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

1 files changed, 0 insertions, 1350 deletions

diff --git a/web/javascript/webqtl.js b/web/javascript/webqtl.js
deleted file mode 100755
index 536e7d26..00000000
--- a/web/javascript/webqtl.js
+++ /dev/null
@@ -1,1350 +0,0 @@
-// var NS4 = (document.layers) ? 1 : 0;
-// var IE4 = (document.all) ? 1 : 0;
-
-function openNewWin(myURL){
-	windowName = 'formTarget' + (new Date().getTime());
-	if (openNewWin.arguments.length == 2){
-  		newWindow = open(myURL,windowName,openNewWin.arguments[1]);
-	}
-	else{
-		newWindow = open(myURL,windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-	}
-}
-
-/*XZ, 9/2/2009*/
-/*submit form to new window*/
-function submitToNewWindow(thisForm){
-        var windowName = genNewWin();
-        newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-        newWindow.focus();
-        thisForm.target = windowName;
-        thisForm.submit();
-}
-
-/*Obsolete and To be mofdified*/
-/*
-function makeTree(thisForm, nnn){
-  	var trait_list2 = new Array();
-	var correlation2 = new Array();
-	var symbol_list2 = new Array();
-	var length = document.showDatabase.searchResult.length;
-	var j = 0
-	for(var i = 0; i < length; i++)
-	{
-		if (document.showDatabase.searchResult[i].checked == true){
-			trait_list2 = trait_list2.concat(trait_list[i]);
-			correlation2 = correlation2.concat(correlation[i]);
-			symbol_list2 = symbol_list2.concat(symbol_list[i]);
-			j += 1;
-		}
-	}
-
-	var windowName = 'formTarget' + (new Date().getTime());
-	var newWindow = open("", windowName,"width=900,menubar=0,toolbar=1,resizable=1,status=1,scrollbars=1");
-	var html = "";
-	if (j > 0)
-	{
-		var waithtml1 ="<Blockquote class='title' id='red'>Your list of "+j+" transcripts is being exported to the Gene Ontology Tree Machine for analysis. This window will soon be replaced with the main GOTM results.</Blockquote>";
-	}
-	else
-	{
-		var waithtml1 ="<Blockquote class='title' id='red'>Your should select at least one transcript to export to the Gene Ontology Tree Machine for analysis.</Blockquote>";
-	}
-  	html +=  waithtml1;
-  	//newWindow.document.write(html);
-  	//newWindow.document.close();
-  	newWindow.focus();
-  	if (j > 0)
-  	{
-		thisForm.trait_list.value = trait_list2.join(',');
-		thisForm.correlation.value = correlation2.join(',');
-		thisForm.symbol_list.value = symbol_list2.join(',');
-		thisForm.target = windowName;
-		thisForm.submit();
-	}
-}
-*/
-
-function showCorrelationPlot(ProbeSetID,CellID){
-	windowName = 'formTarget' + (new Date().getTime());
-	newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-	document.showDatabase.target = windowName;
-	document.showDatabase.FormID.value = "showCorrelationPlot";
-	document.showDatabase.ProbeSetID.value = ProbeSetID;
-	document.showDatabase.CellID.value = CellID;
-	document.showDatabase.submit();
-}
-
-
-function showPairPlot(ChrA,ChrB){
-	windowName = 'formTarget' + (new Date().getTime());
-	newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-	document.showPairPlot.target = windowName;
-	document.showPairPlot.Chr_A.value = ChrA;
-	document.showPairPlot.Chr_B.value = ChrB;
-	document.showPairPlot.submit();
-}
-
-function showCorrelationPlot2(db, ProbeSetID, CellID, db2, ProbeSetID2, CellID2, rank){
-	windowName = 'formTarget' + (new Date().getTime());
-	newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-	document.showDatabase.target = windowName;
-	document.showDatabase.FormID.value = "showCorrelationPlot";
-	document.showDatabase.database.value = db;
-	document.showDatabase.ProbeSetID.value = ProbeSetID;
-	document.showDatabase.CellID.value = CellID;
-	document.showDatabase.database2.value = db2;
-	document.showDatabase.ProbeSetID2.value = ProbeSetID2;
-	document.showDatabase.CellID2.value = CellID2;
-	document.showDatabase.rankOrder.value = rank;
-
-	//This is to make sure the type of correlation is Sample Correlation
-	if(typeof(document.showDatabase.X_geneSymbol) !== 'undefined'){
-		document.showDatabase.X_geneSymbol.value = null;
-		document.showDatabase.Y_geneSymbol.value = null;
-	}
-
-	document.showDatabase.submit();
-}
-
-
-function showProbeInfo(Database,ProbeSetID,CellID){
-	windowName = 'formTarget' + (new Date().getTime());
-	newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-	document.showDatabase.target = windowName;
-	document.showDatabase.FormID.value = "showProbeInfo";
-	document.showDatabase.database.value = Database;
-	document.showDatabase.ProbeSetID.value = ProbeSetID;
-	document.showDatabase.CellID.value = CellID;
-	document.showDatabase.submit();
-}
-
-
-function showDatabase(ProbeSetID,CellID){
-	windowName = 'formTarget' + (new Date().getTime());
-	newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-	document.showDatabase.target = windowName;
-	document.showDatabase.FormID.value = "showDatabase";
-	document.showDatabase.ProbeSetID.value = ProbeSetID;
-	document.showDatabase.CellID.value = CellID;
-	document.showDatabase.submit();
-}
-
-
-
-function showDatabase2(Database,ProbeSetID,CellID){
-	windowName = 'formTarget' + (new Date().getTime());
-	newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-	document.showDatabase.target = windowName;
