Add all the source codes into the github.

1 files changed, 695 insertions, 0 deletions

diff --git a/web/webqtl/collection/AddToSelectionPage.py b/web/webqtl/collection/AddToSelectionPage.py
new file mode 100644
index 00000000..2a99e8c1
--- /dev/null
+++ b/web/webqtl/collection/AddToSelectionPage.py
@@ -0,0 +1,695 @@
+#AddToSelectionPage.py
+
+import string
+from htmlgen import HTMLgen2 as HT
+import os
+import cPickle
+import reaper
+
+from base import webqtlConfig
+from base.templatePage import templatePage
+from utility.THCell import THCell
+from utility.TDCell import TDCell
+from utility import webqtlUtil
+from showTrait import ShowProbeInfoPage
+# NL, 07/27/2010: add 'import webqtlDatabaseFunction' for retrieveSpecies function
+from dbFunction import webqtlDatabaseFunction
+from base.webqtlTrait import webqtlTrait
+
+	
+#########################################
+#      Add to Selection Page
+#########################################
+class AddToSelectionPage(templatePage):
+
+	def __init__(self,fd):
+
+		templatePage.__init__(self, fd)
+
+		if not self.openMysql():
+			return
+
+		if not fd.genotype:
+			fd.readGenotype()
+		
+		self.searchResult = fd.formdata.getvalue('searchResult', [])
+		if type("1") == type(self.searchResult):
+			self.searchResult = [self.searchResult]
+		if fd.formdata.getvalue('fromDataEditingPage'):
+			searchResult2 = fd.formdata.getvalue('fullname')
+			if searchResult2:
+				self.searchResult.append(searchResult2)
+		
+		if self.searchResult:
+			pass
+		else:
+			templatePage.__init__(self, fd)
+			heading = 'Add Collections'
+			detail = ['You need to select at least one trait to add to your selection.']
+			self.error(heading=heading,detail=detail)
+			return
+
+		if self.genSelection(fd=fd):
+			self.writeHTML(fd)
+
+
+		
+	def genSelection(self, fd=None, checkPreSelection = 1):
+		collectionName = '%s_Select' % fd.RISet
+
+		if checkPreSelection:
+			try:
+				preSelection = fd.input_session_data[collectionName]
+				preSelection = list(string.split(preSelection,','))
+			except:
+				preSelection = []
+		else:
+			preSelection = []
+
+		if preSelection:
+			for item in preSelection:
+				if item not in self.searchResult:
+					self.searchResult.append(item)
+
+		self.searchResult = map(self.transfer2NewName, self.searchResult)
+
+		for item in self.searchResult:
+			if not item:
+				self.searchResult.remove(item)
+
+		if len(self.searchResult) > 3000:
+                        heading = 'Add Collections'
+                        detail = ['You are adding over 3000 traits to selections, please reduce your number of traits.']
+                        self.error(heading=heading,detail=detail)
+                        return 0
+	
+		searchResult2 = []
+		self.theseTraits = []
+		for item in self.searchResult:
+			try:
+				thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
+				thisTrait.retrieveInfo(QTL=1)
+				self.theseTraits.append(thisTrait)
+				searchResult2.append(item)
+			except:
+				pass
+
+		allTraitStr = string.join(searchResult2,',')
+
+		self.session_data_changed[collectionName] = allTraitStr
+
+		return 1
+
+
+	
+	def writeHTML(self,fd):
+		TD_LR = HT.TD(height=100,width="100%",bgColor='#eeeeee',valign="top")
+		pageTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left")
+		tbl = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0, align="Left")
+		seq = 1
+		SelectionHeading = HT.Paragraph('%s Trait Collection' % fd.RISet, Class="title")
+		
+		mintmap = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'showIntMap');}")
+		mintmap_img = HT.Image("/images/multiple_interval_mapping1_final.jpg", name='mintmap', alt="Multiple Interval Mapping", title="Multiple Interval Mapping", style="border:none;")
+		mintmap.append(mintmap_img)
+		mcorr = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'compCorr');}")
+		mcorr_img = HT.Image("/images/compare_correlates2_final.jpg", name='comparecorr', alt="Compare Correlates", title="Compare Correlates", style="border:none;")
+		mcorr.append(mcorr_img)
+		cormatrix = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'corMatrix');}")
+		cormatrix_img = HT.Image("/images/correlation_matrix1_final.jpg", name='corrmatrix', alt="Correlation Matrix and PCA", title="Correlation Matrix and PCA", style="border:none;")
+		cormatrix.append(cormatrix_img)
