9 files changed, 1532 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("&nbsp;"*1,"Select"), HT.TD("Deselect"), HT.TD("&nbsp;"*1,"Invert"), HT.TD("&nbsp;"*1,"Remove"), HT.TD("&nbsp;"*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("&nbsp;"*2,HT.Text("Graph")), HT.TD("&nbsp;"*2,HT.Text("Matrix")), HT.TD("&nbsp;"*2, HT.Text("Partial")), HT.TD(HT.Text("Compare")))
+        	else:
+        		labelRow = HT.TR(HT.TD("&nbsp;"*2,HT.Text("Graph")), HT.TD("&nbsp;"*2,HT.Text("Matrix")), HT.TD("&nbsp;"*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("&nbsp;"), height="10"), HT.TR(HT.TD(HT.Div(fewerOptions, Class="toggleShowHide"))))
+            	    containerTable.append(HT.TR(HT.TD("&nbsp;"), height="10"), HT.TR(HT.TD(HT.Div(fewerOptions, Class="toggleShowHide"))))
+        	else:	
+            	    postContainerTable.append(HT.TR(HT.TD("&nbsp;"), height="10"), HT.TR(HT.TD(HT.Div(moreOptions, Class="toggleShowHide"))))
+            	    containerTable.append(HT.TR(HT.TD("&nbsp;"), 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("&nbsp;"*2, HT.Text("GCAT")), HT.TD("&nbsp;"*3, HT.Text("ODE")), style="display:none;", Class="extra_options")
+        	LinkOutTable.append(LinkOutRow,LinkOutLabels)
+        	postContainerTable.append(HT.TR(HT.TD("&nbsp;"), height=10), HT.TR(HT.TD(LinkOutTable)))
+        	containerTable.append(HT.TR(HT.TD("&nbsp;"), 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("&nbsp;")))
+        	if len(self.theseTraits) > 20:
+            	    pageTable.append(HT.TR(HT.TD(postContainerTable)))
+        	pageTable.append(HT.TR(HT.TD(importFile, ' ', importMenu, ' ', importButton, '&nbsp;'*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 ""
+		
diff --git a/web/webqtl/collection/AddUserInputToSelectionPage.py b/web/webqtl/collection/AddUserInputToSelectionPage.py
new file mode 100755
index 00000000..2c69a047
--- /dev/null
+++ b/web/webqtl/collection/AddUserInputToSelectionPage.py
@@ -0,0 +1,97 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+#AddUserInputToSelectionPage.py
+
+import time
+
+from base import webqtlConfig
+from base.templatePage import templatePage
+from utility import webqtlUtil
+from AddToSelectionPage import AddToSelectionPage	
+			
+#########################################
+#      Add UserInput to Selection Page
+#########################################
+class AddUserInputToSelectionPage(AddToSelectionPage):
+
+	def __init__(self, fd):
+
+		templatePage.__init__(self, fd)
+
+		if not self.openMysql():
+			return
+
+		if not fd.genotype:
+			fd.readData(incf1 = 1)
+			
+		self.strainlist = []
+		self.vals = []
+		for i, strain in enumerate(fd.f1list + fd.strainlist):
+			if fd.allTraitData.has_key(strain) and fd.allTraitData[strain].val != None:
+				self.strainlist.append(strain)
+				self.vals.append([fd.allTraitData[strain].val, fd.allTraitData[strain].var])
+		
+		if len(self.strainlist) > webqtlConfig.KMININFORMATIVE:
+			pass
+		else:
+			templatePage.__init__(self, fd)
+			heading = 'Add to Collection'
+			detail = ['The number of informative strains in your trait is less than %d, this trait can not be added to the selection' % webqtlConfig.KMININFORMATIVE]
+			self.error(heading=heading,detail=detail)
+			return
+		
+		self.cursor.execute('delete Temp, TempData from Temp, TempData where Temp.DataId = TempData.Id and UNIX_TIMESTAMP()-UNIX_TIMESTAMP(CreateTime)>%d;' % webqtlConfig.MAXLIFE)
+		ct0 = time.localtime(time.time())
+		ct = time.strftime("%B/%d %H:%M:%S",ct0)
+		if not fd.identification:
+			fd.identification = "Unnamed Trait"
+		user_ip = fd.remote_ip
+		newDescription = '%s entered at %s from IP %s' % (fd.identification,ct,user_ip)
+		newProbeSetID = webqtlUtil.genRandStr("USER_Tmp_")
