path: root/web/webqtl/showTrait/DataEditingPage.py

import string
import os
import cPickle
import pyXLWriter as xl

from htmlgen import HTMLgen2 as HT

from base import webqtlConfig
from utility import webqtlUtil, Plot
from base.webqtlTrait import webqtlTrait
from dbFunction import webqtlDatabaseFunction
from base.templatePage import templatePage
from basicStatistics import BasicStatisticsFunctions


#########################################
#      DataEditingPage
#########################################
class DataEditingPage(templatePage):

	def __init__(self, fd, thisTrait=None):

		templatePage.__init__(self, fd)

		self.dict['title'] = 'Data Editing' 
		TD_LR = HT.TD(valign="top",width="100%",bgcolor="#fafafa")
		
		if not self.openMysql():
			return
		if not fd.genotype:
			fd.readData(incf1=1)
	
		#############################
		# determine data editing page format
		#############################
		varianceDataPage = 0
		if fd.formID == 'varianceChoice':
			varianceDataPage = 1
		
		if varianceDataPage:
			fmID='dataEditing'
			nCols = 6
		else:
			if fd.enablevariance:
				fmID='pre_dataEditing'
				nCols = 4
			else:
				fmID='dataEditing'
				nCols = 4
		
		#############################
		##      titles, etc.
		#############################
			
		titleTop = HT.Div()
				
		title1 = HT.Paragraph("  Details and Links", style="border-radius: 5px;", Id="title1", Class="sectionheader")	
		title1Body = HT.Paragraph(Id="sectionbody1")
		
		if fd.enablevariance and not varianceDataPage:
			title2 = HT.Paragraph("  Submit Variance", style="border-radius: 5px;", Id="title2", Class="sectionheader")
		else:
			title2 = HT.Paragraph("  Basic Statistics", style="border-radius: 5px;", Id="title2", Class="sectionheader")
		title2Body = HT.Paragraph(Id="sectionbody2")		
		
		title3 = HT.Paragraph("  Calculate Correlations", style="border-radius: 5px;", Id="title3", Class="sectionheader")
		title3Body = HT.Paragraph(Id="sectionbody3")
		
		title4 = HT.Paragraph("  Mapping Tools", style="border-radius: 5px;", Id="title4", Class="sectionheader")
		title4Body = HT.Paragraph(Id="sectionbody4")
		
		title5 = HT.Paragraph("  Review and Edit Data", style="border-radius: 5px;", Id="title5", Class="sectionheader")
		title5Body = HT.Paragraph(Id="sectionbody5")

		#############################
		##     Hidden field
		#############################
		
		# Some fields, like method, are defaulted to None; otherwise in IE the field can't be changed using jquery
		hddn = {'FormID':fmID, 'RISet':fd.RISet, 'submitID':'', 'scale':'physic', 'additiveCheck':'ON', 'showSNP':'ON', 'showGenes':'ON', 'method':None,\
		'parentsf14regression':'OFF', 'stats_method':'1', 'chromosomes':'-1', 'topten':'', 'viewLegend':'ON', 'intervalAnalystCheck':'ON', 'valsHidden':'OFF',\
 		'database':'', 'criteria':None, 'MDPChoice':None, 'bootCheck':None, 'permCheck':None, 'applyVarianceSE':None, 'strainNames':'_', 'strainVals':'_',\
		'strainVars':'_', 'otherStrainNames':'_', 'otherStrainVals':'_', 'otherStrainVars':'_', 'extra_attributes':'_', 'other_extra_attributes':'_'}
		
		if fd.enablevariance:
			hddn['enablevariance']='ON'
		if fd.incparentsf1:
			hddn['incparentsf1']='ON'
		
		if thisTrait:
			hddn['fullname'] = str(thisTrait)
			try:
				hddn['normalPlotTitle'] = thisTrait.symbol
				hddn['normalPlotTitle'] += ": "
				hddn['normalPlotTitle'] += thisTrait.name
			except:
				hddn['normalPlotTitle'] = str(thisTrait.name)
			hddn['fromDataEditingPage'] = 1	
			if thisTrait.db and thisTrait.db.type and thisTrait.db.type == 'ProbeSet':
				hddn['trait_type'] = thisTrait.db.type
				if thisTrait.cellid:
					hddn['cellid'] = thisTrait.cellid		
				else:
					self.cursor.execute("SELECT h2 from ProbeSetXRef WHERE DataId = %d" % thisTrait.mysqlid)
					heritability = self.cursor.fetchone()
					hddn['heritability'] = heritability	
				
				hddn['attribute_names'] = ""			

		hddn['mappingMethodId'] = webqtlDatabaseFunction.getMappingMethod (cursor=self.cursor, groupName=fd.RISet)

		#############################
		##  Display Trait Information 
		#############################
		
		headSpan = self.dispHeader(fd,thisTrait) #Draw header
		
		titleTop.append(headSpan)
		
		if fd.identification:
			hddn['identification'] = fd.identification
			
		else:
			hddn['identification'] = "Un-named trait"  #If no identification, set identification to un-named
			
		self.dispTraitInformation(fd, title1Body, hddn, thisTrait) #Display trait information + function buttons	
		
		#############################
		##  Generate form and buttons
		#############################

		mainForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), 
		    name='dataInput', submit=HT.Input(type='hidden'))
		
		next=HT.Input(type='submit', name='submit',value='Next',Class="button")
		reset=HT.Input(type='Reset',name='',value=' Reset ',Class="button")
		correlationMenus = []
		
		if thisTrait == None:
			thisTrait = webqtlTrait(data=fd.allTraitData, db=None)			
		
		# Variance submit page only
		if fd.enablevariance and not varianceDataPage:
			title2Body.append("Click the next button to go to the variance submission form.", 
				HT.Center(next,reset))
		else:
			self.dispBasicStatistics(fd, title2Body, thisTrait)
			self.dispCorrelationTools(fd, title3Body, thisTrait)
			self.dispMappingTools(fd, title4Body, thisTrait)
		
		#############################
		##  Trait Value Table
		#############################

		self.dispTraitValues(fd, title5Body, varianceDataPage, nCols, mainForm, thisTrait)
		
		if fd.allstrainlist:
			hddn['allstrainlist'] = string.join(fd.allstrainlist, ' ') 
		for key in hddn.keys():
			mainForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
	
		if fd.enablevariance and not varianceDataPage:
			#pre dataediting page, need to submit variance
			mainForm.append(titleTop, title1,title1Body,title2,title2Body,title3,title3Body,title4,title4Body,title5,title5Body)
		else:
			mainForm.append(titleTop, title1,title1Body,title2,title2Body,title3,title3Body,title4,title4Body,title5,title5Body)
		TD_LR.append(HT.Paragraph(mainForm))
		self.dict['body'] = str(TD_LR)
	
	##########################################
	##  Function to display header
	##########################################	
	def dispHeader(self, fd, thisTrait):
		headSpan = HT.Div(style="font-size:14px;")

		#If trait, use trait name; otherwise, use identification value
		if thisTrait:
			if thisTrait.cellid:
				headSpan.append(HT.Strong('Trait Data and Analysis ', style='font-size:16px;'),' for Probe ID ', thisTrait.cellid)
			else:
				headSpan.append(HT.Strong('Trait Data and Analysis ', style='font-size:16px;'),' for Record ID ', thisTrait.name)
		else:
			if fd.identification:
				headSpan.append(HT.Strong('Trait ID ', style='font-size:16px;'),fd.identification)
			else:
				headSpan.append(HT.Strong('Un-named Trait', style='font-size:16px;'))
		
		return headSpan

	##########################################
	##  Function to display trait infos
	##########################################
	def dispTraitInformation(self, fd, title1Body, hddn, thisTrait):

		_Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
		
		tbl = HT.TableLite(cellpadding=2, Class="collap", style="margin-left:20px;", width="840", valign="top", id="target1")

		reset=HT.Input(type='Reset',name='',value=' Reset ',Class="button")
	
		#XZ, August 02, 2011: The display of icons is decided by the trait type (if trait exists), along with user log-in status. Note that the new submitted trait might not be trait object.	
		addSelectionButton = ""
		verifyButton = ""
		rnaseqButton = ""
		geneWikiButton = ""
		probeButton = ""
		similarButton = ""
		snpBrowserButton = ""
		updateButton = ""

		addSelectionText = ""
		verifyText = ""
		rnaseqText = ""
		geneWikiText = ""
		probeText = ""
		similarText = ""
		snpBrowserText = ""
		updateText = ""

		if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['user']:

			if thisTrait==None or thisTrait.db.type=='Temp':
				updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'addPublish');")
				updateButton_img = HT.Image("/images/edit_icon.jpg", name="addnew", alt="Add To Publish", title="Add To Publish", style="border:none;")
				updateButton.append(updateButton_img)
				updateText = "Edit"
			elif thisTrait.db.type != 'Temp':
				if thisTrait.db.type == 'Publish' and thisTrait.confidential: #XZ: confidential phenotype trait
					if webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users):
						updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'updateRecord');")
						updateButton_img = HT.Image("/images/edit_icon.jpg", name="update", alt="Edit", title="Edit", style="border:none;")
						updateButton.append(updateButton_img)
						updateText = "Edit"
				else:
					updateButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('dataInput')[0],'updateRecord');")
					updateButton_img = HT.Image("/images/edit_icon.jpg", name="update", alt="Edit", title="Edit", style="border:none;")
					updateButton.append(updateButton_img)
					updateText = "Edit"
			else:
				pass

		self.cursor.execute('SELECT Name FROM InbredSet WHERE Name="%s"' % fd.RISet)
		if thisTrait:
			addSelectionButton = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('%s')[0], 'addToSelection');" % (fd.RISet, 'dataInput'))
			addSelectionButton_img = HT.Image("/images/add_icon.jpg", name="addselect", alt="Add To Collection", title="Add To Collection", style="border:none;")
			addSelectionButton.append(addSelectionButton_img)
			addSelectionText = "Add"		
		elif self.cursor.fetchall():
			addSelectionButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('%s')[0], 'addRecord');" % ('dataInput'))
			addSelectionButton_img = HT.Image("/images/add_icon.jpg", name="", alt="Add To Collection", title="Add To Collection", style="border:none;")
			addSelectionButton.append(addSelectionButton_img)
			addSelectionText = "Add"				
		else:
			pass			
					

		# Microarray database information to display
		if thisTrait and thisTrait.db and thisTrait.db.type == 'ProbeSet': #before, this line was only reached if thisTrait != 0, but now we need to check
			try:
				hddn['GeneId'] = int(string.strip(thisTrait.geneid))
			except:
				pass
				
			Info2Disp = HT.Paragraph()

			#XZ: Gene Symbol
			if thisTrait.symbol:
				#XZ: Show SNP Browser only for mouse
				if _Species == 'mouse':
					self.cursor.execute("select geneSymbol from GeneList where geneSymbol = %s", thisTrait.symbol)
					geneName = self.cursor.fetchone()
					if geneName:
						snpurl = os.path.join(webqtlConfig.CGIDIR, "main.py?FormID=SnpBrowserResultPage&submitStatus=1&diffAlleles=True&customStrain=True") + "&geneName=%s" % geneName[0]	
					else:
						if thisTrait.chr and thisTrait.mb:
							snpurl = os.path.join(webqtlConfig.CGIDIR, "main.py?FormID=SnpBrowserResultPage&submitStatus=1&diffAlleles=True&customStrain=True") + \
								"&chr=%s&start=%2.6f&end=%2.6f" % (thisTrait.chr, thisTrait.mb-0.002, thisTrait.mb+0.002)
						else:
							snpurl = ""

					if snpurl:
						snpBrowserButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % snpurl)
						snpBrowserButton_img = HT.Image("/images/snp_icon.jpg", name="snpbrowser", alt=" View SNPs and Indels ", title=" View SNPs and Indels ", style="border:none;")
						snpBrowserButton.append(snpBrowserButton_img)	
						snpBrowserText = "SNPs"				