-	document.showDatabase.FormID.value = "showDatabase";
-	document.showDatabase.database.value = Database;
-	document.showDatabase.ProbeSetID.value = ProbeSetID;
-	document.showDatabase.CellID.value = CellID;
-	document.showDatabase.submit();
-}
-
-
-function showDatabase3(formName, Database,ProbeSetID,CellID){
-	windowName = 'formTarget' + (new Date().getTime());
-	newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-	document[formName].target = windowName;
-	document[formName].FormID.value = "showDatabase";
-	document[formName].database.value = Database;
-	document[formName].ProbeSetID.value = ProbeSetID;
-	document[formName].CellID.value = CellID;
-	console.log("formName:", formName)
-	console.log("document[formName]:", document[formName])
-	console.log("submit turned off for debugging")
-	console.log("showDatabase3 is deprecated for the flask version of this site")
-	//document[formName].submit();
-}
-
-
-function showTextResult(){
-	windowName = 'formTarget' + (new Date().getTime());
-	newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-	document.SEARCHFORM.target = windowName;
-	document.SEARCHFORM.submit();
-	newWindow.focus()
-}
-
-/*New form name independent function*/
-function getForm(fmName){
-	var match = 0;
-	for (i=0; i< document.forms.length;i++){
-		if (document.forms[i].name == fmName){
-			thisForm = document.forms[i];
-			match = 1;
-			return thisForm;
-		}
-	}
-	if (match == 0)
-		return null;
-}
-
-function genNewWin(){
-	windowName = 'formTarget' + (new Date().getTime());
-	newWindow = open("",windowName, "menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-	return windowName;
-}
-
-function showTrait(fmName){
-	var thisForm = getForm(fmName);
-	if (thisForm == null || showTrait.arguments.length < 2)
-		return;
-
-	windowName = genNewWin();
-	thisForm.target = windowName;
-
-	thisForm.FormID.value = "showDatabase";
-	thisForm.ProbeSetID.value = showTrait.arguments[1];
-	if (showTrait.arguments.length > 2)
-		thisForm.CellID.value = showTrait.arguments[2];
-	else
-		thisForm.CellID.value = "";
-	thisForm.submit();
-}
-
-function showCateGraph(fmName){
-	var thisForm = getForm(fmName);
-	if (thisForm == null || showCateGraph.arguments.length < 2)
-		return;
-
-	windowName = genNewWin();
-	thisForm.target = windowName;
-
-	thisForm.FormID.value = "showCategoryGraph";
-	thisForm.interval1.value = showCateGraph.arguments[1];
-	thisForm.interval2.value = showCateGraph.arguments[2];
-	thisForm.submit();
-}
-
-function showCorrPlot(fmName){
-	var thisForm = getForm(fmName);
-	if (thisForm == null || showCorrPlot.arguments.length < 2)
-		return;
-
-	windowName = genNewWin();
-	thisForm.target = windowName;
-
-	thisForm.FormID.value = "showCorrelationPlot";
-	thisForm.ProbeSetID.value = showCorrPlot.arguments[1];
-	if (showCorrPlot.arguments.length > 2)
-		thisForm.CellID.value = showCorrPlot.arguments[2];
-	else
-		thisForm.CellID.value = "";
-
-	thisForm.X_geneSymbol.value = null;
-	thisForm.Y_geneSymbol.value = null;
-
-	thisForm.submit();
-
-}
-
-
-function showCorrPlotThird(fmName){
-	var thisForm = getForm(fmName);
-	if (thisForm == null || showCorrPlotThird.arguments.length < 3)
-		return;
-
-	windowName = genNewWin();
-	thisForm.target = windowName;
-
-	var olddb = thisForm.database.value;
-
-	thisForm.FormID.value = "showCorrelationPlot";
-	thisForm.database.value = showCorrPlotThird.arguments[1];
-	thisForm.ProbeSetID.value = showCorrPlotThird.arguments[2];
-	if (showCorrPlotThird.arguments.length > 3)
-		thisForm.CellID.value = showCorrPlotThird.arguments[3];
-	else
-		thisForm.CellID.value = "";
-	thisForm.submit();
-	thisForm.database.value = olddb;
-}
-
-/*
-function ODE(thisForm, script){
-	var trait_list_all = new Array();
-	var correlation_all = new Array();
-	var llid_list_all = new Array();
-  	var trait_list2 = new Array();
-	var correlation2 = new Array();
-	var llid_list2 = new Array();
-	var length = thisForm.searchResult.length;
-	var j = 0;
-	for(var i = 0; i < length; i++){
-		var p = corrArray[thisForm.searchResult[i].value];
-		if (thisForm.searchResult[i].checked == true){
-			trait_list2 = trait_list2.concat(p.name);
-			correlation2 = correlation2.concat(p.corr);
-			llid_list2 = llid_list2.concat(p.geneid);
-			j += 1;
-		}
-		trait_list_all = trait_list_all.concat(p.name);
-		correlation_all = correlation_all.concat(p.corr);
-		llid_list_all = llid_list_all.concat(p.geneid);
-	}
-	var windowName = 'formTarget' + (new Date().getTime());
-	var newWindow = open("", windowName, "width=900,menubar=0,toolbar=1,resizable=1,status=1,scrollbars=1");
-	var html = "";
-	if (j == 0){
-		j = length;
-		trait_list2 = trait_list_all;
-		correlation2 = correlation_all;
-		llid_list2 = llid_list_all;
-	}
-
-	var waithtml1 ="<Blockquote class='title' id='red'>Your list of "+j+" transcripts is being exported to the ODE for analysis. This window will soon be replaced with the results.</Blockquote>";
-
-  	html +=  waithtml1;
-  	newWindow.document.write(html);
-  	newWindow.document.close();
-  	newWindow.focus();
-  	if (j > 0){
-		thisForm.id_list.value = trait_list2.join(',');