+		networkGraph = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'networkGraph');}")
+		networkGraph_img = HT.Image("/images/network_graph1_final.jpg", name='networkgraph', alt="Network Graphs", title="Network Graphs", style="border:none;")
+		networkGraph.append(networkGraph_img)
+		heatmap = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'heatmap');}")
+		heatmap_img = HT.Image("/images/heatmap2_final.jpg", name='heatmap', alt="QTL Heat Map and Clustering", title="QTL Heatmap and Clustering", style="border:none;")
+		heatmap.append(heatmap_img)
+		partialCorr = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'partialCorrInput');}")
+		partialCorr_img = HT.Image("/images/partial_correlation_final.jpg", name='partialCorr', alt="Partial Correlation", title="Partial Correlation", style="border:none;")
+		partialCorr.append(partialCorr_img)
+
+		BN = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'BNInput');}")
+		networkGraph_img = HT.Image("/images/network_graph1_final.jpg", name='BayesianNetwork', alt="Bayesian Network", title="Bayesian Network", style="border:none;")
+		BN.append(networkGraph_img)
+
+		removeselect = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('showDatabase')[0], 'removeSelection');" % fd.RISet)
+		removeselect_img = HT.Image("/images/remove_selection1_final.jpg", name="removeselect", alt="Remove Selection", title="Remove Selection", style="border:none;")
+		removeselect.append(removeselect_img)	
+		selectall = HT.Href(url="#redirect", onClick="$('.checkallbox').attr('checked', true);")
+		selectall_img = HT.Image("/images/select_all2_final.jpg", name="selectall", alt="Select All", title="Select All", style="border:none;")
+		selectall.append(selectall_img)
+		reset = HT.Href(url="#redirect", onClick="$('.checkallbox').attr('checked', false);")
+		reset_img = HT.Image("/images/select_none2_final.jpg", alt="Select None", title="Select None", style="border:none;")
+		reset.append(reset_img)
+		exportSelect = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'exportSelectionDetailInfo');")
+		exportSelect_img = HT.Image("/images/export2_final.jpg", name="exportSelection", alt="Export Selection", title="Export Selection", style="border:none;")
+		exportSelect.append(exportSelect_img)
+		selectinvert = HT.Href(url="#redirect", onClick = "checkInvert(document.getElementsByName('showDatabase')[0]);")
+		selectinvert_img = HT.Image("/images/invert_selection2_final.jpg", name="selectinvert", alt="Invert Selection", title="Invert Selection", style="border:none;")
+		selectinvert.append(selectinvert_img)
+
+		chrMenu = HT.Input(type='hidden',name='chromosomes',value='all')
+		
+		importFile = HT.Input(type='file', name='importfile', size=15)
+		importButton = HT.Input(type='button',name='importSelection',value='Load Collection', onClick="addRmvSelection('%s', this.form, 'importSelect');" % fd.RISet,Class="button")
+		exportButton = HT.Input(type='button' ,name='exportSelection',value='Save Collection', onClick="databaseFunc(this.form,'exportSelect');", Class="button")
+		importMenu = HT.Select(name='importmethod')
+		importMenu.append(('append','append'))
+		importMenu.append(('replace','replace'))            
+	
+		ODE = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'ODE');")
+		ODE_img = HT.Image("/images/ODE_logo_final.jpg", name="ode", alt="ODE", title="ODE", style="border:none")
+		ODE.append(ODE_img)
+	        
+		GCATButton = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'GCAT');")
+		GCATButton_img = HT.Image("/images/GCAT_logo_final.jpg", name="GCAT", alt="GCAT", title="GCAT", style="border:none")
+		GCATButton.append(GCATButton_img)
+		
+        	GeneSet = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0],'GOTree');")
+        	GeneSet_img = HT.Image("/images/webgestalt_icon_final.jpg", name="webgestalt", alt="Gene Set Analysis Toolkit", title="Gene Set Analysis Toolkit", style="border:none")        
+        	GeneSet.append(GeneSet_img)      
+
+		#need to be refined
+        	if fd.genotype.Mbmap:
+            	    scale = HT.Input(name="scale", value="physic", type="hidden")
+        	else:
+            	    scale = ""
+ 
+        	formMain = HT.Form(cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showDatabase', submit=HT.Input(type='hidden'))
+
+		#XZ, July 22, 2011: I add parameters for interval mapping
