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

7 files changed, 0 insertions, 3568 deletions

diff --git a/web/webqtl/utility/AJAX_table.py b/web/webqtl/utility/AJAX_table.py
deleted file mode 100755
index 963a530e..00000000
--- a/web/webqtl/utility/AJAX_table.py
+++ /dev/null
@@ -1,153 +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 cPickle
-import os
-import MySQLdb
-import time
-import pyXLWriter as xl
-
-from htmlgen import HTMLgen2 as HT
-
-from base import webqtlConfig
-from THCell import THCell
-from TDCell import TDCell
-import webqtlUtil
-
-
-class AJAX_table:
-	def __init__(self, fd):
-		file = fd.formdata.getfirst("file", "")
-		sort = fd.formdata.getfirst("sort", "")
-		order = fd.formdata.getfirst("order", "up")
-		cmd = fd.formdata.getfirst("cmd", "")
-		tableID = fd.formdata.getfirst("tableID", "")
-		addIndex = fd.formdata.getfirst("addIndex", "1")
-		hiddenColumnsString = fd.formdata.getfirst("hiddenColumns", "")
-		hiddenColumns = hiddenColumnsString.split(',')
-
-		try:
-			fp = open(os.path.join(webqtlConfig.TMPDIR, file + '.obj'), 'rb')
-			tblobj = cPickle.load(fp)
-			fp.close()
-		
-			if cmd == 'addCorr':
-				dbId = int(fd.formdata.getfirst("db"))
-				dbFullName = fd.formdata.getfirst("dbname")
-				trait = fd.formdata.getfirst("trait")
-				form = fd.formdata.getfirst("form")
-				ids = fd.formdata.getfirst("ids")
-				vals = fd.formdata.getfirst("vals")
-				ids = eval(ids) 
-				nnCorr = len(ids)
-				vals = eval(vals)
-	
-				workbook = xl.Writer('%s.xls' % (webqtlConfig.TMPDIR+file))
-				worksheet = workbook.add_worksheet()
-	
-				con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD)
-				cursor = con.cursor()
-			
-				cursor.execute("Select name, ShortName from ProbeSetFreeze where Id = %s", dbId)
-				dbName, dbShortName = cursor.fetchone()
-			
-				tblobj['header'][0].append(
-					THCell(HT.TD(dbShortName, Class="fs11 ffl b1 cw cbrb"), 
-					text="%s" % dbShortName, idx=tblobj['header'][0][-1].idx + 1),
-				)
-	            
-				headingStyle = workbook.add_format(align = 'center', bold = 1, border = 1, size=13, fg_color = 0x1E, color="white")
-				for i, item in enumerate(tblobj['header'][0]):
-                    			if (i > 0):
-						worksheet.write([8, i-1], item.text, headingStyle)
-						worksheet.set_column([i-1, i-1], 2*len(item.text))  
-			
-				for i, row in enumerate(tblobj['body']):
-					ProbeSetId = row[1].text
-					#XZ, 03/02/2009: Xiaodong changed Data to ProbeSetData
-					cursor.execute("""
-						Select ProbeSetData.StrainId, ProbeSetData.Value
-						From ProbeSetData, ProbeSetXRef, ProbeSet
-						where ProbeSetXRef.ProbeSetFreezeId = %d AND
-							ProbeSetXRef.DataId = ProbeSetData.Id AND
-							ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-							ProbeSet.Name = '%s'
-					""" % (dbId, ProbeSetId))
-					results = cursor.fetchall()
-					vdict = {}
-					for item in results:
-						vdict[item[0]] = item[1]
-					newvals = []
-					for id in ids:
-						if vdict.has_key(id):
-							newvals.append(vdict[id])
-						else:
-							newvals.append(None)
-					corr,nOverlap= webqtlUtil.calCorrelation(newvals,vals,nnCorr)
-					repr = '%0.4f' % corr
-					row.append(
-						TDCell(HT.TD(HT.Href(text=repr, url="javascript:showCorrPlotThird('%s', '%s', '%s')" % (form, dbName, ProbeSetId), Class="fs11 fwn ffl"), " / ", nOverlap, Class="fs11 fwn ffl b1 c222", align="middle"),repr,abs(corr))
-					)
-	                
-					last_row=0
-					for j, item in enumerate(tblobj['body'][i]):
-						if (j > 0):
-							worksheet.write([9+i, j-1], item.text)
-							last_row = 9+i
-					last_row += 1
-	                              
-				titleStyle = workbook.add_format(align = 'left', bold = 0, size=14, border = 1, border_color="gray")
-				##Write title Info
-				# Modified by Hongqiang Li 
-				worksheet.write([0, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle)
-				worksheet.write([1, 0], "Trait : %s" % trait, titleStyle)
-				worksheet.write([2, 0], "Database : %s" % dbFullName, 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)
-				#Write footer info
-				worksheet.write([1 + last_row, 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 + last_row, 0], "PLEASE RETAIN DATA SOURCE INFORMATION WHENEVER POSSIBLE", titleStyle)    
-	                    
-				cursor.close()
-				workbook.close()
-	            
-				objfile = open(os.path.join(webqtlConfig.TMPDIR, file + '.obj'), 'wb')
-				cPickle.dump(tblobj, objfile)
-				objfile.close()
-			else:
-				pass
-
-			self.value = str(webqtlUtil.genTableObj(tblobj=tblobj, file=file, sortby=(sort, order), tableID = tableID, addIndex = addIndex, hiddenColumns = hiddenColumns))
-
-		except:
-			self.value = "<span class='fs16 fwb cr ffl'>The table is no longer available on this server</span>"
-
-	def __str__(self):
-		return self.value
-
-	def write(self):
-		return str(self)
diff --git a/web/webqtl/utility/Plot.py b/web/webqtl/utility/Plot.py
deleted file mode 100755
index 2401c85c..00000000
--- a/web/webqtl/utility/Plot.py
+++ /dev/null
@@ -1,1283 +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 piddle as pid
-from math import *
-import random
-import sys, os
-from numarray import linear_algebra as la
-from numarray import ones, array, dot, swapaxes
-
-import reaper
-
-import svg
-import webqtlUtil
-from base import webqtlConfig
-
-
-def cformat(d, rank=0):
-	'custom string format'
-	strD = "%2.6f" % d
-	
-	if rank == 0:
-		while strD[-1] in ('0','.'):
-			if strD[-1] == '0' and strD[-2] == '.' and len(strD) <= 4:
-				break
-			elif strD[-1] == '.':
-				strD = strD[:-1]
-				break
-			else:
-				strD = strD[:-1]
-	
-	else:
-		strD = strD.split(".")[0]		
-
-	if strD == '-0.0':
-		strD = '0.0'
-	return strD
-	
-def frange(start, end=None, inc=1.0): 
-	"A faster range-like function that does accept float increments..." 
-	if end == None: 
-		end = start + 0.0 
-		start = 0.0 
-	else: 
-		start += 0.0 # force it to be a float 
-	count = int((end - start) / inc) 
-	if start + count * inc != end: 
-	# Need to adjust the count. AFAICT, it always comes up one short. 
-		count += 1 
-	L = [start] * count 
-	for i in xrange(1, count): 
-		L[i] = start + i * inc 
-	return L 
-
-
-def gammln(xx):
-	cof=[76.18009173,-86.50532033,24.01409822,-1.231739516,0.120858003e-2,-0.536382e-5]
-	x=xx-1.0
-	tmp=x+5.5
-	tmp -=(x+0.5)*log(tmp)
-	ser=1.0
-	for item in cof:
-		x+=1.0
-		ser+=item/x
-	
-	return -tmp+log(2.50662827465*ser)
-	
-
-def gser(a,x):
-	gln=gammln(a)
-	ITMAX=100
-	EPS=3.0e-7
-	
-	if x<=0.0:
-		gamser=0.0
-		return [gamser,gln]
-	else:
-		ap=a
-		sum=1.0/a
-		dele=sum
-		for i in range(1,ITMAX+1):
-			ap+=1.0
-			dele*=x/ap
-			sum+=dele
-			if abs(dele)<abs(sum)*EPS:
-				gamser=sum*exp(-x+a*log(x)-gln)
-				return [gamser,gln]
-	return None
-	
-def gcf(a,x):
-	ITMAX=100
-	EPS=3.0e-7
-	gold=0.0
-	fac=1
-	b1=1.0
-	b0=0.0
-	a0=1.0
-	gln=gammln(a)
-	
-	a1=x
-	for n in range(1,ITMAX+1):
-		an=n+0.0
-		ana=an-a
-		a0=(a1+a0*ana)*fac
-		b0=(b1+b0*ana)*fac
-		anf=an*fac
-		a1=x*a0+anf*a1
-		b1=x*b0+anf*b1
-		if (a1):
-			fac=1.0/a1
-			g=b1*fac
-			if abs((g-gold)/g)<EPS:
-				gammcf=exp(-x+a*log(x)-gln)*g
-				return [gammcf,gln]
-			gold=g
-	return None
-	
-def gammp(a,x):
-	if x<0.0 or a<=0.0:
-		return None
-	if x<(a+1.0):
-		a=gser(a,x)[0]
-		return a
-	else:
-		a=gcf(a,x)[0]
-		return 1.0-a
-def U(n):
-	x=pow(0.5,1.0/n)
-	m=[1-x]
-	for i in range(2,n):
-		a=(i-0.3175)/(n+0.365)
-		m.append(a)
-	m.append(x)
-	return m
-		
-def erf(x):
-	if x<0.0:
-		return -gammp(0.5,x*x)
-	else:
-		return gammp(0.5,x*x)
-
-def erfcc(x):
-	z=abs(x)
-	t=1.0/(1.0+0.5*z)
-	ans=t*exp(-z*z-1.26551223+t*(1.00002368+t*(0.37409196+t*(0.09678418+t*(-0.18628806+t*(0.27886807+t*(-1.13520398+t*(1.48851587+t*(-0.82215223+t*0.17087277)))))))))
-	if x>=0.0:
-		return ans
-	else:
-		return 2.0-ans
-		
-def calMeanVar(data):
-	n=len(data)
-	if n<2:
-		return None
-	else:
-		sum=reduce(lambda x,y:x+y,data,0.0)
-		mean=sum/n
-		z=data[:]
-		for i in range(n):
-			z[i]=z[i]-mean
-		variance=reduce(lambda x,y:x+y*y,z,0.0)
-		variance /= n-1
-		variance =sqrt(variance)
-		for i in range(n):
-			z[i]=z[i]/variance
-		return z
-		
-def inverseCumul(p):
-	#Coefficients in rational approximations.
-	a = [-3.969683028665376e+01,2.209460984245205e+02,-2.759285104469687e+02,1.383577518672690e+02,-3.066479806614716e+01,2.506628277459239e+00]
-
-	b = [-5.447609879822406e+01,1.615858368580409e+02,-1.556989798598866e+02,6.680131188771972e+01,-1.328068155288572e+01]
-
-	c = [-7.784894002430293e-03,-3.223964580411365e-01,-2.400758277161838e+00,-2.549732539343734e+00,4.374664141464968e+00,2.938163982698783e+00]
-
-	d =  [7.784695709041462e-03,3.224671290700398e-01,2.445134137142996e+00,3.754408661907416e+00]
-
-	#Define break-points.
-
-	p_low  = 0.02425
-	p_high = 1 - p_low
-
-	#Rational approximation for lower region.
-
-	if p > 0 and p < p_low:
-   		q = sqrt(-2*log(p))
-   		x = (((((c[0]*q+c[1])*q+c[2])*q+c[3])*q+c[4])*q+c[5]) / ((((d[0]*q+d[1])*q+d[2])*q+d[3])*q+1)
-
-
-	#Rational approximation for central region.
-
-	elif p>= p_low and p <= p_high:
-   		q = p - 0.5
-   		r = q*q
-   		x = (((((a[0]*r+a[1])*r+a[2])*r+a[3])*r+a[4])*r+a[5])*q /(((((b[0]*r+b[1])*r+b[2])*r+b[3])*r+b[4])*r+1)
-
-	#Rational approximation for upper region.