-		thisForm.correlation.value = correlation2.join(',');
-		thisForm.id_value.value = thisForm.correlation.value;
-		thisForm.llid_list.value = llid_list2.join(',');
-
-		// ODE
-
-		thisForm.idtype.value = thisForm.id_type.value;
-		thisForm.species.value = thisForm.org.value;
-		thisForm.list.value = thisForm.id_list.value;
-		thisForm.client.value = "genenetwork";
-
-		thisForm.target = windowName;
-		var oldaction = thisForm.action;
-		thisForm.action = script;
-		thisForm.submit();
-		thisForm.action = oldaction;
-	}
-}
-*/
-// 02/12/2009
-// Lei Yan
-
-/*scripts in the Dataediting form*/
-
-function dataEditingFunc(thisForm,submitIdValue){
-
-	windowName = 'formTarget' + (new Date().getTime());
-
-	if (thisForm.FormID.value!='secondRegression'){
-		thisForm.FormID.value = 'dataEditing';
-	}
-
-	if ((submitIdValue == "markerRegression")||(submitIdValue == "compositeRegression")){
-		thisForm.topten.value = "";
-	}
-
-	else if (submitIdValue == "addRecord"){
-		windowName = thisForm.RISet.value;
-		var name = thisForm.identification.value;
-		if (name != ""){
-		}
-		else{
-			name = "Unnamed Trait";
-    		}
-		Namebox = prompt("Name of your trait",name);
-		thisForm.identification.value = Namebox;
-	}
-
-	else{
-	}
-
-	newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-	thisForm.target = windowName;
-	newWindow.focus();
-	thisForm.submitID.value = submitIdValue;
-	thisForm.submit();
-}
-
-/*searchForm etc.*/
-function databaseFunc(thisForm,formIdValue){
-	if(formIdValue=="GOTree" && typeof(corrArray)!='undefined' && corrArray!=null){
-                makeListCorrelation(thisForm);
-        }
-
-	windowName = 'formTarget' + (new Date().getTime());
-	newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-	if (databaseFunc.arguments.length > 2){
-  		newWindow.document.write("<center><H3><font color='black' face='verdana'>" + databaseFunc.arguments[2]+ "</font></h3></center>");
-  		newWindow.document.close();
-	}
-	newWindow.focus();
-	thisForm.target = windowName;
-	thisForm.FormID.value = formIdValue;
-	thisForm.submit();
-}
-
-/* make a list of correlation values for GOTree */
-function makeListCorrelation(thisForm){
-	var correlation = new Array();
-	for(var i = 0; i < thisForm.searchResult.length; i++){
-		if (thisForm.searchResult[i].checked == true){
-			var p = corrArray[thisForm.searchResult[i].value];
-			correlation = correlation.concat(p.corr);
-		}
-	}
-	thisForm.correlation.value = correlation.join(',');
-}
-
-/*add/remove selection*/
-
-function addRmvSelection(windowName, thisForm, addORrmv){
-	var newWindow = window.open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-	thisForm.target = windowName;
-	thisForm.FormID.value = addORrmv;
-	thisForm.submit();
-	newWindow.focus();
-}
-
-function batchSelection(thisForm){
-  	var select = thisForm.RISet;
-  	var windowName = select.options[select.selectedIndex].value;
-	var newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-	newWindow.focus();
-	thisForm.target = windowName;
-	thisForm.submit();
-}
-
-/*opener involved*/
-
-function showTop10(formName, submitIdValue){
-	var match = 0;
-	for (i=0; i< window.opener.document.forms.length;i++){
-		if (window.opener.document.forms[i].name == formName){
-			thisForm = window.opener.document.forms[i];
-			match = 1;
-			break;
-		}
-	}
-	if (match == 0)
-		return;
-
-	thisForm.target = self.name;
-	if ((submitIdValue == "markerRegression")||(submitIdValue == "compositeRegression")){
-		thisForm.topten.value = "topten";
-	}
-
-	thisForm.submitID.value = submitIdValue;
-	thisForm.submit();
-}
-
-
-function showIndividualChromosome(formName, submitIdValue, ii){
-	var match = 0;
-	for (i=0; i< window.opener.document.forms.length;i++){
-		if (window.opener.document.forms[i].name == formName){
-			thisForm = window.opener.document.forms[i];
-			match = 1;
-			break;
-		}
-	}
-	if (match == 0)
-		return;
-
-	windowName = 'formTarget' + (new Date().getTime());
-	newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-	newWindow.focus();
-	thisForm.target = windowName;
-
-	if (submitIdValue == "showIntMap"){
-		thisForm.chromosomes.value = ii;
-	}
-	else{
-		thisForm.chromosomes.selectedIndex = ii;
-	}
-
-	thisForm.FormID.value = submitIdValue;
-	thisForm.submit();
-
-}
-
-/*end of opener*/
-
-function showSample(thisForm){
-	thisForm.submitID.value = "sample";
-	thisForm.submit();
-}
-
-function showNext(thisForm){
-	thisForm.submitID.value = "next";
-	thisForm.submit();
-}
-
-
-function changeStatusSubmit(thisForm, status) {
-	thisForm.status.value = status;
-        thisForm.submit();
-}
-
-function editHTML(thisForm, execCommand){
-	if (execCommand == "preview"){
-		windowName = 'formTarget' + (new Date().getTime());
-		newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-		newWindow.focus();
-		thisForm.target = windowName;
-		thisForm.preview.value = "newWindow";
-		thisForm.submit();
-	}
-	else if (execCommand == "submit"){
-		//thisForm.target = window;
-		thisForm.preview.value = "";
-		thisForm.submit();
-	}
-	else{
-	}
-}
-
-function dataWindow(form){
-  var SaveAs = (document.execCommand) ? 1 : 0;
-  newWindow = open("", "thankYouWin","width=600,menubar=1,toolbar=1,height=300,resizable=0,status=1,scrollbars=1");
