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

1 files changed, 0 insertions, 453 deletions

diff --git a/web/javascript/correlationMatrix.js b/web/javascript/correlationMatrix.js
deleted file mode 100755
index d3ca195e..00000000
--- a/web/javascript/correlationMatrix.js
+++ /dev/null
@@ -1,453 +0,0 @@
-
-/*For Tissue Correlation Page; Default Export Tissue Text*/
-function exportTissueText(items){
-	var windowName = 'ExportTissueText';
-	var newWindow = open("", windowName,"width=900,menubar=0,toolbar=1,resizable=1,status=1,scrollbars=1");
-	var html = '<PRE>';
-	
-	for (i=0;i<items.length;i++){
-		for (j=0;j<items[i].length;j++){
-			if ((i>0) && (j>0)){
-				html += items[i][j].slice(0,items[i][j].indexOf('/'));}
-			else if (((i>0) && (j == 0)) || ((i == 0) && (j > 0))){
-				html += items[i][j].slice(0, items[i][j].indexOf('/'));
-				}
-				
-			else {
-				html += "Correlation";}
-			html += '\t';}
-		html += '\n';}
-	html += '</PRE>';
-	
-	html += '<BR><BR>';
-	
-	html += '<PRE>';
-	for (i=0;i<items.length;i++){
-		for (j=0;j<items[i].length;j++){
-			if ((i>0) && (j>0)){
-				html += items[i][j].slice(items[i][j].indexOf('/')+1, items[i][j].length);}
-			else if (((i>0) && (j == 0)) || ((i == 0) && (j > 0))){
-				html += items[i][j].slice(0, items[i][j].indexOf('/'));}
-			else {
-				html += 'P Value';}
-			html += '\t';}
-		html += '\n';}
-	html += '</PRE>';
-	
-  	newWindow.document.write(html);
-  	newWindow.document.close();
-  	newWindow.focus();/**/
-}
-
-/*Export Tissue Text for long label*/
-function exportTissueVerboseText(items){
-	var windowName = 'ExportVerboseText';
-	var newWindow = open("", windowName,"width=900,menubar=0,toolbar=1,resizable=1,status=1,scrollbars=1");
-	var html = '<PRE>';
-	
-	for (i=0;i<items.length;i++){
-		for (j=0;j<items[i].length;j++){
-			if ((i>0) && (j>0)){
-				html += items[i][j].slice(0,items[i][j].indexOf('/'));}
-			else if ((i>0) && (j == 0)){
-				position1 = items[i][j].indexOf('/') + 1;
-				position2 = items[i][j].indexOf('/', position1);
-				html += items[i][j].slice(position2 + 1, items[i][j].length);}
-			else if ((i == 0) && (j>0)){
-				html += items[i][j].slice(0, items[i][j].indexOf('/')) ;}
-			else {
-				html += "Correlation";}
-			html += '\t';}
-		html += '\n';}
-	html += '</PRE>';
-	
-	html += '<BR><BR>';
-	
-	html += '<PRE>';
-	for (i=0;i<items.length;i++){
-		for (j=0;j<items[i].length;j++){
-			if ((i>0) && (j>0)){
-				html += items[i][j].slice(items[i][j].indexOf('/')+1, items[i][j].length);}
-			else if ((i>0) && (j == 0)){
-				position1 = items[i][j].indexOf('/') + 1;
-				position2 = items[i][j].indexOf('/', position1) + 1;
-				html += items[i][j].slice(position2, items[i][j].length);}
-			else if ((i == 0) && (j>0)){
-				html += items[i][j].slice(0, items[i][j].indexOf('/'));}
-			else {
-				html += 'P Value';}
-			html += '\t';}
-		html += '\n';}
-	html += '</PRE>';
-	
-  	newWindow.document.write(html);
-  	newWindow.document.close();
-  	newWindow.focus();/**/
-}
-
-/*For Tissue Correlation Page; Default Save function for results of symbol count =1*/
-function exportAllTissueText(items){
-	var windowName = 'ExportTissueText';
-	var newWindow = open("", windowName,"width=900,menubar=0,toolbar=1,resizable=1,status=1,scrollbars=1");
-	var html = '<PRE>';
-	
-	for (i=0;i<items.length;i++){
-		for (j=0;j<items[i].length;j++){
-			if ((i>0) && (j>0)){
-				html += items[i][j].slice(0,items[i][j].indexOf('/'));}
-			else if (((i>0) && (j == 0)) || ((i == 0) && (j > 0))){
-				html += items[i][j].slice(0, items[i][j].indexOf('/'));
-				}
-				
-			else {
-				html += "Correlation";}
-			html += '\t';}
-		html += '\n';}
-	html += '</PRE>';
-	
-  	newWindow.document.write(html);
-  	newWindow.document.close();
-  	newWindow.focus();/**/
-}
