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+/*
+ jquery part
+*/
+
+/*
+used by index (base/indexBody.py)
+*/
+
+$(document).ready(function(){
+ options_visible = 0; //Whether advanced options are being shown
+
+ $('tr .advanced_option').hide();
+
+ $('.toggle_advanced').click(function(){
+ $('tr .advanced_option').toggle();
+
+ if (options_visible = 0) {
+ $('.full_search_td').css('display','none;');
+ $('.search_td').css('display','inline');
+ options_visible = 1;
+ }
+ else {
+ if ($('#type_menu.type_menu').val() = 'Hippocampus'){
+ $('.search_td').css('display','none;');
+ $('.full_search_td').css('display','inline');
+ }
+ options_visible = 0;
+ }
+ });
+
+ $('#full_search').click(function(){
+ gene_symbol = $('input[name=keyword]').val();
+ scriptable_interface_url = 'http://alexandria.uthsc.edu:89/webqtl/main.py?cmd=sch&gene=' + gene_symbol;
+ window.open(scriptable_interface_url,'_self');
+ });
+});
+
+$('select.type_menu').live('change', function() {
+ var trait_type = $('select.type_menu option:selected').val();
+ $('#tissue').val(trait_type);
+ $('#tissue').trigger('change');
+});
+
+
+/*
+used by CorrelationPage.py, AddToSelectionPage.py, and SearchResultPage.py
+*/
+$(document).ready(function(){
+ $('img[name=addselect], img[name=networkgraph], img[name=corrmatrix], img[name=partialCorr], img[name=comparecorr], img[name=mintmap], img[name=heatmap]').click(function(){
+ if ($('input[name=searchResult]:checked').length < 1){
+ for (i=0; i<10; i++){
+ $('input[name=searchResult]:eq('+i+')').attr('checked',true);
+ }
+ }
+ });
+
+ $('img[name=addselect]').click(function(){
+ addRmvSelection($('input[name=RISet]').val(), document.getElementsByName('showDatabase'+ $('input[name=RISet]').val())[0], 'addToSelection');
+ });
+
+ $('.toggleShowHide').click(function(){
+ var className = '.extra_options';
+ if ($(className).css('display') == 'none'){
+ var less = 'less';
+ $('input[name=showHideOptions]').val(less);
+ $(className).show();
+ $('input[name=options]').val('Fewer Options');
+ var display = $('input[name=options]').css('display')
+ $(display).val('block');
+ }
+ else {
+ var more = 'more';
+ $('input[name=showHideOptions]').val(more);
+ $(className).hide();
+ $('input[name=options]').val('More Options');
+ var display = $('input[name=showHideOptions]').css('display')
+ $(display).val('block');
+ }
+ });
+});
+
+/*
+used by AddToSelectionPage.py
+*/
+function validateTraitNumber() {
+ var checkBoxes = $('.checkallbox');
+ if (checkBoxes.filter(":checked").length < 2) {
+ alert("Please select at least two traits.");
+ return false;
+ }
+ else {
+ return true;
+ }
+}
+
+/*
+used by TextSearchPage.py
+*/
+$(document).ready(function(){
+
+ $('.add_traits').click(function(){
+ $('input[name=searchResult]').each(function(){
+ if ($(this).is(':checked')){
+ groupName = $(this).parents().next().next().children('[href]').text();
+ addORrmv = 'addToSelection';
+ thisForm = $('form[name=showDatabase]');
+ addRmvSelection_allGroups(groupName, thisForm, addORrmv);
+ }
+ });
+ });
+
+ function addRmvSelection_allGroups(groupName, thisForm, addORrmv){
+ thisForm.attr('target',groupName);
+ thisForm.children('input[name=FormID]:hidden').val(addORrmv);
+ thisForm.children('input[name=RISet]:hidden').val(groupName);
+ var newWindow = open("",thisForm.attr('target'),"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
+ thisForm.submit();
+ }
+
+ $('.tab_content').hide(); //Hide all tab content
+ $('div.tab_container').each(function(){
+ $(this).parent('td').find('div.tab_container:first').find('div.tab_content:first').show();
+ });
+ $('ul.tabs').each(function(){
+ $(this).find('li:first').addClass('active');
+ });
+ $('ul.tabs:first').find('li:first').show();
+ $('.tab_container:first').find('.tab_content:first').show();
+
+ //On Click Event
+ $('ul.tabs li').click(function() {
+ $('ul.tabs').find('li').removeClass('last_viewed');
+ if($(this).parent('ul.tabs').next('div.tab_container').attr('id').indexOf('stats') != 1){
+ $(this).addClass('last_viewed');
+ }
+ $(this).parent('ul.tabs').find('li').removeClass('active');
+ $(this).addClass('active');
+ $(this).parent('ul.tabs').next('div.tab_container').find('.tab_content').hide();
+ var activeTab = $(this).find('a').attr('href');
+ if ($.browser.msie)
+ {$(activeTab).show();}
+ else
+ {$(activeTab).fadeIn();} //Fade in the active ID content
+
+ return false;
+ });
+
+});
+
+/*
+used by DataEditingPage.py
+*/
+$(document).ready(function() {
+
+ // ZS: This checks the number of columns in order to determine which column to not sort; in this case the plus-minus symbol shouldn't be sortable
+ $('#sortable1,#sortable2').find('th').each(function() {
+ if ($(this).text() == 'SE'){
+ $.tablesorter.defaults.headers = { 3: {sorter: false} };
+ return false;
+ }
+ });
+
+/*
+ ZS: This segment is called by tablesorter.js; it determines where to get the text used when sorting, based on the type of cell.