+        	hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','RISet':fd.RISet,'incparentsf1':'ON','showHideOptions':'more','scale':'physic','additiveCheck':'ON', 'showSNP':'ON', 'showGenes':'ON', 'intervalAnalystCheck':'ON','bootCheck':None, 'permCheck':None, 'applyVarianceSE':None}
+        	for key in hddn.keys():
+            	    formMain.append(HT.Input(name=key, value=hddn[key], type='hidden'))
+
+        	if not self.searchResult:
+            	    SelectionHeading = HT.Paragraph('%s Trait Collection' % fd.RISet, Class="title")
+            	    formMain.append(HT.HR(width="70%", color = "blue"),importFile, ' ', importMenu, ' ', importButton)
+            	    TD_LR.append(SelectionHeading,HT.Blockquote('No trait has been added to this selection.'), HT.Center(HT.BR(), HT.BR(), HT.BR(), HT.BR(), formMain))
+            	    self.dict['body'] = str(TD_LR)
+            	    self.dict['title'] = "%s Trait Collection" % fd.RISet
+            	    return
+
+		#########################################
+		# Creating table object for AJAX table  #
+		#########################################
+		tblobj = {}
+		mainfmName = 'showDatabase'
+		# NL, 07/27/2010. retrieveSpecies function has been moved from webqtlTrait.py to webqtlDatabaseFunction.py;
+		species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
+		if species == 'human':
+			chrMenu = scale = mintmap = heatmap = ""
+
+		tblobj['header'] = self.getCollectionTableHeader()
+
+		sortby = self.getSortByValue()
+
+		thisRISet = fd.RISet
+		tblobj['body'] = self.getCollectionTableBody(RISet=thisRISet, traitList=self.theseTraits, formName=mainfmName, species=species)
+
+		filename= webqtlUtil.genRandStr("Search_")
+
+		objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb')
+		cPickle.dump(tblobj, objfile)
+		objfile.close()
+
+
+		div = HT.Div(webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=sortby, tableID = "sortable", addIndex = "1"), Id="sortable")		
+
+
+        	containerTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0,align="Left")
+        	postContainerTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0,align="Left")
+
+        	optionsTable = HT.TableLite(cellSpacing=2, cellPadding=0,width="400", border=0, align="Left")
+        	optionsTable.append(HT.TR(HT.TD(selectall), HT.TD(reset), HT.TD(selectinvert), HT.TD(removeselect), HT.TD(exportSelect)))
+        	optionsTable.append(HT.TR(HT.TD(" "*1,"Select"), HT.TD("Deselect"), HT.TD(" "*1,"Invert"), HT.TD(" "*1,"Remove"), HT.TD(" "*1,"Export")))
+        	postContainerTable.append(HT.TR(HT.TD(optionsTable)))
+        	containerTable.append(HT.TR(HT.TD(optionsTable)))
+
+        	functionTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="480",border=0, align="Left")
+        	functionRow = HT.TR(HT.TD(networkGraph, width="16.7%"), HT.TD(cormatrix, width="16.7%"), HT.TD(partialCorr, width="16.7%"), HT.TD(mcorr, width="16.7%"), HT.TD(mintmap, width="16.7%"), HT.TD(heatmap))
+        	if species == "human":
+        	    labelRow = HT.TR(HT.TD(" "*2,HT.Text("Graph")), HT.TD(" "*2,HT.Text("Matrix")), HT.TD(" "*2, HT.Text("Partial")), HT.TD(HT.Text("Compare")))
+        	else:
+        		labelRow = HT.TR(HT.TD(" "*2,HT.Text("Graph")), HT.TD(" "*2,HT.Text("Matrix")), HT.TD(" "*2, HT.Text("Partial")), HT.TD(HT.Text("Compare")), HT.TD(HT.Text("QTL Map")), HT.TD(HT.Text(text="Heat Map")))
+        	functionTable.append(functionRow, labelRow)
+        	postContainerTable.append(HT.TR(HT.TD(functionTable)))
+        	containerTable.append(HT.TR(HT.TD(functionTable)))
+
+        	moreOptions = HT.Input(type='button',name='options',value='More Options', onClick="",Class="toggle")
+        	fewerOptions = HT.Input(type='button',name='options',value='Fewer Options', onClick="",Class="toggle")
+        	
+        	
+
+        	if (fd.formdata.getvalue('showHideOptions') == 'less'):		
+            	    postContainerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(fewerOptions, Class="toggleShowHide"))))
+            	    containerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(fewerOptions, Class="toggleShowHide"))))
+        	else:	
+            	    postContainerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(moreOptions, Class="toggleShowHide"))))
+            	    containerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(moreOptions, Class="toggleShowHide"))))	
+
+