-
-	elif p>p_high and  p < 1:
-   		q = sqrt(-2*log(1-p))
-   		x = -(((((c[0]*q+c[1])*q+c[2])*q+c[3])*q+c[4])*q+c[5]) /((((d[0]*q+d[1])*q+d[2])*q+d[3])*q+1)
-
-	else:
-		return None
-
-	if p>0 and p < 1:
-   		e = 0.5 * erfcc(-x/sqrt(2)) - p 
-   		u = e * sqrt(2*pi) * exp(x*x/2)
-   		x = x - u/(1 + x*u/2)
-		return x
-	else:
-		return None
-
-def gmean(lst):
-	N = len(lst)
-	if N == 0:
-		return 0
-	else:
-		return (reduce(lambda x,y: x+y, lst, 0.0))/N
-
-def gmedian(lst2):
-	lst = lst2[:]
-	N = len(lst)
-	if N == 0:
-		return 0
-	else:
-		lst.sort()
-		if N % 2 == 0:
-			return (lst[N/2]+lst[(N-2)/2])/2.0
-		else:
-			return lst[(N-1)/2]
-			
-def gpercentile(lst2, np):
-	lst = lst2[:]
-	N = len(lst)
-	if N == 0 or np > 100 or np < 0:
-		return None
-	else:
-		lst.sort()
-		pNadd1 = (np/100.0)*N
-		k = int(pNadd1)
-		d = pNadd1 - k
-		if k == 0:
-			return lst[0]
-		elif k >= N-1:
-			return lst[N-1]
-		else:
-			return lst[k-1] + d*(lst[k] - lst[k-1])
-		
-def findOutliers(vals):
-	
-	valsOnly = []
-	dataXZ = vals[:]
-	for i in range(len(dataXZ)):
-		valsOnly.append(dataXZ[i][1])
-		
-	data = [('', valsOnly[:])]	
-	
-	for item in data:
-		itemvalue = item[1]
-		nValue = len(itemvalue)
-		catValue = []
-		
-		for item2 in itemvalue:
-			try:
-				tstrain, tvalue = item2
-			except:
-				tvalue = item2
-			if nValue <= 4:
-				continue
-			else:
-				catValue.append(tvalue)
-				
-		if catValue != []:
-			lowHinge = gpercentile(catValue, 25)
-			upHinge = gpercentile(catValue, 75)
-			Hstep = 1.5*(upHinge - lowHinge)
-			
-			outlier = []
-			extreme = []
-			
-			upperBound = upHinge + Hstep
-			lowerBound = lowHinge - Hstep
-			
-			for item in catValue:
-				if item >= upHinge + 2*Hstep:
-					extreme.append(item)
-				elif item >= upHinge + Hstep:
-					outlier.append(item)
-				else:
-					pass
-				
-			for item in catValue:
-				if item <= lowHinge - 2*Hstep:
-					extreme.append(item)
-				elif item <= lowHinge - Hstep:
-					outlier.append(item)
-				else:
-					pass
-		else:
-			upperBound = 1000
-			lowerBound = -1000
-				
-	return upperBound, lowerBound
-					
-					
-def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabel="Value"):
-	xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-	plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
-	plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
-	iValues = []
-	for item in data:
-		for item2 in item[1]:
-			try:
-				iValues.append(item2[1])
-			except:
-				iValues.append(item2)
-	
-	#draw frame		
-	max_Y = max(iValues)
-	min_Y = min(iValues)
-	scaleY = 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 = 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(data)
-	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 data:
-		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)
-		
-		nValue = len(itemvalue)
-		catValue = []
-		for item2 in itemvalue:
-			try:
-				tstrain, tvalue = item2
-			except:
-				tvalue = item2
-			if nValue <= 4:
-				canvas.drawCross(XCoord, plotHeight + yTopOffset - (tvalue-Yll)*plotHeight/(Yur - Yll), color=pid.red,size=5)
-			else:
-				catValue.append(tvalue)
-		if catValue != []:
-			catMean = gmean(catValue)
-			catMedian = gmedian(catValue)
-			lowHinge = gpercentile(catValue, 25)
-			upHinge = gpercentile(catValue, 75)
-			Hstep = 1.5*(upHinge - lowHinge)
-			
-			outlier = []
-			extrem = []
-			
-			upperAdj = None
-			for item in catValue:
-				if item >= upHinge + 2*Hstep:
-					extrem.append(item)
-				elif item >= upHinge + Hstep:
-					outlier.append(item)
-				elif item > upHinge and  item < upHinge + Hstep:
-					if upperAdj == None or item > upperAdj:
-						upperAdj = item
-				else:
-					pass
-			lowerAdj = None
-			for item in catValue:
-				if item <= lowHinge - 2*Hstep:
-					extrem.append(item)
-				elif item <= lowHinge - Hstep:
-					outlier.append(item)
-				if item < lowHinge and  item > lowHinge - Hstep:
-					if lowerAdj == None or item < lowerAdj:
-						lowerAdj = item
-					else:
-						pass
-			canvas.drawRect(XCoord-20, plotHeight + yTopOffset - (lowHinge-Yll)*plotHeight/(Yur - Yll), \
-				XCoord+20, plotHeight + yTopOffset - (upHinge-Yll)*plotHeight/(Yur - Yll))
-			canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (catMedian-Yll)*plotHeight/(Yur - Yll), \
-				XCoord+20, plotHeight + yTopOffset - (catMedian-Yll)*plotHeight/(Yur - Yll))
-			if upperAdj != None:
-				canvas.drawLine(XCoord, plotHeight + yTopOffset - (upHinge-Yll)*plotHeight/(Yur - Yll), \
-				XCoord, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll))
-				canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll), \
-				XCoord+20, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll))
-			if lowerAdj != None:
-				canvas.drawLine(XCoord, plotHeight + yTopOffset - (lowHinge-Yll)*plotHeight/(Yur - Yll), \
-				XCoord, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll))
-				canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll), \
-				XCoord+20, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll))
-			
-			outlierFont = pid.Font(ttf="cour",size=12,bold=0)
-			if outlier != []:
-				for item in outlier:
-					yc = plotHeight + yTopOffset - (item-Yll)*plotHeight/(Yur - Yll)
-					#canvas.drawEllipse(XCoord-3, yc-3, XCoord+3, yc+3)
-					canvas.drawString('o', XCoord-3, yc+5, font=outlierFont, color=pid.orange)
-			if extrem != []:
-				for item in extrem:
-					yc = plotHeight + yTopOffset - (item-Yll)*plotHeight/(Yur - Yll)
-					#canvas.drawEllipse(XCoord-3, yc-3, XCoord+3, yc+3)
-					canvas.drawString('*', XCoord-3, yc+6, font=outlierFont, color=pid.red)
-			
-			canvas.drawCross(XCoord, plotHeight + yTopOffset - (catMean-Yll)*plotHeight/(Yur - Yll), \
-				color=pid.blue,size=3)
-			#print (catMean, catMedian, cat25per, cat75per)
-			pass
-		
-		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(YLabel,xLeftOffset-40, YCoord-(plotHeight -canvas.stringWidth(YLabel,font=labelFont))/2.0,\
-	 font=labelFont, angle =90)
-
-def plotSecurity(canvas, text="12345"):
-	if not text:
-		return
-
-	plotWidth = canvas.size[0]
-	plotHeight = canvas.size[1]
-	if plotHeight<=0 or plotWidth<=0:
-		return
-		
-	bgColor = pid.Color(0.6+0.4*random.random(), 0.6+0.4*random.random(), 0.6+0.4*random.random())
-	canvas.drawRect(0,0,plotWidth,plotHeight, edgeColor=bgColor, fillColor=bgColor)
-	
-	for i in range(30):
-		randomColor = pid.Color(0.6+0.4*random.random(), 0.6+0.4*random.random(), 0.6+0.4*random.random())
-		scaleFont=pid.Font(ttf="cour",size=random.choice(range(20, 50)))
-		canvas.drawString(random.choice('abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'), 
-			int(random.random()*plotWidth), int(random.random()*plotHeight), font=scaleFont, 
-			color=randomColor, angle=random.choice(range(-45, 50)))
-			
-	step = (plotWidth-20)/len(text)
-	startX = 20
-	for item in text:
-		randomColor = pid.Color(0.6*random.random(),0.6*random.random(), 0.6*random.random())
-		scaleFont=pid.Font(ttf="verdana",size=random.choice(range(50, 60)),bold=1)
-		canvas.drawString(item, startX, plotHeight/2-10, font=scaleFont, 
-			color=randomColor, angle=random.choice(range(-45, 50)))
-		startX += step
- 
-# parameter: data is either object returned by reaper permutation function (called by MarkerRegressionPage.py)
-# or the first object returned by direct (pair-scan) permu function (called by DirectPlotPage.py)	 
-def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, offset= (60, 20, 40, 40), zoom = 1):
-	
-	xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-	
-	plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
-	plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
-	if plotHeight<=0 or plotWidth<=0:
-		return
-		
-	if len(data) < 2:
-		return
-		
-	max_D = max(data)
-	min_D = min(data)
-	#add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong
-	if max_D == float('inf') or max_D>webqtlConfig.MAXLRS:
-		max_D=webqtlConfig.MAXLRS #maximum LRS value
-		
-	xLow, xTop, stepX = detScale(min_D, max_D)
-	
-	#reduce data
-	step = ceil((xTop-xLow)/50.0)
-	j = xLow
-	dataXY = []
-	Count = []
-	while j <= xTop:
-		dataXY.append(j)
-		Count.append(0)
-		j += step 
-	
-	for i, item in enumerate(data):
-		if item == float('inf') or item>webqtlConfig.MAXLRS:
-			item = webqtlConfig.MAXLRS #maximum LRS value
-		j = int((item-xLow)/step)
-		Count[j] += 1	
-		
-	yLow, yTop, stepY=detScale(0,max(Count))
-	
-	#draw data
-	xScale = plotWidth/(xTop-xLow)
-	yScale = plotHeight/(yTop-yLow)
-	barWidth = xScale*step
-	
-	for i, count in enumerate(Count):
-		if count:
-			xc = (dataXY[i]-xLow)*xScale+xLeftOffset
-			yc =-(count-yLow)*yScale+yTopOffset+plotHeight
-			canvas.drawRect(xc+2,yc,xc+barWidth-2,yTopOffset+plotHeight,edgeColor=barColor,fillColor=barColor)
-	
-	#draw drawing region
-	canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight)
-
-	#draw scale
-	scaleFont=pid.Font(ttf="cour",size=11,bold=1)
-	x=xLow
-	for i in range(stepX+1):
-		xc=xLeftOffset+(x-xLow)*xScale
-		canvas.drawLine(xc,yTopOffset+plotHeight,xc,yTopOffset+plotHeight+5, color=axesColor)
-		strX = cformat(d=x, rank=0)
-		canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+14,font=scaleFont)
-		x+= (xTop - xLow)/stepX
-		
-	y=yLow
-	for i in range(stepY+1):
-		yc=yTopOffset+plotHeight-(y-yLow)*yScale
-		canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor)
-		strY = "%d" %y
-		canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont)
-		y+= (yTop - yLow)/stepY
-	
-	#draw label
-	labelFont=pid.Font(ttf="tahoma",size=17,bold=0)
-	if XLabel:
-		canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,
-			yTopOffset+plotHeight+yBottomOffset-10,font=labelFont,color=labelColor)
-	
-	if YLabel:
-		canvas.drawString(YLabel, 19, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,
-			font=labelFont,color=labelColor,angle=90)
-
-	labelFont=pid.Font(ttf="verdana",size=16,bold=0)
-	if title:
-		canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0,
-			20,font=labelFont,color=labelColor)
-
-def plotBarText(canvas, data, label, variance=None, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, sLabel = None, offset= (80, 20, 40, 100), barSpace = 2, zoom = 1):
-	xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-	plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
-	plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
-	if plotHeight<=0 or plotWidth<=0:
-		return
-	
-	NNN = len(data)
-	if NNN < 2 or NNN != len(label):
-		return
-	if variance and len(variance)!=NNN:
-		variance = []
-	
-	Y2 = data[:]
-	if variance:
-		for i in range(NNN):
-			if variance[i]:
-				Y2 += [data[i]-variance[i]]
-				
-	#Y axis
-	YLow, YTop, stepY = detScale(min(Y2), max(Y2))
-	YScale = plotHeight/(YTop - YLow)
-	
-	if YLow < 0  and  YTop > 0:
-		drawZero = 1
-	else:
-		drawZero = 0
-		
-	#X axis
-	X = range(NNN)
-	Xll= 0 
-	Xur= NNN-1
-	
-	
-	if drawZero:
-		YZero = yTopOffset+plotHeight-YScale*(0-YLow)
-		canvas.drawLine(xLeftOffset, YZero, xLeftOffset+plotWidth, YZero)
-	else:
-		YZero = yTopOffset+plotHeight
-	#draw data
-	spaceWidth = barSpace
-	if spaceWidth < 1:
-		spaceWidth = 1
-	barWidth = int((plotWidth - (NNN-1.0)*spaceWidth)/NNN)
-	
-	xc= xLeftOffset
-	scaleFont=pid.Font(ttf="verdana",size=11,bold=0)	
-	for i in range(NNN):
-		yc = yTopOffset+plotHeight-(data[i]-YLow)*YScale
-		canvas.drawRect(xc,YZero,xc+barWidth-1, yc, edgeColor=barColor,fillColor=barColor)
-		if variance and variance[i]:
-			varlen = variance[i]*YScale
-			if yc-varlen < yTopOffset:
-				topYd = yTopOffset
-			else:
-				topYd = yc-varlen
-				canvas.drawLine(xc+barWidth/2-2,yc-varlen,xc+barWidth/2+2,yc-varlen,color=pid.red)
-			canvas.drawLine(xc+barWidth/2,yc+varlen,xc+barWidth/2,topYd,color=pid.red)
-			canvas.drawLine(xc+barWidth/2-2,yc+varlen,xc+barWidth/2+2,yc+varlen,color=pid.red)
-		strX = label[i]
-		canvas.drawString(strX,xc+barWidth/2.0+2,yTopOffset+plotHeight+2+canvas.stringWidth(strX,font=scaleFont),font=scaleFont,angle=90)
-		xc += barWidth + spaceWidth	
-		
-	#draw drawing region
-	canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight)
-	
-	#draw Y scale
-	scaleFont=pid.Font(ttf="cour",size=16,bold=1)		
-	y=YLow
-	for i in range(stepY+1):
-		yc=yTopOffset+plotHeight-(y-YLow)*YScale
-		canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor)
-		strY = cformat(d=y, rank=0)
-		canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont)
-		y+= (YTop - YLow)/stepY
-	
-	#draw label
-	labelFont=pid.Font(ttf="verdana",size=17,bold=0)
-	if XLabel:
-		canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,yTopOffset+plotHeight+65,font=labelFont,color=labelColor)
-	
-	if YLabel:
-		canvas.drawString(YLabel,xLeftOffset-50, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,font=labelFont,color=labelColor,angle=90)
-	
-	labelFont=pid.Font(ttf="verdana",size=18,bold=0)
-	if title:
-		canvas.drawString(title,xLeftOffset,yTopOffset-15,font=labelFont,color=labelColor)
-		
-	return
-		
-def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, axesColor=pid.black, labelColor=pid.black, lineSize="thin", lineColor=pid.grey, idFont="arial", idColor=pid.blue, idSize="14", symbolColor=pid.black, symbolType="circle", filled="yes", symbolSize="tiny", XLabel=None, YLabel=None, title=None, fitcurve=None, connectdot=1, displayR=None, loadingPlot = 0, offset= (80, 20, 40, 60), zoom = 1, specialCases=[], showLabel = 1, bufferSpace = 15):
-	'displayR : correlation scatter plot, loadings : loading plot'
-	
-	dataXRanked, dataYRanked = webqtlUtil.calRank(dataX, dataY, len(dataX))
-		
-	#get ID font size
-	idFontSize = int(idSize)	
-	
-	#If filled is yes, set fill color
-	if filled == "yes":
-		fillColor = symbolColor
