Add all the source codes into the github.

3 files changed, 841 insertions, 0 deletions

diff --git a/web/webqtl/genomeGraph/__init__.py b/web/webqtl/genomeGraph/__init__.py
new file mode 100755
index 00000000..e69de29b
--- /dev/null
+++ b/web/webqtl/genomeGraph/__init__.py
diff --git a/web/webqtl/genomeGraph/cmdGenomeScanPage.py b/web/webqtl/genomeGraph/cmdGenomeScanPage.py
new file mode 100755
index 00000000..d880ce69
--- /dev/null
+++ b/web/webqtl/genomeGraph/cmdGenomeScanPage.py
@@ -0,0 +1,532 @@
+# 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
+import math
+
+from htmlgen import HTMLgen2 as HT
+
+from utility import svg
+from base import webqtlConfig
+from utility import Plot
+from utility import webqtlUtil
+from base.webqtlDataset import webqtlDataset
+from base.templatePage import templatePage
+
+
+######################################### 
+#      Genome Scan PAGE
+#########################################
+class cmdGenomeScanPage(templatePage):
+	def __init__(self,fd):
+		templatePage.__init__(self,fd)
+		if not self.openMysql():
+			return
+		self.database = fd.formdata.getvalue('database', '')
+		db = webqtlDataset(self.database, self.cursor)
+
+		try:
+			self.openURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + \
+				'?FormID=showDatabase&database=%s&incparentsf1=1&ProbeSetID=' % self.database
+				
+			if db.type != "ProbeSet" or not db.id:
+				raise DbNameError
+			
+			self.cursor.execute("""
+				Select 
+					InbredSet.Name
+				From
+					ProbeSetFreeze, ProbeFreeze, InbredSet
+				whERE
+					ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND
+					ProbeFreeze.InbredSetId = InbredSet.Id AND
+					ProbeSetFreeze.Id = %d
+				""" % db.id)
+			thisRISet = self.cursor.fetchone()[0]
+			if thisRISet =='BXD300':
+				thisRISet = 'BXD'
+
+			##################################################
+			#  exon data is too huge for GenoGraph, skip it  #
+			##################################################
+			self.cursor.execute('select count(*) from ProbeSetXRef where ProbeSetFreezeId=%d' % db.id)
+			amount = self.cursor.fetchall()
+			if amount:
+				amount = amount[0][0]
+				if amount>100000:
+					heading = "Whole Transcriptome Mapping"
+					detail = ["Whole Transcriptome Mapping is not available for this data set."]
+					self.error(heading=heading,detail=detail)
+					return
+
+			self.cursor.execute("""
+				Select 
+					ProbeSet.Id, ProbeSet.Name, ProbeSet.Chr, ProbeSet.Mb, ProbeSetXRef.Locus, ProbeSetXRef.pValue
+				From
+					ProbeSet, ProbeSetXRef
+				whERE
+					ProbeSetXRef.ProbeSetFreezeId = %d AND
+					ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+					ProbeSetXRef.Locus is not NULL 
+				""" % db.id)
+			results = self.cursor.fetchall()
+
+			if results:
+				self.mouseChrLengthDict, sum = self.readMouseGenome(thisRISet)
+				
+				import reaper
+				markerGMb = {}
+				genotype_1 = reaper.Dataset()
+				genotype_1.read(os.path.join(webqtlConfig.GENODIR, thisRISet + '.geno'))
+				for chr in genotype_1:
+					chrlen = self.mouseChrLengthDict[chr.name]
+
+					for locus in chr:	
+						markerGMb[locus.name] = locus.Mb + chrlen
+  				
+				try:
+					FDR = float(fd.formdata.getvalue("fdr", ""))
+				except:
+					FDR = 0.2
+				self.grid = fd.formdata.getvalue("grid", "")
+				
+				NNN = len(results)
+				results = list(results)
+				results.sort(self.cmppValue)
+
+				MbCoord = []
+				MbCoord2 = []
+
+				for j in range(NNN, 0, -1):
+					if results[j-1][-1] <= (FDR*j)/NNN:
+						break
+
+				if j > 0:
+					for i in range(j-1, -1, -1):
+						_Id, _probeset, _chr, _Mb, _marker, _pvalue = results[i]
+						try:
+							MbCoord.append([markerGMb[_marker], _Mb+self.mouseChrLengthDict[string.strip(_chr)], _probeset, _chr, _Mb, _marker, _pvalue])
+						except:
+							pass
+          	
+				filename=webqtlUtil.genRandStr("gScan_")
+				canvas = pid.PILCanvas(size=(1280,880))