+        	LinkOutTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="320",border=0, align="Left")
+        	LinkOutRow = HT.TR(HT.TD(GeneSet, width="33%"), HT.TD(GCATButton, width="33%"), HT.TD(ODE, width="33%"), style="display:none;", Class="extra_options")
+        	LinkOutLabels = HT.TR(HT.TD(HT.Text("Gene Set")), HT.TD(" "*2, HT.Text("GCAT")), HT.TD(" "*3, HT.Text("ODE")), style="display:none;", Class="extra_options")
+        	LinkOutTable.append(LinkOutRow,LinkOutLabels)
+        	postContainerTable.append(HT.TR(HT.TD(" "), height=10), HT.TR(HT.TD(LinkOutTable)))
+        	containerTable.append(HT.TR(HT.TD(" "), height=10), HT.TR(HT.TD(LinkOutTable)))      
+                
+        	pageTable.append(HT.TR(HT.TD(containerTable)))
+        	chrMenu = scale = ""
+
+        	pageTable.append(HT.TR(HT.TD(div)))
+        	pageTable.append(HT.TR(HT.TD(" ")))
+        	if len(self.theseTraits) > 20:
+            	    pageTable.append(HT.TR(HT.TD(postContainerTable)))
+        	pageTable.append(HT.TR(HT.TD(importFile, ' ', importMenu, ' ', importButton, ' '*10, exportButton)))
+		    #Took out scaleMenu since it will be replaced with a jquery popup in the future - Zach 5/10/2010
+        	formMain.append(chrMenu,scale,pageTable)
+		    
+		#Updated by NL, deleted showHideJS, moved jquery to jqueryFunction.js 
+		self.dict['js1'] = ''
+            	TD_LR.append(SelectionHeading,formMain)
+
+        	self.dict['body'] = str(TD_LR)
+        	self.dict['js2'] = 'onLoad="pageOffset()"'
+        	self.dict['layer'] = self.generateWarningLayer()       	
+        	self.dict['title'] = "%s Trait Collection" % thisRISet
+
+	def transfer2NewName(self, str):
+		"this is temporary"
+		if str.find("::") < 0:
+			return str.replace(":", "::")
+		else:
+			return str
+		
+	def generateWarningLayer(self):
+
+		layerString = """
+			<!-- BEGIN FLOATING LAYER CODE //-->
+			<div id="warningLayer" style="padding:3px; border: 1px solid #222;
+  			background-color: #fff; position:absolute;width:250px;left:100;top:100;visibility:hidden">			
+				<table border="0" width="250" class="cbrb" cellspacing="0" cellpadding="5">
+					<tr>
+						<td width="100%">
+  							<table border="0" width="100%" cellspacing="0" cellpadding="0" height="36">
+  								<tr>
+  									<td class="cbrb cw ff15 fwb" align="Center" width="100%" style="padding:4px">
+        									Sort Table
+  									</td>
+  								</tr>
+  								<tr>
+  									<td width="100%" bgcolor="#eeeeee" align="Center" style="padding:4px">
+										<!-- PLACE YOUR CONTENT HERE //-->
+										Resorting this table <br>
+										<!-- END OF CONTENT AREA //-->
+  									</td>
+  								</tr>
+  							</table>
+						</td>
+					</tr>
+				</table>
+			</div>
+			<!-- END FLOATING LAYER CODE //-->
+
+            		"""
+
+		return layerString		
+		
+	def getCollectionTableHeader(self):
+
+		tblobj_header = []
+
+		className = "fs13 fwb ffl b1 cw cbrb"
+
+		tblobj_header = [[THCell(HT.TD(' ', Class=className, nowrap="on"), sort=0), 
+			THCell(HT.TD('Dataset', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="dataset", idx=1),
+			THCell(HT.TD('Trait', HT.BR(), 'ID', HT.BR(), valign="top", Class=className, nowrap="on"), text="name", idx=2),
+			THCell(HT.TD('Symbol', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="symbol", idx=3),
+			THCell(HT.TD('Description', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="desc", idx=4),
+			THCell(HT.TD('Location', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="location", idx=5),
+			THCell(HT.TD('Mean', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="mean", idx=6),
+			THCell(HT.TD('N', HT.BR(), 'Cases', HT.BR(), valign="top", Class=className, nowrap="on"), text="samples", idx=7),
+			THCell(HT.TD('Max LRS', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="lrs", idx=8),
+			THCell(HT.TD('Max LRS Location',HT.BR(),'Chr and Mb', HT.BR(), valign="top", Class=className, nowrap="on"), text="lrs_location", idx=9)]]
+
+		return tblobj_header
+
+	def getCollectionTableBody(self, RISet=None, traitList=None, formName=None, species=''):
+
+		tblobj_body = []
+
+		className = "fs12 fwn b1 c222"
+
+		for thisTrait in traitList:
+			tr = []
+
+			if not thisTrait.haveinfo:
+				thisTrait.retrieveInfo(QTL=1)
+
+			if thisTrait.riset != RISet:
+				continue	
+
+			trId = str(thisTrait)
+