-	else:
-		fillColor = None	
-	
-	if symbolSize == "large":
-		sizeModifier = 7
-		fontModifier = 12
-	elif symbolSize == "medium":
-		sizeModifier = 5
-		fontModifier = 8
-	elif symbolSize == "small":
-		sizeModifier = 3
-		fontModifier = 3
-	else:
-		sizeModifier = 1
-		fontModifier = -1	
-			
-	if rank == 0:    # Pearson correlation
-		bufferSpace = 0
-		dataXPrimary = dataX
-		dataYPrimary = dataY
-		dataXAlt = dataXRanked    #Values used just for printing the other corr type to the graph image
-		dataYAlt = dataYRanked    #Values used just for printing the other corr type to the graph image
-	else:    # Spearman correlation: Switching Ranked and Unranked X and Y values
-		dataXPrimary = dataXRanked
-		dataYPrimary = dataYRanked
-		dataXAlt = dataX    #Values used just for printing the other corr type to the graph image
-		dataYAlt = dataY    #Values used just for printing the other corr type to the graph image
-	
-	xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-	plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
-	plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
-	if plotHeight<=0 or plotWidth<=0:
-		return
-	if len(dataXPrimary) < 1 or  len(dataXPrimary) != len(dataYPrimary) or (dataLabel and len(dataXPrimary) != len(dataLabel)):
-		return
-	
-	max_X=max(dataXPrimary)
-	min_X=min(dataXPrimary)
-	max_Y=max(dataYPrimary)
-	min_Y=min(dataYPrimary)
-	
-	#for some reason I forgot why I need to do this
-	if loadingPlot:
-		min_X = min(-0.1,min_X)
-		max_X = max(0.1,max_X)
-		min_Y = min(-0.1,min_Y)
-		max_Y = max(0.1,max_Y)
-	
-	xLow, xTop, stepX=detScale(min_X,max_X)
-	yLow, yTop, stepY=detScale(min_Y,max_Y)
-	xScale = plotWidth/(xTop-xLow)
-	yScale = plotHeight/(yTop-yLow)
-	
-	#draw drawing region
-	canvas.drawRect(xLeftOffset-bufferSpace, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight+bufferSpace)
-	canvas.drawRect(xLeftOffset-bufferSpace+1, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight+bufferSpace-1)
-
-	#calculate data points	
-	data = map(lambda X, Y: (X, Y), dataXPrimary, dataYPrimary)
-	xCoord = map(lambda X, Y: ((X-xLow)*xScale + xLeftOffset, yTopOffset+plotHeight-(Y-yLow)*yScale), dataXPrimary, dataYPrimary)
-
-	labelFont=pid.Font(ttf=idFont,size=idFontSize,bold=0)
-
-	if loadingPlot:
-		xZero = -xLow*xScale+xLeftOffset
-		yZero = yTopOffset+plotHeight+yLow*yScale
-		for point in xCoord:
-			canvas.drawLine(xZero,yZero,point[0],point[1],color=pid.red)
-	else:
-		if connectdot:
-			canvas.drawPolygon(xCoord,edgeColor=plotColor,closed=0)
-		else:
-			pass
-
-	symbolFont = pid.Font(ttf="fnt_bs", size=12+fontModifier,bold=0)
-
-	for i, item in enumerate(xCoord):
-		if dataLabel and dataLabel[i] in specialCases:
-			canvas.drawRect(item[0]-3, item[1]-3, item[0]+3, item[1]+3, edgeColor=pid.green)
-			#canvas.drawCross(item[0],item[1],color=pid.blue,size=5)
-		else:
-			if symbolType == "vertRect":
-				canvas.drawRect(x1=item[0]-sizeModifier+2,y1=item[1]-sizeModifier-2, x2=item[0]+sizeModifier-1,y2=item[1]+sizeModifier+2, edgeColor=symbolColor, edgeWidth=1, fillColor=fillColor)
-			elif (symbolType == "circle" and filled != "yes"):
-				canvas.drawString(":", item[0]-canvas.stringWidth(":",font=symbolFont)/2+1,item[1]+2,color=symbolColor, font=symbolFont)
-			elif (symbolType == "circle" and filled == "yes"):
-				canvas.drawString("5", item[0]-canvas.stringWidth("5",font=symbolFont)/2+1,item[1]+2,color=symbolColor, font=symbolFont)
-			elif symbolType == "horiRect":
-				canvas.drawRect(x1=item[0]-sizeModifier-1,y1=item[1]-sizeModifier+3, x2=item[0]+sizeModifier+3,y2=item[1]+sizeModifier-2, edgeColor=symbolColor, edgeWidth=1, fillColor=fillColor)
-			elif (symbolType == "square"):
-				canvas.drawRect(x1=item[0]-sizeModifier+1,y1=item[1]-sizeModifier-4, x2=item[0]+sizeModifier+2,y2=item[1]+sizeModifier-3, edgeColor=symbolColor, edgeWidth=1, fillColor=fillColor)
-			elif (symbolType == "diamond" and filled != "yes"):
-				canvas.drawString(",", item[0]-canvas.stringWidth(",",font=symbolFont)/2+2, item[1]+6, font=symbolFont, color=symbolColor)
-			elif (symbolType == "diamond" and filled == "yes"):
-				canvas.drawString("D", item[0]-canvas.stringWidth("D",font=symbolFont)/2+2, item[1]+6, font=symbolFont, color=symbolColor)	
-			elif symbolType == "4-star":
-				canvas.drawString("l", item[0]-canvas.stringWidth("l",font=symbolFont)/2+1, item[1]+3, font=symbolFont, color=symbolColor)	
-			elif symbolType == "3-star":
-				canvas.drawString("k", item[0]-canvas.stringWidth("k",font=symbolFont)/2+1, item[1]+3, font=symbolFont, color=symbolColor)	
-			else:	
-				canvas.drawCross(item[0],item[1]-2,color=symbolColor, size=sizeModifier+2)
-
-		if showLabel and dataLabel:
-			if (symbolType == "vertRect" or symbolType == "diamond"):
-				labelGap = 15
-			elif (symbolType == "4-star" or symbolType == "3-star"):
-				labelGap = 12
-			else:
-			    labelGap = 11
-			canvas.drawString(dataLabel[i], item[0]- canvas.stringWidth(dataLabel[i],
-				font=labelFont)/2 + 1, item[1]+(labelGap+sizeModifier+(idFontSize-12)), font=labelFont, color=idColor)
-                        	
-	#draw scale
-	scaleFont=pid.Font(ttf="cour",size=16,bold=1)
-	
-
-	x=xLow
-	for i in range(stepX+1):
-		xc=xLeftOffset+(x-xLow)*xScale
-		if ((x == 0) & (rank == 1)):
-			pass
-		else:
-			canvas.drawLine(xc,yTopOffset+plotHeight + bufferSpace,xc,yTopOffset+plotHeight+5 + bufferSpace, color=axesColor)		
-		strX = cformat(d=x, rank=rank)
-		if ((strX == "0") & (rank == 1)):
-			pass
-		else:
-			canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+20 + bufferSpace,font=scaleFont)
-		x+= (xTop - xLow)/stepX
-	
-	y=yLow
-	for i in range(stepY+1):
-		yc=yTopOffset+plotHeight-(y-yLow)*yScale
-		if ((y == 0) & (rank == 1)):
-			pass
-		else:
-			canvas.drawLine(xLeftOffset - bufferSpace,yc,xLeftOffset-5 - bufferSpace,yc, color=axesColor)
-		strY = cformat(d=y, rank=rank)
-		if ((strY == "0") & (rank == 1)):
-			pass
-		else:
-			canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)- 10 - bufferSpace,yc+4,font=scaleFont)
-		y+= (yTop - yLow)/stepY
-			
-	#draw label
-
-	labelFont=pid.Font(ttf="verdana",size=canvas.size[0]/45,bold=0)
-	titleFont=pid.Font(ttf="verdana",size=canvas.size[0]/40,bold=0)
-		
-	if (rank == 1 and not title):
-		canvas.drawString("Spearman Rank Correlation", xLeftOffset-canvas.size[0]*.025+(plotWidth-canvas.stringWidth("Spearman Rank Correlation",font=titleFont))/2.0,
-						  25,font=titleFont,color=labelColor)
-	elif (rank == 0 and not title):
-		canvas.drawString("Pearson Correlation", xLeftOffset-canvas.size[0]*.025+(plotWidth-canvas.stringWidth("Pearson Correlation",font=titleFont))/2.0,
-						  25,font=titleFont,color=labelColor)
-		
-	if XLabel:
-		canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,
-			yTopOffset+plotHeight+yBottomOffset-25,font=labelFont,color=labelColor)
-	
-	if YLabel:
-		canvas.drawString(YLabel, xLeftOffset-65, yTopOffset+plotHeight- (plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,
-			font=labelFont,color=labelColor,angle=90)
-
-	labelFont=pid.Font(ttf="verdana",size=20,bold=0)
-	if title:
-		canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0,
-			20,font=labelFont,color=labelColor)
-	
-	if fitcurve:
-		import sys
-		sys.argv = [ "mod_python" ]
-		#from numarray import linear_algebra as la
-		#from numarray import ones, array, dot, swapaxes
-		fitYY = array(dataYPrimary)
-		fitXX = array([ones(len(dataXPrimary)),dataXPrimary])
-		AA = dot(fitXX,swapaxes(fitXX,0,1))
-		BB = dot(fitXX,fitYY)
-		bb = la.linear_least_squares(AA,BB)[0]
-		
-		xc1 = xLeftOffset
-		yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale 
-		if yc1 > yTopOffset+plotHeight:
-			yc1 = yTopOffset+plotHeight
-			xc1 = (yLow-bb[0])/bb[1]
-			xc1=(xc1-xLow)*xScale+xLeftOffset
-		elif yc1 < yTopOffset:
-			yc1 = yTopOffset
-			xc1 = (yTop-bb[0])/bb[1]
-			xc1=(xc1-xLow)*xScale+xLeftOffset
-		else:
-			pass
-		
-		xc2 = xLeftOffset + plotWidth 
-		yc2 = yTopOffset+plotHeight-(bb[0]+bb[1]*xTop-yLow)*yScale
-		if yc2 > yTopOffset+plotHeight:
-			yc2 = yTopOffset+plotHeight
-			xc2 = (yLow-bb[0])/bb[1]
-			xc2=(xc2-xLow)*xScale+xLeftOffset
-		elif yc2 < yTopOffset:
-			yc2 = yTopOffset
-			xc2 = (yTop-bb[0])/bb[1]
-			xc2=(xc2-xLow)*xScale+xLeftOffset
-		else:
-			pass
-
-		canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace,xc2,yc2,color=lineColor)
-		if lineSize == "medium":
-			canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace+1,xc2,yc2+1,color=lineColor)
-		if lineSize == "thick":
-			canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace+1,xc2,yc2+1,color=lineColor)
-			canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace-1,xc2,yc2-1,color=lineColor)
-		
-		
-	if displayR:
-		labelFont=pid.Font(ttf="trebuc",size=canvas.size[0]/60,bold=0)
-		NNN = len(dataX)
-		corr = webqtlUtil.calCorrelation(dataXPrimary,dataYPrimary,NNN)[0]
-
-		if NNN < 3:
-			corrPValue = 1.0
-		else:
-			if abs(corr) >= 1.0:
-				corrPValue = 0.0
-			else:
-				ZValue = 0.5*log((1.0+corr)/(1.0-corr))
-				ZValue = ZValue*sqrt(NNN-3)
-				corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue)))
-				
-		NStr = "N = %d" % NNN
-		strLenN = canvas.stringWidth(NStr,font=labelFont)
-
-		if rank == 1:
-		    if corrPValue < 0.0000000000000001:
-				corrStr = "Rho = %1.3f P < 1.00 E-16" % (corr)
-		    else:
-				corrStr = "Rho = %1.3f P = %3.2E" % (corr, corrPValue)
-		else:
-		    if corrPValue < 0.0000000000000001:
-				corrStr = "r = %1.3f P < 1.00 E-16" % (corr)
-		    else:
-				corrStr = "r = %1.3f P = %3.2E" % (corr, corrPValue)
-		strLen = canvas.stringWidth(corrStr,font=labelFont)
-
-		canvas.drawString(NStr,xLeftOffset,yTopOffset-10,font=labelFont,color=labelColor)
-		canvas.drawString(corrStr,xLeftOffset+plotWidth-strLen,yTopOffset-10,font=labelFont,color=labelColor)
-
-	return xCoord
-
-def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black", axesColor="black", labelColor="black", symbolColor="red", XLabel=None, YLabel=None, title=None, fitcurve=None, connectdot=1, displayR=None, loadingPlot = 0, offset= (80, 20, 40, 60), zoom = 1, specialCases=[], showLabel = 1):
-	'displayR : correlation scatter plot, loadings : loading plot'
-	
-	dataXRanked, dataYRanked = webqtlUtil.calRank(dataX, dataY, len(dataX))
-			
-	# Switching Ranked and Unranked X and Y values if a Spearman Rank Correlation			
-	if rank == 0:
-		dataXPrimary = dataX
-		dataYPrimary = dataY
-		dataXAlt = dataXRanked
-		dataYAlt = dataYRanked		
-	
-	else:	
-		dataXPrimary = dataXRanked
-		dataYPrimary = dataYRanked
-		dataXAlt = dataX
-		dataYAlt = dataY
-
-
-	
-	xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-	plotWidth = drawSpace.attributes['width'] - xLeftOffset - xRightOffset
-	plotHeight = drawSpace.attributes['height'] - yTopOffset - yBottomOffset
-	if plotHeight<=0 or plotWidth<=0:
-		return
-	if len(dataXPrimary) < 1 or  len(dataXPrimary) != len(dataYPrimary) or (dataLabel and len(dataXPrimary) != len(dataLabel)):
-		return
-	
-	max_X=max(dataXPrimary)
-	min_X=min(dataXPrimary)
-	max_Y=max(dataYPrimary)
-	min_Y=min(dataYPrimary)
-	
-	#for some reason I forgot why I need to do this
-	if loadingPlot:
-		min_X = min(-0.1,min_X)
-		max_X = max(0.1,max_X)
-		min_Y = min(-0.1,min_Y)
-		max_Y = max(0.1,max_Y)
-	
-	xLow, xTop, stepX=detScale(min_X,max_X)
-	yLow, yTop, stepY=detScale(min_Y,max_Y)
-	xScale = plotWidth/(xTop-xLow)
-	yScale = plotHeight/(yTop-yLow)
-	
-	#draw drawing region
-	r = svg.rect(xLeftOffset, yTopOffset, plotWidth,  plotHeight, 'none', axesColor, 1)
-	drawSpace.addElement(r)
-	
-	#calculate data points	
-	data = map(lambda X, Y: (X, Y), dataXPrimary, dataYPrimary)
-	xCoord = map(lambda X, Y: ((X-xLow)*xScale + xLeftOffset, yTopOffset+plotHeight-(Y-yLow)*yScale), dataXPrimary, dataYPrimary)
-	labelFontF = "verdana"
-	labelFontS = 11
-	
-	if loadingPlot:
-		xZero = -xLow*xScale+xLeftOffset
-		yZero = yTopOffset+plotHeight+yLow*yScale
-		for point in xCoord:
-			drawSpace.addElement(svg.line(xZero,yZero,point[0],point[1], "red", 1))
-	else:
-		if connectdot:
-			pass
-			#drawSpace.drawPolygon(xCoord,edgeColor=plotColor,closed=0)
-		else:
-			pass
-			
-	for i, item in enumerate(xCoord):
-		if dataLabel and dataLabel[i] in specialCases:
-			drawSpace.addElement(svg.rect(item[0]-3, item[1]-3, 6, 6, "none", "green", 0.5))
-			#drawSpace.drawCross(item[0],item[1],color=pid.blue,size=5)
-		else:
-			drawSpace.addElement(svg.line(item[0],item[1]+5,item[0],item[1]-5,symbolColor,1))
-			drawSpace.addElement(svg.line(item[0]+5,item[1],item[0]-5,item[1],symbolColor,1))
-		if showLabel and dataLabel:
-			pass
-			drawSpace.addElement(svg.text(item[0], item[1]+14, dataLabel[i], labelFontS, 
-				labelFontF, text_anchor="middle", style="stroke:blue;stroke-width:0.5;"))
-			#canvas.drawString(, item[0]- canvas.stringWidth(dataLabel[i],
-			#	font=labelFont)/2, item[1]+14, font=labelFont, color=pid.blue)
-	
-	#draw scale
-	#scaleFont=pid.Font(ttf="cour",size=14,bold=1)
-	x=xLow
-	for i in range(stepX+1):
-		xc=xLeftOffset+(x-xLow)*xScale
-		drawSpace.addElement(svg.line(xc,yTopOffset+plotHeight,xc,yTopOffset+plotHeight+5, axesColor, 1))
-		strX = cformat(d=x, rank=rank)
-		drawSpace.addElement(svg.text(xc,yTopOffset+plotHeight+20,strX,13, "courier", text_anchor="middle"))
-		x+= (xTop - xLow)/stepX
-		
-	y=yLow
-	for i in range(stepY+1):
-		yc=yTopOffset+plotHeight-(y-yLow)*yScale
-		drawSpace.addElement(svg.line(xLeftOffset,yc,xLeftOffset-5,yc, axesColor, 1))
-		strY = cformat(d=y, rank=rank)
-		drawSpace.addElement(svg.text(xLeftOffset-10,yc+5,strY,13, "courier", text_anchor="end"))
-		y+= (yTop - yLow)/stepY
-			
