- SNP Browser is mostly complete; just need to test more and add SNP density chart if results exceed some number (5000 on GN1)

- Removed unnecessary options from the mode bar for the trait page Plotly figures and changed the default to highlight points the mouse is hovering over

- Changed some file/function names related to mapping, which previously were erroneously named "marker_regression"

14 files changed, 497 insertions, 121 deletions

diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 4708bf0a..c9052c83 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -34,6 +34,10 @@ PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=
 UCSC_BLAT = 'http://genome.ucsc.edu/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
 UTHSC_BLAT = 'http://ucscbrowser.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
 UTHSC_BLAT2 = 'http://ucscbrowserbeta.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
+GENOMEBROWSER_URL="https://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=%s"
+NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=%s"
+ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Transcript/Idhistory?t=%s"
+DBSNP = 'http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s'
 
 # Temporary storage (note that this TMPDIR can be set as an
 # environment variable - use utility.tools.TEMPDIR when you
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 21dd897a..09646f57 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -51,7 +51,7 @@ logger = utility.logger.getLogger(__name__ )
 #########################################
 #      Inteval Mapping Plot Page
 #########################################
-class MarkerRegression(object):
+class DisplayMappingResults(object):
     cMGraphInterval = 5
     GRAPH_MIN_WIDTH = 900
     GRAPH_MAX_WIDTH = 10000 # Don't set this too high
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 17089c13..b604b467 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -45,7 +45,7 @@ from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR
 import utility.logger
 logger = utility.logger.getLogger(__name__ )
 
-class MarkerRegression(object):
+class RunMapping(object):
 
     def __init__(self, start_vars, temp_uuid):
 
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index df68d4a0..393b8507 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -8,21 +8,27 @@ from utility.logger import getLogger
 logger = getLogger(__name__ )
 
 from base import species
+from base import webqtlConfig
 
 class SnpBrowser(object):
 
     MAXSNPRETURN = 5000
 
     def __init__(self, start_vars):
-        self.strain_list = get_browser_sample_list()
+        self.strain_lists = get_browser_sample_lists()
         self.initialize_parameters(start_vars)
 
         if self.first_run == "false":
             if self.limit_strains == "true":
                 self.header_fields = get_header_list(self.variant_type, self.chosen_strains)
             else:
-                self.header_fields = get_header_list(self.variant_type, self.strain_list)
-            self.filtered_results = self.get_table_results()
+                self.header_fields = get_header_list(self.variant_type, self.strain_lists, self.species_name)
+            self.filtered_results = self.get_browser_results()
+
+            if len(self.filtered_results) <= 5000:
+                self.table_rows = self.get_table_rows()
+            else:
+                self.table_rows = []
 
     def initialize_parameters(self, start_vars):
         self.first_run = "true"
@@ -39,7 +45,7 @@ class SnpBrowser(object):
                 self.species_id = 0 #Using this to indicate "All Species"
  
             #ZS: Currently this is just assuming mouse for determining the chromosomes. 
-            #    This logic may have to change depending upon what other species are added or how we want to deal with an "All Species" option
+            #    This logic may have to change depending upon what other species are added
             self.chr_list = []
             species_ob = species.TheSpecies(species_name="Mouse")
             for key in species_ob.chromosomes.chromosomes:
@@ -61,7 +67,14 @@ class SnpBrowser(object):
                 self.limit_strains = "true"
             else:
                 self.limit_strains = "false"
-            self.chosen_strains = start_vars['chosen_strains'].split(",")
+            self.chosen_strains_mouse = start_vars['chosen_strains_mouse'].split(",")
+            self.chosen_strains_rat = start_vars['chosen_strains_rat'].split(",")
+
+            if self.species_id == 1:
+                self.chosen_strains = self.chosen_strains_mouse
+            elif self.species_id == 2:
+                self.chosen_strains = self.chosen_strains_rat
+
             self.domain = start_vars['domain']
             self.function = start_vars['function']
             self.source = start_vars['source']
@@ -89,15 +102,19 @@ class SnpBrowser(object):
 
             self.limit_strains = "true"
 
-            self.chosen_strains = ["C57BL/6J",
-                                   "DBA/2J",
-                                   "A/J",
-                                   "129S1/SvImJ",
-                                   "NOD/ShiLtJ",
-                                   "NZO/HlLtJ",
-                                   "WSB/EiJ",
-                                   "PWK/PhJ",
-                                   "CAST/EiJ"]
+            self.chosen_strains_mouse = ["C57BL/6J",
+                                         "DBA/2J",
+                                         "A/J",
+                                         "129S1/SvImJ",
+                                         "NOD/ShiLtJ",
+                                         "NZO/HlLtJ",
+                                         "WSB/EiJ",
+                                         "PWK/PhJ",
+                                         "CAST/EiJ"]
+            self.chosen_strains_rat = ["F344"]
+            self.chosen_strains_all = self.chosen_strains_mouse + self.chosen_strains_rat
+
+            self.chosen_strains = self.chosen_strains_mouse
             
             self.domain = "All"
             self.function = "All"
@@ -108,11 +125,14 @@ class SnpBrowser(object):
             self.redundant = "false"
             self.diff_alleles = "true"
 
