path: root/wqflask/wqflask/marker_regression/MarkerRegressionPage.py

# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
# as published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the GNU Affero General Public License for more details.
#
# This program is available from Source Forge: at GeneNetwork Project
# (sourceforge.net/projects/genenetwork/).
#
# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
#
# This module is used by GeneNetwork project (www.genenetwork.org)
#
# Created by GeneNetwork Core Team 2010/08/10
#
# Last updated by GeneNetwork Core Team 2010/10/20

import time
import string
import math
from math import *
import piddle as pid
import sys,os
import httplib, urllib

from htmlgen import HTMLgen2 as HT
from utility import Plot
from intervalAnalyst import GeneUtil
from base.webqtlTrait import webqtlTrait
from base.templatePage import templatePage
from utility import webqtlUtil
from base import webqtlConfig
from dbFunction import webqtlDatabaseFunction
from base.GeneralObject import GeneralObject

import reaper
import cPickle
from utility.THCell import THCell
from utility.TDCell import TDCell

class MarkerRegressionPage(templatePage):

    def __init__(self, fd):

        templatePage.__init__(self, fd)

        if not self.openMysql():
            return

        self.initializeParameters(fd)

        filename= webqtlUtil.genRandStr("Itvl_")
        ChrList,ChrNameOrderIdDict,ChrOrderIdNameDict,ChrLengthMbList= self.getChrNameOrderIdLength(RISet=fd.RISet)

        if self.mappingMethodId == '4': # For PLINK

            traitInfoList = string.split(string.strip(fd.identification),':')
            probesetName = string.strip(traitInfoList[-1])
            plinkOutputFileName= webqtlUtil.genRandStr("%s_%s_"%(fd.RISet,probesetName))

            # get related values from fd.allTraitData; the format of 'allTraitValueDict'is {strainName1: value=-0.2...}
            fd.readData()
            allTraitValueDict = fd.allTraitData

            #automatically generate pheno txt file for PLINK
            self.genPhenoTxtFileForPlink(phenoFileName=plinkOutputFileName,RISetName=fd.RISet,probesetName=probesetName, valueDict=allTraitValueDict)
            # os.system full path is required for input and output files; specify missing value is -9999
            plink_command = '%splink/plink --noweb --ped %splink/%s.ped --no-fid --no-parents --no-sex --no-pheno --map %splink/%s.map --pheno %s/%s.txt --pheno-name %s --missing-phenotype -9999 --out %s%s --assoc ' % (webqtlConfig.HTMLPATH, webqtlConfig.HTMLPATH,  fd.RISet, webqtlConfig.HTMLPATH, fd.RISet, webqtlConfig.TMPDIR, plinkOutputFileName, probesetName, webqtlConfig.TMPDIR, plinkOutputFileName)

            os.system(plink_command)

            if fd.identification:
                heading2 = HT.Paragraph('Trait ID: %s' % fd.identification)
                heading2.__setattr__("class","subtitle")
                self.dict['title'] = '%s: Genome Association' % fd.identification
            else:
                heading2 = ""
                self.dict['title'] = 'Genome Association'

            if fd.traitInfo:
                symbol,chromosome,MB = string.split(fd.traitInfo,'\t')
                heading3 = HT.Paragraph('[ ',HT.Strong(HT.Italic('%s' % symbol,id="green")),' on Chr %s @ %s Mb ]' % (chromosome,MB))
            else:
                heading3 = ""

            heading = HT.Paragraph('Trait Data Entered for %s Set' % fd.RISet)
            heading.__setattr__("class","title")

            # header info part:Trait Data Entered for HLC Set & Trait ID:
            headerdiv = HT.TR(HT.TD(heading, heading2,heading3, width='45%',valign='top', align='left', bgColor='#eeeeee'))

            self.ChrList=ChrList  # get chr name from '1' to 'X'
            self.ChrLengthMbList = ChrLengthMbList

            # build plink result dict based on chr, key is chr name, value is in list type including Snpname, bp and pvalue info
            plinkResultDict={}
            count,minPvalue,plinkResultDict =self.getPlinkResultDict(outputFileName=plinkOutputFileName,thresholdPvalue=self.pValue,ChrOrderIdNameDict=ChrOrderIdNameDict)

            # if can not find results which are matched with assigned p-value, system info will show up
            if count >0:

                #for genome association report table
                reportTable=""
                # sortable table object
                resultstable,tblobj,bottomInfo = self.GenReportForPLINK(ChrNameOrderIdDict=ChrNameOrderIdDict, RISet=fd.RISet,plinkResultDict=plinkResultDict,thresholdPvalue=self.pValue,chrList=self.ChrList)

                # creat object for result table for sort function
                objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb')
                cPickle.dump(tblobj, objfile)
                objfile.close()

                sortby = ("Index", "up")
                reportTable =HT.Div(webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=sortby, tableID = "sortable", addIndex = "0"), Id="sortable")

                descriptionTable =  HT.TableLite(border=0, cellpadding=0, cellspacing=0)
                descriptionTable.append(HT.TR(HT.TD(reportTable, colspan=3)))
                descriptionTable.append(HT.TR(HT.TD(HT.BR(),HT.BR())))
                descriptionTable.append(bottomInfo)

                # get each chr's length
                self.ChrLengthMbList = map(lambda x: x/1000000.0, self.ChrLengthMbList) # change unit from bp to mb
                self.ChrLengthMbSum = reduce(lambda x, y:x+y, self.ChrLengthMbList, 0.0)# get total length of all chrs
                if self.ChrLengthMbList:
                    self.GraphInterval = self.ChrLengthMbSum/(len(self.ChrLengthMbList)*12) #Empirical Mb interval
                else:
                    self.GraphInterval = 1

                # for human data, there's no CM value
                self.ChrLengthCMList = []
                self.ChrLengthCMSum = 0

                # begin: common part with human data
                intCanvas = pid.PILCanvas(size=(self.graphWidth,self.graphHeight))
                gifmap = self.plotIntMappingForPLINK(fd, intCanvas, startMb = self.startMb, endMb = self.endMb, plinkResultDict=plinkResultDict)

                intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, filename), format='png')
                intImg=HT.Image('/image/'+filename+'.png', border=0, usemap='#WebQTLImageMap')

                TD_LR = HT.TR(HT.TD(HT.Blockquote(gifmap,intImg, HT.P()), bgColor='#eeeeee', height = 200))
                self.dict['body'] = str(headerdiv)+str(TD_LR)+str(resultstable)+str(HT.TR(HT.TD(descriptionTable)))

            else:
                heading = "Genome Association"
                detail = ['There is no association with marker that meets this criteria. Please provide a less stringend threshold. The minimun p-value is %s.'%minPvalue]
                self.error(heading=heading,detail=detail)
                return

        elif self.mappingMethodId == '1': # QTLreaper result
            if not fd.genotype:
                fd.readData()

            fd.parentsf14regression = fd.formdata.getvalue('parentsf14regression')
            weightedRegression = fd.formdata.getvalue('applyVarianceSE')

            if fd.parentsf14regression and fd.genotype_2:
                _genotype = fd.genotype_2
            else:
                _genotype = fd.genotype_1

            _strains, _vals, _vars, N = fd.informativeStrains(_genotype.prgy, weightedRegression)

            if fd.identification:
                heading2 = HT.Paragraph('Trait ID: %s' % fd.identification)
                heading2.__setattr__("class","subtitle")
                self.dict['title'] = '%s: Genome Association' % fd.identification
            else:
                heading2 = ""
                self.dict['title'] = 'Genome Association'

            if fd.traitInfo:
                symbol,chromosome,MB = string.split(fd.traitInfo,'\t')
                heading3 = HT.Paragraph('[ ',HT.Strong(HT.Italic('%s' % symbol,id="green")),' on Chr %s @ %s Mb ]' % (chromosome,MB))
            else:
                heading3 = ""

            if N < webqtlConfig.KMININFORMATIVE:
                heading = "Genome Association"
                detail = ['Fewer than %d strain data were entered for %s data set. No mapping attempted.' % (webqtlConfig.KMININFORMATIVE, fd.RISet)]
                self.error(heading=heading,detail=detail)
                return
            else:
                heading = HT.Paragraph('Trait Data Entered for %s Set' % fd.RISet)
                heading.__setattr__("class","title")

                datadiv = HT.TD(heading, heading2,heading3, width='45%',valign='top', align='left', bgColor='#eeeeee')
                resultstable,tblobj,bottomInfo  = self.GenReport(ChrNameOrderIdDict,fd, _genotype, _strains, _vals, _vars)
                #resultstable = self.GenReport(fd, _genotype, _strains, _vals, _vars)