-  var html = "";
-  for (var i=0; i < form.length; i++)
-   {
-        if (form.elements[i].type == "text")
-        {
-                if (form.elements[i].value=="")
-                   html +="x ";
-                else
-                   html += form.elements[i].value+" ";
-        }
-   }
-  newWindow.document.open();
-  newWindow.document.write(html);
-  newWindow.document.close();
-  newWindow.focus();
-
-  if (!SaveAs)
-	{alert("Feature is not avaiable in current type of browser,You \nneed to manually save the content into a text format \nfile, The window will be automatically closed in 20 \nseconds!");
-	setTimeout("newWindow.close()", 20000);}
-  else
-    {
-	  if (newWindow.document.execCommand('SaveAs',false,'.txt'))
-		{newWindow.close();}
-	  else{
-	    alert("Either you cancelled the SaveAs Dialog, or this feature \nis not avaiable in current type of browser, You \ncan manually save the content into a text format file.");
-	    setTimeout("newWindow.close()", 20000);
-	  }
-	}
-}
-
-
-function xchange() {
-  var select = document.crossChoice.RISet;
-  var value = select.options[select.selectedIndex].value;
-
-  if (value !="BDAI") return;
-  document.crossChoice.variance.checked = false;
-}
-
-/*display Info Page and Data Set buttom Added by A. Centeno*/
-
-function datasetinfo(){
-    var windowName = 'dataset_info' + (new Date().getTime());
-    var select = document.SEARCHFORM.database;
-    var database = select.options[select.selectedIndex].value;
-	var page = '/webqtl/main.py?FormID=sharinginfo&InfoPageName=' + database;
-    newWindow = open(page,windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-    newWindow.focus();
-}
-
-function databaseinfo(){
-    var windowName = 'database_info' + (new Date().getTime());
-    var select = document.SEARCHFORM.database;
-    var database = select.options[select.selectedIndex].value;
-    var page = '/webqtl/main.py?FormID=sharinginfo&InfoPageName=' + database;
-    newWindow = open(page,windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-    newWindow.focus();
-}
-
-function crossinfo(){
-    var windowName = 'cross_info';
-    var select0 = document.SEARCHFORM.species;
-    var select1 = document.SEARCHFORM.cross;
-    var specie = select0.options[select0.selectedIndex].value;
-    var database = select1.options[select1.selectedIndex].value;
-    var page = '/' + specie + 'Cross.html#' + database;
-    newWindow = open(page,windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-    newWindow.focus();
-}
-
-function crossinfo2(){
-    var windowName = 'cross_info';
-    var select = document.crossChoice.RISet;
-    var database = select.options[select.selectedIndex].value;
-    var page = '/cross.html#' + database;
-    newWindow = open(page,windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-    newWindow.focus()
-}
-
-
-function checkWidth(){
-	var width = document.getElementsByName('plotSize')[0].value
-
-	if (width < 600) {
-		alert("Plot size is too small - setting size to 600")
-		document.getElementsByName('plotSize')[0].value = 600
-	}
-}
-
-function changeLineColor(){
-	var lineColor = document.getElementsByName('lineColorSel')[0].value
-
-	document.getElementsByName('lineColor')[0].value = lineColor
-}
-
-function changeLineSize(){
-	var lineSize = document.getElementsByName('lineSizeSel')[0].value
-
-	document.getElementsByName('lineSize')[0].value = lineSize
-}
-
-function changeIdColor(){
-	var idColor = document.getElementsByName('idColorSel')[0].value
-
-	document.getElementsByName('idColor')[0].value = idColor
-}
-
-function changeIdFont(){
-	var idFont = document.getElementsByName('idFontSel')[0].value
-
-	document.getElementsByName('idFont')[0].value = idFont
-}
-
-function changeIdSize(){
-	var idSize = document.getElementsByName('idSizeSel')[0].value
-
-	document.getElementsByName('idSize')[0].value = idSize
-}
-
-function changeSymbolColor(){
-	var symbolColor = document.getElementsByName('colorSel')[0].value
-
-	document.getElementsByName('symbolColor')[0].value = symbolColor
-}
-
-function changeSymbol(){
-	var symbol = document.getElementsByName('symbolSel')[0].value
-
-	document.getElementsByName('symbol')[0].value = symbol
-}
-
-function changeFilled(){
-	var filled = document.getElementsByName('fillSel')[0].value
-
-	document.getElementsByName('filled')[0].value = filled
-}
-
-function changeSize(){
-	var symbolSize = document.getElementsByName('sizeSel')[0].value
-
-	document.getElementsByName('symbolSize')[0].value = symbolSize
-}
-
-
-function checkAll(thisForm){
-	var length = thisForm.searchResult.length;
-	for(var i = 0; i < length; i++)
-	{
-		thisForm.searchResult[i].checked = true;
-		highlight(thisForm.searchResult[i]);
-	}
-}
-
-function checkNone(thisForm){
-	var length = thisForm.searchResult.length;
-	for(var i = 0; i < length; i++)
-	{
-		thisForm.searchResult[i].checked = false;
-		highlight(thisForm.searchResult[i]);
-	}
-}
-
-function checkInvert(thisForm){
-	var length = thisForm.searchResult.length;
-	for(var i = 0; i < length; i++)
-	{
-		thisForm.searchResult[i].checked = !(thisForm.searchResult[i].checked);