+ If a cell has a text input field, it gets the text from its class, which is changed when the user changes the value.
+
+ This segment is repeated twice. Ideally this wouldn't be the case, but I can't find a way to reuse the inner textExtraction function.
+*/
+
+ //ZS: Defining these here, so they don't need to be searched for in the DOM for every single node
+ primaryTable = $("#sortable1");
+ otherTable = $("#sortable2");
+
+ primaryValueHeader = primaryTable.find('th:contains("Value"):eq(0)');
+ primarySEHeader = primaryTable.find('th:contains("SE"):eq(0)');
+ otherValueHeader = otherTable.find('th:contains("Value"):eq(1)');
+ otherSEHeader = otherTable.find('th:contains("SE"):eq(1)');
+
+ $("#sortable1").tablesorter({
+ textExtraction: function(node) {
+ if ((node.children[0] == "[object HTMLInputElement]" && node.children[0].type == "text") || (/\S/.test(node.id))) {
+ cellId = node.id;
+ thisCell = $('#'+cellId).children(':eq(0)')
+ valueClassNames = thisCell.attr('class').split(/\s+/);
+ capitalized_column_name = cellId.split('_')[0].charAt(0).toUpperCase() + cellId.split('_')[0].slice(1);
+ value = valueClassNames[valueClassNames.length - 1];
+ newValue = thisCell.val();
+
+ if (newValue == 'x' || value == '9999' || value == '-9999') {
+ valueType = cellId.split('_')[0];
+ if (valueType == 'value'){
+ header = primaryValueHeader;
+ } else {
+ header = primarySEHeader;
+ }
+
+ if (header.hasClass('headerSortUp')){
+ sort_order = 'desc';
+ } else if (header.hasClass('headerSortDown')){
+ sort_order = 'asc';
+ } else {
+ sort_order = 'desc';
+ }
+
+ if (sort_order == 'desc') {
+ value = 9999;
+ thisCell.removeClass(value).addClass('9999');
+ } else if (sort_order == 'asc'){
+ value = -9999;
+ thisCell.removeClass(value).addClass('-9999');
+ } else {
+ value = 9999;
+ thisCell.removeClass(value).addClass('9999');
+ }
+ }
+
+ text = value;
+ }
+
+ else {
+ if (node.textContent) {
+ text = node.textContent;
+ } else {
+ if (node.childNodes[0] && node.childNodes[0].hasChildNodes()) {
+ text = node.childNodes[0].innerHTML;
+ } else {
+ text = node.innerText;
+ }
+ }
+ }
+ return text
+ }
+ });
+
+ $("#sortable2").tablesorter({
+ textExtraction: function(node) {
+ if ((node.children[0] == "[object HTMLInputElement]" && node.children[0].type == "text") || (/\S/.test(node.id))) {
+ cellId = node.id;
+ thisCell = $('#'+cellId).children(':eq(0)')
+ valueClassNames = thisCell.attr('class').split(/\s+/);
+ capitalized_column_name = cellId.split('_')[0].charAt(0).toUpperCase() + cellId.split('_')[0].slice(1);
+ value = valueClassNames[valueClassNames.length - 1];
+ newValue = thisCell.val();
+
+ if (newValue == 'x' || value == '9999' || value == '-9999') {
+ valueType = cellId.split('_')[0];
+ if (valueType == 'value'){
+ header = otherValueHeader;
+ } else {
+ header = otherSEHeader;
+ }
+
+ if (header.hasClass('headerSortUp')){
+ sort_order = 'desc';
+ } else if (header.hasClass('headerSortDown')){
+ sort_order = 'asc';
+ } else {
+ sort_order = 'desc';
+ }
+
+ if (sort_order == 'desc') {
+ value = 9999;
+ thisCell.removeClass(value).addClass('9999');
+ } else if (sort_order == 'asc'){
+ value = -9999;
+ thisCell.removeClass(value).addClass('-9999');
+ } else {
+ value = 9999;
+ thisCell.removeClass(value).addClass('9999');
+ }
+ }
+
+ text = value;
+ }
+
+ else {
+ if (node.textContent) {
+ text = node.textContent;
+ } else {
+ if (node.childNodes[0] && node.childNodes[0].hasChildNodes()) {
+ text = node.childNodes[0].innerHTML;
+ } else {
+ text = node.innerText;
+ }
+ }
+ }
+ return text
+ }
+ });
+
+/*
+ ZS: When the user changes the value in the text field, the new value is added as a class. This is because
+ $('input[type=text]').val() gets the value attribute, which is always the default value, instead of the
+ value property (which can be changed)
+*/
+
+ var thisTable = $('#sortable1,#sortable2');
+
+ thisTable.bind("update propertychange keyup input paste", function(e){
+
+ var target = e.target;
+ $target = $(target);
+
+ if (target.nodeName.toLowerCase() == 'input'){