-    def get_table_results(self):
+    def get_browser_results(self):
         self.snp_list = None
 
         if self.gene_name != "":
-            query = "SELECT geneSymbol, chromosome, txStart, txEnd FROM GeneList WHERE SpeciesId = %s AND geneSymbol = %s" % (self.species_id, self.gene_name)
+            if self.species_id != 0:
+                query = "SELECT geneSymbol, chromosome, txStart, txEnd FROM GeneList WHERE SpeciesId = %s AND geneSymbol = '%s'" % (self.species_id, self.gene_name)
+            else:
+                query = "SELECT geneSymbol, chromosome, txStart, txEnd FROM GeneList WHERE geneSymbol = '%s'" % (self.gene_name)
             result = g.db.execute(query).fetchone()
             if result:
                 self.gene_name, self.chr, self.start_mb, self.end_mb = result
@@ -120,9 +140,12 @@ class SnpBrowser(object):
                 result_snp = None
                 if self.variant_type == "SNP":
                     if self.gene_name[:2] == "rs":
-                        query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll WHERE Rs = %s" % self.gene_name
+                        query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll WHERE Rs = '%s'" % self.gene_name
                     else:
-                        query = "SELECT Id, Chromosome, Position, Position+0.000001 ForM SnpAll where SpeciesId = %s AND SnpName = %s" % (self.species_id, self.gene_name)
+                        if self.species_id != 0:
+                            query = "SELECT Id, Chromosome, Position, Position+0.000001 ForM SnpAll where SpeciesId = %s AND SnpName = '%s'" % (self.species_id, self.gene_name)
+                        else:
+                            query = "SELECT Id, Chromosome, Position, Position+0.000001 ForM SnpAll where SnpName = '%s'" % (self.gene_name)
                     result_snp = g.db.execute(query).fetchall()
                     if result_snp:
                         self.snp_list = [item[0] for item in result_snp]
@@ -133,7 +156,10 @@ class SnpBrowser(object):
                         return
                 elif self.variant_type == "InDel":
                     if self.gene_name[0] == "I":
-                        query = "SELECT Id, Chromosome, Mb_start, Mb_end FROM IndelAll WHERE SpeciesId = %s AND Name = %s" % (self.species_id, self.gene_name)
+                        if self.species_id != 0:
+                            query = "SELECT Id, Chromosome, Mb_start, Mb_end FROM IndelAll WHERE SpeciesId = %s AND Name = '%s'" % (self.species_id, self.gene_name)
+                        else:
+                            query = "SELECT Id, Chromosome, Mb_start, Mb_end FROM IndelAll WHERE Name = '%s'" % (self.gene_name)
                         result_snp = g.db.execute(query).fetchall()
                     if result_snp:
                         self.snp_list = [item[0] for item in result_snp]
@@ -144,29 +170,59 @@ class SnpBrowser(object):
                         return
 
         if self.variant_type == "SNP":
-            query = """
+            mouse_query = """
                        SELECT
-                               a.*, b.*
+                           a.*, b.*
                        FROM
-                               SnpAll a, SnpPattern b
+                           SnpAll a, SnpPattern b
                        WHERE
-                               a.SpeciesId = %s AND a.Chromosome = '%s' AND
-                               a.Position >= %.6f AND a.Position < %.6f AND
-                               a.Id = b.SnpId
+                           a.SpeciesId = %s AND a.Chromosome = '%s' AND
+                           a.Position >= %.6f AND a.Position < %.6f AND
+                           a.Id = b.SnpId
                        ORDER BY a.Position
                     """ % (self.species_id, self.chr, self.start_mb, self.end_mb)
-        elif self.variant_type == "InDel":
-            query = """
+
+            rat_query = """
                        SELECT
-                               DISTINCT a.Name, a.Chromosome, a.SourceId, a.Mb_start, a.Mb_end, a.Strand, a.Type, a.Size, a.InDelSequence, b.Name
+                           a.*, b.*
                        FROM
-                               IndelAll a, SnpSource b
+                           SnpAll a, RatSnpPattern b
                        WHERE
+                           a.SpeciesId = %s AND a.Chromosome = '%s' AND
+                           a.Position >= %.6f AND a.Position < %.6f AND
+                           a.Id = b.SnpId
+                       ORDER BY a.Position
+                    """ % (self.species_id, self.chr, self.start_mb, self.end_mb)
+            if self.species_id == 1:
+                query = mouse_query
+            elif self.species_id == 2:
+                query = rat_query
+
+        elif self.variant_type == "InDel":
+            if species_id != 0:
+                query = """
+                           SELECT
+                               DISTINCT a.Name, a.Chromosome, a.SourceId, a.Mb_start, a.Mb_end, a.Strand, a.Type, a.Size, a.InDelSequence, b.Name
+                           FROM
+                               IndelAll a, SnpSource b
+                           WHERE
                                a.SpeciesId = '%s' AND a.Chromosome = '%s' AND
                                a.Mb_start >= %2.6f AND a.Mb_start < (%2.6f+.0010) AND
                                b.Id = a.SourceId
-                       ORDER BY a.Mb_start
-                    """ % (self.species_id, self.chr, self.start_mb, self.end_mb)
+                           ORDER BY a.Mb_start
+                        """ % (self.species_id, self.chr, self.start_mb, self.end_mb)
+            else:
+                query = """
+                           SELECT
+                               DISTINCT a.Name, a.Chromosome, a.SourceId, a.Mb_start, a.Mb_end, a.Strand, a.Type, a.Size, a.InDelSequence, b.Name
+                           FROM
+                               IndelAll a, SnpSource b
+                           WHERE
+                               a.Chromosome = '%s' AND
+                               a.Mb_start >= %2.6f AND a.Mb_start < (%2.6f+.0010) AND
+                               b.Id = a.SourceId
+                           ORDER BY a.Mb_start
+                        """ % (self.chr, self.start_mb, self.end_mb)
 
         results_all = g.db.execute(query).fetchall()
 