-
-/* Display Short Label for Tissue */
-function displayTissueShortName(){
-	var geneSymbols = document.getElementsByName("Symbol");
-	
-	var exportButton = document.getElementsByName("export")[0];
-	var shortNameCheck = document.getElementById("shortName_1"); // to check if currently short
-	
-	if (shortNameCheck.style.display == 'none'){
-		exportButton.value="Export";
-		exportButton.onclick = function(){exportTissueText(allCorrelations);};
-	}
-	else {
-		exportButton.value="Export";
-		exportButton.onclick = function(){exportTissueText(allCorrelations);};
-	}
-	
-	for (i=0; i < geneSymbols.length; i++){
-		var shortName = document.getElementById("shortName_" + String(i));
-		var verboseName = document.getElementById("verboseName_" + String(i));
-		var verboseName2 = document.getElementById("verboseName2_" + String(i));
-		var verboseName3 = document.getElementById("verboseName3_" + String(i));
-		
-		
-		if (shortName.style.display == 'block') {
-			shortName.style.display = 'none';
-		}		
-	
-		else if (shortName.style.display == 'none') {
-			if (verboseName.style.display == 'block'){
-				verboseName.style.display = 'none';
-				verboseName2.style.display = 'none';
-				verboseName3.style.display = 'none';
-			}	
-			shortName.style.display = 'block';
-		}
-	}
-}
-
-/* Display Long Label for Tissue */
-function displayTissueVerboseName(){
-	var geneSymbols = document.getElementsByName("Symbol");
-	
-	var exportButton = document.getElementsByName("export")[0];
-	var verboseNameCheck = document.getElementById("verboseName_0"); // to check if currently verbose
-	
-	if (verboseNameCheck.style.display == 'none'){
-		exportButton.value="Export";
-		exportButton.onclick = function(){exportTissueVerboseText(allCorrelations);};
-	}
-	else {
-		exportButton.value="Export";
-		exportButton.onclick = function(){exportTissueText(allCorrelations);};
-	}
-	
-	for (i=0; i < geneSymbols.length; i++){
-		var verboseName = document.getElementById("verboseName_" + String(i));
-		var verboseName2 = document.getElementById("verboseName2_" + String(i));
-		var verboseName3 = document.getElementById("verboseName3_" + String(i));
-		var shortName = document.getElementById("shortName_" + String(i));
-		
-		
-		if (verboseName.style.display == 'block') {
-			verboseName.style.display = 'none';
-			verboseName2.style.display = 'none';
-			verboseName3.style.display = 'none';
-		}
-		
-		else if (verboseName.style.display == 'none'){
-			if (shortName.style.display == 'block'){
-				shortName.style.display = 'none';
-			}
-			verboseName.style.display = 'block';
-			verboseName2.style.display = 'block';
-			verboseName3.style.display = 'block';
-		}	
-	}
-	
-}
-
-/* Info page for dataset of tissue correlation */
-function tissueDatasetInfo(thisForm,dataSetNames){
-    var windowName = 'dataset_info';
-    var Index = thisForm.selectedIndex;
-	var datasetName =dataSetNames[Index]
-    var page = '/dbdoc/' + datasetName + '.html';
-    newWindow = open(page,windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-    newWindow.focus()
-}
-
-
-/*for correlation matrix page*/
-/* Display Short Label in Correlation Matrix */
-function displayShortName(){
-	var traitList = document.getElementsByName("traitList")[0].value.split("\t");
-	var exportButton = document.getElementsByName("export")[0];
-	var shortNameCheck = document.getElementById("shortName_1"); // to check if currently short
-	
-	if (shortNameCheck.style.display == 'none'){
-		exportButton.value="Export";
-		exportButton.onclick = function(){exportAbbreviationText(allCorrelations);};
-	}
-	else {
-		exportButton.value="Export";
-		exportButton.onclick = function(){exportText(allCorrelations);};
-	}
-	
-	for (i=0; i < traitList.length; i++){
-		var shortName = document.getElementById("shortName_" + String(i));