+				self.drawGraph(canvas, MbCoord, cLength=sum)
+		
+				canvas.save(os.path.join(webqtlConfig.IMGDIR, filename), format='png')
+	
+				canvasSVG = self.drawSVG(MbCoord, cLength=sum, size=(1280,880))
+				canvasSVG.toXml(os.path.join(webqtlConfig.IMGDIR, filename+'.svg')) #and write it to file
+				
+				img  = HT.Embed(src='/image/'+filename+'.png', width=1280, height=880, border=0, alt='Genome Scan')
+				img2 = HT.Embed(src='/image/'+filename+'.svg', width=1280, height=880, border=0)
+				TD_LR = HT.TD(colspan=2,height=200,width="100%",bgColor='#eeeeee')
+				
+				heading = HT.Paragraph('Whole Transcriptome Mapping')
+				heading.__setattr__("class","title")
+				intro = HT.Blockquote()
+				intro.append('The plot below is the Whole Transcriptome Mapping of Database ') 
+				intro.append(HT.Href(text=db.fullname, url = webqtlConfig.INFOPAGEHREF % db.name ,target='_blank',Class="normalsize"))
+				intro.append(". %d from a total of %d ProbeSets were utilized to generate this graph." % (len(MbCoord), len(results)))
+				
+				mainfm = HT.Form(cgi = os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE),  enctype='multipart/form-data', \
+					name=webqtlUtil.genRandStr("fm_"), submit=HT.Input(type='hidden'))
+				mainfm.append(HT.Input(name='database', value=self.database, type='hidden'))
+				mainfm.append(HT.Input(name='FormID', value='transciptMapping', type='hidden'))
+				
+				mainfm.append("<BLOCKQUOTE>")
+				mainfm.append("0 < FDR <= 1.0 ")
+				mainfm.append(HT.Input(name='fdr', value=FDR, type='text'))
+			
+				mainfm.append(HT.Input(name='submit', value='Redraw Graph', type='submit', Class='button'))
+				mainfm.append("</BLOCKQUOTE>")
+				mainfm.append("""
+<center>
+<div id="gallery">
+<div class="on"  title="img1"><span>Static</span></div>
+<div class="off" title="img2"><span>Interactive</span></div>
+</div>
+
+<div id="img1" class="show">
+""")           
+				mainfm.append(img)
+				mainfm.append("""
+</div>
+
+<div id="img2" class="hide">
+""")
+				mainfm.append(img2)
+				mainfm.append("""
+</div>
+</center>
+""")
+
+				TD_LR.append(heading, intro, HT.Paragraph(mainfm))
+				
+				self.dict['title'] = 'Whole Transcriptome Mapping'
+				self.dict['body'] = TD_LR
+			else:
+				heading = "Whole Transcriptome Mapping"
+				detail = ["Database calculation is not finished."]
+				self.error(heading=heading,detail=detail)
+				return
+		except:
+			heading = "Whole Transcriptome Mapping"
+			detail = ["Whole Transcriptome Mapping only apply to Microarray database."]
+			self.error(heading=heading,detail=detail)
+			return
+			
+	def drawSVG(self, data, cLength = 2500, offset= (80, 160, 60, 60), size=(1280,880), 
+			XLabel="Marker GMb", YLabel="Transcript GMb"):
+		entities = {
+				"colorText" : "fill:darkblue;",
+				"strokeText" : ";stroke:none;stroke-width:0;",
+				"allText" : "font-family:Helvetica;", 
+				"titleText" : "font-size:22;font-weight:bold;", 
+				"subtitleText" : "font-size:18;font-weight:bold;", 
+				"headlineText" : "font-size:14;font-weight:bold;", 
+				"normalText" : "font-size:12;", 
+				"legendText" : "font-size:11;text-anchor:end;", 
+				"valuesText" : "font-size:12;", 
+				"boldValuesText" : "font-size:12;font-weight:bold;", 
+				"smallText" : "font-size:10;", 
+				"vText" : "writing-mode:tb-rl",
+				"rightText" : "text-anchor:end;", 
+				"middleText" : "text-anchor:middle;", 
+				"bezgrenzstyle" : "fill:none;stroke:#11A0FF;stroke-width:40;stroke-antialiasing:true;", 
+				"rectstyle" : "fill:lightblue;stroke:none;opacity:0.2;", 
+				"fillUnbebaut" : "fill:#CCFFD4;stroke:none;", 
+				"fillNodata" : "fill:#E7E7E7;stroke:black;stroke-width:2;stroke-antialiasing:true;", 
+				"fillNodataLegend" : "fill:#E7E7E7;stroke:black;stroke-width:0.5;stroke-antialiasing:true;", 
+				"grundzeitstyle" : "fill:none;stroke:#E00004;stroke-width:60;stroke-antialiasing:true;", 
