Add all the source codes into the github.

1 files changed, 453 insertions, 0 deletions

diff --git a/web/javascript/correlationMatrix.js b/web/javascript/correlationMatrix.js
new file mode 100755
index 00000000..d3ca195e
--- /dev/null
+++ b/web/javascript/correlationMatrix.js
@@ -0,0 +1,453 @@
+
+/*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;
+	}
+
+}