Add all the source codes into the github.

1 files changed, 2454 insertions, 0 deletions

diff --git a/web/webqtl/intervalMapping/IntervalMappingPage.py b/web/webqtl/intervalMapping/IntervalMappingPage.py
new file mode 100644
index 00000000..4bdf45ab
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+++ b/web/webqtl/intervalMapping/IntervalMappingPage.py
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+# 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 Zach 12/14/2010
+
+
+import time
+import string
+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
+
+#########################################
+#      Inteval Mapping Plot Page
+#########################################
+class IntervalMappingPage(templatePage):
+	cMGraphInterval = 5
+	maxBootStrap = 50
+	GRAPH_MIN_WIDTH = 900
+	GRAPH_MAX_WIDTH = 10000 # Don't set this too high
+	GRAPH_DEFAULT_WIDTH = 1280
+	MULT_GRAPH_DEFAULT_WIDTH = 2000
+	MULT_GRAPH_MIN_WIDTH = 1400
+	MULT_GRAPH_DEFAULT_WIDTH = 1600
+	GRAPH_DEFAULT_HEIGHT = 600
+
+
+	# Display order:
+	# UCSC BAND =========
+	# ENSEMBL BAND -=-=-=
+	# ** GENES **********
+	BAND_SPACING = 4
+
+	#ENSEMBL_BAND_Y      = UCSC_BAND_Y + UCSC_BAND_HEIGHT + BAND_SPACING
+	UCSC_BAND_HEIGHT = 10
+	ENSEMBL_BAND_HEIGHT = 10
+	WEBQTL_BAND_HEIGHT = 10
+
+	#GENE_START_Y        = ENSEMBL_BAND_Y + ENSEMBL_BAND_HEIGHT + BAND_SPACING
+	NUM_GENE_ROWS       = 10
+	EACH_GENE_HEIGHT    = 6  # number of pixels tall, for each gene to display
+	EACH_GENE_ARROW_WIDTH = 5
+	EACH_GENE_ARROW_SPACING = 14
+	DRAW_DETAIL_MB = 4
+	DRAW_UTR_LABELS_MB = 4
+
+	MIN_PIXELS_BETWEEN_LABELS = 50
+	
+	qmarkImg = HT.Image('/images/qmarkBoxBlue.gif', width=10, height=13, border=0, alt='Glossary')
+	# Note that "qmark.gif" is a similar, smaller, rounded-edges question mark. It doesn't look
+	# like the ones on the image, though, which is why we don't use it here.
+	
+	HELP_WINDOW_NAME = 'helpWind'
+	
+	## BEGIN HaplotypeAnalyst
+	NR_INDIVIDUALS = 0
+	## END HaplotypeAnalyst
+	
+	ALEX_DEBUG_BOOL_COLORIZE_GENES = 1 # 0=don't colorize, 1=colorize
+	ALEX_DEBUG_BOOL_PRINT_GENE_LIST = 1
+	
+	kWIDTH_DEFAULT=1
+	
+	kONE_MILLION = 1000000
+	
+	LODFACTOR = 4.61
+	
+	SNP_COLOR           = pid.orange # Color for the SNP "seismograph"
+	TRANSCRIPT_LOCATION_COLOR = pid.mediumpurple
+	
+	GENE_FILL_COLOR     = pid.HexColor(0x6666FF)
+	GENE_OUTLINE_COLOR  = pid.HexColor(0x000077)
+	BOOTSTRAP_BOX_COLOR = pid.yellow
+	LRS_COLOR           = pid.HexColor(0x0000FF)
+	LRS_LINE_WIDTH = 2
+	SIGNIFICANT_COLOR   = pid.HexColor(0xEBC7C7)
+	SUGGESTIVE_COLOR    = pid.gainsboro
+	SIGNIFICANT_WIDTH = 5
+	SUGGESTIVE_WIDTH = 5
+	ADDITIVE_COLOR_POSITIVE = pid.green
+	ADDITIVE_COLOR_NEGATIVE = pid.red
+	ADDITIVE_COLOR = ADDITIVE_COLOR_POSITIVE
+	DOMINANCE_COLOR_POSITIVE = pid.darkviolet
+	DOMINANCE_COLOR_NEGATIVE = pid.orange
+	
+	## BEGIN HaplotypeAnalyst
+	HAPLOTYPE_POSITIVE = pid.green
+	HAPLOTYPE_NEGATIVE = pid.red
+	HAPLOTYPE_HETEROZYGOUS = pid.blue
+	HAPLOTYPE_RECOMBINATION = pid.darkgray
+	## END HaplotypeAnalyst
+	
+	QMARK_EDGE_COLOR    = pid.HexColor(0x718118)
+	QMARK_FILL_COLOR    = pid.HexColor(0xDEE3BB)
+	
+	TOP_RIGHT_INFO_COLOR = pid.black
+	X_AXIS_LABEL_COLOR  = pid.black #HexColor(0x505050)
+	
+	MINI_VIEW_MAGNIFIED_REGION_COLOR = pid.HexColor(0xCC0000)
+	MINI_VIEW_OUTSIDE_REGION_COLOR   = pid.HexColor(0xEEEEEE)
+	MINI_VIEW_BORDER_COLOR           = pid.black
+	
+	CLICKABLE_WEBQTL_REGION_COLOR     = pid.HexColor(0xF5D3D3)
+	CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR = pid.HexColor(0xFCE9E9)
+	CLICKABLE_WEBQTL_TEXT_COLOR       = pid.HexColor(0x912828)
+	
+	CLICKABLE_UCSC_REGION_COLOR     = pid.HexColor(0xDDDDEE)
+	CLICKABLE_UCSC_REGION_OUTLINE_COLOR = pid.HexColor(0xEDEDFF)
+	CLICKABLE_UCSC_TEXT_COLOR       = pid.HexColor(0x333366)
+	
+	CLICKABLE_ENSEMBL_REGION_COLOR  = pid.HexColor(0xEEEEDD)
+	CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR = pid.HexColor(0xFEFEEE)
+	CLICKABLE_ENSEMBL_TEXT_COLOR    = pid.HexColor(0x555500)
+	
+	GRAPH_BACK_LIGHT_COLOR = pid.HexColor(0xFBFBFF)
+	GRAPH_BACK_DARK_COLOR  = pid.HexColor(0xF1F1F9)
+	
+	HELP_PAGE_REF = '/glossary.html'
+	
+	DRAW_UTR_LABELS=0
+	
+	def __init__(self,fd):
+
+		templatePage.__init__(self, fd)
+
+		if not self.openMysql():
+			return
+
+		#RISet and Species
+		if not fd.genotype:
+			fd.readGenotype()
+		
+		fd.parentsf14regression = fd.formdata.getvalue('parentsf14regression')
+		
+		if ((fd.parentsf14regression == 'on') and fd.genotype_2):
+			fd.genotype = fd.genotype_2
+		else:
+			fd.genotype = fd.genotype_1
+		fd.strainlist = list(fd.genotype.prgy)
+
+		self.species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
+		if self.species == "rat":
+			self._ucscDb = "rn3"
+		elif self.species == "mouse":
+			self._ucscDb = "mm9"
+		else:
+			self._ucscDb = ""
+
+		#####################################
+		# Options
+		#####################################
+		#Mapping options
+		self.plotScale = fd.formdata.getvalue('scale', 'physic')
+		if self.plotScale == 'physic' and not fd.genotype.Mbmap:
+			self.plotScale = 'morgan'
+		self.permChecked = fd.formdata.getvalue('permCheck')
+		self.bootChecked = fd.formdata.getvalue('bootCheck', '')
+		self.controlLocus = fd.formdata.getvalue('controlLocus', '')
+		try:
+			self.selectedChr = int(fd.formdata.getvalue('chromosomes', "-1"))
+		except:
+			self.selectedChr = -1
+
+		#whether include parents and F1 for InbredSet
+		fd.parentsf14regression = fd.formdata.getvalue('parentsf14regression')
+		if ((fd.parentsf14regression == 'on') and fd.genotype_2):
+			fd.genotype = fd.genotype_2
+		else:
+			fd.genotype = fd.genotype_1
+		self.strainlist = list(fd.genotype.prgy)
+		self.genotype = fd.genotype
+
+		#Darwing Options
+		try:
+			if self.selectedChr > -1:
+				self.graphWidth  = min(self.GRAPH_MAX_WIDTH, max(self.GRAPH_MIN_WIDTH, int(fd.formdata.getvalue('graphWidth'))))
+			else:
+				self.graphWidth  = min(self.GRAPH_MAX_WIDTH, max(self.MULT_GRAPH_MIN_WIDTH, int(fd.formdata.getvalue('graphWidth'))))
+		except:
+			if self.selectedChr > -1:
+				self.graphWidth  = self.GRAPH_DEFAULT_WIDTH
+			else:
+				self.graphWidth  = self.MULT_GRAPH_DEFAULT_WIDTH
+				
+## BEGIN HaplotypeAnalyst
+		self.haplotypeAnalystChecked = fd.formdata.getvalue('haplotypeAnalystCheck')
+## END HaplotypeAnalyst
+
+
+		self.graphHeight = self.GRAPH_DEFAULT_HEIGHT
+		self.additiveChecked = fd.formdata.getvalue('additiveCheck')
+		self.dominanceChecked = fd.formdata.getvalue('dominanceCheck')
+		self.LRS_LOD = fd.formdata.getvalue('LRSCheck', 'LRS')
+		self.intervalAnalystChecked = fd.formdata.getvalue('intervalAnalystCheck')
+		self.legendChecked = fd.formdata.getvalue('viewLegend')
+		self.geneChecked = fd.formdata.getvalue('showGenes')
+		self.SNPChecked  = fd.formdata.getvalue('showSNP')
+		self.draw2X = fd.formdata.getvalue('draw2X')
+		self.lrsMax = float(fd.formdata.getvalue('lrsMax', 0))
+
+		self.startMb  = fd.formdata.getvalue('startMb', "-1")
+		self.endMb  = fd.formdata.getvalue('endMb', "-1")
+		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
+		#Trait Infos
+		self.identification = fd.formdata.getvalue('identification', "")
+
+		################################################################
+		# Generate Chr list and Retrieve Length Information
+		################################################################
+		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)
+
+		if self.plotScale == 'physic':
+			self.GraphInterval = self.MbGraphInterval #Mb
+		else:
+			self.GraphInterval = self.cMGraphInterval #cM
+
+
+		################################################################
+		# Get Trait Values and Infomation
+		################################################################
+		#input from search page or selection page
+		self.searchResult = fd.formdata.getvalue('searchResult')
+		#convert single selection into a list
+		if type("1") == type(self.searchResult):
+			self.searchResult = string.split(self.searchResult,'\t')
+		
+		self.traitList = []
+		if self.searchResult and len(self.searchResult) > webqtlConfig.MULTIPLEMAPPINGLIMIT:
+			heading = 'Multiple Interval Mapping'
+			detail = ['In order to get clear result, do not select more than %d traits for \
+				Multiple Interval Mapping analysis.' % webqtlConfig.MULTIPLEMAPPINGLIMIT]
+			self.error(heading=heading,detail=detail)
+			return
+		elif self.searchResult:
+			self.dataSource = 'selectionPage'
+			for item in self.searchResult:
+				thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
+				thisTrait.retrieveInfo()
+				thisTrait.retrieveData(fd.strainlist)
+				self.traitList.append(thisTrait)
+		else:
+			#input from data editing page
+			fd.readData()
+			if not fd.allTraitData:
+				heading = "Mapping"
+				detail = ['No trait data was selected for %s data set. No mapping attempted.' % fd.RISet]
+				self.error(heading=heading,detail=detail)
+				return
+			
+			self.dataSource = 'editingPage'
+			fullname = fd.formdata.getvalue('fullname', '')
+			if fullname:
+				thisTrait = webqtlTrait(fullname=fullname, data=fd.allTraitData, cursor=self.cursor)
+				thisTrait.retrieveInfo()
+			else:
+				thisTrait = webqtlTrait(data=fd.allTraitData)
+			self.traitList.append(thisTrait)
+
+
+
+
+
+
+	
+## BEGIN HaplotypeAnalyst
+## count the amount of individuals to be plotted, and increase self.graphHeight
+		if self.haplotypeAnalystChecked and self.selectedChr > -1:
+			thisTrait = self.traitList[0]
+			_strains, _vals, _vars = thisTrait.exportInformative()
+			smd=[]
+			for ii, _val in enumerate(_vals):
+				temp = GeneralObject(name=_strains[ii], value=_val)
+				smd.append(temp)
+			bxdlist=list(self.genotype.prgy)
+			for j,_geno in enumerate (self.genotype[0][1].genotype):
+				for item in smd:
+					if item.name == bxdlist[j]:
+						self.NR_INDIVIDUALS = self.NR_INDIVIDUALS + 1
+## default: 
+			self.graphHeight = self.graphHeight + 2 * (self.NR_INDIVIDUALS+10) * self.EACH_GENE_HEIGHT
+## for paper: 
+			#self.graphHeight = self.graphHeight + 1 * self.NR_INDIVIDUALS * self.EACH_GENE_HEIGHT - 180
+
+
+			
+## END HaplotypeAnalyst
+
+		################################################################
+		# Calculations QTL goes here
+		################################################################
+		self.multipleInterval = len(self.traitList) > 1
+		errorMessage = self.calculateAllResult(fd)
+		if errorMessage:
+			heading = "Mapping"
+			detail = ['%s' % errorMessage]
+			self.error(heading=heading,detail=detail)
+			return
+
+		if self.multipleInterval:
+			self.colorCollection = Plot.colorSpectrum(len(self.qtlresults))
+		else:
+			self.colorCollection = [self.LRS_COLOR]
+
+
+		#########################
+		## Get the sorting column