@@ -179,7 +235,7 @@ class SnpBrowser(object):
 
         if self.limit_strains == "true" and len(self.chosen_strains) > 0:
             for item in self.chosen_strains:
-                index = self.strain_list.index(item)
+                index = self.strain_lists[self.species_name.lower()].index(item)
                 strain_index_list.append(index)
 
         for seq, result in enumerate(results):
@@ -189,11 +245,17 @@ class SnpBrowser(object):
                 display_strains = []
                 snp_id, species_id, snp_name, rs, chr, mb, mb_2016, alleles, snp_source, conservation_score = result[:10]
                 effect_list = result[10:26]
-                self.allele_list = result[27:]
+                if self.species_id == 1:
+                    self.allele_list = result[27:]
+                elif self.species_id == 2:
+                    self.allele_list = result[28:]
 
                 if self.limit_strains == "true" and len(self.chosen_strains) > 0:
                     for index in strain_index_list:
-                        display_strains.append(result[27+index])
+                        if self.species_id == 1:
+                            display_strains.append(result[27+index])
+                        elif self.species_id == 2:
+                            display_strains.append(result[28+index])
                     self.allele_list = display_strains
 
                 effect_info_dict = get_effect_info(effect_list)
@@ -266,6 +328,150 @@ class SnpBrowser(object):
 
         return filtered_results
 
+    def get_table_rows(self):
+        """ Take results and put them into the order and format necessary for the tables rows """
+
+        if self.variant_type == "SNP":
+            gene_name_list = []
+            for item in self.filtered_results:
+                if item[5] and item[5] != "":
+                    gene_name = item[5][1]
+                    # eliminate duplicate gene_name
+                    if gene_name and (gene_name not in gene_name_list):
+                        gene_name_list.append(gene_name)
+            if len(gene_name_list) > 0:
+                gene_id_name_dict = get_gene_id_name_dict(gene_name_list)
+
+        the_rows = []
+        for result in self.filtered_results:
+            this_row = []
+            if self.variant_type == "SNP":
+                snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, function, function_details, snp_source, conservation_score, snp_id = result[:14]
+                allele_value_list = result[14:]
+                if rs:
+                    snp_url = webqtlConfig.DBSNP % (rs)
+                    snp_name = rs
+                else:
+                    rs = ""
+                    start_bp = int(mb*1000000 - 100)
+                    end_bp = int(mb*1000000 + 100)
+                    position_info = "chr%s:%d-%d" % (chr, start_bp, end_bp)
+                    if self.species_id == 2:
+                        snp_url = webqtlConfig.GENOMEBROWSER_URL % ("rn6", position_info)
+                    else:
+                        snp_url = webqtlConfig.GENOMEBROWSER_URL % ("mm10", position_info)
+
+                mb = float(mb)
+                mb_formatted = "%2.6f" % mb
+
+                if snp_source == "Sanger/UCLA":
+                    source_url_1 = "http://www.sanger.ac.uk/resources/mouse/genomes/"
+                    source_url_2 = "http://mouse.cs.ucla.edu/mousehapmap/beta/wellcome.html"
+                    source_urls = [source_url_1, source_url_2]
+                else:
+                    source_urls = []
+
+                if not conservation_score:
+                    conservation_score = ""
+
+                if gene:
+                    gene_name = gene[1]
+                    # if gene_name has related gene_id, use gene_id for NCBI search
+                    if (gene_name in gene_id_name_dict) and (gene_id_name_dict[gene_name] != None and gene_id_name_dict[gene_name] != ""):
+                        gene_id = gene_id_name_dict[gene[1]]
+                        gene_link = webqtlConfig.NCBI_LOCUSID % gene_id
+                    else:
+                        gene_link = "http://www.ncbi.nln.nih.gov/entrez/query.fcgi?CMD=search&DB=gene&term=%s" % gene_name
+                else:
+                    gene_name = ""
+                    gene_link = ""
+
+                if transcript:
+                    transcript_link = webqtlConfig.ENSEMBLETRANSCRIPT_URL % (transcript)
+                else:
+                    transcript_link = ""
+
+                if exon:
+                    exon = exon[1] # exon[0] is exon_id, exon[1] is exon_rank
+                else:
+                    exon = "1"
+
+                if domain:
+                    domain_1 = domain[0]
+                    domain_2 = domain[1]
+                    if domain_1 == "Exon":
+                        domain_1 = domain_1 + " " + exon
+
+                function_list = []
+                if function_details:
+                    function_list = string.split(string.strip(function_details), ",")
+                    function_list = map(string.strip, function_list)
+                    function_list[0] = function_list[0].title()
+                    function_details = ", ".join(item for item in function_list)
+                    function_details = function_details.replace("_", " ")
+                    function_details = function_details.replace("/", " -> ")
+                    if function_details == "Biotype: Protein Coding":
+                        function_details = function_details + ", Coding Region Unknown"
+                    
+                #[snp_href, chr, mb_formatted, alleles, snp_source_cell, conservation_score, gene_name_cell, transcript_href, exon, domain_1, domain_2, function, function_details]
+
+                base_color_dict = {"A": "#C33232", "C": "#1569C7", "T": "#CFCF32", "G": "#32C332", 
+                                   "t": "#FF6", "c": "#5CB3FF", "a": "#F66", "g": "#CF9", ":": "#FFFFFF", "-": "#FFFFFF", "?": "#FFFFFF"}
+
+
+                the_bases = []
+                for j, item in enumerate(allele_value_list):
+                    if item:
+                        this_base = [item, base_color_dict[item]]
+                    else:
+                        this_base = ""
+
+                    the_bases.append(this_base)
+
+                this_row = {
+                    "rs": rs,
+                    "snp_url": snp_url,
+                    "snp_name": snp_name,
+                    "chr": chr,
+                    "mb_formatted": mb_formatted,
+                    "alleles": alleles,
+                    "snp_source": snp_source,
+                    "source_urls": source_urls,
+                    "conservation_score": conservation_score,
+                    "gene_name": gene_name,
+                    "gene_link": gene_link,
+                    "transcript": transcript,
+                    "transcript_link": transcript_link,
+                    "exon": exon,
+                    "domain_1": domain_1,
+                    "domain_2": domain_2,
+                    "function": function, 
+                    "function_details": function_details,
+                    "allele_value_list": the_bases
+                }
+
+            elif self.variant_type == "InDel":
+                indel_name, indel_chr, indel_mb_s, indel_mb_e, indel_strand, indel_type, indel_size, indel_sequence, source_name = result
+                this_row = {
+                    "indel_name": indel_name,
+                    "indel_chr": indel_chr,
+                    "indel_mb_s": indel_mb_s,
+                    "indel_mb_e": indel_mb_e,
+                    "indel_strand": indel_strand,
+                    "indel_type": indel_type,
+                    "indel_size": indel_size,
+                    "indel_sequence": indel_sequence,
+                    "source_name": source_name
+                }
+                #this_row = [indel_name, indel_chr, indel_mb_s, indel_mb_e, indel_strand, indel_type, indel_size, indel_sequence, source_name]
+            else:
+                this_row = {}
+
+            the_rows.append(this_row)
+
+        return the_rows
+                
+
     def include_record(self, domain, function, snp_source, conservation_score):
         """ Decide whether to add this record """
 
