_you.js
+++ b/wqflask/wqflask/static/new/javascript/thank_you.js
@@ -1,10 +1,6 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-
-  $(function() {
-    console.log("Starting transform");
-    $('#login_out').text('Sign out').attr('href', '/logout').removeClass('modalize');
-    return console.log("Transformed to sign out I hope");
-  });
-
-}).call(this);
+// Generated by CoffeeScript 1.7.1
+$(function() {
+  console.log("Starting transform");
+  $('#login_out').text('Sign out').attr('href', '/logout').removeClass('modalize');
+  return console.log("Transformed to sign out I hope");
+});
diff --git a/wqflask/wqflask/static/new/javascript/validation.js b/wqflask/wqflask/static/new/javascript/validation.js
index 275bcaa0..9536491b 100755
--- a/wqflask/wqflask/static/new/javascript/validation.js
+++ b/wqflask/wqflask/static/new/javascript/validation.js
@@ -1,51 +1,47 @@
-// Generated by CoffeeScript 1.6.1
-(function() {
-
-  $(function() {
-    var remove_samples_is_valid, validate_remove_samples;
-    remove_samples_is_valid = function(input) {
-      var new_splats, pattern, splat, splats, _i, _len;
-      if (_.trim(input).length === 0) {
-        return true;
-      }
-      splats = input.split(",");
-      new_splats = (function() {
-        var _i, _len, _results;
-        _results = [];
-        for (_i = 0, _len = splats.length; _i < _len; _i++) {
-          input = splats[_i];
-          _results.push(_.trim(input));
-        }
-        return _results;
-      })();
-      console.log("new_splats:", new_splats);
-      pattern = /^\d+\s*(?:-\s*\d+)?\s*$/;
-      for (_i = 0, _len = new_splats.length; _i < _len; _i++) {
-        splat = new_splats[_i];
-        console.log("splat is:", splat);
-        if (!splat.match(pattern)) {
-          return false;
-        }
-      }
+// Generated by CoffeeScript 1.7.1
+$(function() {
+  var remove_samples_is_valid, validate_remove_samples;
+  remove_samples_is_valid = function(input) {
+    var new_splats, pattern, splat, splats, _i, _len;
+    if (_.trim(input).length === 0) {
       return true;
-    };
-    validate_remove_samples = function() {
-      /*
-      Check if input for the remove samples function is valid and notify the user if not
-      */
-
-      var input;
-      input = $('#remove_samples_field').val();
-      console.log("input is:", input);
-      if (remove_samples_is_valid(input)) {
-        console.log("input is valid");
-        return $('#remove_samples_invalid').hide();
-      } else {
-        console.log("input isn't valid");
-        return $('#remove_samples_invalid').show();
+    }
+    splats = input.split(",");
+    new_splats = (function() {
+      var _i, _len, _results;
+      _results = [];
+      for (_i = 0, _len = splats.length; _i < _len; _i++) {
+        input = splats[_i];
+        _results.push(_.trim(input));
+      }
+      return _results;
+    })();
+    console.log("new_splats:", new_splats);
+    pattern = /^\d+\s*(?:-\s*\d+)?\s*$/;
+    for (_i = 0, _len = new_splats.length; _i < _len; _i++) {
+      splat = new_splats[_i];
+      console.log("splat is:", splat);
+      if (!splat.match(pattern)) {
+        return false;
       }
-    };
-    return $('#remove_samples_field').change(validate_remove_samples);
-  });
+    }
+    return true;
+  };
+  validate_remove_samples = function() {
 
-}).call(this);
+    /*
+    Check if input for the remove samples function is valid and notify the user if not
+     */
+    var input;
+    input = $('#remove_samples_field').val();
+    console.log("input is:", input);
+    if (remove_samples_is_valid(input)) {
+      console.log("input is valid");
+      return $('#remove_samples_invalid').hide();
+    } else {
+      console.log("input isn't valid");
+      return $('#remove_samples_invalid').show();
+    }
+  };
+  return $('#remove_samples_field').change(validate_remove_samples);
+});
diff --git a/wqflask/wqflask/templates/interval_mapping.html b/wqflask/wqflask/templates/interval_mapping.html
index ad174b7b..25ee22ac 100755
--- a/wqflask/wqflask/templates/interval_mapping.html
+++ b/wqflask/wqflask/templates/interval_mapping.html
@@ -5,6 +5,7 @@
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />

     <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />

     <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />

+    <link rel="stylesheet" type="text/css" href="/static/new/css/interval_mapping.css" />

     <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />

     <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />

 {% endblock %}

@@ -18,9 +19,16 @@
             <h2>

                 Whole Genome Mapping

             </h2>

+            <form id="exportform" action="export" method="post">

+              <input type="hidden" id="data" name="data" value="">

+              <input type="hidden" id="filename" name="filename" value="">

+              <input type="submit" id="export" value="Download SVG">

+            </form>

         </div>

-        <div class="qtlcharts" id="topchart">

-            

+        <div id="chart_container">

+            <div class="qtlcharts" id="topchart">

+                

+            </div>

         </div>

         <div>

             <h2>

@@ -32,12 +40,10 @@
                 <tr>

                     <td>Index</td>

                     <td>LRS Score</td>

-                    {% if method == "qtl_reaper" %}

-                    <td>Additive Effect</td>

-                    {% endif %}

                     <td>Chr</td>

                     <td>Mb</td>

                     <td>Locus</td>

+                    <td>Additive Effect</td>

                 </tr>

             </thead>

             <tbody>

@@ -45,12 +51,10 @@
                 <tr>

                     <td>{{ loop.index }}</td>

                     <td>{{ marker.lrs_value|float }}</td>

-                    {% if method == "qtl_reaper" %}

-                    <td>{{ marker.additive|float }}</td>

-                    {% endif %}

                     <td>{{ marker.chr|int }}</td>

                     <td>{{ marker.Mb|float  }}</td>

                     <td>{{ marker.name }}</td>

+                    <td>{{ marker.additive|float }}</td>

                 </tr>

                 {% endfor %}

             </tbody>

@@ -73,8 +77,9 @@
     <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>

     <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>

     <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>

+    <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_interval_map.js"></script>

     <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>

-    <script language="javascript" type="text/javascript" src="/static/new/javascript/interval_map_new.js"></script>

+    <script language="javascript" type="text/javascript" src="/static/new/javascript/create_interval_map.js"></script>

     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>

     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>

     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>

diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html
index defcd929..3dce5266 100755
--- a/wqflask/wqflask/templates/marker_regression.html
+++ b/wqflask/wqflask/templates/marker_regression.html
@@ -1,106 +1,121 @@
-{% extends "base.html" %}
-{% block title %}Marker Regression{% endblock %}
-{% block css %}
-    <link rel="stylesheet" type="text/css" href="/static/packages/jqplot/jquery.jqplot.min.css" />
-    <link rel="stylesheet" type="text/css" href="/static/new/css/marker_regression.css" />
-    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
-    <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
-    <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
-{% endblock %}
-{% block content %} <!-- Start of body -->
-
-    {{ header("Marker Regression",
-        '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
-
-    <div class="container">
-        <div>
-            <h2>
-                Manhattan Plot
-            </h2>
-        </div>
-        <div id="manhattan_plot_container" class="manhattan_plot_container">
-            <div id="manhattan_plot" class="manhattan_plots">
-                
-            </div>
-        </div>
-        <div>
-            <h2>
-                Genome Association Results
-            </h2>
-        </div>
-
-        <table cellpadding="0" cellspacing="0" border="0" id="qtl_results" class="table table-hover table-striped table-bordered">
-            <thead>
-                <tr>
-                    <td>Index</td>
-                    <td>LOD Score</td>
-                    <td>Chr</td>
-                    <td>Mb</td>
-                    <td>Locus</td>
-                </tr>
-            </thead>
-            <tbody>
-                {% for marker in filtered_markers %}
-                    {% if marker.lod_score > lod_cutoff %}
-                    <tr>
-                        <td>{{loop.index}}</td>
-                        <td>{{marker.lod_score}}</td>
-                        <td>{{marker.chr}}</td>
-                        <td>{{marker.Mb}}</td>
-                        <td>{{marker.name}}</td>
-                    </tr>
-                    {% endif %}
-                {% endfor %}
-            </tbody>
-        </table>
-    </div>
-
-    <!-- End of body -->
-
-{% endblock %}
-
-{% block js %}  
-    <script>
-        js_data = {{ js_data | safe }}
-    </script>
-
-    <!--[if lt IE 9]>
-<!--        <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script>-->
-    <![endif]-->
-    <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_manhattan_plot.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/javascript/marker_regression.js"></script>
-
-    
-    <script type="text/javascript" charset="utf-8">
-        $(document).ready( function () {
-            console.time("Creating table");
-            $('#qtl_results').dataTable( {
-                //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
-                "sDom": "lTftipr",
-                "oTableTools": {
-                    "aButtons": [
-                        "copy",
-                        "print",
-                        {
-                            "sExtends":    "collection",
-                            "sButtonText": 'Save <span class="caret" />',
-                            "aButtons":    [ "csv", "xls", "pdf" ]
-                        }
-                    ],
-                    "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf"
-                },
-                "iDisplayLength": 50,
-                "bLengthChange": true,
-                "bDeferRender": true,
-                "bSortClasses": false
-            } );
-            console.timeEnd("Creating table");
-        });
-    </script>
+{% extends "base.html" %}