-		highlight(thisForm.searchResult[i]);
-	}
-}
-
-/*Not used anymore*/
-function checkTraits2(thisForm){
-	var length = thisForm.searchResult.length;
-	var category = thisForm.selectmenu.value;
-	for(var i = 0; i < length; i++)
-	{
-		if (category == 'gt0.8')
-		{
-			if (correlation[i] > 0.8)
-				{thisForm.searchResult[i].checked = true;}
-			else
-				{thisForm.searchResult[i].checked = false;}
-		}
-		else if (category == 'gt0.4')
-		{
-			if (correlation[i] > 0.4)
-				{thisForm.searchResult[i].checked = true;}
-			else
-				{thisForm.searchResult[i].checked = false;}
-		}
-		else if (category == 'gt0.0')
-		{
-			if (correlation[i] > 0.0)
-				{thisForm.searchResult[i].checked = true;}
-			else
-				{thisForm.searchResult[i].checked = false;}
-		}
-		else if (category == 'lt0.0')
-		{
-			if (correlation[i] < 0.0)
-				{thisForm.searchResult[i].checked = true;}
-			else
-				{thisForm.searchResult[i].checked = false;}
-		}
-		else if (category == 'lt-0.4')
-		{
-			if (correlation[i] < -0.4)
-				{thisForm.searchResult[i].checked = true;}
-			else
-				{thisForm.searchResult[i].checked = false;}
-		}
-		else if (category == 'lt-0.8')
-		{
-			if (correlation[i] < -0.8)
-				{thisForm.searchResult[i].checked = true;}
-			else
-				{thisForm.searchResult[i].checked = false;}
-		}
-		else
-			{}
-	}
-}
-
-
-function checkNumeric(field,limit,resetvalue,compares,fdname)
-	{
-		pattern = /^-?[0-9]*\.?[0-9]*$/;
-		if(pattern.test(field.value)==false)
-		{
-			alert("Not numeric in " + fdname);
-			field.value = resetvalue;
-		}
-		else
-		{
-			if (compares == 'gthan') {
-			if(field.value > limit)
-			{
-				alert("Out of range in " + fdname);
-				field.value = resetvalue;
-			}}
-			else {
-			if(field.value < limit)
-			{
-				alert("Out of range in " + fdname);
-				field.value = resetvalue;
-			}}
-		}
-	}
-
-function checkTraits(thisForm){
-	var length = thisForm.searchResult.length;
-	var andor = thisForm.selectandor.value;
-	var gthan = parseFloat(thisForm.selectgt.value);
-	var lthan = parseFloat(thisForm.selectlt.value);
-	//alert(length + ' / ' + andor  + ' / ' + gthan + ' / ' + lthan);
-	for(var i = 0; i < length; i++)
-	{
-		var p = corrArray[thisForm.searchResult[i].value];
-		if (andor == 'and')
-		{
-			if ((p.corr > gthan) && ( p.corr < lthan))
-				{thisForm.searchResult[i].checked = true;}
-			else
-				{thisForm.searchResult[i].checked = false;}
-		}
-		else if (andor == 'or')
-		{
-			if ((p.corr > gthan) || ( p.corr < lthan))
-				{thisForm.searchResult[i].checked = true;}
-			else
-				{thisForm.searchResult[i].checked = false;}
-		}
-		else
-			{}
-		highlight(thisForm.searchResult[i]);
-	}
-
-
-}
-
-
-function checkPM(thisForm){
-	var length = thisForm.searchResult.length;
-	for(var i = 0; i < length; i++)
-	{
-		curStr = thisForm.searchResult[i].value;
-		//alert(curStr.charAt(curStr.length - 1));
-		if ((curStr.charAt(curStr.length - 1) % 2) == 1)
-			{thisForm.searchResult[i].checked = true;}
-		else
-			{thisForm.searchResult[i].checked = false;}
-		highlight(thisForm.searchResult[i]);
-	}
-}
-function checkMM(thisForm){
-	var length = thisForm.searchResult.length;
-	for(var i = 0; i < length; i++)
-	{
-		curStr = thisForm.searchResult[i].value;
-		if ((curStr.charAt(curStr.length - 1) % 2) == 0)
-			{thisForm.searchResult[i].checked = true;}
-		else
-			{thisForm.searchResult[i].checked = false;}
-		highlight(thisForm.searchResult[i]);
-	}
-}
-
-
-function directPermuAlert(thisForm){
-	if (thisForm.directPermuCheckbox.checked){
-		alert("Interaction permutation will take long time to compute.\n Check this box only when necessary.");
-	}
-}
-
-function cliqueDatabase(pid){
-	var windowName = 'clique';
-	var newWindow = open("", windowName,"width=900,menubar=0,toolbar=1,resizable=1,status=1,scrollbars=1");
-	var html = '<form name=info action=http://compbio1.uthsc.edu/clique_go/results.php method=post><center><table cellspacing=0 cellpadding=0 border=0 width=50%><tr><td><font size=+1> ProbsetId </font><input type=text name=pid value=';
-	html += pid;
-  	html += ' size=20 maxlength=30 ></td><tr><td><font size=+1> p-value range: between </font><input type=text name=pval_1 value=0 size=8 maxlength=20 > and <input type=text name=pval_2 value=0.01 size=8 maxlength=20></td><td><input type=submit value=Search Clique onclick=return check();></td></tr></table></center></form>';
-	newWindow.document.write(html);
-  	newWindow.document.close();
-  	newWindow.focus();
-}
-
-function getCookie(NameOfCookie){
-	if (document.cookie.length > 0){
-		begin = document.cookie.indexOf(NameOfCookie+"=");
-		if (begin != -1){
-			begin += NameOfCookie.length+1;
-			end = document.cookie.indexOf(";", begin);
-			if (end == -1) end = document.cookie.length;
-			return unescape(document.cookie.substring(begin, end));
-			}
-	}
-	return null;
-}
-
-function setCookie(NameOfCookie, value, expiredays){
-	var ExpireDate = new Date ();
-	ExpireDate.setTime(ExpireDate.getTime() + (expiredays * 24 * 3600 * 1000));
-	document.cookie = NameOfCookie + "=" + escape(value) + ((expiredays == null) ? "" : "; expires=" + ExpireDate.toGMTString()) + "; path=/";
-}
-
-