				#XZ: Show GeneWiki for all species
				geneWikiButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) + "?FormID=geneWiki&symbol=%s" % thisTrait.symbol))
				geneWikiButton_img = HT.Image("/images/genewiki_icon.jpg", name="genewiki", alt=" Write or review comments about this gene ", title=" Write or review comments about this gene ", style="border:none;")
				geneWikiButton.append(geneWikiButton_img)
				geneWikiText = 'GeneWiki'					

				#XZ: display similar traits in other selected datasets
				if thisTrait and thisTrait.db and thisTrait.db.type=="ProbeSet" and thisTrait.symbol:
					 if _Species in ("mouse", "rat", "human"):
						similarUrl = "%s?cmd=sch&gene=%s&alias=1&species=%s" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), thisTrait.symbol, _Species)
						similarButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % similarUrl)
						similarButton_img = HT.Image("/images/find_icon.jpg", name="similar", alt=" Find similar expression data ", title=" Find similar expression data ", style="border:none;")
						similarButton.append(similarButton_img)
						similarText = "Find"		
				else:
				     pass	
				tbl.append(HT.TR(
					HT.TD('Gene Symbol: ', Class="fwb fs13", valign="top", nowrap="on", width=90),
					HT.TD(width=10, valign="top"),
					HT.TD(HT.Span('%s' % thisTrait.symbol, valign="top", Class="fs13 fsI"), valign="top", width=740)
					))
			else:
				tbl.append(HT.TR(
					HT.TD('Gene Symbol: ', Class="fwb fs13", valign="top", nowrap="on"),
					HT.TD(width=10, valign="top"),
					HT.TD(HT.Span('Not available', Class="fs13 fsI"), valign="top")
					))

			#XZ: Gene Alias
			if thisTrait.alias:
				alias = string.replace(thisTrait.alias, ";", " ")
				alias = string.join(string.split(alias), ", ")
				tbl.append(HT.TR(
					HT.TD('Aliases: ', Class="fwb fs13", valign="top", nowrap="on"),
					HT.TD(width=10, valign="top"),
					HT.TD(HT.Span(alias, Class="fs13 fsI"), valign="top")
					))

			#XZ: Description
			if thisTrait.description:
				tSpan = HT.Span(thisTrait.description, Class="fs13")
				if thisTrait.probe_target_description: 
					tSpan.append('; ', thisTrait.probe_target_description)
			else:
				tSpan = HT.Span('Not available', Class="fs13")
			tbl.append(HT.TR(
				HT.TD('Description: ', Class="fwb fs13", valign="top", nowrap="on"),
				HT.TD(width=10, valign="top"),
				HT.TD(tSpan, valign="top")
				))

			#XZ: Location

			#XZ: deal with Chr and Mb
			if thisTrait.chr and thisTrait.mb:
				tSpan = HT.Span('Chr %s @ %s Mb'  % (thisTrait.chr,thisTrait.mb),Class="fs13")
			elif (thisTrait.chr):
			    	tSpan = HT.Span('Chr %s @ Unknown position' % (thisTrait.chr), Class="fs13")
			else:
				tSpan = HT.Span('Not available', Class="fs13")

			#XZ: deal with direction				
			if thisTrait.strand_probe == '+':
				tSpan.append(' on the plus strand ')
			elif thisTrait.strand_probe == '-':
				tSpan.append(' on the minus strand ')
			else:
				pass
			
			tbl.append(HT.TR(
				HT.TD('Location: ', Class="fwb fs13", valign="top", nowrap="on"),
				HT.TD(width=10, valign="top"),
				HT.TD(tSpan, valign="top")
				))			
			
			##display Verify Location button
			try:
				blatsequence = thisTrait.blatseq
				if not blatsequence:
					#XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead.
					self.cursor.execute("""SELECT Probe.Sequence, Probe.Name
                                                               FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef
                                                               WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
                                                                     ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
                                                                     ProbeSetFreeze.Name = '%s' AND
                                                                     ProbeSet.Name = '%s' AND
                                                                     Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (thisTrait.db.name, thisTrait.name) )
					seqs = self.cursor.fetchall()
					if not seqs:
						raise ValueError
					else:
						blatsequence = ''
						for seqt in seqs:
							if int(seqt[1][-1]) % 2 == 1:
								blatsequence += string.strip(seqt[0])	

				#--------Hongqiang add this part in order to not only blat ProbeSet, but also blat Probe
				blatsequence = '%3E'+thisTrait.name+'%0A'+blatsequence+'%0A'
				#XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead.
				self.cursor.execute("""SELECT Probe.Sequence, Probe.Name
                                                       FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef
                                                       WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
                                                             ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
                                                             ProbeSetFreeze.Name = '%s' AND
                                                             ProbeSet.Name = '%s' AND
                                                             Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (thisTrait.db.name, thisTrait.name) )

				seqs = self.cursor.fetchall()
				for seqt in seqs:
					if int(seqt[1][-1]) %2 == 1:
						blatsequence += '%3EProbe_'+string.strip(seqt[1])+'%0A'+string.strip(seqt[0])+'%0A'
				#--------
				#XZ, 07/16/2009: targetsequence is not used, so I comment out this block
				#targetsequence = thisTrait.targetseq
				#if targetsequence==None:   
				#	targetsequence = ""

				#XZ: Pay attention to the parameter of version (rn, mm, hg). They need to be changed if necessary.
				if _Species == "rat":
					UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', blatsequence)
					UTHSC_BLAT_URL = ""
				elif _Species == "mouse":
					UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', blatsequence)
					UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm9', blatsequence)
				elif _Species == "human":
					UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence)
					UTHSC_BLAT_URL = ""
				else:
					UCSC_BLAT_URL = ""
					UTHSC_BLAT_URL = ""
				
				if UCSC_BLAT_URL:
					verifyButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UCSC_BLAT_URL)
					verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", 
						title=" Check probe locations at UCSC ", style="border:none;")
					verifyButton.append(verifyButtonImg)
					verifyText = 'Verify'
				if UTHSC_BLAT_URL:	
					rnaseqButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UTHSC_BLAT_URL)
					rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", 
						title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;")
					rnaseqButton.append(rnaseqButtonImg)
					rnaseqText = 'RNA-seq'											
				tSpan.append(HT.BR())
			except:
				pass

			#Display probe information (if any)
			if thisTrait.db.name.find('Liver') >= 0 and thisTrait.db.name.find('F2') < 0:
				pass
			else:
				#query database for number of probes associated with trait; if count > 0, set probe tool button and text	
	                        self.cursor.execute("""SELECT count(*)
                                                           FROM Probe, ProbeSet
                                                           WHERE ProbeSet.Name = '%s' AND Probe.ProbeSetId = ProbeSet.Id""" % (thisTrait.name))

				probeResult = self.cursor.fetchone()
				if probeResult[0] > 0:
					probeurl = "%s?FormID=showProbeInfo&database=%s&ProbeSetID=%s&CellID=%s&RISet=%s&incparentsf1=ON" \
						% (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), thisTrait.db, thisTrait.name, thisTrait.cellid, fd.RISet)
					probeButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % probeurl)
					probeButton_img = HT.Image("/images/probe_icon.jpg", name="probe", alt=" Check sequence of probes ", title=" Check sequence of probes ", style="border:none;")
					probeButton.append(probeButton_img)
					probeText = "Probes"	

			tSpan = HT.Span(Class="fs13")			

			#XZ: deal with blat score and blat specificity.
			if thisTrait.probe_set_specificity or thisTrait.probe_set_blat_score:
				if thisTrait.probe_set_specificity:
					tSpan.append(HT.Href(url="/blatInfo.html", target="_blank", title="Values higher than 2 for the specificity are good", text="BLAT specificity", Class="non_bold"),": %.1f" % float(thisTrait.probe_set_specificity), "&nbsp;"*3)
				if thisTrait.probe_set_blat_score:
					tSpan.append("Score: %s" % int(thisTrait.probe_set_blat_score), "&nbsp;"*2)					

			onClick="openNewWin('/blatInfo.html')"

			tbl.append(HT.TR(
				HT.TD('Target Score: ', Class="fwb fs13", valign="top", nowrap="on"),
				HT.TD(width=10, valign="top"),
				HT.TD(tSpan, valign="top")
				))
			
			tSpan = HT.Span(Class="fs13")
			tSpan.append(str(_Species).capitalize(), ", ", fd.RISet)
			
			tbl.append(HT.TR(
				HT.TD('Species and Group: ', Class="fwb fs13", valign="top", nowrap="on"),
				HT.TD(width=10, valign="top"),
				HT.TD(tSpan, valign="top")
				))			
			
			if thisTrait.cellid:
				self.cursor.execute("""
						select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze 
							where 
						ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND
						ProbeSetFreeze.Id = %d""" % thisTrait.db.id)
				probeDBName = self.cursor.fetchone()[0]
				tbl.append(HT.TR(
					HT.TD('Database: ', Class="fs13 fwb", valign="top", nowrap="on"),
					HT.TD(width=10, valign="top"),
					HT.TD(HT.Span('%s' % probeDBName, Class="non_bold"), valign="top")
					))				
			else:
				tbl.append(HT.TR(
					HT.TD('Database: ', Class="fs13 fwb", valign="top", nowrap="on"),
					HT.TD(width=10, valign="top"),
					HT.TD(HT.Href(text=thisTrait.db.fullname, url = webqtlConfig.INFOPAGEHREF % thisTrait.db.name,
					target='_blank', Class="fs13 fwn non_bold"), valign="top")
					))					
			
			#XZ: ID links
			if thisTrait.genbankid or thisTrait.geneid or thisTrait.unigeneid or thisTrait.omim or thisTrait.homologeneid:
				idStyle = "background:#dddddd;padding:2"
				tSpan = HT.Span(Class="fs13")
				if thisTrait.geneid:
					gurl = HT.Href(text= 'Gene', target='_blank',\
						url=webqtlConfig.NCBI_LOCUSID % thisTrait.geneid, Class="fs14 fwn", title="Info from NCBI Entrez Gene")
					tSpan.append(HT.Span(gurl, style=idStyle), "&nbsp;"*2)
				if thisTrait.omim:
					gurl = HT.Href(text= 'OMIM', target='_blank', \
						url= webqtlConfig.OMIM_ID % thisTrait.omim,Class="fs14 fwn", title="Summary from On Mendelian Inheritance in Man")
					tSpan.append(HT.Span(gurl, style=idStyle), "&nbsp;"*2)
				if thisTrait.unigeneid:
					try:
						gurl = HT.Href(text= 'UniGene',target='_blank',\
							url= webqtlConfig.UNIGEN_ID % tuple(string.split(thisTrait.unigeneid,'.')[:2]),Class="fs14 fwn", title="UniGene ID")
						tSpan.append(HT.Span(gurl, style=idStyle), "&nbsp;"*2)
					except:
						pass
				if thisTrait.genbankid: 
					thisTrait.genbankid = '|'.join(thisTrait.genbankid.split('|')[0:10])
					if thisTrait.genbankid[-1]=='|':
						thisTrait.genbankid=thisTrait.genbankid[0:-1]
					gurl = HT.Href(text= 'GenBank', target='_blank', \
						url= webqtlConfig.GENBANK_ID % thisTrait.genbankid,Class="fs14 fwn", title="Find the original GenBank sequence used to design the probes")
					tSpan.append(HT.Span(gurl, style=idStyle), "&nbsp;"*2)
                                if thisTrait.homologeneid:
                                       	hurl = HT.Href(text= 'HomoloGene', target='_blank',\
                                               	url=webqtlConfig.HOMOLOGENE_ID % thisTrait.homologeneid, Class="fs14 fwn", title="Find similar genes in other species")
                                        tSpan.append(HT.Span(hurl, style=idStyle), "&nbsp;"*2)

				tbl.append(
					HT.TR(HT.TD(colspan=3,height=6)),
					HT.TR(
					HT.TD('Resource Links: ', Class="fwb fs13", valign="top", nowrap="on"),
					HT.TD(width=10, valign="top"),
					HT.TD(tSpan, valign="top")
					))			
			