+{% block title %}Interval Mapping{% endblock %}

+{% block css %}

+<!--    <link rel="stylesheet" type="text/css" href="/static/new/css/interval_mapping.css" />-->

+    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />

+    <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />

+    <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />

+    <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />

+    <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />

+{% endblock %}

+{% block content %} <!-- Start of body -->

+

+    {{ header("Mapping",

+        '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}

+

+    <div class="container">

+        <div>

+            <h2>

+                Whole Genome Mapping

+            </h2>

+            <form id="exportform" action="export" method="post">

+              <input type="hidden" id="data" name="data" value="">

+              <input type="hidden" id="filename" name="filename" value="">

+              <input type="submit" id="export" value="Download SVG">

+            </form>

+<!--            <button id="export_pdf" class="btn">Export PDF</button>-->

+        </div>

+        <div id="chart_container">

+            <div class="qtlcharts" id="topchart">

+                

+            </div>

+        </div>

+        <div>

+            <h2>

+                Results

+            </h2>

+        </div>

+        <table cellpadding="0" cellspacing="0" border="0" id="qtl_results" class="table table-hover table-striped table-bordered">

+            <thead>

+                <tr>

+                    <td>Index</td>

+                    <td>LOD Score</td>

+                    <td>Chr</td>

+                    <td>Mb</td>

+                    <td>Locus</td>

+                </tr>

+            </thead>

+            <tbody>

+                {% for marker in filtered_markers %}

+                    {% if marker.lod_score > lod_cutoff %}

+                    <tr>

+                        <td>{{loop.index}}</td>

+                        <td>{{marker.lod_score}}</td>

+                        <td>{{marker.chr}}</td>

+                        <td>{{marker.Mb}}</td>

+                        <td>{{marker.name}}</td>

+                    </tr>

+                    {% endif %}

+                {% endfor %}

+            </tbody>

+        </table>

+    

+    </div>

+

+    <!-- End of body -->

+

+{% endblock %}

+

+{% block js %}  

+    <script>

+        js_data = {{ js_data | safe }}

+    </script>

+

+    <!--[if lt IE 9]>

+<!--        <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script>-->

+    <![endif]-->

+    <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>

+    <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>

+<!--    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.js"></script>

+    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/FileSaver.js/FileSaver.js"></script>

+    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/Blob.js/BlobBuilder.js"></script>

+    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.standard_fonts_metrics.js"></script>

+    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.from_html.js"></script>-->

+    <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>

+    <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_manhattan_plot.js"></script>

+    <script language="javascript" type="text/javascript" src="/static/new/javascript/manhattan_plot.js"></script>

+    <script language="javascript" type="text/javascript" src="/static/new/javascript/create_manhattan_plot.js"></script>

+    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>

+    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>

+    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>

+    <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>

+    <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>

+    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>

+

+    <script type="text/javascript" charset="utf-8">

+        $(document).ready( function () {

+            console.time("Creating table");

+            $('#qtl_results').dataTable( {

+                //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",

+                "sDom": "lTftipr",

+                "oTableTools": {

+                    "aButtons": [

+                        "copy",

+                        "print",

+                        {

+                            "sExtends":    "collection",

+                            "sButtonText": 'Save <span class="caret" />',

+                            "aButtons":    [ "csv", "xls", "pdf" ]

