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

4 files changed, 0 insertions, 943 deletions

diff --git a/web/webqtl/pairScan/CategoryGraphPage.py b/web/webqtl/pairScan/CategoryGraphPage.py
deleted file mode 100755
index 696c05ce..00000000
--- a/web/webqtl/pairScan/CategoryGraphPage.py
+++ /dev/null
@@ -1,199 +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 GeneNetwork Core Team 2010/10/20
-
-import string
-import piddle as pid
-from htmlgen import HTMLgen2 as HT
-
-from utility import Plot
-from base.templatePage import templatePage
-from utility import webqtlUtil
-from base import webqtlConfig
-
-#########################################
-#      Category Graph Page
-#########################################
-class CategoryGraphPage(templatePage):
-	def __init__(self, fd):
-
-		LRSFullThresh = 30
-		LRSInteractThresh = 25
-		maxPlotSize = 800
-		mainfmName = webqtlUtil.genRandStr("fm_")
-
-		templatePage.__init__(self, fd)
-
-		if not fd.genotype:
-			fd.readData()
-
-		##Remove F1 and Parents
-		fd.genotype = fd.genotype_1
-
-		plotType = fd.formdata.getvalue('plotType')
-		self.dict['title'] = '%s Plot' % plotType
-		main_title = HT.Paragraph("%s Plot" % plotType)
-		main_title.__setattr__("class","title")
-
-		interval1 = fd.formdata.getvalue('interval1')
-		interval2 = fd.formdata.getvalue('interval2')
-
-		flanka1, flanka2, chram = string.split(interval1)
-		flankb1, flankb2, chrbm = string.split(interval2)
-
-		traitValues = string.split(fd.formdata.getvalue('traitValues'), ',')
-		traitValues = map(webqtlUtil.StringAsFloat, traitValues)
-		traitStrains = string.split(fd.formdata.getvalue('traitStrains'), ',')
-
-		flankaGeno = []
-		flankbGeno = []
-
-		for chr in fd.genotype:
-			for locus in chr:
-				if locus.name in (flanka1, flankb1):
-					if locus.name == flanka1:
-						flankaGeno = locus.genotype[:]
-					else:
-						flankbGeno = locus.genotype[:]
-			if flankaGeno and flankbGeno:
-				break
-
-		flankaDict = {}
-		flankbDict = {}
-		for i in range(len(fd.genotype.prgy)):
-			flankaDict[fd.genotype.prgy[i]] = flankaGeno[i]
-			flankbDict[fd.genotype.prgy[i]] = flankbGeno[i]
-
-		BB = []
-		BD = []
-		DB = []
-		DD = []
-
-		iValues = []
-		for i in range(len(traitValues)):
-			if traitValues[i] != None:
-				iValues.append(traitValues[i])
-				thisstrain = traitStrains[i]
-				try:
-					a1 = flankaDict[thisstrain]
-					b1 = flankbDict[thisstrain]
-				except:
-					continue
-				if a1 == -1.0:
-					if b1 == -1.0:
-						BB.append((thisstrain, traitValues[i]))
-					elif b1 == 1.0:
-						BD.append((thisstrain, traitValues[i]))
-				elif a1 == 1.0:
-					if b1 == -1.0:
-						DB.append((thisstrain, traitValues[i]))
-					elif b1 == 1.0:
-						DD.append((thisstrain, traitValues[i]))
-				else:
-					pass
-
-		#print BB, BD, DB, DD, max(iValues), min(iValues)
-
-		plotHeight = 400
-		plotWidth = 600
-		xLeftOffset = 60
-		xRightOffset = 40
-		yTopOffset = 40
-		yBottomOffset = 60
-
-		canvasHeight = plotHeight + yTopOffset + yBottomOffset
-		canvasWidth = plotWidth + xLeftOffset + xRightOffset
-		canvas = pid.PILCanvas(size=(canvasWidth,canvasHeight))
-		XXX = [('Mat/Mat', BB), ('Mat/Pat', BD), ('Pat/Mat', DB), ('Pat/Pat', DD)]
-		XLabel = "Interval 1 / Interval 2"
-
-		if plotType == "Box":
-			Plot.plotBoxPlot(canvas, XXX, offset=(xLeftOffset, xRightOffset, yTopOffset, yBottomOffset), XLabel = XLabel)
-		else:
-			#Could be a separate function, but seems no other uses
-			max_Y = max(iValues)
-			min_Y = min(iValues)
-			scaleY = Plot.detScale(min_Y, max_Y)
-			Yll = scaleY[0]
-			Yur = scaleY[1]
-			nStep = scaleY[2]
-			stepY = (Yur - Yll)/nStep
-			stepYPixel = plotHeight/(nStep)
-			canvas.drawRect(plotWidth+xLeftOffset, plotHeight + yTopOffset, xLeftOffset, yTopOffset)
-
-			##draw Y Scale
-			YYY = Yll
-			YCoord = plotHeight + yTopOffset
-			scaleFont=pid.Font(ttf="cour",size=11,bold=1)
-			for i in range(nStep+1):
-				strY = Plot.cformat(d=YYY, rank=0)
-				YCoord = max(YCoord, yTopOffset)
-				canvas.drawLine(xLeftOffset,YCoord,xLeftOffset-5,YCoord)
-				canvas.drawString(strY,	xLeftOffset -30,YCoord +5,font=scaleFont)
-				YYY += stepY
-				YCoord -= stepYPixel
-
-
-			##draw X Scale
-			stepX = plotWidth/len(XXX)
-			XCoord = xLeftOffset + 0.5*stepX
-			YCoord = plotHeight + yTopOffset
-			scaleFont = pid.Font(ttf="tahoma",size=12,bold=0)
-			labelFont = pid.Font(ttf="tahoma",size=13,bold=0)
-			for item in XXX:
-				itemname, itemvalue = item
-				canvas.drawLine(XCoord, YCoord,XCoord, YCoord+5, color=pid.black)
-				canvas.drawString(itemname, XCoord - canvas.stringWidth(itemname,font=labelFont)/2.0,YCoord +20,font=labelFont)
-				itemvalue.sort(webqtlUtil.cmpOrder2)
-				j = 0
-				for item2 in itemvalue:
-					tstrain, tvalue = item2
-					canvas.drawCross(XCoord, plotHeight + yTopOffset - (tvalue-Yll)*plotHeight/(Yur - Yll), color=pid.red,size=5)
-					if j % 2 == 0:
-						canvas.drawString(tstrain, XCoord+5, plotHeight + yTopOffset - \
-						(tvalue-Yll)*plotHeight/(Yur - Yll) +5, font=scaleFont, color=pid.blue)
-					else:
-						canvas.drawString(tstrain, XCoord-canvas.stringWidth(tstrain,font=scaleFont)-5, \
-						plotHeight + yTopOffset - (tvalue-Yll)*plotHeight/(Yur - Yll) +5, font=scaleFont, color=pid.blue)
-					j += 1
-				XCoord += stepX
-
-