@@ -304,7 +510,10 @@ class SnpBrowser(object):
                     function_satisfied = False
             else:
                 function_satisfied = False
-                if function.startswith(self.function):
+                if self.function != "All":
+                    if function.startswith(self.function):
+                        function_satisfied = True
+                else:
                     function_satisfied = True
         else:
             if self.function != "All":
@@ -358,23 +567,39 @@ class SnpBrowser(object):
 
         return domain_satisfied and function_satisfied and source_satisfied and score_satisfied and different_alleles_satisfied
 
-def get_browser_sample_list(species_id=1):
-    sample_list = []
+def get_browser_sample_lists(species_id=1):
+    strain_lists = {}
+    mouse_strain_list = []
     query = "SHOW COLUMNS FROM SnpPattern;"
     results = g.db.execute(query).fetchall();
     for result in results[1:]:
-        sample_list.append(result[0])
+        mouse_strain_list.append(result[0])
+
+    rat_strain_list = []
+    query = "SHOW COLUMNS FROM RatSnpPattern;"
+    results = g.db.execute(query).fetchall();
+    for result in results[2:]:
+        rat_strain_list.append(result[0])
+
+    strain_lists['mouse'] = mouse_strain_list
+    strain_lists['rat'] = rat_strain_list
 
-    return sample_list
+    return strain_lists
 
-def get_header_list(variant_type, strain_list):
+def get_header_list(variant_type, strains, species = None):
+    if species == "Mouse":
+        strain_list = strains['mouse']
+    elif species == "Rat":
+        strain_list = strains['rat']
+    else:
+        strain_list = strains
+
+    header_fields = []
     if variant_type == "SNP":
-        header_fields = ['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'Source', 'ConScore', 'Gene', 'Transcript', 'Exon', 'Domain 1', 'Domain 2', 'Function', 'Details']
-        header_fields.extend(strain_list)
+        header_fields.append(['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'Source', 'ConScore', 'Gene', 'Transcript', 'Exon', 'Domain 1', 'Domain 2', 'Function', 'Details'])
+        header_fields.append(strain_list)
     elif variant_type == "InDel":
         header_fields = ['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source']
-    else:
-        header_fields = []
 
     return header_fields
 
@@ -454,7 +679,7 @@ def get_effect_info(effect_list):
                 effect_detail_list = get_effect_details_by_category(effect_name='Splice Site', effect_value=splice_site)
                 effect_info_dict[domain] = effect_detail_list
             if nonsplice_site:
-                domain = "Downstream"
+                domain = "Nonsplice Site"
                 effect_detail_list = get_effect_details_by_category(effect_name='Nonsplice Site', effect_value=nonsplice_site)
                 effect_info_dict[domain] = effect_detail_list
         # get gene, transcript_list, and exon info
@@ -498,3 +723,29 @@ def get_effect_info(effect_list):
             effect_info_dict[domain] = effect_detail_list
 
     return effect_info_dict
+
+def get_gene_id_name_dict(gene_name_list):
+    gene_id_name_dict = {}
+    if len(gene_name_list) == 0:
+        return ""
+    gene_name_str_list = ["'" + gene_name + "'" for gene_name in gene_name_list]
+    gene_name_str = string.join(gene_name_str_list, ",")
+
+    query = """
+                SELECT
+                        geneId, geneSymbol
+                FROM
+                        GeneList
+                WHERE
+                        SpeciesId = 1 AND geneSymbol in (%s)
+            """ % gene_name_str
+
+    results = g.db.execute(query).fetchall()
+
+    if len(results) > 0:
+        for item in results:
+            gene_id_name_dict[item[1]] = item[0]
+    else:
+        pass
+
+    return gene_id_name_dict
diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index 1e9fd4df..135a7643 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -8,4 +8,8 @@ tr .outlier {
 