			#XZ: Resource Links:			
			if thisTrait.symbol:
				linkStyle = "background:#dddddd;padding:2"
				tSpan = HT.Span(style="font-family:verdana,serif;font-size:13px")

				#XZ,12/26/2008: Gene symbol may contain single quotation mark.
				#For example, Affymetrix, mouse430v2, 1440338_at, the symbol is 2'-Pde (geneid 211948)
				#I debug this by using double quotation marks.
				if _Species == "rat":

					#XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more
					#symatlas_species = "Rattus norvegicus"

					#self.cursor.execute("SELECT kgID, chromosome,txStart,txEnd FROM GeneList_rn33 WHERE geneSymbol = '%s'" % thisTrait.symbol)
                                        self.cursor.execute('SELECT kgID, chromosome,txStart,txEnd FROM GeneList_rn33 WHERE geneSymbol = "%s"' % thisTrait.symbol)
					try:
						kgId, chr, txst, txen = self.cursor.fetchall()[0]
						if chr and txst and txen and kgId:
							txst = int(txst*1000000)
							txen = int(txen*1000000)
							tSpan.append(HT.Span(HT.Href(text= 'UCSC',target="mainFrame",\
								title= 'Info from UCSC Genome Browser', url = webqtlConfig.UCSC_REFSEQ % ('rn3',kgId,chr,txst,txen),Class="fs14 fwn"), style=linkStyle)
								, "&nbsp;"*2)
					except:
						pass
				if _Species == "mouse":

					#XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more
					#symatlas_species = "Mus musculus"

					#self.cursor.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = '%s'" % thisTrait.symbol)
                                        self.cursor.execute('SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = "%s"' % thisTrait.symbol)
					try:
						chr, txst, txen = self.cursor.fetchall()[0]
						if chr and txst and txen and thisTrait.refseq_transcriptid :
							txst = int(txst*1000000)
							txen = int(txen*1000000)
							tSpan.append(HT.Span(HT.Href(text= 'UCSC',target="mainFrame",\
								title= 'Info from UCSC Genome Browser', url = webqtlConfig.UCSC_REFSEQ % ('mm9',thisTrait.refseq_transcriptid,chr,txst,txen),
								Class="fs14 fwn"), style=linkStyle)
								, "&nbsp;"*2)
					except:
						pass

				#XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more
				#tSpan.append(HT.Span(HT.Href(text= 'SymAtlas',target="mainFrame",\
				#	url="http://symatlas.gnf.org/SymAtlas/bioentry?querytext=%s&query=14&species=%s&type=Expression" \
				#	% (thisTrait.symbol,symatlas_species),Class="fs14 fwn", \
				#	title="Expression across many tissues and cell types"), style=linkStyle), "&nbsp;"*2)
				if thisTrait.geneid and (_Species == "mouse" or _Species == "rat" or _Species == "human"):
					tSpan.append(HT.Span(HT.Href(text= 'BioGPS',target="mainFrame",\
						url="http://biogps.gnf.org/?org=%s#goto=genereport&id=%s" \
						% (_Species, thisTrait.geneid),Class="fs14 fwn", \
						title="Expression across many tissues and cell types"), style=linkStyle), "&nbsp;"*2)
				tSpan.append(HT.Span(HT.Href(text= 'STRING',target="mainFrame",\
					url="http://string.embl.de/newstring_cgi/show_link_summary.pl?identifier=%s" \
					% thisTrait.symbol,Class="fs14 fwn", \
					title="Protein interactions: known and inferred"), style=linkStyle), "&nbsp;"*2)
				if thisTrait.symbol:
					#ZS: The "species scientific" converts the plain English species names we're using to their scientific names, which are needed for PANTHER's input
					#We should probably use the scientific name along with the English name (if not instead of) elsewhere as well, given potential non-English speaking users
					if _Species == "mouse":
						species_scientific = "Mus%20musculus"
					elif _Species == "rat":
						species_scientific = "Rattus%20norvegicus"
					elif _Species == "human":
						species_scientific = "Homo%20sapiens"
					elif _Species == "drosophila":
						species_scientific = "Drosophila%20melanogaster"
					else:
						species_scientific = "all"

					species_scientific
					tSpan.append(HT.Span(HT.Href(text= 'PANTHER',target="mainFrame", \
						url="http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=%s&listType=1&fieldValue=%s"  \
						% (species_scientific, thisTrait.symbol),Class="fs14 fwn", \
					title="Gene and protein data resources from Celera-ABI"), style=linkStyle), "&nbsp;"*2)
				else:
					pass
				#tSpan.append(HT.Span(HT.Href(text= 'BIND',target="mainFrame",\
				#	url="http://bind.ca/?textquery=%s" \
				#	% thisTrait.symbol,Class="fs14 fwn", \
				#	title="Protein interactions"), style=linkStyle), "&nbsp;"*2)
				if thisTrait.geneid and (_Species == "mouse" or _Species == "rat" or _Species == "human"):
					tSpan.append(HT.Span(HT.Href(text= 'Gemma',target="mainFrame",\
						url="http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=%s" \
						% thisTrait.geneid, Class="fs14 fwn", \
						title="Meta-analysis of gene expression data"), style=linkStyle), "&nbsp;"*2)
				tSpan.append(HT.Span(HT.Href(text= 'SynDB',target="mainFrame",\
					url="http://lily.uthsc.edu:8080/20091027_GNInterfaces/20091027_redirectSynDB.jsp?query=%s" \
					% thisTrait.symbol, Class="fs14 fwn", \
					title="Brain synapse database"), style=linkStyle), "&nbsp;"*2)
				if _Species == "mouse":
                                                tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\
                                                        url="http://mouse.brain-map.org/brain/%s.html" \
                                                        % thisTrait.symbol, Class="fs14 fwn", \
                                                        title="Allen Brain Atlas"), style=linkStyle), "&nbsp;"*2)

				if thisTrait.geneid:
					#if _Species == "mouse":
					#	tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\
					#		url="http://www.brain-map.org/search.do?queryText=egeneid=%s" \
					#		% thisTrait.geneid, Class="fs14 fwn", \
					#		title="Allen Brain Atlas"), style=linkStyle), "&nbsp;"*2)
                                        if _Species == "human":
                                                tSpan.append(HT.Span(HT.Href(text= 'ABA',target="mainFrame",\
                                                        url="http://humancortex.alleninstitute.org/has/human/imageseries/search/1.html?searchSym=t&searchAlt=t&searchName=t&gene_term=&entrez_term=%s" \
                                                        % thisTrait.geneid, Class="fs14 fwn", \
                                                        title="Allen Brain Atlas"), style=linkStyle), "&nbsp;"*2)
				tbl.append(
					HT.TR(HT.TD(colspan=3,height=6)),
					HT.TR(
					HT.TD(' '),
					HT.TD(width=10, valign="top"),
					HT.TD(tSpan, valign="top")))                                                                     
                                                
			menuTable = HT.TableLite(cellpadding=2, Class="collap", width="620", id="target1")
			menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(similarButton, align="center"),HT.TD(verifyButton, align="center"),HT.TD(geneWikiButton, align="center"),HT.TD(snpBrowserButton, align="center"),HT.TD(rnaseqButton, align="center"),HT.TD(probeButton, align="center"),HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))     
			menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(similarText, align="center"),HT.TD(verifyText, align="center"),HT.TD(geneWikiText, align="center"),HT.TD(snpBrowserText, align="center"),HT.TD(rnaseqText, align="center"),HT.TD(probeText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))                         
				
			
			#for zhou mi's cliques, need to be removed
			#if self.database[:6]  == 'BXDMic' and self.ProbeSetID in cliqueID:
			#	Info2Disp.append(HT.Strong('Clique Search: '),HT.Href(text='Search',\
			#		url ="http://compbio1.utmem.edu/clique_go/results.php?pid=%s&pval_1=0&pval_2=0.001" \
			#		% self.ProbeSetID,target='_blank',Class="normalsize"),HT.BR())
			
			#linkTable.append(HT.TR(linkTD))
			#Info2Disp.append(linkTable)
			title1Body.append(tbl, HT.BR(), menuTable)
			
		elif thisTrait and thisTrait.db and thisTrait.db.type =='Publish': #Check if trait is phenotype

			if thisTrait.confidential:
				tbl.append(HT.TR(
						HT.TD('Pre-publication Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90),
						HT.TD(width=10, valign="top"),
						HT.TD(HT.Span(thisTrait.pre_publication_description, Class="fs13"), valign="top", width=740)
						))
				if webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users):
					tbl.append(HT.TR(
							HT.TD('Post-publication Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90),
							HT.TD(width=10, valign="top"),
							HT.TD(HT.Span(thisTrait.post_publication_description, Class="fs13"), valign="top", width=740)
                                                        ))
					tbl.append(HT.TR(
							HT.TD('Pre-publication Abbreviation: ', Class="fs13 fwb", valign="top", nowrap="on", width=90),
							HT.TD(width=10, valign="top"),
							HT.TD(HT.Span(thisTrait.pre_publication_abbreviation, Class="fs13"), valign="top", width=740)
							))
					tbl.append(HT.TR(
							HT.TD('Post-publication Abbreviation: ', Class="fs13 fwb", valign="top", nowrap="on", width=90),
							HT.TD(width=10, valign="top"),
							HT.TD(HT.Span(thisTrait.post_publication_abbreviation, Class="fs13"), valign="top", width=740)
							))
					tbl.append(HT.TR(
							HT.TD('Lab code: ', Class="fs13 fwb", valign="top", nowrap="on", width=90),
							HT.TD(width=10, valign="top"),
							HT.TD(HT.Span(thisTrait.lab_code, Class="fs13"), valign="top", width=740)
							))
				tbl.append(HT.TR(
						HT.TD('Owner: ', Class="fs13 fwb", valign="top", nowrap="on", width=90),
						HT.TD(width=10, valign="top"),
						HT.TD(HT.Span(thisTrait.owner, Class="fs13"), valign="top", width=740)
						))
			else:
				tbl.append(HT.TR(
						HT.TD('Phenotype: ', Class="fs13 fwb", valign="top", nowrap="on", width=90),
						HT.TD(width=10, valign="top"),
						HT.TD(HT.Span(thisTrait.post_publication_description, Class="fs13"), valign="top", width=740)
						))
			tbl.append(HT.TR(
					HT.TD('Authors: ', Class="fs13 fwb", 
						valign="top", nowrap="on", width=90),
					HT.TD(width=10, valign="top"),
					HT.TD(HT.Span(thisTrait.authors, Class="fs13"), 
						valign="top", width=740)
					))
			tbl.append(HT.TR(
					HT.TD('Title: ', Class="fs13 fwb", 
						valign="top", nowrap="on", width=90),
					HT.TD(width=10, valign="top"),
					HT.TD(HT.Span(thisTrait.title, Class="fs13"), 
						valign="top", width=740)
					))
			if thisTrait.journal:
				journal = thisTrait.journal
				if thisTrait.year:
					journal = thisTrait.journal + " (%s)" % thisTrait.year
					
				tbl.append(HT.TR(
					HT.TD('Journal: ', Class="fs13 fwb", 
						valign="top", nowrap="on", width=90),
					HT.TD(width=10, valign="top"),
					HT.TD(HT.Span(journal, Class="fs13"), 
						valign="top", width=740)
					))
			PubMedLink = ""
			if thisTrait.pubmed_id:
				PubMedLink = webqtlConfig.PUBMEDLINK_URL % thisTrait.pubmed_id
			if PubMedLink:
				tbl.append(HT.TR(
					HT.TD('Link: ', Class="fs13 fwb", 
						valign="top", nowrap="on", width=90),
					HT.TD(width=10, valign="top"),
					HT.TD(HT.Span(HT.Href(url=PubMedLink, text="PubMed",target='_blank',Class="fs14 fwn"),
						style = "background:#cddcff;padding:2"), valign="top", width=740)
					))

			menuTable = HT.TableLite(cellpadding=2, Class="collap", width="150", id="target1")
			menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))
			menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))

			title1Body.append(tbl, HT.BR(), menuTable)
			
		elif thisTrait and thisTrait.db and thisTrait.db.type == 'Geno': #Check if trait is genotype