+				"bezgrenzstyle" : "fill:none;stroke:#11A0FF;stroke-width:40;stroke-antialiasing:true;", 
+				"mapAuthor" : "A. Neumann", 
+				}
+		cWidth, cHeight = size		
+		canvasSVG = svg.drawing(entities) #create a drawing
+		drawSpace=svg.svg((0, 0, cWidth, cHeight), cWidth, cHeight, xml__space="preserve", 
+			zoomAndPan="disable", onload="initMap(evt);", 
+			xmlns__a3="http://ns.adobe.com/AdobeSVGViewerExtensions/3.0/",
+			a3__scriptImplementation="Adobe") #create a svg drawingspace
+		canvasds=svg.description('Genome Graph') #define a description
+		drawSpace.addElement(canvasds) #add the description to the svg
+		
+		#need to be modified or deleted
+		xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+		plotWidth = cWidth - xLeftOffset - xRightOffset
+		plotHeight = cHeight - yTopOffset - yBottomOffset
+		drawSpace.addElement(svg.script("", language="javascript", xlink__href="/javascript/svg.js"))
+		
+		#add defs
+		defs = svg.defs()
+		symbol1= svg.symbol(id="magnifyer", overflow="visible", 
+			style="fill:white;stroke:orange;stroke-width:2;")
+		symbol1.addElement(svg.line(0, 0, -8, 20))
+		symbol1.addElement(svg.circle(0, 0, 8))
+		symbol1.addElement(svg.line(-4, 0, 4, 0, style="stroke:orange;stroke-width:2;"))
+		defs.addElement(symbol1)
+		symbol2= svg.symbol(id="magnifyerZoomIn",overflow="visible")
+		symbol2.addElement(svg.use(link="#magnifyer", id="zoomIn"))
+		symbol2.addElement(svg.line(0, -4, 0, 4, style="stroke:orange;stroke-width:2;"))
+		defs.addElement(symbol2)
+		drawSpace.addElement(defs)
+		
+		symbol3= svg.symbol(id="msgbox", overflow="visible", 
+			style="fill:white;stroke:orange;stroke-width:1;opacity:0.8;")
+		symbol3.addElement(svg.rect(-80, -190, 300, 150, rx=10, ry=10))
+		symbol3.addElement(svg.line(21, -40, 58, -40, style="stroke:white;"))
+		symbol3.addElement(svg.polyline([[20, -40], [0, 0], [60, -40]]))
+		symbol3.addElement(svg.text(-60, -160, "ProbeSet ", style="&colorText; &allText; &subtitleText; &strokeText;"))
+		symbol3.addElement(svg.text(-60, -125, "Marker ", style="&colorText; &allText; &subtitleText; &strokeText;"))
+		symbol3.addElement(svg.text(-60, -90, "LRS ", style="&colorText; &allText; &subtitleText; &strokeText;"))
+		symbol3.addElement(svg.text(-60, -55, "P value ", style="&colorText; &allText; &subtitleText; &strokeText;"))
+		defs.addElement(symbol3)
+		
+		g = svg.group("title")
+		g.addElement(svg.text(cWidth-40, 30, "Genome Graph", style="&colorText; &allText; &titleText; &rightText;"))
+		g.addElement(svg.text(cWidth-40, 50, "Whole Transcriptome Mapping", style="&colorText; &allText; &subtitleText; &rightText;"))
+		drawSpace.addElement(g)
+		
+		#draw Main display area border
+		mainSquare = cHeight-60
+		cordZOOM = 10
+		drawSpace.addElement(svg.rect(8, 8, mainSquare+4, mainSquare+4,'none',"orange",0.5, rx="5", ry="5"))
+		drawSpace.addElement(svg.text(10+mainSquare/2, 40+mainSquare,'Marker GMb', 
+			style="&colorText; &allText; &titleText; &middleText;", id="XLabel"))
+		drawSpace.addElement(svg.text(mainSquare + 80, 10+mainSquare/2,'Transcript GMb', 
+			style="&colorText; &allText; &titleText; &middleText; &vText;", id="YLabel"))
+		
+		#draw overview display area
+		drawSpace.addElement(svg.rect(cWidth-40-260, 60, 260, 260,'none',"orange",0.5, rx="5", ry="5"))
+		drawSpaceThumb= svg.svg(id="overviewPlot",x=cWidth-40-260,y="60",width="260",
+			height="260",viewBox=(0, 0, mainSquare*cordZOOM, mainSquare*cordZOOM))
+		g = svg.group(style="&bezgrenzstyle;")
+		g.addElement(svg.use("#grid"))
+		drawSpaceThumb.addElement(g)
+		drawSpaceThumb.addElement(svg.rect(id="overviewRect",style="&rectstyle;",
+			x="0",y="0",width=mainSquare*cordZOOM,height=mainSquare*cordZOOM, 
+			onmouseover="statusChange('click and drag rectangle to change extent');",
+			onmousedown="beginPan(evt);", onmousemove="doPan(evt);", 