+ thisClassNames = $target.attr('class').split(/\s+/);
+ valueClass = thisClassNames[thisClassNames.length - 1];
+ newValue = $target.val();
+ thisParent = $target.parent('td');
+ thisParentId = thisParent.attr('id');
+
+ $target.removeClass(valueClass);
+
+ if (newValue == 'x'){
+ thisParent.parent('tr').addClass('blocked');
+ } else {
+ $('#'+thisParentId).children('input.valueField:eq(0)').addClass(newValue);
+ }
+ }
+ });
+
+ ////////////////////////////////////
+ // Initially close tabs
+ ////////////////////////////////////
+
+ thisForm = $('form[name="dataInput"]');
+
+ $('#sectionbody2').hide();
+ $('#sectionbody3').hide();
+ $('#sectionbody4').hide();
+
+ $('#title1').click(function() {
+ $('#sectionbody1').toggle();
+ return false;
+ });
+ $('#title2').click(function() {
+ $('#sectionbody2').toggle();
+ return false;
+ });
+ $('#title3').click(function() {
+ $('#sectionbody3').toggle();
+ return false;
+ });
+ $('#title4').click(function() {
+ $('#sectionbody4').toggle();
+ return false;
+ });
+ $('#title5').click(function() {
+ $('#sectionbody5').toggle();
+ return false;
+ });
+
+
+
+ //////////////////////////////////////////////////////////////
+ // Switch out + and - icon when you click each section header
+ //////////////////////////////////////////////////////////////
+
+ var expand_html = "<span class=\"expand_container\">&nbsp;&nbsp;<IMG src=\"/images/Expand.gif\" alt=\"Expand\"></span>";
+ var contract_html = "<span class=\"contract_container\">&nbsp;&nbsp;<IMG src=\"/images/Contract.gif\" alt=\"Contract\"></span>";
+
+ $('#title2, #title3, #title4').prepend(expand_html).addClass('1');
+
+ $('#title1, #title5').prepend(contract_html).addClass('0');
+
+ for(i=1;i<=5;i++){
+ $('#title'+i).click(function(){
+ if ($(this).hasClass('0')) {
+ $(this).find('span').replaceWith(expand_html);
+ $(this).removeClass('0');
+ $(this).addClass('1');
+ }
+ else {
+ $(this).find('span').replaceWith(contract_html);
+ $(this).removeClass('1');
+ $(this).addClass('0');
+ }
+ });
+ }
+
+ // Exclude cases by attributes
+
+ $('div.attribute_values:first').css('display', 'inline'); //Display the dropdown menu with the first attribute's distinct values
+
+ $('select[name=exclude_menu]').change(function(){
+ $('div.attribute_values').css('display', 'none'); //clear all other menus when a new attribute is selected
+ attribute = $(this).val();
+ //attribute = $('select[name=exclude_menu]').val();
+ menu = $('div.attribute_values').find('[name=\''+attribute+'\']');
+ menu.parent().css('display', 'inline');
+ });
+
+ primary_row_count = $('#primary').find('tr').length - 1;
+ other_row_count = $('#other').find('tr').length - 1;
+
+ if (primary_row_count >= other_row_count) {
+ row_count = primary_row_count;
+ }
+ else {
+ row_count = other_row_count;
+ }
+
+ $('div.attribute_values').children('select').change(function(){
+ exclude_value = $(this).val();
+ });
+});
+
+$(window).load(function(){
+
+ //ZS: These are needed in a few places; looping through rows by index is faster than doing a "find" search
+ numPrimaryRows = $('#sortable1').find('tr').length;
+ numOtherRows = $('#sortable2').find('tr').length;
+
+
+///////////////////////////////
+//Basic Statistics
+///////////////////////////////
+
+ /////////////////////////////////////////////////////////////////
+ // Hide unselected Basic Statistics tabs (when just BXD strains
+ // are selected, hide the results for all strains/non-BXD)
+ /////////////////////////////////////////////////////////////////
+
+ $('#stats_tabs1').hide();
+ $('#stats_tabs2').hide();
+
+ $('#sectionbody2').find('select[name=stats_mdp]').change(function(){
+ selected = $('#sectionbody2').find('select[name=stats_mdp] option:selected').val();
+ for (i=0;i<=2;i++){
+ $('#stats_tabs'+i).hide();
+ }
+ $('#stats_tabs'+selected).show();
+ });
+
+ ////////////////////////////////////////////////////////////////////////
+ // Select the same tab across each sample group (when a Box Plot is
+ // selected for BXD, switching to Non-BXD will also display a Box Plot)
+ ////////////.///////////////////////////////////////////////////////////