-	#draw label
-	labelFontF = "verdana"
-	labelFontS = 17
-	if XLabel:
-		drawSpace.addElement(svg.text(xLeftOffset+plotWidth/2.0,
-			yTopOffset+plotHeight+yBottomOffset-10,XLabel,
-			labelFontS, labelFontF, text_anchor="middle"))
-	
-	if YLabel:
-		drawSpace.addElement(svg.text(xLeftOffset-50,
-			 yTopOffset+plotHeight/2,YLabel,
-			labelFontS, labelFontF, text_anchor="middle", style="writing-mode:tb-rl", transform="rotate(270 %d %d)" % (xLeftOffset-50,  yTopOffset+plotHeight/2)))
-		#drawSpace.drawString(YLabel, xLeftOffset-50, yTopOffset+plotHeight- (plotHeight-drawSpace.stringWidth(YLabel,font=labelFont))/2.0,
-		#	font=labelFont,color=labelColor,angle=90)
-
-
-	if fitcurve:
-		sys.argv = [ "mod_python" ]
-                #from numarray import linear_algebra as la
-		#from numarray import ones, array, dot, swapaxes
-		fitYY = array(dataYPrimary)
-		fitXX = array([ones(len(dataXPrimary)),dataXPrimary])
-		AA = dot(fitXX,swapaxes(fitXX,0,1))
-		BB = dot(fitXX,fitYY)
-		bb = la.linear_least_squares(AA,BB)[0]
-		
-		xc1 = xLeftOffset
-		yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale 
-		if yc1 > yTopOffset+plotHeight:
-			yc1 = yTopOffset+plotHeight
-			xc1 = (yLow-bb[0])/bb[1]
-			xc1=(xc1-xLow)*xScale+xLeftOffset
-		elif yc1 < yTopOffset:
-			yc1 = yTopOffset
-			xc1 = (yTop-bb[0])/bb[1]
-			xc1=(xc1-xLow)*xScale+xLeftOffset
-		else:
-			pass
-		
-		xc2 = xLeftOffset + plotWidth 
-		yc2 = yTopOffset+plotHeight-(bb[0]+bb[1]*xTop-yLow)*yScale
-		if yc2 > yTopOffset+plotHeight:
-			yc2 = yTopOffset+plotHeight
-			xc2 = (yLow-bb[0])/bb[1]
-			xc2=(xc2-xLow)*xScale+xLeftOffset
-		elif yc2 < yTopOffset:
-			yc2 = yTopOffset
-			xc2 = (yTop-bb[0])/bb[1]
-			xc2=(xc2-xLow)*xScale+xLeftOffset
-		else:
-			pass
-
-		drawSpace.addElement(svg.line(xc1,yc1,xc2,yc2,"green", 1))
-	
-	if displayR:		
-		labelFontF = "trebuc"
-		labelFontS = 14
-		NNN = len(dataX)
-
-		corr = webqtlUtil.calCorrelation(dataXPrimary,dataYPrimary,NNN)[0]
-
-		if NNN < 3:
-			corrPValue = 1.0
-		else:
-			if abs(corr) >= 1.0:
-				corrPValue = 0.0
-			else:
-				ZValue = 0.5*log((1.0+corr)/(1.0-corr))
-				ZValue = ZValue*sqrt(NNN-3)
-				corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue)))
-				
-		NStr = "N of Cases=%d" % NNN
-		
-		if rank == 1:
-			corrStr = "Spearman's r=%1.3f P=%3.2E" % (corr, corrPValue)
-		else:
-			corrStr = "Pearson's r=%1.3f P=%3.2E" % (corr, corrPValue)
-		
-		drawSpace.addElement(svg.text(xLeftOffset,yTopOffset-10,NStr,
-			labelFontS, labelFontF, text_anchor="start"))
-		drawSpace.addElement(svg.text(xLeftOffset+plotWidth,yTopOffset-25,corrStr,
-			labelFontS, labelFontF, text_anchor="end"))
-	"""	
-	"""
-	return
-
-
-# This function determines the scale of the plot	
-def detScaleOld(min,max):
-	if min>=max:
-		return None
-	elif min == -1.0 and max == 1.0:
-		return [-1.2,1.2,12]
-	else:
-		a=max-min
-		b=floor(log10(a))
-		c=pow(10.0,b)
-		if a < c*5.0:
-			c/=2.0
-		#print a,b,c
-		low=c*floor(min/c)
-		high=c*ceil(max/c)
-		return [low,high,round((high-low)/c)]
-
-def detScale(min=0,max=0,bufferSpace=3):
-
-	if min>=max:
-		return None
-	elif min == -1.0 and max == 1.0:
-		return [-1.2,1.2,12]
-	else:
-		a=max-min
-		if max != 0:
-			max += 0.1*a
-		if min != 0:
-			if min > 0 and min < 0.1*a:
-				min = 0.0
-			else:
-				min -= 0.1*a
-		a=max-min
-		b=floor(log10(a))
-		c=pow(10.0,b)
-		low=c*floor(min/c)
-		high=c*ceil(max/c)
-		n = round((high-low)/c)
-		div = 2.0
-		while n < 5 or n > 15:
-			if n < 5:
-				c /= div
-			else:
-				c *= div
-			if div == 2.0:
-				div =5.0
-			else:
-				div =2.0
-			low=c*floor(min/c)
-			high=c*ceil(max/c)
-			n = round((high-low)/c)
-
-		return [low,high,n]
-
-
-
-def colorSpectrumOld(n):
-	if n == 1:
-		return [pid.Color(1,0,0)]
-	elif n == 2:
-		return [pid.Color(1,0,0),pid.Color(0,0,1)]
-	elif n == 3:
-		return [pid.Color(1,0,0),pid.Color(0,1,0),pid.Color(0,0,1)]
-	else:
-		step = 2.0/(n-1)
-		red = 1.0
-		green = 0.0
-		blue = 0.0
-		colors = [pid.Color(red,green,blue)]
-		i = 1
-		greenpeak = 0
-		while i < n:
-			if red >= step:
-				red -= step
-				green += step
-				if green >= 1.0:
-					greenpeak = 1
-					blue += green -1.0
-					green = 1.0
-			else:
-				red = 0.0
-				if greenpeak:
-					green -= step
-					blue += step
-				else:
-					green += step
-				if green >= 1.0:
-					greenpeak = 1
-					blue += green -1.0
-					green = 2.0 -green
-				elif green < 0.0:
-					green = 0.0
-				else:
-					pass
-			colors.append(pid.Color(red,green,blue))
-			i += 1
-		return colors
-		
-		
-
-
-def bluefunc(x):
-	return 1.0 / (1.0 + exp(-10*(x-0.6)))
-
-
-def redfunc(x):
-	return 1.0 / (1.0 + exp(10*(x-0.5)))
-
-def greenfunc(x):
-	return 1 - pow(redfunc(x+0.2),2) - bluefunc(x-0.3)
-
-def colorSpectrum(n=100):
-	multiple = 10
-	if n == 1:
-		return [pid.Color(1,0,0)]
-	elif n == 2:
-		return [pid.Color(1,0,0),pid.Color(0,0,1)]
-	elif n == 3:
-		return [pid.Color(1,0,0),pid.Color(0,1,0),pid.Color(0,0,1)]
-	N = n*multiple
-	out = [None]*N;
-	for i in range(N):
-		x = float(i)/N
-		out[i] = pid.Color(redfunc(x), greenfunc(x), bluefunc(x));
-	out2 = [out[0]]
-	step = N/float(n-1)
-	j = 0
-	for i in range(n-2):
-		j += step
-		out2.append(out[int(j)])
-	out2.append(out[-1])
-	return out2
-
-
-def colorSpectrumSVG(n=100):
-	multiple = 10
-	if n == 1:
-		return ["rgb(255,0,0)"]
-	elif n == 2:
-		return ["rgb(255,0,0)","rgb(0,0,255)"]
-	elif n == 3:
-		return ["rgb(255,0,0)","rgb(0,255,0)","rgb(0,0,255)"]
-	N = n*multiple
-	out = [None]*N;
-	for i in range(N):
-		x = float(i)/N
-		out[i] = "rgb(%d, %d, %d)" % (redfunc(x)*255, greenfunc(x)*255, bluefunc(x)*255);
-	out2 = [out[0]]
-	step = N/float(n-1)
-	j = 0
-	for i in range(n-2):
-		j += step
-		out2.append(out[int(j)])
-	out2.append(out[-1])
-	return out2
-
-
-def BWSpectrum(n=100):
-	multiple = 10
-	if n == 1:
-		return [pid.Color(0,0,0)]
-	elif n == 2:
-		return [pid.Color(0,0,0),pid.Color(1,1,1)]
-	elif n == 3:
-		return [pid.Color(0,0,0),pid.Color(0.5,0.5,0.5),pid.Color(1,1,1)]
-	
-	step = 1.0/n
-	x = 0.0
-	out = []
-	for i in range(n):
-		out.append(pid.Color(x,x,x));
-		x += step
-	return out
diff --git a/web/webqtl/utility/TDCell.py b/web/webqtl/utility/TDCell.py
deleted file mode 100755
index 76b9c5db..00000000
--- a/web/webqtl/utility/TDCell.py
+++ /dev/null
@@ -1,42 +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
-
-##########################################################
-#
-#    Table Cell Class
-#
-##########################################################
-
-		
-class TDCell:
-	def __init__(self, html="", text="", val=0.0):
-		self.html = html	#html, for web page
-		self.text = text	#text value, for output to a text file
-		self.val = val		#sort by value
-	
-	def __str__(self):
-		return self.text
-
diff --git a/web/webqtl/utility/THCell.py b/web/webqtl/utility/THCell.py
deleted file mode 100755
index a96b9e49..00000000
--- a/web/webqtl/utility/THCell.py
+++ /dev/null
@@ -1,44 +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
-
-##########################################################
-#
-#    Table Header Class
-#
-##########################################################
-
-
-class THCell:
-	def __init__(self, html="", text="", sort=1, idx=-1):
-		self.html = html	#html, for web page
-		self.text = text	#Column text value
-		self.sort = sort	#0: not sortable, 1: yes
-		self.idx = idx		#sort by value
-	
-	def __str__(self):
-		return self.text
-		
-
diff --git a/web/webqtl/utility/__init__.py b/web/webqtl/utility/__init__.py
deleted file mode 100755
index e69de29b..00000000
--- a/web/webqtl/utility/__init__.py
+++ /dev/null
diff --git a/web/webqtl/utility/svg.py b/web/webqtl/utility/svg.py
deleted file mode 100755
index e49a6c3c..00000000
--- a/web/webqtl/utility/svg.py
+++ /dev/null
@@ -1,1069 +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
-
-#!/usr/bin/env python
-##Copyright (c) 2002, Fedor Baart & Hans de Wit (Stichting Farmaceutische Kengetallen)
-##All rights reserved.
-##
-##Redistribution and use in source and binary forms, with or without modification,
-##are permitted provided that the following conditions are met:
-##
-##Redistributions of source code must retain the above copyright notice, this
-##list of conditions and the following disclaimer.
-##
-##Redistributions in binary form must reproduce the above copyright notice,
-##this list of conditions and the following disclaimer in the documentation and/or
-##other materials provided with the distribution.
-##
-##Neither the name of the Stichting Farmaceutische Kengetallen nor the names of
-##its contributors may be used to endorse or promote products derived from this
-##software without specific prior written permission.
-##
-##THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-##AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-##IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-##DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
-##FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-##DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-##SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-##CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-##OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-##OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-##Thanks to Gerald Rosennfellner for his help and useful comments.
-
-__doc__="""Use SVGdraw to generate your SVGdrawings.
-
-SVGdraw uses an object model drawing and a method toXML to create SVG graphics
-by using easy to use classes and methods usualy you start by creating a drawing eg
-
-    d=drawing()
-    #then you create a SVG root element
-    s=svg()
-    #then you add some elements eg a circle and add it to the svg root element
-    c=circle()
-    #you can supply attributes by using named arguments.
-    c=circle(fill='red',stroke='blue')
-    #or by updating the attributes attribute:
-    c.attributes['stroke-width']=1
-    s.addElement(c)
-    #then you add the svg root element to the drawing
-    d.setSVG(s)
-    #and finaly you xmlify the drawing
-    d.toXml()
-    
-
-this results in the svg source of the drawing, which consists of a circle
-on a white background. Its as easy as that;)
-This module was created using the SVG specification of www.w3c.org and the
-O'Reilly (www.oreilly.com) python books as information sources. A svg viewer
-is available from www.adobe.com"""
-
-__version__="1.0"
-
-# there are two possibilities to generate svg:
-# via a dom implementation and directly using <element>text</element> strings
-# the latter is way faster (and shorter in coding)
-# the former is only used in debugging svg programs
-# maybe it will be removed alltogether after a while
-# with the following variable you indicate whether to use the dom implementation
-# Note that PyXML is required for using the dom implementation.
-# It is also possible to use the standard minidom. But I didn't try that one.
-# Anyway the text based approach is about 60 times faster than using the full dom implementation.
-use_dom_implementation=0
-
-
-import exceptions
-if use_dom_implementation<>0:
-    try:
-        from xml.dom import implementation
-        from xml.dom.ext import PrettyPrint
-    except:
-        raise exceptions.ImportError, "PyXML is required for using the dom implementation"
-#The implementation is used for the creating the XML document.
-#The prettyprint module is used for converting the xml document object to a xml file
-
-import sys
-assert sys.version_info[0]>=2
-if sys.version_info[1]<2:
-    True=1
-    False=0
-    file=open
-    
-sys.setrecursionlimit=50
-#The recursion limit is set conservative so mistakes like s=svg() s.addElement(s)
-#won't eat up too much processor time.
-
-#the following code is pasted form xml.sax.saxutils
-#it makes it possible to run the code without the xml sax package installed
-#To make it possible to have <rubbish> in your text elements, it is necessary to escape the texts
-def _escape(data, entities={}):
-    """Escape &, <, and > in a string of data.
-
-    You can escape other strings of data by passing a dictionary as
-    the optional entities parameter.  The keys and values must all be
-    strings; each key will be replaced with its corresponding value.
-    """
-    #data = data.replace("&", "&amp;")
-    data = data.replace("<", "&lt;")
-    data = data.replace(">", "&gt;")
-    for chars, entity in entities.items():
-        data = data.replace(chars, entity)
-    return data
-
-def _quoteattr(data, entities={}):
-    """Escape and quote an attribute value.
-
-    Escape &, <, and > in a string of data, then quote it for use as
-    an attribute value.  The \" character will be escaped as well, if
-    necessary.
-
-    You can escape other strings of data by passing a dictionary as
-    the optional entities parameter.  The keys and values must all be
-    strings; each key will be replaced with its corresponding value.
-    """
-    data = _escape(data, entities)
-    if '"' in data:
-        if "'" in data:
-            data = '"%s"' % data.replace('"', "&quot;")
-        else:
-            data = "'%s'" % data
-    else:
-        data = '"%s"' % data
-    return data
-
-
-
-def _xypointlist(a):
-    """formats a list of xy pairs"""
-    s=''
-    for e in a: #this could be done more elegant
-        s+=str(e)[1:-1] +'  '
-    return s
-
-def _viewboxlist(a):
-    """formats a tuple"""
-    s=''
-    for e in a: 
-        s+=str(e)+' '
-    return s
-
-def _pointlist(a):
-    """formats a list of numbers"""
-    return str(a)[1:-1]
-
-class pathdata:
-    """class used to create a pathdata object which can be used for a path.