+			onmouseup="endPan();", onmouseout="endPan();"))
+		drawSpace.addElement(drawSpaceThumb)
+		
+		#draw navigator
+		g = svg.group(id="navigatorElements")
+		g.addElement(svg.use("#magnifyerZoomIn", id="zoomIn", transform="translate(%d,350)" % (cWidth-40-130-20), 
+			onmouseover="magnify(evt,1.3,'in');", onmouseout="magnify(evt,1,'in');", onclick="zoomIt('in');"))
+		g.addElement(svg.use("#magnifyer", id="zoomOut", transform="translate(%d,350)" % (cWidth-40-130+20),
+			onmouseover="magnify(evt,1.3,'out');",onmouseout="magnify(evt,1,'out');", onclick="zoomIt('out');"))
+		
+		drawSpace.addElement(g)
+		
+		g = svg.group(id="statusBar")
+		g.addElement(svg.text(cWidth-40-260, 360, "ZOOM: 100%", style="fill:orange; font-size:14;", id="zoomValueObj"))
+		g.addElement(svg.text(cWidth-40-260, 380, "Status:", style="&colorText; &allText; &smallText;"))
+		g.addElement(svg.text(cWidth-40-260, 395, "Loading Plot", style="&colorText; &allText; &smallText;", id="statusText"))
+		drawSpace.addElement(g)
+		
+		#draw main display area
+		drawSpaceMain= svg.svg((0, 0, mainSquare*cordZOOM, mainSquare*cordZOOM), mainSquare, mainSquare, 
+			id="mainPlot",x="10",y="10")
+		mPlotWidth = mPlotHeight = 0.8*mainSquare*cordZOOM
+		
+		drawSpaceMain.addElement(svg.rect(mainSquare*cordZOOM*0.1, mainSquare*cordZOOM*0.1, mPlotWidth, mPlotHeight,style="fill:white",
+			onmousemove="showChr(evt);", onmouseover="showChr(evt);", onmouseout="showNoChr(evt);"))
+		#draw grid
+		g = svg.group("grid", style="stroke:lightblue;stroke-width:3", 
+			transform="translate(%d,%d)" % (mainSquare*cordZOOM*0.1, mainSquare*cordZOOM*0.1))
+			
+		if 1: #self.grid == "on":
+			js = [] 
+			for key in self.mouseChrLengthDict.keys():
+				length = self.mouseChrLengthDict[key]
+				js.append(mPlotWidth*length/cLength)
+				if length != 0:
+					yCoord = mPlotHeight*(1.0-length/cLength)
+					l = svg.line(0,yCoord ,mPlotWidth, yCoord)
+					g.addElement(l)	
+					xCoord = mPlotWidth*length/cLength
+					l = svg.line(xCoord, 0 ,xCoord, mPlotHeight)
+					g.addElement(l)
+			js.sort()
+			drawSpace.addElement(svg.script("",language="javascript", cdata="var openURL=\"%s\";\nvar chrLength=%s;\n" % (self.openURL, js)))
+		
+		g.addElement(svg.rect(0, 0, mPlotWidth, mPlotHeight,'none','black',10))
+		drawSpaceMain.addElement(g)
+		
+		#draw Scale
+		g = svg.group("scale", style="stroke:black;stroke-width:0", 
+			transform="translate(%d,%d)" % (mainSquare*cordZOOM*0.1, mainSquare*cordZOOM*0.1))
+		i = 100
+		scaleFontSize = 11*cordZOOM
+		while i < cLength:
+			yCoord = mPlotHeight - mPlotHeight*i/cLength
+			l = svg.line(0,yCoord ,-5*cordZOOM, yCoord)
+			g.addElement(l)
+			t = svg.text(-40*cordZOOM, yCoord +5*cordZOOM, "%d"% i, 100, "verdana") # coordinate tag Y
+			g.addElement(t)
+			xCoord = mPlotWidth*i/cLength
+			l = svg.line(xCoord, mPlotHeight, xCoord, mPlotHeight+5*cordZOOM)
+			g.addElement(l)
+			if i%200 == 0:
+				t = svg.text(xCoord, mPlotHeight+10*cordZOOM, "%d"% i, 100, "verdana") # coordinate tag X
+				g.addElement(t)
+			i += 100
+			
+		drawSpaceMain.addElement(g)
+		#draw Points
+		finecolors = Plot.colorSpectrumSVG(12)
+		finecolors.reverse()
+		g = preColor = ""
+		for item in data:
+			_probeset, _chr, _Mb, _marker, _pvalue = item[2:]
+			try:
+				_idx = int((-math.log10(_pvalue))*12/6.0) # add module name
+				_color = finecolors[_idx]
+			except:
+				_color = finecolors[-1]
+			if _color != preColor:
+				preColor = _color
+				if g:
+					drawSpaceMain.addElement(g)
+				g = svg.group("points", style="stroke:%s;stroke-width:5" % _color, 
+					transform="translate(%d,%d)" % (mainSquare*cordZOOM*0.1, mainSquare*cordZOOM*0.1),
+					onmouseover="mvMsgBox(evt);", onmouseout="hdMsgBox();", onmousedown="openPage(evt);")
+			else:
+				pass
+			px = mPlotWidth*item[0]/cLength
+			py = mPlotHeight*(1.0-item[1]/cLength)