-function delCookie (NameOfCookie){
-	if (getCookie(NameOfCookie)){
-		document.cookie = NameOfCookie + "=" + "; expires=Thu, 01-Jan-70 00:00:01 GMT";
-	}
-}
-
-
-function highlight(chkbox){
-	var tr = document.getElementById(chkbox.value);
-	if (tr){
-		if (chkbox.checked == true)
-			tr.bgColor='#FFEE99';
-		else
-			tr.bgColor='#eeeeee';
-	}
-}
-
-/* refresh function option when domain options change */
-function snpbrowser_function_refresh() {
-   var idx = document.newSNPPadding.domain.selectedIndex;
-   if (idx != 1) {
-      document.newSNPPadding.exonfunction.options[0].selected=true;
-      for (var i=1; i<document.newSNPPadding.exonfunction.length; i++) {
-          document.newSNPPadding.exonfunction.options[i].selected=false;
-      }
-   }
-}
-
-function snpbrowser_domain_refresh() {
-   /* to refresh domain option when function option change */
-   var form = document.newSNPPadding;
-   var idx = form.exonfunction.selectedIndex;
-   if (idx != 0) {
-        form.domain.options[0].selected = false;
-        form.domain.options[1].selected = true;
-        for (var i=2; i<form.domain.length; i++) {
-             form.domain.options[i].selected = false;
-        }
-   }
-}
-
-function showHideOptions() {
-	var options = document.getElementById("options");
-	var showOptions = document.getElementsByName("showOptions")[0];
-	var optionsButton = document.getElementsByName("optionsButton")[0];
-
-	if (showOptions.value == '0') {
-		showOptions.value = '1';
-		optionsButton.value = "Hide Options";
-	}
-	else {
-		showOptions.value = '0';
-		optionsButton.value = "Show Options";
-	}
-
-	options.style.display = (options.style.display != 'none' ? 'none' : '' );
-}
-
-function editPCAName(thisForm) {
-	var pcaTraits = document.getElementsByName("searchResult");
-
-	var nameArray = new Array();
-
-	for (j=1; j<=pcaTraits.length; j++){
-		var traitName = "pcaTrait" + String(j);
-		var pcaTrait = document.getElementById(traitName).childNodes[0].innerHTML;
-		var editID = "editName" + String(j);
-		var editName = document.getElementsByName(editID)[0].value;
-		var originalName = pcaTrait.split(":")[3];
-
-		if (editName.length < 1) {
-			nameArray.push(originalName);
-		}
-		else {
-			nameArray.push(editName);
-		}
-	}
-
-	var newNames = nameArray.join(",");
-
-	thisForm.newNames.value = newNames;
-	thisForm.searchResult = thisForm.oldSearchResult;
-	thisForm.FormID.value = "corMatrix";
-
-	thisForm.submit();
-}
-
-
-/*
-Used by GoTreePage.py,ODEPage.py ,add the parameter 'methodName'
-*/
-function mixedChipError(methodName){
-	str ='Sorry, the analysis was interrupted because your selections from GeneNetwork apparently include data from more than one array platform (ie., Affymetrix U74A and M430 2.0). Most ' + methodName + ' analyses assume that you are using a single array type and compute statistical values on the basis of that particular array. Please reselect traits from a single platform and submit again.';
-	alert(str);
-	window.close();
-}
-
-/*
-Used by GoTreePage.py, add the parameter 'chipName'
-*/
-function unknownChipError(chipName){
-	alert("Sorry, the analysis was interrupted because your selections from GeneNetwork apparently include data from platform "+ chipName +" which is unknown by WebGestalt. Please reselect traits and submit again.");
-	window.close();
-}
-
-/*
-Used by PartialCorrInputPage.py,
-*/
-function validateTrait(thisForm, inputRadioNames, type, method)
-{
-    var radioArray = new Array();
-    radioArray = inputRadioNames.split(',');
-
-    var value = null;
-    var primaryCount = 0;
-    var controlCount = 0;
-    var targetCount = 0;
-    var primaryString = '';
-    var controlString = '';
-    var targetString = '';
-
-    for (var i = 0; i < radioArray.length; i++)
-    {
-        radioElement = thisForm[radioArray[i]]
-
-        for (var j = 0; j < radioElement.length; j++)
-        {
-            if (radioElement[j].checked) {
-                value = radioElement[j].value;
-            }
-        }
-
-        if (value == "primary") {
-            primaryCount += 1;
-            primaryString += radioElement[0].name + ',';
-        }
-        else if (value == "control") {
-            controlCount += 1;
-            controlString += radioElement[0].name + ',';
-        }
-        else if (value == "target") {
-            targetCount += 1;
-            targetString += radioElement[0].name + ',';
-        }
-    }
-
-    primaryString = primaryString.slice(0,primaryString.length-1);
-    controlString = controlString.slice(0,controlString.length-1);
-    targetString = targetString.slice(0,targetString.length-1);
-
-    if (primaryCount < 1) {
-        alert("You must select one primary trait!");
-    }
-    else if (primaryCount > 1) {
-        alert("You selected multiple primary traits. Please just select one primary trait!");
-    }
-    else if (controlCount < 1) {
-        alert("You must select at least one control trait!");
-    }
-    else if (controlCount > 3) {
-        alert("You selected more than three control traits. Please select no more than three control trait!");
-    }
-    else if (targetCount < 1 && type == 0) {