+		self.cursor.execute('SelecT max(id) from TempData')
+		try:
+			DataId = self.cursor.fetchall()[0][0] + 1
+		except:
+			DataId = 1
+		self.cursor.execute('SelecT Id  from InbredSet where Name = "%s"' % fd.RISet)
+		InbredSetId = self.cursor.fetchall()[0][0]
+				
+		self.cursor.execute('insert into Temp(Name,description, createtime,DataId,InbredSetId,IP) values(%s,%s,Now(),%s,%s,%s)' ,(newProbeSetID, newDescription, DataId,InbredSetId,user_ip))
+		
+		k = 0	
+		for Strain in self.strainlist:
+			self.cursor.execute('SelecT Strain.Id  from Strain,StrainXRef where Strain.Name = "%s" and Strain.Id = StrainXRef.StrainId and StrainXRef.InbredSetId=%d' % (Strain, InbredSetId))
+			StrainId = self.cursor.fetchall()[0][0]
+			self.cursor.execute('insert into TempData(Id, StrainId, value, SE) values(%s,%s,%s,%s)' , (DataId, StrainId, self.vals[k][0], self.vals[k][1]))
+			k += 1
+
+		self.searchResult = ['Temp::%s'	% newProbeSetID]
+
+		if self.genSelection(fd=fd):
+			self.writeHTML(fd)
+
+
diff --git a/web/webqtl/collection/BatchSubmitSelectionPage.py b/web/webqtl/collection/BatchSubmitSelectionPage.py
new file mode 100755
index 00000000..743606b2
--- /dev/null
+++ b/web/webqtl/collection/BatchSubmitSelectionPage.py
@@ -0,0 +1,225 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+#BatchSubmitSelectionPage.py
+
+import string
+import time
+
+from base import webqtlConfig
+from base.templatePage import templatePage
+from utility import webqtlUtil
+from AddToSelectionPage import AddToSelectionPage
+	
+
+#########################################
+#     batch submission result Page
+#########################################
+class BatchSubmitSelectionPage(AddToSelectionPage):
+
+	def __init__(self, fd):
+
+		templatePage.__init__(self, fd)
+
+		if not self.openMysql():
+			return
+		if not fd.genotype:
+			fd.readGenotype()
+		
+		heading = 'Batch Submission'
+		
+		self.batchDataFile = fd.formdata.getvalue('batchdatafile')
+		if not self.batchDataFile:
+			templatePage.__init__(self, fd)
+			detail = ['The file you choose to import from doesn\'t exist.']
+			self.error(heading=heading,detail=detail)
+			return
+		self.batchDataFile = string.replace(self.batchDataFile, '\r', '\n')
+		self.batchDataFile = string.replace(self.batchDataFile, '\n\n', '\n')
+		self.batchDataFile = string.split(self.batchDataFile, '\n')
+		self.batchDataFile = map(string.strip, self.batchDataFile)
+		
+		traitNames, strainNames, traitValues, SE, NStrain = self.parseDataFile()
+		strainIds = []
+		
+		#print 'Content-type: text/html\n'
+		#print len(traitNames), len(strainNames) , len(strainIds), len(traitValues) , len(SE), "<BR><BR>", len(NStrain)
+		#return
+		
+		try:
+			
+			if not traitNames or not strainNames or not traitValues or len(traitNames) != len(traitValues) or len(traitNames) != len(SE) or len(traitNames) != len(NStrain):
+				raise 'ValueError'
+			for item in traitValues:
+				if len(strainNames) != len(item):
+					raise 'ValueError'
+			for item in SE:
+				if len(strainNames) != len(item):
+					raise 'ValueError'
+			for item in NStrain:
+				if len(strainNames) != len(item):
+					raise 'ValueError'
+			for item in strainNames:
+ 				self.cursor.execute('''Select 
+ 								Strain.Id 
+ 							from Strain, StrainXRef,InbredSet 
+ 							where 
+ 								Strain.Name = "%s" AND
+ 								StrainXRef.StrainId = Strain.Id AND
+ 								StrainXRef.InbredSetId = InbredSet.Id AND
+ 								InbredSet.Name = "%s"
+ 							''' % (item, fd.RISet))
+ 				strainId = self.cursor.fetchone()[0]
+ 				strainIds.append(strainId)
+ 		except:
+			templatePage.__init__(self, fd)
+			detail = ['The format of the file is incorrect, or it contains unknown strains.']