+		#########################
+		RISet = fd.RISet
+		if RISet in ('AXB', 'BXA', 'AXBXA'):
+			self.diffCol = ['B6J', 'A/J']
+		elif RISet in ('BXD', 'BXD300', 'B6D2F2', 'BDF2-2005', 'BDF2-1999', 'BHHBF2'):
+			self.diffCol = ['B6J', 'D2J']
+		elif RISet in ('CXB'):
+			self.diffCol = ['CBY', 'B6J']
+		elif RISet in ('BXH', 'BHF2'):
+			self.diffCol = ['B6J', 'C3H']
+		elif RISet in ('B6BTBRF2'):
+			self.diffCol = ['B6J', 'BTB']
+		elif RISet in ('LXS'):
+			self.diffCol = ['ILS', 'ISS']
+		else:
+			self.diffCol= []
+
+		for i, strain in enumerate(self.diffCol):
+			self.cursor.execute("select Id from Strain where Symbol = %s", strain)
+			self.diffCol[i] = self.cursor.fetchone()[0]
+		#print self.diffCol
+		
+		################################################################
+		# GeneCollection goes here
+		################################################################
+		if self.plotScale == 'physic':
+			#StartMb or EndMb
+			if self.startMb < 0 or self.endMb < 0:
+				self.startMb = 0
+				self.endMb = self.ChrLengthMbList[self.selectedChr]
+
+		geneTable = ""
+		if self.plotScale == 'physic' and self.selectedChr > -1 and (self.intervalAnalystChecked  or self.geneChecked):
+			chrName = self.genotype[0].name
+			# Draw the genes for this chromosome / region of this chromosome
+			if self.traitList and self.traitList[0] and len(self.traitList) == 1 and self.traitList[0].db:
+				webqtldatabase = self.traitList[0].db.name
+			else:
+				webqtldatabase = None
+
+			self.geneCol = None
+
+			if self.species == "mouse":
+				self.geneCol = GeneUtil.loadGenes(self.cursor, chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "mouse")
+			elif self.species == "rat":
+				self.geneCol = GeneUtil.loadGenes(self.cursor, chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "rat")
+			else:
+				self.geneCol = None
+
+			if self.geneCol and self.intervalAnalystChecked:
+				#######################################################################
+				#Nick use GENEID as RefGene to get Literature Correlation Informations#
+				#For Interval Mapping, Literature Correlation isn't useful, so skip it#
+				#through set GENEID is None                                           #
+				########################################################################
+
+				#GENEID = fd.formdata.getvalue('GeneId') or None
+				GENEID = None
+				geneTable = self.geneTables(self.geneCol,GENEID)
+
+		else:
+			self.geneCol = None
+
+		################################################################
+		# Plots goes here
+		################################################################
+		if self.plotScale != 'physic' or self.multipleInterval:
+			showLocusForm =  webqtlUtil.genRandStr("fm_")
+		else:
+			showLocusForm = ""
+		intCanvas = pid.PILCanvas(size=(self.graphWidth,self.graphHeight))
+		gifmap = self.plotIntMapping(fd, intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm)
+
+		filename= webqtlUtil.genRandStr("Itvl_")
+		intCanvas.save(os.path.join(webqtlConfig.IMGDIR, filename), format='png')
+		intImg=HT.Image('/image/'+filename+'.png', border=0, usemap='#WebQTLImageMap')
+
+		if self.draw2X:
+			intCanvasX2 = pid.PILCanvas(size=(self.graphWidth*2,self.graphHeight*2))
+			gifmapX2 = self.plotIntMapping(fd, intCanvasX2, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm, zoom=2)
+			intCanvasX2.save(os.path.join(webqtlConfig.IMGDIR, filename+"X2"), format='png')
+			DLintImgX2=HT.Href(text='Download',url = '/image/'+filename+'X2.png', Class='smallsize', target='_blank')
+
+		textUrl = self.writeQTL2Text(fd, filename)
+
+		################################################################
+		# Info tables goes here
+		################################################################
+		traitInfoTD = self.traitInfoTD(fd)
+		
+		if self.draw2X:
+			traitInfoTD.append(HT.P(), DLintImgX2, ' a higher resolution 2X image. ')
+		else:
+			traitInfoTD.append(HT.P())
+			
+		if textUrl:
+			traitInfoTD.append(HT.BR(), textUrl, ' results in tab-delimited text format.')
+		traitRemapTD = self.traitRemapTD(self.cursor, fd)
+		
+		topTable = HT.TableLite(HT.TR(traitInfoTD, HT.TD("&nbsp;", width=25), traitRemapTD), border=0, cellspacing=0, cellpadding=0)
+		
+		################################################################
+		# Outputs goes here
+		################################################################
+		#this form is used for opening Locus page or trait page, only available for genetic mapping
+		if showLocusForm:
+			showLocusForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', 
+				name=showLocusForm, submit=HT.Input(type='hidden'))
+			hddn = {'FormID':'showDatabase', 'ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'}
+			for key in hddn.keys():
+				showLocusForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
+			showLocusForm.append(intImg)
+		else:
+			showLocusForm = intImg
+		
+		################################################################
+		# 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)
+		
+		if self.traitList and self.traitList[0].db and self.traitList[0].db.type == 'Geno':
+			btminfo.append(HT.BR(), 'Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.')
+			
+		TD_LR = HT.TD(HT.Blockquote(topTable), HT.Blockquote(gifmap, showLocusForm, HT.P(), btminfo), bgColor='#eeeeee', height = 200)
+		
+		if geneTable:
+			iaForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, "main.py?FormID=intervalAnalyst"), enctype='multipart/form-data', 
+				name="iaForm", submit=HT.Input(type='hidden'))
+			hddn = {'chromosome':self.genotype[0].name, 'species':self.species,'startMb':self.startMb,'endMb':self.endMb}
+			if self.diffCol:
+				hddn['s1'] = self.diffCol[0] 
+				hddn['s2'] = self.diffCol[1]
+			for key in hddn.keys():
+				iaForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
+			iaForm.append(HT.Paragraph("Interval Analyst : Chr %s from %2.6f to %2.6f Mb" % (self.genotype[0].name, self.startMb, self.endMb), 
+				HT.Input(name='customize', value='Customize', onClick= "formInNewWindow(this.form);", type='button', Class="button"), Class="subtitle"))
+			TD_LR.append(HT.Blockquote(iaForm, geneTable))
+		
+		self.dict['body'] = TD_LR
+		self.dict['title'] = "Mapping"
+
+	def writeQTL2Text(self, fd, filename):
+		if self.multipleInterval:
+			return ""
+		_dominance = (self.genotype.type == 'intercross') 
+		_Mb = self.genotype.Mbmap
+		
+		###Write to text file
+		fpText = open(os.path.join(webqtlConfig.TMPDIR, filename) + '.txt','wb')
+
+		fpText.write("Source: WebQTL, The GeneNetwork (%s)\n" % webqtlConfig.PORTADDR)
+		#
+		fpText.write("Site: %s\n" % webqtlConfig.SITENAME)
+		fpText.write("Page: Map Viewer\n")
+		fpText.write(time.strftime("Date and Time (US Center): %b %d, %Y at %I.%M %p\n", time.localtime()))
+		fpText.write("Trait ID: %s\n" % fd.identification)
+		fpText.write("Suggestive LRS = %0.2f\n" % self.suggestive)
+		fpText.write("Significant LRS = %0.2f\n" % self.significance)
+		"""
+		if fd.traitInfo:
+			writeSymbol, writeChromosome, writeMb = string.split(fd.traitInfo)
+		else:
+			writeSymbol, writeChromosome, writeMb = (" ", " ", " ")
+		fpText.write("Gene Symbol: %s\n" % writeSymbol)
+		fpText.write("Location: Chr %s @ %s Mb\n" % (writeChromosome, writeMb))
+		selectedChr = self.indexToChrName(int(fd.formdata.getvalue('chromosomes', -1)))
+		fpText.write("Chromosome: %s\n" % selectedChr)
+		fpText.write("Region: %0.6f-%0.6f Mb\n\n" % (self.startMb, self.endMb))
+		"""
+
+		if hasattr(self, 'LRSArray'):		
+			if _dominance:
+				fpText.write('Chr\tLocus\tcM\tMb\tLRS\tP-value\tAdditive\tDominance\n')
+			else:
+				fpText.write('Chr\tLocus\tcM\tMb\tLRS\tP-value\tAdditive\n')
+		else:
+			if _dominance:
+                                fpText.write('Chr\tLocus\tcM\tMb\tLRS\tAdditive\tDominance\n')
+                        else:
+                                fpText.write('Chr\tLocus\tcM\tMb\tLRS\tAdditive\n')
+			
+		i = 0
+		for qtlresult in self.qtlresults[0]:
+			if _Mb:
+				locusMb = '%2.3f' % qtlresult.locus.Mb
+			else:
+				locusMb = 'N/A'
+
+			if hasattr(self, 'LRSArray'):
+				P_value = self.calculatePValue(qtlresult.lrs, self.LRSArray)
+
+				if _dominance:
+					fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\t%2.3f\t%2.3f\t%2.3f\n" %(qtlresult.locus.chr, \
+						qtlresult.locus.name, qtlresult.locus.cM, locusMb , qtlresult.lrs, P_value,  qtlresult.additive, qtlresult.dominance))
+				else:
+					fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\t%2.3f\t%2.3f\n" %(qtlresult.locus.chr, \
+						qtlresult.locus.name, qtlresult.locus.cM, locusMb , qtlresult.lrs, P_value,  qtlresult.additive))
+			else:
+				if _dominance:
+					fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\t%2.3f\t%2.3f\n" %(qtlresult.locus.chr, \
+						qtlresult.locus.name, qtlresult.locus.cM, locusMb , qtlresult.lrs, qtlresult.additive, qtlresult.dominance))
+				else:
+					fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\t%2.3f\n" %(qtlresult.locus.chr, \
+						qtlresult.locus.name, qtlresult.locus.cM, locusMb , qtlresult.lrs, qtlresult.additive))
+
+			i += 1
+
+		fpText.close()
+		textUrl = HT.Href(text = 'Download', url= '/tmp/'+filename+'.txt', target = "_blank", Class='smallsize')
+		return textUrl
+	
+	def plotIntMapping(self, fd, canvas, offset= (80, 120, 20, 80), zoom = 1, startMb = None, endMb = None, showLocusForm = ""):
+		#calculating margins
+		xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+		if self.multipleInterval:
+			yTopOffset = max(80, yTopOffset)
+		else:
+			if self.legendChecked:
+				yTopOffset = max(80, yTopOffset)
+			else:
+				pass
+		
+		if self.plotScale != 'physic':
+			yBottomOffset = max(120, yBottomOffset)
+		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:
+			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:
+				drawAreaHeight -= 30
+
+## BEGIN HaplotypeAnalyst
+		if self.haplotypeAnalystChecked and self.selectedChr > -1:
+			drawAreaHeight -= self.EACH_GENE_HEIGHT * (self.NR_INDIVIDUALS+10) * 2 * zoom
+## END HaplotypeAnalyst
+
+		#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 bootstap
+		if self.bootChecked and not self.multipleInterval:
+			self.drawBootStrapResult(canvas, fd.nboot, drawAreaHeight, plotXScale, offset=newoffset)
+		
+		# Draw clickable region and gene band if selected
+		if self.plotScale == 'physic' and self.selectedChr > -1:
+			self.drawClickBand(canvas, gifmap, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
+			if self.geneChecked and self.geneCol:
+				self.drawGeneBand(canvas, gifmap, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
+			if self.SNPChecked:
+				self.drawSNPTrackNew(canvas, offset=newoffset, zoom= 2*zoom, startMb=startMb, endMb = endMb)
+## BEGIN HaplotypeAnalyst
+			if self.haplotypeAnalystChecked:
+				self.drawHaplotypeBand(canvas, gifmap, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
+## END HaplotypeAnalyst		
+		# 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
+	
+	def drawBootStrapResult(self, canvas, nboot, drawAreaHeight, 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
+		yZero = canvas.size[1] - yBottomOffset
+		fontZoom = zoom
+		if zoom == 2:
+			fontZoom = 1.5
+		
+		bootHeightThresh = drawAreaHeight*3/4
+		
+		#break bootstrap result into groups
+		BootCoord = []
+		i = 0
+		startX = xLeftOffset
+		for j, _chr in enumerate(self.genotype):
+			BootCoord.append( [])
+			for _locus in _chr:
+				if self.plotScale == 'physic':
+					Xc = startX + (_locus.Mb-self.startMb)*plotXScale
+				else:
+					Xc = startX + (_locus.cM-_chr[0].cM)*plotXScale
+				BootCoord[-1].append([Xc, self.bootResult[i]])
+				i += 1
+			startX += (self.ChrLengthDistList[j] + self.GraphInterval)*plotXScale
+		
+		#reduce bootResult
+		if self.selectedChr > -1:
+			maxBootBar = 80.0
+		else:
+			maxBootBar = 200.0
+		stepBootStrap = plotWidth/maxBootBar
+		reducedBootCoord = []
+		maxBootCount = 0
+		
+		for BootChrCoord in BootCoord:
+			nBoot = len(BootChrCoord)
+			bootStartPixX = BootChrCoord[0][0]
+			bootCount = BootChrCoord[0][1]
+			for i in range(1, nBoot):
+				if BootChrCoord[i][0] - bootStartPixX < stepBootStrap:
+					bootCount += BootChrCoord[i][1]
+					continue
+				else:
+					if maxBootCount < bootCount:
+						maxBootCount = bootCount
+					# end if
+					reducedBootCoord.append([bootStartPixX, BootChrCoord[i][0], bootCount])
+					bootStartPixX = BootChrCoord[i][0]
+					bootCount = BootChrCoord[i][1]
+				# end else
+			# end for
+			#add last piece		
+			if BootChrCoord[-1][0] - bootStartPixX  > stepBootStrap/2.0:
+				reducedBootCoord.append([bootStartPixX, BootChrCoord[-1][0], bootCount])
+			else:
+				reducedBootCoord[-1][2] += bootCount
+				reducedBootCoord[-1][1] = BootChrCoord[-1][0]
+			# end else
+			if maxBootCount < reducedBootCoord[-1][2]:
+				maxBootCount = reducedBootCoord[-1][2]
+			# end if
+		for item in reducedBootCoord:
+			if item[2] > 0:
+				if item[0] < xLeftOffset:
+					item[0] = xLeftOffset
+				if item[0] > xLeftOffset+plotWidth:
+					item[0] = xLeftOffset+plotWidth
+				if item[1] < xLeftOffset:
+					item[1] = xLeftOffset
+				if item[1] > xLeftOffset+plotWidth:
+					item[1] = xLeftOffset+plotWidth
+				if item[0] != item[1]:
+					canvas.drawRect(item[0], yZero, item[1], yZero - item[2]*bootHeightThresh/maxBootCount, 
+					fillColor=self.BOOTSTRAP_BOX_COLOR)
+					
+		###draw boot scale	
+		highestPercent = (maxBootCount*100.0)/nboot
+		bootScale = Plot.detScale(0, highestPercent)
+		bootScale = Plot.frange(bootScale[0], bootScale[1], bootScale[1]/bootScale[2])
+		bootScale = bootScale[:-1] + [highestPercent]
+		
+		bootOffset = 50*fontZoom
+		bootScaleFont=pid.Font(ttf="verdana",size=13*fontZoom,bold=0)
+		canvas.drawRect(canvas.size[0]-bootOffset,yZero-bootHeightThresh,canvas.size[0]-bootOffset-15*zoom,yZero,fillColor = pid.yellow)
+		canvas.drawLine(canvas.size[0]-bootOffset+4, yZero, canvas.size[0]-bootOffset, yZero, color=pid.black)
+		canvas.drawString('0%' ,canvas.size[0]-bootOffset+10,yZero+5,font=bootScaleFont,color=pid.black)
+		for item in bootScale:
+			if item == 0:
+				continue
+			bootY = yZero-bootHeightThresh*item/highestPercent
+			canvas.drawLine(canvas.size[0]-bootOffset+4,bootY,canvas.size[0]-bootOffset,bootY,color=pid.black)
+			canvas.drawString('%2.1f'%item ,canvas.size[0]-bootOffset+10,bootY+5,font=bootScaleFont,color=pid.black)
+		
+		if self.legendChecked:
+			startPosY = 30
+			nCol = 2
+			smallLabelFont = pid.Font(ttf="trebuc", size=12, bold=1)
+			leftOffset = xLeftOffset+(nCol-1)*200
+			canvas.drawRect(leftOffset,startPosY-6, leftOffset+12,startPosY+6, fillColor=pid.yellow)
+			canvas.drawString('Frequency of the Peak LRS',leftOffset+ 20, startPosY+5,font=smallLabelFont,color=pid.black)
+			
+	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
+			Mb = self.traitList[0].mb
+		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)
+			
+	
+	def drawSNPTrackNew(self, canvas, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+		if self.plotScale != 'physic' or self.selectedChr == -1 or not self.diffCol:
+			return
+		
+		SNP_HEIGHT_MODIFIER = 18.0
+
+		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
+			
+		drawSNPLocationY = yTopOffset + plotHeight
+		chrName = self.genotype[0].name
+		
+		stepMb = (endMb-startMb)/plotWidth
+		strainId1, strainId2 = self.diffCol
+		SNPCounts = []
+
+		while startMb<endMb:
+			self.cursor.execute("""
+				select
+					count(*) from BXDSnpPosition
+				where
+					Chr = '%s' AND Mb >= %2.6f AND Mb < %2.6f AND
+					StrainId1 = %d AND StrainId2 = %d
+				""" % (chrName, startMb, startMb+stepMb, strainId1, strainId2))
+			SNPCounts.append(self.cursor.fetchone()[0])
+			startMb += stepMb
+
+		if (len(SNPCounts) > 0):
+			maxCount = max(SNPCounts)
+			if maxCount>0:						
+				for i in range(xLeftOffset, xLeftOffset + plotWidth):
+					snpDensity = float(SNPCounts[i-xLeftOffset]*SNP_HEIGHT_MODIFIER/maxCount)
+					canvas.drawLine(i, drawSNPLocationY+(snpDensity)*zoom, i, drawSNPLocationY-(snpDensity)*zoom, color=self.SNP_COLOR, width=1)
+		
+	def drawMultiTraitName(self, fd, canvas, gifmap, showLocusForm, offset= (40, 120, 80, 10), zoom = 1, locLocation= None):
+		nameWidths = []
+		yPaddingTop = 10
+		colorFont=pid.Font(ttf="trebuc",size=12,bold=1)
+		if len(self.qtlresults) >20 and self.selectedChr > -1:
+			rightShift = 20
+			rightShiftStep = 60
+			rectWidth = 10
+		else:
+			rightShift = 40
+			rightShiftStep = 80
+			rectWidth = 15
+			
+		for k, thisTrait in enumerate(self.traitList):
+			thisLRSColor = self.colorCollection[k]
+			kstep = k % 4
+			if k!=0 and kstep==0:
+				if nameWidths:
+					rightShiftStep = max(nameWidths[-4:]) + rectWidth + 20
+				rightShift += rightShiftStep
+
+			name = thisTrait.displayName()
+			nameWidth = canvas.stringWidth(name,font=colorFont)
+			nameWidths.append(nameWidth)
+	
+			canvas.drawRect(rightShift,yPaddingTop+kstep*15, rectWidth+rightShift,yPaddingTop+10+kstep*15, fillColor=thisLRSColor)
+			canvas.drawString(name,rectWidth+2+rightShift,yPaddingTop+10+kstep*15,font=colorFont,color=pid.black)
+			if thisTrait.db:
+
+				COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift,yPaddingTop+kstep*15,rectWidth+2+rightShift+nameWidth,yPaddingTop+10+kstep*15,)
+				HREF= "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name)
+				Areas = HT.Area(shape='rect',coords=COORDS,href=HREF)
+				gifmap.areas.append(Areas)
+				
+
+	def drawLegendPanel(self, fd, canvas, offset= (40, 120, 80, 10), zoom = 1, locLocation= 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
+			
+		
+		labelFont=pid.Font(ttf="trebuc",size=12, bold=1)
+		startPosY = 15
+		stepPosY = 12
+		canvas.drawLine(xLeftOffset,startPosY,xLeftOffset+32,startPosY,color=self.LRS_COLOR, width=2)
+		canvas.drawString(self.LRS_LOD, xLeftOffset+40,startPosY+5,font=labelFont,color=pid.black)
+		startPosY += stepPosY
+
+		if self.additiveChecked:
+			startPosX = xLeftOffset
+			canvas.drawLine(startPosX,startPosY,startPosX+17,startPosY,color=self.ADDITIVE_COLOR_POSITIVE, width=2)
+			canvas.drawLine(startPosX+18,startPosY,startPosX+32,startPosY,color=self.ADDITIVE_COLOR_NEGATIVE, width=2)			
+			canvas.drawString('Additive Effect',startPosX+40,startPosY+5,font=labelFont,color=pid.black)
+	
+		if self.genotype.type == 'intercross' and self.dominanceChecked:
+			startPosX = xLeftOffset
+			startPosY += stepPosY
+			canvas.drawLine(startPosX,startPosY,startPosX+17,startPosY,color=self.DOMINANCE_COLOR_POSITIVE, width=4)
+			canvas.drawLine(startPosX+18,startPosY,startPosX+35,startPosY,color=self.DOMINANCE_COLOR_NEGATIVE, width=4)				
+			canvas.drawString('Dominance Effect',startPosX+42,startPosY+5,font=labelFont,color=pid.black)
+			
+		if self.haplotypeAnalystChecked:
+			startPosY += stepPosY
+			startPosX = xLeftOffset
+			canvas.drawLine(startPosX,startPosY,startPosX+17,startPosY,color=self.HAPLOTYPE_POSITIVE, width=4)
+			canvas.drawLine(startPosX+18,startPosY,startPosX+35,startPosY,color=self.HAPLOTYPE_NEGATIVE, width=4)	
+			canvas.drawLine(startPosX+36,startPosY,startPosX+53,startPosY,color=self.HAPLOTYPE_HETEROZYGOUS, width=4)			
+			canvas.drawLine(startPosX+54,startPosY,startPosX+67,startPosY,color=self.HAPLOTYPE_RECOMBINATION, width=4)	
+			canvas.drawString('Haplotypes (Pat, Mat, Het, Unk)',startPosX+76,startPosY+5,font=labelFont,color=pid.black)
+			
+		if self.permChecked:
+			startPosY += stepPosY	
+			startPosX = xLeftOffset
+			canvas.drawLine(startPosX, startPosY, startPosX + 32, startPosY, color=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH)
+			canvas.drawLine(startPosX, startPosY + stepPosY, startPosX + 32, startPosY + stepPosY, color=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH)
+			lod = 1
+			if self.LRS_LOD == 'LOD':
+				lod = self.LODFACTOR
+			canvas.drawString('Significant %s = %2.2f' % (self.LRS_LOD, self.significance/lod),xLeftOffset+42,startPosY +5,font=labelFont,color=pid.black)
+			canvas.drawString('Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive/lod),xLeftOffset+42,startPosY + 5 +stepPosY,font=labelFont,color=pid.black)				
+			
+			
+			
+		labelFont=pid.Font(ttf="verdana",size=12)
+		labelColor = pid.black
+		if self.selectedChr == -1:	
+			string1 = 'Mapping for Dataset: %s, mapping on All Chromosomes' % fd.RISet
+		else:	
+			string1 = 'Mapping for Dataset: %s, mapping on Chromosome %s' % (fd.RISet,self.genotype[0].name)
+		if self.controlLocus:
+			string2 = 'Using %s as control' % self.controlLocus
+		else:
+			string2 = 'Using Haldane mapping function with no control for other QTLs'
+		d = 4+ max(canvas.stringWidth(string1,font=labelFont),canvas.stringWidth(string2,font=labelFont))
+		if fd.identification:
+			identification = "Trait ID: %s" % fd.identification
+			canvas.drawString(identification,canvas.size[0] - xRightOffset-d,20,font=labelFont,color=labelColor)
+
+		canvas.drawString(string1,canvas.size[0] - xRightOffset-d,35,font=labelFont,color=labelColor)
+		canvas.drawString(string2,canvas.size[0] - xRightOffset-d,50,font=labelFont,color=labelColor)
+	
+
+	def drawGeneBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+		if self.plotScale != 'physic' or self.selectedChr == -1 or not self.geneCol:
+			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
+
+		yPaddingTop = yTopOffset
+
+		displayStartInBases = startMb*self.kONE_MILLION