-    although most methods are pretty straightforward it might be useful to look at the SVG specification."""
-    #I didn't test the methods below. 
-    def __init__(self,x=None,y=None):
-        self.path=[]
-        if x is not None and y is not None:
-            self.path.append('M '+str(x)+' '+str(y))
-    def closepath(self):
-        """ends the path"""
-        self.path.append('z')
-    def move(self,x,y):
-        """move to absolute"""
-        self.path.append('M '+str(x)+' '+str(y))
-    def relmove(self,x,y):
-        """move to relative"""
-        self.path.append('m '+str(x)+' '+str(y))
-    def line(self,x,y):
-        """line to absolute"""
-        self.path.append('L '+str(x)+' '+str(y))
-    def relline(self,x,y):
-        """line to relative"""
-        self.path.append('l '+str(x)+' '+str(y))
-    def hline(self,x):
-        """horizontal line to absolute"""
-        self.path.append('H'+str(x))
-    def relhline(self,x):
-        """horizontal line to relative"""
-        self.path.append('h'+str(x))
-    def vline(self,y):
-        """verical line to absolute"""
-        self.path.append('V'+str(y))
-    def relvline(self,y):
-        """vertical line to relative"""
-        self.path.append('v'+str(y))
-    def bezier(self,x1,y1,x2,y2,x,y):
-        """bezier with xy1 and xy2 to xy absolut"""
-        self.path.append('C'+str(x1)+','+str(y1)+' '+str(x2)+','+str(y2)+' '+str(x)+','+str(y))
-    def relbezier(self,x1,y1,x2,y2,x,y):
-        """bezier with xy1 and xy2 to xy relative"""
-        self.path.append('c'+str(x1)+','+str(y1)+' '+str(x2)+','+str(y2)+' '+str(x)+','+str(y))
-    def smbezier(self,x2,y2,x,y):
-        """smooth bezier with xy2 to xy absolut"""
-        self.path.append('S'+str(x2)+','+str(y2)+' '+str(x)+','+str(y))
-    def relsmbezier(self,x2,y2,x,y):
-        """smooth bezier with xy2 to xy relative"""
-        self.path.append('s'+str(x2)+','+str(y2)+' '+str(x)+','+str(y))
-    def qbezier(self,x1,y1,x,y):
-        """quadratic bezier with xy1 to xy absolut"""
-        self.path.append('Q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y))
-    def relqbezier(self,x1,y1,x,y):
-        """quadratic bezier with xy1 to xy relative"""
-        self.path.append('q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y))
-    def smqbezier(self,x,y):
-        """smooth quadratic bezier to xy absolut"""
-        self.path.append('T'+str(x)+','+str(y))
-    def relsmqbezier(self,x,y):
-        """smooth quadratic bezier to xy relative"""
-        self.path.append('t'+str(x)+','+str(y))
-    def ellarc(self,rx,ry,xrot,laf,sf,x,y):
-        """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag  to xy absolut"""
-        self.path.append('A'+str(rx)+','+str(ry)+' '+str(xrot)+' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y))
-    def relellarc(self,rx,ry,xrot,laf,sf,x,y):
-        """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag  to xy relative"""
-        self.path.append('a'+str(rx)+','+str(ry)+' '+str(xrot)+' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y))
-    def __repr__(self):
-        return ' '.join(self.path)
-    
-
-
-      
-class SVGelement:
-    """SVGelement(type,attributes,elements,text,namespace,**args)
-    Creates a arbitrary svg element and is intended to be subclassed not used on its own.
-    This element is the base of every svg element it defines a class which resembles
-    a xml-element. The main advantage of this kind of implementation is that you don't
-    have to create a toXML method for every different graph object. Every element
-    consists of a type, attribute, optional subelements, optional text and an optional
-    namespace. Note the elements==None, if elements = None:self.elements=[] construction.
-    This is done because if you default to elements=[] every object has a reference
-    to the same empty list."""
-    def __init__(self,type='',attributes=None,elements=None,text='',namespace='',cdata=None, **args):
-        self.type=type
-        if attributes==None:
-            self.attributes={}
-        else:
-            self.attributes=attributes
-        if elements==None:
-            self.elements=[]
-        else:
-            self.elements=elements
-        self.text=text
-        self.namespace=namespace
-        self.cdata=cdata
-        for arg in args.keys():
-            arg2 = arg.replace("__", ":")
-            arg2 = arg2.replace("_", "-")
-            self.attributes[arg2]=args[arg]
-    def addElement(self,SVGelement):
-        """adds an element to a SVGelement
-
-        SVGelement.addElement(SVGelement)
-        """
-        self.elements.append(SVGelement)
-
-    def toXml(self,level,f):
-        f.write('\t'*level)
-        f.write('<'+self.type)
-        for attkey in self.attributes.keys():
-            f.write(' '+_escape(str(attkey))+'='+_quoteattr(str(self.attributes[attkey])))
-        if self.namespace:
-            f.write(' xmlns="'+ _escape(str(self.namespace))+'" xmlns:xlink="http://www.w3.org/1999/xlink"')
-        if self.elements or self.text or self.cdata:
-            f.write('>')
-        if self.elements:
-            f.write('\n')
-        for element in self.elements:
-            element.toXml(level+1,f)
-        if self.cdata:
-            f.write('\n'+'\t'*(level+1)+'<![CDATA[')
-            for line in self.cdata.splitlines():
-               f.write('\n'+'\t'*(level+2)+line)
-            f.write('\n'+'\t'*(level+1)+']]>\n')
-        if self.text:
-            if type(self.text)==type(''): #If the text is only text
-                f.write(_escape(str(self.text)))
-            else:                         #If the text is a spannedtext class
-                f.write(str(self.text))
-        if self.elements:
-            f.write('\t'*level+'</'+self.type+'>\n')
-        elif self.text: 
-            f.write('</'+self.type+'>\n')
-        elif self.cdata:
-            f.write('\t'*level+'</'+self.type+'>\n')
-        else:
-            f.write('/>\n')
-            
-class tspan(SVGelement):
-    """ts=tspan(text='',**args)
-
-    a tspan element can be used for applying formatting to a textsection
-    usage:
-    ts=tspan('this text is bold')
-    ts.attributes['font-weight']='bold'
-    st=spannedtext()
-    st.addtspan(ts)
-    t=text(3,5,st)
-    """
-    def __init__(self,text=None,**args):
-        SVGelement.__init__(self,'tspan',**args)
-        if self.text<>None:
-            self.text=text
-    def __repr__(self):
-        s="<tspan"
-        for key,value in self.attributes.items():
-         s+= ' %s="%s"' % (key,value)
-        s+='>'
-        s+=self.text
-        s+='</tspan>'
-        return s
-    
-class tref(SVGelement):
-    """tr=tref(link='',**args)
-
-    a tref element can be used for referencing text by a link to its id.
-    usage:
-    tr=tref('#linktotext')
-    st=spannedtext()
-    st.addtref(tr)
-    t=text(3,5,st)
-    """
-    def __init__(self,link,**args):
-        SVGelement.__init__(self,'tref',{'xlink:href':link},**args)
-    def __repr__(self):
-        s="<tref"
-        
-        for key,value in self.attributes.items():
-         s+= ' %s="%s"' % (key,value)
-        s+='/>'
-        return s
-    
-class spannedtext:
-    """st=spannedtext(textlist=[])
-
-    a spannedtext can be used for text which consists of text, tspan's and tref's
-    You can use it to add to a text element or path element. Don't add it directly
-    to a svg or a group element.
-    usage:
-    
-    ts=tspan('this text is bold')
-    ts.attributes['font-weight']='bold'
-    tr=tref('#linktotext')
-    tr.attributes['fill']='red'
-    st=spannedtext()
-    st.addtspan(ts)
-    st.addtref(tr)
-    st.addtext('This text is not bold')
-    t=text(3,5,st)
-    """
-    def __init__(self,textlist=None):
-        if textlist==None:
-            self.textlist=[]
-        else:
-            self.textlist=textlist
-    def addtext(self,text=''):
-        self.textlist.append(text)
-    def addtspan(self,tspan):
-        self.textlist.append(tspan)
-    def addtref(self,tref):
-        self.textlist.append(tref)
-    def __repr__(self):
-        s=""
-        for element in self.textlist:
-            s+=str(element)
-        return s
-    
-class rect(SVGelement):
-    """r=rect(width,height,x,y,fill,stroke,stroke_width,**args)
-    
-    a rectangle is defined by a width and height and a xy pair 
-    """
-    def __init__(self,x=None,y=None,width=None,height=None,fill=None,stroke=None,stroke_width=None,**args):
-        if width==None or height==None:
-            if width<>None:
-                raise ValueError, 'height is required'
-            if height<>None:
-                raise ValueError, 'width is required'
-            else:
-                raise ValueError, 'both height and width are required'
-        SVGelement.__init__(self,'rect',{'width':width,'height':height},**args)
-        if x<>None:
-            self.attributes['x']=x
-        if y<>None:
-            self.attributes['y']=y
-        if fill<>None:
-            self.attributes['fill']=fill
-        if stroke<>None:
-            self.attributes['stroke']=stroke
-        if stroke_width<>None:
-            self.attributes['stroke-width']=stroke_width
-            
-class ellipse(SVGelement):
-    """e=ellipse(rx,ry,x,y,fill,stroke,stroke_width,**args)
-
-    an ellipse is defined as a center and a x and y radius.
-    """
-    def __init__(self,cx=None,cy=None,rx=None,ry=None,fill=None,stroke=None,stroke_width=None,**args):
-        if rx==None or ry== None:
-            if rx<>None:
-                raise ValueError, 'rx is required'
-            if ry<>None:
-                raise ValueError, 'ry is required'
-            else:
-                raise ValueError, 'both rx and ry are required'
-        SVGelement.__init__(self,'ellipse',{'rx':rx,'ry':ry},**args)
-        if cx<>None:
-            self.attributes['cx']=cx
-        if cy<>None:
-            self.attributes['cy']=cy
-        if fill<>None:
-            self.attributes['fill']=fill
-        if stroke<>None:
-            self.attributes['stroke']=stroke
-        if stroke_width<>None:
-            self.attributes['stroke-width']=stroke_width
-        
-   
-class circle(SVGelement):
-    """c=circle(x,y,radius,fill,stroke,stroke_width,**args)
-
-    The circle creates an element using a x, y and radius values eg
-    """
-    def __init__(self,cx=None,cy=None,r=None,fill=None,stroke=None,stroke_width=None,**args):
-        if r==None:
-            raise ValueError, 'r is required'
-        SVGelement.__init__(self,'circle',{'r':r},**args)
-        if cx<>None:
-            self.attributes['cx']=cx
-        if cy<>None:
-            self.attributes['cy']=cy
-        if fill<>None:
-            self.attributes['fill']=fill
-        if stroke<>None:
-            self.attributes['stroke']=stroke
-        if stroke_width<>None:
-            self.attributes['stroke-width']=stroke_width
-
-class point(circle):
-    """p=point(x,y,color)
-    
-    A point is defined as a circle with a size 1 radius. It may be more efficient to use a
-    very small rectangle if you use many points because a circle is difficult to render.
-    """
-    def __init__(self,x,y,fill='black',**args):
-        circle.__init__(self,x,y,1,fill,**args)
-
-class line(SVGelement):
-    """l=line(x1,y1,x2,y2,stroke,stroke_width,**args)
-    
-    A line is defined by a begin x,y pair and an end x,y pair
-    """
-    def __init__(self,x1=None,y1=None,x2=None,y2=None,stroke=None,stroke_width=None,**args):
-        SVGelement.__init__(self,'line',**args)
-        if x1<>None:
-            self.attributes['x1']=x1
-        if y1<>None:
-            self.attributes['y1']=y1
-        if x2<>None:
-            self.attributes['x2']=x2
-        if y2<>None:
-            self.attributes['y2']=y2
-        if stroke_width<>None:
-            self.attributes['stroke-width']=stroke_width
-        if stroke<>None:
-            self.attributes['stroke']=stroke
-            
-class polyline(SVGelement):
-    """pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)
-    
-    a polyline is defined by a list of xy pairs
-    """
-    def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args):
-        SVGelement.__init__(self,'polyline',{'points':_xypointlist(points)},**args)
-        if fill<>None:
-            self.attributes['fill']=fill
-        if stroke_width<>None:
-            self.attributes['stroke-width']=stroke_width
-        if stroke<>None:
-            self.attributes['stroke']=stroke
-
-class polygon(SVGelement):
-    """pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)
-    
-    a polygon is defined by a list of xy pairs
-    """
-    def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args):
-        SVGelement.__init__(self,'polygon',{'points':_xypointlist(points)},**args)
-        if fill<>None:
-            self.attributes['fill']=fill
-        if stroke_width<>None:
-            self.attributes['stroke-width']=stroke_width
-        if stroke<>None:
-            self.attributes['stroke']=stroke
-
-class path(SVGelement):
-    """p=path(path,fill,stroke,stroke_width,**args)
-
-    a path is defined by a path object and optional width, stroke and fillcolor
-    """
-    def __init__(self,pathdata,fill=None,stroke=None,stroke_width=None,id=None,**args):
-        SVGelement.__init__(self,'path',{'d':str(pathdata)},**args)
-        if stroke<>None:
-            self.attributes['stroke']=stroke
-        if fill<>None:
-            self.attributes['fill']=fill
-        if stroke_width<>None:
-            self.attributes['stroke-width']=stroke_width
-        if id<>None:
-            self.attributes['id']=id
-        
-        
-class text(SVGelement):
-    """t=text(x,y,text,font_size,font_family,**args)
-    
-    a text element can bge used for displaying text on the screen
-    """
-    def __init__(self,x=None,y=None,text=None,font_size=None,font_family=None,text_anchor=None,**args):
-        SVGelement.__init__(self,'text',**args)
-        if x<>None:
-            self.attributes['x']=x
-        if y<>None:
-            self.attributes['y']=y
-        if font_size<>None:
-            self.attributes['font-size']=font_size
-        if font_family<>None:
-            self.attributes['font-family']=font_family
-        if text<>None:
-            self.text=text
-        if text_anchor<>None:
-            self.attributes['text-anchor']=text_anchor
-
-
-class textpath(SVGelement):
-    """tp=textpath(text,link,**args)
-
-    a textpath places a text on a path which is referenced by a link.   
-    """
-    def __init__(self,link,text=None,**args):
-        SVGelement.__init__(self,'textPath',{'xlink:href':link},**args)
-        if text<>None:
-            self.text=text
-
-class pattern(SVGelement):
-    """p=pattern(x,y,width,height,patternUnits,**args)
-
-    A pattern is used to fill or stroke an object using a pre-defined
-    graphic object which can be replicated ("tiled") at fixed intervals
-    in x and y to cover the areas to be painted.
-    """
-    def __init__(self,x=None,y=None,width=None,height=None,patternUnits=None,**args):
-        SVGelement.__init__(self,'pattern',**args)
-        if x<>None:
-            self.attributes['x']=x
-        if y<>None:
-            self.attributes['y']=y
-        if width<>None:
-            self.attributes['width']=width
-        if height<>None:
-            self.attributes['height']=height
-        if patternUnits<>None:
-            self.attributes['patternUnits']=patternUnits
-
-class title(SVGelement):
-    """t=title(text,**args)
-    
-    a title is a text element. The text is displayed in the title bar
-    add at least one to the root svg element
-    """
-    def __init__(self,text=None,**args):
-        SVGelement.__init__(self,'title',**args)
-        if text<>None:
-            self.text=text
-
-class description(SVGelement):
-    """d=description(text,**args)
-    
-    a description can be added to any element and is used for a tooltip
-    Add this element before adding other elements.