			GenoInfo = HT.Paragraph()
			if thisTrait.chr and thisTrait.mb:
				location = ' Chr %s @ %s Mb' % (thisTrait.chr,thisTrait.mb)
			else:
				location = "not available"				
				
			if thisTrait.sequence and len(thisTrait.sequence) > 100:
				if _Species == "rat":
					UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', thisTrait.sequence)
					UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('rat', 'rn3', thisTrait.sequence)
				elif _Species == "mouse":
					UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', thisTrait.sequence)
					UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm9', thisTrait.sequence)
				elif _Species == "human":
					UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence)
					UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('human', 'hg19', thisTrait.sequence)
				else:
					UCSC_BLAT_URL = ""
					UTHSC_BLAT_URL = ""
				if UCSC_BLAT_URL:
					#verifyButton = HT.Href(url="#", onClick="openNewWin('%s')" % UCSC_BLAT_URL)
					verifyButton = HT.Href(url="#")
					verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;")
					verifyButton.append(verifyButtonImg)	
					verifyText = "Verify"
					rnaseqButton = HT.Href(url="#", onClick="openNewWin('%s')" % UTHSC_BLAT_URL)
					rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;")
					rnaseqButton.append(rnaseqButtonImg)			
					rnaseqText = "RNA-seq"								

			tbl.append(HT.TR(
					HT.TD('Location: ', Class="fs13 fwb", 
						valign="top", nowrap="on", width=90),
					HT.TD(width=10, valign="top"),
					HT.TD(HT.Span(location, Class="fs13"), valign="top", width=740)
					),
				HT.TR(
					HT.TD('SNP Search: ', Class="fs13 fwb", 
						valign="top", nowrap="on", width=90),
					HT.TD(width=10, valign="top"),
					HT.TD(HT.Href("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=snp&cmd=search&term=%s" % thisTrait.name, 'NCBI',Class="fs13"), 
						valign="top", width=740)
					))
			
    			menuTable = HT.TableLite(cellpadding=2, Class="collap", width="275", id="target1")
    			menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(verifyButton, align="center"),HT.TD(rnaseqButton, align="center"), HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))     
    			menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(verifyText, align="center"),HT.TD(rnaseqText, align="center"), HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))          					
					
			title1Body.append(tbl, HT.BR(), menuTable)
			
		elif (thisTrait == None or thisTrait.db.type == 'Temp'): #if temporary trait (user-submitted trait or PCA trait)	
			
			TempInfo = HT.Paragraph()
			if thisTrait != None:
				if thisTrait.description:
					tbl.append(HT.TR(HT.TD(HT.Strong('Description: '),' %s ' % thisTrait.description,HT.BR()), colspan=3, height=15))
			else:
				tbl.append(HT.TR(HT.TD(HT.Strong('Description: '),'not available',HT.BR(),HT.BR()), colspan=3, height=15))
			
			if (updateText == "Edit"):
				menuTable = HT.TableLite(cellpadding=2, Class="collap", width="150", id="target1")
			else:
				menuTable = HT.TableLite(cellpadding=2, Class="collap", width="80", id="target1")

			menuTable.append(HT.TR(HT.TD(addSelectionButton, align="right"),HT.TD(updateButton, align="right"), colspan=3, height=50, style="vertical-align:bottom;")	)	
			menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))					

			title1Body.append(tbl, HT.BR(), menuTable)
			
		else:
			pass	
	

	##########################################
	##  Function to display analysis tools
	##########################################
	def dispBasicStatistics(self, fd, title2Body, thisTrait):

		#XZ, June 22, 2011: The definition and usage of primary_strains, other_strains, specialStrains, all_strains are not clear and hard to understand. But since they are only used in this function for draw graph purpose, they will not hurt the business logic outside. As of June 21, 2011, this function seems work fine, so no hurry to clean up. These parameters and code in this function should be cleaned along with fd.f1list, fd.parlist, fd.strainlist later.
		stats_row = HT.TR()
		stats_cell = HT.TD()

		if fd.genotype.type == "riset":
			strainlist = fd.f1list + fd.strainlist
		else:
			strainlist = fd.f1list + fd.parlist + fd.strainlist	

		other_strains = [] #XZ: strain that is not of primary group
		specialStrains = [] #XZ: This might be replaced by other_strains / ZS: It is just other strains without parent/f1 strains.
		all_strains = []
		primary_strains = [] #XZ: strain of primary group, e.g., BXD, LXS

		MDP_menu = HT.Select(name='stats_mdp', Class='stats_mdp')		

		for strain in thisTrait.data.keys():
			strainName = strain.replace("_2nd_", "")
			if strain not in strainlist:
				if (thisTrait.data[strainName].val != None):
					if strain.find('F1') < 0:
						specialStrains.append(strain)	
					if (thisTrait.data[strainName].val != None) and (strain not in (fd.f1list + fd.parlist)):											
						other_strains.append(strain) #XZ: at current stage, other_strains doesn't include parent strains and F1 strains of primary group					
			else:		
				if (thisTrait.data[strainName].val != None) and (strain not in (fd.f1list + fd.parlist)):
					primary_strains.append(strain) #XZ: at current stage, the primary_strains is the same as fd.strainlist / ZS: I tried defining primary_strains as fd.strainlist instead, but in some cases it ended up including the parent strains (1436869_at BXD)

		if len(other_strains) > 3:
			other_strains.sort(key=webqtlUtil.natsort_key)
			primary_strains.sort(key=webqtlUtil.natsort_key)
			primary_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_strains #XZ: note that fd.f1list and fd.parlist are added.
			all_strains = primary_strains + other_strains			
			other_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + other_strains	#XZ: note that fd.f1list and fd.parlist are added.
			MDP_menu.append(('All Cases','0'))
			MDP_menu.append(('%s Only' % fd.RISet,'1'))
			MDP_menu.append(('Non-%s Only' % fd.RISet,'2'))
			stats_row.append("Include: ", MDP_menu, HT.BR(), HT.BR())
		else:				
			if (len(other_strains) > 0) and (len(primary_strains) + len(other_strains) > 3):
				MDP_menu.append(('All Cases','0'))
				MDP_menu.append(('%s Only' % fd.RISet,'1'))
				MDP_menu.append(('Non-%s Only' % fd.RISet,'2'))					
				stats_row.append("Include: ", MDP_menu, "&nbsp;"*3)
				all_strains = primary_strains
				all_strains.sort(key=webqtlUtil.natsort_key)	
				all_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + all_strains 			
				primary_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_strains	
			else:	
				all_strains = strainlist				
	
			other_strains.sort(key=webqtlUtil.natsort_key)
			all_strains = all_strains + other_strains
			pass	

		update_button = HT.Input(type='button',value=' Update Figures ', Class="button update") #This is used to reload the page and update the Basic Statistics figures with user-edited data
		stats_row.append(update_button, HT.BR(), HT.BR())
		
		if (len(other_strains)) > 0 and (len(primary_strains) + len(other_strains) > 4):
			#One set of vals for all, selected strain only, and non-selected only
			vals1 = []
			vals2 = []
			vals3 = []			
			
			#Using all strains/cases for values
			for i, strainNameOrig in enumerate(all_strains):
				strainName = strainNameOrig.replace("_2nd_", "")
				
				try:
					thisval = thisTrait.data[strainName].val
					thisvar = thisTrait.data[strainName].var
					thisValFull = [strainName,thisval,thisvar]
				except:
					continue
	
				vals1.append(thisValFull)
				
			#Using just the RISet strain
			for i, strainNameOrig in enumerate(primary_strains):
				strainName = strainNameOrig.replace("_2nd_", "")
				
				try:
					thisval = thisTrait.data[strainName].val
					thisvar = thisTrait.data[strainName].var
					thisValFull = [strainName,thisval,thisvar]
				except:
					continue
	
				vals2.append(thisValFull)
					
			#Using all non-RISet strains only
			for i, strainNameOrig in enumerate(other_strains):
				strainName = strainNameOrig.replace("_2nd_", "")
				
				try:
					thisval = thisTrait.data[strainName].val
					thisvar = thisTrait.data[strainName].var
					thisValFull = [strainName,thisval,thisvar]
				except:
					continue
	
				vals3.append(thisValFull)				
			
			vals_set = [vals1,vals2,vals3]
			
		else:
			vals = []
					
			#Using all strains/cases for values
			for i, strainNameOrig in enumerate(all_strains):
				strainName = strainNameOrig.replace("_2nd_", "")
				
				try:
					thisval = thisTrait.data[strainName].val
					thisvar = thisTrait.data[strainName].var
					thisValFull = [strainName,thisval,thisvar]
				except:
					continue
	
				vals.append(thisValFull)
				
			vals_set = [vals]
			
		stats_script = HT.Script(language="Javascript") #script needed for tabs			

		for i, vals in enumerate(vals_set):
			if i == 0 and len(vals) < 4:			
				stats_container = HT.Div(id="stats_tabs", style="padding:10px;", Class="ui-tabs") #Needed for tabs; notice the "stats_script_text" below referring to this element
				stats_container.append(HT.Div(HT.Italic("Fewer than 4 case data were entered. No statistical analysis has been attempted.")))				
				stats_script_text = """$(function() { $("#stats_tabs").tabs();});"""
				stats_cell.append(stats_container)
				break
			elif (i == 1 and len(primary_strains) < 4):	
				stats_container = HT.Div(id="stats_tabs%s" % i, Class="ui-tabs")
				stats_container.append(HT.Div(HT.Italic("Fewer than 4 " + fd.RISet + " case data were entered. No statistical analysis has been attempted.")))											
			elif (i == 2 and len(other_strains) < 4):
				stats_container = HT.Div(id="stats_tabs%s" % i, Class="ui-tabs")
				stats_container.append(HT.Div(HT.Italic("Fewer than 4 non-" + fd.RISet + " case data were entered. No statistical analysis has been attempted.")))			
				stats_script_text = """$(function() { $("#stats_tabs0").tabs(); $("#stats_tabs1").tabs(); $("#stats_tabs2").tabs();});"""	
			else:	
				stats_container = HT.Div(id="stats_tabs%s" % i, Class="ui-tabs")
				stats_script_text = """$(function() { $("#stats_tabs0").tabs(); $("#stats_tabs1").tabs(); $("#stats_tabs2").tabs();});"""
			if len(vals) > 4:
				stats_tab_list = [HT.Href(text="Basic Table", url="#statstabs-1", Class="stats_tab"),HT.Href(text="Probability Plot", url="#statstabs-5", Class="stats_tab"), 
								  HT.Href(text="Bar Graph (by name)", url="#statstabs-3", Class="stats_tab"), HT.Href(text="Bar Graph (by rank)", url="#statstabs-4", Class="stats_tab"), 
								  HT.Href(text="Box Plot", url="#statstabs-2", Class="stats_tab")]
				stats_tabs = HT.List(stats_tab_list)
				stats_container.append(stats_tabs)
		
				table_div = HT.Div(id="statstabs-1")
				table_container = HT.Paragraph()				
		
				statsTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
				
				if thisTrait.db:
					if thisTrait.cellid:
						statsTableCell = BasicStatisticsFunctions.basicStatsTable(vals=vals, trait_type=thisTrait.db.type, cellid=thisTrait.cellid)
					else:
						statsTableCell = BasicStatisticsFunctions.basicStatsTable(vals=vals, trait_type=thisTrait.db.type)
				else:
					  statsTableCell = BasicStatisticsFunctions.basicStatsTable(vals=vals)

				statsTable.append(HT.TR(HT.TD(statsTableCell)))
				