+			#XZ: check box column
+			tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class="checkallbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", Class=className)))
+
+			#XZ: Dataset column
+			tr.append(TDCell(HT.TD(thisTrait.db.name, Class="fs12 fwn b1 c222"), thisTrait.db.name, thisTrait.db.name.upper()))
+
+			#XZ: Trait ID column
+			if thisTrait.cellid:
+				tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.cellid,url="javascript:showDatabase3('%s','%s','%s','%s')" % (formName, thisTrait.db.name, thisTrait.name, thisTrait.cellid), Class="fs12 fwn"), nowrap="yes",align="left", Class=className),str(thisTrait.cellid), thisTrait.cellid))
+			else:
+				tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.getGivenName(),url="javascript:showDatabase3('%s','%s','%s','')" % (formName, thisTrait.db.name, thisTrait.name), Class="fs12 fwn"), nowrap="yes",align="left", Class=className),str(thisTrait.name), thisTrait.name))
+
+			#XZ: Symbol column and Description column
+			if (thisTrait.db.type == "Publish"):
+				AbbreviationString = "--"
+				if (thisTrait.post_publication_abbreviation != None):
+					AbbreviationString = thisTrait.post_publication_abbreviation
+				PhenotypeString = thisTrait.post_publication_description
+				if thisTrait.confidential:
+					if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users):
+						if thisTrait.pre_publication_abbreviation:
+							AbbreviationString = thisTrait.pre_publication_abbreviation
+						else:
+							AbbreviationString = "--"
+						PhenotypeString = thisTrait.pre_publication_description
+
+				if AbbreviationString == "--":
+					tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
+				else:
+					tr.append(TDCell(HT.TD(AbbreviationString, Class=className), AbbreviationString, AbbreviationString.upper()))
+
+				tr.append(TDCell(HT.TD(PhenotypeString, Class=className), PhenotypeString, PhenotypeString.upper()))
+
+
+			elif (thisTrait.db.type == "ProbeSet" or thisTrait.db.type == "Temp"):
+				description_string = str(thisTrait.description).strip()
+				if (thisTrait.db.type == "ProbeSet"):
+					if (thisTrait.symbol != None):
+           					if thisTrait.geneid:
+                        				symbolurl = HT.Href(text=thisTrait.symbol,target='_blank',url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" % thisTrait.geneid, Class="font_black fs12 fwn")
+            					else:
+                        				symbolurl = HT.Href(text=thisTrait.symbol,target='_blank',url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=gene&term=%s" % thisTrait.symbol, Class="font_black fs12 fwn")
+						tr.append(TDCell(HT.TD(symbolurl, align="left", Class="fs12 fwn b1 c222 fsI"), thisTrait.symbol, thisTrait.symbol))
+            				else:
+						tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
+					target_string = str(thisTrait.probe_target_description).strip()
+
+            				description_display = ''
+
+					if len(description_string) > 1 and description_string != 'None':
+						description_display = description_string
+					else:
+           		    			description_display = thisTrait.symbol
+
+            				if len(description_display) > 1 and description_display != 'N/A' and len(target_string) > 1 and target_string != 'None':
+                				description_display = description_display + '; ' + target_string.strip()
+					
+					description_string = description_display
+				else:
+					tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
+            			tr.append(TDCell(HT.TD(description_string, Class=className), description_string, description_string))
+			else:
+				if (thisTrait.name != None):
+					tr.append(TDCell(HT.TD(thisTrait.name, Class="fs12 fwn b1 c222"), thisTrait.name, thisTrait.name))
+				else:
+					tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
+				tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
+
+			#XZ: Location column
+			if (thisTrait.db.type == "Publish"):
+				tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
+			else:
+				if thisTrait.db.type == "ProbeSet" and thisTrait.cellid:
+					EnsemblProbeSetID = thisTrait.name
+					if '_at' in thisTrait.name:
+						EnsemblProbeSetID = thisTrait.name[0:thisTrait.name.index('_at')+3]	
+
+					#These tables (Ensembl) were created by Xusheng Wang in 2010 and are mm9 (so they'll need to be changed at some point to be mm10.