+			l = svg.line("%2.1f" % (px-3*cordZOOM), "%2.1f" % py, "%2.1f" % (px+3*cordZOOM), "%2.1f" % py, ps=_probeset, mk=_marker)
+			g.addElement(l)	
+
+		drawSpaceMain.addElement(g)
+		
+		"""
+		#draw spectrum
+		i = 0
+		j = 0
+		middleoffsetX = 40
+		labelFont=pid.Font(ttf="tahoma",size=12,bold=0)
+		for dcolor in finecolors:
+			drawSpace.drawLine(xLeftOffset+ plotWidth + middleoffsetX -15 , plotHeight + yTopOffset - i, \
+				xLeftOffset+ plotWidth + middleoffsetX+15 , plotHeight + yTopOffset - i, color=dcolor)
+			if i % 50 == 0:
+				drawSpace.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i,  \
+				xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i, color=pid.black)
+				drawSpace.drawString("%1.1f" % -j , xLeftOffset+ plotWidth +middleoffsetX+25 ,plotHeight + yTopOffset - i+5, font = labelFont)
+				j += 1
+			i += 1
+		drawSpace.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i+1,  \
+			xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i+1, color=pid.black)	
+		drawSpace.drawString("%1.1f" % -j , xLeftOffset+ plotWidth +middleoffsetX+25 ,plotHeight + yTopOffset - i+6, font = labelFont)
+		labelFont=pid.Font(ttf="tahoma",size=14,bold=1)	
+		drawSpace.drawString("Log(pValue)" , xLeftOffset+ plotWidth +middleoffsetX+60 ,plotHeight + yTopOffset - 100, font = labelFont, angle =90)
+		
+		labelFont=pid.Font(ttf="verdana",size=18,bold=0)
+		drawSpace.drawString(XLabel, xLeftOffset + (plotWidth -drawSpace.stringWidth(XLabel,font=labelFont))/2.0, plotHeight + yTopOffset +40, color=pid.blue, font=labelFont)
+		drawSpace.drawString(YLabel,xLeftOffset-60, plotHeight + yTopOffset-(plotHeight -drawSpace.stringWidth(YLabel,font=labelFont))/2.0, color=pid.blue, font=labelFont, angle =90)			
+		"""
+		drawSpace.addElement(drawSpaceMain)
+		
+		g= svg.group(id="dispBox", overflow="visible", 
+			style="fill:white;stroke:orange;stroke-width:1;opacity:0.85;",
+			transform="translate(%d,650)" % (cWidth-40-300), visibility="hidden")
+		g.addElement(svg.rect(-80, -190, 300, 150, rx=10, ry=10))
+		g.addElement(svg.line(21, -40, 58, -40, style="stroke:white;"))
+		g.addElement(svg.polyline([[20, -40], [0, 0], [60, -40]]))
+		g.addElement(svg.text(-60, -160, "ProbeSet ", style="&colorText; &allText; &subtitleText; &strokeText;", id="_probeset"))
+		g.addElement(svg.text(-60, -125, "Marker ", style="&colorText; &allText; &subtitleText; &strokeText;", id="_marker"))
+
+		drawSpace.addElement(g)
+
+		canvasSVG.setSVG(drawSpace) #set the svg of the drawing to the svg
+		return canvasSVG
+			
+
+	def drawGraph(self, canvas, data, cLength = 2500, offset= (80, 160, 60, 60), XLabel="QTL location (GMb)", YLabel="Gene location (GMb)"):
+		xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+		plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
+		plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
+		
+		#draw Frame
+		canvas.drawRect(plotWidth+xLeftOffset, plotHeight + yTopOffset, xLeftOffset, yTopOffset)
+		
+		#draw Scale
+		i = 100
+		scaleFont=pid.Font(ttf="cour",size=11,bold=1)
+		while i < cLength:
+			yCoord = plotHeight + yTopOffset - plotHeight*i/cLength
+			canvas.drawLine(xLeftOffset,yCoord ,xLeftOffset-5, yCoord)
+			canvas.drawString("%d"% i,	xLeftOffset -40, yCoord +5,font=scaleFont)
+			xCoord = xLeftOffset + plotWidth*i/cLength
+			canvas.drawLine(xCoord, plotHeight + yTopOffset ,xCoord, plotHeight + yTopOffset+5)
+			canvas.drawString("%d"% i,	xCoord -10, plotHeight + yTopOffset+15,font=scaleFont)
+			i += 100
+
+		#draw Points
+		finecolors = Plot.colorSpectrum(300)
+		finecolors.reverse()
+		for item in data:
+			_pvalue = item[-1]
+			try:
+				_idx = int((-math.log10(_pvalue))*300/6.0) # XZ, 09/11/2008: add module name
+				_color = finecolors[_idx]
+			except:
+				_color = finecolors[-1]
+				
+			canvas.drawCross(xLeftOffset + plotWidth*item[0]/cLength, plotHeight + yTopOffset - plotHeight*item[1]/cLength, color=_color,size=3)
+		