                # creat object for result table for sort function
                objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb')
                cPickle.dump(tblobj, objfile)
                objfile.close()

                sortby = ("Index", "up")
                reportTable =HT.Div(webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=sortby, tableID = "sortable", addIndex = "0"), Id="sortable")

                descriptionTable =  HT.TableLite(border=0, cellpadding=0, cellspacing=0)
                descriptionTable.append(HT.TR(HT.TD(reportTable, colspan=3)))
                descriptionTable.append(HT.TR(HT.TD(HT.BR(),HT.BR())))
                descriptionTable.append(bottomInfo)

                self.traitList=_vals

                ##########################plot#######################

                ################################################################
                # Generate Chr list and Retrieve Length Information
                ################################################################
                self.genotype= _genotype
                self.ChrList = [("All", -1)]

                for i, indChr in enumerate(self.genotype):
                    self.ChrList.append((indChr.name, i))

                self.cursor.execute("""
                        Select
                                Length from Chr_Length, InbredSet
                        where
                                Chr_Length.SpeciesId = InbredSet.SpeciesId AND
                                InbredSet.Name = '%s' AND
                                Chr_Length.Name in (%s)
                        Order by
                                OrderId
                        """ % (fd.RISet, string.join(map(lambda X: "'%s'" % X[0], self.ChrList[1:]), ", ")))

                self.ChrLengthMbList = self.cursor.fetchall()
                self.ChrLengthMbList = map(lambda x: x[0]/1000000.0, self.ChrLengthMbList)
                self.ChrLengthMbSum = reduce(lambda x, y:x+y, self.ChrLengthMbList, 0.0)
                if self.ChrLengthMbList:
                    self.MbGraphInterval = self.ChrLengthMbSum/(len(self.ChrLengthMbList)*12) #Empirical Mb interval
                else:
                    self.MbGraphInterval = 1

                self.ChrLengthCMList = []
                for i, _chr in enumerate(self.genotype):
                    self.ChrLengthCMList.append(_chr[-1].cM - _chr[0].cM)
                self.ChrLengthCMSum = reduce(lambda x, y:x+y, self.ChrLengthCMList, 0.0)# used for calculate plot scale

                self.GraphInterval = self.MbGraphInterval #Mb

                # begin: common part with human data
                intCanvas = pid.PILCanvas(size=(self.graphWidth,self.graphHeight))
                gifmap = self.plotIntMapping(fd, intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= "")
                filename= webqtlUtil.genRandStr("Itvl_")
                intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, filename), format='png')
                intImg=HT.Image('/image/'+filename+'.png', border=0, usemap='#WebQTLImageMap')

                ################################################################
                # footnote goes here
                ################################################################
                btminfo = HT.Paragraph(Id="smallsize") #Small('More information about this graph is available here.')

                if (self.additiveChecked):
                    btminfo.append(HT.BR(), 'A positive additive coefficient (', HT.Font('green', color='green'), ' line) indicates that %s alleles increase trait values. In contrast, a negative additive coefficient (' % fd.ppolar, HT.Font('red', color='red'), ' line) indicates that %s alleles increase trait values.' % fd.mpolar)


                TD_LR = HT.TR(HT.TD(HT.Blockquote(gifmap,intImg, HT.P()), bgColor='#eeeeee', height = 200))

                self.dict['body'] = str(datadiv)+str(TD_LR)+str(resultstable)+str(HT.TR(HT.TD(descriptionTable)))

                # end: common part with human data

        else:
            pass


    # add by NL 10-2-2011
    def initializeParameters(self, fd):
        """
        Initializes all of the MarkerRegressionPage class parameters,
        acquiring most values from the formdata (fd)
        """
        ###################################
        # manhattam plot parameters
        ###################################

        self.graphHeight = 600
        self.graphWidth  = 1280
        self.plotScale = 'physic'
        self.selectedChr = -1
        self.GRAPH_BACK_DARK_COLOR  = pid.HexColor(0xF1F1F9)
        self.GRAPH_BACK_LIGHT_COLOR = pid.HexColor(0xFBFBFF)
        self.LRS_COLOR  = pid.HexColor(0x0000FF)
        self.LRS_LOD ='LRS'
        self.lrsMax = float(fd.formdata.getvalue('lrsMax', 0))
        self.startMb  = fd.formdata.getvalue('startMb', "-1")
        self.endMb  = fd.formdata.getvalue('endMb', "-1")
        self.mappingMethodId  = fd.formdata.getvalue('mappingMethodId', "0")
        self.permChecked=True
        self.multipleInterval=False
        self.SIGNIFICANT_WIDTH = 5
        self.SUGGESTIVE_WIDTH = 5
        self.SIGNIFICANT_COLOR   = pid.HexColor(0xEBC7C7)
        self.SUGGESTIVE_COLOR    = pid.gainsboro
        self.colorCollection = [self.LRS_COLOR]
        self.additiveChecked= True
        self.ADDITIVE_COLOR_POSITIVE = pid.green
        self.legendChecked =False
        self.pValue=float(fd.formdata.getvalue('pValue',-1))

        # allow user to input p-value greater than 1,
        # in this case, the value will be treated as -lgP value. so the input value needs to be transferred to power of 10 format
        if self.pValue >1:
            self.pValue =10**-(self.pValue)

        try:
            self.startMb = float(self.startMb)
            self.endMb = float(self.endMb)
            if self.startMb > self.endMb:
                temp = self.startMb
                self.startMb = self.endMb
                self.endMb = temp
            #minimal distance 10bp
            if self.endMb - self.startMb < 0.00001:
                self.endMb = self.startMb + 0.00001
        except:
            self.startMb = self.endMb = -1

    def GenReportForPLINK(self, ChrNameOrderIdDict={},RISet='',plinkResultDict= {},thresholdPvalue=-1,chrList=[]):

        'Create an HTML division which reports any loci which are significantly associated with the submitted trait data.'
        #########################################
        #      Genome Association report
        #########################################
        locusFormName = webqtlUtil.genRandStr("fm_")
        locusForm = HT.Form(cgi = os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), \
                enctype='multipart/form-data', name=locusFormName, submit=HT.Input(type='hidden'))
        hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':RISet+"Geno",'CellID':'_', \
                'RISet':RISet, 'incparentsf1':'on'}
        for key in hddn.keys():
            locusForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))

        regressionHeading = HT.Paragraph('Genome Association Report')
        regressionHeading.__setattr__("class","title")

        filename= webqtlUtil.genRandStr("GenomeAsscociation_")
        fpText = open('%s.txt' % (webqtlConfig.TMPDIR+filename), 'wb')
        fpText.write('The loci meet the criteria of P-Value <= %3.6f.\n'%thresholdPvalue)
        pValueInfo =HT.Paragraph('The loci meet the criteria of P-Value <= %3.6f.\n'%thresholdPvalue)

        textUrl = HT.Href(text = 'Download', url= '/tmp/'+filename+'.txt', target = "_blank", Class='fs12 fwn')
        bottomInfo = HT.TR(HT.TD(HT.Paragraph(textUrl, ' result in tab-delimited text format.', HT.BR(), HT.BR(),Class="fs12 fwn"), colspan=3))

        tblobj={}       # build dict for genTableObj function; keys include header and body
        tblobj_header = [] # value of key 'header'
        tblobj_body=[]          # value of key 'body'
        reportHeaderRow=[]      # header row list for tblobj_header (html part)
        headerList=['Index','SNP Name','Chr','Mb','-log(P)']
        headerStyle="fs14 fwb ffl b1 cw cbrb" # style of the header
        cellColorStyle = "fs13 b1 fwn c222" # style of the cells

        if headerList:
            for ncol, item in enumerate(headerList):
                reportHeaderRow.append(THCell(HT.TD(item, Class=headerStyle, valign='bottom',nowrap='ON'),text=item, idx=ncol))
            #download file for table headers' names
            fpText.write('SNP_Name\tChromosome\tMb\t-log(P)\n')

        tblobj_header.append(reportHeaderRow)
        tblobj['header']=tblobj_header

        index=1
        for chr in chrList:

            if plinkResultDict.has_key(chr):
                if chr in ChrNameOrderIdDict.keys():
                    chrOrderId =ChrNameOrderIdDict[chr]
                else:
                    chrOrderId=chr

                valueList=plinkResultDict[chr]

                for value in valueList:
                    reportBodyRow=[]        # row list for tblobj_body (html part)
                    snpName=value[0]
                    bp=value[1]
                    mb=int(bp)/1000000.0

                    try:
                        pValue =float(value[2])
                    except:
                        pValue =1
                    formattedPvalue = -math.log10(pValue)

                    formattedPvalue = webqtlUtil.SciFloat(formattedPvalue)
                    dbSnprs=snpName.replace('rs','')
                    SnpHref = HT.Href(text=snpName, url="http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=%s"%dbSnprs, target="_blank")

                    selectCheck=HT.Input(type="checkbox", Class="checkbox", name="index",value=index, onClick="highlight(this)")
                    reportBodyRow.append(TDCell(HT.TD(str(index),selectCheck, align='right',Class=cellColorStyle,nowrap='ON'),str(index),index))
                    reportBodyRow.append(TDCell(HT.TD(SnpHref, Class=cellColorStyle,nowrap='ON'),snpName, snpName))
                    reportBodyRow.append(TDCell(HT.TD(chr, Class=cellColorStyle, align="center",nowrap='ON'),chr, chrOrderId))
                    reportBodyRow.append(TDCell(HT.TD('%3.6f'%mb, Class=cellColorStyle, align="center",nowrap='ON'),mb, mb))
                    reportBodyRow.append(TDCell(HT.TD(formattedPvalue, Class=cellColorStyle, align="center",nowrap='ON'),formattedPvalue, float(formattedPvalue)))

                    fpText.write('%s\t%s\t%3.6f\t%s\n' % (snpName, str(chr), mb, formattedPvalue))
                    index+=1

                    tblobj_body.append(reportBodyRow)

        tblobj['body']=tblobj_body
        rv=HT.TR(HT.TD(regressionHeading,pValueInfo, locusForm, HT.P(), width='55%',valign='top', align='left',bgColor='#eeeeee'))

        return rv, tblobj,bottomInfo


    def GenReport(self, ChrNameOrderIdDict,fd, _genotype, _strains, _vals, _vars= []):
        'Create an HTML division which reports any loci which are significantly associated with the submitted trait data.'
        #calculate QTL for each trait
        self.qtlresults = []
        if webqtlUtil.ListNotNull(_vars):
            qtlresults = _genotype.regression(strains = _strains, trait = _vals, variance = _vars)
            LRSArray = _genotype.permutation(strains = _strains, trait = _vals, variance = _vars, nperm=fd.nperm)
        else:
            qtlresults = _genotype.regression(strains = _strains, trait = _vals)
            LRSArray = _genotype.permutation(strains = _strains, trait = _vals,nperm=fd.nperm)

        self.qtlresults.append(qtlresults)

        filename= webqtlUtil.genRandStr("GenomeAsscociation_")