+                        }

+                    ],

+                    "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf"

+                },

+                "iDisplayLength": 50,

+                "bLengthChange": true,

+                "bDeferRender": true,

+                "bSortClasses": false

+            } );

+            console.timeEnd("Creating table");

+        });

+    </script>

 {% endblock %}
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index ae4adf25..f20d66ed 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -2,7 +2,6 @@
 {% block title %}Trait Data and Analysis{% endblock %}
 {% block css %}
     <link rel="stylesheet" type="text/css" href="/static/new/css/marker_regression.css" />
-    <link rel="stylesheet" type="text/css" href="/static/new/css/interval_mapping.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/bar_chart.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/box_plot.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 07f33d28..f8542c78 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -9,12 +9,14 @@
                 <li>
                     <a href="#pylmm" data-toggle="tab">pyLMM</a>
                 </li>
+                {% if dataset.group.species == 'human' %}
                 <li>
                     <a href="#plink" data-toggle="tab">PLINK</a>
                 </li>
                 <li>
                     <a href="#gemma" data-toggle="tab">GEMMA</a>
                 </li>
+                {% endif %}
                 <!--<li>
                     <a href="#pair_scan" data-toggle="tab">Pair Scan</a>
                 </li>-->
@@ -22,7 +24,7 @@
 
             <div class="tab-content">
                 <div class="tab-pane active" id="interval_mapping">
-                    <div class="control-group">
+<!--                <div class="control-group">
                         <label for="mapping_method" class="control-label">Mapping Method</label>
                         <div class="controls" id="mapping_method_choice">
                             <select name="mapping_method">
@@ -42,7 +44,7 @@
                                 {% endfor %}
                             </select>
                         </div>
-                    </div>
+                    </div>-->
     
                     <div class="control-group mapping_method_fields">
                         <label for="mapping_permutations" class="control-label">Permutations (n)</label>
@@ -75,7 +77,7 @@
                         </div>
                     </div>
 
-                    <div class="control-group mapping_method_fields">
+<!--                    <div class="control-group mapping_method_fields">
                         <label class="control-label"><b>Composite Mapping</b></label>
                         <div class="controls" id="use_composite_choice">                      
                             <label class="radio inline">
@@ -113,7 +115,7 @@
                             <input name="control_locus" placeholder="rs12345" id="control_locus"
                                     type="text" disabled />
                         </div>
-                    </div>
+                    </div>-->
 
                     <div class="control-group">
                         <div class="controls">
@@ -149,7 +151,7 @@
                         </div>
                     </div>
                     
-<!--                    <div class="control-group">
+<!--                <div class="control-group">
                         <label for="marker_reg_permutations" class="control-label">Permutations (n)</label>
                         <div class="controls">
                             <input name="num_perm" value="2000" type="text" />
@@ -169,6 +171,7 @@
                     
                 </div>
                 
+                {% if dataset.group.species == 'human' %}
                 <div class="tab-pane" id="plink">
                     <div class="control-group" id="display_all_div">
                         <label class="control-label">Display all</label>
@@ -250,9 +253,8 @@
                             </button>
                         </div>
                     </div>
-                    
                 </div>
-
+                {% endif %}
             </div>
         </div>
     </div>
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 2ee5bbca..12ff851e 100755
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -164,7 +164,6 @@ class UsersManager(object):
         print("Users are:", self.users)
 
 
-
 class UserManager(object):
     def __init__(self, kw):
         self.user_id = kw['user_id']
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 7a484898..6315260d 100755
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -260,6 +260,16 @@ def marker_regression_page():
 
     return rendered_template
 
+@app.route("/export", methods = ('POST',))
+def export():
+    print("request.form:", request.form)
+    svg_xml = request.form.get("data", "Invalid data")
+    filename = request.form.get("filename", "manhattan_plot_snp")
+    response = Response(svg_xml, mimetype="image/svg+xml")
+    response.headers["Content-Disposition"] = "attchment; filename=%s"%filename
+    return response
+
+
 @app.route("/interval_mapping", methods=('POST',))
 def interval_mapping_page():
     initial_start_vars = request.form