+		#draw grid / always draw grid
+		if 1: #self.grid == "on":
+			for key in self.mouseChrLengthDict.keys():
+				length = self.mouseChrLengthDict[key]
+				if length != 0:
+					yCoord = plotHeight + yTopOffset - plotHeight*length/cLength
+					canvas.drawLine(xLeftOffset,yCoord ,xLeftOffset+plotWidth, yCoord, color=pid.lightgrey)
+					xCoord = xLeftOffset + plotWidth*length/cLength
+					canvas.drawLine(xCoord, plotHeight + yTopOffset ,xCoord, yTopOffset, color=pid.lightgrey)
+		
+		#draw spectrum
+		i = 0
+		j = 0
+		middleoffsetX = 40
+		labelFont=pid.Font(ttf="tahoma",size=12,bold=0)
+		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:
+				canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i,  \
+				xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i, color=pid.black)
+				canvas.drawString("%1.1f" % -j , xLeftOffset+ plotWidth +middleoffsetX+25 ,plotHeight + yTopOffset - i+5, font = labelFont)
+				j += 1
+			i += 1
+		canvas.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i+1,  \
+			xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i+1, color=pid.black)	
+		canvas.drawString("%1.1f" % -j , xLeftOffset+ plotWidth +middleoffsetX+25 ,plotHeight + yTopOffset - i+6, font = labelFont)
+		labelFont=pid.Font(ttf="tahoma",size=14,bold=1)	
+		canvas.drawString("Log(pValue)" , xLeftOffset+ plotWidth +middleoffsetX+60 ,plotHeight + yTopOffset - 100, font = labelFont, angle =90)
+		
+		labelFont=pid.Font(ttf="verdana",size=18,bold=0)
+		canvas.drawString(XLabel, xLeftOffset + (plotWidth -canvas.stringWidth(XLabel,font=labelFont))/2.0, plotHeight + yTopOffset +40, color=pid.blue, font=labelFont)
+		canvas.drawString(YLabel,xLeftOffset-60, plotHeight + yTopOffset-(plotHeight -canvas.stringWidth(YLabel,font=labelFont))/2.0, color=pid.blue, font=labelFont, angle =90)			
+		return
+	
+	def readMouseGenome(self, RISet):
+		ldict = {}
+		lengths = []
+		sum = 0
+		#####################################
+		# Retrieve Chr Length Information
+		#####################################
+		self.cursor.execute("""
+			Select 
+				Chr_Length.Name, Length from Chr_Length, InbredSet 
+			where 
+				Chr_Length.SpeciesId = InbredSet.SpeciesId AND
+				InbredSet.Name = '%s'
+			Order by 
+				OrderId
+			""" % RISet)
+		lengths = self.cursor.fetchall()
+		ldict[lengths[0][0]] = 0
+		prev = lengths[0][1]/1000000.0
+		sum += lengths[0][1]/1000000.0
+		for item in lengths[1:]:
+			ldict[item[0]] = prev
+			prev += item[1]/1000000.0
+			sum += item[1]/1000000.0
+		return ldict, sum
+	
+	def cmppValue(self, A,B):
+		if A[-1] < B[-1]:
+			return -1
+		elif A[-1] == B[-1]:
+			return 0
+		else:
+			return 1
+			
diff --git a/web/webqtl/genomeGraph/genAllDbResultPage.py b/web/webqtl/genomeGraph/genAllDbResultPage.py
new file mode 100755
index 00000000..f0663a7c
--- /dev/null
+++ b/web/webqtl/genomeGraph/genAllDbResultPage.py
@@ -0,0 +1,309 @@
+# 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 os
+import time
+
+from htmlgen import HTMLgen2 as HT
+
+from base import webqtlConfig
+from utility import webqtlUtil
+from base.webqtlDataset import webqtlDataset
+from base.templatePage import templatePage
+			
+
+######################################### 
+#      Genome Scan PAGE
+#########################################
+class genAllDbResultPage(templatePage):
+
+	def __init__(self,fd):
+
+		templatePage.__init__(self,fd)
+
+		if not self.openMysql():
+			return
+
+		self.database = fd.formdata.getvalue('database', '')
+		db = webqtlDataset(self.database, self.cursor)
+
+		try:
+			if db.type != "ProbeSet" or not db.id:
+				raise DbNameError
+		except:
+			print 'Content-type: text/html\n'
+			heading = "Download Results"
+			detail = ["Only results of microarray database are available to download."]
+			self.error(heading=heading,detail=detail)
+			self.write()
+			return
+
+
+                #XZ, protect confidential dataset.