				table_container.append(statsTable)
				table_div.append(table_container)
				stats_container.append(table_div)
				
				normalplot_div = HT.Div(id="statstabs-5")
				normalplot_container = HT.Paragraph()
				normalplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")

				try:
					plotTitle = thisTrait.symbol
					plotTitle += ": "
					plotTitle += thisTrait.name
				except:
					plotTitle = str(thisTrait.name)

				normalplot_img = BasicStatisticsFunctions.plotNormalProbability(vals=vals, RISet=fd.RISet, title=plotTitle, specialStrains=specialStrains)
				normalplot.append(HT.TR(HT.TD(normalplot_img)))
				normalplot.append(HT.TR(HT.TD(HT.BR(),HT.BR(),"This plot evaluates whether data are \
				normally distributed. Different symbols represent different groups.",HT.BR(),HT.BR(),
				"More about ", HT.Href(url="http://en.wikipedia.org/wiki/Normal_probability_plot", 
						 target="_blank", text="Normal Probability Plots"), " and more about interpreting these plots from the ", HT.Href(url="/glossary.html#normal_probability", target="_blank", text="glossary"))))				
				normalplot_container.append(normalplot)
				normalplot_div.append(normalplot_container)
				stats_container.append(normalplot_div)	
				
				boxplot_div = HT.Div(id="statstabs-2")
				boxplot_container = HT.Paragraph()
				boxplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
				boxplot_img, boxplot_link = BasicStatisticsFunctions.plotBoxPlot(vals)
				boxplot.append(HT.TR(HT.TD(boxplot_img, HT.P(), boxplot_link, align="left")))		
				boxplot_container.append(boxplot)
				boxplot_div.append(boxplot_container)
				stats_container.append(boxplot_div)				
				
				
				barName_div = HT.Div(id="statstabs-3")
				barName_container = HT.Paragraph()
				barName = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
				barName_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="name")
				barName.append(HT.TR(HT.TD(barName_img)))		
				barName_container.append(barName)
				barName_div.append(barName_container)
				stats_container.append(barName_div)			
				
				barRank_div = HT.Div(id="statstabs-4")
				barRank_container = HT.Paragraph()
				barRank = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
				barRank_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="rank")
				barRank.append(HT.TR(HT.TD(barRank_img)))	
				barRank_container.append(barRank)
				barRank_div.append(barRank_container)
				stats_container.append(barRank_div)
				
			stats_cell.append(stats_container)
		
		stats_script.append(stats_script_text)	

		submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target2")
		stats_row.append(stats_cell)
		
		submitTable.append(stats_row)
		submitTable.append(stats_script)
		
		title2Body.append(submitTable)


	def dispCorrelationTools(self, fd, title3Body, thisTrait):
	
		_Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
	
		RISetgp = fd.RISet
		if RISetgp[:3] == 'BXD':
			RISetgp = 'BXD'
		
		if RISetgp:
			sample_correlation = HT.Input(type='button',name='sample_corr', value=' Compute ', Class="button sample_corr")
			lit_correlation = HT.Input(type='button',name='lit_corr', value=' Compute ', Class="button lit_corr")
			tissue_correlation = HT.Input(type='button',name='tiss_corr', value=' Compute ', Class="button tiss_corr")						
			methodText = HT.Span("Calculate:", Class="ffl fwb fs12") 

			databaseText = HT.Span("Database:", Class="ffl fwb fs12") 
			databaseMenu1 = HT.Select(name='database1')
			databaseMenu2 = HT.Select(name='database2')
			databaseMenu3 = HT.Select(name='database3')			
			
			nmenu = 0
			self.cursor.execute('SELECT PublishFreeze.FullName,PublishFreeze.Name FROM \
				PublishFreeze,InbredSet WHERE PublishFreeze.InbredSetId = InbredSet.Id \
				and InbredSet.Name = "%s" and PublishFreeze.public > %d' % \
				(RISetgp,webqtlConfig.PUBLICTHRESH))
			for item in self.cursor.fetchall():
				databaseMenu1.append(item)
				databaseMenu2.append(item)
				databaseMenu3.append(item)
				nmenu += 1
			self.cursor.execute('SELECT GenoFreeze.FullName,GenoFreeze.Name FROM GenoFreeze,\
				InbredSet WHERE GenoFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = \
				"%s" and GenoFreeze.public > %d' % (RISetgp,webqtlConfig.PUBLICTHRESH))
			for item in self.cursor.fetchall():
				databaseMenu1.append(item)
				databaseMenu2.append(item)
				databaseMenu3.append(item)
				nmenu += 1
			#03/09/2009: Xiaodong changed the SQL query to order by Name as requested by Rob.
			self.cursor.execute('SELECT Id, Name FROM Tissue order by Name')
			for item in self.cursor.fetchall():
				TId, TName = item
				databaseMenuSub = HT.Optgroup(label = '%s ------' % TName)
				self.cursor.execute('SELECT ProbeSetFreeze.FullName,ProbeSetFreeze.Name FROM ProbeSetFreeze, ProbeFreeze, \
				InbredSet WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = %d and \
				ProbeSetFreeze.public > %d and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name like "%s%%" \
				order by ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId '  % (TId,webqtlConfig.PUBLICTHRESH, RISetgp))
				for item2 in self.cursor.fetchall():
					databaseMenuSub.append(item2)
					nmenu += 1
				databaseMenu1.append(databaseMenuSub)
				databaseMenu2.append(databaseMenuSub)
				databaseMenu3.append(databaseMenuSub)
			if nmenu:
				if thisTrait and thisTrait.db != None:
					databaseMenu1.selected.append(thisTrait.db.fullname)
					databaseMenu2.selected.append(thisTrait.db.fullname)
					databaseMenu3.selected.append(thisTrait.db.fullname)
				
				criteriaText = HT.Span("Return:", Class="ffl fwb fs12") 

				criteriaMenu1 = HT.Select(name='criteria1', selected='500', onMouseOver="if (NS4 || IE4) activateEl('criterias', event);")
				criteriaMenu1.append(('top 100','100'))
				criteriaMenu1.append(('top 200','200'))
				criteriaMenu1.append(('top 500','500'))
				criteriaMenu1.append(('top 1000','1000'))
				criteriaMenu1.append(('top 2000','2000'))
				criteriaMenu1.append(('top 5000','5000'))
				criteriaMenu1.append(('top 10000','10000'))
				criteriaMenu1.append(('top 15000','15000'))
				criteriaMenu1.append(('top 20000','20000'))

				criteriaMenu2 = HT.Select(name='criteria2', selected='500', onMouseOver="if (NS4 || IE4) activateEl('criterias', event);")
				criteriaMenu2.append(('top 100','100'))
				criteriaMenu2.append(('top 200','200'))
				criteriaMenu2.append(('top 500','500'))
				criteriaMenu2.append(('top 1000','1000'))
				criteriaMenu2.append(('top 2000','2000'))
				criteriaMenu2.append(('top 5000','5000'))
				criteriaMenu2.append(('top 10000','10000'))
				criteriaMenu2.append(('top 15000','15000'))
				criteriaMenu2.append(('top 20000','20000'))

				criteriaMenu3 = HT.Select(name='criteria3', selected='500', onMouseOver="if (NS4 || IE4) activateEl('criterias', event);")
				criteriaMenu3.append(('top 100','100'))
				criteriaMenu3.append(('top 200','200'))
				criteriaMenu3.append(('top 500','500'))
				criteriaMenu3.append(('top 1000','1000'))
				criteriaMenu3.append(('top 2000','2000'))								
				criteriaMenu3.append(('top 5000','5000'))
				criteriaMenu3.append(('top 10000','10000'))
				criteriaMenu3.append(('top 15000','15000'))
				criteriaMenu3.append(('top 20000','20000'))


				self.MDPRow1 = HT.TR(Class='mdp1')
				self.MDPRow2 = HT.TR(Class='mdp2')
				self.MDPRow3 = HT.TR(Class='mdp3')
				
				correlationMenus1 = HT.TableLite( 
					HT.TR(HT.TD(databaseText), HT.TD(databaseMenu1, colspan="3")),
					HT.TR(HT.TD(criteriaText), HT.TD(criteriaMenu1)),
				    self.MDPRow1, cellspacing=0, width="619px", cellpadding=2)
				correlationMenus1.append(HT.Input(name='orderBy', value='2', type='hidden'))    # to replace the orderBy menu
				correlationMenus2 = HT.TableLite( 
					HT.TR(HT.TD(databaseText), HT.TD(databaseMenu2, colspan="3")),
					HT.TR(HT.TD(criteriaText), HT.TD(criteriaMenu2)),
				    self.MDPRow2, cellspacing=0, width="619px", cellpadding=2)
				correlationMenus2.append(HT.Input(name='orderBy', value='2', type='hidden'))
				correlationMenus3 = HT.TableLite( 
					HT.TR(HT.TD(databaseText), HT.TD(databaseMenu3, colspan="3")),
					HT.TR(HT.TD(criteriaText), HT.TD(criteriaMenu3)),
				    self.MDPRow3, cellspacing=0, width="619px", cellpadding=2)
				correlationMenus3.append(HT.Input(name='orderBy', value='2', type='hidden'))
				
			else:
				correlationMenus = ""
	
	
		corr_row = HT.TR()
		corr_container = HT.Div(id="corr_tabs", Class="ui-tabs")
		
		if (thisTrait.db != None and thisTrait.db.type =='ProbeSet'):
				corr_tab_list = [HT.Href(text='Sample r', url="#corrtabs-1"), HT.Href(text='Literature r',  url="#corrtabs-2"), HT.Href(text='Tissue r', url="#corrtabs-3")]
		else:
			corr_tab_list = [HT.Href(text='Sample r', url="#corrtabs-1")]
		
		corr_tabs = HT.List(corr_tab_list)
		corr_container.append(corr_tabs)
	
		if correlationMenus1 or correlationMenus2 or correlationMenus3:
			sample_div = HT.Div(id="corrtabs-1")
			sample_container = HT.Span()
			
			sample_type = HT.Input(type="radio", name="sample_method", value="1", checked="checked")
			sample_type2 = HT.Input(type="radio", name="sample_method", value="2")
			
			sampleTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
			sampleTD = HT.TD(correlationMenus1, HT.BR(),
						   "Pearson", sample_type, "&nbsp;"*3, "Spearman Rank", sample_type2, HT.BR(), HT.BR(),
						   sample_correlation, HT.BR(), HT.BR())
			
			sampleTD.append(HT.Span("The ",HT.Href(url="/correlationAnnotation.html#sample_r", target="_blank", text="Sample Correlation")," is computed between trait data and",
											" any ",HT.BR()," other traits in the sample database selected above. Use ", 
											HT.Href(url="/glossary.html#Correlations", target="_blank", text="Spearman Rank"),
											HT.BR(),"when the sample size is small (<20) or when there are influential \
											outliers.", HT.BR(),Class="fs12"))
			
			sampleTable.append(sampleTD)
			
			sample_container.append(sampleTable)
			sample_div.append(sample_container)
			corr_container.append(sample_div)
			
			literature_div = HT.Div(id="corrtabs-2")
			literature_container = HT.Span()			
			
			literatureTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
			literatureTD = HT.TD(correlationMenus2,HT.BR(),lit_correlation, HT.BR(), HT.BR())
			literatureTD.append(HT.Span("The ", HT.Href(url="/correlationAnnotation.html", target="_blank",text="Literature Correlation"), " (Lit r) between this gene and all other genes is computed",HT.BR(),
			                            "using the ", HT.Href(url="https://grits.eecs.utk.edu/sgo/sgo.html", target="_blank", text="Semantic Gene Organizer"),
			                            " and human, rat, and mouse data from PubMed. ", HT.BR(),"Values are ranked by Lit r, \
			                            but Sample r and Tissue r are also displayed.", HT.BR(), HT.BR(), 
			                            HT.Href(url="/glossary.html#Literature", target="_blank", text="More on using Lit r"), Class="fs12"))
			literatureTable.append(literatureTD)	
			