+					self.cursor.execute('''
+							SELECT EnsemblProbeLocation.* 
+							FROM EnsemblProbeLocation, EnsemblProbe, EnsemblChip, GeneChipEnsemblXRef, ProbeFreeze, ProbeSetFreeze
+							WHERE EnsemblProbeLocation.ProbeId=EnsemblProbe.Id and EnsemblProbe.ChipId=GeneChipEnsemblXRef.EnsemblChipId and
+								GeneChipEnsemblXRef.GeneChipId=ProbeFreeze.ChipId and EnsemblProbe.Name=%s and EnsemblProbe.ProbeSet=%s and
+								ProbeSetFreeze.Id=%s and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id group by Chr, Start, End'''
+							,(thisTrait.cellid, EnsemblProbeSetID, thisTrait.db.id))
+					LocationFields = self.cursor.fetchall()
+
+					Chr=''
+					Mb=''
+					Start=''
+					End=''
+					if (len(LocationFields)>=1):
+						Chr,Start,End,Strand,MisMatch,ProbeId = map(self.nullRecord,LocationFields[0])
+						Start /= 1000000.0
+						End /= 1000000.0
+						Mb = Start
+					if (len(LocationFields)>1):
+						self.cursor.execute('''
+								SELECT ProbeSet.Chr, ProbeSet.Mb FROM ProbeSet, ProbeFreeze, ProbeSetFreeze 
+								WHERE ProbeSet.ChipId=ProbeFreeze.ChipId and ProbeSet.Name=%s and ProbeSetFreeze.Id=%s and
+									ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id'''
+								,(thisTrait.name, thisTrait.db.id))
+						ProbeSetChr, ProbeSetMb = map(self.nullRecord,self.cursor.fetchall()[0])
+					
+						self.cursor.execute('''
+								SELECT EnsemblProbeLocation.*, ABS(EnsemblProbeLocation.Start/1000000-%s) as Mb 
+								FROM EnsemblProbeLocation, EnsemblProbe, EnsemblChip, GeneChipEnsemblXRef, ProbeFreeze
+								WHERE EnsemblProbeLocation.ProbeId=EnsemblProbe.Id and EnsemblProbe.ChipId=GeneChipEnsemblXRef.EnsemblChipId and
+									GeneChipEnsemblXRef.GeneChipId=ProbeFreeze.ChipId and EnsemblProbe.Name=%s and EnsemblProbe.ProbeSet=%s and
+									EnsemblProbeLocation.Chr=%s and ProbeSetFreezeId=%s and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id order by Mb limit 1'''
+								,(ProbeSetMb, thisTrait.cellid, EnsemblProbeSetID, ProbeSetChr, thisTrait.db.id))
+						NewLocationFields = self.cursor.fetchall()
+						if (len(NewLocationFields)>0):
+							Chr,Start,End,Strand,MisMatch,ProbeId,Mb = map(self.nullRecord,NewLocationFields[0])
+							Start /= 1000000.0
+							End /= 1000000.0
+							Mb = Start
+
+					#ZS: trait_location_value is used for sorting
+					trait_location_repr = "--"
+					trait_location_value = 1000000
+
+					if Chr and Mb:
+						try:
+							trait_location_value = int(Chr)*1000 + Mb
+						except:
+							if Chr.upper() == "X":
+								trait_location_value = 20*1000 + Mb
+							else:
+								trait_location_value = ord(str(Chr).upper()[0])*1000 + Mb
+					
+						trait_location_repr = "Chr%s: %.6f" % (Chr, float(Mb) )
+			
+					tr.append(TDCell(HT.TD(trait_location_repr, nowrap='ON', Class=className), trait_location_repr, trait_location_value))
+				
+				else:
+
+					#ZS: trait_location_value is used for sorting
+					trait_location_repr = "--"
+					trait_location_value = 1000000
+
+					if hasattr(thisTrait, 'chr') and hasattr(thisTrait, 'mb') and thisTrait.chr and thisTrait.mb:
+						try:
+							trait_location_value = int(thisTrait.chr)*1000 + thisTrait.mb
+						except:
+							if thisTrait.chr.upper() == "X":
+								trait_location_value = 20*1000 + thisTrait.mb
+							else:
+								trait_location_value = ord(str(thisTrait.chr).upper()[0])*1000 + thisTrait.mb
+					
+						trait_location_repr = "Chr%s: %.6f" % (thisTrait.chr, float(thisTrait.mb) )
+			
+					tr.append(TDCell(HT.TD(trait_location_repr, nowrap='ON', Class=className), trait_location_repr, trait_location_value))
+
+			#XZ: Mean column