-			labelFont=pid.Font(ttf="verdana",size=18,bold=0)
-			canvas.drawString(XLabel, xLeftOffset + (plotWidth -canvas.stringWidth(XLabel,font=labelFont))/2.0, YCoord +40, font=labelFont)
-			canvas.drawString("Value",xLeftOffset-40,  YCoord-(plotHeight -canvas.stringWidth("Value",font=labelFont))/2.0, font=labelFont, angle =90)
-
-
-		filename= webqtlUtil.genRandStr("Cate_")
-		canvas.save(webqtlConfig.IMGDIR+filename, format='gif')
-		img=HT.Image('/image/'+filename+'.gif',border=0)
-
-		TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign='top')
-		TD_LR.append(main_title, HT.Center(img))#, traitValues , len(traitValues), traitStrains, len(traitStrains), len(fd.genotype.prgy))
-		#TD_LR.append(main_title, HT.BR(), flanka1, flanka2, chram, HT.BR(), flankb1, flankb2, chrbm)
-		self.dict['body'] = str(TD_LR)
-
-
-
diff --git a/web/webqtl/pairScan/DirectPlotPage.py b/web/webqtl/pairScan/DirectPlotPage.py
deleted file mode 100755
index 4c3b9075..00000000
--- a/web/webqtl/pairScan/DirectPlotPage.py
+++ /dev/null
@@ -1,430 +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 GeneNetwork Core Team 2010/10/20
-
-import string
-import piddle as pid
-from math import *
-import os
-
-import direct
-from htmlgen import HTMLgen2 as HT
-
-from utility import Plot
-from base.webqtlTrait import webqtlTrait
-from base.templatePage import templatePage
-from utility import webqtlUtil
-from base import webqtlConfig
-
-
-
-class DirectPlotPage(templatePage):
-	def __init__(self, fd):
-
-		LRSFullThresh = 30
-		LRSInteractThresh = 25
-
-		templatePage.__init__(self, fd)
-
-		if not fd.genotype:
-			fd.readData()
-
-		incVars = 0
-		_genotype = fd.genotype_1
-		_strains, _vals, _vars, N = fd.informativeStrains(_genotype.prgy, incVars)
-
-		self.dict['title'] = 'Pair-Scan Plot'
-		if not self.openMysql():
-			return
-
-		iPermuCheck = fd.formdata.getvalue('directPermuCheckbox')
-
-		try:
-			graphtype = int(fd.formdata.getvalue('graphtype'))
-		except:
-			graphtype = 1
-		try:
-			graphsort = int(fd.formdata.getvalue('graphSort'))
-		except:
-			graphsort = 1
-		try:
-			returnIntervalPairNum = int(fd.formdata.getvalue('pairScanReturn'))
-		except:
-			returnIntervalPairNum = 50
-
-		pairIntro = HT.Blockquote("The graph below displays pair-scan results for the trait ",HT.Strong(" %s" % fd.identification))
-		if not graphsort:
-			tblIntro = HT.Blockquote('This table lists LRS scores for the top %d pairs of intervals (Interval 1 on the left and Interval 2 on the right). Pairs are sorted by the "LRS Full" column. Both intervals are defined by proximal and distal markers that flank the single best position.' % returnIntervalPairNum)
-		else:
-			tblIntro = HT.Blockquote('This table lists LRS scores for the top %d pairs of intervals (Interval 1 on the left and Interval 2 on the right). Pairs are sorted by the "LRS Interaction" column. Both intervals are defined by proximal and distal markers that flank the single best position.' % returnIntervalPairNum)
-
-		try:
-			thisTrait = webqtlTrait(fullname=fd.formdata.getvalue("fullname"), cursor=self.cursor)
-			pairIntro.append(' from the database ' , thisTrait.db.genHTML())
-		except:
-			pass
-
-		pairIntro.append('. The upper left half of the plot highlights any epistatic interactions (corresponding to the column labeled "LRS Interact"). In contrast, the lower right half provides a summary of LRS of the full model, representing cumulative effects of linear and non-linear terms (column labeled "LRS Full"). The WebQTL implementation of the scan for 2-locus epistatic interactions is based on the DIRECT global optimization algorithm developed by ',HT.Href(text ="Ljungberg",url='http://user.it.uu.se/~kl/qtl_software.html',target="_blank", Class = "fs14 fwn"),', Holmgren, and Carlborg (',HT.Href(text = "2004",url='http://bioinformatics.oupjournals.org/cgi/content/abstract/bth175?ijkey=21Pp0pgOuBL6Q&keytype=ref', Class = "fs14 fwn"),').')
-
-		main_title = HT.Paragraph("Pair-Scan Results: An Analysis of Epistatic Interactions")
-		main_title.__setattr__("class","title")
-
-		subtitle1 = HT.Paragraph("Pair-Scan Graph")
-		subtitle3 = HT.Paragraph("Pair-Scan Top LRS")
-		subtitle1.__setattr__("class","subtitle")
-		subtitle3.__setattr__("class","subtitle")
-
-		self.identification = "unnamed trait"
-		if fd.identification:
-			self.identification = fd.identification
-			self.dict['title'] = self.identification + ' / '+self.dict['title']
-
-		#####################################
-		#
-		# Remove the Parents & F1 data
-		#
-		#####################################
-
-		if _vals:
-			if len(_vals) > webqtlConfig.KMININFORMATIVE:
-				ResultFull = []
-				ResultInteract = []
-				ResultAdd = []
-
-				#permutation test
-				subtitle2 = ''
-				permuTbl = ''
-				permuIntro = ''
-				if iPermuCheck:
-					subtitle2 = HT.Paragraph("Pair-Scan Permutation Results")
-					subtitle2.__setattr__("class","subtitle")
-					permuIntro = HT.Blockquote("Phenotypes were randomly permuted 500 times among strains or individuals and reanalyzed using the pair-scan algorithm. We extracted the single highest LRS for the full model for each of these permuted data sets. The histograms of these highest LRS values provide an empirical way to estimate the probability of obtaining an LRS above suggestive or significant thresholds.")