        # set suggestive, significant and highly significant LRS
        if fd.suggestive == None:
            fd.suggestive = LRSArray[int(fd.nperm*0.37-1)]
        else:
            fd.suggestive = float(fd.suggestive)
        if fd.significance == None:
            fd.significance = LRSArray[int(fd.nperm*0.95-1)]
        else:
            fd.significance = float(fd.significance)

        self.significance =fd.significance
        self.suggestive = fd.suggestive
        self.highlysignificant = LRSArray[int(fd.nperm*0.99-1)]
        _dispAllLRS = 0
        if fd.formdata.getvalue('displayAllLRS'):
            _dispAllLRS = 1
        qtlresults2 = []
        if _dispAllLRS:
            filtered = qtlresults[:]
        else:
            filtered = filter(lambda x, y=fd.suggestive: x.lrs > y, qtlresults)
        if len(filtered) == 0:
            qtlresults2 = qtlresults[:]
            qtlresults2.sort()
            filtered = qtlresults2[-10:]

        #########################################
        #      Permutation Graph
        #########################################
        myCanvas = pid.PILCanvas(size=(400,300))
        #plotBar(myCanvas,10,10,390,290,LRSArray,XLabel='LRS',YLabel='Frequency',title=' Histogram of Permutation Test',identification=fd.identification)
        Plot.plotBar(myCanvas, LRSArray,XLabel='LRS',YLabel='Frequency',title=' Histogram of Permutation Test')
        filename= webqtlUtil.genRandStr("Reg_")
        myCanvas.save(webqtlConfig.GENERATED_IMAGE_DIR+filename, format='gif')
        img=HT.Image('/image/'+filename+'.gif',border=0,alt='Histogram of Permutation Test')
            
        if fd.suggestive == None:
            fd.suggestive = LRSArray[int(fd.nperm*0.37-1)]
        else:
            fd.suggestive = float(fd.suggestive)
        if fd.significance == None:
            fd.significance = LRSArray[int(fd.nperm*0.95-1)]
        else:
            fd.significance = float(fd.significance)

        permutationHeading = HT.Paragraph('Histogram of Permutation Test')
        permutationHeading.__setattr__("class","title")

        permutation = HT.TableLite()
        permutation.append(HT.TR(HT.TD(img)))


        #########################################
        #      Genome Association report
        #########################################
        locusFormName = webqtlUtil.genRandStr("fm_")
        locusForm = HT.Form(cgi = os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), \
                enctype='multipart/form-data', name=locusFormName, submit=HT.Input(type='hidden'))
        hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_', \
                'RISet':fd.RISet, 'incparentsf1':'on'}
        for key in hddn.keys():
            locusForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))

        regressionHeading = HT.Paragraph('Genome Association Report')
        regressionHeading.__setattr__("class","title")
        # report is the info part above report table
        if qtlresults2 != []:
            report = HT.Blockquote(HT.Font('No association ',color="#FF0000"),HT.Font('with a likelihood ratio statistic greater than %3.1f was found. Here are the top 10 LRSs.' % fd.suggestive,color="#000000"))
        else:
            report = HT.Blockquote('The following loci in the %s data set have associations with the above trait data.\n' % fd.RISet, HT.P())
        report.__setattr__("class","normalsize")

        fpText = open('%s.txt' % (webqtlConfig.TMPDIR+filename), 'wb')
        fpText.write('Suggestive LRS =%3.2f\n'%self.suggestive)
        fpText.write('Significant LRS =%3.2f\n'%self.significance)
        fpText.write('Highly Significant LRS =%3.2f\n'%self.highlysignificant)
        LRSInfo =HT.Paragraph('&nbsp;&nbsp;&nbsp;&nbsp;Suggestive LRS =%3.2f\n'%fd.suggestive, HT.BR(), '&nbsp;&nbsp;&nbsp;&nbsp;Significant LRS =%3.2f\n'%fd.significance,HT.BR(),'&nbsp;&nbsp;&nbsp;&nbsp;Highly Significant LRS =%3.2f\n' % self.highlysignificant)

        textUrl = HT.Href(text = 'Download', url= '/tmp/'+filename+'.txt', target = "_blank", Class='fs12 fwn')

        bottomInfo = HT.TR(HT.TD(HT.Paragraph(textUrl, ' result in tab-delimited text format.', HT.BR(), HT.BR(),'LRS values marked with',HT.Font(' * ',color="red"), 'are greater than the significance threshold (specified by you or by permutation test). ' , HT.BR(), HT.BR(), HT.Strong('Additive Effect'), ' is half the difference in the mean phenotype of all cases that are homozygous for one parental allel at this marker minus the mean of all cases that are homozygous for the other parental allele at this marker. ','In the case of %s strains, for example,' % fd.RISet,' A positive additive effect indicates that %s alleles increase trait values. Negative additive effect indicates that %s alleles increase trait values.'% (fd.ppolar,fd.mpolar),Class="fs12 fwn")))

        tblobj={}       # build dict for genTableObj function; keys include header and body
        tblobj_header = [] # value of key 'header'
        tblobj_body=[]          # value of key 'body'
        reportHeaderRow=[]      # header row list for tblobj_header (html part)
        headerStyle="fs14 fwb ffl b1 cw cbrb" # style of the header
        cellColorStyle = "fs13 b1 fwn c222" # style of the cells

        headerList=['Index','LRS','Chr','Mb','Locus','Additive Effect']
        for ncol, item in enumerate(headerList):
            reportHeaderRow.append(THCell(HT.TD(item, Class=headerStyle, valign='bottom',nowrap='ON'),text=item, idx=ncol))

        if fd.genotype.type == 'intercross':
            ncol =len(headerList)
            reportHeaderRow.append(THCell(HT.TD('Dominance Effect', Class=headerStyle, valign='bottom',nowrap='ON'),text='Dominance Effect', idx=ncol))

            #download file for table headers' names
            fpText.write('LRS\tChromosome\tMb\tLocus\tAdditive Effect\tDominance Effect\n')

            index=1
            for ii in filtered:
                #add by NL 06-20-2011: set LRS to 460 when LRS is infinite,
                if ii.lrs==float('inf') or ii.lrs>webqtlConfig.MAXLRS:
                    LRS=webqtlConfig.MAXLRS #maximum LRS value
                else:
                    LRS=ii.lrs

                if LRS > fd.significance:
                    lrs = HT.TD(HT.Font('%3.3f*' % LRS, color='#FF0000'),Class=cellColorStyle)
                else:
                    lrs = HT.TD('%3.3f' % LRS,Class=cellColorStyle)

                if ii.locus.chr in ChrNameOrderIdDict.keys():
                    chrOrderId =ChrNameOrderIdDict[ii.locus.chr]
                else:
                    chrOrderId=ii.locus.chr

                reportBodyRow=[]        # row list for tblobj_body (html part)
                selectCheck=HT.Input(type="checkbox", Class="checkbox", name="index",value=index, onClick="highlight(this)")
                reportBodyRow.append(TDCell(HT.TD(str(index),selectCheck, align='right',Class=cellColorStyle,nowrap='ON'),str(index),index))
                reportBodyRow.append(TDCell(lrs,LRS, LRS))
                reportBodyRow.append(TDCell(HT.TD(ii.locus.chr, Class=cellColorStyle, align="center",nowrap='ON'),ii.locus.chr, chrOrderId))
                reportBodyRow.append(TDCell(HT.TD('%3.6f'%ii.locus.Mb, Class=cellColorStyle, align="center",nowrap='ON'),ii.locus.Mb, ii.locus.Mb))
                reportBodyRow.append(TDCell(HT.TD(HT.Href(text=ii.locus.name, url = "javascript:showTrait('%s','%s');" % (locusFormName, ii.locus.name), Class='normalsize'), Class=cellColorStyle, align="center",nowrap='ON'),ii.locus.name, ii.locus.name))
                reportBodyRow.append(TDCell(HT.TD('%3.3f' % ii.additive, Class=cellColorStyle, align="center",nowrap='ON'),ii.additive, ii.additive))
                reportBodyRow.append(TDCell(HT.TD('%3.3f' % ii.dominance, Class=cellColorStyle, align="center",nowrap='ON'),ii.dominance, ii.dominance))

                fpText.write('%2.3f\t%s\t%3.6f\t%s\t%2.3f\t%2.3f\n' % (LRS, ii.locus.chr, ii.locus.Mb, ii.locus.name, ii.additive, ii.dominance))
                index+=1
                tblobj_body.append(reportBodyRow)
        else:
            #download file for table headers' names
            fpText.write('LRS\tChromosome\tMb\tLocus\tAdditive Effect\n')

            index=1
            for ii in filtered:
                #add by NL 06-20-2011: set LRS to 460 when LRS is infinite,
                if ii.lrs==float('inf') or ii.lrs>webqtlConfig.MAXLRS:
                    LRS=webqtlConfig.MAXLRS #maximum LRS value
                else:
                    LRS=ii.lrs