+			if (thisTrait.db.type == "ProbeSet"):
+				if thisTrait.cellid:
+					mean = -10000.0
+					try:
+						thisTrait.retrieveData()
+						mean, median, var, stdev, sem, N = reaper.anova(thisTrait.exportInformative()[1])
+					except:
+						pass
+					repr = '%2.3f' % mean
+					mean = '%2.2f' % mean
+            				tr.append(TDCell(HT.TD(repr, Class=className, align='right', nowrap='ON'),repr, mean))	
+				else:
+           	 			self.cursor.execute("""
+                   	 			select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet
+                   	 			where ProbeSetXRef.ProbeSetFreezeId = %d and
+                        	  			ProbeSet.Id = ProbeSetXRef.ProbeSetId and
+                        	  			ProbeSet.Name = '%s'
+            				""" % (thisTrait.db.id, thisTrait.name))
+            				result = self.cursor.fetchone()
+            				if result:
+                				if result[0]:
+                    					mean = result[0]
+                				else:
+                    					mean=0
+            				else:
+                				mean = 0
+
+					#XZ, 06/05/2009: It is neccessary to turn on nowrap
+            				repr = "%2.3f" % mean
+            				tr.append(TDCell(HT.TD(repr, Class=className, align='right', nowrap='ON'),repr, mean))	
+
+			elif (thisTrait.db.type == "Publish"):
+				self.cursor.execute("""
+				select count(PublishData.value), sum(PublishData.value) from PublishData, PublishXRef, PublishFreeze
+				where PublishData.Id = PublishXRef.DataId and 
+					PublishXRef.Id = %s and
+					PublishXRef.InbredSetId = PublishFreeze.InbredSetId and
+					PublishFreeze.Id = %d
+				""" % (thisTrait.name, thisTrait.db.id))
+				result = self.cursor.fetchone()
+
+				if result:
+					if result[0] and result[1]:
+						mean = result[1]/result[0]
+					else:	
+						mean = 0
+				else:
+					mean = 0
+
+				repr = "%2.3f" % mean
+				tr.append(TDCell(HT.TD(repr, Class=className, align='right', nowrap='ON'),repr, mean))		
+			else:
+				tr.append(TDCell(HT.TD("--", Class=className, align='left', nowrap='ON'),"--", 0))			
+			
+			#Number of cases
+			n_cases_value = 0
+			n_cases_repr = "--"
+			if (thisTrait.db.type == "Publish"):
+				self.cursor.execute("""
+				select count(PublishData.value) from PublishData, PublishXRef, PublishFreeze
+				where PublishData.Id = PublishXRef.DataId and 
+					PublishXRef.Id = %s and
+					PublishXRef.InbredSetId = PublishFreeze.InbredSetId and
+					PublishFreeze.Id = %d
+				""" % (thisTrait.name, thisTrait.db.id))
+				result = self.cursor.fetchone()
+
+				if result:
+					if result[0]:
+						n_cases_value = result[0]
+						n_cases_repr = result[0]
+
+				if (n_cases_value == "--"):
+					tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value))
+				else:
+					tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='right', nowrap="on"), n_cases_repr, n_cases_value))	
+			
+			elif (thisTrait.db.type == "ProbeSet"):
+				self.cursor.execute("""
+				select count(ProbeSetData.value) from ProbeSet, ProbeSetXRef, ProbeSetData, ProbeSetFreeze
+				where ProbeSet.Name='%s' and
+					ProbeSetXRef.ProbeSetId = ProbeSet.Id and
+					ProbeSetXRef.DataId = ProbeSetData.Id and
+					ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and
+					ProbeSetFreeze.Name = '%s'
+				""" % (thisTrait.name, thisTrait.db.name))
+				result = self.cursor.fetchone()
+
+				if result:
+					if result[0]:
+						n_cases_value = result[0]
+						n_cases_repr = result[0]
+				if (n_cases_value == "--"):
+					tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value))
+				else:
+					tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='right', nowrap="on"), n_cases_repr, n_cases_value))