+		displayEndInBases = endMb*self.kONE_MILLION
+
+		for gIndex, theGO in enumerate(self.geneCol):
+			geneNCBILink = 'http://www.ncbi.nlm.nih.gov/gene?term=%s'
+			if self.species == "mouse":
+				txStart = theGO["TxStart"]
+				txEnd = theGO["TxEnd"]
+				geneLength = (txEnd - txStart)*1000.0
+				tenPercentLength = geneLength*0.0001
+				SNPdensity = theGO["snpCount"]/geneLength
+
+				exonStarts = map(float, theGO['exonStarts'].split(",")[:-1])
+				exonEnds = map(float, theGO['exonEnds'].split(",")[:-1])
+				cdsStart = theGO['cdsStart']
+				cdsEnd = theGO['cdsEnd']
+				accession = theGO['NM_ID']
+				geneId = theGO['GeneID']
+				geneSymbol = theGO["GeneSymbol"]
+				strand = theGO["Strand"]
+				exonCount = theGO["exonCount"]
+
+				geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb)
+				geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) #at least one pixel
+
+				if (geneEndPix < xLeftOffset):
+					return; # this gene is not on the screen
+				elif (geneEndPix > xLeftOffset + plotWidth):
+					geneEndPix = xLeftOffset + plotWidth; # clip the last in-range gene
+				if (geneStartPix > xLeftOffset + plotWidth):
+					return; # we are outside the valid on-screen range, so stop drawing genes
+				elif (geneStartPix < xLeftOffset):
+					geneStartPix = xLeftOffset; # clip the first in-range gene
+
+				#color the gene based on SNP density
+
+				
+				#found earlier, needs to be recomputed as snps are added
+				
+				#always apply colors now, even if SNP Track not checked - Zach 11/24/2010
+				
+				densities=[1.0000000000000001e-05, 0.094094033555233408, 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0]
+				if SNPdensity < densities[0]:
+					myColor = pid.black
+				elif SNPdensity < densities[1]:
+					myColor = pid.purple
+				elif SNPdensity < densities[2]:
+					myColor = pid.darkblue
+				elif SNPdensity < densities[3]:
+					myColor = pid.darkgreen
+				elif SNPdensity < densities[4]:
+					myColor = pid.gold
+				elif SNPdensity < densities[5]:
+					myColor = pid.darkorange
+				else:
+					myColor = pid.darkred
+
+				outlineColor = myColor
+				fillColor    = myColor
+
+				TITLE = "Gene: %s (%s)\nFrom %2.3f to %2.3f Mb (%s)\nNum. exons: %d." % (geneSymbol, accession, float(txStart), float(txEnd), strand, exonCount)
+				# NL: 06-02-2011 Rob required to change this link for gene related
+				HREF=geneNCBILink %geneSymbol
+				
+			elif self.species == "rat":
+				exonStarts = []
+				exonEnds = []
+				txStart = theGO["TxStart"]
+				txEnd = theGO["TxEnd"]
+				cdsStart = theGO["TxStart"]
+				cdsEnd = theGO["TxEnd"]
+				geneId = theGO["GeneID"]
+				geneSymbol = theGO["GeneSymbol"]
+				strand = theGO["Strand"]
+				exonCount = 0
+
+				geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb)
+				geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) #at least one pixel
+
+				if (geneEndPix < xLeftOffset):
+					return; # this gene is not on the screen
+				elif (geneEndPix > xLeftOffset + plotWidth):
+					geneEndPix = xLeftOffset + plotWidth; # clip the last in-range gene
+				if (geneStartPix > xLeftOffset + plotWidth):
+					return; # we are outside the valid on-screen range, so stop drawing genes
+				elif (geneStartPix < xLeftOffset):
+					geneStartPix = xLeftOffset; # clip the first in-range gene
+
+				outlineColor = pid.darkblue
+				fillColor = pid.darkblue
+				TITLE = "Gene: %s\nFrom %2.3f to %2.3f Mb (%s)" % (geneSymbol, float(txStart), float(txEnd), strand)
+				# NL: 06-02-2011 Rob required to change this link for gene related
+				HREF=geneNCBILink %geneSymbol
+			else:
+				outlineColor = pid.orange
+				fillColor = pid.orange
+				TITLE = "Gene: %s" % geneSymbol
+
+			#Draw Genes
+			geneYLocation = yPaddingTop + (gIndex % self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT*zoom
+
+			if 1:#drawClickableRegions:
+				geneYLocation += self.UCSC_BAND_HEIGHT + self.BAND_SPACING + self.ENSEMBL_BAND_HEIGHT + self.BAND_SPACING + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING
+			else:
+				geneYLocation += self.BAND_SPACING
+
+			#draw the detail view
+			if self.endMb - self.startMb <= self.DRAW_DETAIL_MB and geneEndPix - geneStartPix > self.EACH_GENE_ARROW_SPACING * 3:
+				utrColor = pid.Color(0.66, 0.66, 0.66)
+				arrowColor = pid.Color(0.7, 0.7, 0.7)
+
+			        #draw the line that runs the entire length of the gene
+				#canvas.drawString(str(geneStartPix), 300, 400)
+				canvas.drawLine(geneStartPix, geneYLocation + self.EACH_GENE_HEIGHT/2*zoom, geneEndPix, geneYLocation + self.EACH_GENE_HEIGHT/2*zoom, color=outlineColor, width=1)
+
+			        #draw the arrows
+				for xCoord in range(0, geneEndPix-geneStartPix):
+
+					if (xCoord % self.EACH_GENE_ARROW_SPACING == 0 and xCoord + self.EACH_GENE_ARROW_SPACING < geneEndPix-geneStartPix) or xCoord == 0:
+						if strand == "+":
+							canvas.drawLine(geneStartPix + xCoord, geneYLocation, geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, geneYLocation +(self.EACH_GENE_HEIGHT / 2)*zoom, color=arrowColor, width=1)
+							canvas.drawLine(geneStartPix + xCoord, geneYLocation + self.EACH_GENE_HEIGHT*zoom, geneStartPix + xCoord+self.EACH_GENE_ARROW_WIDTH, geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom, color=arrowColor, width=1)
+						else:
+							canvas.drawLine(geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, geneYLocation, geneStartPix + xCoord, geneYLocation +(self.EACH_GENE_HEIGHT / 2)*zoom, color=arrowColor, width=1)
+							canvas.drawLine(geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, geneYLocation + self.EACH_GENE_HEIGHT*zoom, geneStartPix + xCoord, geneYLocation + (self.EACH_GENE_HEIGHT / 2)*zoom, color=arrowColor, width=1)
+
+				#draw the blocks for the exon regions
+				for i in range(0, len(exonStarts)):
+					exonStartPix = (exonStarts[i]-startMb)*plotXScale + xLeftOffset 
+					exonEndPix = (exonEnds[i]-startMb)*plotXScale + xLeftOffset 
+					if (exonStartPix < xLeftOffset):
+						exonStartPix = xLeftOffset
+					if (exonEndPix < xLeftOffset):
+						exonEndPix = xLeftOffset
+					if (exonEndPix > xLeftOffset + plotWidth):
+						exonEndPix = xLeftOffset + plotWidth
+					if (exonStartPix > xLeftOffset + plotWidth):
+						exonStartPix = xLeftOffset + plotWidth
+					canvas.drawRect(exonStartPix, geneYLocation, exonEndPix, (geneYLocation + self.EACH_GENE_HEIGHT*zoom), edgeColor = outlineColor, fillColor = fillColor)
+
+				#draw gray blocks for 3' and 5' UTR blocks
+				if cdsStart and cdsEnd:
+
+					utrStartPix = (txStart-startMb)*plotXScale + xLeftOffset 
+					utrEndPix = (cdsStart-startMb)*plotXScale + xLeftOffset 
+					if (utrStartPix < xLeftOffset):
+						utrStartPix = xLeftOffset
+					if (utrEndPix < xLeftOffset):
+						utrEndPix = xLeftOffset
+					if (utrEndPix > xLeftOffset + plotWidth):
+						utrEndPix = xLeftOffset + plotWidth
+					if (utrStartPix > xLeftOffset + plotWidth):
+						utrStartPix = xLeftOffset + plotWidth
+					canvas.drawRect(utrStartPix, geneYLocation, utrEndPix, (geneYLocation+self.EACH_GENE_HEIGHT*zoom), edgeColor=utrColor, fillColor =utrColor)
+
+					if self.DRAW_UTR_LABELS and self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB:
+						if strand == "-":
+							labelText = "3'"
+						else:
+							labelText = "5'"
+						canvas.drawString(labelText, utrStartPix-9, geneYLocation+self.EACH_GENE_HEIGHT, pid.Font(face="helvetica", size=2))
+
+					#the second UTR region
+
+					utrStartPix = (cdsEnd-startMb)*plotXScale + xLeftOffset 
+					utrEndPix = (txEnd-startMb)*plotXScale + xLeftOffset 
+					if (utrStartPix < xLeftOffset):
+						utrStartPix = xLeftOffset
+					if (utrEndPix < xLeftOffset):
+						utrEndPix = xLeftOffset
+					if (utrEndPix > xLeftOffset + plotWidth):
+						utrEndPix = xLeftOffset + plotWidth
+					if (utrStartPix > xLeftOffset + plotWidth):
+						utrStartPix = xLeftOffset + plotWidth
+					canvas.drawRect(utrStartPix, geneYLocation, utrEndPix, (geneYLocation+self.EACH_GENE_HEIGHT*zoom), edgeColor=utrColor, fillColor =utrColor)
+
+					if self.DRAW_UTR_LABELS and self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB:
+						if tstrand == "-":
+							labelText = "5'"
+						else:
+							labelText = "3'"
+						canvas.drawString(labelText, utrEndPix+2, geneYLocation+self.EACH_GENE_HEIGHT, pid.Font(face="helvetica", size=2))
+
+			#draw the genes as rectangles
+			else:
+				canvas.drawRect(geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT*zoom), edgeColor = outlineColor, fillColor = fillColor)
+
+			COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT))
+			# NL: 06-02-2011 Rob required to display NCBI info in a new window
+			gifmap.areas.append(HT.Area(shape='rect',coords=COORDS,href=HREF, title=TITLE,target="_blank"))
+
+## BEGIN HaplotypeAnalyst
+	def drawHaplotypeBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+		if self.plotScale != 'physic' or self.selectedChr == -1 or not self.geneCol:
+			return
+
+
+		fpText = open(os.path.join(webqtlConfig.TMPDIR, "hallo") + '.txt','wb')
+
+		clickableRegionLabelFont=pid.Font(ttf="verdana", size=9, bold=0)
+
+		xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+		plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
+		plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
+		yZero = canvas.size[1] - yBottomOffset
+		fontZoom = zoom
+		widthMultiplier = 1
+			
+		yPaddingTop = yTopOffset
+
+		exprdrawn = 0
+
+		thisTrait = self.traitList[0]
+		_strains, _vals, _vars = thisTrait.exportInformative()
+
+		smd=[]
+		for ii, _val in enumerate(_vals):
+			temp = GeneralObject(name=_strains[ii], value=_val)
+			smd.append(temp)
+
+		smd.sort(lambda A, B: cmp(A.value, B.value))
+
+		bxdlist=list(self.genotype.prgy)
+
+		oldgeneEndPix = -1
+		#Initializing plotRight, error before
+		plotRight = xRightOffset
+		
+#### find out PlotRight
+		for i, _locus in enumerate(self.genotype[0]):
+			txStart = self.genotype[0][i].Mb 
+			txEnd   = self.genotype[0][i].Mb 
+
+			geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb)  - 0
+			geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) - 0			
+
+			drawit = 1
+			if (geneStartPix < xLeftOffset):
+				drawit = 0;
+			if (geneStartPix > xLeftOffset + plotWidth):
+				drawit = 0;
+
+			if drawit == 1:
+
+				if self.genotype[0][i].name != " - " :
+
+					plotRight = geneEndPix + 4
+			
+			
+
+#### end find out PlotRight
+
+		firstGene = 1
+		lastGene = 0
+		
+		#Sets the length to the length of the strain list. Beforehand, "oldgeno = self.genotype[0][i].genotype" 
+		#was the only place it was initialized, which worked as long as the very start (startMb = None/0) wasn't being mapped.