+			self.error(heading=heading,detail=detail)
+			return
+		
+		self.searchResult = []	
+		self.addToTable(traitNames, strainNames,strainIds, traitValues,SE, NStrain, fd)
+		
+		if self.genSelection(fd=fd):
+			self.writeHTML(fd)
+	
+	def parseDataFile(self):
+		rchSartPos = 0
+		header = []
+		traits = []
+		data = []
+		se = []
+		nstrain = []
+		strains = []
+		
+		if 1:
+			for line in  self.batchDataFile:
+				line = line.strip()
+				if line == '' or line[0] == '#':
+					continue
+					
+				columns = string.split(line, '\t')
+				columns = map(string.strip, columns)
+				
+				if rchSartPos == 'column':
+					strains.append(columns[0])
+					tdata = map(webqtlUtil.StringAsFloat,columns[1:])
+					for j, item in enumerate(tdata):
+						if  posIdx[j][0] == 'data':
+							data[posIdx[j][1]].append(item)
+						elif  posIdx[j][0] == 'n':
+							if item != None:
+								nstrain[posIdx[j][1]].append(int(item))
+							else:
+								nstrain[posIdx[j][1]].append(item)
+						else:
+							se[posIdx[j][1]].append(item)
+							
+				elif rchSartPos == 'row':
+					if columns[0].lower() == 'se':
+						se.append(map(webqtlUtil.StringAsFloat,columns[1:]))
+					elif columns[0].lower() == 'n':
+						nstrain.append(map(webqtlUtil.IntAsFloat,columns[1:]))
+					else:
+						while (len(data) > len(se)):
+							se.append([None] * len(data[-1]))
+						while (len(data) > len(nstrain)):
+							nstrain.append([None] * len(data[-1]))
+						header.append(columns[0])
+						data.append(map(webqtlUtil.StringAsFloat,columns[1:]))
+ 				elif columns[0] == '@format=column':
+					rchSartPos = 'column'
+					posIdx = []
+					j = 0
+					for item in columns[1:]:
+						#assign column type
+						if string.lower(item) == 'se':
+							posIdx.append(('se',j-1))
+						elif string.lower(item) == 'n':
+							posIdx.append(('n',j-1))
+						else:
+							header.append(item)
+							posIdx.append(('data',j))
+							j += 1
+					
+					for i in range(len(header)):
+						data.append([])
+						se.append([])
+						nstrain.append([])
+ 				elif columns[0] == '@format=row':
+					rchSartPos = 'row'
+					strains = columns[1:]
+				else:
+					pass
+			#modify
+			for i in range(len(se)):
+				if se[i] == []:
+					se[i] = [None] * len(data[-1])
+			for i in range(len(nstrain)):
+				if nstrain[i] == []:
+					nstrain[i] = [None] * len(data[-1])
+			if len(data) > len(se):
+				se.append([None] * len(data[-1]))
+			if len(data) > len(nstrain):
+				nstrain.append([None] * len(data[-1]))
+			
+			return header,strains,data,se, nstrain
+		else:
+			return [],[],[],[], []
+
+
+	#XZ, add items to self.searchResult	
+	def addToTable(self, traitNames, strainNames,strainIds, traitValues, SE, NStrain, fd):
+		self.cursor.execute('delete Temp, TempData from Temp, TempData where Temp.DataId = TempData.Id and UNIX_TIMESTAMP()-UNIX_TIMESTAMP(CreateTime)>%d;' % webqtlConfig.MAXLIFE)
+		
+		i = 0
+		for trait in traitNames:
+			ct0 = time.localtime(time.time())
+			ct = time.strftime("%B/%d %H:%M:%S",ct0)
+			if trait == '':
+				trait = "Unnamed Trait"
+			user_ip = fd.remote_ip
+			newDescription = '%s entered at %s from IP %s' % (trait,ct,user_ip)
+			newProbeSetID = webqtlUtil.genRandStr('Usr_TMP_')
+			
+			self.cursor.execute('SelecT max(id) from TempData')
+			try:
+				DataId = self.cursor.fetchall()[0][0] + 1
+			except:
+				DataId = 1
+			
+			self.cursor.execute('Select Id  from InbredSet where Name = "%s"' % fd.RISet)
+			InbredSetId = self.cursor.fetchall()[0][0]
+					
+			self.cursor.execute('insert into Temp(Name,description, createtime,DataId,InbredSetId,IP) values(%s,%s,Now(),%s,%s,%s)' ,(newProbeSetID, newDescription, DataId,InbredSetId,user_ip))
+			
+			for k in range(len(traitValues[i])):
+				if traitValues[i][k] != None:
+					self.cursor.execute('insert into TempData(Id, StrainId, value, SE, NStrain) values(%s, %s, %s, %s, %s)' , (DataId, strainIds[k], traitValues[i][k],SE[i][k],NStrain[i][k]))