-
-					prtmuTblIntro1 = HT.Paragraph("The following table gives threshold values for Suggestive (P=0.63) and Significant associations (P=0.05) defined by Lander & Kruglyak and for the slightly more stringent P=0.01 level. (The Highly Significant level of Lander & Kruglyak corresponds to P=0.001 and cannot be estimated with 500 permutations.)")
-					prtmuTblIntro2 = HT.Paragraph("If the full model exceeds the permutation-based Significant threshold, then different models for those locations can be tested by conventional chi-square tests at P<0.01. Interaction is significant if LRS Interact exceeds 6.64 for RI strains or 13.28 for an F2. If interaction is not significant, the two-QTL model is better than a one-QTL model if LRS Additive exceeds LRS 1 or LRS 2 by 6.64 for RI strains or 9.21 for an F2.")
-					ResultFull, ResultInteract, ResultAdd = direct.permu(webqtlConfig.GENODIR, _vals, _strains, fd.RISet, 500) #XZ, 08/14/2008: add module name webqtlConfig
-					ResultFull.sort()
-					ResultInteract.sort()
-					ResultAdd.sort()
-					nPermuResult = len(ResultFull)
-					# draw Histogram
-					cFull = pid.PILCanvas(size=(400,300))
-					Plot.plotBar(cFull, ResultFull,XLabel='LRS',YLabel='Frequency',title=' Histogram of LRS Full')
-					#plotBar(cFull,10,10,390,290,ResultFull,XLabel='LRS',YLabel='Frequency',title=' Histogram of LRS Full')
-					filename= webqtlUtil.genRandStr("Pair_")
-					cFull.save(webqtlConfig.IMGDIR+filename, format='gif')
-					imgFull=HT.Image('/image/'+filename+'.gif',border=0,alt='Histogram of LRS Full')
-
-
-					superPermuTbl = HT.TableLite(border=0, cellspacing=0, cellpadding=0,bgcolor ='#999999')
-					permuTbl2 = HT.TableLite(border=0, cellspacing= 1, cellpadding=5)
-					permuTbl2.append(HT.TR(HT.TD(HT.Font('LRS', color = '#FFFFFF')), HT.TD(HT.Font('p = 0.63', color = '#FFFFFF'), width = 150, align='Center'), HT.TD(HT.Font('p = 0.05', color = '#FFFFFF'), width = 150, align='Center'), HT.TD(HT.Font('p = 0.01', color = '#FFFFFF'), width = 150, align='Center'),bgColor='royalblue'))
-					permuTbl2.append(HT.TR(HT.TD('Full'), HT.TD('%2.1f' % ResultFull[int(nPermuResult*0.37 -1)], align="Center"), HT.TD('%2.1f' % ResultFull[int(nPermuResult*0.95 -1)], align="Center"), HT.TD('%2.1f' % ResultFull[int(nPermuResult*0.99 -1)], align="Center"),bgColor="#eeeeee"))
-					superPermuTbl.append(HT.TD(HT.TD(permuTbl2)))
-
-					permuTbl1 = HT.TableLite(border=0, cellspacing= 0, cellpadding=5,width='100%')
-					permuTbl1.append(HT.TR(HT.TD(imgFull, align="Center", width = 410), HT.TD(prtmuTblIntro1, superPermuTbl, prtmuTblIntro2, width = 490)))
-
-					permuTbl = HT.Center(permuTbl1, HT.P())
-
-					#permuTbl.append(HT.TR(HT.TD(HT.BR(), 'LRS Full  = %2.1f, ' % ResultFull[int(nPermuResult*0.37 -1)], 'LRS Full  = %2.1f, ' % ResultFull[int(nPermuResult*0.95 -1)], 'LRS Full highly significant (p=0.001) = %2.1f, ' % ResultFull[int(nPermuResult*0.999 -1)] , HT.BR(), 'LRS Interact suggestive (p=0.63) = %2.1f, ' % ResultInteract[int(nPermuResult*0.37 -1)], 'LRS Interact significant (p=0.05) = %2.1f, ' % ResultInteract[int(nPermuResult*0.95 -1)], 'LRS Interact  = %2.1f, ' % ResultInteract[int(nPermuResult*0.999 -1)] , HT.BR(),'LRS Additive suggestive (p=0.63) = %2.1f, ' % ResultAdd[int(nPermuResult*0.37 -1)], 'LRS Additive significant (p=0.05) = %2.1f, ' % ResultAdd[int(nPermuResult*0.95 -1)], 'LRS Additive highly significant (p=0.001) = %2.1f, ' % ResultAdd[int(nPermuResult*0.999 -1)], HT.BR(), 'Total number of permutation is %d' % nPermuResult, HT.BR(), HT.BR(),colspan=2)))
-					#tblIntro.append(HT.P(), HT.Center(permuTbl))
-
-				#print vals, strains, fd.RISet
-				d = direct.direct(webqtlConfig.GENODIR, _vals, _strains, fd.RISet, 8000)#XZ, 08/14/2008: add module name webqtlConfig
-				chrsInfo = d[2]
-				sum = 0
-				offsets = [0]
-				i = 0
-				for item in chrsInfo:
-					if i > 0:
-						offsets.append(sum)
-					sum += item[0]
-					i += 1
-				offsets.append(sum)
-				#print sum,offset,d[2]
-				canvasWidth = 880
-				canvasHeight = 880
-				if graphtype:
-					colorAreaWidth = 230
-				else:
-					colorAreaWidth = 0
-				c = pid.PILCanvas(size=(canvasWidth + colorAreaWidth ,canvasHeight))
-				xoffset = 40
-				yoffset = 40
-				width = canvasWidth - xoffset*2
-				height = canvasHeight - yoffset*2
-
-				xscale = width/sum
-				yscale = height/sum
-
-				rectInfo = d[1]
-				rectInfo.sort(webqtlUtil.cmpLRSFull)
-
-				finecolors = Plot.colorSpectrum(250)
-				finecolors.reverse()
-				regLRS = [0]*height
-				#draw LRS Full
-
-				for item in rectInfo:
-					LRSFull,LRSInteract,LRSa,LRSb,chras,chram,chrae,chrbs,chrbm,chrbe,chra,chrb,flanka,flankb = item
-					if LRSFull > 30:
-						dcolor = pid.red
-					elif LRSFull > 20:
-						dcolor = pid.orange
-					elif LRSFull > 10:
-						dcolor = pid.olivedrab
-					elif LRSFull > 0:
-						dcolor = pid.grey
-					else:
-						LRSFull = 0
-						dcolor = pid.grey
-
-					chras += offsets[chra]
-					chram += offsets[chra]