-    """
-    def __init__(self,text=None,**args):
-        SVGelement.__init__(self,'desc',**args)
-        if text<>None:
-            self.text=text
-
-class lineargradient(SVGelement):
-    """lg=lineargradient(x1,y1,x2,y2,id,**args)
-
-    defines a lineargradient using two xy pairs.
-    stop elements van be added to define the gradient colors.
-    """
-    def __init__(self,x1=None,y1=None,x2=None,y2=None,id=None,**args):
-        SVGelement.__init__(self,'linearGradient',**args)
-        if x1<>None:
-            self.attributes['x1']=x1
-        if y1<>None:
-            self.attributes['y1']=y1
-        if x2<>None:
-            self.attributes['x2']=x2
-        if y2<>None:
-            self.attributes['y2']=y2
-        if id<>None:
-            self.attributes['id']=id
-
-class radialgradient(SVGelement):
-    """rg=radialgradient(cx,cy,r,fx,fy,id,**args)
-
-    defines a radial gradient using a outer circle which are defined by a cx,cy and r and by using a focalpoint.
-    stop elements van be added to define the gradient colors.
-    """
-    def __init__(self,cx=None,cy=None,r=None,fx=None,fy=None,id=None,**args):
-        SVGelement.__init__(self,'radialGradient',**args)
-        if cx<>None:
-            self.attributes['cx']=cx
-        if cy<>None:
-            self.attributes['cy']=cy
-        if r<>None:
-            self.attributes['r']=r
-        if fx<>None:
-            self.attributes['fx']=fx
-        if fy<>None:
-            self.attributes['fy']=fy
-        if id<>None:
-            self.attributes['id']=id
-            
-class stop(SVGelement):
-    """st=stop(offset,stop_color,**args)
-
-    Puts a stop color at the specified radius
-    """
-    def __init__(self,offset,stop_color=None,**args):
-        SVGelement.__init__(self,'stop',{'offset':offset},**args)
-        if stop_color<>None:
-            self.attributes['stop-color']=stop_color
-            
-class style(SVGelement):
-    """st=style(type,cdata=None,**args)
-
-    Add a CDATA element to this element for defing in line stylesheets etc..
-    """
-    def __init__(self,type,cdata=None,**args):
-        SVGelement.__init__(self,'style',{'type':type},cdata=cdata, **args)
-        
-            
-class image(SVGelement):
-    """im=image(url,width,height,x,y,**args)
-
-    adds an image to the drawing. Supported formats are .png, .jpg and .svg.
-    """
-    def __init__(self,url,x=None,y=None,width=None,height=None,**args):
-        if width==None or height==None:
-            if width<>None:
-                raise ValueError, 'height is required'
-            if height<>None:
-                raise ValueError, 'width is required'
-            else:
-                raise ValueError, 'both height and width are required'
-        SVGelement.__init__(self,'image',{'xlink:href':url,'width':width,'height':height},**args)
-        if x<>None:
-            self.attributes['x']=x
-        if y<>None:
-            self.attributes['y']=y
- 
-class cursor(SVGelement):
-    """c=cursor(url,**args)
-
-    defines a custom cursor for a element or a drawing
-    """
-    def __init__(self,url,**args):
-        SVGelement.__init__(self,'cursor',{'xlink:href':url},**args)
-
-    
-class marker(SVGelement):
-    """m=marker(id,viewbox,refX,refY,markerWidth,markerHeight,**args)
-    
-    defines a marker which can be used as an endpoint for a line or other pathtypes
-    add an element to it which should be used as a marker.
-    """
-    def __init__(self,id=None,viewBox=None,refx=None,refy=None,markerWidth=None,markerHeight=None,**args):
-        SVGelement.__init__(self,'marker',**args)
-        if id<>None:
-            self.attributes['id']=id
-        if viewBox<>None:
-            self.attributes['viewBox']=_viewboxlist(viewBox)
-        if refx<>None:
-            self.attributes['refX']=refx
-        if refy<>None:
-            self.attributes['refY']=refy
-        if markerWidth<>None:
-            self.attributes['markerWidth']=markerWidth
-        if markerHeight<>None:
-            self.attributes['markerHeight']=markerHeight
-        
-class group(SVGelement):
-    """g=group(id,**args)
-    
-    a group is defined by an id and is used to contain elements
-    g.addElement(SVGelement)
-    """
-    def __init__(self,id=None,**args):
-        SVGelement.__init__(self,'g',**args)
-        if id<>None:
-            self.attributes['id']=id
-
-class symbol(SVGelement):
-    """sy=symbol(id,viewbox,**args)
-
-    defines a symbol which can be used on different places in your graph using
-    the use element. A symbol is not rendered but you can use 'use' elements to
-    display it by referencing its id.
-    sy.addElement(SVGelement)
-    """
-    
-    def __init__(self,id=None,viewBox=None,**args):
-        SVGelement.__init__(self,'symbol',**args)
-        if id<>None:
-            self.attributes['id']=id
-        if viewBox<>None:
-            self.attributes['viewBox']=_viewboxlist(viewBox)
-            
-class defs(SVGelement):
-    """d=defs(**args)
-
-    container for defining elements
-    """
-    def __init__(self,**args):
-        SVGelement.__init__(self,'defs',**args)
-
-class switch(SVGelement):
-    """sw=switch(**args)
-
-    Elements added to a switch element which are "switched" by the attributes
-    requiredFeatures, requiredExtensions and systemLanguage.
-    Refer to the SVG specification for details.
-    """
-    def __init__(self,**args):
-        SVGelement.__init__(self,'switch',**args)
-
-        
-class use(SVGelement):
-    """u=use(link,x,y,width,height,**args)
-    
-    references a symbol by linking to its id and its position, height and width
-    """
-    def __init__(self,link,x=None,y=None,width=None,height=None,**args):
-        SVGelement.__init__(self,'use',{'xlink:href':link},**args)
-        if x<>None:
-            self.attributes['x']=x
-        if y<>None:
-            self.attributes['y']=y
-
-        if width<>None:
-            self.attributes['width']=width
-        if height<>None:
-            self.attributes['height']=height
-            
-            
-class link(SVGelement):
-    """a=link(url,**args)
-
-    a link  is defined by a hyperlink. add elements which have to be linked
-    a.addElement(SVGelement)
-    """
-    def __init__(self,link='',**args):
-        SVGelement.__init__(self,'a',{'xlink:href':link},**args)
-        
-class view(SVGelement):
-    """v=view(id,**args)
-
-    a view can be used to create a view with different attributes"""
-    def __init__(self,id=None,**args):
-        SVGelement.__init__(self,'view',**args)
-        if id<>None:
-            self.attributes['id']=id
-
-class script(SVGelement):
-    """sc=script(type,type,cdata,**args)
-
-    adds a script element which contains CDATA to the SVG drawing
-
-    """
-    def __init__(self,type,cdata=None,**args):
-        SVGelement.__init__(self,'script',{'type':type},cdata=cdata,**args)
-        
-class animate(SVGelement):
-    """an=animate(attribute,from,to,during,**args)
-
-    animates an attribute.    
-    """
-    def __init__(self,attribute,fr=None,to=None,dur=None,**args):
-        SVGelement.__init__(self,'animate',{'attributeName':attribute},**args)
-        if fr<>None:
-            self.attributes['from']=fr
-        if to<>None:
-            self.attributes['to']=to
-        if dur<>None:
-            self.attributes['dur']=dur
-        
-class animateMotion(SVGelement):
-    """an=animateMotion(pathdata,dur,**args)
-
-    animates a SVGelement over the given path in dur seconds
-    """
-    def __init__(self,pathdata,dur,**args):
-        SVGelement.__init__(self,'animateMotion',**args)
-        if pathdata<>None:
-            self.attributes['path']=str(pathdata)
-        if dur<>None:
-            self.attributes['dur']=dur
-
-class animateTransform(SVGelement):
-    """antr=animateTransform(type,from,to,dur,**args)
-    
-    transform an element from and to a value.
-    """
-    def __init__(self,type=None,fr=None,to=None,dur=None,**args):
-        SVGelement.__init__(self,'animateTransform',{'attributeName':'transform'},**args)
-        #As far as I know the attributeName is always transform
-        if type<>None:
-            self.attributes['type']=type
-        if fr<>None:
-            self.attributes['from']=fr
-        if to<>None:
-            self.attributes['to']=to
-        if dur<>None:
-            self.attributes['dur']=dur
-class animateColor(SVGelement):
-    """ac=animateColor(attribute,type,from,to,dur,**args)
-
-    Animates the color of a element
-    """
-    def __init__(self,attribute,type=None,fr=None,to=None,dur=None,**args):
-        SVGelement.__init__(self,'animateColor',{'attributeName':attribute},**args)
-        if type<>None:
-            self.attributes['type']=type
-        if fr<>None:
-            self.attributes['from']=fr
-        if to<>None:
-            self.attributes['to']=to
-        if dur<>None:
-            self.attributes['dur']=dur        
-class set(SVGelement):
-    """st=set(attribute,to,during,**args)
-    
-    sets an attribute to a value for a
-    """
-    def __init__(self,attribute,to=None,dur=None,**args):
-        SVGelement.__init__(self,'set',{'attributeName':attribute},**args)
-        if to<>None:
-            self.attributes['to']=to
-        if dur<>None:
-            self.attributes['dur']=dur
-
-
-            
-class svg(SVGelement):
-    """s=svg(viewbox,width,height,**args)
-    
-    a svg or element is the root of a drawing add all elements to a svg element.
-    You can have different svg elements in one svg file
-    s.addElement(SVGelement)
-
-    eg
-    d=drawing()
-    s=svg((0,0,100,100),'100%','100%')
-    c=circle(50,50,20)
-    s.addElement(c)
-    d.setSVG(s)
-    d.toXml()
-    """
-    def __init__(self,viewBox=None, width=None, height=None,**args):
-        SVGelement.__init__(self,'svg',**args)
-        if viewBox<>None:
-            self.attributes['viewBox']=_viewboxlist(viewBox)
-        if width<>None:
-            self.attributes['width']=width
-        if height<>None:
-            self.attributes['height']=height
-        self.namespace="http://www.w3.org/2000/svg"
-        
-class drawing:
-    """d=drawing()
-
-    this is the actual SVG document. It needs a svg element as a root.
-    Use the addSVG method to set the svg to the root. Use the toXml method to write the SVG
-    source to the screen or to a file
-    d=drawing()
-    d.addSVG(svg)
-    d.toXml(optionalfilename)
-    """
-
-    def __init__(self, entity={}):
-        self.svg=None
-        self.entity = entity
-    def setSVG(self,svg):
-        self.svg=svg
-        #Voeg een element toe aan de grafiek toe.
-    if use_dom_implementation==0:      
-        def toXml(self, filename='',compress=False):
-            import cStringIO
-            xml=cStringIO.StringIO()
-            xml.write("<?xml version='1.0' encoding='UTF-8'?>\n")
-            xml.write("<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.0//EN\" \"http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd\"")
-            if self.entity:
-            	xml.write(" [\n")
-            	for item in self.entity.keys():
-            		xml.write("<!ENTITY %s \"%s\">\n" % (item, self.entity[item]))
-            	xml.write("]")
-            xml.write(">\n")
-            self.svg.toXml(0,xml)
-            if not filename:
-                if compress:
-                    import gzip
-                    f=cStringIO.StringIO()
-                    zf=gzip.GzipFile(fileobj=f,mode='wb')
-                    zf.write(xml.getvalue())
-                    zf.close()
-                    f.seek(0)
-                    return f.read()
-                else:
-                    return xml.getvalue()
-            else:
-                if filename[-4:]=='svgz':
-                    import gzip
-                    f=gzip.GzipFile(filename=filename,mode="wb", compresslevel=9)
-                    f.write(xml.getvalue())
-                    f.close()
-                else:
-                    f=file(filename,'w')
-                    f.write(xml.getvalue())
-                    f.close()
-
-    else:
-        def toXml(self,filename='',compress=False):
-            """drawing.toXml()        ---->to the screen
-            drawing.toXml(filename)---->to the file
-            writes a svg drawing to the screen or to a file
-            compresses if filename ends with svgz or if compress is true
-            """
-            doctype = implementation.createDocumentType('svg',"-//W3C//DTD SVG 1.0//EN""",'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ')
-        
-            global root
-            #root is defined global so it can be used by the appender. Its also possible to use it as an arugument but
-            #that is a bit messy.
-            root=implementation.createDocument(None,None,doctype)
-            #Create the xml document.