+			
+			self.searchResult.append('Temp::%s'	% newProbeSetID)
+			i += 1
+	
diff --git a/web/webqtl/collection/DisplaySelectionPage.py b/web/webqtl/collection/DisplaySelectionPage.py
new file mode 100755
index 00000000..02d4d4b8
--- /dev/null
+++ b/web/webqtl/collection/DisplaySelectionPage.py
@@ -0,0 +1,51 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+#DisplaySelectionPage.py
+
+from base.templatePage import templatePage
+from AddToSelectionPage import AddToSelectionPage
+
+#########################################
+#     Display Selection Page
+#########################################
+class DisplaySelectionPage(AddToSelectionPage):
+
+	def __init__(self, fd):
+
+		templatePage.__init__(self, fd)
+
+		if not self.openMysql():
+			return
+
+		if not fd.genotype:
+			fd.readGenotype()
+
+		self.searchResult = []
+
+		self.genSelection(fd=fd)
+
+		self.writeHTML(fd)
diff --git a/web/webqtl/collection/ExportSelectionDetailInfoPage.py b/web/webqtl/collection/ExportSelectionDetailInfoPage.py
new file mode 100755
index 00000000..69f293b2
--- /dev/null
+++ b/web/webqtl/collection/ExportSelectionDetailInfoPage.py
@@ -0,0 +1,197 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+#ExportSelectionDetailInfoPage.py
+
+import string
+from htmlgen import HTMLgen2 as HT
+import os
+import time
+import pyXLWriter as xl
+
+import reaper
+
+from base import webqtlConfig
+from base.templatePage import templatePage
+from utility import webqtlUtil
+from base.webqtlTrait import webqtlTrait
+	
+		
+#########################################
+#      Export Selection DetailInfo Page
+#########################################
+class ExportSelectionDetailInfoPage(templatePage):
+
+	def __init__(self,fd):
+
+		templatePage.__init__(self, fd)
+		
+		if not self.openMysql():
+			return
+		
+		fd.incparentsf1 = 1
+		if not fd.genotype:
+			fd.readGenotype()
+
+		locusChr = {}
+		locusMb = {}
+		for chr in fd.genotype:
+			for locus in chr:
+				locusChr[locus.name] = locus.chr
+				locusMb[locus.name] = locus.Mb
+				
+		self.searchResult = fd.formdata.getvalue('searchResult')
+		
+		if not self.searchResult:
+			templatePage.__init__(self, fd)
+			heading = 'Export Collection'
+			detail = ['You need to select at least one trait to export.']
+			self.error(heading=heading,detail=detail)
+			return
+			
+		self.RISet = fd.formdata.getvalue("RISet")	
+		self.cursor.execute("Select Species.Name from Species, InbredSet where InbredSet.SpeciesId = Species.Id and InbredSet.Name = '%s'" % self.RISet)
+		self.Species = self.cursor.fetchone()[0]
+		
+		if type("1") == type(self.searchResult):
+			self.searchResult = string.split(self.searchResult,'\t')
+		strainlist = fd.f1list + fd.strainlist
+		fields = ["ID", "Species", "Cross", "Database", "ProbeSetID / RecordID", "Symbol", "Description", "ProbeTarget", "PubMed_ID", "Phenotype", "Chr", "Mb", "Alias", "Gene_ID", "HomoloGene_ID", "UniGene_ID", "Strand_Probe ", "Strand_Gene ", "Probe_set_specificity", "Probe_set_BLAT_score", "Probe_set_BLAT_Mb_start", "Probe_set_BLAT_Mb_end ", "QTL_Chr", "QTL_Mb", "Locus_at_Peak", "Max_LRS", "P_value_of_MAX", "Mean_Expression"] + strainlist
+		
+		if self.searchResult:
+			traitList = []
+			for item in self.searchResult:
+				thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
+				thisTrait.retrieveInfo(QTL=1)
+				thisTrait.retrieveData(strainlist=strainlist)
+				traitList.append(thisTrait)
+
+			text = [fields]
+			for i, thisTrait in enumerate(traitList):
+				if thisTrait.db.type == 'ProbeSet':
+					if not thisTrait.cellid: #ProbeSet
+						#12/22/2009, XZ: We calculated LRS for each marker(locus) in geno file and record the max LRS and its corresponding marker in MySQL database. But after the calculation, Rob deleted several markers. If one of the deleted markers happen to be the one recorded in database, error will occur. So we have to deal with this situation.