                if LRS > fd.significance:
                    lrs = HT.TD(HT.Font('%3.3f*' % LRS, color='#FF0000'),Class=cellColorStyle)
                else:
                    lrs = HT.TD('%3.3f' % LRS,Class=cellColorStyle)

                if ii.locus.chr in ChrNameOrderIdDict.keys():
                    chrOrderId =ChrNameOrderIdDict[ii.locus.chr]
                else:
                    chrOrderId=ii.locus.chr

                reportBodyRow=[]        # row list for tblobj_body (html part)
                selectCheck=HT.Input(type="checkbox", Class="checkbox", name="index",value=index, onClick="highlight(this)")
                reportBodyRow.append(TDCell(HT.TD(str(index),selectCheck, align='right',Class=cellColorStyle,nowrap='ON'),str(index),index))
                reportBodyRow.append(TDCell(lrs,LRS, LRS))
                reportBodyRow.append(TDCell(HT.TD(ii.locus.chr, Class=cellColorStyle, align="center",nowrap='ON'),ii.locus.chr, chrOrderId))
                reportBodyRow.append(TDCell(HT.TD('%3.6f'%ii.locus.Mb, Class=cellColorStyle, align="center",nowrap='ON'),ii.locus.Mb, ii.locus.Mb))
                reportBodyRow.append(TDCell(HT.TD(HT.Href(text=ii.locus.name, url = "javascript:showTrait('%s','%s');" % (locusFormName, ii.locus.name), Class='normalsize'), Class=cellColorStyle, align="center",nowrap='ON'),ii.locus.name, ii.locus.name))
                reportBodyRow.append(TDCell(HT.TD('%3.3f' % ii.additive, Class=cellColorStyle, align="center",nowrap='ON'),ii.additive, ii.additive))

                fpText.write('%2.3f\t%s\t%3.6f\t%s\t%2.3f\n' % (LRS, ii.locus.chr, ii.locus.Mb, ii.locus.name, ii.additive))
                index+=1
                tblobj_body.append(reportBodyRow)

        tblobj_header.append(reportHeaderRow)
        tblobj['header']=tblobj_header
        tblobj['body']=tblobj_body

        rv=HT.TD(regressionHeading,LRSInfo,report, locusForm, HT.P(),width='55%',valign='top', align='left', bgColor='#eeeeee')
        if fd.genotype.type == 'intercross':
            bottomInfo.append(HT.BR(), HT.BR(), HT.Strong('Dominance Effect'),' is the difference between the mean trait value of cases heterozygous at a marker and the average mean for the two groups homozygous at this marker: e.g.,  BD - (BB+DD)/2]. A positive dominance effect indicates that the average phenotype of BD heterozygotes exceeds the mean of BB and DD homozygotes. No dominance deviation can be computed for a set of recombinant inbred strains or for a backcross.')
            return rv,tblobj,bottomInfo

        return rv,tblobj,bottomInfo

    def plotIntMappingForPLINK(self, fd, canvas, offset= (80, 120, 20, 80), zoom = 1, startMb = None, endMb = None, showLocusForm = "",plinkResultDict={}):
        #calculating margins
        xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset

        fontZoom = zoom
        if zoom == 2:
            fontZoom = 1.5

        xLeftOffset = int(xLeftOffset*fontZoom)
        xRightOffset = int(xRightOffset*fontZoom)
        yBottomOffset = int(yBottomOffset*fontZoom)

        cWidth = canvas.size[0]
        cHeight = canvas.size[1]
        plotWidth = cWidth - xLeftOffset - xRightOffset
        plotHeight = cHeight - yTopOffset - yBottomOffset
        startPixelX = xLeftOffset
        endPixelX   = (xLeftOffset + plotWidth)

        #Drawing Area Height
        drawAreaHeight = plotHeight
        if self.plotScale == 'physic' and self.selectedChr > -1: # for single chr
            drawAreaHeight -= self.ENSEMBL_BAND_HEIGHT + self.UCSC_BAND_HEIGHT+ self.WEBQTL_BAND_HEIGHT + 3*self.BAND_SPACING+ 10*zoom
            if self.geneChecked:
                drawAreaHeight -= self.NUM_GENE_ROWS*self.EACH_GENE_HEIGHT + 3*self.BAND_SPACING + 10*zoom
        else:
            if self.selectedChr > -1:
                drawAreaHeight -= 20
            else:# for all chrs
                drawAreaHeight -= 30

        #Image map
        gifmap = HT.Map(name='WebQTLImageMap')

        newoffset = (xLeftOffset, xRightOffset, yTopOffset, yBottomOffset)
        # Draw the alternating-color background first and get plotXScale
        plotXScale = self.drawGraphBackgroundForPLINK(canvas, gifmap, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb,plinkResultDict=plinkResultDict)

        # Draw X axis
        self.drawXAxisForPLINK(fd, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
        # Draw manhattam plot
        self.drawManhattanPlotForPLINK(canvas, drawAreaHeight, gifmap, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb,plinkResultDict=plinkResultDict,thresholdPvalue=self.pValue)

        return gifmap


    def plotIntMapping(self, fd, canvas, offset= (80, 120, 20, 80), zoom = 1, startMb = None, endMb = None, showLocusForm = ""):
        #calculating margins
        xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset

        fontZoom = zoom
        if zoom == 2:
            fontZoom = 1.5

        xLeftOffset = int(xLeftOffset*fontZoom)
        xRightOffset = int(xRightOffset*fontZoom)
        yBottomOffset = int(yBottomOffset*fontZoom)

        cWidth = canvas.size[0]
        cHeight = canvas.size[1]
        plotWidth = cWidth - xLeftOffset - xRightOffset
        plotHeight = cHeight - yTopOffset - yBottomOffset
        startPixelX = xLeftOffset
        endPixelX   = (xLeftOffset + plotWidth)

        #Drawing Area Height
        drawAreaHeight = plotHeight
        if self.plotScale == 'physic' and self.selectedChr > -1: # for single chr
            drawAreaHeight -= self.ENSEMBL_BAND_HEIGHT + self.UCSC_BAND_HEIGHT+ self.WEBQTL_BAND_HEIGHT + 3*self.BAND_SPACING+ 10*zoom
            if self.geneChecked:
                drawAreaHeight -= self.NUM_GENE_ROWS*self.EACH_GENE_HEIGHT + 3*self.BAND_SPACING + 10*zoom
        else:# for all chrs
            if self.selectedChr > -1:
                drawAreaHeight -= 20
            else:
                drawAreaHeight -= 30

        #Image map
        gifmap = HT.Map(name='WebQTLImageMap')

        newoffset = (xLeftOffset, xRightOffset, yTopOffset, yBottomOffset)
        # Draw the alternating-color background first and get plotXScale
        plotXScale = self.drawGraphBackground(canvas, gifmap, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)

        # Draw X axis
        self.drawXAxis(fd, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
        # Draw QTL curve
        self.drawQTL(canvas, drawAreaHeight, gifmap, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)

        #draw legend
        if self.multipleInterval:
            self.drawMultiTraitName(fd, canvas, gifmap, showLocusForm, offset=newoffset)
        elif self.legendChecked:
            self.drawLegendPanel(fd, canvas, offset=newoffset)
        else:
            pass

        #draw position, no need to use a separate function
        if fd.genotype.Mbmap:
            self.drawProbeSetPosition(canvas, plotXScale, offset=newoffset)

        return gifmap


    # functions for manhattam plot of markers
    def drawManhattanPlotForPLINK(self, canvas, drawAreaHeight, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None,plinkResultDict={},thresholdPvalue=-1):

        xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
        plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
        plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
        fontZoom = zoom
        if zoom == 2:
            fontZoom = 1.5

        # INTERCROSS = (self.genotype.type=="intercross")
        INTERCROSS ='' #??????

        ChrLengthDistList = self.ChrLengthMbList
        drawRegionDistance = self.ChrLengthMbSum
        GraphInterval=self.GraphInterval
        pvalueHeightThresh = drawAreaHeight - 80 #ZS: Otherwise the plot gets very close to the chromosome labels

        #draw the pvalue scale
        #We first determine whether or not we are using a sliding scale.
        #If so, we need to compute the maximum pvalue value to determine where the max y-value should be, and call this pvalueMax.
        #pvalueTop is then defined to be above the pvalueMax by enough to add one additional pvalueScale increment.
        #if we are using a set-scale, then we set pvalueTop to be the user's value, and pvalueMax doesn't matter.