-					chrae += offsets[chra]
-					chrbs += offsets[chrb]
-					chrbm += offsets[chrb]
-					chrbe += offsets[chrb]
-
-					regLRSD = int(chram*yscale)
-					if regLRS[regLRSD] < LRSa:
-						regLRS[regLRSD] = LRSa
-					regLRSD = int(chrbm*yscale)
-					if regLRS[regLRSD] < LRSb:
-						regLRS[regLRSD] = LRSb
-
-					if graphtype:
-						colorIndex = int(LRSFull *250 /LRSFullThresh)
-						if colorIndex >= 250:
-							colorIndex = 249
-						dcolor = finecolors[colorIndex]
-						if chra != chrb or ((chrbe - chrae) > 10 and (chrbs - chras) > 10):
-							c.drawRect(xoffset+chrbs*xscale,yoffset+height-chras*yscale,xoffset+chrbe*xscale,yoffset+height-chrae*yscale,edgeColor=dcolor,fillColor=dcolor,edgeWidth = 0)
-						else:
-							c.drawPolygon([(xoffset+chrbs*xscale,yoffset+height-chras*yscale),(xoffset+chrbe*xscale,yoffset+height-chras*yscale),(xoffset+chrbe*xscale,yoffset+height-chrae*yscale)],edgeColor=dcolor,fillColor=dcolor,edgeWidth = 0,closed =1)
-					else:
-						c.drawCross(xoffset+chrbm*xscale,yoffset+height-chram*yscale,color=dcolor,size=2)
-				#draw Marker Regression LRS
-				if graphtype:
-					"""
-					maxLRS = max(regLRS)
-					pts = []
-					i = 0
-					for item in regLRS:
-						pts.append((xoffset+width+35+item*50/maxLRS, yoffset+height-i))
-						i += 1
-					c.drawPolygon(pts,edgeColor=pid.blue,edgeWidth=1,closed=0)
-					"""
-					LRS1Thresh = 16.2
-					i = 0
-					for item in regLRS:
-						colorIndex = int(item *250 /LRS1Thresh)
-						if colorIndex >= 250:
-							colorIndex = 249
-						dcolor = finecolors[colorIndex]
-						c.drawLine(xoffset+width+35,yoffset+height-i,xoffset+width+55,yoffset+height-i,color=dcolor)
-						i += 1
-					labelFont=pid.Font(ttf="arial",size=20,bold=0)
-					c.drawString('Single Locus Regression',xoffset+width+90,yoffset+height, font = labelFont,color=pid.dimgray,angle=90)
-				#draw LRS Interact
-				rectInfo.sort(webqtlUtil.cmpLRSInteract)
-				for item in rectInfo:
-					LRSFull,LRSInteract,LRSa,LRSb,chras,chram,chrae,chrbs,chrbm,chrbe,chra,chrb,flanka,flankb = item
-					if LRSInteract > 30:
-						dcolor = pid.red
-					elif LRSInteract > 20:
-						dcolor = pid.orange
-					elif LRSInteract > 10:
-						dcolor = pid.olivedrab
-					elif LRSInteract > 0:
-						dcolor = pid.grey
-					else:
-						LRSInteract = 0
-						dcolor = pid.grey
-					chras += offsets[chra]
-					chram += offsets[chra]
-					chrae += offsets[chra]
-					chrbs += offsets[chrb]
-					chrbm += offsets[chrb]
-					chrbe += offsets[chrb]
-					if graphtype:
-						colorIndex = int(LRSInteract *250 / LRSInteractThresh )
-						if colorIndex >= 250:
-							colorIndex = 249
-						dcolor = finecolors[colorIndex]
-						if chra != chrb or ((chrbe - chrae) > 10 and (chrbs - chras) > 10):
-							c.drawRect(xoffset+chras*xscale,yoffset+height-chrbs*yscale,xoffset+chrae*xscale,yoffset+height-chrbe*yscale,edgeColor=dcolor,fillColor=dcolor,edgeWidth = 0)
-						else:
-							c.drawPolygon([(xoffset+chras*xscale,yoffset+height-chrbs*yscale),(xoffset+chras*xscale,yoffset+height-chrbe*yscale),(xoffset+chrae*xscale,yoffset+height-chrbe*yscale)],edgeColor=dcolor,fillColor=dcolor,edgeWidth = 0,closed =1)
-					else:
-						c.drawCross(xoffset+chram*xscale,yoffset+height-chrbm*yscale,color=dcolor,size=2)
-				#draw chromosomes label
-				labelFont=pid.Font(ttf="tahoma",size=24,bold=0)
-				i = 0
-				for item in chrsInfo:
-					strWidth = c.stringWidth(item[1],font=labelFont)
-					c.drawString(item[1],xoffset+offsets[i]*xscale +(item[0]*xscale-strWidth)/2,canvasHeight -15,font = labelFont,color=pid.dimgray)
-					c.drawString(item[1],xoffset+offsets[i]*xscale +(item[0]*xscale-strWidth)/2,yoffset-10,font = labelFont,color=pid.dimgray)
-					c.drawString(item[1],xoffset-strWidth-5,yoffset+height - offsets[i]*yscale -(item[0]*yscale-22)/2,font = labelFont,color=pid.dimgray)
-					c.drawString(item[1],canvasWidth-xoffset+5,yoffset+height - offsets[i]*yscale -(item[0]*yscale-22)/2,font = labelFont,color=pid.dimgray)
-					i += 1
-
-
-				c.drawRect(xoffset,yoffset,xoffset+width,yoffset+height)
-				for item in offsets:
-					c.drawLine(xoffset,yoffset+height-item*yscale,xoffset+width,yoffset+height-item*yscale)
-					c.drawLine(xoffset+item*xscale,yoffset,xoffset+item*xscale,yoffset+height)
-
-				#draw pngMap
-				pngMap = HT.Map(name='pairPlotMap')
-				#print offsets, len(offsets)
-				for i in range(len(offsets)-1):
-					for j in range(len(offsets)-1):
-						COORDS = "%d,%d,%d,%d" %(xoffset+offsets[i]*xscale, yoffset+height-offsets[j+1]*yscale, xoffset+offsets[i+1]*xscale, yoffset+height-offsets[j]*yscale)
-						HREF = "javascript:showPairPlot(%d,%d);" % (i,j)
-						Areas = HT.Area(shape='rect',coords=COORDS,href=HREF)
-						pngMap.areas.append(Areas)
-
-				#draw spectrum
-				if graphtype:
-					i = 0
-					labelFont=pid.Font(ttf="tahoma",size=14,bold=0)
-					middleoffsetX = 180
-					for dcolor in finecolors:
-						if i % 50 == 0:
-							c.drawLine(xoffset+ width +middleoffsetX-15 , height + yoffset -i, xoffset+ width +middleoffsetX-20,height + yoffset -i, color=pid.black)
-							c.drawString('%d' % int(LRSInteractThresh*i/250.0),xoffset+ width+ middleoffsetX-40,height + yoffset -i +5, font = labelFont,color=pid.black)
-							c.drawLine(xoffset+ width +middleoffsetX+15 , height + yoffset -i, xoffset+ width +middleoffsetX+20 ,height + yoffset -i, color=pid.black)
-							c.drawString('%d' % int(LRSFullThresh*i/250.0),xoffset+ width + middleoffsetX+25,height + yoffset -i +5, font = labelFont,color=pid.black)
-						c.drawLine(xoffset+ width +middleoffsetX-15 , height + yoffset -i, xoffset+ width +middleoffsetX+15 ,height + yoffset -i, color=dcolor)
-						i += 1
-
-					if i % 50 == 0:
-						i -= 1
-						c.drawLine(xoffset+ width +middleoffsetX-15 , height + yoffset -i, xoffset+ width +middleoffsetX-20,height + yoffset -i, color=pid.black)
-						c.drawString('%d' % ceil(LRSInteractThresh*i/250.0),xoffset+ width + middleoffsetX-40,height + yoffset -i +5, font = labelFont,color=pid.black)
-						c.drawLine(xoffset+ width +middleoffsetX+15 , height + yoffset -i, xoffset+ width +middleoffsetX+20 ,height + yoffset -i, color=pid.black)
-						c.drawString('%d' % ceil(LRSFullThresh*i/250.0),xoffset+ width + middleoffsetX+25,height + yoffset -i +5, font = labelFont,color=pid.black)
-
-					labelFont=pid.Font(ttf="verdana",size=20,bold=0)
-					c.drawString('LRS Interaction',xoffset+ width + middleoffsetX-50,height + yoffset, font = labelFont,color=pid.dimgray,angle=90)
-					c.drawString('LRS Full',xoffset+ width + middleoffsetX+50,height + yoffset, font = labelFont,color=pid.dimgray,angle=90)
-
-				filename= webqtlUtil.genRandStr("Pair_")
-				c.save(webqtlConfig.IMGDIR+filename, format='png')
-				img2=HT.Image('/image/'+filename+'.png',border=0,usemap='#pairPlotMap')
-
-
-				form0 = HT.Form( cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showPairPlot', submit=HT.Input(type='hidden'))
-				hddn0 = {'FormID':'pairPlot','Chr_A':'_','Chr_B':'','idata':string.join(map(str, _vals), ','),'istrain':string.join(_strains, ','),'RISet':fd.RISet}
-				for key in hddn0.keys():
-					form0.append(HT.Input(name=key, value=hddn0[key], type='hidden'))
-
-				form0.append(img2, pngMap)
-
-				mainfmName = webqtlUtil.genRandStr("fm_")
-				txtform = HT.Form( cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name=mainfmName, submit=HT.Input(type='hidden'))
-				hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_','RISet':fd.RISet}
-				#XZ, Aug 11, 2010: The variable traitStrains is not assigned right values before (should not be assigned fd.strainlist).
-				#hddn['traitStrains'] = string.join(fd.strainlist, ',')
-				hddn['traitStrains'] = string.join(_strains, ',')
-				hddn['traitValues'] = string.join(map(str, _vals), ',')
-				hddn['interval1'] = ''
-				hddn['interval2'] = ''
-				if fd.incparentsf1:
-					hddn['incparentsf1']='ON'
-				for key in hddn.keys():
-					txtform.append(HT.Input(name=key, value=hddn[key], type='hidden'))
-
-				tbl = HT.TableLite(Class="collap", cellspacing=1, cellpadding=5,width=canvasWidth + colorAreaWidth)
-
-				c1 = HT.TD('Interval 1',colspan=3,align="Center", Class="fs13 fwb ffl b1 cw cbrb")
-				c2 = HT.TD('Interval 2',colspan=3,align="Center", Class="fs13 fwb ffl b1 cw cbrb")
-				c11 = HT.TD('Position',rowspan=2,align="Center", Class="fs13 fwb ffl b1 cw cbrb")
-				c12 = HT.TD('Flanking Markers',colspan=2,align="Center", Class="fs13 fwb ffl b1 cw cbrb")
-				c111 = HT.TD('Proximal',align="Center", Class="fs13 fwb ffl b1 cw cbrb")
-				c112 = HT.TD('Distal',align="Center", Class="fs13 fwb ffl b1 cw cbrb")
-
-
-				c3 = HT.TD('LRS Full',rowspan=3,align="Center", Class="fs13 fwb ffl b1 cw cbrb")
-				c4 = HT.TD('LRS Additive',rowspan=3,align="Center", Class="fs13 fwb ffl b1 cw cbrb")
-				c5 = HT.TD('LRS Interact',rowspan=3,align="Center", Class="fs13 fwb ffl b1 cw cbrb")
-				c6 = HT.TD('LRS 1',rowspan=3,align="Center", Class="fs13 fwb ffl b1 cw cbrb")
-				c7 = HT.TD('LRS 2',rowspan=3,align="Center", Class="fs13 fwb ffl b1 cw cbrb")
-
-
-				tbl.append(HT.TR(c1,c3,c4,c5,c6,c7,c2))
-
-				tbl.append(HT.TR(c11,c12,c11,c12))
-				tbl.append(HT.TR(c111,c112,c111,c112))
-				if not graphsort: #Sort by LRS Full
-					rectInfo.sort(webqtlUtil.cmpLRSFull)
-				rectInfoReturned = rectInfo[len(rectInfo) - returnIntervalPairNum:]
-				rectInfoReturned.reverse()
-
-				for item in rectInfoReturned:
-					LRSFull,LRSInteract,LRSa,LRSb,chras,chram,chrae,chrbs,chrbm,chrbe,chra,chrb,flanka,flankb = item
-					LRSAdditive = LRSFull - LRSInteract
-					flanka1,flanka2 = string.split(flanka)
-					flankb1,flankb2 = string.split(flankb)
-					urla1 = HT.Href(text = flanka1, url = "javascript:showTrait('%s','%s');" % (mainfmName, flanka1),Class= "fs12 fwn")
-					urla2 = HT.Href(text = flanka2, url = "javascript:showTrait('%s','%s');" % (mainfmName, flanka2),Class= "fs12 fwn")
