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-rwxr-xr-xweb/javascript/webqtl.js1350
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diff --git a/web/javascript/webqtl.js b/web/javascript/webqtl.js
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--- 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 =''
-
-}
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-24 06:20:40 +0000