        # for human data we use p value instead of lrs
        pValueList=[]
        for key in plinkResultDict:
            valueList = plinkResultDict[key]
            for item in valueList:
                pValue = item[-1]
                pValueList.append(pValue)

        formattedPValueList=[]
        for pValue in pValueList:
            try:
                pValue=float(pValue)
            except:
                pValue =1
            formattedpValue = -math.log10(pValue)
            formattedPValueList.append(formattedpValue)

        #sliding scale
        pvalueMax = max(formattedPValueList)
        #pvalueMax =pvalueMax +1
        # no permutation result for plink  func: GenReport()
        pvalueMin = int(-math.log10(thresholdPvalue))

        if pvalueMax> 100:
            pvalueScale = 20.0
        elif pvalueMax > 20:
            pvalueScale = 5.0
        elif pvalueMax > 7.5:
            pvalueScale = 2.5
        else:
            pvalueScale = 1.0

        # the base line for x-axis is -log(thresholdPvalue)
        pvalueAxisList = Plot.frange(pvalueMin, pvalueMax, pvalueScale)
        #make sure the user's value appears on the y-axis
        #ZS: There is no way to do this without making the position of the points not directly proportional to a given distance on the y-axis
        #tempPvalueMax=round(pvalueMax)
        tempPvalueMax = pvalueAxisList[len(pvalueAxisList)-1] + pvalueScale
        pvalueAxisList.append(tempPvalueMax)

        #ZS: I don't understand this; the if statement will be true for any number that isn't exactly X.5.
        #if abs(tempPvalueMax-pvalueMax) <0.5:
        #       tempPvalueMax=tempPvalueMax+1
        #       pvalueAxisList.append(tempPvalueMax)

        #draw the "pvalue" string to the left of the axis
        pvalueScaleFont=pid.Font(ttf="verdana", size=14*fontZoom, bold=0)
        pvalueLODFont=pid.Font(ttf="verdana", size=14*zoom*1.5, bold=0)
        yZero = yTopOffset + plotHeight

        #yAxis label display area
        yAxis_label ='-log(P)'
        canvas.drawString(yAxis_label, xLeftOffset - canvas.stringWidth("999.99", font=pvalueScaleFont) - 10*zoom, \
                                          yZero - 150, font=pvalueLODFont, color=pid.black, angle=90)

        for i,item in enumerate(pvalueAxisList):
            ypvalue = yZero - (float(i)/float(len(pvalueAxisList) - 1)) * pvalueHeightThresh
            canvas.drawLine(xLeftOffset, ypvalue, xLeftOffset - 4, ypvalue, color=self.LRS_COLOR, width=1*zoom)
            scaleStr = "%2.1f" % item
            #added by NL 6-24-2011:Y-axis scale display
            canvas.drawString(scaleStr, xLeftOffset-4-canvas.stringWidth(scaleStr, font=pvalueScaleFont)-5, ypvalue+3, font=pvalueScaleFont, color=self.LRS_COLOR)

        ChrList=self.ChrList
        startPosX = xLeftOffset

        for i, chr in enumerate(ChrList):

            if      plinkResultDict.has_key(chr):
                plinkresultList = plinkResultDict[chr]

                m = 0
                #add by NL 06-24-2011: for mahanttam plot
                symbolFont = pid.Font(ttf="fnt_bs", size=5,bold=0)
                # color for point in each chr
                chrCount=len(ChrList)
                chrColorDict =self.getColorForMarker(chrCount=chrCount,flag=1)
                for j, item in enumerate(plinkresultList):
                    try :
                        mb=float(item[1])/1000000.0
                    except:
                        mb=0

                    try :
                        pvalue =float(item[-1])
                    except:
                        pvalue =1

                    try:
                        snpName = item[0]
                    except:
                        snpName=''

                    formattedPvalue = -math.log10(pvalue)

                    Xc = startPosX + (mb-startMb)*plotXScale
                    Yc = yZero - (formattedPvalue-pvalueMin)*pvalueHeightThresh/(tempPvalueMax - pvalueMin)
                    canvas.drawString("5", Xc-canvas.stringWidth("5",font=symbolFont)/2+1,Yc+2,color=chrColorDict[i], font=symbolFont)
                    m += 1

            startPosX +=  (ChrLengthDistList[i]+GraphInterval)*plotXScale

        canvas.drawLine(xLeftOffset, yZero, xLeftOffset, yTopOffset, color=self.LRS_COLOR, width=1*zoom)  #the blue line running up the y axis

    def drawQTL(self, canvas, drawAreaHeight, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):

        xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
        plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
        plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
        fontZoom = zoom
        if zoom == 2:
            fontZoom = 1.5

        INTERCROSS = (self.genotype.type=="intercross")

        ChrLengthDistList = self.ChrLengthMbList
        GraphInterval=self.GraphInterval
        LRSHeightThresh = drawAreaHeight
        AdditiveHeightThresh = drawAreaHeight/2
        DominanceHeightThresh = drawAreaHeight/2

        #draw the LRS scale
        #We first determine whether or not we are using a sliding scale.
        #If so, we need to compute the maximum LRS value to determine where the max y-value should be, and call this LRSMax.
        #LRSTop is then defined to be above the LRSMax by enough to add one additional LRSScale increment.
        #if we are using a set-scale, then we set LRSTop to be the user's value, and LRSMax doesn't matter.

        if self.LRS_LOD == 'LOD':
            lodm = self.LODFACTOR
        else:
            lodm = 1.0

        if self.lrsMax <= 0:  #sliding scale
            LRSMax = max(map(max, self.qtlresults)).lrs
            #genotype trait will give infinite LRS
            LRSMax = min(LRSMax, webqtlConfig.MAXLRS)
            LRSMax = max(self.significance, LRSMax)
        else:
            LRSMax = self.lrsMax*lodm

        if LRSMax/lodm > 100:
            LRSScale = 20.0
        elif LRSMax/lodm > 20:
            LRSScale = 5.0
        elif LRSMax/lodm > 7.5:
            LRSScale = 2.5
        else:
            LRSScale = 1.0

        LRSAxisList = Plot.frange(LRSScale, LRSMax/lodm, LRSScale)
        #make sure the user's value appears on the y-axis
        #update by NL 6-21-2011: round the LOD value to 100 when LRSMax is equal to 460
        LRSAxisList.append(round(LRSMax/lodm))

        #draw the "LRS" or "LOD" string to the left of the axis
        LRSScaleFont=pid.Font(ttf="verdana", size=14*fontZoom, bold=0)
        LRSLODFont=pid.Font(ttf="verdana", size=14*zoom*1.5, bold=0)
        yZero = yTopOffset + plotHeight

        #yAxis label display area
        canvas.drawString(self.LRS_LOD, xLeftOffset - canvas.stringWidth("999.99", font=LRSScaleFont) - 10*zoom, \
                                          yZero - 150, font=LRSLODFont, color=pid.black, angle=90)

        for item in LRSAxisList:
            yLRS = yZero - (item*lodm/LRSMax) * LRSHeightThresh
            canvas.drawLine(xLeftOffset, yLRS, xLeftOffset - 4, yLRS, color=self.LRS_COLOR, width=1*zoom)
            scaleStr = "%2.1f" % item
            #added by NL 6-24-2011:Y-axis scale display
            canvas.drawString(scaleStr, xLeftOffset-4-canvas.stringWidth(scaleStr, font=LRSScaleFont)-5, yLRS+3, font=LRSScaleFont, color=self.LRS_COLOR)


        #"Significant" and "Suggestive" Drawing Routine
        # ======= Draw the thick lines for "Significant" and "Suggestive" =====  (crowell: I tried to make the SNPs draw over these lines, but piddle wouldn't have it...)
        if self.permChecked and not self.multipleInterval:
            significantY = yZero - self.significance*LRSHeightThresh/LRSMax
            suggestiveY = yZero - self.suggestive*LRSHeightThresh/LRSMax


            startPosX = xLeftOffset
            for i, _chr in enumerate(self.genotype):
                rightEdge = int(startPosX + self.ChrLengthDistList[i]*plotXScale - self.SUGGESTIVE_WIDTH/1.5)
                #added by NL 6-24-2011:draw suggestive line (grey one)
                canvas.drawLine(startPosX+self.SUGGESTIVE_WIDTH/1.5, suggestiveY, rightEdge, suggestiveY, color=self.SUGGESTIVE_COLOR,
                        width=self.SUGGESTIVE_WIDTH*zoom, clipX=(xLeftOffset, xLeftOffset + plotWidth-2))
                #added by NL 6-24-2011:draw significant line (pink one)
                canvas.drawLine(startPosX+self.SUGGESTIVE_WIDTH/1.5, significantY, rightEdge, significantY, color=self.SIGNIFICANT_COLOR,
                        width=self.SIGNIFICANT_WIDTH*zoom, clipX=(xLeftOffset, xLeftOffset + plotWidth-2))
                sugg_coords = "%d, %d, %d, %d" % (startPosX, suggestiveY-2, rightEdge + 2*zoom, suggestiveY+2)
                sig_coords = "%d, %d, %d, %d" % (startPosX, significantY-2, rightEdge + 2*zoom, significantY+2)
                if self.LRS_LOD == 'LRS':
                    sugg_title = "Suggestive LRS = %0.2f" % self.suggestive
                    sig_title = "Significant LRS = %0.2f" % self.significance
                else:
                    sugg_title = "Suggestive LOD = %0.2f" % (self.suggestive/4.61)
                    sig_title = "Significant LOD = %0.2f" % (self.significance/4.61)
                Areas1 = HT.Area(shape='rect',coords=sugg_coords,title=sugg_title)
                Areas2 = HT.Area(shape='rect',coords=sig_coords,title=sig_title)
                gifmap.areas.append(Areas1)
                gifmap.areas.append(Areas2)

                startPosX +=  (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale


        if self.multipleInterval:
            lrsEdgeWidth = 1
        else:
            additiveMax = max(map(lambda X : abs(X.additive), self.qtlresults[0]))
            if INTERCROSS:
                dominanceMax = max(map(lambda X : abs(X.dominance), self.qtlresults[0]))
            else:
                dominanceMax = -1
            lrsEdgeWidth = 2
        for i, qtlresult in enumerate(self.qtlresults):
            m = 0
            startPosX = xLeftOffset
            thisLRSColor = self.colorCollection[i]