+						if locusChr.has_key(thisTrait.locus) and locusMb.has_key(thisTrait.locus):
+							text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, thisTrait.symbol, thisTrait.description, thisTrait.probe_target_description,"", "", thisTrait.chr, thisTrait.mb, thisTrait.alias, thisTrait.geneid, thisTrait.homologeneid, thisTrait.unigeneid, thisTrait.strand_probe, thisTrait.strand_gene, thisTrait.probe_set_specificity, thisTrait.probe_set_blat_score, thisTrait.probe_set_blat_mb_start, thisTrait.probe_set_blat_mb_end, locusChr[thisTrait.locus], locusMb[thisTrait.locus], thisTrait.locus, thisTrait.lrs, thisTrait.pvalue])
+						else:
+                                                        text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, thisTrait.symbol, thisTrait.description, thisTrait.probe_target_description,"", "", thisTrait.chr, thisTrait.mb, thisTrait.alias, thisTrait.geneid, thisTrait.homologeneid, thisTrait.unigeneid, thisTrait.strand_probe, thisTrait.strand_gene, thisTrait.probe_set_specificity, thisTrait.probe_set_blat_score, thisTrait.probe_set_blat_mb_start, thisTrait.probe_set_blat_mb_end, "", "", "", "", ""])
+                                        else: #Probe
+                                                text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name + " : " + thisTrait.cellid, thisTrait.symbol, thisTrait.description, thisTrait.probe_target_description,"", "", thisTrait.chr, thisTrait.mb, thisTrait.alias, thisTrait.geneid, thisTrait.homologeneid, thisTrait.unigeneid, "", "", "", "", "", "", "", "", "", "", ""])
+
+				elif thisTrait.db.type == 'Publish':
+					#XZ: need to consider confidential phenotype
+					PhenotypeString = thisTrait.post_publication_description
+					if thisTrait.confidential:
+						if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users):
+							PhenotypeString = thisTrait.pre_publication_description
+					text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, "", "", "", thisTrait.pubmed_id, PhenotypeString, "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""])
+				elif thisTrait.db.type == 'Temp':
+					text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, "", thisTrait.description, "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "","", ""])
+				elif thisTrait.db.type == 'Geno':
+					text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, "", thisTrait.name,"", "", "", thisTrait.chr, thisTrait.mb, "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""])
+				else:
+					continue
+				
+				testval = thisTrait.exportData(strainlist)
+				try:
+					mean = reaper.anova(testval)[0]
+				except:
+					count = 0
+					sum = 0
+					for oneValue in testval:
+						try:
+							oneValue = float(oneValue)
+							sum = sum + oneValue
+							count = count + 1
+						except:
+							pass
+					mean = sum/count
+				text[-1].append(mean)
+				text[-1] += testval
+			if len(text[0]) < 255 or len(text) < 255:
+				transpose = 0
+				if len(text[0]) >= 255:
+					text = webqtlUtil.transpose(text)
+					transpose = 1
+				filename = os.path.join(webqtlConfig.TMPDIR, webqtlUtil.generate_session() +'.xls')
+							
+				# Create a new Excel workbook
+				workbook = xl.Writer(filename)
+				worksheet = workbook.add_worksheet()
+				headingStyle = workbook.add_format(align = 'center', bold = 1, size=13, color = 'green')
+				titleStyle = workbook.add_format(align = 'left', bold = 0, size=13, border = 1, border_color="gray")
+				
+				##Write title Info
+				# Modified by Hongqiang Li
+				# worksheet.write([0, 0], "Data source: The GeneNetwork at web2qtl.utmem.edu:88", titleStyle)
+				# worksheet.write([1, 0], "Citations: Please see web2qtl.utmem.edu:88/reference.html", titleStyle)
+				worksheet.write([0, 0], "Data source: The GeneNetwork at %s" % webqtlConfig.PORTADDR, titleStyle)