-            global appender
-            def appender(element,elementroot):
-                """This recursive function appends elements to an element and sets the attributes
-                and type. It stops when alle elements have been appended"""
-                if element.namespace:
-                    e=root.createElementNS(element.namespace,element.type)
-                else:
-                    e=root.createElement(element.type)
-                if element.text:
-                    textnode=root.createTextNode(element.text)
-                    e.appendChild(textnode)
-                for attribute in element.attributes.keys():   #in element.attributes is supported from python 2.2
-                    e.setAttribute(attribute,str(element.attributes[attribute]))
-                if element.elements:
-                    for el in element.elements:
-                        e=appender(el,e)
-                elementroot.appendChild(e)
-                return elementroot
-            root=appender(self.svg,root)
-            if not filename:
-                import cStringIO
-                xml=cStringIO.StringIO()
-                PrettyPrint(root,xml)
-                if compress:
-                    import gzip
-                    f=cStringIO.StringIO()
-                    zf=gzip.GzipFile(fileobj=f,mode='wb')
-                    zf.write(xml.getvalue())
-                    zf.close()
-                    f.seek(0)
-                    return f.read()
-                else:
-                    return xml.getvalue()
-            else:
-                try:
-                    if filename[-4:]=='svgz':
-                        import gzip
-                        import cStringIO
-                        xml=cStringIO.StringIO()
-                        PrettyPrint(root,xml)
-                        f=gzip.GzipFile(filename=filename,mode='wb',compresslevel=9)
-                        f.write(xml.getvalue())
-                        f.close()
-                    else:
-                        f=open(filename,'w')
-                        PrettyPrint(root,f)
-                        f.close()
-                except:
-                    print "Cannot write SVG file: " + filename
-    def validate(self):
-        try:
-            import xml.parsers.xmlproc.xmlval
-        except:
-            raise exceptions.ImportError,'PyXml is required for validating SVG'
-        svg=self.toXml()
-        xv=xml.parsers.xmlproc.xmlval.XMLValidator()
-        try:
-            xv.feed(svg)
-        except:
-            raise "SVG is not well formed, see messages above"
-        else:
-            print "SVG well formed"
-if __name__=='__main__':
-
-    
-    d=drawing()
-    s=svg((0,0,100,100))
-    r=rect(-100,-100,300,300,'cyan')
-    s.addElement(r)
-    
-    t=title('SVGdraw Demo')
-    s.addElement(t)
-    g=group('animations')
-    e=ellipse(0,0,5,2)
-    g.addElement(e)
-    c=circle(0,0,1,'red')
-    g.addElement(c)
-    pd=pathdata(0,-10)
-    for i in range(6):
-        pd.relsmbezier(10,5,0,10)
-        pd.relsmbezier(-10,5,0,10)
-    an=animateMotion(pd,10)
-    an.attributes['rotate']='auto-reverse'
-    an.attributes['repeatCount']="indefinite"
-    g.addElement(an)
-    s.addElement(g)
-    for i in range(20,120,20):
-        u=use('#animations',i,0)
-        s.addElement(u)
-    for i in range(0,120,20):
-        for j in range(5,105,10):
-            c=circle(i,j,1,'red','black',.5)
-            s.addElement(c)
-    d.setSVG(s)
-     
-    print d.toXml()
-
diff --git a/web/webqtl/utility/webqtlUtil.py b/web/webqtl/utility/webqtlUtil.py
deleted file mode 100755
index 6af7f846..00000000
--- a/web/webqtl/utility/webqtlUtil.py
+++ /dev/null
@@ -1,977 +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 time
-import re
-import math
-from math import *
-
-from htmlgen import HTMLgen2 as HT
-
-from base import webqtlConfig
-
-
-
-
-# NL, 07/27/2010. moved from webqtlForm.py
-#Dict of Parents and F1 information, In the order of [F1, Mat, Pat]
-ParInfo ={
-'BXH':['BHF1', 'HBF1',  'C57BL/6J', 'C3H/HeJ'],
-'AKXD':['AKF1', 'KAF1', 'AKR/J', 'DBA/2J'],
-'BXD':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
-'BXD300':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
-'B6BTBRF2':['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'],
-'BHHBF2':['B6HF2','HB6F2','C57BL/6J','C3H/HeJ'],
-'BHF2':['B6HF2','HB6F2','C57BL/6J','C3H/HeJ'],
-'B6D2F2':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
-'BDF2-1999':['B6D2F2', 'D2B6F2', 'C57BL/6J', 'DBA/2J'],
-'BDF2-2005':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
-'CTB6F2':['CTB6F2','B6CTF2','C57BL/6J','Castaneous'],
-'CXB':['CBF1', 'BCF1', 'C57BL/6ByJ', 'BALB/cByJ'],
-'AXBXA':['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
-'AXB':['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
-'BXA':['BAF1', 'ABF1', 'C57BL/6J', 'A/J'],
-'LXS':['LSF1', 'SLF1', 'ISS', 'ILS'],
-'HXBBXH':['HSRBNF1', 'BNHSRF1', 'BN', 'HSR'],
-'BayXSha':['BayXShaF1', 'ShaXBayF1', 'Bay-0','Shahdara'],
-'ColXBur':['ColXBurF1', 'BurXColF1', 'Col-0','Bur-0'],
-'ColXCvi':['ColXCviF1', 'CviXColF1', 'Col-0','Cvi'],
-'SXM':['SMF1', 'MSF1', 'Steptoe','Morex']
-}
-
-
-# NL, 07/27/2010. moved from template.py
-IMGSTEP1 = HT.Image('/images/step1.gif', alt='STEP 1',border=0) #XZ, Only be used in inputPage.py
-IMGSTEP2 = HT.Image('/images/step2.gif', alt='STEP 2',border=0) #XZ, Only be used in inputPage.py
-IMGSTEP3 = HT.Image('/images/step3.gif', alt='STEP 3',border=0) #XZ, Only be used in inputPage.py
-IMGNEXT = HT.Image('/images/arrowdown.gif', alt='NEXT',border=0) #XZ, Only be used in inputPage.py
-
-IMGASC = HT.Image("/images/sortup.gif", border=0)
-IMGASCON = HT.Image("/images/sortupon.gif", border=0)
-IMGDESC = HT.Image("/images/sortdown.gif", border=0)
-IMGDESCON = HT.Image("/images/sortdownon.gif", border=0)
-
-"""
-IMGASC = HT.Image("/images/sortup_icon.gif", border=0)
-IMGASCON = HT.Image("/images/sortupon.gif", border=0)
-IMGDESC = HT.Image("/images/sortdown_icon.gif", border=0)
-IMGDESCON = HT.Image("/images/sortdownon.gif", border=0)
-IMG_UNSORTED = HT.Image("/images/unsorted_icon.gif", border=0)
-"""
-
-PROGRESSBAR = HT.Image('/images/waitAnima2.gif', alt='checkblue',align="middle",border=0)
-
-#########################################
-#      Accessory Functions
-#########################################
-
-def decodeEscape(str):
-	a = str
-	pattern = re.compile('(%[0-9A-Fa-f][0-9A-Fa-f])')
-	match = pattern.findall(a)
-	matched = []
-	for item in match:
-		if item not in matched:
-			a = a.replace(item, '%c' % eval("0x"+item[-2:]))
-		matched.append(item)
-	return a
-	
-def exportData(hddn, tdata, NP = None):
-	for key in tdata.keys():
-		_val, _var, _N = tdata[key].val, tdata[key].var, tdata[key].N
-		if _val != None:
-			hddn[key] = _val
-			if _var != None:
-				hddn['V'+key] = _var
-			if NP and _N != None:
-				hddn['N'+key] = _N
-	
-def genShortStrainName(RISet='', input_strainName=''):
-	#aliasStrainDict = {'C57BL/6J':'B6','DBA/2J':'D2'}
-	strainName = input_strainName
-	if RISet != 'AXBXA':
-		if RISet == 'BXD300':
-			this_RISet = 'BXD'
-		elif RISet == 'BDF2-2005':
-			this_RISet = 'CASE05_'
-		else:
-			this_RISet = RISet
-		strainName = string.replace(strainName,this_RISet,'')
-		strainName = string.replace(strainName,'CASE','')
-		try:
-			strainName = "%02d" % int(strainName)
-		except:
-			pass
-	else:
-		strainName = string.replace(strainName,'AXB','A')
-		strainName = string.replace(strainName,'BXA','B')
-		try:
-			strainName = strainName[0] + "%02d" % int(strainName[1:])
-		except:
-			pass
-	return strainName
-
-def toInt(in_str):
-	"Converts an arbitrary string to an unsigned integer"
-	start = -1
-	end = -1
-	for i, char in enumerate(in_str):
-		if char >= '0' and char <= '9':
-			if start < 0:
-				start = i
-			end = i+1
-		else:
-			if start >= 0:
-				break
-	if start < end:
-		return int(in_str[start:end])
-	else:
-		return  -1
-
-def transpose(m):
-	'transpose a matrix'
-	n = len(m)
-	return [[m[j][i] for i in range(len(m[0])) for j in range(n)][k*n:k*n+n] for k in range(len(m[0]))]
-
-def asymTranspose(m):
-	'transpose a matrix'
-	t = max(map(len, m))
-	n = len(m)
-	m2 = [["-"]]*n
-	for i in range(n):
-		m2[i] = m[i] + [""]*(t- len(m[i]))
-	return [[m2[j][i] for i in range(len(m2[0])) for j in range(n)][k*n:k*n+n] for k in range(len(m2[0]))]
-
-def genRandStr(prefix = "", length=8, chars=string.letters+string.digits):
-	from random import choice
-	_str = prefix[:]
-	for i in range(length):
-		_str += choice(chars)
-	return _str
-
-def generate_session():
-	import sha
-	return sha.new(str(time.time())).hexdigest()
-
-def cvt2Dict(x):
-	tmp = {}
-	for key in x.keys():
-		tmp[key] = x[key]
-	return tmp
-
-def dump_session(session_obj, filename):
-	"It seems mod python can only cPickle most basic data type"
-	import cPickle
-	session_file = open(filename, 'wb')
-	#try:
-	#	pass
-	#except:
-	#	pass
-	cPickle.dump(session_obj, session_file)
-	session_file.close()
-	
-def StringAsFloat(str):
-	'Converts string to float but catches any exception and returns None'
-	try:
-		return float(str)
-	except:
-		return None
-	
-def IntAsFloat(str):
-	'Converts string to Int but catches any exception and returns None'
-	try:
-		return int(str)
-	except:
-		return None
-		
-def FloatAsFloat(flt):
-	'Converts float to string but catches any exception and returns None'
-	try:
-		return float("%2.3f" % flt)
-	except:
-		return None
-
-def RemoveZero(flt):
-	'Converts string to float but catches any exception and returns None'
-	try:
-		if abs(flt) < 1e-6:
-			return None
-		else:
-			return flt
-	except:
-		return None
-
-
-def SciFloat(d):
-	'Converts string to float but catches any exception and returns None'
-
-	try:
-		if abs(d) <= 1.0e-4:	
-			return "%1.2e" % d
-		else:
-			return "%1.5f" % d
-	except:
-		return None
-
-###To be removed
-def FloatList2String(lst):
-	'Converts float list to string but catches any exception and returns None'
-	tt=''
-	try:
-		for item in lst:
-			if item == None:
-				tt += 'X '
-			else:
-				tt += '%f ' % item
-		return tt
-	except:
-		return ""
-
-def ListNotNull(lst):
-	'Determine if the elements in a list are all null'
-	for item in lst:
-		if item is not None:
-			return 1
-	return None
-	
-###To be removed
-def FileDataProcess(str):
-	'Remove the description text from the input file if theres any'
-	i=0
-	while i<len(str):
-		if str[i]<'\x7f' and str[i]>'\x20':
-			break
-		else:
-			i+=1
-	str=str[i:]
-	str=string.join(string.split(str,'\000'),'')
-	i=string.find(str,"*****")
-	if i>-1:
-		return str[i+5:]
-	else:
-		return str
-
-def rank(a,lst,offset=0):
-	"""Calculate the integer rank of a number in an array, can be used to calculate p-value"""
-	n = len(lst)
-	if n == 2:
-		if a <lst[0]:
-			return offset
-		elif a > lst[1]: 
-			return offset + 2 	
-		else:
-			return offset +1	
-	elif n == 1:
-		if a <lst[0]:
-			return offset
-		else:
-			return offset +1
-	elif n== 0:
-		return offset
-	else:
-		mid = n/2
-		if a < lst[mid]:
-			return rank(a,lst[:mid-1],offset)
-		else:
-			return rank(a,lst[mid:],offset+mid)
-
-def cmpScanResult(A,B):
-	try:
-		if A.LRS > B.LRS:
-			return 1
-		elif A.LRS == B.LRS:
-			return 0
-		else:
-			return -1	
-	except:
-		return 0
-
-	
-def cmpScanResult2(A,B):
-	try:
-		if A.LRS < B.LRS:
-			return 1
-		elif A.LRS == B.LRS:
-			return 0
-		else:
-			return -1	
-	except:
-		return 0
-
-def cmpOrder(A,B):
-	try:
-		if A[1] < B[1]:
-			return -1
-		elif A[1] == B[1]:
-			return 0
-		else:
-			return 1
-	except:
-		return 0
-
-def cmpOrder2(A,B):
-	try:
-		if A[-1] < B[-1]:
-			return -1
-		elif A[-1] == B[-1]:
-			return 0
-		else:
-			return 1	
-	except:
-		return 0
-
-
-
-
-def calRank(xVals, yVals, N): ###  Zach Sloan, February 4 2010
-	""" 
-	Returns a ranked set of X and Y values. These are used when generating
-	a Spearman scatterplot. Bear in mind that this sets values equal to each 
-	other as the same rank.
-	"""
-	XX = []
-	YY = []
-	X = [0]*len(xVals)
-	Y = [0]*len(yVals)
-	j = 0
-	
-	for i in range(len(xVals)):
-		
-		if xVals[i] != None and yVals[i] != None:
-			XX.append((j, xVals[i]))
-			YY.append((j, yVals[i]))
-			j = j + 1
-		
-	NN = len(XX)
-	
-	XX.sort(cmpOrder2)
-	YY.sort(cmpOrder2)
-
-	j = 1
-	rank = 0.0
-	
-	while j < NN:
-
-		if XX[j][1] != XX[j-1][1]:	
-			X[XX[j-1][0]] = j
-			j = j+1 
-		
-		else:
-			jt = j+1
-			ji = j
-			for jt in range(j+1, NN):
-				 if (XX[jt][1] != XX[j-1][1]):
-				 	break
-			rank = 0.5*(j+jt)
-			for ji in range(j-1, jt):
-				 X[XX[ji][0]] = rank
-			if (jt == NN-1):
-				if (XX[jt][1] == XX[j-1][1]):
-					X[XX[NN-1][0]] = rank
-			j = jt+1
-				 	
-	if j == NN:
-		if X[XX[NN-1][0]] == 0:
-			X[XX[NN-1][0]] = NN
-		
-	j = 1
-	rank = 0.0
-
-	while j < NN:
-
-		if YY[j][1] != YY[j-1][1]:	
-			Y[YY[j-1][0]] = j
-			j = j+1
-		else:
-			jt = j+1
-			ji = j
-			for jt in range(j+1, NN):
-				 if (YY[jt][1] != YY[j-1][1]):
-				 	break
-			rank = 0.5*(j+jt)
-			for ji in range(j-1, jt):
-				 Y[YY[ji][0]] = rank
-			if (jt == NN-1):
-				if (YY[jt][1] == YY[j-1][1]):
-					Y[YY[NN-1][0]] = rank
-			j = jt+1
-			
-	if j == NN:
-		if Y[YY[NN-1][0]] == 0:
-			Y[YY[NN-1][0]] = NN
-		
-	return (X,Y)	 
-
-def calCorrelationRank(xVals,yVals,N):
-	"""
-	Calculated Spearman Ranked Correlation. The algorithm works
-	by setting all tied ranks to the average of those ranks (for 
-	example, if ranks 5-10 all have the same value, each will be set
-	to rank 7.5).
-	"""
-	
-	XX = []
-	YY = []
-	j = 0
-	
-	for i in range(len(xVals)):
-		if xVals[i]!= None and yVals[i]!= None:
-			XX.append((j,xVals[i]))
-			YY.append((j,yVals[i]))
-			j = j+1
-			
-	NN = len(XX)
-	if NN <6:
-		return (0.0,NN)
-	XX.sort(cmpOrder2)
-	YY.sort(cmpOrder2)
-	X = [0]*NN
-	Y = [0]*NN
-	
-	j = 1
-	rank = 0.0
-	t = 0.0
-	sx = 0.0
-	
-	while j < NN:
-
-		if XX[j][1] != XX[j-1][1]:	
-			X[XX[j-1][0]] = j
-			j = j+1 
-		
-		else:
-			jt = j+1
-			ji = j
-			for jt in range(j+1, NN):
-				 if (XX[jt][1] != XX[j-1][1]):
-				 	break
-			rank = 0.5*(j+jt)
-			for ji in range(j-1, jt):
-				 X[XX[ji][0]] = rank
-			t = jt-j
-			sx = sx + (t*t*t-t)
-			if (jt == NN-1):
-				if (XX[jt][1] == XX[j-1][1]):
-					X[XX[NN-1][0]] = rank
-			j = jt+1
-				 	
-	if j == NN:
-		if X[XX[NN-1][0]] == 0:
-			X[XX[NN-1][0]] = NN
-		
-	j = 1
-	rank = 0.0
-	t = 0.0
-	sy = 0.0
-
-	while j < NN:
-
-		if YY[j][1] != YY[j-1][1]:	
-			Y[YY[j-1][0]] = j
-			j = j+1
-		else:
-			jt = j+1
-			ji = j
-			for jt in range(j+1, NN):
-				 if (YY[jt][1] != YY[j-1][1]):
-				 	break
-			rank = 0.5*(j+jt)
-			for ji in range(j-1, jt):
-				 Y[YY[ji][0]] = rank
-			t = jt - j
-			sy = sy + (t*t*t-t)
-			if (jt == NN-1):
-				if (YY[jt][1] == YY[j-1][1]):
-					Y[YY[NN-1][0]] = rank
-			j = jt+1
-			
-	if j == NN:
-		if Y[YY[NN-1][0]] == 0:
-			Y[YY[NN-1][0]] = NN
-				
-	D = 0.0
-	
-	for i in range(NN):
-		D += (X[i]-Y[i])*(X[i]-Y[i])
-		
-	fac = (1.0 -sx/(NN*NN*NN-NN))*(1.0-sy/(NN*NN*NN-NN))
-	
-	return ((1-(6.0/(NN*NN*NN-NN))*(D+(sx+sy)/12.0))/math.sqrt(fac),NN)
-	
-	
-def calCorrelationRankText(dbdata,userdata,N): ### dcrowell = David Crowell, July 2008
-        """Calculates correlation ranks with data formatted from the text file.
