Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'

1 files changed, 0 insertions, 2454 deletions

diff --git a/web/webqtl/intervalMapping/IntervalMappingPage.py b/web/webqtl/intervalMapping/IntervalMappingPage.py
deleted file mode 100755
index c3ef1cbd..00000000
--- a/web/webqtl/intervalMapping/IntervalMappingPage.py
+++ /dev/null
@@ -1,2454 +0,0 @@
-# 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