+				worksheet.write([1, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle)
+				#
+				worksheet.write([2, 0], "Date : %s" % time.strftime("%B %d, %Y", time.gmtime()), titleStyle)
+				worksheet.write([3, 0], "Time : %s GMT" % time.strftime("%H:%M ", time.gmtime()), titleStyle)
+			
+				# Modified by Hongqiang Li	
+				# worksheet.write([4, 0], "Status of data ownership: Possibly unpublished data; please see web2qtl.utmem.edu:88/statusandContact.html for details on sources, ownership, and usage of these data.", titleStyle)
+				worksheet.write([4, 0], "Status of data ownership: Possibly unpublished data; please see %s/statusandContact.html for details on sources, ownership, and usage of these data." % webqtlConfig.PORTADDR, titleStyle)
+				#
+				worksheet.write([6, 0], "This output file contains data from %d GeneNetwork databases listed below" % len(traitList), titleStyle)
+			
+				# Row and column are zero indexed
+				nrow = startRow = 8
+				for row in text:
+				    for ncol, cell in enumerate(row):
+				    	if nrow == startRow:
+				        	worksheet.write([nrow, ncol], cell.strip(), headingStyle)
+				        	worksheet.set_column([ncol, ncol], 2*len(cell))
+				    	else:
+				        	worksheet.write([nrow, ncol], cell)
+				    nrow += 1
+				
+				worksheet.write([nrow+1, 0], "Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA 21131), NCI MMHCC (U01CA105417), and NCRR (U24 RR021760)", titleStyle)
+				worksheet.write([nrow+2, 0], "PLEASE RETAIN DATA SOURCE INFORMATION WHENEVER POSSIBLE", titleStyle)
+				workbook.close()
+								
+				fp = open(filename, 'rb')
+				text = fp.read()
+				fp.close()
+				
+				self.content_type = 'application/xls'
+				self.content_disposition = 'attachment; filename=%s' % ('export-%s.xls' % time.strftime("%y-%m-%d-%H-%M"))
+				self.attachment = text
+			else:
+				self.content_type = 'application/xls'
+				self.content_disposition = 'attachment; filename=%s' % ('export-%s.txt' % time.strftime("%y-%m-%d-%H-%M"))
+				for item in text:
+					self.attachment += string.join(map(str, item), '\t')+ "\n"
+			self.cursor.close()
+		else:
+			fd.req.content_type = 'text/html'
+			heading = 'Export Collection'
+			detail = [HT.Font('Error : ',color='red'),HT.Font('Error occurs while retrieving data from database.',color='black')]
+			self.error(heading=heading,detail=detail)
+			
+			
diff --git a/web/webqtl/collection/ExportSelectionPage.py b/web/webqtl/collection/ExportSelectionPage.py
new file mode 100755
index 00000000..df401e9e
--- /dev/null
+++ b/web/webqtl/collection/ExportSelectionPage.py
@@ -0,0 +1,67 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+#ExportSelectionPage.py
+
+import string
+import time
+
+from base.templatePage import templatePage
+	
+
+#########################################
+#     Export Selection Page
+#########################################
+class ExportSelectionPage(templatePage):
+
+	def __init__(self, fd):
+
+		templatePage.__init__(self, fd)
+
+		collectionName = '%s_Select' % fd.RISet
+
+		try:
+			preSelection = fd.input_session_data[collectionName]
+			preSelection = list(string.split(preSelection,','))
+		except:
+			preSelection = []
+
+		for item in preSelection:
+                        if not item:
+                                preSelection.remove(item)
+
+		if preSelection:
+			self.content_type = 'application/txt'
+			self.content_disposition = 'attachment; filename=%s' % (fd.RISet+'_export-%s.txt' % time.strftime("%y-%m-%d-%H-%M"))
+			self.attachment += fd.RISet+"\n"
+			for item in preSelection:
+				self.attachment += item+"\n"
+		else:
+			heading = 'Export Collection'
+                        detail = ['This collection is empty. No trait could be exported.']