-		var verboseName = document.getElementById("verboseName_" + String(i));
-		var verboseName2 = document.getElementById("verboseName2_" + String(i));
-		var verboseName3 = document.getElementById("verboseName3_" + String(i));
-		
-		
-		if (shortName.style.display == 'block') {
-			shortName.style.display = 'none';
-		}		
-	
-		else if (shortName.style.display == 'none') {
-			if (verboseName.style.display == 'block'){
-				verboseName.style.display = 'none';
-				verboseName2.style.display = 'none';
-				verboseName3.style.display = 'none';
-			}	
-			shortName.style.display = 'block';
-		}
-	}
-}
-
-/* Display Long Label in Correlation Matrix*/
-function displayVerboseName(){
-	var traitList = document.getElementsByName("traitList")[0].value.split("\t");
-	var exportButton = document.getElementsByName("export")[0];
-	var verboseNameCheck = document.getElementById("verboseName_0"); // to check if currently verbose
-	
-	if (verboseNameCheck.style.display == 'none'){
-		exportButton.value="Export";
-		exportButton.onclick = function(){exportVerboseText(allCorrelations);};
-	}
-	else {
-		exportButton.value="Export";
-		exportButton.onclick = function(){exportText(allCorrelations);};
-	}
-	
-	for (i=0; i < traitList.length; i++){
-		var verboseName = document.getElementById("verboseName_" + String(i));
-		var verboseName2 = document.getElementById("verboseName2_" + String(i));
-		var verboseName3 = document.getElementById("verboseName3_" + String(i));
-		var shortName = document.getElementById("shortName_" + String(i));
-		
-		if (verboseName.style.display == 'block') {
-			verboseName.style.display = 'none';
-			verboseName2.style.display = 'none';
-			verboseName3.style.display = 'none';
-		}
-		
-		else if (verboseName.style.display == 'none'){
-			if (shortName.style.display == 'block'){
-				shortName.style.display = 'none';
-			}
-			verboseName.style.display = 'block';
-			verboseName2.style.display = 'block';
-			verboseName3.style.display = 'block';
-		}	
-	}
-	
-}
-
-/*Export for long label in Correlation Matrix*/
-function exportVerboseText(items){
-	var windowName = 'ExportVerboseText';
-	var newWindow = open("", windowName,"width=900,menubar=0,toolbar=1,resizable=1,status=1,scrollbars=1");
-	var html = '<PRE>';
-	
-	for (i=0;i<items.length;i++){
-		for (j=0;j<items[i].length;j++){
-			if ((i>0) && (j>0)){
-				html += items[i][j].slice(0,items[i][j].indexOf('/'));}
-			else if ((i>0) && (j == 0)){
-				position1 = items[i][j].indexOf('/') + 1;
-				position2 = items[i][j].indexOf('/', position1);
-				html += "Trait " + String(i) + ": " + items[i][j].slice(position2 + 1, items[i][j].length);}
-			else if ((i == 0) && (j>0)){
-				html += items[i][j];}
-			else {
-				html += "Correlation";}
-			html += '\t';}
-		html += '\n';}
-	html += '</PRE>';
-	
-	html += '<BR><BR>';
-	
-	html += '<PRE>';
-	for (i=0;i<items.length;i++){
-		for (j=0;j<items[i].length;j++){
-			if ((i>0) && (j>0)){
-				html += items[i][j].slice(items[i][j].indexOf('/')+1, items[i][j].length);}
-			else if ((i>0) && (j == 0)){
-				position1 = items[i][j].indexOf('/') + 1;
-				position2 = items[i][j].indexOf('/', position1) + 1;
-				html += "Trait " + String(i) + ": " + items[i][j].slice(position2, items[i][j].length);}
-			else if ((i == 0) && (j>0)){
-				html += items[i][j];}
-			else {
-				html += 'N';}
-			html += '\t';}
-		html += '\n';}
-	html += '</PRE>';
-	
-  	newWindow.document.write(html);
-  	newWindow.document.close();
-  	newWindow.focus();/**/
-}
-
-/*Default Export for labels in Correlation Matrix*/
-function exportText(items){
-	var windowName = 'ExportText';
-	var newWindow = open("", windowName,"width=900,menubar=0,toolbar=1,resizable=1,status=1,scrollbars=1");
-	var html = '<PRE>';
-	for (i=0;i<items.length;i++){