            #add by NL 06-24-2011: for mahanttam plot
            symbolFont = pid.Font(ttf="fnt_bs", size=5,bold=0)

            for j, _chr in enumerate(self.genotype):
                chrCount=len(self.genotype)
                chrColorDict =self.getColorForMarker(chrCount=chrCount,flag=1)
                LRSCoordXY = []
                AdditiveCoordXY = []
                DominanceCoordXY = []
                for k, _locus in enumerate(_chr):
                    if self.plotScale == 'physic':
                        Xc = startPosX + (_locus.Mb-startMb)*plotXScale
                    else:
                        Xc = startPosX + (_locus.cM-_chr[0].cM)*plotXScale
                    # updated by NL 06-18-2011:
                    # fix the over limit LRS graph issue since genotype trait may give infinite LRS;
                    # for any lrs is over than 460(LRS max in this system), it will be reset to 460
                    if      qtlresult[m].lrs> 460 or qtlresult[m].lrs=='inf':
                        Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSMax
                    else:
                        Yc = yZero - qtlresult[m].lrs*LRSHeightThresh/LRSMax

                    LRSCoordXY.append((Xc, Yc))
                    #add by NL 06-24-2011: for mahanttam plot
                    #self.significance/4.61  consider chr and LOD
                    # significantY = yZero - self.significance*LRSHeightThresh/LRSMax
                    # if Yc >significantY:
                        # canvas.drawString(":", Xc-canvas.stringWidth(":",font=symbolFont)/2+1,Yc+2,color=pid.black, font=symbolFont)
                    # else:
                        # canvas.drawString(":", Xc-canvas.stringWidth(":",font=symbolFont)/2+1,Yc+2,color=pid.black, font=symbolFont)

                    # add by NL 06-27-2011: eliminate imputed value when locus name is equal to '-'
                    if (qtlresult[m].locus.name) and (qtlresult[m].locus.name!=' - '):
                        canvas.drawString("5", Xc-canvas.stringWidth("5",font=symbolFont)/2+1,Yc+2,color=chrColorDict[j], font=symbolFont)

                    if not self.multipleInterval and self.additiveChecked:
                        Yc = yZero - qtlresult[m].additive*AdditiveHeightThresh/additiveMax
                        AdditiveCoordXY.append((Xc, Yc))
                    if not self.multipleInterval and INTERCROSS and self.additiveChecked:
                        Yc = yZero - qtlresult[m].dominance*DominanceHeightThresh/dominanceMax
                        DominanceCoordXY.append((Xc, Yc))
                    m += 1

                startPosX +=  (ChrLengthDistList[j]+GraphInterval)*plotXScale


        ###draw additive scale
        if not self.multipleInterval and self.additiveChecked:
            additiveScaleFont=pid.Font(ttf="verdana",size=12*fontZoom,bold=0)
            additiveScale = Plot.detScaleOld(0,additiveMax)
            additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
            additiveAxisList = Plot.frange(0, additiveScale[1], additiveStep)
            maxAdd =  additiveScale[1]
            addPlotScale = AdditiveHeightThresh/additiveMax

            additiveAxisList.append(additiveScale[1])
            for item in additiveAxisList:
                additiveY = yZero - item*addPlotScale
                canvas.drawLine(xLeftOffset + plotWidth,additiveY,xLeftOffset+4+ plotWidth,additiveY,color=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)
                scaleStr = "%2.3f" % item
                canvas.drawString(scaleStr,xLeftOffset + plotWidth +6,additiveY+5,font=additiveScaleFont,color=self.ADDITIVE_COLOR_POSITIVE)

            canvas.drawLine(xLeftOffset+plotWidth,additiveY,xLeftOffset+plotWidth,yZero,color=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)

        canvas.drawLine(xLeftOffset, yZero, xLeftOffset, yTopOffset, color=self.LRS_COLOR, width=1*zoom)  #the blue line running up the y axis

    def drawGraphBackgroundForPLINK(self, canvas, gifmap, offset= (80, 120, 80, 50), zoom = 1, startMb = None, endMb = None,plinkResultDict={} ):

        xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
        plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
        plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
        fontZoom = zoom
        if zoom == 2:
            fontZoom = 1.5

        #calculate plot scale
        #XZ: all of these global variables should be passed from function signiture
        ChrLengthDistList = self.ChrLengthMbList
        drawRegionDistance = self.ChrLengthMbSum
        GraphInterval=self.GraphInterval
        ChrList =self.ChrList

        #multiple chromosome view
        plotXScale = plotWidth / ((len(ChrList)-1)*GraphInterval + drawRegionDistance)

        startPosX = xLeftOffset
        chrLabelFont=pid.Font(ttf="verdana",size=24*fontZoom,bold=0)

        for i, _chr in enumerate(ChrList):

            if (i % 2 == 0):
                theBackColor = self.GRAPH_BACK_DARK_COLOR
            else:
                theBackColor = self.GRAPH_BACK_LIGHT_COLOR
            # NL:resize chr width for drawing
            if float(ChrLengthDistList[i])<90:
                ChrLengthDistList[i]=90
            #draw the shaded boxes and the sig/sug thick lines
            canvas.drawRect(startPosX, yTopOffset, startPosX + ChrLengthDistList[i]*plotXScale, \
                            yTopOffset+plotHeight, edgeColor=pid.gainsboro,fillColor=theBackColor)

            chrNameWidth = canvas.stringWidth(_chr, font=chrLabelFont)
            chrStartPix = startPosX + (ChrLengthDistList[i]*plotXScale -chrNameWidth)/2
            chrEndPix = startPosX + (ChrLengthDistList[i]*plotXScale +chrNameWidth)/2

            canvas.drawString(_chr, chrStartPix, yTopOffset +20,font = chrLabelFont,color=pid.dimgray)
            COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix,yTopOffset +20)

            #add by NL 09-03-2010
            HREF = "javascript:changeView(%d,%s);" % (i,ChrLengthDistList)
            Areas = HT.Area(shape='rect',coords=COORDS,href=HREF)
            gifmap.areas.append(Areas)
            startPosX +=  (ChrLengthDistList[i]+GraphInterval)*plotXScale

        return plotXScale


    def drawGraphBackground(self, canvas, gifmap, offset= (80, 120, 80, 50), zoom = 1, startMb = None, endMb = None):
        ##conditions
        ##multiple Chromosome view
        ##single Chromosome Physical
        ##single Chromosome Genetic
        xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
        plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
        plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
        fontZoom = zoom
        if zoom == 2:
            fontZoom = 1.5

        #calculate plot scale
        if self.plotScale != 'physic':
            self.ChrLengthDistList = self.ChrLengthCMList
            drawRegionDistance = self.ChrLengthCMSum
        else:
            self.ChrLengthDistList = self.ChrLengthMbList
            drawRegionDistance = self.ChrLengthMbSum

        if self.selectedChr > -1: #single chromosome view
            spacingAmt = plotWidth/13.5
            i = 0
            for startPix in Plot.frange(xLeftOffset, xLeftOffset+plotWidth, spacingAmt):
                if (i % 2 == 0):
                    theBackColor = self.GRAPH_BACK_DARK_COLOR
                else:
                    theBackColor = self.GRAPH_BACK_LIGHT_COLOR
                i += 1
                canvas.drawRect(startPix, yTopOffset, min(startPix+spacingAmt, xLeftOffset+plotWidth), \
                        yTopOffset+plotHeight, edgeColor=theBackColor, fillColor=theBackColor)

            drawRegionDistance = self.ChrLengthDistList[self.selectedChr]
            self.ChrLengthDistList = [drawRegionDistance]
            if self.plotScale == 'physic':
                plotXScale = plotWidth / (endMb-startMb)
            else:
                plotXScale = plotWidth / drawRegionDistance

        else:   #multiple chromosome view
            plotXScale = plotWidth / ((len(self.genotype)-1)*self.GraphInterval + drawRegionDistance)

            startPosX = xLeftOffset
            chrLabelFont=pid.Font(ttf="verdana",size=24*fontZoom,bold=0)

            for i, _chr in enumerate(self.genotype):

                if (i % 2 == 0):
                    theBackColor = self.GRAPH_BACK_DARK_COLOR
                else:
                    theBackColor = self.GRAPH_BACK_LIGHT_COLOR

                #draw the shaded boxes and the sig/sug thick lines
                canvas.drawRect(startPosX, yTopOffset, startPosX + self.ChrLengthDistList[i]*plotXScale, \
                                yTopOffset+plotHeight, edgeColor=pid.gainsboro,fillColor=theBackColor)

                chrNameWidth = canvas.stringWidth(_chr.name, font=chrLabelFont)
                chrStartPix = startPosX + (self.ChrLengthDistList[i]*plotXScale -chrNameWidth)/2
                chrEndPix = startPosX + (self.ChrLengthDistList[i]*plotXScale +chrNameWidth)/2

                canvas.drawString(_chr.name, chrStartPix, yTopOffset +20,font = chrLabelFont,color=pid.dimgray)
                COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix,yTopOffset +20)

                #add by NL 09-03-2010
                HREF = "javascript:changeView(%d,%s);" % (i,self.ChrLengthMbList)
                Areas = HT.Area(shape='rect',coords=COORDS,href=HREF)
                gifmap.areas.append(Areas)
                startPosX +=  (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale

        return plotXScale

    # XZ: The only difference of function drawXAxisForPLINK and function drawXAxis are the function name and the self.plotScale condition.
    def drawXAxisForPLINK(self, fd, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
        xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
        plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
        plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
        yZero = canvas.size[1] - yBottomOffset
        fontZoom = zoom
        if zoom == 2:
            fontZoom = 1.5

        #Parameters
        ChrLengthDistList = self.ChrLengthMbList
        GraphInterval=self.GraphInterval

        NUM_MINOR_TICKS = 5 # Number of minor ticks between major ticks
        X_MAJOR_TICK_THICKNESS = 2
        X_MINOR_TICK_THICKNESS = 1
        X_AXIS_THICKNESS = 1*zoom