 div.sample_group {
     overflow: auto; # needed because it contains float dataTable wrapper
+}
+
+.js-plotly-plot .plotly .modebar {
+  left: 100px;
 }
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/css/snp_browser.css b/wqflask/wqflask/static/new/css/snp_browser.css
new file mode 100644
index 00000000..c1adaf20
--- /dev/null
+++ b/wqflask/wqflask/static/new/css/snp_browser.css
@@ -0,0 +1,22 @@
+.form_group {
+    margin-bottom 5px;
+}
+
+table.dataTable thead th {
+  vertical-align: bottom;
+}
+
+table.dataTable thead .sorting,
+table.dataTable thead .sorting_asc,
+table.dataTable thead .sorting_desc,
+table.dataTable thead .sorting_asc_disabled,
+table.dataTable thead .sorting_desc_disabled {
+  background-repeat: no-repeat;
+  background-position: bottom right;
+}
+
+table.dataTable thead th{
+  border-right: 1px solid white;
+  color: white;
+  background-color: royalblue;
+}
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
index be0b96a1..a74c99d3 100644
--- a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
+++ b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
@@ -23,7 +23,8 @@ var layout = {
         visible: true,
         linecolor: 'black',
         linewidth: 1,
-    }
+    },
+    hovermode: "closest"
 }
 
 cofactor1_dict = {}
diff --git a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
index ad06ff6a..1585b0ad 100644
--- a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
+++ b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
@@ -183,7 +183,8 @@
             visible: true,
             linecolor: 'black',
             linewidth: 1,
-        }
+        },
+        hovermode: "closest"
     }
 
     var primary_trace = {
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index a0a98437..a3edd0e6 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -776,6 +776,12 @@
         sample_group_list = [js_data.sample_group_types['samples_primary']]
     }
 
+    // Define Plotly Options (for the options bar at the top of each figure)
+
+    root.modebar_options = {
+      modeBarButtonsToRemove:['hoverClosest', 'hoverCompare', 'hoverClosestCartesian', 'hoverCompareCartesian', 'lasso2d', 'toggleSpikelines']
+    }
+
     // Bar Chart
 
     root.errors_exist = get_sample_errors(sample_lists[0])[1]
@@ -822,7 +828,13 @@
             range_bottom = 0
         }
     }
-    if (get_sample_vals(sample_lists[0]).length < 256) {
+
+    total_sample_count = 0
+    for (i = 0, i < sample_lists.length; i++) {
+      total_sample_count += get_sample_vals(sample_lists[i]).length
+    }
+
+    if (total_sample_count < 256) {
       bar_chart_width = 25 * get_sample_vals(sample_lists[0]).length
 
       var layout = {
@@ -839,7 +851,7 @@
         }
       };
       root.bar_layout = layout
-      Plotly.newPlot('bar_chart', root.bar_data, root.bar_layout)
+      Plotly.newPlot('bar_chart', root.bar_data, root.bar_layout, root.modebar_options)
     }
 
     if (full_sample_lists.length > 1) {
@@ -947,14 +959,14 @@
       data: box_data,
       layout: root.box_layout
     }
-    Plotly.newPlot('box_plot', obj);
+    Plotly.newPlot('box_plot', obj, root.modebar_options);
 
     // Violin Plot
 
     if (full_sample_lists.length > 1) {
         root.violin_layout = {
           title: "Violin Plot",
-          xaxis: {
+          yaxis: {
             range: [range_bottom, range_top],
             zeroline: false
           },
@@ -963,12 +975,12 @@
           margin: {
                 l: 50,
                 r: 30,
-                t: 30,
+                t: 80,
                 b: 80
           }
         };
         var trace1 = {
-            x: get_sample_vals(full_sample_lists[2]),
+            y: get_sample_vals(full_sample_lists[2]),
             type: 'violin',
             points: 'none',
             box: {
@@ -981,10 +993,10 @@
               visible: true
             },
             name: sample_group_list[2],
-            y0: sample_group_list[2]
+            x0: sample_group_list[2]
         }
         var trace2 = {
-            x: get_sample_vals(full_sample_lists[1]),
+            y: get_sample_vals(full_sample_lists[1]),
             type: 'violin',
             points: 'none',
             box: {
@@ -997,10 +1009,10 @@
               visible: true
             },
             name: sample_group_list[1],
-            y0: sample_group_list[1]
+            x0: sample_group_list[1]
         }
         var trace3 = {
-            x: get_sample_vals(full_sample_lists[0]),
+            y: get_sample_vals(full_sample_lists[0]),
             type: 'violin',
             points: 'none',
             box: {
@@ -1013,13 +1025,13 @@
               visible: true
             },
             name: sample_group_list[0],
-            y0: sample_group_list[0]
+            x0: sample_group_list[0]
         }
         violin_data = [trace1, trace2, trace3]
     } else {
         root.violin_layout = {
           title: "Violin Plot",
-          xaxis: {
+          yaxis: {
             range: [range_bottom, range_top],
             zeroline: false
           },
@@ -1028,13 +1040,13 @@
           margin: {
                 l: 50,
                 r: 30,
-                t: 30,
+                t: 80,
                 b: 80
           }
         };
         violin_data = [
           {
-            x: get_sample_vals(full_sample_lists[0]),
+            y: get_sample_vals(full_sample_lists[0]),
             type: 'violin',
             points: 'none',
             box: {
@@ -1047,7 +1059,7 @@
               visible: true
             },
             name: sample_group_list[0],
-            y0: sample_group_list[0]
+            x0: sample_group_list[0]
           }
         ]
     }
@@ -1057,7 +1069,7 @@
       layout: root.violin_layout
     }
 