+			
+			elif (thisTrait.db.type == "Geno"):
+				self.cursor.execute("""
+				select count(GenoData.value) from GenoData, GenoXRef, GenoFreeze, Geno, Strain
+				where Geno.SpeciesId = %s and Geno.Name='%s' and
+					GenoXRef.GenoId = Geno.Id and
+					GenoXRef.DataId = GenoData.Id and
+					GenoXRef.GenoFreezeId = GenoFreeze.Id and
+					GenoData.StrainId = Strain.Id and
+					GenoFreeze.Name = '%s'
+				""" % (webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, thisTrait.db.riset), thisTrait.name, thisTrait.db.name))
+				result = self.cursor.fetchone()
+
+				if result:
+					if result[0]:
+						n_cases_value = result[0]
+						n_cases_repr = result[0]
+				if (n_cases_value == "--"):
+					tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value))
+				else:
+					tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='right', nowrap="on"), n_cases_repr, n_cases_value))
+
+			else:
+				tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value))
+
+			#XZ: Max LRS column and Max LRS Location column
+			if (thisTrait.db.type != "Geno"):
+            			#LRS and its location
+            			LRS_score_repr = '--'
+            			LRS_score_value = 0
+            			LRS_location_repr = '--'
+            			LRS_location_value = 1000000
+            			LRS_flag = 1
+
+            			#Max LRS and its Locus location
+            			if hasattr(thisTrait, 'lrs') and hasattr(thisTrait, 'locus') and thisTrait.lrs and thisTrait.locus:
+                			self.cursor.execute("""
+                    			select Geno.Chr, Geno.Mb from Geno, Species
+                    			where Species.Name = '%s' and
+                          			Geno.Name = '%s' and
+                          			Geno.SpeciesId = Species.Id
+                			""" % (species, thisTrait.locus))
+                			result = self.cursor.fetchone()
+
+                			if result:
+                    				if result[0] and result[1]:
+                        				LRS_Chr = result[0]
+                        				LRS_Mb = result[1]
+
+                        				#XZ: LRS_location_value is used for sorting
+                        				try:
+								LRS_location_value = int(LRS_Chr)*1000 + float(LRS_Mb)
+							except:
+								if LRS_Chr.upper() == 'X':
+									LRS_location_value = 20*1000 + float(LRS_Mb)
+								else:
+									LRS_location_value = ord(str(LRS_chr).upper()[0])*1000 + float(LRS_Mb)
+
+
+                        				LRS_score_repr = '%3.1f' % thisTrait.lrs
+                        				LRS_score_value = thisTrait.lrs
+                        				LRS_location_repr = 'Chr%s: %.6f' % (LRS_Chr, float(LRS_Mb) )
+                        				LRS_flag = 0
+
+                        				tr.append(TDCell(HT.TD(LRS_score_repr, Class=className, align='right', nowrap="on"), LRS_score_repr, LRS_score_value))
+                        				tr.append(TDCell(HT.TD(LRS_location_repr, Class=className), LRS_location_repr, LRS_location_value))
+
+            			if LRS_flag:
+                			tr.append(TDCell(HT.TD(LRS_score_repr, Class=className), LRS_score_repr, LRS_score_value))
+                			tr.append(TDCell(HT.TD(LRS_location_repr, Class=className), LRS_location_repr, LRS_location_value))
+			else:
+                		tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", 0))
+                		tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", 1000000))							
+
+			tblobj_body.append(tr)
+
+		return tblobj_body		
+		
+	def getSortByValue(self):
+
+		sortby = ("pv", "up")
+
+		return sortby
+
+	def nullRecord(self,x):
+		if x or x == 0:
+			return x
+		else:
+			return ""
+