        # ======= Alex: Draw the X-axis labels (megabase location)
        MBLabelFont = pid.Font(ttf="verdana", size=12*fontZoom, bold=0)
        xMajorTickHeight = 15 # How high the tick extends below the axis
        xMinorTickHeight = 5*zoom
        xAxisTickMarkColor = pid.black
        xAxisLabelColor = pid.black
        fontHeight = 12*fontZoom # How tall the font that we're using is
        spacingFromLabelToAxis = 20
        spacingFromLineToLabel = 3

        if self.plotScale == 'physic':
            strYLoc = yZero + spacingFromLabelToAxis + canvas.fontHeight(MBLabelFont)
            ###Physical single chromosome view
            if self.selectedChr > -1:
                graphMbWidth  = endMb - startMb
                XScale = Plot.detScale(startMb, endMb)
                XStart, XEnd, XStep = XScale
                if XStep < 8:
                    XStep *= 2
                spacingAmtX = spacingAmt = (XEnd-XStart)/XStep

                j = 0
                while  abs(spacingAmtX -int(spacingAmtX)) >= spacingAmtX/100.0 and j < 6:
                    j += 1
                    spacingAmtX *= 10

                formatStr = '%%2.%df' % j

                for counter, _Mb in enumerate(Plot.frange(XStart, XEnd, spacingAmt / NUM_MINOR_TICKS)):
                    if _Mb < startMb or _Mb > endMb:
                        continue
                    Xc = xLeftOffset + plotXScale*(_Mb - startMb)
                    if counter % NUM_MINOR_TICKS == 0: # Draw a MAJOR mark, not just a minor tick mark
                        canvas.drawLine(Xc, yZero, Xc, yZero+xMajorTickHeight, color=xAxisTickMarkColor, width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark
                        labelStr = str(formatStr % _Mb) # What Mbase location to put on the label
                        strWidth = canvas.stringWidth(labelStr, font=MBLabelFont)
                        drawStringXc = (Xc - (strWidth / 2.0))
                        canvas.drawString(labelStr, drawStringXc, strYLoc, font=MBLabelFont, color=xAxisLabelColor, angle=0)
                    else:
                        canvas.drawLine(Xc, yZero, Xc, yZero+xMinorTickHeight, color=xAxisTickMarkColor, width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark
                    # end else

            ###Physical genome wide view
            else:
                distScale = 0
                startPosX = xLeftOffset
                for i, distLen in enumerate(ChrLengthDistList):
                    if distScale == 0: #universal scale in whole genome mapping
                        if distLen > 75:
                            distScale = 25
                        elif distLen > 30:
                            distScale = 10
                        else:
                            distScale = 5
                    for tickdists in range(distScale, ceil(distLen), distScale):
                        canvas.drawLine(startPosX + tickdists*plotXScale, yZero, startPosX + tickdists*plotXScale, yZero + 7, color=pid.black, width=1*zoom)
                        canvas.drawString(str(tickdists), startPosX+tickdists*plotXScale, yZero + 10*zoom, color=pid.black, font=MBLabelFont, angle=270)
                    startPosX +=  (ChrLengthDistList[i]+GraphInterval)*plotXScale

            megabaseLabelFont = pid.Font(ttf="verdana", size=14*zoom*1.5, bold=0)
            canvas.drawString("Megabases", xLeftOffset + (plotWidth -canvas.stringWidth("Megabases", font=megabaseLabelFont))/2,
                    strYLoc + canvas.fontHeight(MBLabelFont) + 5*zoom, font=megabaseLabelFont, color=pid.black)
            pass

        canvas.drawLine(xLeftOffset, yZero, xLeftOffset+plotWidth, yZero, color=pid.black, width=X_AXIS_THICKNESS) # Draw the X axis itself

    def drawXAxis(self, fd, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
        xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
        plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
        plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
        yZero = canvas.size[1] - yBottomOffset
        fontZoom = zoom
        if zoom == 2:
            fontZoom = 1.5

        #Parameters
        NUM_MINOR_TICKS = 5 # Number of minor ticks between major ticks
        X_MAJOR_TICK_THICKNESS = 2
        X_MINOR_TICK_THICKNESS = 1
        X_AXIS_THICKNESS = 1*zoom

        # ======= Alex: Draw the X-axis labels (megabase location)
        MBLabelFont = pid.Font(ttf="verdana", size=12*fontZoom, bold=0)
        xMajorTickHeight = 15 # How high the tick extends below the axis
        xMinorTickHeight = 5*zoom
        xAxisTickMarkColor = pid.black
        xAxisLabelColor = pid.black
        fontHeight = 12*fontZoom # How tall the font that we're using is
        spacingFromLabelToAxis = 20
        spacingFromLineToLabel = 3

        if self.plotScale == 'physic':
            strYLoc = yZero + spacingFromLabelToAxis + canvas.fontHeight(MBLabelFont)
            ###Physical single chromosome view
            if self.selectedChr > -1:
                graphMbWidth  = endMb - startMb
                XScale = Plot.detScale(startMb, endMb)
                XStart, XEnd, XStep = XScale
                if XStep < 8:
                    XStep *= 2
                spacingAmtX = spacingAmt = (XEnd-XStart)/XStep

                j = 0
                while  abs(spacingAmtX -int(spacingAmtX)) >= spacingAmtX/100.0 and j < 6:
                    j += 1
                    spacingAmtX *= 10

                formatStr = '%%2.%df' % j

                for counter, _Mb in enumerate(Plot.frange(XStart, XEnd, spacingAmt / NUM_MINOR_TICKS)):
                    if _Mb < startMb or _Mb > endMb:
                        continue
                    Xc = xLeftOffset + plotXScale*(_Mb - startMb)
                    if counter % NUM_MINOR_TICKS == 0: # Draw a MAJOR mark, not just a minor tick mark
                        canvas.drawLine(Xc, yZero, Xc, yZero+xMajorTickHeight, color=xAxisTickMarkColor, width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark
                        labelStr = str(formatStr % _Mb) # What Mbase location to put on the label
                        strWidth = canvas.stringWidth(labelStr, font=MBLabelFont)
                        drawStringXc = (Xc - (strWidth / 2.0))
                        canvas.drawString(labelStr, drawStringXc, strYLoc, font=MBLabelFont, color=xAxisLabelColor, angle=0)
                    else:
                        canvas.drawLine(Xc, yZero, Xc, yZero+xMinorTickHeight, color=xAxisTickMarkColor, width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark
                    # end else

            ###Physical genome wide view
            else:
                distScale = 0
                startPosX = xLeftOffset
                for i, distLen in enumerate(self.ChrLengthDistList):
                    if distScale == 0: #universal scale in whole genome mapping
                        if distLen > 75:
                            distScale = 25
                        elif distLen > 30:
                            distScale = 10
                        else:
                            distScale = 5
                    for tickdists in range(distScale, ceil(distLen), distScale):
                        canvas.drawLine(startPosX + tickdists*plotXScale, yZero, startPosX + tickdists*plotXScale, yZero + 7, color=pid.black, width=1*zoom)
                        canvas.drawString(str(tickdists), startPosX+tickdists*plotXScale, yZero + 10*zoom, color=pid.black, font=MBLabelFont, angle=270)
                    startPosX +=  (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale

            megabaseLabelFont = pid.Font(ttf="verdana", size=14*zoom*1.5, bold=0)
            canvas.drawString("Megabases", xLeftOffset + (plotWidth -canvas.stringWidth("Megabases", font=megabaseLabelFont))/2,
                    strYLoc + canvas.fontHeight(MBLabelFont) + 5*zoom, font=megabaseLabelFont, color=pid.black)
            pass
        else:
            ChrAInfo = []
            preLpos = -1
            distinctCount = 0.0
            if len(self.genotype) > 1:
                for i, _chr in enumerate(self.genotype):
                    thisChr = []
                    Locus0CM = _chr[0].cM
                    nLoci = len(_chr)
                    if  nLoci <= 8:
                        for _locus in _chr:
                            if _locus.name != ' - ':
                                if _locus.cM != preLpos:
                                    distinctCount += 1
                                preLpos = _locus.cM
                                thisChr.append([_locus.name, _locus.cM-Locus0CM])
                    else:
                        for j in (0, nLoci/4, nLoci/2, nLoci*3/4, -1):
                            while _chr[j].name == ' - ':
                                j += 1
                            if _chr[j].cM != preLpos:
                                distinctCount += 1
                            preLpos = _chr[j].cM
                            thisChr.append([_chr[j].name, _chr[j].cM-Locus0CM])
                    ChrAInfo.append(thisChr)
            else:
                for i, _chr in enumerate(self.genotype):
                    thisChr = []
                    Locus0CM = _chr[0].cM
                    for _locus in _chr:
                        if _locus.name != ' - ':
                            if _locus.cM != preLpos:
                                distinctCount += 1
                            preLpos = _locus.cM
                            thisChr.append([_locus.name, _locus.cM-Locus0CM])
                    ChrAInfo.append(thisChr)