-    Plotly.plot('violin_plot', obj)
+    Plotly.plot('violin_plot', obj, root.modebar_options)
 
     // Histogram
     var hist_trace = {
@@ -1077,7 +1089,7 @@
           b: 60
       }
     };
-    Plotly.newPlot('histogram', data, layout)
+    Plotly.newPlot('histogram', data, layout, root.modebar_options)
 
     update_histogram_width()
 
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 3df4c81a..81c04db5 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -52,6 +52,9 @@
                             </a>
                         </li>
                         <li class="">
+                            <a href="/snp_browser">SNP Browser</a>
+                        </li>
+                        <li class="">
                             <a href="/help">Help</a>
                         </li>
                         <li class="">
diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html
index 43488c75..99fa4a89 100644
--- a/wqflask/wqflask/templates/loading.html
+++ b/wqflask/wqflask/templates/loading.html
@@ -1,6 +1,6 @@
 <title>Loading Mapping Results</title>
 <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.css" />
-<form method="post" action="/marker_regression" name="loading_form" id="loading_form" class="form-horizontal">
+<form method="post" action="/run_mapping" name="loading_form" id="loading_form" class="form-horizontal">
   {% for key, value in start_vars.iteritems() %}
   <input type="hidden" name="{{ key }}" value="{{ value }}">
   {% endfor %}
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/mapping_results.html
index fd083983..5fb2c95e 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -10,7 +10,7 @@
 {% from "base_macro.html" import header %}
 {% block content %}
     <div class="container">
-        <form method="post" target="_blank" action="/marker_regression" name="marker_regression" id="marker_regression_form">
+        <form method="post" target="_blank" action="/run_mapping" name="marker_regression" id="marker_regression_form">
         <input type="hidden" name="temp_uuid" value="{{ temp_uuid }}">
         <input type="hidden" name="trait_id" value="{{ this_trait.name }}">
         <input type="hidden" name="dataset" value="{{ dataset.name }}">
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index cbce1449..578bd2fc 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -9,9 +9,10 @@
   <div class="container-fluid">
     <h2>Variant Browser <a class="btn btn-primary" href="http://genenetwork.org/snpbrowser.html" role="button">Info</a></h2>
 
-    <div class="container" style="border-style: double; position: relative; width: 60%; padding-top: 10px; padding-right: 40px;">
+    <div class="container" style="border-style: double; position: relative; width: 950px; padding-top: 10px; padding-right: 40px;">
       <form id="snp_browser_form" method="get" action="/snp_browser">
-        <input type="hidden" name="chosen_strains">
+        <input type="hidden" name="chosen_strains_mouse" value="{{ chosen_strains_mouse|join(",") }}">
+        <input type="hidden" name="chosen_strains_rat" value="{{ chosen_strains_rat|join(",") }}">
         <div class="col-xs-4" style="padding-left: 0px;">
           <div class="form-group row" style="margin-bottom: 5px;">
             <label for="snp_or_indel" style="text-align: right;" class="col-xs-4 col-form-label"><b>Type:</b></label>
@@ -25,17 +26,16 @@
           <div class="form-group row" style="margin-bottom: 5px;">
             <label for="species" style="text-align: right;" class="col-xs-4 col-form-label"><b>Species:</b></label>
             <div class="col-xs-8">
-              <select name="species">
-                <option value="Mouse" selected>Mouse</option>
-                <option value="Rat">Rat</option>
-                <option value="All" selected>All</option>
+              <select id="species_select" name="species">
+                <option value="Mouse" {% if species_name == "Mouse" %}selected{% endif %}>Mouse</option>
+                <option value="Rat" {% if species_name == "Rat" %}selected{% endif %}>Rat</option>
               </select>
             </div>
           </div>
           <div class="form-group row" style="margin-bottom: 5px;">
             <label for="gene_or_id" style="text-align: right;" class="col-xs-4 col-form-label"><b>Gene or ID:</b></label>
             <div class="col-xs-8">
-              <input type="text" name="gene_name" size="12">
+              <input type="text" name="gene_name" size="12" value="{{ gene_name }}">
             </div>
           </div>
           <div class="form-group row">
@@ -75,15 +75,16 @@
           <div class="form-group row" style="margin-bottom: 10px;">
             <label for="strains" style="text-align: right;" class="col-xs-4 col-form-label"><b>Strains:</b></label>
             <div class="col-xs-8">
-              <select name="strains" style="width: 70%;">
-                <optgroup label="Mouse">
-                  {% for strain in strain_list[:-1] %}
+              <select id="strain_select" name="strains" style="width: 70%;">
+                  {% if species_name == "Mouse" %}
+                  {% for strain in strain_lists['mouse'] %}
                   <option value="{{ strain }}" {% if loop.index == 1 %}selected{% endif %}>{{ strain }}</option>
                   {% endfor %}
-                </optgroup>
-                <optgroup label="Rat">
-                  <option value="BN">BN</option>
-                </optgroup>
+                  {% elif species_name == "Rat" %}
+                  {% for strain in strain_lists['rat'] %}
+                  <option value="{{ strain }}" {% if loop.index == 1 %}selected{% endif %}>{{ strain }}</option>
+                  {% endfor %}
+                  {% endif %}
               </select>
               <div style="float: right; line-height: 20px;">
                 <input class="btn btn-primary" type="button" name="add_strain" value="Add" style="vertical-align: middle;">
@@ -177,32 +178,57 @@
       </form>
     </div>
 