-					urlb1 = HT.Href(text = flankb1, url = "javascript:showTrait('%s','%s');" % (mainfmName, flankb1),Class= "fs12 fwn")
-					urlb2 = HT.Href(text = flankb2, url = "javascript:showTrait('%s','%s');" % (mainfmName, flankb2),Class= "fs12 fwn")
-					urlGenGraph = HT.Href(text = "Plot", url = "javascript:showCateGraph('%s',  '%s %s %2.3f', '%s %s %2.3f');" % (mainfmName, flanka1, flanka2, chram, flankb1, flankb2, chrbm),Class= "fs12 fwn")
-					tr1 = HT.TR(
-						HT.TD('Chr %s @ %2.1f cM ' % (chrsInfo[chra][1],chram),Class= "fs12 b1 fwn"),
-						HT.TD(urla1,Class= "fs12 b1 fwn"),
-						HT.TD(urla2,Class= "fs12 b1 fwn"),
-						HT.TD('%2.3f ' % LRSFull, urlGenGraph,Class= "fs12 b1 fwn"),
-						HT.TD('%2.3f' % LRSAdditive,Class= "fs12 b1 fwn"),
-						HT.TD('%2.3f' % LRSInteract,Class= "fs12 b1 fwn"),
-						HT.TD('%2.3f' % LRSa,Class= "fs12 b1 fwn"),
-						HT.TD('%2.3f' % LRSb,Class= "fs12 b1 fwn"),
-						HT.TD('Chr %s @ %2.1f cM' % (chrsInfo[chrb][1],chrbm),Class= "fs12 b1 fwn"),
-						HT.TD(urlb1,Class= "fs12 b1 fwn"),
-						HT.TD(urlb2,Class= "fs12 b1 fwn"))
-					tbl.append(tr1)
-
-				plotType1 = HT.Input(type="radio", name="plotType", value ="Dot", checked=1)
-				plotType2 = HT.Input(type="radio", name="plotType", value ="Box")
-				plotText = HT.Paragraph("Plot Type : ", plotType1, " Dot ", plotType2, " Box",  )
-
-				txtform.append(plotText, tbl)
-				TD_LR = HT.TD(colspan=2,height=200,width="100%",bgColor='#eeeeee')
-				TD_LR.append(main_title,HT.Blockquote(subtitle1, pairIntro, HT.P(), HT.Center(form0,HT.P())),HT.Blockquote(subtitle2, permuIntro,HT.P(), HT.Center(permuTbl)), HT.Blockquote(subtitle3, tblIntro, HT.P(),HT.Center(txtform), HT.P()))
-				self.dict['body'] = str(TD_LR)
-			else:
-				heading = "Direct Plot"
-				detail = ['Fewer than %d strain data were entered for %s data set. No statitical analysis has been attempted.' % (webqtlConfig.KMININFORMATIVE, fd.RISet)]
-				self.error(heading=heading,detail=detail)
-				return
-		else:
-			heading = "Direct Plot"
-			detail = ['Empty data set, please check your data.']
-			self.error(heading=heading,detail=detail)
-			return
-
diff --git a/web/webqtl/pairScan/PairPlotPage.py b/web/webqtl/pairScan/PairPlotPage.py
deleted file mode 100755
index 3f72bd74..00000000
--- a/web/webqtl/pairScan/PairPlotPage.py
+++ /dev/null
@@ -1,314 +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 GeneNetwork Core Team 2010/10/20
-
-import string
-import piddle as pid
-import os
-
-from htmlgen import HTMLgen2 as HT
-import direct
-
-from utility import Plot
-from base.templatePage import templatePage
-from utility import webqtlUtil
-from base import webqtlConfig
-
-#########################################
-#      PairPlotPage
-#########################################
-class PairPlotPage(templatePage):
-	def __init__(self, fd):
-
-		LRSFullThresh = 30
-		LRSInteractThresh = 25
-		maxPlotSize = 1000
-		mainfmName = webqtlUtil.genRandStr("fm_")
-
-		templatePage.__init__(self, fd)
-
-		self.dict['title'] = 'Pair-Scan Plot'
-
-		if not self.openMysql():
-			return
-
-		TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee')
-		vals = fd.formdata.getvalue('idata')
-		vals = map(float,string.split(vals,','))
-		strains = fd.formdata.getvalue('istrain')
-		strains = string.split(strains,',')
-		Chr_A = int(fd.formdata.getvalue('Chr_A'))
-		Chr_B = int(fd.formdata.getvalue('Chr_B'))
-		if len(vals) > webqtlConfig.KMININFORMATIVE:
-			d = direct.exhaust(webqtlConfig.GENODIR, vals, strains, fd.RISet, Chr_A, Chr_B)#XZ, 08/14/2008: add module name webqtlConfig
-			chrsInfo = d[2]
-			longerChrLen = max(chrsInfo[Chr_A][0], chrsInfo[Chr_B][0])
-			shorterChrlen = min(chrsInfo[Chr_A][0], chrsInfo[Chr_B][0])
-
-			plotHeight = int(chrsInfo[Chr_B][0]*maxPlotSize/longerChrLen)
-			plotWidth = int(chrsInfo[Chr_A][0]*maxPlotSize/longerChrLen)
-
-
-			xLeftOffset = 200
-			xRightOffset = 40
-			yTopOffset = 40
-			yBottomOffset = 200
-			colorAreaWidth = 120
-
-			canvasHeight = plotHeight + yTopOffset + yBottomOffset
-			canvasWidth = plotWidth + xLeftOffset + xRightOffset + colorAreaWidth
-
-
-			canvas = pid.PILCanvas(size=(canvasWidth,canvasHeight))
-			plotScale = plotHeight/chrsInfo[Chr_B][0]
-
-			rectInfo = d[1]
-			finecolors = Plot.colorSpectrum(250)
-			finecolors.reverse()
-			#draw LRS Full
-			for item in rectInfo:
-				LRSFull,LRSInteract,LRSa,LRSb,chras,chram,chrae,chrbs,chrbm,chrbe,chra,chrb,flanka,flankb = item
-				if Chr_A > Chr_B:
-					colorIndex = int(LRSFull *250 /LRSFullThresh)
-				else:
-					colorIndex = int(LRSInteract *250 /LRSInteractThresh)
-				if colorIndex >= 250:
-					colorIndex = 249
-				elif colorIndex < 0:
-					colorIndex = 0
-				dcolor = finecolors[colorIndex]
-				if chra != chrb or (abs(chrbe - chrae) > 10 and abs(chrbs - chras) > 10):
-					canvas.drawRect(xLeftOffset+chras*plotScale,yTopOffset+plotHeight- \
-					chrbs*plotScale,xLeftOffset+chrae*plotScale,yTopOffset+plotHeight- \