+		#Now there should always be some value set for "oldgeno" - Zach 12/14/2010
+		oldgeno = [None]*len(self.strainlist) 
+
+		for i, _locus in enumerate(self.genotype[0]):
+			txStart = self.genotype[0][i].Mb 
+			txEnd   = self.genotype[0][i].Mb 
+			
+			geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb)  - 0
+			geneEndPix   = xLeftOffset + plotXScale*(float(txEnd)   - startMb)  + 0
+
+			if oldgeneEndPix >= xLeftOffset:
+				drawStart = oldgeneEndPix + 4
+			else:
+				drawStart = xLeftOffset + 3
+
+			drawEnd = plotRight - 9			
+
+			drawit = 1
+			
+			if (geneStartPix < xLeftOffset):
+				if firstGene == 1:
+					drawit = 1
+				else:
+					drawit = 0
+				
+			elif (geneStartPix > (xLeftOffset + plotWidth - 3)):
+				if lastGene == 0:
+					drawit = 1
+					drawEnd = xLeftOffset + plotWidth - 6
+					lastGene = 1
+				else:
+					break
+			
+			else:
+				firstGene = 0
+				drawit = 1
+
+			if drawit == 1:				
+				myColor = pid.darkblue
+				outlineColor = myColor
+				fillColor    = myColor
+
+				maxind=0
+
+				#Draw Genes
+
+				geneYLocation = yPaddingTop + self.NUM_GENE_ROWS * (self.EACH_GENE_HEIGHT)*zoom
+
+				if 1:#drawClickableRegions:
+					geneYLocation += self.UCSC_BAND_HEIGHT + self.BAND_SPACING + self.ENSEMBL_BAND_HEIGHT + self.BAND_SPACING + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING
+				else:
+					geneYLocation += self.BAND_SPACING
+					
+				if self.genotype[0][i].name != " - " :
+					
+					if (firstGene == 1) and (lastGene != 1):
+						oldgeneEndPix = drawStart = xLeftOffset
+						oldgeno = self.genotype[0][i].genotype
+						continue
+					
+					for j,_geno in enumerate (self.genotype[0][i].genotype):
+
+						plotbxd=0
+						for item in smd:
+							if item.name == bxdlist[j]:
+								plotbxd=1
+								
+						if (plotbxd == 1):
+							ind = 0
+							counter = 0
+							for item in smd:
+								counter = counter + 1
+								if item.name == bxdlist[j]:
+									ind = counter
+							maxind=max(ind,maxind)		
+
+							# lines
+							if (oldgeno[j] == -1 and _geno == -1):
+								mylineColor = self.HAPLOTYPE_NEGATIVE
+							elif (oldgeno[j] == 1 and _geno == 1):
+								mylineColor = self.HAPLOTYPE_POSITIVE
+							elif (oldgeno[j] == 0 and _geno == 0):
+								mylineColor = self.HAPLOTYPE_HETEROZYGOUS							
+							else:
+								mylineColor = self.HAPLOTYPE_RECOMBINATION # XZ: Unknown
+	
+							canvas.drawLine(drawStart, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, drawEnd, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, color = mylineColor, width=zoom*(self.EACH_GENE_HEIGHT+2))
+
+							fillColor=pid.black
+							outlineColor=pid.black
+							if lastGene == 0:
+								canvas.drawRect(geneStartPix, geneYLocation+2*ind*self.EACH_GENE_HEIGHT*zoom, geneEndPix, geneYLocation+2*ind*self.EACH_GENE_HEIGHT+ 2*self.EACH_GENE_HEIGHT*zoom, edgeColor = outlineColor, fillColor = fillColor)
+
+
+							COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation+ind*self.EACH_GENE_HEIGHT, geneEndPix+1, (geneYLocation + ind*self.EACH_GENE_HEIGHT))
+							TITLE = "Strain: %s, marker (%s) \n Position  %2.3f Mb." % (bxdlist[j], self.genotype[0][i].name, float(txStart))
+							HREF = ''
+							gifmap.areas.append(HT.Area(shape='rect',coords=COORDS,href=HREF, title=TITLE))
+							
+							# if there are no more markers in a chromosome, the plotRight value calculated above will be before the plotWidth
+							# resulting in some empty space on the right side of the plot area. This draws an "unknown" bar from plotRight to the edge.
+							if (plotRight < (xLeftOffset + plotWidth - 3)) and (lastGene == 0):
+								drawEnd = xLeftOffset + plotWidth - 6
+								mylineColor = self.HAPLOTYPE_RECOMBINATION
+								canvas.drawLine(plotRight, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, drawEnd, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, color = mylineColor, width=zoom*(self.EACH_GENE_HEIGHT+2))								
+							
+							
+					if lastGene == 0:
+						canvas.drawString("%s" % (self.genotype[0][i].name), geneStartPix , geneYLocation+17+2*maxind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black, angle=-90)					
+				
+					oldgeneEndPix = geneEndPix;
+					oldgeno = self.genotype[0][i].genotype
+					firstGene = 0
+				else:
+					lastGene = 0					
+		
+		for j,_geno in enumerate (self.genotype[0][1].genotype):
+
+			plotbxd=0
+			for item in smd:
+				if item.name == bxdlist[j]:
+					plotbxd=1
+					
+			if (plotbxd == 1):
+
+				ind = 0
+				counter = 0
+				expr = 0
+				for item in smd:
+					counter = counter + 1
+					if item.name == bxdlist[j]:
+						ind = counter
+						expr = item.value
+				
+				# Place where font is hardcoded
+				canvas.drawString("%s" % (bxdlist[j]), (xLeftOffset + plotWidth + 10) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black)
+				canvas.drawString("%2.2f" % (expr), (xLeftOffset + plotWidth + 60) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black)
+
+		fpText.close()
+ 
+## END HaplotypeAnalyst
+
+	def drawClickBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+		if self.plotScale != 'physic' or self.selectedChr == -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
+
+		# only draw this many clickable regions (if you set it higher, you get more precision in clicking,
+		# but it makes the HTML huge, and takes forever to render the page in the first place)
+		# Draw the bands that you can click on to go to UCSC / Ensembl
+		MAX_CLICKABLE_REGION_DIVISIONS = 100
+		clickableRegionLabelFont=pid.Font(ttf="verdana", size=9, bold=0)
+		pixelStep = max(5, int(float(plotWidth)/MAX_CLICKABLE_REGION_DIVISIONS))
+		# pixelStep: every N pixels, we make a new clickable area for the user to go to that area of the genome.
+
+		numBasesCurrentlyOnScreen = self.kONE_MILLION*abs(startMb - endMb) # Number of bases on screen now
+		flankingWidthInBases = int ( min( (float(numBasesCurrentlyOnScreen) / 2.0), (5*self.kONE_MILLION) ) )
+		webqtlZoomWidth = numBasesCurrentlyOnScreen / 16.0
+		# Flanking width should be such that we either zoom in to a 10 million base region, or we show the clicked region at the same scale as we are currently seeing.