-		for (j=0;j<items[i].length;j++){
-			//alert(" i="+i+"---j="+j+"----item[i][j]=="+items[i][j]);
-			if ((i>0) && (j>0)){
-				html += items[i][j].slice(0,items[i][j].indexOf('/'));}
-			else if (((i>0) && (j == 0)) || ((i == 0) && (j > 0))){
-				html += items[i][j].slice(0, items[i][j].indexOf('/'));}
-			else {
-				html += "Correlation";}
-			html += '\t';}
-		html += '\n';}
-	html += '</PRE>';
-	
-	html += '<BR><BR>';
-	
-	html += '<PRE>';
-	for (i=0;i<items.length;i++){
-		for (j=0;j<items[i].length;j++){
-			if ((i>0) && (j>0)){
-				html += items[i][j].slice(items[i][j].indexOf('/')+1, items[i][j].length);}
-			else if (((i>0) && (j == 0)) || ((i == 0) && (j > 0))){
-				html += items[i][j].slice(0, items[i][j].indexOf('/'));}
-			else {
-				html += 'N';}
-			html += '\t';}
-		html += '\n';}
-	html += '</PRE>';
-	
-  	newWindow.document.write(html);
-  	newWindow.document.close();
-  	newWindow.focus();/**/
-}
-
-/*Export for short label in Correlation Matrix*/
-function exportAbbreviationText(items){
-	var windowName = 'ExportAbbreviationText';
-	var newWindow = open("", windowName,"width=900,menubar=0,toolbar=1,resizable=1,status=1,scrollbars=1");
-	var html = '<PRE>';
-	
-	for (i=0;i<items.length;i++){
-		for (j=0;j<items[i].length;j++){
-			if ((i>0) && (j>0)){
-				html += items[i][j].slice(0,items[i][j].indexOf('/'));}
-			else if ((i>0) && (j == 0)){
-				position1 = items[i][j].indexOf('/') + 1;
-				position2 = items[i][j].indexOf('/', position1);
-				html += "Trait " + String(i) + ": " + items[i][j].slice(position1, position2);}
-			else if ((i == 0) && (j>0)){
-				html += items[i][j];}
-			else {
-				html += "Correlation";}
-			html += '\t';}
-		html += '\n';}
-	html += '</PRE>';
-	
-	html += '<BR><BR>';
-	
-	html += '<PRE>';
-	for (i=0;i<items.length;i++){
-		for (j=0;j<items[i].length;j++){
-			if ((i>0) && (j>0)){
-				html += items[i][j].slice(items[i][j].indexOf('/')+1, items[i][j].length);}
-			else if ((i>0) && (j == 0)){
-				position1 = items[i][j].indexOf('/') + 1;
-				position2 = items[i][j].indexOf('/', position1);
-				html += "Trait " + String(i) + ": " + items[i][j].slice(position1, position2);}
-			else if ((i == 0) && (j>0)){
-				html += items[i][j];}
-			else {
-				html += 'N';}
-			html += '\t';}
-		html += '\n';}
-	html += '</PRE>';
-	
-  	newWindow.document.write(html);
-  	newWindow.document.close();
-  	newWindow.focus();/**/
-}
-
-/*dynamic change formID for process bar display issue. Only Single symbol result page needs process bar*/
-function selectFormIdForTissueCorr(fmName){
-
-	var thisForm = getForm(fmName);
-	var geneSymbolStr =thisForm.geneSymbols.value;	
-	var geneSymbolStrSplit =geneSymbolStr.split(/\n/);//delimiter is very important here
-
-	len=geneSymbolStrSplit.length;
-	if (len==1){
-		thisForm.FormID.value="dispTissueCorrelationResult";
-	}
-	else{
-		thisForm.FormID.value="dispMultiSymbolsResult";
-	}
-	thisForm.submit()
-}
-
-/*make default for dropdown menu in tissue correlation page*/
-function makeTissueCorrDefault(thisform){
-	setCookie('cookieTest', 'cookieTest', 1);
-	var cookieTest = getCookie('cookieTest');
-	delCookie('cookieTest');
-	if (cookieTest){
-		var defaultTissueDataset = thisform.tissueProbeSetFeezeId.value;
-		setCookie('defaultTissueDataset', defaultTissueDataset, 10);
-		alert("The current dataset is set to default.");
-	}
-	else{
-		alert("You need to enable Cookies in your browser.");
-	}
-
-}
-
-/*set default selected value for tissue correlation dataset Id*/
-function getTissueCorrDefault(fmName){
-	var thisForm = getForm(fmName);
-	if (getCookie('defaultTissueDataset')){
-		thisForm.tissueProbeSetFeezeId.selectedIndex =(getCookie('defaultTissueDataset'))-1;
-	}
-	else{
-		thisForm.tissueProbeSetFeezeId.selectedIndex =0;
-	}
-
-}