+    <div style="margin-top: 20px;">
     {% if filtered_results is defined %}
-    <table class="cell-border nowrap" id="results_table" style="float: left;">
+    {% if filtered_results|length > 5000 %}
+    There are more than 5000 results. Consider limiting your search to a smaller range.
+    {% else %}
+    <table class="dataTable cell-border nowrap" id="results_table" style="float: left;">
       <thead>
         <tr>
           <th></th>
+          {% if header_fields|length == 2 %}
+          {% for header in header_fields[0] %}
+          <th data-export="{{ header }}">{{ header }}</th>
+          {% endfor %}
+          {% for strain in header_fields[1] %}
+          <th data-export="{{ strain }}" style="align: center; text-align: center; line-height: 15px;">{% for letter in strain %}<div style="transform: rotate(90deg);">{{ letter }}</div>{% endfor %}</th>
+          {% endfor %}
+          {% else %}
           {% for header in header_fields %}
           <th data-export="{{ header }}">{{ header }}</th>
           {% endfor %}
+          {% endif %}
         </tr>
       </thead>
       <tbody>
-        {% for result in filtered_results %}
+        {% for row in table_rows %}
         <tr>
           <td><input type="checkbox" name="trait_check"></td>
           <td align="right">{{ loop.index }}</td>
-          {% for item in result %}
-          {% if loop.index > 1 %}
-          <td>{{ item }}</td>
-          {% endif %}
+          <td>{% if row.rs != "" %}<b><a href="{{ row.snp_url }}">{{ row.snp_name }}</a></b>{% else %}<a href="{{ row.snp_url }}">{{ row.snp_name }}</a>{% endif %}</td>
+          <td>{{ row.chr }}</td>
+          <td>{{ row.mb_formatted }}</td>
+          <td>{{ row.alleles }}</td>
+          <td>{% if row.snp_source == "Sanger/UCLA" %}<a href="{{ row.source_urls[0] }}">Sanger</a>/<a href="{{ row.source_urls[1] }}">UCLA</a>{% else %}{{ row.snp_source }}{% endif %}</td>
+          <td>{{ row.conservation_score }}</td>
+          <td>{% if row.gene_name != "" %}<i>{{ row.gene_name }}</i><br><a href="{{ row.gene_link }}">NCBI</a>{% else %}{% endif %}</td>
+          <td><a href="{{ row.transcript_link }}">{{ row.transcript }}</a></td>
+          <td>{{ row.exon }}</td>
+          <td>{{ row.domain_1 }}</td>
+          <td>{{ row.domain_2 }}</td>
+          <td>{{ row.function }}</td>
+          <td>{{ row.function_details }}</td>
+          {% for item in row.allele_value_list %}
+          <td style="background-color: {{ item[1] }};">{{ item[0] }}</td>
           {% endfor %}
         </tr>
         {% endfor %}
       </tbody>
     </table>
+    {% endif %}
     {% endif %}     
-
+    </div>
   </div>
 
 {% endblock %}
@@ -213,6 +239,18 @@
 
     {% if filtered_results is defined %}
     $("#results_table").DataTable( {
+      {% if variant_type == "SNP" %}
+      "columnDefs": [ {
+        "targets": [0, {% for n in range(15, 15 + allele_list|length) %}, {{ n }}{% endfor %}],
+        "orderable": false
+       } ],
+      {% else %}
+      "columnDefs": [ {
+        "targets": 0,
+        "orderable": false
+       } ],
+      {% endif %}
+      "order": [[1, "asc" ]],
       "sDom": "tir",
       "iDisplayLength": -1,
       "autoWidth": true,
@@ -220,14 +258,74 @@
     });
     {% endif %}
 
+    $("#species_select").change(function() {
+        this_species = $(this).val();
+        $("#strain_select").empty()
+        $("#chosen_strains_select").empty()
+
+        if (this_species == "Mouse") {
+            {% for strain in strain_lists["mouse"] %}
+            var option = $('<option></option>').attr("value", "{{ strain }}").text("{{ strain }}");
+            $("select[name=strains]").append(option);
+            {% endfor %}
+
+            chosen_strains = $("input[name=chosen_strains_mouse]").val().split(",")
+        } else if (this_species == "Rat") {
+            {% for strain in strain_lists["rat"] %}
+            var option = $('<option></option>').attr("value", "{{ strain }}").text("{{ strain }}");
+            $("select[name=strains]").append(option);
+            {% endfor %}
+
+            chosen_strains = $("input[name=chosen_strains_rat]").val().split(",")
+        }
+
+        for (i=0; i < chosen_strains.length; i++) {
+            var option = $('<option></option>').attr("value", chosen_strains[i]).text(chosen_strains[i]);
+            $("#chosen_strains_select").append(option)
+        }
+    });
+
     $("input[name=add_strain]").click(function() {
       var selected_strain = $("select[name=strains] option:selected").val();
       $("#chosen_strains_select").append("<option value='" + selected_strain + "'>" + selected_strain + "</option>");
+
+      var current_species = $("#species_select").val();
+      if (current_species == "Mouse") {
+          stored_strains = $("input[name=chosen_strains_mouse]").val().split(",")
+          stored_strains.push(selected_strain)
+          $("input[name=chosen_strains_mouse]").val(stored_strains.join(","))
+      } else if (current_species == "Rat") {
+          stored_strains = $("input[name=chosen_strains_rat]").val().split(",")
+          stored_strains.push(selected_strain)
+          $("input[name=chosen_strains_rat]").val(stored_strains.join(","))
+      }
     });
 