+
+ var $tabs1 = $('#stats_tabs0').tabs();
+ var $tabs2 = $('#stats_tabs1').tabs();
+ var $tabs3 = $('#stats_tabs2').tabs();
+
+ $tabs1.tabs({
+ show: function(event, ui) {
+ var selected = $tabs1.tabs('option','selected');
+ $tabs2.tabs('select',selected);
+ $tabs3.tabs('select',selected);
+ }
+ });
+ $tabs2.tabs({
+ show: function(event, ui) {
+ var selected = $tabs2.tabs('option','selected');
+ $tabs1.tabs('select',selected);
+ $tabs3.tabs('select',selected);
+ }
+ });
+ $tabs3.tabs({
+ show: function(event, ui) {
+ var selected = $tabs3.tabs('option','selected');
+ $tabs1.tabs('select',selected);
+ $tabs2.tabs('select',selected);
+ }
+ });
+
+
+///////////////////////////////
+//Calculate Correlations
+///////////////////////////////
+
+ $('#sectionbody3').find('input[name="sample_corr"]').click(function() {
+ dbValue = $('select[name=database1] option:selected').val();
+ $('input[name=database]').val(dbValue);
+ criteriaValue = $('select[name=criteria1] option:selected').val();
+ $('input[name=criteria]').val(criteriaValue);
+ MDPValue = $('select[name=MDPChoice1] option:selected').val();
+ $('input[name=MDPChoice]').val(MDPValue);
+
+ methodValue = $('input[name=sample_method]:checked').val();
+
+ //This simple method can be used now that 'method' is defaulted to None instead of ''
+ if (methodValue == "1"){
+ $('input[name=method]').val('1');
+ }
+ else{
+ $('input[name=method]').val('2');
+ }
+
+ dataEditingFunc(this.form,'correlation');
+ });
+
+ $('#sectionbody3').find('input[name="lit_corr"]').click(function() {
+ dbValue = $('select[name=database2] option:selected').val();
+ $('input[name=database]').val(dbValue);
+ criteriaValue = $('select[name=criteria2] option:selected').val();
+ $('input[name=criteria]').val(criteriaValue);
+ MDPValue = $('select[name=MDPChoice2] option:selected').val();
+ $('input[name=MDPChoice]').val(MDPValue);
+
+ $('input[name=method]').val('3');
+
+ dataEditingFunc(this.form,'correlation');
+ });
+
+ $('#sectionbody3').find('input[name="tiss_corr"]').click(function() {
+ dbValue = $('select[name=database3] option:selected').val();
+ $('input[name=database]').val(dbValue);
+ criteriaValue = $('select[name=criteria3] option:selected').val();
+ $('input[name=criteria]').val(criteriaValue);
+ MDPValue = $('select[name=MDPChoice3] option:selected').val();
+ $('input[name=MDPChoice]').val(MDPValue);
+
+ methodValue = $('input[name=tissue_method]:checked').val();
+
+ if (methodValue == "4"){
+ $('input[name=method]').val('4');
+ }
+ else{
+ $('input[name=method]').val('5');
+ }
+ dataEditingFunc(this.form,'correlation');
+ });
+
+///////////////////////////////
+//Mapping Tools
+///////////////////////////////
+
+ $('#sectionbody4').find('input[name=interval]').click(function() {
+ chrValue = $('select[name=chromosomes1] option:selected').val();
+ $('input[name=chromosomes]').val(chrValue);
+ scaleValue = $('select[name=scale1] option:selected').val();
+ $('input[name=scale]').val(scaleValue);
+ $('input[name=controlLocus]').val('');
+
+ //Changed the way permValue, bootValue, and parentsValue are acquired; before it was $(____).is(':checked');
+ permValue = $('input[name=permCheck1]:checked').val();
+ $('input[name=permCheck]').val(permValue);
+
+ bootValue = $('input[name=bootCheck1]:checked').val();
+ $('input[name=bootCheck]').val(bootValue);
+
+ if ($('input[name=parentsf14regression1]:checked').length > 0){
+ $('input[name=parentsf14regression]').val('on');
+ } else {
+ $('input[name=parentsf14regression]').val('off');
+ }
+
+ varValue = $('input[name=applyVarianceSE1]:checked').val();
+ $('input[name=applyVarianceSE]').val(varValue);
+
+ dataEditingFunc(this.form,'intervalMap');
+ });
+
+ var tiptext = "e.g., rs12345";
+ controlLocus = $('#sectionbody4').find('input[name=controlLocus]');
+
+ if(controlLocus.val() == '' || controlLocus == tiptext) {
+ controlLocus.addClass('searchtip').val(tiptext);
+ }
+
+ controlLocus.focus(function(e) {
+ if(controlLocus.val() == tiptext) {
+ controlLocus.val('');
+ }