+		userExist = None
+                self.cursor.execute('SELECT Id, Name, FullName, confidentiality, AuthorisedUsers FROM ProbeSetFreeze WHERE Name = "%s"' %  self.database)
+                indId, indName, indFullName, indConfid, AuthorisedUsers = self.cursor.fetchall()[0]
+                if indConfid == 1 and userExist == None:
+                    try:
+
+                        userExist = self.userName
+
+                        #for the dataset that confidentiality is 1
+                        #1. 'admin' and 'root' can see all of the dataset
+                        #2. 'user' can see the dataset that AuthorisedUsers contains his id(stored in the Id field of User table)
+                        if webqtlConfig.USERDICT[self.privilege] < webqtlConfig.USERDICT['admin']:
+                            if not AuthorisedUsers:
+                                userExist=None
+                            else:
+                                AuthorisedUsersList=AuthorisedUsers.split(',')
+                                if not AuthorisedUsersList.__contains__(self.userName):
+                                    userExist=None
+                    except:
+                        pass
+
+                    if not userExist:
+                        #Error, Confidential Database
+                        heading = "Correlation Table"
+                        detail = ["The %s database you selected is not open to the public at this time, please go back and select other database." % indFullName]
+                        self.error(heading=heading,detail=detail,error="Confidential Database")
+                        return
+	
+		self.cursor.execute("""
+				Select 
+					InbredSet.Name
+				From
+					ProbeSetFreeze, ProbeFreeze, InbredSet
+				whERE
+					ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND
+					ProbeFreeze.InbredSetId = InbredSet.Id AND
+					ProbeSetFreeze.Id = %d
+				""" % db.id)
+		thisRISet = self.cursor.fetchone()[0]
+		if thisRISet =='BXD300':
+			thisRISet = 'BXD'
+
+		#XZ, 06/26/2009: It seems that this query is not neccessary. It doesn't return any result.
+		#XZ: It seems it is just for test purpose. The next try-except block does the real work.
+		#XZ: I think it should be deleted to shorten the response time.	
+		#self.cursor.execute("""
+		#		Select 
+		#			ProbeSet.Name, ProbeSet.symbol, ProbeSet.description, ProbeSet.Chr, ProbeSet.Mb, ProbeSetXRef.Locus, 
+		#			ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.additive, ProbeSetXRef.mean
+		#		From
+		#			ProbeSet, ProbeSetXRef
+		#		whERE
+		#			ProbeSetXRef.ProbeSetFreezeId = %d AND
+		#			ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+		#			ProbeSetXRef.Locus is not NULL 
+		#		Order by
+		#			ProbeSet.name_num
+		#		""" % db.id)
+		
+		filename = os.path.join(webqtlConfig.SECUREDIR, db.name+'.result.xls')
+
+		try:
+			import random234
+			if random.choice(range(10)) == 0:
+				raise "ReCalculate"
+			fp = open(filename, 'rb')
+			text = fp.read()
+			fp.close()
+		except:
+			self.cursor.execute("Select ProbeSetXRef.ProbeSetId from ProbeSetXRef where ProbeSetFreezeId=%d" % db.id)
+			ProbeSetIds = self.cursor.fetchall()
+			self.mouseChrLengthDict, sum = self.readMouseGenome(thisRISet)
+
+			if ProbeSetIds:
+				import reaper
+				markerGMb = {}
+				genotype_1 = reaper.Dataset()
+				genotype_1.read(os.path.join(webqtlConfig.GENODIR, thisRISet + '.geno'))
+				for chr in genotype_1:
+					chrlen = self.mouseChrLengthDict[chr.name]
+					for locus in chr:	
+						markerGMb[locus.name] = [chr.name, locus.Mb, locus.Mb + chrlen]
+				
+				text = []
+				text.append(['ProbeSetId', 'Symbol', 'Description', 'Target Description', 'Chr', 'TMb', 'TGMb', 'Locus', 'LRS', 'Additive', 'pvalue', 'markerChr', 'markerMb', 'markerGMb', 'meanExpression'])
+				ProbeSetIdList = []
+				for ProbeSetId in ProbeSetIds:
+					ProbeSetIdList.append(ProbeSetId[0])
+					if len(ProbeSetIdList)==1000:
+						ProbeSetIdStr = ','.join(map(str, ProbeSetIdList))
+						ProbeSetIdList = []
+
+						cmd = """
+							Select 
+								ProbeSet.Name, ProbeSet.symbol, ProbeSet.description,ProbeSet.Probe_Target_Description,ProbeSet.Chr, ProbeSet.Mb, 
+								ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, 
+								ProbeSetXRef.additive, ProbeSetXRef.mean
+							From
+								ProbeSet, ProbeSetXRef
+							Where
+								ProbeSetXRef.ProbeSetFreezeId = %s AND
+								ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+								ProbeSetXRef.Locus is not NULL AND
+								ProbeSet.Id in (%s)
+							Order by
+								ProbeSet.name_num
+						""" % (db.id, ProbeSetIdStr)
+
+						self.cursor.execute(cmd)
+						results = self.cursor.fetchall()
+
+						for result in results:
+							_Id, _symbol, _desc,_targetDesc, _chr, _TMb, _marker, _lrs, _pvalue, _additive, _mean = result
+							if _marker == "-":
+								continue
+							if not _additive:
+								_additive = ""
+						
+							try:
+								_TGMb = _TMb + self.mouseChrLengthDict[string.strip(_chr)]
+							except:
+								_TGMb = ""
+
+							result2 = [_Id, _symbol, _desc, _targetDesc, _chr, _TMb, _TGMb, _marker, _lrs, _additive, _pvalue]
+							try:
+								result2 += markerGMb[_marker]
+							except:
+								result2 += ['', '', '']
+							result2 += [_mean]
+							text.append(map(str, result2))
+
+				#XZ, 06/29/2007: This block is dealing with the last several probesets that fall out of the 1000-probeset block. 