+
+		currentChromosome = self.genotype[0].name
+		i = 0
+		for pixel in range(xLeftOffset, xLeftOffset + plotWidth, pixelStep):
+
+			calBase = self.kONE_MILLION*(startMb + (endMb-startMb)*(pixel-xLeftOffset-0.0)/plotWidth)
+
+			xBrowse1 = pixel
+			xBrowse2 = min(xLeftOffset + plotWidth, (pixel + pixelStep - 1))
+
+			paddingTop = yTopOffset
+			ucscPaddingTop = paddingTop + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING
+			ensemblPaddingTop = ucscPaddingTop + self.UCSC_BAND_HEIGHT + self.BAND_SPACING
+
+			WEBQTL_COORDS = "%d, %d, %d, %d" % (xBrowse1, paddingTop, xBrowse2, (paddingTop+self.WEBQTL_BAND_HEIGHT))
+			bandWidth = xBrowse2 - xBrowse1
+			WEBQTL_HREF = "javascript:centerIntervalMapOnRange2('%s', %f, %f, document.changeViewForm)" % (currentChromosome, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0)
+
+			WEBQTL_TITLE = "Click to view this section of the genome in WebQTL"
+			gifmap.areas.append(HT.Area(shape='rect',coords=WEBQTL_COORDS,href=WEBQTL_HREF, title=WEBQTL_TITLE))
+			canvas.drawRect(xBrowse1, paddingTop, xBrowse2, (paddingTop + self.WEBQTL_BAND_HEIGHT), edgeColor=self.CLICKABLE_WEBQTL_REGION_COLOR, fillColor=self.CLICKABLE_WEBQTL_REGION_COLOR)
+			canvas.drawLine(xBrowse1, paddingTop, xBrowse1, (paddingTop + self.WEBQTL_BAND_HEIGHT), color=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR)
+
+			UCSC_COORDS = "%d, %d, %d, %d" %(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.UCSC_BAND_HEIGHT))
+			if self.species == "mouse":
+				UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=%s/snp/chr%s" % (self._ucscDb, currentChromosome, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases, webqtlConfig.PORTADDR, currentChromosome)
+			else:
+				UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, currentChromosome, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
+			UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser"
+			gifmap.areas.append(HT.Area(shape='rect',coords=UCSC_COORDS,href=UCSC_HREF, title=UCSC_TITLE))
+			canvas.drawRect(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.UCSC_BAND_HEIGHT), edgeColor=self.CLICKABLE_UCSC_REGION_COLOR, fillColor=self.CLICKABLE_UCSC_REGION_COLOR)
+			canvas.drawLine(xBrowse1, ucscPaddingTop, xBrowse1, (ucscPaddingTop+self.UCSC_BAND_HEIGHT), color=self.CLICKABLE_UCSC_REGION_OUTLINE_COLOR)
+
+			ENSEMBL_COORDS = "%d, %d, %d, %d" %(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.ENSEMBL_BAND_HEIGHT))
+			if self.species == "mouse":
+				ENSEMBL_HREF = "http://www.ensembl.org/Mus_musculus/contigview?highlight=&chr=%s&vc_start=%d&vc_end=%d&x=35&y=12" % (currentChromosome, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
+			else:
+				ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (currentChromosome, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
+			ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser"
+			gifmap.areas.append(HT.Area(shape='rect',coords=ENSEMBL_COORDS,href=ENSEMBL_HREF, title=ENSEMBL_TITLE))
+			canvas.drawRect(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.ENSEMBL_BAND_HEIGHT), edgeColor=self.CLICKABLE_ENSEMBL_REGION_COLOR, fillColor=self.CLICKABLE_ENSEMBL_REGION_COLOR)
+			canvas.drawLine(xBrowse1, ensemblPaddingTop, xBrowse1, (ensemblPaddingTop+self.ENSEMBL_BAND_HEIGHT), color=self.CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR)
+		# end for
+
+		canvas.drawString("Click to view the corresponding section of the genome in an 8x expanded WebQTL map", (xLeftOffset + 10), paddingTop + self.WEBQTL_BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_WEBQTL_TEXT_COLOR)
+		canvas.drawString("Click to view the corresponding section of the genome in the UCSC Genome Browser", (xLeftOffset + 10), ucscPaddingTop + self.UCSC_BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_UCSC_TEXT_COLOR)
+		canvas.drawString("Click to view the corresponding section of the genome in the Ensembl Genome Browser", (xLeftOffset+10), ensemblPaddingTop + self.ENSEMBL_BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_ENSEMBL_TEXT_COLOR)
+
+		#draw the gray text
+		chrFont = pid.Font(ttf="verdana", size=26, bold=1)
+		traitFont = pid.Font(ttf="verdana", size=14, bold=0)
+		chrX = xLeftOffset + plotWidth - 2 - canvas.stringWidth("Chr %s" % currentChromosome, font=chrFont)
+		canvas.drawString("Chr %s" % currentChromosome, chrX, ensemblPaddingTop-5, font=chrFont, color=pid.gray)
+		traitX = chrX - 28 - canvas.stringWidth("database", font=traitFont)
+		# end of drawBrowserClickableRegions
+
+		pass
+
+	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 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")
+		
+		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)
+			if self.permChecked and not self.multipleInterval:
+				self.significance = min(self.significance, webqtlConfig.MAXLRS)
+				self.suggestive = min(self.suggestive, 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
+		
+
+		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
+			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)
+				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))
+				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]
+			for j, _chr in enumerate(self.genotype):
+				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))
+					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
+				canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+				if not self.multipleInterval and self.additiveChecked:
+					plusColor = self.ADDITIVE_COLOR_POSITIVE
+					minusColor = self.ADDITIVE_COLOR_NEGATIVE
+					for k, aPoint in enumerate(AdditiveCoordXY):
+						if k > 0:
+							Xc0, Yc0 = AdditiveCoordXY[k-1]
+							Xc, Yc = aPoint
+							if (Yc0-yZero)*(Yc-yZero) < 0:
+								if Xc == Xc0: #genotype , locus distance is 0
+									Xcm = Xc
+								else:	
+									Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0
+								if Yc0 < yZero:
+									canvas.drawLine(Xc0, Yc0, Xcm, yZero, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+									canvas.drawLine(Xcm, yZero, Xc, yZero-(Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+								else:
+									canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xcm, yZero, color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+									canvas.drawLine(Xcm, yZero, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+							elif (Yc0-yZero)*(Yc-yZero) > 0:
+								if Yc < yZero:
+									canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+								else:
+									canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+							else:
+								minYc = min(Yc-yZero, Yc0-yZero)
+								if minYc < 0:
+									canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+								else:
+									canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+				if not self.multipleInterval and INTERCROSS and self.dominanceChecked:
+					plusColor = self.DOMINANCE_COLOR_POSITIVE
+					minusColor = self.DOMINANCE_COLOR_NEGATIVE
+					for k, aPoint in enumerate(DominanceCoordXY):
+						if k > 0:
+							Xc0, Yc0 = DominanceCoordXY[k-1]
+							Xc, Yc = aPoint
+							if (Yc0-yZero)*(Yc-yZero) < 0:
+								if Xc == Xc0: #genotype , locus distance is 0
+									Xcm = Xc
+								else:	
+									Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0
+								if Yc0 < yZero:
+									canvas.drawLine(Xc0, Yc0, Xcm, yZero, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+									canvas.drawLine(Xcm, yZero, Xc, yZero-(Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+								else:
+									canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xcm, yZero, color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+									canvas.drawLine(Xcm, yZero, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+							elif (Yc0-yZero)*(Yc-yZero) > 0:
+								if Yc < yZero:
+									canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+								else:
+									canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+							else:
+								minYc = min(Yc-yZero, Yc0-yZero)
+								if minYc < 0:
+									canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+								else:
+									canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+				startPosX +=  (self.ChrLengthDistList[j]+self.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 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
+
+	def calculateAllResult(self, fd):
+
+		weightedRegression = fd.formdata.getvalue('applyVarianceSE')
+		
+		self.genotype = self.genotype.addinterval()
+		resultSlice = []
+		controlGeno = []
+		
+		if self.multipleInterval:
+			self.suggestive = 0
+			self.significance = 0
+			if self.selectedChr > -1:
+				self.genotype.chromosome = [self.genotype[self.selectedChr]]
+		else:
+			#single interval mapping
+			try:
+				self.suggestive = float(fd.formdata.getvalue('permSuggestive'))
+				self.significance = float(fd.formdata.getvalue('permSignificance'))
+			except:
+				self.suggestive = None
+				self.significance = None
+			
+			_strains, _vals, _vars = self.traitList[0].exportInformative(weightedRegression)
+			
+			if webqtlUtil.ListNotNull(_vars):
+				pass
+			else:
+				weightedRegression = 0
+				_strains, _vals, _vars = self.traitList[0].exportInformative()
+				
+			##locate genotype of control Locus
+			if self.controlLocus:
+				controlGeno2 = []
+				_FIND = 0
+				for _chr in self.genotype:
+					for _locus in _chr:
+						if _locus.name == self.controlLocus:
+							controlGeno2 = _locus.genotype
+							_FIND = 1
+							break
+					if _FIND:
+						break
+				if controlGeno2:
+					_prgy = list(self.genotype.prgy)
+					for _strain in _strains:
+						_idx = _prgy.index(_strain)
+						controlGeno.append(controlGeno2[_idx])
+				else:
+					return "The control marker you selected is not in the genofile."
+
+			
+			if self.significance and self.suggestive:
+				pass
+			else:
+				if self.permChecked:
+					if weightedRegression:
+						self.LRSArray = self.genotype.permutation(strains = _strains, trait = _vals, 
+							variance = _vars, nperm=fd.nperm)
+					else:
+						self.LRSArray = self.genotype.permutation(strains = _strains, trait = _vals, 
+							nperm=fd.nperm)
+					self.suggestive = self.LRSArray[int(fd.nperm*0.37-1)]
+					self.significance = self.LRSArray[int(fd.nperm*0.95-1)]
+
+				else:
+					self.suggestive = 9.2
+					self.significance = 16.1
+
+			#calculating bootstrap
+			#from now on, genotype could only contain a single chromosome 
+			#permutation need to be performed genome wide, this is not the case for bootstrap
+			
+			#due to the design of qtlreaper, composite regression need to be performed genome wide
+			if not self.controlLocus and self.selectedChr > -1:
+				self.genotype.chromosome = [self.genotype[self.selectedChr]]
+			elif self.selectedChr > -1: #self.controlLocus and self.selectedChr > -1
+				lociPerChr = map(len, self.genotype)
+				resultSlice = reduce(lambda X, Y: X+Y, lociPerChr[:self.selectedChr], 0)
+				resultSlice = [resultSlice,resultSlice+lociPerChr[self.selectedChr]]
+			else:
+				pass
+			
+		#calculate QTL for each trait
+		self.qtlresults = []
+
+		for thisTrait in self.traitList:
+			_strains, _vals, _vars = thisTrait.exportInformative(weightedRegression)
+			if self.controlLocus:
+				if weightedRegression:
+					qtlresult = self.genotype.regression(strains = _strains, trait = _vals, 
+							variance = _vars, control = self.controlLocus)
+				else:
+					qtlresult = self.genotype.regression(strains = _strains, trait = _vals,
+						control = self.controlLocus)
+				if resultSlice:
+					qtlresult = qtlresult[resultSlice[0]:resultSlice[1]]
+			else:
+				if weightedRegression:
+					qtlresult = self.genotype.regression(strains = _strains, trait = _vals, 
+							variance = _vars)
+				else:
+					qtlresult = self.genotype.regression(strains = _strains, trait = _vals)
+
+			self.qtlresults.append(qtlresult)
+		
+		if not self.multipleInterval:
+			if self.controlLocus and self.selectedChr > -1:
+				self.genotype.chromosome = [self.genotype[self.selectedChr]]
+				
+			if self.bootChecked:
+				if controlGeno:
+					self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals,
+						control = controlGeno, nboot=fd.nboot)
+				elif weightedRegression:
+					self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals, 
+						variance = _vars, nboot=fd.nboot)
+				else:
+					self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals, 
+						nboot=fd.nboot)
+			else:
+				self.bootResult = []
+
+	def calculatePValue (self, query_LRS, permutation_LRS_array):
+		query_index = len(permutation_LRS_array)
+		for i, one_permutation_LRS in enumerate(permutation_LRS_array):
+			if one_permutation_LRS >= query_LRS:
+				query_index = i
+				break
+
+		P_value = float(len(permutation_LRS_array) - query_index) / len(permutation_LRS_array)
+
+		return P_value
+
+	def helpButton(self, anchor):
+		return HT.Href(self.HELP_PAGE_REF + '#%s' % anchor, self.qmarkImg, target=self.HELP_WINDOW_NAME)
+
+		
+	def traitRemapTD(self, cursor, fd):
+		chrList = HT.Select(name="chromosomes", data=self.ChrList, selected=[self.selectedChr], 
+			onChange="chrLength(this.form.chromosomes.value, this.form.scale.value, this.form, self.ChrLengthMbList);")
+		
+		physicOnly = HT.Span(' *', Class="cr")
+					
+		showSNPCheck   = HT.Input(type='checkbox', Class='checkbox', name='showSNP', value='ON', checked=self.SNPChecked)
+		showSNPText    = HT.Span('SNP Track ', self.helpButton("snpSeismograph"), Class="fs12 fwn")
+	
+		showGenesCheck = HT.Input(type='checkbox', Class='checkbox', name='showGenes', value='ON', checked=self.geneChecked)
+		showGenesText  = HT.Span('Gene Track', Class="fs12 fwn")
+
+		showIntervalAnalystCheck = HT.Input(type='checkbox', Class='checkbox', name='intervalAnalystCheck', value='ON', checked=self.intervalAnalystChecked)
+		showIntervalAnalystText = HT.Span('Interval Analyst', Class="fs12 fwn")
+## BEGIN HaplotypeAnalyst
+		
+		showHaplotypeAnalystCheck = HT.Input(type='checkbox', Class='checkbox', name='haplotypeAnalystCheck', value='ON', checked=self.haplotypeAnalystChecked)
+		showHaplotypeAnalystText = HT.Span('Haplotype Analyst', Class="fs12 fwn")
+## END HaplotypeAnalyst
+
+		leftBox = HT.Input(type="text", name="startMb", size=10)
+		rightBox = HT.Input(type="text", name="endMb", size=10)
+		if self.selectedChr > -1 and self.plotScale=='physic':
+			leftBox.value = self.startMb
+			rightBox.value = self.endMb
+			
+		scaleBox = HT.Select(name="scale", onChange="chrLength(this.form.chromosomes.value, this.form.scale.value, this.form, self.ChrLengthMbList);")
+		scaleBox.append(("Genetic", "morgan"))
+		if fd.genotype.Mbmap:
+			 scaleBox.append(("Physical", "physic"))
+		scaleBox.selected.append(self.plotScale)
+		
+		permBox = HT.Input(type="checkbox", name="permCheck", value='ON', checked=self.permChecked, Class="checkbox")
+		permText = HT.Span("Permutation Test ", self.helpButton("Permutation"), Class="fs12 fwn")
+		bootBox = HT.Input(type="checkbox", name="bootCheck", value='ON', checked=self.bootChecked, Class="checkbox")
+		bootText = HT.Span("Bootstrap Test ", self.helpButton("bootstrap"), Class="fs12 fwn")
+		additiveBox = HT.Input(type="checkbox", name="additiveCheck", value='ON', checked=self.additiveChecked, Class="checkbox")
+		additiveText = HT.Span("Allele Effects ", self.helpButton("additive"), Class="fs12 fwn")
+		dominanceBox = HT.Input(type="checkbox", name="dominanceCheck", value='ON', checked=self.dominanceChecked, Class="checkbox")
+		dominanceText = HT.Span("Dominance Effects ", self.helpButton("Dominance"), Class="fs12 fwn")
+		
+		lrsRadio = HT.Input(type="radio", name="LRSCheck", value='LRS', checked = (self.LRS_LOD == "LRS"))
+		lodRadio = HT.Input(type="radio", name="LRSCheck", value='LOD', checked = (self.LRS_LOD != "LRS"))
+		lrsMaxBox = HT.Input(type="text", name="lrsMax", value=self.lrsMax, size=3)
+		widthBox = HT.Input(type="text", name="graphWidth", size=5, value=str(self.graphWidth))
+		legendBox = HT.Input(type="checkbox", name="viewLegend", value='ON', checked=self.legendChecked, Class="checkbox")			
+		legendText = HT.Span("Legend", Class="fs12 fwn")
+		
+		draw2XBox = HT.Input(type="checkbox", name="draw2X", value='ON', Class="checkbox")			
+		draw2XText = HT.Span("2X Plot", Class="fs12 fwn")
+		
+		regraphButton = HT.Input(type="button", Class="button", onClick="javascript:databaseFunc(this.form,'showIntMap');", value="Remap")
+		
+		controlsForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype="multipart/form-data", name="changeViewForm", submit=HT.Input(type='hidden'))
+		controlsTable = HT.TableLite(border=0)
+		innerControlsTable = HT.TableLite(border=0)
+		if self.selectedChr == -1:
+			minimumGraphWidth = self.MULT_GRAPH_MIN_WIDTH
+		else:
+			minimumGraphWidth = self.GRAPH_MIN_WIDTH
+		
+		innerControlsTable.append(
+			HT.TR(HT.TD("Chr: ", Class="fs12 fwb ffl"),HT.TD(chrList, scaleBox, regraphButton)),
+			HT.TR(HT.TD("View: ", Class="fs12 fwb ffl"),HT.TD(leftBox, " to ", rightBox, "Mb", physicOnly, NOWRAP="on")),
+			HT.TR(HT.TD("Units: ", Class="fs12 fwb ffl"), HT.TD(lrsRadio, "LRS ", lodRadio, "LOD ", self.helpButton("LOD"))),
+			HT.TR(HT.TD(" ", Class="fs12 fwb ffl"), HT.TD(lrsMaxBox, "units on Y-axis (0 for default)", Class="fs11 fwn")),
+			HT.TR(HT.TD("Width: ", Class="fs12 fwb ffl"), HT.TD(widthBox, "pixels (minimum=%d)" % minimumGraphWidth, Class="fs11 fwn "))
+		)
+		#whether SNP
+		cursor.execute("Select Species.Id from SnpAll, Species where SnpAll.SpeciesId = Species.Id and Species.Name = %s limit 1", self.species)
+		SNPorNot = cursor.fetchall()
+		#Whether Gene 
+		cursor.execute("Select Species.Id from GeneList, Species where GeneList.SpeciesId = Species.Id and Species.Name = %s limit 1", self.species)
+		GeneorNot = cursor.fetchall()
+		
+		if self.multipleInterval:
+			optionPanel = HT.TD(valign="top", NOWRAP="on")
+		else:
+			optionPanel = HT.TD(permBox, permText, HT.BR(), bootBox, bootText, HT.BR(), additiveBox, additiveText, HT.BR(), valign="top", NOWRAP="on")
+		#whether dominance
+		if self.genotype.type == 'intercross':
+			optionPanel.append(dominanceBox, dominanceText, HT.BR())
+		if SNPorNot:
+			optionPanel.append(showSNPCheck, showSNPText, physicOnly, HT.BR())
+		if GeneorNot:
+			optionPanel.append(showGenesCheck, showGenesText, physicOnly, HT.BR(), 
+				showIntervalAnalystCheck, showIntervalAnalystText, physicOnly, HT.BR())
+## BEGIN HaplotypeAnalyst
+		optionPanel.append(showHaplotypeAnalystCheck, showHaplotypeAnalystText, physicOnly, HT.BR())
+## END HaplotypeAnalyst		
+		optionPanel.append(legendBox, legendText, HT.BR(),draw2XBox, draw2XText)
+		controlsTable.append(
+			HT.TR(HT.TD(innerControlsTable, valign="top"), 
+				HT.TD("&nbsp;", width=15), optionPanel),
+			HT.TR(HT.TD(physicOnly, " only apply to single chromosome physical mapping", align="Center", colspan=3, Class="fs11 fwn"))
+				)
+		controlsForm.append(controlsTable)
+		
+		controlsForm.append(HT.Input(name="permSuggestive", value=self.suggestive, type="hidden"))
+		controlsForm.append(HT.Input(name="permSignificance", value=self.significance, type="hidden"))
+
+## BEGIN HaplotypeAnalyst #### haplotypeAnalystCheck added below
+## END HaplotypeAnalyst		
+
+		for key in fd.formdata.keys():
+			if key == "searchResult" and type([]) == type(fd.formdata.getvalue(key)):
+				controlsForm.append(HT.Input(name=key, value=string.join(fd.formdata.getvalue(key), "\t"), type="hidden"))
+			elif key not in ("endMb",  "startMb",  "chromosomes", "scale", "permCheck", "bootCheck",  "additiveCheck", "dominanceCheck", 
+				"LRSCheck", "intervalAnalystCheck", "haplotypeAnalystCheck", "lrsMax", "graphWidth", "viewLegend", 'showGenes', 'showSNP', 'draw2X',
+				'permSuggestive', "permSignificance"):
+				controlsForm.append(HT.Input(name=key, value=fd.formdata.getvalue(key), type="hidden"))
+			else:
+				pass
+		
+		# updated by NL, move function changeView(i) to webqtl.js and change it to function changeView(i, Chr_Mb_list)
+		#                move function chrLength(a, b, c) to webqtl.js and change it to function chrLength(a, b, c, Chr_Mb_list)
+		self.dict['js1'] = ''
+		
+		return HT.TD(controlsForm, Class="doubleBorder", width=400)
+		
+	def traitInfoTD(self, fd):
+		if self.selectedChr == -1:
+			intMapHeading = HT.Paragraph('Map Viewer: Whole Genome', Class="title")
+		else:
+			intMapHeading = HT.Paragraph('Map Viewer: Chr %s' % self.genotype[0].name, Class="title")
+		
+		heading2 = HT.Paragraph(HT.Strong('Population: '), "%s %s" % (self.species.title(), fd.RISet) , HT.BR())
+		#Trait is from an database 
+		if self.traitList and self.traitList[0] and self.traitList[0].db:
+			#single trait
+			if len(self.traitList) == 1: 
+				thisTrait = self.traitList[0]
+				trait_url = HT.Href(text=thisTrait.name, url = os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) + \
+					"?FormID=showDatabase&incparentsf1=1&database=%s&ProbeSetID=%s" % (thisTrait.db.name, thisTrait.name), \
+					target='_blank', Class="normalsize")
+				heading2.append(HT.Strong("Database: "), HT.Href(text=thisTrait.db.fullname, url = webqtlConfig.INFOPAGEHREF % thisTrait.db.name ,\
+					target='_blank',Class="normalsize"),HT.BR())
+				if thisTrait.db.type == 'ProbeSet':
+					heading2.append(HT.Strong('Trait ID: '), trait_url, HT.BR(), 
+						HT.Strong("Gene Symbol: "), HT.Italic('%s' % thisTrait.symbol,id="green"),HT.BR())
+					if thisTrait.chr and thisTrait.mb:
+						heading2.append(HT.Strong("Location: "), 'Chr %s @ %s Mb' % (thisTrait.chr, thisTrait.mb))
+				elif thisTrait.db.type == 'Geno':
+					heading2.append(HT.Strong('Locus : '), trait_url, HT.BR())
+					if thisTrait.chr and thisTrait.mb:
+						heading2.append(HT.Strong("Location: "), 'Chr %s @ %s Mb' % (thisTrait.chr, thisTrait.mb))
+				elif thisTrait.db.type == 'Publish':
+					heading2.append(HT.Strong('Record ID: '), trait_url, HT.BR())
+				else:
+					pass
+			else:
+				heading2.append(HT.Strong("Traits: "), "Multiple Traits")
+		else:
+			heading2.append(HT.Strong("Trait Name: "), fd.identification)
+		return HT.TD(intMapHeading, heading2, valign="top")
+		
+	def geneTables(self, geneCol, refGene=None):
+		SNPLink = 0
+		tableIterationsCnt = 0
+		if self.species == "mouse":
+			geneTableMain = HT.TableLite(border=0, width=1280, cellpadding=0, cellspacing=0, Class="collap")
+			columns = HT.TR(HT.TD(' ', Class="fs14 fwb ffl b1 cw cbrb"),
+			HT.TD('Gene Symbol',Class="fs14 fwb ffl b1 cw cbrb", colspan=2),
+			HT.TD('Mb Start (mm9)',Class="fs14 fwb ffl b1 cw cbrb", width=1),
+			HT.TD('Gene Length (Kb)',Class="fs14 fwb ffl b1 cw cbrb", width=1),
+			HT.TD("SNP Count", Class="fs14 fwb ffl b1 cw cbrb", width=1),
+			HT.TD("SNP Density (SNP/Kb)", Class="fs14 fwb ffl b1 cw cbrb", width=1),
+			HT.TD('Avg. Expr. Value', Class="fs14 fwb ffl b1 cw cbrb", width=1), # Max of all transcripts
+			HT.TD('Human Chr',Class="fs14 fwb ffl b1 cw cbrb", width=1),
+			HT.TD('Mb Start (hg19)', Class="fs14 fwb ffl b1 cw cbrb", width=1))
+			
+			# http://compbio.uthsc.edu/miRSNP/
+
+			td_pd = HT.TD(Class="fs14 fwb ffl b1 cw cbrb")
+			td_pd.append(HT.Text("PolymiRTS"))
+			td_pd.append(HT.BR())
+			td_pd.append(HT.Text("Database"))
+			td_pd.append(HT.BR())
+			td_pd.append(HT.Href(url='http://compbio.uthsc.edu/miRSNP/', text='>>', target="_blank", Class="normalsize"))
+						   
+                        if refGene: 
+				columns.append(HT.TD('Literature Correlation', Class="fs14 fwb ffl b1 cw cbrb", width=1))
+	                columns.append(HT.TD('Gene Description',Class="fs14 fwb ffl b1 cw cbrb"))
+	                columns.append(td_pd)
+			geneTableMain.append(columns)
+			
+			# polymiRTS
+			# http://lily.uthsc.edu:8080/20090422_UTHSC_cuiyan/PolymiRTS_CLS?chrom=2&chrom_from=115&chrom_to=125
+			#XZ: We can NOT assume their web service is always on. We must put this block of code in try except.