+ controlLocus.removeClass('searchtip');
+ });
+
+ controlLocus.blur(function(e) {
+ if(controlLocus.val() == '') {
+ controlLocus.addClass('searchtip').val(tiptext);
+ } else if(controlLocus.val() == tiptext) {
+ controlLocus.addClass('searchtip');
+ } else {
+ controlLocus.removeClass('searchtip');
+ }
+ });
+
+ $('#sectionbody4').find('input[name=composite]').click(function() {
+ chrValue = $('select[name=chromosomes2] option:selected').val();
+ $('input[name=chromosomes]').val(chrValue);
+ scaleValue = $('select[name=scale2] option:selected').val();
+ $('input[name=scale]').val(scaleValue);
+ controlValue = controlLocus.val();
+ if (controlValue != tiptext){
+ controlLocus.val(controlValue);
+ }
+ else{
+ controlLocus.val('');
+ }
+
+ //Changed the way permValue, bootValue, and parentsValue are acquired; before it was $(____).is(':checked');
+ permValue = $('input[name=permCheck2]:checked').val();
+ $('input[name=permCheck]').val(permValue);
+
+ bootValue = $('input[name=bootCheck2]:checked').val();
+ $('input[name=bootCheck]').val(bootValue);
+
+ if ($('input[name=parentsf14regression3]:checked').length > 0){
+ $('input[name=parentsf14regression]').val('on');
+ } else {
+ $('input[name=parentsf14regression]').val('off');
+ }
+
+ dataEditingFunc(this.form,'intervalMap');
+
+ });
+
+ $('#sectionbody4').find('input[name=marker]').click(function() {
+ //Changed the way parentsValue is acquired; before it was $(____).is(':checked');
+ if ($('input[name=parentsf14regression2]:checked').length > 0){
+ $('input[name=parentsf14regression]').val('on');
+ } else {
+ $('input[name=parentsf14regression]').val('off');
+ }
+
+ varValue = $('input[name=applyVarianceSE2]:checked').val();
+ $('input[name=applyVarianceSE]').val(varValue);
+
+ dataEditingFunc(this.form,'markerRegression');
+ });
+
+///////////////////////////////
+//Review and Edit Data
+///////////////////////////////
+
+ $('input[name=excludeGroup]').click(function(){
+ for (i = 1;i <= Math.max(primary_row_count,other_row_count)-1; i++){
+ valueExists = 0;
+ $('#Primary_'+i+',#Other_'+i).children().each(function(){
+ if ($(this).text() == exclude_value) {
+ $('#Primary_'+i+',#Other_'+i).addClass('blocked').find('input[type=text]').val('x');
+ valueExists = 1;
+ return false;
+ }
+ });
+ }
+ });
+
+ $('.update').click(function(){
+ windowName = 'formTarget' + (new Date().getTime());
+ newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=0,directories=1,width=900");
+ document.dataInput.target = windowName;
+ document.dataInput.submitID.value = "basicStatistics";
+
+ primaryData = getTraitData()[0];
+ otherData = getTraitData()[1];
+ allData = getTraitData()[2];
+
+ if (otherData[0].length > 0) {
+ if ($('select[name="stats_mdp"] option:selected').val() == 0) {
+ document.dataInput.strainNames.value = allData[0].toString();
+ document.dataInput.strainVals.value = allData[1].toString();
+ document.dataInput.strainVars.value = allData[2].toString();
+ }
+ else if ($('select[name="stats_mdp"] option:selected').val() == 1) {
+ document.dataInput.strainNames.value = primaryData[0].toString();
+ document.dataInput.strainVals.value = primaryData[1].toString();
+ document.dataInput.strainVars.value = primaryData[2].toString();
+ }
+ else {
+ document.dataInput.strainNames.value = otherData[0].toString();
+ document.dataInput.strainVals.value = otherData[1].toString();
+ document.dataInput.strainVars.value = otherData[2].toString();
+ }
+ }
+ else {
+ document.dataInput.strainNames.value = allData[0].toString();
+ document.dataInput.strainVals.value = allData[1].toString();
+ document.dataInput.strainVars.value = allData[2].toString();
+ }
+
+ document.dataInput.submit();
+ });
+
+ $('input[name="export"]').click(function(){
+ windowName = 'formTarget' + (new Date().getTime());
+ newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=0,directories=1,width=900");
+ document.dataInput.target = windowName;
+ document.dataInput.submitID.value = "exportData";
+
+ primaryData = getTraitData()[0];
+ otherData = getTraitData()[1];
+