-        dbdata, userdata are lists of strings.  N is an int.  Returns a float.
-        Used by correlationPage"""
-        XX = []
-        YY = []
-        j = 0
-        for i in range(N):
-                if (dbdata[i]!= None and userdata[i]!=None) and (dbdata[i]!= 'None' and userdata[i]!='None'):
-                        XX.append((j,float(dbdata[i])))
-                        YY.append((j,float(userdata[i])))
-                        j += 1
-	NN = len(XX)
-	if NN <6:
-		return (0.0,NN)
-	XX.sort(cmpOrder2)
-	YY.sort(cmpOrder2)
-	X = [0]*NN
-	Y = [0]*NN
-	
-	j = 1
-	rank = 0.0
-	t = 0.0
-	sx = 0.0
-	
-	while j < NN:
-
-		if XX[j][1] != XX[j-1][1]:	
-			X[XX[j-1][0]] = j
-			j = j+1 
-		
-		else:
-			jt = j+1
-			ji = j
-			for jt in range(j+1, NN):
-				 if (XX[jt][1] != XX[j-1][1]):
-				 	break
-			rank = 0.5*(j+jt)
-			for ji in range(j-1, jt):
-				 X[XX[ji][0]] = rank
-			t = jt-j
-			sx = sx + (t*t*t-t)
-			if (jt == NN-1):
-				if (XX[jt][1] == XX[j-1][1]):
-					X[XX[NN-1][0]] = rank
-			j = jt+1
-				 	
-	if j == NN:
-		if X[XX[NN-1][0]] == 0:
-			X[XX[NN-1][0]] = NN
-		
-	j = 1
-	rank = 0.0
-	t = 0.0
-	sy = 0.0
-
-	while j < NN:
-
-		if YY[j][1] != YY[j-1][1]:	
-			Y[YY[j-1][0]] = j
-			j = j+1
-		else:
-			jt = j+1
-			ji = j
-			for jt in range(j+1, NN):
-				 if (YY[jt][1] != YY[j-1][1]):
-				 	break
-			rank = 0.5*(j+jt)
-			for ji in range(j-1, jt):
-				 Y[YY[ji][0]] = rank
-			t = jt - j
-			sy = sy + (t*t*t-t)
-			if (jt == NN-1):
-				if (YY[jt][1] == YY[j-1][1]):
-					Y[YY[NN-1][0]] = rank
-			j = jt+1
-			
-	if j == NN:
-		if Y[YY[NN-1][0]] == 0:
-			Y[YY[NN-1][0]] = NN
-				
-	D = 0.0
-	
-	for i in range(NN):
-		D += (X[i]-Y[i])*(X[i]-Y[i])
-		
-	fac = (1.0 -sx/(NN*NN*NN-NN))*(1.0-sy/(NN*NN*NN-NN))
-	
-	return ((1-(6.0/(NN*NN*NN-NN))*(D+(sx+sy)/12.0))/math.sqrt(fac),NN)
-
-
-
-def calCorrelation(dbdata,userdata,N):
-	X = []
-	Y = []
-	for i in range(N):
-		if dbdata[i]!= None and userdata[i]!= None:
-			X.append(dbdata[i])
-			Y.append(userdata[i])
-	NN = len(X)
-	if NN <6:
-		return (0.0,NN)
-	sx = reduce(lambda x,y:x+y,X,0.0)
-	sy = reduce(lambda x,y:x+y,Y,0.0)
-	meanx = sx/NN
-	meany = sy/NN
-	xyd = 0.0
-	sxd = 0.0
-	syd = 0.0
-	for i in range(NN):
-		xyd += (X[i] - meanx)*(Y[i]-meany)
-		sxd += (X[i] - meanx)*(X[i] - meanx)
-		syd += (Y[i] - meany)*(Y[i] - meany)
-	try:
-		corr = xyd/(sqrt(sxd)*sqrt(syd))
-	except:
-		corr = 0
-	return (corr,NN)
-
-def calCorrelationText(dbdata,userdata,N): ### dcrowell July 2008
-        """Calculates correlation coefficients with values formatted from text files. dbdata, userdata are lists of strings.  N is an int.  Returns a float
-        Used by correlationPage"""
-        X = []
-        Y = []
-        for i in range(N):
-                #if (dbdata[i]!= None and userdata[i]!= None) and (dbdata[i]!= 'None' and userdata[i]!= 'None'):
-                #               X.append(float(dbdata[i]))
-                #               Y.append(float(userdata[i]))
-                if dbdata[i] == None or dbdata[i] == 'None' or userdata[i] == None or userdata[i] == 'None':
-                        continue
-                else:
-                        X.append(float(dbdata[i]))
-                        Y.append(float(userdata[i]))
-        NN = len(X)
-        if NN <6:
-                return (0.0,NN)
-        sx = sum(X)
-        sy = sum(Y)
-        meanx = sx/float(NN)
-        meany = sy/float(NN)
-        xyd = 0.0
-        sxd = 0.0
-        syd = 0.0
-        for i in range(NN):
-                x1 = X[i]-meanx
-                y1 = Y[i]-meany
-                xyd += x1*y1
-                sxd += x1**2
-                syd += y1**2
-        try:
-                corr = xyd/(sqrt(sxd)*sqrt(syd))
-        except:
-                corr = 0
-        return (corr,NN)
-
-
-def readLineCSV(line): ### dcrowell July 2008
-        """Parses a CSV string of text and returns a list containing each element as a string.
-        Used by correlationPage"""
-        returnList = line.split('","')
-        returnList[-1]=returnList[-1][:-2]
-        returnList[0]=returnList[0][1:]
-        return returnList
-
-
-def cmpCorr(A,B):
-	try:
-		if abs(A[1]) < abs(B[1]):
-			return 1
-		elif abs(A[1]) == abs(B[1]):
-			return 0
-		else:
-			return -1	
-	except:
-		return 0
-
-def cmpLitCorr(A,B):
-	try:
-		if abs(A[3]) < abs(B[3]): return 1
-		elif abs(A[3]) == abs(B[3]):
-                     if abs(A[1]) < abs(B[1]): return 1
-		     elif abs(A[1]) == abs(B[1]): return 0
-                     else: return -1
-		else: return -1	
-	except:
-		return 0
-
-def cmpPValue(A,B):
-	try:
-		if A.corrPValue < B.corrPValue:
-			return -1
-		elif A.corrPValue == B.corrPValue:
-			if abs(A.corr) > abs(B.corr):
-				return -1
-			elif abs(A.corr) < abs(B.corr):
-				return 1
-			else:
-				return 0
-		else:
-			return 1	
-	except:
-		return 0
-
-def cmpEigenValue(A,B):
-	try:
-		if A[0] > B[0]:
-			return -1
-		elif A[0] == B[0]:
-			return 0
-		else:
-			return 1	
-	except:
-		return 0
-
-
-def cmpLRSFull(A,B):
-	try:
-		if A[0] < B[0]:
-			return -1
-		elif A[0] == B[0]:
-			return 0
-		else:
-			return 1	
-	except:
-		return 0
-
-def cmpLRSInteract(A,B):
-	try:
-		if A[1] < B[1]:
-			return -1
-		elif A[1] == B[1]:
-			return 0
-		else:
-			return 1	
-	except:
-		return 0
-
-	
-def cmpPos(A,B):
-	try:
-		try: 
-			AChr = int(A.chr)
-		except:
-			AChr = 20
-		try: 
-			BChr = int(B.chr)
-		except:
-			BChr = 20
-		if AChr > BChr:
-			return 1
-		elif AChr == BChr:
-			if A.mb > B.mb:
-				return 1
-			if A.mb == B.mb:
-				return 0
-			else:
-				return -1
-		else:
-			return -1	
-	except:
-		return 0
-	
-def cmpGenoPos(A,B):
-	try:
-		A1 = A.chr
-		B1 = B.chr
-		try:
-			A1 = int(A1)
-		except:
-			A1 = 25
-		try:
-			B1 = int(B1)
-		except:
-			B1 = 25
-		if A1 > B1:
-			return 1
-		elif A1 == B1:
-			if A.mb > B.mb:
-				return 1
-			if A.mb == B.mb:
-				return 0
-			else:
-				return -1
-		else:
-			return -1	
-	except:
-		return 0
-
-#XZhou: Must use "BINARY" to enable case sensitive comparison.
-def authUser(name,password,db, encrypt=None):
-	try:
-		if encrypt:
-			query = 'SELECT privilege, id,name,password, grpName FROM User WHERE name= BINARY \'%s\' and password= BINARY \'%s\'' % (name,password)
-		else:
-			query = 'SELECT privilege, id,name,password, grpName FROM User WHERE name= BINARY \'%s\' and password= BINARY SHA(\'%s\')' % (name,password)
-		db.execute(query)
-		records = db.fetchone()
-		if not records:
-			raise ValueError
-		return records#(privilege,id,name,password,grpName)
-	except:
-		return (None, None, None, None, None)
-
-
-def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users):
-    access_to_confidential_phenotype_trait = 0
-    if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']:
-        access_to_confidential_phenotype_trait = 1
-    else:
-        AuthorizedUsersList=map(string.strip, string.split(authorized_users, ','))
-        if AuthorizedUsersList.__contains__(userName):
-            access_to_confidential_phenotype_trait = 1
-    return access_to_confidential_phenotype_trait
-
-
-class VisualizeException(Exception):
-    def __init__(self, message):
-	        self.message = message	
-    def __str__(self):
-                return self.message
-
-# safeConvert : (string -> A) -> A -> A
-# to convert a string to type A, using the supplied default value
-# if the given conversion function doesn't work
-def safeConvert(f, value, default):
-    try:
-        return f(value)
-    except:
-        return default
-    
-# safeFloat : string -> float -> float
-# to convert a string to a float safely
-def safeFloat(value, default):
-    return safeConvert(float, value, default)
-    
-# safeInt: string -> int -> int
-# to convert a string to an int safely
-def safeInt(value, default):
-    return safeConvert(int, value, default)
-
-# safeString : string -> (arrayof string) -> string -> string
-# if a string is not in a list of strings to pick a default value
-# for that string
-def safeString(value, validChoices, default):
-    if value in validChoices:
-        return value
-    else:
-        return default
-
-# yesNoToInt: string -> int
-# map "yes" -> 1 and "no" -> 0
-def yesNoToInt(value):
-    if value == "yes":
-        return 1
-    elif value == "no":
-       	return 0
-    else:
-        return None
-
-# IntToYesNo: int -> string
-# map 1 -> "yes" and 0 -> "no"
-def intToYesNo(value):
-    if value == 1:
-        return "yes"
-    elif value == 0:
-        return "no"
-    else:
-        return None	
-       
-def formatField(name):
-	name = name.replace("_", " ")
-	name = name.title()
-        #name = name.replace("Mb Mm6", "Mb");  
-	return name.replace("Id", "ID")  
-
-#XZ, 03/27/2009: This function is very specific.
-#It is used by AJAX_table.py, correlationPage.py and dataPage.py
-
-
-def genTableObj(tblobj=None, file="", sortby = ("", ""), tableID = "sortable", addIndex = "1", hiddenColumns=[]):
-	header = tblobj['header']
-	body = tblobj['body']
-	field, order = sortby
-	
-	#ZAS 9/12/2011 - The hiddenColumns array needs to be converted into a string so they can be placed into the javascript of each up/down button
-	hiddenColumnsString = ",".join(hiddenColumns)
-
-	tbl = HT.TableLite(Class="collap b2", cellspacing=1, cellpadding=5)
-
-	hiddenColumnIdx = [] #indices of columns to hide
-	idx = -1
-	last_idx = 0 #ZS: This is the index of the last item in the regular table header (without any extra parameters). It is used to determine the index of each extra parameter.
-	for row in header:
-		hr = HT.TR()
-		for i, item in enumerate(row):
-			if (item.text == '') or (item.text not in hiddenColumns):
-				if item.sort and item.text:			
-					down = HT.Href("javascript:xmlhttpPost('%smain.py?FormID=AJAX_table', '%s', 'sort=%s&order=down&file=%s&tableID=%s&addIndex=%s&hiddenColumns=%s')" % (webqtlConfig.CGIDIR, tableID, item.text, file, tableID, addIndex, hiddenColumnsString),IMGDESC)		
-					up = HT.Href("javascript:xmlhttpPost('%smain.py?FormID=AJAX_table', '%s', 'sort=%s&order=up&file=%s&tableID=%s&addIndex=%s&hiddenColumns=%s')" % (webqtlConfig.CGIDIR, tableID, item.text, file, tableID, addIndex, hiddenColumnsString),IMGASC)
-					if item.text == field:	
-						idx = item.idx
-						last_idx = idx
-						if order == 'up':
-							up = IMGASCON
-						elif order == 'down':
-							down = IMGDESCON
-					item.html.append(HT.Div(up, down, style="float: bottom;"))
-				hr.append(item.html)
-			else:
-				hiddenColumnIdx.append(i)
-		tbl.append(hr)
-
-	for i, row in enumerate(body):
-		for j, item in enumerate(row):
-			if order == 'down':
-				if (item.val == '' or item.val == 'x' or item.val == 'None'):
-					item.val = 0 
-			if order == 'up':
-				if (item.val == '' or item.val == 'x' or item.val == 'None'):
-					item.val = 'zzzzz' 
-
-	if idx >= 0:
-		if order == 'down':
-			body.sort(lambda A, B: cmp(B[idx].val, A[idx].val), key=natsort_key)
-		elif order == 'up':
-			body.sort(lambda A, B: cmp(A[idx].val, B[idx].val), key=natsort_key)
-		else:
-			pass
-			
-	for i, row in enumerate(body):
-		hr = HT.TR(Id = row[0].text)
-		for j, item in enumerate(row):
-			if (j not in hiddenColumnIdx):
-				if j == 0:
-					if addIndex == "1":
-						item.html.contents = [i+1] + item.html.contents
-				hr.append(item.html)
-		tbl.append(hr)
-
-	return tbl	
-
-def natsort_key(string):
-    r = []
-    for c in string:
-        try:
-            c = int(c)
-            try: r[-1] = r[-1] * 10 + c
-            except: r.append(c)
-        except:
-            r.append(c)
-    return r
-