-					chrbe*plotScale,edgeColor=dcolor,fillColor=dcolor,edgeWidth = 0)
-				elif chrbs >= chras:
-					canvas.drawPolygon([(xLeftOffset+chras*plotScale,yTopOffset+plotHeight-chrbs*plotScale),\
-					(xLeftOffset+chras*plotScale,yTopOffset+plotHeight-chrbe*plotScale),\
-					(xLeftOffset+chrae*plotScale,yTopOffset+plotHeight-chrbe*plotScale)],\
-					edgeColor=dcolor,fillColor=dcolor,edgeWidth = 0,closed =1)
-				else:
-					canvas.drawPolygon([(xLeftOffset+chras*plotScale,yTopOffset+plotHeight-chrbs*plotScale),\
-					(xLeftOffset+chrae*plotScale,yTopOffset+plotHeight-chrbs*plotScale), \
-					(xLeftOffset+chrae*plotScale,yTopOffset+plotHeight-chrbe*plotScale)], \
-					edgeColor=dcolor,fillColor=dcolor,edgeWidth = 0,closed =1)
-
-			labelFont=pid.Font(ttf="verdana",size=24,bold=0)
-			chrName = "chromosome %s" % chrsInfo[Chr_A][1]
-			canvas.drawString(chrName,xLeftOffset + (plotWidth - canvas.stringWidth(chrName,font=labelFont))/2,\
-			yTopOffset+plotHeight+ 170,font=labelFont)
-			chrName = "chromosome %s" % chrsInfo[Chr_B][1]
-			canvas.drawString(chrName, 30, yTopOffset +(canvas.stringWidth(chrName,font=labelFont) + plotHeight)/2,\
-			font=labelFont, angle = 90)
-			if Chr_A == Chr_B:
-				infoStr = "minimum distance = 10 cM"
-				infoStrWidth = canvas.stringWidth(infoStr,font=labelFont)
-				canvas.drawString(infoStr, xLeftOffset + (plotWidth-infoStrWidth*0.707)/2, yTopOffset + \
-				(plotHeight+infoStrWidth*0.707)/2,font=labelFont, angle = 45, color=pid.red)
-
-			labelFont=pid.Font(ttf="verdana",size=12,bold=0)
-			gifmap = HT.Map(name='markerMap')
-
-			lineColor = pid.lightblue
-			#draw ChrA Loci
-			ChrAInfo = d[3]
-			preLpos = -1
-			i = 0
-			for item in ChrAInfo:
-				Lname,Lpos = item
-				if Lpos != preLpos:
-					i += 1
-				preLpos = Lpos
-			stepA = float(plotWidth)/i
-
-			offsetA = -stepA
-			LRectWidth = 10
-			LRectHeight = 3
-			i = 0
-			preLpos = -1
-			for item in ChrAInfo:
-				Lname,Lpos = item
-				if Lpos != preLpos:
-					offsetA += stepA
-					differ = 1
-				else:
-					differ = 0
-				preLpos = Lpos
-				Lpos *= plotScale
-				Zorder = i % 5
-				"""
-				LStrWidth = canvas.stringWidth(Lname,font=labelFont)
-				canvas.drawString(Lname,xLeftOffset+offsetA+4,yTopOffset+plotHeight+140,\
-				font=labelFont,color=pid.blue,angle=90)
-				canvas.drawLine(xLeftOffset+Lpos,yTopOffset+plotHeight,xLeftOffset+offsetA,\
-				yTopOffset+plotHeight+25,color=lineColor)
-				canvas.drawLine(xLeftOffset+offsetA,yTopOffset+plotHeight+25,xLeftOffset+offsetA,\
-				yTopOffset+plotHeight+140-LStrWidth,color=lineColor)
-				COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA+4,yTopOffset+plotHeight+140,\
-				xLeftOffset+offsetA-6,yTopOffset+plotHeight+140-LStrWidth)
-				"""
-				if differ:
-					canvas.drawLine(xLeftOffset+Lpos,yTopOffset+plotHeight,xLeftOffset+offsetA,\
-					yTopOffset+plotHeight+25,color=lineColor)
-					canvas.drawLine(xLeftOffset+offsetA,yTopOffset+plotHeight+25,xLeftOffset+offsetA,\
-					yTopOffset+plotHeight+80+Zorder*(LRectWidth+3),color=lineColor)
-					rectColor = pid.orange
-				else:
-					canvas.drawLine(xLeftOffset+offsetA, yTopOffset+plotHeight+80+Zorder*(LRectWidth+3)-3,\
-					xLeftOffset+offsetA, yTopOffset+plotHeight+80+Zorder*(LRectWidth+3),color=lineColor)
-					rectColor = pid.deeppink
-				canvas.drawRect(xLeftOffset+offsetA, yTopOffset+plotHeight+80+Zorder*(LRectWidth+3),\
-					xLeftOffset+offsetA-LRectHeight,yTopOffset+plotHeight+80+Zorder*(LRectWidth+3)+LRectWidth,\
-					edgeColor=rectColor,fillColor=rectColor,edgeWidth = 0)
-				COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA, yTopOffset+plotHeight+80+Zorder*(LRectWidth+3),\
-					xLeftOffset+offsetA-LRectHeight,yTopOffset+plotHeight+80+Zorder*(LRectWidth+3)+LRectWidth)
-				HREF="javascript:showTrait('%s','%s');" % (mainfmName, Lname)
-				Areas=HT.Area(shape='rect',coords=COORDS,href=HREF, title="Locus : " + Lname)
-				gifmap.areas.append(Areas)
-				i += 1
-				#print (i , offsetA, Lname, Lpos, preLpos)
-				#print "<BR>"
-
-			#draw ChrB Loci
-			ChrBInfo = d[4]
-			preLpos = -1
-			i = 0
-			for item in ChrBInfo:
-				Lname,Lpos = item
-				if Lpos != preLpos:
-					i += 1
-				preLpos = Lpos
-			stepB = float(plotHeight)/i
-
-			offsetB = -stepB
-			LRectWidth = 10
-			LRectHeight = 3
-			i = 0
-			preLpos = -1
-			for item in ChrBInfo:
-				Lname,Lpos = item
-				if Lpos != preLpos:
-					offsetB += stepB
-					differ = 1
-				else:
-					differ = 0
-				preLpos = Lpos
-				Lpos *= plotScale
-				Zorder = i % 5
-				Lname,Lpos = item
-				Lpos *= plotScale
-				"""
-				LStrWidth = canvas.stringWidth(Lname,font=labelFont)
-				canvas.drawString(Lname, 45,yTopOffset+plotHeight-offsetB+4,font=labelFont,color=pid.blue)
-				canvas.drawLine(45+LStrWidth,yTopOffset+plotHeight-offsetB,xLeftOffset-25,\
-				yTopOffset+plotHeight-offsetB,color=lineColor)
-				canvas.drawLine(xLeftOffset-25,yTopOffset+plotHeight-offsetB,xLeftOffset,\
-				yTopOffset+plotHeight-Lpos,color=lineColor)