+ document.dataInput.strainNames.value = primaryData[0].toString();
+ document.dataInput.strainVals.value = primaryData[1].toString();
+ document.dataInput.strainVars.value = primaryData[2].toString();
+
+ document.dataInput.otherStrainNames.value = otherData[0].toString();
+ document.dataInput.otherStrainVals.value = otherData[1].toString();
+ document.dataInput.otherStrainVars.value = otherData[2].toString();
+
+ attribute_names = new Array();
+ $('#primary,#other').find('th.attribute_name').each(function(){
+ attribute_names.push($(this).val().toString());
+ });
+
+ primary_attribute_values = ""; //This string will be structured as a dictionary with a set of values for each attribute; it will be parsed in the ExportPage class
+ other_attribute_values = "";
+
+ attr_counter = 1; // Counter for each different attribute
+ row_counter = 1; // Counter for each value for each attribute
+ while (attr_counter <= attribute_names.length){
+ attribute_name = $('#primary,#other').find('th.attribute_name:eq('+ (attr_counter-1).toString() + ')').text();
+ primary_row_count = $('#primary').find('tr').length - 1;
+ other_row_count = $('#other').find('tr').length - 1;
+
+ primary_attribute_values += attribute_name + " : ";
+ other_attribute_values += attribute_name + " : ";
+
+ primary_value_string = ""; //This string of values (in the format 'a,b,c', etc) will be appended to the primary_attribute_values string
+ for (row_counter = 1;row_counter <= numPrimaryRows; row_counter++){
+ value = $('#primary_attribute'+attr_counter.toString()+'_sample'+row_counter.toString()).text();
+ if (row_counter == primary_row_count) {
+ primary_value_string += (value + " / ");
+ }
+ else{
+ primary_value_string += (value + ",");
+ }
+ }
+
+ primary_attribute_values += primary_value_string;
+
+ other_value_string = ""; //This string of values (in the format 'a,b,c', etc) will be appended to the other_attribute_values string
+ for (row_counter = 1;row_counter <= numOtherRows; row_counter++){
+ value = $('#other_attribute'+attr_counter.toString()+'_sample'+row_counter.toString()).text();
+ if (row_counter == other_row_count) {
+ other_value_string += (value + " / ");
+ }
+ else{
+ other_value_string += (value + ",");
+ }
+ }
+ other_attribute_values += other_value_string;
+ attr_counter += 1
+ }
+
+ document.dataInput.extra_attributes.value = primary_attribute_values;
+ document.dataInput.other_extra_attributes.value = other_attribute_values;
+
+ document.dataInput.submit();
+ });
+
+ var thisTable = $('#sortable1,#sortable2'); //ZS: variable representing each table, because it's used often
+
+ thisTable.find('input[name="selectCheck"]').click(function(){
+ if($(this).is(':checked')){
+ $(this).parent("").parent("").children("td").css("background-color", "yellow");
+ }
+ else{
+ if(!($(this).parent().parent().hasClass('outlier'))){
+ $(this).parent().parent().children("td").css("background-color", "white");
+ }
+ }
+ });
+
+ $('input[name=resetButton]').click(function(){
+
+ //ZS: Reset "hide no value" and "hide outliers"
+ $('#showHideOptions').find('input[name=showHideNoValue]').val(' Hide No Value ');
+ $('#showHideOptions').find('input[name=showHideOutliers]').val(' Hide Outliers ');
+ noValShown = 1;
+ outliersShown = 1;
+
+ for (i=1;i<=numPrimaryRows-1;i++){
+ var thisRow = $('#Primary_'+i);
+ if (thisRow.is('.invisible')){
+ thisRow.removeClass('invisible');
+ }
+ if (thisRow.is('.blocked')){
+ thisRow.removeClass('blocked');
+ }
+ if (thisRow.is(':not(.outlier)')){
+ thisRow.css("background-color", "white");
+ }
+
+ var thisValueField = thisRow.find('.valueField');
+
+ var originalValue = thisValueField[0].defaultValue;
+ var thisClassNames = thisRow.find('input:eq(1)').attr('class').split(/\s+/);
+ var valueClass = thisClassNames[thisClassNames.length-1];
+ thisRow.find('input:eq(1)').removeClass(valueClass).addClass(originalValue).val(originalValue);
+
+ if (thisValueField.length > 1){
+ var originalValue = thisValueField[1].defaultValue;
+ var thisClassNames = thisRow.find('input:eq(2)').attr('class').split(/\s+/);
+ var valueClass = thisClassNames[thisClassNames.length-1];