-        alert("You must select at least one target trait!");
-    }
-    else {
-        thisForm.primaryTrait.value = primaryString;
-        thisForm.controlTraits.value = controlString;
-        thisForm.targetTraits.value = targetString;
-
-        if (type == 0){
-            if (method == 1) {
-                thisForm.pcMethod.value = "pearson";
-            }
-            else {
-                thisForm.pcMethod.value = "spearman";
-            }
-
-            databaseFunc(thisForm,'calPartialCorrTrait');
-        }
-        if (type == 1){
-            databaseFunc(thisForm,'calPartialCorrDB');
-        }
-
-    }
-
-}
-
-/*
-used by IntervalMappingPage.py
-*/
-function changeView(i, Chr_Mb_list){
-	var oldwidth= document.changeViewForm.graphWidth.value;
-	var oldselect= document.changeViewForm.chromosomes.selectedIndex;
-	var oldstart= document.changeViewForm.startMb.value;
-	var oldend= document.changeViewForm.startMb.value;
-	windowName = 'formTarget' + (new Date().getTime());
-	newWindow = open('',windowName,'menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900');
-	document.changeViewForm.target = windowName;
-	document.changeViewForm.chromosomes.selectedIndex = i+1;
-	document.changeViewForm.startMb.value = '0.000000';
-	document.changeViewForm.endMb.value = Chr_Mb_list[i];
-	document.changeViewForm.graphWidth.value = 1280;
-	document.changeViewForm.submit();
-	document.changeViewForm.graphWidth.value = oldwidth;
-	document.changeViewForm.chromosomes.selectedIndex = oldselect;
-	document.changeViewForm.startMb.value = oldstart;
-	document.changeViewForm.endMb.value = oldend;
-	newWindow.focus();
-}
-
-/*
-used by IntervalMappingPage.py
-*/
-function chrLength(a, b, c, Chr_Mb_list) {
- if (b=='physic' && a>-1) {
-  c.startMb.value = '0.000000';
-  c.endMb.value = Chr_Mb_list[a];
- } else {
-  c.startMb.value = '';
-  c.endMb.value = '';
- }
- if (a>-1) c.graphWidth.value = 1280;
- else c.graphWidth.value = 1600;
-}
-
-/*
-used by networkGraphPageBody.py
-*/
-function changeFormat(graphName){
-	var graphFormat = document.getElementById('exportFormat').value;
-	var traitType = document.getElementById('traitType').value;
-
-	if (graphFormat=="xgmml"){
-		if (traitType=="symbol"){
-			var graphname = graphName+ "_xgmml_symbol.txt";
-			document.getElementById('exportGraphFile').onclick = function() { window.open(graphname) };
-		}
-		else if (traitType=="name"){
-			var graphname = graphName+ "_xgmml_name.txt";
-			document.getElementById('exportGraphFile').onclick = function() { window.open(graphname) };
-		}
-	}
-
-	else if (graphFormat=="plain")
-	{
-		if (traitType=="symbol")
-		{
-			var graphname = graphName+ "_plain_symbol.txt";
-			document.getElementById('exportGraphFile').onclick = function() { window.open(graphname) };
-		}
-		else if (traitType=="name")
-		{
-			var graphname = graphName+ "_plain_name.txt";
-			document.getElementById('exportGraphFile').onclick = function() { window.open(graphname) };
-		}
-	}
-
-}
-
-
-/*
-used by snpBrowserPage.py
-*/
-function set_customStrains_cookie() {
-    var options = document.newSNPPadding.chosenStrains.options;
-    var size = options.length;
-    strains = "";
-    if (size > 0) {
-       strains = strains + options[0].text+":"+options[0].value;
-    }
-    for (var i=1; i<size; i++) {
-       strains = strains + "," + options[i].text + ":" +
-                      options[i].value;
-    }
-    var exdate = new Date();
-    exdate.setDate(exdate.getDate()+100);
-    document.cookie = "customStrains1="+strains+
-           ";expires="+exdate.toGMTString()
-}
-
-/*
-* moved from beta2.js
-*/
-function centerIntervalMapOnRange2(chr, start, stop, form) {
-	var oldindex = form.chromosomes.selectedIndex;
-	var oldstart = form.startMb.value;
-	var oldend = form.endMb.value;
-
-	for (var i = 1; i < form.chromosomes.length; i++){
-		if(form.chromosomes.options[i].text == chr){
-			form.chromosomes.selectedIndex = i;
-			break;
-		}
-	}
-	form.startMb.value = start;
-	form.endMb.value = stop;
-	databaseFunc(form,'showIntMap');
-	form.chromosomes.selectedIndex = oldindex;
-	form.startMb.value = oldstart;
-	form.endMb.value = oldend;
-
-}
-
-/*
-* moved from index3.html
-*/
-
-String.prototype.trim = function(){
-	return this.replace(/(^\s*)|(\s*$)/g, "");
-}
-
-function asearch(thisform){
-	//
-	var orkeyword = thisform.ORkeyword.value.trim();
-	//
-	var any_position_chr = thisform.any_position_chr.value.trim();
-	var any_position_from = thisform.any_position_from.value.trim();
-	var any_position_to = thisform.any_position_to.value.trim();
-	if(0<any_position_chr.length && 0<any_position_from.length && 0<any_position_to.length){
-		orkeyword += ' position=('+any_position_chr+' '+any_position_from+' '+any_position_to+')';
-	}
-	//
-	var any_mean_from = thisform.any_mean_from.value.trim();
-	var any_mean_to = thisform.any_mean_to.value.trim();
-	if(0<any_mean_from.length && 0<any_mean_to.length){
-		orkeyword += ' mean=('+any_mean_from+' '+any_mean_to+')';
-	}
-	//
-	var any_range_from = thisform.any_range_from.value.trim();
-	var any_range_to = thisform.any_range_to.value.trim();
-	if(0<any_range_from.length && 0<any_range_to.length){