			literature_container.append(literatureTable)
			literature_div.append(literature_container)

			if thisTrait.db != None:
				if (thisTrait.db.type =='ProbeSet'):
					corr_container.append(literature_div)			
			
			tissue_div = HT.Div(id="corrtabs-3")
			tissue_container = HT.Span()			
			
			tissue_type = HT.Input(type="radio", name="tissue_method", value="4", checked="checked")
			tissue_type2 = HT.Input(type="radio", name="tissue_method", value="5")
			
			tissueTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")		
			tissueTD = HT.TD(correlationMenus3,HT.BR(),
						   "Pearson", tissue_type, "&nbsp;"*3, "Spearman Rank", tissue_type2, HT.BR(), HT.BR(),
						   tissue_correlation, HT.BR(), HT.BR())
			tissueTD.append(HT.Span("The ", HT.Href(url="/webqtl/main.py?FormID=tissueCorrelation", target="_blank", text="Tissue Correlation"), 
			" (Tissue r) estimates the similarity of expression of two genes",HT.BR()," or \
			transcripts across different cells, tissues, or organs (",HT.Href(url="/correlationAnnotation.html#tissue_r", target="_blank", text="glossary"),"). \
			Tissue correlations",HT.BR()," are generated by analyzing expression in multiple samples usually taken from \
			single cases.",HT.BR(),HT.Bold("Pearson")," and ",HT.Bold("Spearman Rank")," correlations have been computed for all pairs \
			of genes",HT.BR()," using data from mouse samples.", 
			HT.BR(), Class="fs12"))			   			
			tissueTable.append(tissueTD)
			
			tissue_container.append(tissueTable)
			tissue_div.append(tissue_container)
			if thisTrait.db != None:
				if (thisTrait.db.type =='ProbeSet'):
					corr_container.append(tissue_div)			
	
			corr_row.append(HT.TD(corr_container))
			
			corr_script = HT.Script(language="Javascript")
			corr_script_text = """$(function() { $("#corr_tabs").tabs(); });"""
			corr_script.append(corr_script_text)			
			
			submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target4")
			submitTable.append(corr_row)
			submitTable.append(corr_script)	
			
			title3Body.append(submitTable)


	def dispMappingTools(self, fd, title4Body, thisTrait):
		
		_Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
		
		RISetgp = fd.RISet
		if RISetgp[:3] == 'BXD':
			RISetgp = 'BXD'
			
		#check boxes - one for regular interval mapping, the other for composite
		permCheck1= HT.Input(type='checkbox', Class='checkbox', name='permCheck1',checked="on")
		bootCheck1= HT.Input(type='checkbox', Class='checkbox', name='bootCheck1',checked=0)	
		permCheck2= HT.Input(type='checkbox', Class='checkbox', name='permCheck2',checked="on")
		bootCheck2= HT.Input(type='checkbox', Class='checkbox', name='bootCheck2',checked=0)	
		optionbox1 = HT.Input(type='checkbox', Class='checkbox', name='parentsf14regression1',checked=0)
		optionbox2 = HT.Input(type='checkbox', Class='checkbox', name='parentsf14regression2',checked=0)						
		optionbox3 = HT.Input(type='checkbox', Class='checkbox', name='parentsf14regression3',checked=0)
		applyVariance1 = HT.Input(name='applyVarianceSE1',type='checkbox', Class='checkbox')
		applyVariance2 = HT.Input(name='applyVarianceSE2',type='checkbox', Class='checkbox')
		
		IntervalMappingButton=HT.Input(type='button' ,name='interval',value=' Compute ', Class="button")	
		CompositeMappingButton=HT.Input(type='button' ,name='composite',value=' Compute ', Class="button")
		MarkerRegressionButton=HT.Input(type='button',name='marker', value=' Compute ', Class="button")					
	
		chrText = HT.Span("Chromosome:", Class="ffl fwb fs12") 
	
		# updated by NL 5-28-2010 
		# Interval Mapping 
		chrMenu = HT.Select(name='chromosomes1')
		chrMenu.append(tuple(["All",-1]))
		for i in range(len(fd.genotype)):
			if  len(fd.genotype[i]) > 1:
				chrMenu.append(tuple([fd.genotype[i].name,i]))
		
		#Menu for Composite Interval Mapping		
		chrMenu2 = HT.Select(name='chromosomes2')
		chrMenu2.append(tuple(["All",-1]))
		for i in range(len(fd.genotype)):
			if  len(fd.genotype[i]) > 1:
				chrMenu2.append(tuple([fd.genotype[i].name,i]))		
		
		if fd.genotype.Mbmap:
			scaleText = HT.Span("Mapping Scale:", Class="ffl fwb fs12") 
			scaleMenu1 = HT.Select(name='scale1', onChange="checkUncheck(window.document.dataInput.scale1.value, window.document.dataInput.permCheck1, window.document.dataInput.bootCheck1)")
			scaleMenu1.append(("Megabase",'physic'))
			scaleMenu1.append(("Centimorgan",'morgan'))			
			scaleMenu2 = HT.Select(name='scale2', onChange="checkUncheck(window.document.dataInput.scale2.value, window.document.dataInput.permCheck2, window.document.dataInput.bootCheck2)")
			scaleMenu2.append(("Megabase",'physic'))
			scaleMenu2.append(("Centimorgan",'morgan'))				
		
		controlText = HT.Span("Control Locus:", Class="ffl fwb fs12")
		controlMenu = HT.Input(type="text", name="controlLocus", Class="controlLocus")
				
		if fd.genotype.Mbmap:			
			intMappingMenu = HT.TableLite( 
				HT.TR(HT.TD(chrText), HT.TD(chrMenu, colspan="3")),
				HT.TR(HT.TD(scaleText), HT.TD(scaleMenu1)),
			    cellspacing=0, width="263px", cellpadding=2)		
			compMappingMenu = HT.TableLite( 
				HT.TR(HT.TD(chrText), HT.TD(chrMenu2, colspan="3")),
				HT.TR(HT.TD(scaleText), HT.TD(scaleMenu2)),
				HT.TR(HT.TD(controlText), HT.TD(controlMenu)),
			    cellspacing=0, width="325px", cellpadding=2)
		else:
			intMappingMenu = HT.TableLite( 
				HT.TR(HT.TD(chrText), HT.TD(chrMenu, colspan="3")),
			    cellspacing=0, width="263px", cellpadding=2)		
			compMappingMenu = HT.TableLite( 
				HT.TR(HT.TD(chrText), HT.TD(chrMenu2, colspan="3")),
				HT.TR(HT.TD(controlText), HT.TD(controlMenu)),
			    cellspacing=0, width="325px", cellpadding=2)		
		
		directPlotButton = ""
		directPlotButton = HT.Input(type='button',name='', value=' Compute ',\
			onClick="dataEditingFunc(this.form,'directPlot');",Class="button")
		directPlotSortText = HT.Span(HT.Bold("Sort by: "), Class="ffl fwb fs12")
		directPlotSortMenu = HT.Select(name='graphSort')
		directPlotSortMenu.append(('LRS Full',0))
		directPlotSortMenu.append(('LRS Interact',1))
		directPlotPermuText = HT.Span("Permutation Test (n=500)", Class="ffl fs12")
		directPlotPermu = HT.Input(type='checkbox', Class='checkbox',name='directPermuCheckbox', checked="on")
		pairScanReturnText = HT.Span(HT.Bold("Return: "), Class="ffl fwb fs12")
		pairScanReturnMenu = HT.Select(name='pairScanReturn')
		pairScanReturnMenu.append(('top 50','50'))
		pairScanReturnMenu.append(('top 100','100'))
		pairScanReturnMenu.append(('top 200','200'))
		pairScanReturnMenu.append(('top 500','500'))		
	
		pairScanMenus = HT.TableLite(
			HT.TR(HT.TD(directPlotSortText), HT.TD(directPlotSortMenu)),
			HT.TR(HT.TD(pairScanReturnText), HT.TD(pairScanReturnMenu)),
			cellspacing=0, width="232px", cellpadding=2)		
		
		markerSuggestiveText = HT.Span(HT.Bold("Display LRS greater than:"), Class="ffl fwb fs12")
		markerSuggestive = HT.Input(name='suggestive', size=5, maxlength=8)	
		displayAllText = HT.Span(" Display all LRS ", Class="ffl fs12")
		displayAll = HT.Input(name='displayAllLRS', type="checkbox", Class='checkbox')	
		useParentsText = HT.Span(" Use Parents ", Class="ffl fs12")	
		useParents = optionbox2
		applyVarianceText = HT.Span(" Use Weighted ", Class="ffl fs12")
		
		markerMenu = HT.TableLite(
			HT.TR(HT.TD(markerSuggestiveText), HT.TD(markerSuggestive)),
			HT.TR(HT.TD(displayAll,displayAllText)),
			HT.TR(HT.TD(useParents,useParentsText)),
			HT.TR(HT.TD(applyVariance2,applyVarianceText)),
			cellspacing=0, width="263px", cellpadding=2)				
							
		
		mapping_row = HT.TR()
		mapping_container = HT.Div(id="mapping_tabs", Class="ui-tabs")
		
		mapping_tab_list = [HT.Href(text="Interval", url="#mappingtabs-1"), HT.Href(text="Marker Regression", url="#mappingtabs-2"), HT.Href(text="Composite", url="#mappingtabs-3"), HT.Href(text="Pair-Scan", url="#mappingtabs-4")]
		mapping_tabs = HT.List(mapping_tab_list)
		mapping_container.append(mapping_tabs)
		
		interval_div = HT.Div(id="mappingtabs-1")
		interval_container = HT.Span()
		
		intervalTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
		intTD = HT.TD(valign="top",NOWRAP='ON', Class="fs12 fwn")
		intTD.append(intMappingMenu,HT.BR())

		intTD.append(permCheck1,'Permutation Test (n=2000)',HT.BR(),
		             bootCheck1,'Bootstrap Test (n=2000)', HT.BR(), optionbox1, 'Use Parents', HT.BR(),
		             applyVariance1,'Use Weighted', HT.BR(), HT.BR(),IntervalMappingButton, HT.BR(), HT.BR())
		intervalTable.append(HT.TR(intTD), HT.TR(HT.TD(HT.Span(HT.Href(url='/glossary.html#intmap', target='_blank', text='Interval Mapping'),
			' computes linkage maps for the entire genome or single',HT.BR(),' chromosomes.',
			' The ',HT.Href(url='/glossary.html#permutation', target='_blank', text='Permutation Test'),' estimates suggestive and significant ',HT.BR(),' linkage scores. \
			The ',HT.Href(url='/glossary.html#bootstrap', target='_blank', text='Bootstrap Test'), ' estimates the precision of the QTL location.'
			,Class="fs12"), HT.BR(), valign="top")))
		
		interval_container.append(intervalTable)
		interval_div.append(interval_container)
		mapping_container.append(interval_div)

		# Marker Regression
		
		marker_div = HT.Div(id="mappingtabs-2")
		marker_container = HT.Span()
	
		markerTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")		
		markerTD = HT.TD(valign="top",NOWRAP='ON', Class="fs12 fwn")
		markerTD.append(markerMenu,HT.BR())
		
		markerTD.append(MarkerRegressionButton,HT.BR(),HT.BR())
		
		markerTable.append(HT.TR(markerTD),HT.TR(HT.TD(HT.Span(HT.Href(url='/glossary.html#',target='_blank',text='Marker regression'),
			' computes and displays LRS values for individual markers.',HT.BR(),
			'This function also lists additive effects (phenotype units per allele) and', HT.BR(),
			'dominance deviations for some datasets.', HT.BR(),Class="fs12"), HT.BR(), valign="top")))
		
		marker_container.append(markerTable)
		marker_div.append(marker_container)
		mapping_container.append(marker_div)			
	