     $("input[name=remove_strain]").click(function() {
       var selected_strain = $("#chosen_strains_select option:selected").val();
       $("#chosen_strains_select option[value='" + selected_strain + "']").remove();
+
+      var current_species = $("#species_select").val();
+
+      if (current_species == "Mouse") {
+          stored_strains = $("input[name=chosen_strains_mouse]").val().split(",")
+          for (i=0; i < stored_strains.length; i++) {
+              if (stored_strains[i] == selected_strain) {
+                  stored_strains.splice(i, 1);
+                  break;
+              }
+          }
+          $("input[name=chosen_strains_mouse]").val(stored_strains.join(","))
+      } else if (current_species == "Rat") {
+          stored_strains = $("input[name=chosen_strains_rat]").val().split(",")
+          for (i=0; i < stored_strains.length; i++) {
+              if (stored_strains[i] == selected_strain) {
+                  stored_strains.splice(i, 1);
+                  break;
+              }
+          }
+          $("input[name=chosen_strains_rat]").val(stored_strains.join(","))
+      }
     });
 
     $("#snp_browser_form").submit(function() {
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index fdb80040..27e6eed1 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -44,8 +44,8 @@ from wqflask.show_trait import show_trait
 from wqflask.show_trait import export_trait_data
 from wqflask.heatmap import heatmap
 from wqflask.comparison_bar_chart import comparison_bar_chart
-from wqflask.marker_regression import marker_regression
-from wqflask.marker_regression import marker_regression_gn1
+from wqflask.marker_regression import run_mapping
+from wqflask.marker_regression import display_mapping_results
 from wqflask.network_graph import network_graph
 from wqflask.correlation import show_corr_results
 from wqflask.correlation_matrix import show_corr_matrix
@@ -551,10 +551,10 @@ def loading_page():
 
     return rendered_template
 
-@app.route("/marker_regression", methods=('POST',))
-def marker_regression_page():
+@app.route("/run_mapping", methods=('POST',))
+def mapping_results_page():
     initial_start_vars = request.form
-    logger.debug("Marker regression called with initial_start_vars:", initial_start_vars.items())
+    logger.debug("Mapping called with initial_start_vars:", initial_start_vars.items())
     logger.info(request.url)
     temp_uuid = initial_start_vars['temp_uuid']
     wanted = (
@@ -585,6 +585,7 @@ def marker_regression_page():
         'control_marker',
         'control_marker_db',
         'do_control',
+        'genofile',
         'genofile_string',
         'pair_scan',
         'startMb',
@@ -606,10 +607,10 @@ def marker_regression_page():
     for key, value in initial_start_vars.iteritems():
         if key in wanted or key.startswith(('value:')):
             start_vars[key] = value
-    logger.debug("Marker regression called with start_vars:", start_vars)
+    logger.debug("Mapping called with start_vars:", start_vars)
 
     version = "v3"
-    key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
+    key = "mapping_results:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
     logger.info("key is:", pf(key))
     with Bench("Loading cache"):
         result = None # Just for testing
@@ -625,8 +626,8 @@ def marker_regression_page():
             result = pickle.loads(result)
     else:
         logger.info("Cache miss!!!")
-        with Bench("Total time in MarkerRegression"):
-            template_vars = marker_regression.MarkerRegression(start_vars, temp_uuid)
+        with Bench("Total time in RunMapping"):
+            template_vars = run_mapping.RunMapping(start_vars, temp_uuid)
 
         if template_vars.mapping_method != "gemma" and template_vars.mapping_method != "plink":
             template_vars.js_data = json.dumps(template_vars.js_data,
@@ -648,10 +649,7 @@ def marker_regression_page():
                 result['pair_scan_array'] = bytesarray
                 rendered_template = render_template("pair_scan_results.html", **result)
         else:
-            #for item in template_vars.__dict__.keys():
-            #    logger.info("  ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
-
-            gn1_template_vars = marker_regression_gn1.MarkerRegression(result).__dict__
+            gn1_template_vars = display_mapping_results.DisplayMappingResults(result).__dict__
             #pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
             #logger.info("pickled result length:", len(pickled_result))
             #Redis.set(key, pickled_result)
@@ -660,24 +658,7 @@ def marker_regression_page():
             with Bench("Rendering template"):
                 if (gn1_template_vars['mapping_method'] == "gemma") or (gn1_template_vars['mapping_method'] == "plink"):
                     gn1_template_vars.pop('qtlresults', None)
-                print("TEMPLATE KEYS:", list(gn1_template_vars.keys()))
-                rendered_template = render_template("marker_regression_gn1.html", **gn1_template_vars)
-
-    # with Bench("Rendering template"):
-        # if result['pair_scan'] == True:
-            # img_path = result['pair_scan_filename']
-            # logger.info("img_path:", img_path)
-            # initial_start_vars = request.form
-            # logger.info("initial_start_vars:", initial_start_vars)
-            # imgfile = open(TEMPDIR + '/' + img_path, 'rb')
-            # imgdata = imgfile.read()
-            # imgB64 = imgdata.encode("base64")
-            # bytesarray = array.array('B', imgB64)
-            # result['pair_scan_array'] = bytesarray
-            # rendered_template = render_template("pair_scan_results.html", **result)
-        # else:
-            # rendered_template = render_template("marker_regression.html", **result)
-            # rendered_template = render_template("marker_regression_gn1.html", **gn1_template_vars)
+                rendered_template = render_template("mapping_results.html", **gn1_template_vars)
 
     return rendered_template
 
@@ -693,7 +674,6 @@ def export_mapping_results():
 
     return response
 
-
 @app.route("/export", methods = ('POST',))
 def export():
     logger.info("request.form:", request.form)