            stepA =  (plotWidth+0.0)/distinctCount

            LRectWidth = 10
            LRectHeight = 3
            offsetA = -stepA
            lineColor = pid.lightblue
            startPosX = xLeftOffset
            for j, ChrInfo in enumerate(ChrAInfo):
                preLpos = -1
                for i, item in enumerate(ChrInfo):
                    Lname,Lpos = item
                    if Lpos != preLpos:
                        offsetA += stepA
                        differ = 1
                    else:
                        differ = 0
                    preLpos = Lpos
                    Lpos *= plotXScale
                    if self.selectedChr > -1:
                        Zorder = i % 5
                    else:
                        Zorder = 0
                    if differ:
                        canvas.drawLine(startPosX+Lpos,yZero,xLeftOffset+offsetA,\
                        yZero+25, color=lineColor)
                        canvas.drawLine(xLeftOffset+offsetA,yZero+25,xLeftOffset+offsetA,\
                        yZero+40+Zorder*(LRectWidth+3),color=lineColor)
                        rectColor = pid.orange
                    else:
                        canvas.drawLine(xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3,\
                        xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3),color=lineColor)
                        rectColor = pid.deeppink
                    canvas.drawRect(xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3),\
                            xLeftOffset+offsetA-LRectHeight,yZero+40+Zorder*(LRectWidth+3)+LRectWidth,\
                            edgeColor=rectColor,fillColor=rectColor,edgeWidth = 0)
                    COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\
                            xLeftOffset+offsetA,yZero+40+Zorder*(LRectWidth+3)+LRectWidth)
                    HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname)
                    Areas=HT.Area(shape='rect',coords=COORDS,href=HREF, title="Locus : " + Lname)
                    gifmap.areas.append(Areas)
                ##piddle bug
                if j == 0:
                    canvas.drawLine(startPosX,yZero,startPosX,yZero+40, color=lineColor)
                startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale

        canvas.drawLine(xLeftOffset, yZero, xLeftOffset+plotWidth, yZero, color=pid.black, width=X_AXIS_THICKNESS) # Draw the X axis itself

    def getColorForMarker(self, chrCount,flag):# no change is needed
        chrColorDict={}
        for i in range(chrCount):
            if flag==1: # display blue and lightblue intercross
                chrColorDict[i]=pid.black
            elif flag==0:
                if (i%2==0):
                    chrColorDict[i]=pid.blue
                else:
                    chrColorDict[i]=pid.lightblue
            else:#display different color for different chr
                if i in [0,8,16]:
                    chrColorDict[i]=pid.black
                elif i in [1,9,17]:
                    chrColorDict[i]=pid.red
                elif i in [2,10,18]:
                    chrColorDict[i]=pid.lightgreen
                elif i in [3,11,19]:
                    chrColorDict[i]=pid.blue
                elif i in [4,12]:
                    chrColorDict[i]=pid.lightblue
                elif i in [5,13]:
                    chrColorDict[i]=pid.hotpink
                elif i in [6,14]:
                    chrColorDict[i]=pid.gold
                elif i in [7,15]:
                    chrColorDict[i]=pid.grey

        return chrColorDict


    def drawProbeSetPosition(self, canvas, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
        if len(self.traitList) != 1:
            return

        xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
        plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
        plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
        yZero = canvas.size[1] - yBottomOffset
        fontZoom = zoom
        if zoom == 2:
            fontZoom = 1.5

        try:
            Chr = self.traitList[0].chr # self.traitListChr =self.traitList[0].chr=_vals   need to change to chrList and mbList
            Mb = self.traitList[0].mb # self.traitListMb =self.traitList[0].mb=_vals
        except:
            return

        if self.plotScale == 'physic':
            if self.selectedChr > -1:
                if self.genotype[0].name != Chr or Mb < self.startMb or Mb > self.endMb:
                    return
                else:
                    locPixel = xLeftOffset + (Mb-self.startMb)*plotXScale
            else:
                locPixel = xLeftOffset
                for i, _chr in enumerate(self.genotype):
                    if _chr.name != Chr:
                        locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale
                    else:
                        locPixel += Mb*plotXScale
                        break
        else:
            if self.selectedChr > -1:
                if self.genotype[0].name != Chr:
                    return
                else:
                    for i, _locus in enumerate(self.genotype[0]):
                        #the trait's position is on the left of the first genotype
                        if i==0 and _locus.Mb >= Mb:
                            locPixel=-1
                            break

                        #the trait's position is between two traits
                        if i > 0 and self.genotype[0][i-1].Mb < Mb and _locus.Mb >= Mb:
                            locPixel = xLeftOffset + plotXScale*(self.genotype[0][i-1].cM+(_locus.cM-self.genotype[0][i-1].cM)*(Mb -self.genotype[0][i-1].Mb)/(_locus.Mb-self.genotype[0][i-1].Mb))
                            break

                        #the trait's position is on the right of the last genotype
                        if i==len(self.genotype[0]) and Mb>=_locus.Mb:
                            locPixel = -1
            else:
                locPixel = xLeftOffset
                for i, _chr in enumerate(self.genotype):
                    if _chr.name != Chr:
                        locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale
                    else:
                        locPixel += (Mb*(_chr[-1].cM-_chr[0].cM)/self.ChrLengthCMList[i])*plotXScale
                        break
        if locPixel >= 0:
            traitPixel = ((locPixel, yZero), (locPixel-6, yZero+12), (locPixel+6, yZero+12))
            canvas.drawPolygon(traitPixel, edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1)

        if self.legendChecked:
            startPosY = 15
            nCol = 2
            smallLabelFont = pid.Font(ttf="trebuc", size=12, bold=1)
            leftOffset = xLeftOffset+(nCol-1)*200
            canvas.drawPolygon(((leftOffset+6, startPosY-6), (leftOffset, startPosY+6), (leftOffset+12, startPosY+6)), edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1)
            canvas.drawString("Sequence Site", (leftOffset+15), (startPosY+5), smallLabelFont, self.TOP_RIGHT_INFO_COLOR)

    # build dict based on plink result, key is chr, value is list of [snp,BP,pValue]
    def getPlinkResultDict(self,outputFileName='',thresholdPvalue=-1,ChrOrderIdNameDict={}):

        ChrList =self.ChrList
        plinkResultDict={}

        plinkResultfp = open("%s%s.qassoc"% (webqtlConfig.TMPDIR, outputFileName), "rb")

        headerLine=plinkResultfp.readline()# read header line
        line = plinkResultfp.readline()

        valueList=[] # initialize value list, this list will include snp, bp and pvalue info
        pValueList=[]
        count=0

        while line:
            #convert line from str to list
            lineList=self.buildLineList(line=line)

            # only keep the records whose chromosome name is in db
            if ChrOrderIdNameDict.has_key(int(lineList[0])) and lineList[-1] and lineList[-1].strip()!='NA':

                chrName=ChrOrderIdNameDict[int(lineList[0])]
                snp = lineList[1]
                BP = lineList[2]
                pValue = float(lineList[-1])
                pValueList.append(pValue)

                if plinkResultDict.has_key(chrName):
                    valueList=plinkResultDict[chrName]

                    # pvalue range is [0,1]
                    if thresholdPvalue >=0 and thresholdPvalue<=1:
                        if pValue < thresholdPvalue:
                            valueList.append((snp,BP,pValue))
                            count+=1

                    plinkResultDict[chrName]=valueList
                    valueList=[]
                else:
                    if thresholdPvalue>=0 and thresholdPvalue<=1:
                        if pValue < thresholdPvalue:
                            valueList.append((snp,BP,pValue))
                            count+=1

                    if valueList:
                        plinkResultDict[chrName]=valueList

                    valueList=[]


                line =plinkResultfp.readline()
            else:
                line=plinkResultfp.readline()

        if pValueList:
            minPvalue= min(pValueList)
        else:
            minPvalue=0

        return count,minPvalue,plinkResultDict


    ######################################################
    # input: line: str,one line read from file
    # function: convert line from str to list;
    # output: lineList list
    #######################################################
    def buildLineList(self,line=None):

        lineList = string.split(string.strip(line),' ')# irregular number of whitespaces between columns
        lineList =[ item for item in lineList if item <>'']
        lineList = map(string.strip, lineList)

        return lineList

    #added by NL: automatically generate pheno txt file for PLINK based on strainList passed from dataEditing page
    def genPhenoTxtFileForPlink(self,phenoFileName='', RISetName='', probesetName='', valueDict={}):
        pedFileStrainList=self.getStrainNameFromPedFile(RISetName=RISetName)
        outputFile = open("%s%s.txt"%(webqtlConfig.TMPDIR,phenoFileName),"wb")
        headerLine = 'FID\tIID\t%s\n'%probesetName
        outputFile.write(headerLine)

        newValueList=[]

        #if valueDict does not include some strain, value will be set to -9999 as missing value
        for item in pedFileStrainList:
            try:
                value=valueDict[item]
                value=str(value).replace('value=','')
                value=value.strip()
            except:
                value=-9999

            newValueList.append(value)


        newLine=''
        for i, strain in enumerate(pedFileStrainList):
            j=i+1
            value=newValueList[i]
            newLine+='%s\t%s\t%s\n'%(strain, strain, value)

            if j%1000==0:
                outputFile.write(newLine)
                newLine=''

        if newLine:
            outputFile.write(newLine)

        outputFile.close()

    # get strain name from ped file in order
    def getStrainNameFromPedFile(self, RISetName=''):
        pedFileopen= open("%splink/%s.ped"%(webqtlConfig.HTMLPATH, RISetName),"r")
        line =pedFileopen.readline()
        strainNameList=[]

        while line:
            lineList=string.split(string.strip(line),'\t')
            lineList=map(string.strip,lineList)

            strainName=lineList[0]
            strainNameList.append(strainName)

            line =pedFileopen.readline()

        return strainNameList

    ################################################################
    # 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
                    """ % (RISet)
            self.cursor.execute(query)

            results =self.cursor.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