		# Composite interval mapping		
		composite_div = HT.Div(id="mappingtabs-3")
		composite_container = HT.Span()
		
		compositeTable = HT.TableLite(cellspacing=0, cellpadding=3, width="100%")
		compTD = HT.TD(valign="top",NOWRAP='ON', Class="fs12 fwn")
		compTD.append(compMappingMenu,HT.BR())
		
		compTD.append(permCheck2, 'Permutation Test (n=2000)',HT.BR(),
		             bootCheck2,'Bootstrap Test (n=2000)', HT.BR(), 
		             optionbox3, 'Use Parents', HT.BR(), HT.BR(), CompositeMappingButton, HT.BR(), HT.BR())
		compositeTable.append(HT.TR(compTD), HT.TR(HT.TD(HT.Span(HT.Href(url='/glossary.html#Composite',target='_blank',text='Composite Interval Mapping'),
			" allows you to control for a single marker as",HT.BR()," a cofactor. ",
			"To find a control marker, run the ",HT.Bold("Marker Regression")," function."), 
			HT.BR(), valign="top")))
		
		composite_container.append(compositeTable)
		composite_div.append(composite_container)
		mapping_container.append(composite_div)		
			
		# Pair Scan
		
		pairscan_div = HT.Div(id="mappingtabs-4")
		pairscan_container = HT.Span()
		
		pairScanTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
		pairScanTD = HT.TD(NOWRAP='ON', Class="fs12 fwn")
		pairScanTD.append(pairScanMenus,HT.BR())
		pairScanTD.append(directPlotPermu, directPlotPermuText, HT.BR(), HT.BR(),
						  directPlotButton,HT.BR(),HT.BR())	
		pairScanTable.append(HT.TR(pairScanTD), HT.TR(HT.TD(HT.Span(HT.Href(url='/glossary.html#Pair_Scan', target="_blank", text='Pair-Scan'),
			' searches for pairs of chromosomal regions that are',HT.BR(),
			'involved in two-locus epistatic interactions.'), HT.BR(), valign="top")))
		
		pairscan_container.append(pairScanTable)
		pairscan_div.append(pairscan_container)
		mapping_container.append(pairscan_div)
		
		mapping_row.append(HT.TD(mapping_container))
	
		# Treat Interval Mapping and Marker Regression and Pair Scan as a group for displaying
		#disable Interval Mapping and Marker Regression and Pair Scan for human and the dataset doesn't have genotype file		
		mappingMethodId = webqtlDatabaseFunction.getMappingMethod(cursor=self.cursor, groupName=RISetgp)	
		
		mapping_script = HT.Script(language="Javascript")
		mapping_script_text = """$(function() { $("#mapping_tabs").tabs(); });"""
		mapping_script.append(mapping_script_text)
		
		submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target2")
		
		if mappingMethodId != None:
			if int(mappingMethodId) == 1:
				submitTable.append(mapping_row)
				submitTable.append(mapping_script)
			elif int(mappingMethodId) == 4:
				# NL; 09-26-2011 testing for Human Genome Association function
				mapping_row=HT.TR()
				mapping_container = HT.Div(id="mapping_tabs", Class="ui-tabs")
				
				mapping_tab_list = [HT.Href(text="Genome Association", url="#mappingtabs-1")]
				mapping_tabs = HT.List(mapping_tab_list)
				mapping_container.append(mapping_tabs)
				
				# Genome Association
				markerSuggestiveText = HT.Span(HT.Bold("P Value:"), Class="ffl fwb fs12")
					
				markerSuggestive = HT.Input(name='pValue', value='0.001', size=10, maxlength=20,onClick="this.value='';",onBlur="if(this.value==''){this.value='0.001'};")					
				markerMenu = HT.TableLite(HT.TR(HT.TD(markerSuggestiveText), HT.TD(markerSuggestive),HT.TD(HT.Italic('&nbsp;&nbsp;&nbsp;(e.g. 0.001 or 1e-3 or 1E-3 or 3)'))),cellspacing=0, width="400px", cellpadding=2)
				MarkerRegressionButton=HT.Input(type='button',name='computePlink', value='&nbsp;&nbsp;Compute Using PLINK&nbsp;&nbsp;', onClick= "validatePvalue(this.form);", Class="button")

				marker_div = HT.Div(id="mappingtabs-1")
				marker_container = HT.Span()
				markerTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")		
				markerTD = HT.TD(valign="top",NOWRAP='ON', Class="fs12 fwn")
				markerTD.append(markerMenu,HT.BR())
				markerTD.append(MarkerRegressionButton,HT.BR(),HT.BR())
				markerTable.append(HT.TR(markerTD))
				
				marker_container.append(markerTable)
				marker_div.append(marker_container)
				
				mapping_container.append(marker_div)				
				mapping_row.append(HT.TD(mapping_container))
				submitTable.append(mapping_row)
				submitTable.append(mapping_script)
			else:
				submitTable.append(HT.TR(HT.TD(HT.Div(HT.Italic("mappingMethodId %s has not been implemented for this dataset yet." % mappingMethodId), id="mapping_tabs", Class="ui-tabs"))))
				submitTable.append(mapping_script)

		else:
			submitTable.append(HT.TR(HT.TD(HT.Div(HT.Italic("Mapping options are disabled for data not matched with genotypes."), id="mapping_tabs", Class="ui-tabs"))))
			submitTable.append(mapping_script)
			
		title4Body.append(submitTable)	

		
	def natural_sort(strain_list):
		
	    sorted = []
	    for strain in strain_list:
	        try:
	            strain = int(strain)
	            try: sorted[-1] = sorted[-1] * 10 + strain
	            except: sorted.append(strain)
	        except:
	            sorted.append(strain)
	    return sorted		
		
	##########################################
	##  Function to display trait tables
	##########################################
	def dispTraitValues(self, fd , title5Body, varianceDataPage, nCols, mainForm, thisTrait):
		traitTableOptions = HT.Div(style="border: 3px solid #EEEEEE; -moz-border-radius: 10px; -webkit-border-radius: 10px; width: 625px; padding: 5px 5px 10px 8px; font-size: 12px; background: #DDDDDD;")
		resetButton = HT.Input(type='button',name='resetButton',value=' Reset ',Class="button")
		blockSamplesField = HT.Input(type="text",style="background-color:white;border: 1px solid black;font-size: 14px;", name="removeField")
		blockSamplesButton = HT.Input(type='button',value=' Block ', name='blockSamples', Class="button")
		showHideNoValue = HT.Input(type='button', name='showHideNoValue', value=' Hide No Value ',Class='button')
		blockMenuSpan = HT.Span(Id="blockMenuSpan")
		blockMenu = HT.Select(name='block_method')	
		
		if fd.genotype.type == "riset":
			allstrainlist_neworder = fd.f1list + fd.strainlist
		else:
			allstrainlist_neworder = fd.f1list + fd.parlist + fd.strainlist		

		attribute_ids = []
		attribute_names = []
		try:
			#ZS: Id values for this trait's extra attributes; used to create "Exclude" dropdown and query for attribute values and create
			self.cursor.execute("""SELECT CaseAttribute.Id, CaseAttribute.Name
                                			FROM CaseAttribute, CaseAttributeXRef
                                          	WHERE CaseAttributeXRef.ProbeSetFreezeId = '%s' AND
                                          		CaseAttribute.Id = CaseAttributeXRef.CaseAttributeId
                                                 	group by CaseAttributeXRef.CaseAttributeId""" % (str(thisTrait.db.id)))

			exclude_menu = HT.Select(name="exclude_menu")
			dropdown_menus = [] #ZS: list of dropdown menus with the distinct values of each attribute (contained in DIVs so the style parameter can be edited and they can be hidden) 

			for attribute in self.cursor.fetchall():
				attribute_ids.append(attribute[0])
				attribute_names.append(attribute[1])
			for this_attr_name in attribute_names:
				exclude_menu.append((this_attr_name.capitalize(), this_attr_name))
				self.cursor.execute("""SELECT DISTINCT CaseAttributeXRef.Value
								FROM CaseAttribute, CaseAttributeXRef
								WHERE CaseAttribute.Name = '%s' AND
									CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id""" % (this_attr_name))
				try:
					distinct_values = self.cursor.fetchall()
					attr_value_menu_div = HT.Div(style="display:none;", Class="attribute_values") #container used to show/hide dropdown menus
					attr_value_menu = HT.Select(name=this_attr_name)
                    			attr_value_menu.append(("None", "show_all"))
					for value in distinct_values:
						attr_value_menu.append((str(value[0]), value[0]))
					attr_value_menu_div.append(attr_value_menu)
					dropdown_menus.append(attr_value_menu_div)
				except:
					pass
		except:
			pass

		other_strains = []
		for strain in thisTrait.data.keys():
			if strain not in allstrainlist_neworder:
				other_strains.append(strain)
		
		if other_strains:
			blockMenu.append(('%s Only' % fd.RISet,'1'))
			blockMenu.append(('Non-%s Only' % fd.RISet,'0'))
			blockMenuSpan.append(blockMenu)
		else:
			pass		
		
		showHideOutliers = HT.Input(type='button', name='showHideOutliers', value=' Hide Outliers ', Class='button')
		showHideMenuOptions = HT.Span(Id="showHideOptions", style="line-height:225%;")
		if other_strains:
			showHideMenuOptions.append(HT.Bold("&nbsp;&nbsp;Block samples by index:&nbsp;&nbsp;&nbsp;&nbsp;"), blockSamplesField, "&nbsp;&nbsp;&nbsp;", blockMenuSpan, "&nbsp;&nbsp;&nbsp;", blockSamplesButton, HT.BR())
		else:
			showHideMenuOptions.append(HT.Bold("&nbsp;&nbsp;Block samples by index:&nbsp;&nbsp;&nbsp;&nbsp;"), blockSamplesField, "&nbsp;&nbsp;&nbsp;", blockSamplesButton, HT.BR())

		exportButton = HT.Input(type='button', name='export', value=' Export ', Class='button')
		if len(attribute_names) > 0:
			excludeButton = HT.Input(type='button', name='excludeGroup', value=' Block ', Class='button')
			showHideMenuOptions.append(HT.Bold("&nbsp;&nbsp;Block samples by group:"), "&nbsp;"*5, exclude_menu, "&nbsp;"*5)
			for menu in dropdown_menus:
				showHideMenuOptions.append(menu)
			showHideMenuOptions.append("&nbsp;"*5, excludeButton, HT.BR())
		showHideMenuOptions.append(HT.Bold("&nbsp;&nbsp;Options:"), "&nbsp;"*5, showHideNoValue, "&nbsp;"*5, showHideOutliers, "&nbsp;"*5, resetButton, "&nbsp;"*5, exportButton)
		
		traitTableOptions.append(showHideMenuOptions,HT.BR(),HT.BR())		
		traitTableOptions.append(HT.Span("&nbsp;&nbsp;Outliers highlighted in ", HT.Bold("&nbsp;yellow&nbsp;", style="background-color:yellow;"), " can be hidden using the ", 
								    HT.Strong(" Hide Outliers "), " button,",HT.BR(),"&nbsp;&nbsp;and samples with no value (x) can be hidden by clicking ", 
								    HT.Strong(" Hide No Value "), "."), HT.BR())

		
		dispintro = HT.Paragraph("Edit or delete values in the Trait Data boxes, and use the ", HT.Strong("Reset"), " option as needed.",Class="fs12", style="margin-left:20px;")
		
		table = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target5") #Everything needs to be inside this table object in order for the toggle to work
		container = HT.Div() #This will contain everything and be put into a cell of the table defined above

		container.append(dispintro, traitTableOptions, HT.BR())

		primary_table = HT.TableLite(cellspacing=0, cellpadding=0, Id="sortable1", Class="tablesorter")
		primary_header = self.getTableHeader(fd=fd, thisTrait=thisTrait, nCols=nCols, attribute_names=attribute_names) #Generate header for primary table object
			
		other_strainsExist = False
		for strain in thisTrait.data.keys():
			if strain not in allstrainlist_neworder:
				other_strainsExist = True
				break
				
		primary_body = self.addTrait2Table(fd=fd, varianceDataPage=varianceDataPage, strainlist=allstrainlist_neworder, mainForm=mainForm, thisTrait=thisTrait, other_strainsExist=other_strainsExist, attribute_ids=attribute_ids, attribute_names=attribute_names, strains='primary')		

		primary_table.append(primary_header)
		for i in range(len(primary_body)):
			primary_table.append(primary_body[i])

		other_strains = []
		for strain in thisTrait.data.keys():
			if strain not in allstrainlist_neworder:
				allstrainlist_neworder.append(strain)
				other_strains.append(strain)
		
		if other_strains:
			other_table = HT.TableLite(cellspacing=0, cellpadding=0, Id="sortable2", Class="tablesorter") #Table object with other (for example, non-BXD / MDP) traits
			other_header = self.getTableHeader(fd=fd, thisTrait=thisTrait, nCols=nCols, attribute_names=attribute_names) #Generate header for other table object; same function is used as the one used for the primary table, since the header is the same
			other_strains.sort() #Sort other strains
			other_strains = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + other_strains #Append F1 and parent strains to the beginning of the sorted list of other strains