+ thisRow.find('input:eq(2)').removeClass(valueClass).addClass(originalValue).val(originalValue);
+ }
+ }
+ for (i=1;i<=numOtherRows-1;i++){
+ var thisRow = $('#Other_'+i);
+ if (thisRow.is('.invisible')){
+ thisRow.removeClass('invisible')
+ }
+ if (thisRow.is('.blocked')){
+ thisRow.removeClass('blocked');
+ }
+ if (thisRow.is(':not(.outlier)')){
+ thisRow.css("background-color", "white");
+ }
+
+ var thisValueField = thisRow.find('.valueField');
+
+ var originalValue = thisValueField[0].defaultValue;
+ var thisClassNames = thisRow.find('input:eq(1)').attr('class').split(/\s+/);
+ var valueClass = thisClassNames[thisClassNames.length-1];
+ thisRow.find('input:eq(1)').removeClass(valueClass).addClass(originalValue).val(originalValue);
+
+ if (thisValueField.length > 1){
+ var originalValue = thisValueField[1].defaultValue;
+ var thisClassNames = thisRow.find('input:eq(2)').attr('class').split(/\s+/);
+ var valueClass = thisClassNames[thisClassNames.length-1];
+ thisRow.find('input:eq(2)').removeClass(valueClass).addClass(originalValue).val(originalValue);
+ }
+ }
+ });
+
+ var tiptext2 = "e.g., 4, 6-30, 43";
+ var blockField = $('#showHideOptions').find('input[name=removeField]'); //ZS: Field where user inputs the index of the samples he/she wants to block; created variable because it's used often
+
+ if(blockField.val() == '' || blockField.val() == tiptext2) {
+ blockField.addClass('searchtip');
+ blockField.val(tiptext2);
+ }
+
+ blockField.focus(function(e) {
+ if(blockField.val() == tiptext2) {
+ blockField.val('');
+ }
+ blockField.removeClass('searchtip');
+ });
+
+ blockField.blur(function(e) {
+ if(blockField.val() == '') {
+ blockField.addClass('searchtip');
+ blockField.val(tiptext2);
+ } else if(blockField.val() == tiptext2) {
+ blockField.addClass('searchtip');
+ } else {
+ blockField.removeClass('searchtip');
+ }
+ });
+
+ var noValShown = new Boolean(1);
+ var outliersShown = new Boolean(1);
+
+ $('#showHideOptions').bind('click', function(e){
+ var target = e.target;
+ $target = $(target);
+
+ if (target.name === 'blockSamples'){
+ if (blockField.val() == tiptext2){
+ blockField.val('')
+ }
+ blockedText = blockField.val();
+ blockedTextSplit = new Array();
+ blockedItems = new Array();
+
+ blockedTextSplit = blockedText.split(/\,/);
+
+ for (i=0;i<=blockedTextSplit.length-1;i++) {
+ var item = blockedTextSplit[i];
+ if(item.indexOf('-') != -1){
+ subArray = new Array();
+ subArray = item.split('-');
+ num1 = parseInt(subArray[0]);
+ num2 = parseInt(subArray[1]);
+ for (j=num1;j<=num2;j=j+1){
+ blockedItems.push(j);
+ }
+ }
+ else if(!(isNaN(item))) {
+ blockedItems.push(item);
+ }
+ }
+
+ for (i=0;i<=blockedItems.length-1;i++) {
+ item = blockedItems[i];
+ if ($('select[name=block_method]').val() == '0') {
+ var thisRow = $('#Other_'+item);
+ }
+ else {
+ var thisRow = $('#Primary_'+item);
+ }
+
+ if (thisRow.is('.novalue')) {
+ continue;
+ }
+ else {
+ thisRow.addClass('blocked').find('input.valueField').val('x');
+ }
+
+ //First look at value cell
+ var thisCell = thisRow.find('input:eq(1)');
+ var thisClassNames = thisCell.attr('class').split(/\s+/);
+ var valueClass = thisClassNames[thisClassNames.length-1];
+ var header = thisRow.parents('table.tablesorter').find('th.header:contains("Value"):eq(0)');
+ if (header.hasClass('headerSortUp')){
+ thisCell.removeClass(valueClass).addClass('-9999');
+ } else if (header.hasClass('headerSortDown')){
+ thisCell.removeClass(valueClass).addClass('9999');
+ } else {
+ thisCell.removeClass(valueClass).addClass('-9999');
+ }
+
+ //Check if there is an SE column
+ if (thisRow.find('input.valueField').length > 1) {
+ var thisCell = thisRow.find('input:eq(2)');
+ var thisClassNames = thisCell.attr('class').split(/\s+/);
+ var valueClass = thisClassNames[thisClassNames.length-1];
+ var header = thisRow.parents('table.tablesorter').find('th.header:contains("SE"):eq(0)');
+ if (header.hasClass('headerSortUp')){
+ thisCell.removeClass(valueClass).addClass('-9999');
+ } else if (header.hasClass('headerSortDown')){