+				if ProbeSetIdList:
+					ProbeSetIdStr = ','.join(map(str, ProbeSetIdList))
+
+					cmd = """
+						Select 
+							ProbeSet.Name, ProbeSet.symbol, ProbeSet.description,ProbeSet.Probe_Target_Description, ProbeSet.Chr, ProbeSet.Mb, 
+							ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, 
+							ProbeSetXRef.additive, ProbeSetXRef.mean
+						From
+							ProbeSet, ProbeSetXRef
+						Where
+							ProbeSetXRef.ProbeSetFreezeId = %s AND
+							ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+							ProbeSetXRef.Locus is not NULL AND
+							ProbeSet.Id in (%s)
+						Order by
+							ProbeSet.name_num
+					""" % (db.id, ProbeSetIdStr)
+
+					self.cursor.execute(cmd)
+					results = self.cursor.fetchall()
+
+					for result in results:
+						_Id, _symbol, _desc, _targetDesc,_chr, _TMb, _marker, _lrs, _pvalue, _additive, _mean = result
+						if _marker == "-":
+							continue
+						if not _additive:
+							_additive = ""
+					
+						try:
+							_TGMb = _TMb + self.mouseChrLengthDict[string.strip(_chr)]
+						except:
+							_TGMb = ""
+
+						result2 = [_Id, _symbol, _desc,_targetDesc,  _chr, _TMb, _TGMb, _marker, _lrs, _additive, _pvalue]
+						try:
+							result2 += markerGMb[_marker]
+						except:
+							result2 += ['', '', '']
+						result2 += [_mean]
+						text.append(map(str, result2))
+
+				
+				import pyXLWriter as xl
+				# Create a new Excel workbook
+				workbook = xl.Writer(filename)
+				worksheet = workbook.add_worksheet()
+				heading = workbook.add_format(align = 'center', bold = 1, size=13, color = 'red')
+				titleStyle = workbook.add_format(align = 'left', bold = 0, size=14, border = 1, border_color="gray")
+
+				worksheet.write([0, 0], "Data source: The GeneNetwork at http://www.genenetwork.org", titleStyle)
+				worksheet.write([1, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle)
+				worksheet.write([2, 0], "Database : %s" % db.fullname, titleStyle)
+				worksheet.write([3, 0], "Date : %s" % time.strftime("%B %d, %Y", time.gmtime()), titleStyle)
+				worksheet.write([4, 0], "Time : %s GMT" % time.strftime("%H:%M ", time.gmtime()), titleStyle)
+				worksheet.write([5, 0], "Status of data ownership: Possibly unpublished data; please see %s/statusandContact.html for details on sources, ownership, and usage of these data." % webqtlConfig.PORTADDR, titleStyle)
+
+				table_row_start_index = 7
+				nrow = table_row_start_index
+				for row in text:
+				    for ncol, cell in enumerate(row):
+				    	if nrow == table_row_start_index:
+				        	worksheet.write([nrow, ncol], cell.strip(), heading)
+				        	worksheet.set_column([ncol, ncol], 20)
+				    	else:
+				        	worksheet.write([nrow, ncol], cell.strip())
+				    nrow += 1
+
+				worksheet.write([1+nrow, 0], "Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA21131), NCI MMHCC (U01CA105417), and NCRR (U01NR 105417)", titleStyle)
+				worksheet.write([2+nrow, 0], "PLEASE RETAIN DATA SOURCE INFORMATION WHENEVER POSSIBLE", titleStyle)
+
+				workbook.close()
+								
+				fp = open(filename, 'rb')
+				text = fp.read()
+				fp.close()
+			else:
+				heading = "Download Results"
+				detail = ["Database calculation is not finished."]
+				self.error(heading=heading,detail=detail)
+				return
+				
+		self.content_type = 'application/xls'
+		self.content_disposition = 'attachment; filename=%s' % ('export-%s.xls' % time.strftime("%y-%m-%d-%H-%M"))
+		self.attachment = text
+			
+	def readMouseGenome(self, RISet):
+		ldict = {}
+		lengths = []
+		sum = 0
+		#####################################
+		# Retrieve Chr Length Information
+		#####################################
+		self.cursor.execute("""
+			Select 
+				Chr_Length.Name, Length from Chr_Length, InbredSet 
+			where 
+				Chr_Length.SpeciesId = InbredSet.SpeciesId AND
+				InbredSet.Name = '%s'
+			Order by 
+				OrderId
+			""" % RISet)
+		lengths = self.cursor.fetchall()
+		ldict[lengths[0][0]] = 0
+		prev = lengths[0][1]/1000000.0
+		sum += lengths[0][1]/1000000.0
+		for item in lengths[1:]:
+			ldict[item[0]] = prev
+			prev += item[1]/1000000.0
+			sum += item[1]/1000000.0
+		return ldict, sum