-		orkeyword += ' range=('+any_range_from+' '+any_range_to+')';
-	}
-	//
-	var any_wiki = thisform.any_wiki.value.trim();
-	if(0<any_wiki.length){
-		orkeyword += ' wiki='+any_wiki;
-	}
-	//
-	var any_rif = thisform.any_rif.value.trim();
-	if(0<any_rif.length){
-		orkeyword += ' rif='+any_rif;
-	}
-	//
-	var any_lrs_from = thisform.any_lrs_from.value.trim();
-	var any_lrs_to = thisform.any_lrs_to.value.trim();
-	if(0<any_lrs_from.length && 0<any_lrs_to.length){
-		orkeyword += ' lrs=('+any_lrs_from+' '+any_lrs_to+')';
-	}
-	//
-	var any_pvalue_from = thisform.any_pvalue_from.value.trim();
-	var any_pvalue_to = thisform.any_pvalue_to.value.trim();
-	if(0<any_pvalue_from.length && 0<any_pvalue_to.length){
-		orkeyword += ' pvalue=('+any_pvalue_from+' '+any_pvalue_to+')';
-	}
-	//
-	var any_h2_from = thisform.any_h2_from.value.trim();
-	var any_h2_to = thisform.any_h2_to.value.trim();
-	if(0<any_h2_from.length && 0<any_h2_to.length){
-		orkeyword += ' h2=('+any_h2_from+' '+any_h2_to+')';
-	}
-	//
-	var andkeyword = thisform.ANDkeyword.value;
-	//
-	var all_position_chr = thisform.all_position_chr.value.trim();
-	var all_position_from = thisform.all_position_from.value.trim();
-	var all_position_to = thisform.all_position_to.value.trim();
-	if(0<all_position_chr.length && 0<all_position_from.length && 0<all_position_to.length){
-		andkeyword += ' position=('+all_position_chr+' '+all_position_from+' '+all_position_to+')';
-	}
-	//
-	var all_mean_from = thisform.all_mean_from.value.trim();
-	var all_mean_to = thisform.all_mean_to.value.trim();
-	if(0<all_mean_from.length && 0<all_mean_to.length){
-		andkeyword += ' mean=('+all_mean_from+' '+all_mean_to+')';
-	}
-	//
-	var all_range_from = thisform.all_range_from.value.trim();
-	var all_range_to = thisform.all_range_to.value.trim();
-	if(0<all_range_from.length && 0<all_range_to.length){
-		andkeyword += ' range=('+all_range_from+' '+all_range_to+')';
-	}
-	//
-	var all_wiki = thisform.all_wiki.value.trim();
-	if(0<all_wiki.length){
-		andkeyword += ' wiki='+all_wiki;
-	}
-	//
-	var all_rif = thisform.all_rif.value.trim();
-	if(0<all_rif.length){
-		andkeyword += ' rif='+all_rif;
-	}
-	//
-	var all_lrs_from = thisform.all_lrs_from.value.trim();
-	var all_lrs_to = thisform.all_lrs_to.value.trim();
-	if(0<all_lrs_from.length && 0<all_lrs_to.length){
-		andkeyword += ' lrs=('+all_lrs_from+' '+all_lrs_to+')';
-	}
-	//
-	var all_pvalue_from = thisform.all_pvalue_from.value.trim();
-	var all_pvalue_to = thisform.all_pvalue_to.value.trim();
-	if(0<all_pvalue_from.length && 0<all_pvalue_to.length){
-		andkeyword += ' pvalue=('+all_pvalue_from+' '+all_pvalue_to+')';
-	}
-	//
-	var all_h2_from = thisform.all_h2_from.value.trim();
-	var all_h2_to = thisform.all_h2_to.value.trim();
-	if(0<all_h2_from.length && 0<all_h2_to.length){
-		andkeyword += ' h2=('+all_h2_from+' '+all_h2_to+')';
-	}
-
-	thisform.ORkeyword.value = orkeyword.trim();
-	thisform.ANDkeyword.value = andkeyword.trim();
-
-	thisform.submit();
-        thisform.ORkeyword.value = "";
-        thisform.ANDkeyword.value = "";
-        document.getElementById('tfor').focus();
-}
-
-function searchInitial(){
-        document.getElementById('tfor').value = "";
-    	document.getElementById('tfor').focus();
-}
-
-
-/* set focus function for designated Id in html page */
-function setFocus(Id)
-{
-        document.getElementById(Id).focus();
-}
-/*Tissue correlation plot*/
-function showTissueCorrPlot(fmName,geneSymbol1, geneSymbol2,rank){
-
-    var thisForm = getForm(fmName);
-    if (thisForm == null || showTissueCorrPlot.arguments.length < 3)
-    	return;
-
-	if (rank){
-		thisForm.rankOrder.value = rank;
-	}else{
-		thisForm.rankOrder.value = 0;
-	}
-
-    windowName = genNewWin();
-    thisForm.target = windowName;
-
-    thisForm.FormID.value = "showCorrelationPlot";
-
-    thisForm.X_geneSymbol.value = geneSymbol1;
-    thisForm.Y_geneSymbol.value = geneSymbol2;
-
-    // This is to make sure the type of correlation is Tissue Correlation. Note that the string value 'none' is used to make judgement in PlotCorrelationPage.py.
-    thisForm.ProbeSetID.value = 'none';
-    if(typeof(thisForm.ProbeSetID2) !== 'undefined'){
-    	thisForm.ProbeSetID2.value = 'none';
-    }
-    thisForm.submit();
-}
-
-/* Used by MarkerRegressionPage.py */
-function validatePvalue(thisForm){
-	var pValue=thisForm.pValue.value;
-
-    if (pValue ==""){
-		alert("Please enter the P-Value.");
-		thisForm.pValue.focus();
-	}
-	else if(isNaN(pValue))
-	{
-		alert("Please enter numeric value.");
-		thisForm.pValue.focus();
-	}
-	else if (pValue <0){
-		alert("Please enter the valid P-Value.");
-		thisForm.pValue.focus();
-	}else {
-
-		dataEditingFunc(thisForm,'markerRegression');
-
-	}
-
-
-
-}
-
-function showTissueAbbr(fmName,shortname, fullname){
-    var thisForm = getForm(fmName);
-    windowName = genNewWin();
-    thisForm.target = windowName;
-    thisForm.FormID.value = 'tissueAbbreviation';
-    thisForm.shortTissueName.value=shortname;
-    thisForm.fullTissueName.value=fullname;
-
-    thisForm.submit();
-    thisForm.FormID.value = 'showCorrelationPlot';
-    thisForm.target =''
-
-}