-				COORDS = "%d,%d,%d,%d" %(45,yTopOffset+plotHeight-offsetB+4,45+LStrWidth,\
-				yTopOffset+plotHeight-offsetB-6)
-				"""
-				if differ:
-					canvas.drawLine(xLeftOffset,yTopOffset+plotHeight-Lpos, xLeftOffset-25,\
-					yTopOffset+plotHeight-offsetB,color=lineColor)
-					canvas.drawLine(xLeftOffset -25, yTopOffset+plotHeight-offsetB, \
-					xLeftOffset-80 -Zorder*(LRectWidth+3),yTopOffset+plotHeight-offsetB, color=lineColor)
-					rectColor = pid.orange
-				else:
-					canvas.drawLine(xLeftOffset -80 -Zorder*(LRectWidth+3)+3, yTopOffset+plotHeight-offsetB, \
-					xLeftOffset-80 -Zorder*(LRectWidth+3),yTopOffset+plotHeight-offsetB, color=lineColor)
-					rectColor = pid.deeppink
-				HREF = "javascript:showTrait('%s','%s');" % (mainfmName, Lname)
-				canvas.drawRect(xLeftOffset-80 -Zorder*(LRectWidth+3),yTopOffset+plotHeight-offsetB,\
-					xLeftOffset-80 -Zorder*(LRectWidth+3)-LRectWidth,yTopOffset+plotHeight-offsetB +LRectHeight,\
-					edgeColor=rectColor,fillColor=rectColor,edgeWidth = 0)
-				COORDS="%d,%d,%d,%d"%(xLeftOffset-80 -Zorder*(LRectWidth+3),yTopOffset+plotHeight-offsetB,\
-					xLeftOffset-80 -Zorder*(LRectWidth+3)-LRectWidth,yTopOffset+plotHeight-offsetB +LRectHeight)
-				Areas=HT.Area(shape='rect',coords=COORDS,href=HREF, title="Locus : " + Lname)
-				gifmap.areas.append(Areas)
-				i += 1
-
-			canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight,edgeColor=pid.black)
-
-			#draw spectrum
-			i = 0
-			labelFont=pid.Font(ttf="tahoma",size=14,bold=0)
-			middleoffsetX = 80
-			for dcolor in finecolors:
-				canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX-15 , plotHeight + yTopOffset - i, \
-				xLeftOffset+ plotWidth +middleoffsetX+15 , plotHeight + yTopOffset - i, color=dcolor)
-				if i % 50 == 0:
-					if Chr_A >= Chr_B:
-						canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i, \
-						xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i, color=pid.black)
-						canvas.drawString('%d' % int(LRSFullThresh*i/250.0),xLeftOffset+ plotWidth +middleoffsetX+22,\
-						plotHeight + yTopOffset - i +5, font = labelFont,color=pid.black)
-					if Chr_A <= Chr_B:
-						canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX-15 ,plotHeight + yTopOffset - i, \
-						xLeftOffset+ plotWidth +middleoffsetX-20,plotHeight + yTopOffset - i, color=pid.black)
-						canvas.drawString('%d' % int(LRSInteractThresh*i/250.0),xLeftOffset+plotWidth+middleoffsetX-40,\
-						plotHeight + yTopOffset - i +5, font = labelFont,color=pid.black)
-				i += 1
-			#draw spectrum label
-			labelFont2=pid.Font(ttf="verdana",size=20,bold=0)
-			if i % 50 == 0:
-				i -= 1
-				if Chr_A >= Chr_B:
-					canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i, \
-					xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i, color=pid.black)
-					canvas.drawString('%d' % int(LRSFullThresh*(i+1)/250.0),xLeftOffset+ plotWidth +middleoffsetX+22,\
-					plotHeight + yTopOffset - i +5, font = labelFont,color=pid.black)
-					canvas.drawString('LRS Full',xLeftOffset+ plotWidth +middleoffsetX+50,plotHeight + yTopOffset, \
-					font = labelFont2,color=pid.dimgray,angle=90)
-				if Chr_A <= Chr_B:
-					canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX-15 ,plotHeight + yTopOffset - i, \
-					xLeftOffset+ plotWidth +middleoffsetX-20,plotHeight + yTopOffset - i, color=pid.black)
-					canvas.drawString('%d' % int(LRSInteractThresh*(i+1)/250.0),xLeftOffset+ plotWidth+middleoffsetX-40,\
-					plotHeight + yTopOffset - i +5, font = labelFont,color=pid.black)
-					canvas.drawString('LRS Interaction',xLeftOffset+ plotWidth +middleoffsetX-50,\
-					plotHeight + yTopOffset, font = labelFont2,color=pid.dimgray,angle=90)
-
-			filename= webqtlUtil.genRandStr("Pair_")
-			canvas.save(webqtlConfig.IMGDIR+filename, format='png')
-			img2=HT.Image('/image/'+filename+'.png',border=0,usemap='#markerMap')
-
-			main_title = HT.Paragraph("Pair-Scan Results: Chromosome Pair")
-			main_title.__setattr__("class","title")
-			form = HT.Form(cgi = os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', \
-			name=mainfmName, submit=HT.Input(type='hidden'))
-			hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_','RISet':fd.RISet, 'incparentsf1':'on'}
-			if fd.incparentsf1:
-				hddn['incparentsf1']='ON'
-			for key in hddn.keys():
-				form.append(HT.Input(name=key, value=hddn[key], type='hidden'))
-			form.append(img2,gifmap)
-			TD_LR.append(main_title, HT.Center(form), HT.P())
-		else:
-			heading = "Direct Plot"
-			detail = ['Fewer than %d strain data were entered for %s data set. No statitical analysis has been attempted.'\
-			 % (webqtlConfig.KMININFORMATIVE, fd.RISet)]
-			self.error(heading=heading,detail=detail)
-			return
-		self.dict['body'] = str(TD_LR)
-
-
diff --git a/web/webqtl/pairScan/__init__.py b/web/webqtl/pairScan/__init__.py
deleted file mode 100755
index e69de29b..00000000
--- a/web/webqtl/pairScan/__init__.py
+++ /dev/null