+			try:
+				conn = httplib.HTTPConnection("lily.uthsc.edu:8080")
+				conn.request("GET", "/20090422_UTHSC_cuiyan/PolymiRTS_CLS?chrom=%s&chrom_from=%s&chrom_to=%s" % (self.genotype[0].name, self.startMb, self.endMb))
+				response = conn.getresponse()
+				data = response.read()
+				data = data.split()
+				conn.close()
+				dic = {}
+				index = 0
+				for i in data:
+					if index%3==0:
+						dic[data[index]] = HT.Href(url=data[index+2], text=data[index+1], target="_blank", Class="normalsize")
+					index = index+1
+			except Exception:
+                                dic={}
+				
+			
+			for gIndex, theGO in enumerate(geneCol):
+				geneLength = (theGO["TxEnd"] - theGO["TxStart"])*1000.0
+				tenPercentLength = geneLength*0.0001
+				txStart = theGO["TxStart"]
+				txEnd = theGO["TxEnd"]
+				theGO["snpDensity"] = theGO["snpCount"]/geneLength
+				if (self.ALEX_DEBUG_BOOL_PRINT_GENE_LIST and geneTableMain):
+					#accessionString = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=Display&DB=gene&term=%s'  % theGO["NM_ID"]
+					geneIdString = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s' % theGO["GeneID"]
+
+					allProbeString = '%s?cmd=sch&gene=%s&alias=1' % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), theGO["GeneSymbol"])
+					if theGO["snpCount"]:
+						snpString = HT.Href(url="%s&chr=%s&start=%s&end=%s&geneName=%s&s1=%d&s2=%d" % (os.path.join(webqtlConfig.CGIDIR, 'main.py?FormID=snpBrowser'), 
+							theGO["Chromosome"], theGO["TxStart"], theGO["TxEnd"], theGO["GeneSymbol"], self.diffCol[0], self.diffCol[1]), 
+							text=theGO["snpCount"], target="_blank", Class="normalsize")
+					else:
+						snpString = 0 
+					
+					mouseStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Mouse&db=mm9&position=chr" + theGO["Chromosome"] + "%3A" + str(int(theGO["TxStart"] * 1000000.0))  + "-" + str(int(theGO["TxEnd"]*1000000.0)) +"&pix=620&Submit=submit"
+					
+					if theGO['humanGene']:
+						huGO = theGO['humanGene']
+						if huGO["TxStart"] == '':
+							humanStartDisplay = ""
+						else:
+							humanStartDisplay = "%0.6f" % huGO["TxStart"]
+						humanChr = huGO["Chromosome"]
+						if humanChr.find("q") > -1:
+							humanChr = humanChr[:humanChr.find("q")]
+						if humanChr.find("p") > -1:
+							humanChr = humanChr[:humanChr.find("p")]
+						humanStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg17&position=chr%s:%d-%d" %  (humanChr, int(1000000*huGO["TxStart"]), int(1000000*huGO["TxEnd"]))
+					else:
+						humanStartString = humanChr = humanStartDisplay = ""
+	
+					geneDescription = theGO["GeneDescription"]
+					if len(geneDescription) > 26:
+						geneDescription = geneDescription[:26]+"..."
+					probeSetSearch = HT.Href(allProbeString, HT.Image("/images/webqtl_search.gif", border=0), target="_blank")
+
+					if theGO["snpDensity"] < 0.000001:
+						snpDensityStr = "0"
+					else:
+						snpDensityStr = "%0.6f" % theGO["snpDensity"]
+
+					avgExpr = []#theGO["avgExprVal")
+					if avgExpr in ([], None):
+						avgExpr = ""
+					else:
+						avgExpr = "%0.6f" % avgExpr
+
+					tableIterationsCnt = tableIterationsCnt + 1
+					
+					# polymiRTS
+					polymiRTS = ' '
+					if dic.has_key(theGO["GeneID"]):
+						polymiRTS = dic[theGO["GeneID"]]
+					
+                                        # If we have a referenceGene then we will show the Literature Correlation
+                                        if refGene:
+                                             literatureCorrelation = str(self.getLiteratureCorrelation(self.cursor,refGene,theGO['GeneID']) or "N/A")
+					     geneTableMain.append(HT.TR(HT.TD(tableIterationsCnt, align="right", Class="fs13 b1 cbw c222"),
+							       HT.TD(probeSetSearch, align="center", Class="fs13 bt1 bb1 cbw c222", width=21),
+							       HT.TD(HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank", Class="normalsize"), align='left', Class="fs13 bt1 bb1 cbw c222"),
+							       HT.TD(HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank", Class="normalsize"), align='right', Class="fs13 b1 cbw c222"),
+							       HT.TD(HT.Href("javascript:centerIntervalMapOnRange2('%s', " % theGO["Chromosome"]+str(txStart-tenPercentLength) + ", " + str(txEnd+tenPercentLength) + ", document.changeViewForm)", "%0.3f" % geneLength, Class="normalsize"), align='right', Class="fs13 b1 cbw c222"),
+							       HT.TD(snpString, align="right", Class="fs13 b1 cbw c222"),
+							       HT.TD(snpDensityStr, align='right', Class='fs13 b1 cbw c222'),
+							       HT.TD(avgExpr, align="right", Class="fs13 b1 cbw c222"), # This should have a link to the "basic stats" (button on main selection page) of the gene
+							       HT.TD(humanChr, align="right",Class="fs13 b1 cbw c222"),
+							       HT.TD(HT.Href(humanStartString, humanStartDisplay, target="_blank", Class="normalsize"), align="right", Class="fs13 b1 cbw c222"),
+							       HT.TD(literatureCorrelation, align='left',Class="fs13 b1 cbw c222"),
+							       HT.TD(geneDescription, align='left',Class="fs13 b1 cbw c222"),
+							       HT.TD(polymiRTS, align='left', Class="fs13 b1 cbw c222")))
+					     
+					else:
+                                             geneTableMain.append(HT.TR(HT.TD(tableIterationsCnt, align="right", Class="fs13 b1 cbw c222"),
+							       HT.TD(probeSetSearch, align="center", Class="fs13 bt1 bb1 cbw c222", width=21),
+							       HT.TD(HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank", Class="normalsize"), align='left', Class="fs13 bt1 bb1 cbw c222"),
+							       HT.TD(HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank", Class="normalsize"), align='right', Class="fs13 b1 cbw c222"),
+							       HT.TD(HT.Href("javascript:centerIntervalMapOnRange2('%s', " % theGO["Chromosome"]+str(txStart-tenPercentLength) + ", " + str(txEnd+tenPercentLength) + ", document.changeViewForm)", "%0.3f" % geneLength, Class="normalsize"), align='right', Class="fs13 b1 cbw c222"),
+							       HT.TD(snpString, align="right", Class="fs13 b1 cbw c222"),
+							       HT.TD(snpDensityStr, align='right', Class='fs13 b1 cbw c222'),
+							       HT.TD(avgExpr, align="right", Class="fs13 b1 cbw c222"), # This should have a link to the "basic stats" (button on main selection page) of the gene
+							       HT.TD(humanChr, align="right",Class="fs13 b1 cbw c222"),
+							       HT.TD(HT.Href(humanStartString, humanStartDisplay, target="_blank", Class="normalsize"), align="right", Class="fs13 b1 cbw c222"),
+							       HT.TD(geneDescription, align='left',Class="fs13 b1 cbw c222"),
+							       HT.TD(polymiRTS, align='left', Class="fs13 b1 cbw c222")))
+
+			return geneTableMain	
+		elif self.species == "rat":
+			geneTableMain = HT.TableLite(border=0, width=1050, cellpadding=0, cellspacing=0, Class="collap")
+			geneTableMain.append(HT.TR(HT.TD(' ', Class="fs14 fwb ffl b1 cw cbrb"),
+						   HT.TD('Gene Symbol',Class="fs14 fwb ffl b1 cw cbrb", colspan=2),
+						   HT.TD('Mb Start (rn3)',Class="fs14 fwb ffl b1 cw cbrb", width=1),
+						   HT.TD('Gene Length (Kb)',Class="fs14 fwb ffl b1 cw cbrb", width=1),
+						   HT.TD('Avg. Expr. Value', Class="fs14 fwb ffl b1 cw cbrb", width=1), # Max of all transcripts
+						   HT.TD('Mouse Chr', Class="fs14 fwb ffl b1 cw cbrb", width=1),
+						   HT.TD('Mb Start (mm9)', Class="fs14 fwb ffl b1 cw cbrb", width=1),
+						   HT.TD('Human Chr',Class="fs14 fwb ffl b1 cw cbrb", width=1),
+						   HT.TD('Mb Start (hg19)', Class="fs14 fwb ffl b1 cw cbrb", width=1),
+						   HT.TD('Gene Description',Class="fs14 fwb ffl b1 cw cbrb")))
+						   
+			for gIndex, theGO in enumerate(geneCol):
+				geneDesc = theGO["GeneDescription"]
+				if geneDesc == "---":
+					geneDesc = ""
+				geneLength = (float(theGO["TxEnd"]) - float(theGO["TxStart"]))
+				geneLengthURL = "javascript:centerIntervalMapOnRange2('%s', %f, %f, document.changeViewForm)" % (theGO["Chromosome"], float(theGO["TxStart"])-(geneLength*0.1), float(theGO["TxEnd"])+(geneLength*0.1))
+
+				#the chromosomes for human 1 are 1qXX.XX
+				if theGO['humanGene']:
+					humanChr = theGO['humanGene']["Chromosome"]
+					if 'q' in humanChr:
+						humanChr = humanChr[:humanChr.find("q")]
+					if 'p' in humanChr:
+						humanChr = humanChr[:humanChr.find("p")]
+					humanTxStart = theGO['humanGene']["TxStart"]
+				else:
+					humanChr = humanTxStart = ""
+					
+				#Mouse Gene
+				if theGO['mouseGene']:
+					mouseChr = theGO['mouseGene']["Chromosome"]
+					mouseTxStart = theGO['mouseGene']["TxStart"]
+				else:
+					mouseChr = mouseTxStart = ""
+
+				if theGO["GeneID"] != "":
+					geneSymbolURL = HT.Href("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" % theGO["GeneID"], theGO["GeneSymbol"], Class="normalsize", target="_blanK")
+				else:
+					geneSymbolURL = theGO["GeneSymbol"]
+
+				if len(geneDesc) > 34:
+					geneDesc = geneDesc[:32] + "..."
+
+				avgExprVal = [] #theGO["avgExprVal"]
+				if avgExprVal != "" and avgExprVal:
+					avgExprVal = "%0.5f" % float(avgExprVal)
+				else:
+					avgExprVal = ""
+
+				geneTableMain.append(HT.TR(HT.TD(gIndex+1, align="right", Class="fs13 b1 cbw c222"),
+						       HT.TD(HT.Href(os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)+"?cmd=sch&gene=%s&alias=1&species=rat" % theGO["GeneSymbol"], HT.Image("/images/webqtl_search.gif", border=0), target="_blank"), Class="fs13 bt1 bb1 cbw c222"),
+						       HT.TD(geneSymbolURL, Class="fs13 bt1 bb1 cbw c222"),
+						       HT.TD(theGO["TxStart"], Class="fs13 b1 cbw c222"),
+						       HT.TD(HT.Href(geneLengthURL, "%0.3f" % (geneLength*1000.0), Class="normalsize"), Class="fs13 b1 cbw c222"),
+						       HT.TD(avgExprVal, Class="fs13 b1 cbw c222"),
+						       HT.TD(mouseChr, Class="fs13 b1 cbw c222"),
+						       HT.TD(mouseTxStart, Class="fs13 b1 cbw c222"),
+						       HT.TD(humanChr, Class="fs13 b1 cbw c222"),
+						       HT.TD(humanTxStart, Class="fs13 b1 cbw c222"),
+						       HT.TD(geneDesc, Class="fs13 b1 cbw c222")))
+			return geneTableMain
+		else:
+			return ""
+
+	def getLiteratureCorrelation(cursor,geneId1=None,geneId2=None):
+       		if not geneId1 or not geneId2:  
+        		return None
+        	if geneId1 == geneId2: 
+        		return 1.0
+        	geneId1 = str(geneId1)
+        	geneId2 = str(geneId2)
+        	lCorr = None
+        	try:
+            		query = 'SELECT Value FROM LCorrRamin3 WHERE GeneId1 = %s and GeneId2 = %s'
+            		for x,y in [(geneId1,geneId2),(geneId2,geneId1)]:
+          	    		cursor.execute(query,(x,y))
+		       		lCorr =  cursor.fetchone()
+                 		if lCorr: 
+                     			lCorr = lCorr[0]
+                     			break
+        	except: raise #lCorr = None
+        	return lCorr