+                        self.error(heading=heading,detail=detail)
+		
+
diff --git a/web/webqtl/collection/ImportSelectionPage.py b/web/webqtl/collection/ImportSelectionPage.py
new file mode 100755
index 00000000..0702509b
--- /dev/null
+++ b/web/webqtl/collection/ImportSelectionPage.py
@@ -0,0 +1,92 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+#ImportSelectionPage.py
+
+import string
+
+from base.templatePage import templatePage
+from AddToSelectionPage import AddToSelectionPage
+				
+
+#########################################
+#     Import Selection Page
+#########################################
+class ImportSelectionPage(AddToSelectionPage):
+
+	def __init__(self, fd):
+
+		templatePage.__init__(self, fd)
+
+		if not self.openMysql():
+			return
+
+		if not fd.genotype:
+			fd.readGenotype()
+		
+		self.importFile = fd.formdata.getvalue('importfile')
+		if not self.importFile:
+			templatePage.__init__(self, fd)
+			heading = 'Import Collection'
+			detail = ['The file you choose to import from doesn\'t exist.']
+			self.error(heading=heading,detail=detail)
+			return
+		self.importFile = string.split(self.importFile, '\n')
+		
+		RISetLocate = 0
+		self.searchResult = []
+		for line in self.importFile:
+			if line and line[0] != '#':
+				if not RISetLocate:
+					RISetLocate = line
+					if RISetLocate != fd.RISet:
+						templatePage.__init__(self, fd)
+						heading = 'Import Collection'
+						detail = ['The file you choose to import from doesn\'t contain %s selection.' % fd.RISet]
+						self.error(heading=heading,detail=detail)
+						return
+				else:
+					self.searchResult.append(line)
+		
+		if not self.searchResult:
+			templatePage.__init__(self, fd)
+			heading = 'Import Collection'
+			detail = ['The file you choose to import from is empty.']
+			self.error(heading=heading,detail=detail)
+			return
+				
+		self.importMethod = fd.formdata.getvalue('importmethod')
+		
+		if self.importMethod == 'replace':
+			checkPreSelection = 0
+		else:
+			checkPreSelection = 1
+			
+		if self.genSelection(fd=fd, checkPreSelection = checkPreSelection):
+			self.writeHTML(fd)
+	
+
+		
diff --git a/web/webqtl/collection/RemoveSelectionPage.py b/web/webqtl/collection/RemoveSelectionPage.py
new file mode 100755
index 00000000..b9560c6b
--- /dev/null
+++ b/web/webqtl/collection/RemoveSelectionPage.py
@@ -0,0 +1,108 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+
+
+import string
+
+from base.templatePage import templatePage
+from base.webqtlTrait import webqtlTrait	
+from AddToSelectionPage import AddToSelectionPage
+
+#########################################
+#      Remove Selection Page
+#########################################
+class RemoveSelectionPage(AddToSelectionPage):
+
+	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 self.searchResult:
+			pass
+		else:
+			templatePage.__init__(self, fd)
+			heading = 'Remove Selections'
+			detail = ['You need to select at least one trait to remove from your selection.']
+			self.error(heading=heading,detail=detail)
+			return
+
+		self.genSelection(fd=fd)
+		self.writeHTML(fd)
+
+
+
+	def genSelection(self, fd=None):
+		collectionName = '%s_Select' % fd.RISet
+
+		try:
+			preSelection = fd.input_session_data[collectionName]
+			preSelection = list(string.split(preSelection,','))
+		except:
+			preSelection = []
+		
+		if type("1") == type(self.searchResult):
+			self.searchResult = [self.searchResult]
+		
+		if preSelection:
+			for item in self.searchResult:
+				try:
+					preSelection.remove(item)
+				except:
+					pass
+		self.searchResult = preSelection[:]
+		
+		if not self.searchResult:
+			self.session_data_changed[collectionName] = ""
+			return
+		
+		#self.searchResult.sort()
+		for item in self.searchResult:
+			if not item:
+				self.searchResult.remove(item)
+				
+		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
+
diff --git a/web/webqtl/collection/__init__.py b/web/webqtl/collection/__init__.py
new file mode 100755
index 00000000..e69de29b
--- /dev/null
+++ b/web/webqtl/collection/__init__.py