			MDPText = HT.Span("Samples:", Class="ffl fwb fs12") 
			MDPMenu1 = HT.Select(name='MDPChoice1')
			MDPMenu2 = HT.Select(name='MDPChoice2')
			MDPMenu3 = HT.Select(name='MDPChoice3')
			MDPMenu1.append(('%s Only' % fd.RISet,'1'))
			MDPMenu2.append(('%s Only' % fd.RISet,'1'))
			MDPMenu3.append(('%s Only' % fd.RISet,'1'))
			MDPMenu1.append(('Non-%s Only' % fd.RISet,'2'))
			MDPMenu2.append(('Non-%s Only' % fd.RISet,'2'))
			MDPMenu3.append(('Non-%s Only' % fd.RISet,'2'))
			MDPMenu1.append(('All Cases','0'))
			MDPMenu2.append(('All Cases','0'))
			MDPMenu3.append(('All Cases','0'))
			self.MDPRow1.append(HT.TD(MDPText),HT.TD(MDPMenu1))
			self.MDPRow2.append(HT.TD(MDPText),HT.TD(MDPMenu2))
			self.MDPRow3.append(HT.TD(MDPText),HT.TD(MDPMenu3))

			other_body = self.addTrait2Table(fd=fd, varianceDataPage=varianceDataPage, strainlist=other_strains, mainForm=mainForm, thisTrait=thisTrait, attribute_ids=attribute_ids, attribute_names=attribute_names, strains='other')
			
			other_table.append(other_header)
			for i in range(len(other_body)):
				other_table.append(other_body[i])
		else:
			pass

		if other_strains or (fd.f1list and thisTrait.data.has_key(fd.f1list[0])) \
			or (fd.f1list and thisTrait.data.has_key(fd.f1list[1])):
			fd.allstrainlist = allstrainlist_neworder
		
		if nCols == 6 and fd.varianceDispName != 'Variance':
			mainForm.append(HT.Input(name='isSE', value="yes", type='hidden'))

		primary_div = HT.Div(primary_table, Id="primary") #Container for table with primary (for example, BXD) strain values
		container.append(primary_div)

		if other_strains:
			other_div = HT.Div(other_table, Id="other") #Container for table with other (for example, Non-BXD/MDP) strain values
			container.append(HT.Div('&nbsp;', height=30))
			container.append(other_div)
		
		table.append(HT.TR(HT.TD(container)))
		title5Body.append(table)

	def addTrait2Table(self, fd, varianceDataPage, strainlist, mainForm, thisTrait, other_strainsExist=None, attribute_ids=[], attribute_names=[], strains='primary'):
		#XZ, Aug 23, 2010: I commented the code related to the display of animal case
		#strainInfo = thisTrait.has_key('strainInfo') and thisTrait.strainInfo

		table_body = []
		vals = []
		
		for i, strainNameOrig in enumerate(strainlist):
			strainName = strainNameOrig.replace("_2nd_", "")
								
			try:
				thisval = thisTrait.data[strainName].val
				thisvar = thisTrait.data[strainName].var
				thisValFull = [strainName,thisval,thisvar]
			except:
				continue
			
			vals.append(thisValFull)			
			
		upperBound, lowerBound = Plot.findOutliers(vals) # ZS: Values greater than upperBound or less than lowerBound are considered outliers.

		for i, strainNameOrig in enumerate(strainlist):

			trId = strainNameOrig	
			selectCheck = HT.Input(type="checkbox", name="selectCheck", value=trId, Class="checkbox", onClick="highlight(this)")
				
			strainName = strainNameOrig.replace("_2nd_", "")
			strainNameAdd = ''
			if fd.RISet == 'AXBXA' and strainName in ('AXB18/19/20','AXB13/14','BXA8/17'):
					strainNameAdd = HT.Href(url='/mouseCross.html#AXB/BXA', text=HT.Sup('#'), Class='fs12', target="_blank")
					
			try:
				thisval, thisvar, thisNP = thisTrait.data[strainName].val, thisTrait.data[strainName].var, thisTrait.data[strainName].N
				if thisNP:
					mainForm.append(HT.Input(name='N'+strainName, value=thisNP, type='hidden'))
				else:
					pass
			except:
				thisval = thisvar = 'x'
			
			try:
				traitVal = thisval
				dispVal = "%2.3f" % thisval
			except:
				traitVal = ''
				dispVal = 'x'
			
			strainNameDisp = HT.Span(strainName, Class='fs14 fwn ffl')

			if varianceDataPage:
				try:
					traitVar = thisvar
					dispVar = "%2.3f" % thisvar
				except:
					traitVar = ''
					dispVar = 'x'
			
			if thisval == 'x':
				traitVar = '' #ZS: Used to be 0, but it doesn't seem like a good idea for values of 0 to *always* be at the bottom when you sort; it makes more sense to put "nothing"

				className = 'fs13 b1 c222 '
				valueClassName = 'fs13 b1 c222 valueField '
				rowClassName = 'novalue '		
			else:
				if (thisval >= upperBound) or (thisval <= lowerBound):
					className = 'fs13 b1 c222 outlier '
					valueClassName = 'fs13 b1 c222 valueField '
					rowClassName = 'outlier'
				else:
					className = 'fs13 b1 c222 '
					valueClassName = 'fs13 b1 c222 valueField '
					rowClassName = ' '

			if varianceDataPage:
				varClassName = valueClassName + str(traitVar)
			valueClassName += str(traitVal)

			if strainNameOrig == strainName:
				if other_strainsExist and strainNameOrig in (fd.parlist + fd.f1list):
					########################################################################################################################################################
				      # ZS: Append value and variance to the value and variance input fields' list of classes; this is so the javascript can update the value when the user
				      # changes it. The updated value is then used when the table is sorted (tablesorter.js). This needs to be done because the "value" attribute is immutable. 
					#########################################################################################################################################################

					valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right; background-color:#FFFFFF;", value=dispVal, 
						onChange= "javascript:this.form['_2nd_%s'].value=this.form['%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=valueClassName)
					if varianceDataPage:
						seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar,
							onChange= "javascript:this.form['V_2nd_%s'].value=this.form['V%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=varClassName)
				else:
					valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right; background-color:#FFFFFF;", value=dispVal, Class=valueClassName)
					if varianceDataPage:
						seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, Class=varClassName)
			else:
				valueField = HT.Input(name=strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVal, 
						      onChange= "javascript:this.form['%s'].value=this.form['%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=valueClassName)
				if varianceDataPage:
					seField = HT.Input(name='V'+strainNameOrig, size=8, maxlength=8, style="text-align:right", value=dispVar, 
						onChange= "javascript:this.form['V%s'].value=this.form['V%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=varClassName)

			if (strains == 'primary'):
				table_row = HT.TR(Id="Primary_"+str(i+1), Class=rowClassName)
			else:
				table_row = HT.TR(Id="Other_"+str(i+1), Class=rowClassName)

			if varianceDataPage:
				table_row.append(HT.TD(str(i+1), selectCheck, width=45, align='right', Class=className))
				table_row.append(HT.TD(strainNameDisp, strainNameAdd, align='right', width=100, Class=className))
				table_row.append(HT.TD(valueField, width=70, align='right', Id="value_"+str(i)+"_"+strains, Class=className))
				table_row.append(HT.TD("&plusmn;", width=20, align='center', Class=className))
				table_row.append(HT.TD(seField, width=80, align='right', Id="SE_"+str(i)+"_"+strains, Class=className))		
			else:
				table_row.append(HT.TD(str(i+1), selectCheck, width=45, align='right', Class=className))
				table_row.append(HT.TD(strainNameDisp, strainNameAdd, align='right', width=100, Class=className))
				table_row.append(HT.TD(valueField, width=70, align='right', Id="value_"+str(i)+"_"+strains, Class=className))

			if thisTrait and thisTrait.db and thisTrait.db.type =='ProbeSet':
				if len(attribute_ids) > 0:

					#ZS: Get StrainId value for the next query
					self.cursor.execute("""SELECT Strain.Id
									FROM Strain, StrainXRef, InbredSet 
									WHERE Strain.Name = '%s' and 
										StrainXRef.StrainId = Strain.Id and 
										InbredSet.Id = StrainXRef.InbredSetId and 
										InbredSet.Name = '%s'""" % (strainName, fd.RISet))

					strain_id = self.cursor.fetchone()[0]

					attr_counter = 1 # This is needed so the javascript can know which attribute type to associate this value with for the exported excel sheet (each attribute type being a column).
					for attribute_id in attribute_ids:

						#ZS: Add extra case attribute values (if any)
						self.cursor.execute("""SELECT Value
                                						FROM CaseAttributeXRef
                                          				WHERE ProbeSetFreezeId = '%s' AND
                                          					StrainId = '%s' AND
                                          					CaseAttributeId = '%s'
											group by CaseAttributeXRef.CaseAttributeId""" % (thisTrait.db.id, strain_id, str(attribute_id)))

						attributeValue = self.cursor.fetchone()[0] #Trait-specific attributes, if any

						#ZS: If it's an int, turn it into one for sorting (for example, 101 would be lower than 80 if they're strings instead of ints)
						try:
							attributeValue = int(attributeValue)
						except:
							pass
				
						span_Id = strains+"_attribute"+str(attr_counter)+"_sample"+str(i+1)
						attr_container = HT.Span(attributeValue, Id=span_Id)
						attr_className = str(attributeValue) + "&nbsp;" + className
						table_row.append(HT.TD(attr_container, align='right', Class=attr_className))
						attr_counter += 1

			table_body.append(table_row)	
		return table_body

	def getTableHeader(self, fd, thisTrait, nCols, attribute_names):
	
		table_header = HT.TR()

		col_class = "fs13 fwb ff1 b1 cw cbrb"

		if nCols == 6:
			try:
				if fd.varianceDispName:
					pass
			except:
				fd.varianceDispName = 'Variance'
				
			table_header.append(HT.TH('Index', align='right', width=60, Class=col_class),
				HT.TH('Sample', align='right', width=100, Class=col_class),
				HT.TH('Value', align='right', width=70, Class=col_class),
				HT.TH('&nbsp;', width=20, Class=col_class),
				HT.TH(fd.varianceDispName, align='right', width=80, Class=col_class))

		elif nCols == 4:
			table_header.append(HT.TH('Index', align='right', width=60, Class=col_class),
				HT.TH('Sample', align='right', width=100, Class=col_class),
				HT.TH('Value', align='right', width=70, Class=col_class))

		else:
			pass

		if len(attribute_names) > 0:
			i=0
			for attribute in attribute_names:
				char_count = len(attribute)
				cell_width = char_count * 14
				table_header.append(HT.TH(attribute, align='right', width=cell_width, Class="attribute_name " + col_class))
				i+=1

		return table_header


	def getSortByValue(self):
	
		sortby = ("", "")

		return sortby