+ thisCell.removeClass(valueClass).addClass('9999');
+ } else {
+ thisCell.removeClass(valueClass).addClass('-9999');
+ }
+ }
+ }
+ }
+
+ else if (target.name === 'showHideNoValue'){
+ if (noValShown) {
+ $('#showHideOptions').find('input[name=showHideNoValue]').val(' Show No Value ');
+ for (i=1;i<=Math.max(numPrimaryRows,numOtherRows)-1;i++) {
+ if (i<=numPrimaryRows-1) {
+ var thisRow = $('#Primary_'+i);
+ if (thisRow.is('.novalue:visible') || thisRow.is('.blocked:visible')){
+ jQuery(thisRow).addClass('invisible');
+ }
+ }
+ if (i<=numOtherRows-1){
+ var thisOtherRow = $('#Other_'+i);
+ if (thisOtherRow.is('.novalue:visible') || thisOtherRow.is('.blocked:visible')){
+ if (thisOtherRow.is(':visible')){
+ jQuery(thisOtherRow).addClass('invisible');
+ }
+ }
+ }
+ }
+ noValShown = 0;
+ }
+ else {
+ $('#showHideOptions').find('input[name=showHideNoValue]').val(' Hide No Value ');
+ for (i=1;i<=Math.max(numPrimaryRows,numOtherRows)-1;i++) {
+ if (i<=numPrimaryRows-1) {
+ var thisRow = $('#Primary_'+i);
+ if (thisRow.is('.novalue') || thisRow.is('.blocked')){
+ jQuery(thisRow).removeClass('invisible');
+ if (!(outliersShown)) {
+ if (thisRow.is('.outlier:visible')){
+ jQuery(thisRow).addClass('invisible');
+ }
+ }
+ }
+ }
+ if (i<=numOtherRows-1){
+ var thisOtherRow = $('#Other_'+i);
+ if (thisOtherRow.is('.novalue') || thisOtherRow.is('.blocked')){
+ jQuery(thisOtherRow).removeClass('invisible');
+ if (!(outliersShown)) {
+ if (thisOtherRow.is('.outlier:visible')){
+ jQuery(thisOtherRow).addClass('invisible');
+ }
+ }
+ }
+ }
+ }
+ noValShown = 1;
+ }
+ }
+
+ else if (target.name === 'showHideOutliers'){
+ if (outliersShown){
+ $('#showHideOptions').find('input[name=showHideOutliers]').val(' Show Outliers ');
+ for (i=1;i<=Math.max(numPrimaryRows,numOtherRows)-1;i++) {
+ if (i<=numPrimaryRows-1) {
+ thisRow = $('#Primary_'+i);
+ if (thisRow.is('.outlier:visible') && (!(thisRow.is('.invisible')))) {
+ thisRow.addClass('invisible')
+ }
+ }
+ if (i<=numOtherRows-1) {
+ thisOtherRow = $('#Other_'+i);
+ if (thisOtherRow.is('.outlier:visible') && (!(thisOtherRow.is('.invisible')))) {
+ thisOtherRow.addClass('invisible')
+ }
+ }
+ }
+ outliersShown = 0;
+ }
+ else {
+ $('#showHideOptions').find('input[name=showHideOutliers]').val(' Hide Outliers ');
+ for (i=1;i<=Math.max(numPrimaryRows,numOtherRows)-1;i++) {
+ if (i<=numPrimaryRows-1) {
+ thisRow = $('#Primary_'+i);
+ if (thisRow.is('.outlier') && (!(thisRow.is(':visible')))) {
+ if (!(noValShown)) {
+ if (thisRow.is('.blocked')){
+ continue;
+ }
+ }
+ jQuery(thisRow).removeClass('invisible')
+ }
+ }
+ if (i<=numOtherRows-1) {
+ thisOtherRow = $('#Other_'+i);
+ if (thisOtherRow.is('.outlier') && (!(thisOtherRow.is(':visible')))) {
+ if (!(noValShown)) {
+ if (thisOtherRow.is('.blocked')){
+ continue;
+ }
+ }
+ jQuery(thisOtherRow).removeClass('invisible')
+ }
+ }
+ }
+ outliersShown = 1;
+ }
+ }
+ return false;
+ });
+});
+
+function getTraitData(){
+ primary_row_count = $('#sortable1').find('tr').length - 1;
+ other_row_count = $('#sortable2').find('tr').length - 1;
+
+ primaryStrainNames = new Array();
+ primaryVals = new Array();
+ primaryVars = new Array();
+
+ allStrainNames = new Array();
+ allVals = new Array();
+ allVars = new Array();
+
+ for (i = 1;i <= primary_row_count; i++){
+ thisRow = $('#Primary_'+i);
+ strainName = thisRow.find('span:first').text();
+ primaryStrainNames.push(strainName);
+ allStrainNames.push(strainName);
+ strainVal = thisRow.find('input:eq(1)').val();
+ primaryVals.push(strainVal);
+ allVals.push(strainVal);
+ strainVar = ''; // Just to initialize it in case there is no var
+ strainVar = thisRow.find('input:eq(2)').val();
+ primaryVars.push(strainVar);
+ allVars.push(strainVar);
+ }
+
+ otherStrainNames = new Array();
+ otherVals = new Array();
+ otherVars = new Array();
+
+ for (j = 1;j <= other_row_count; j++){
+ thisRow = $('#Other_'+j)
+ strainName = thisRow.find('span:first').text();
+ otherStrainNames.push(strainName);
+ strainVal = thisRow.find('input:eq(1)').val();
+ otherVals.push(strainVal);
+ strainVar = ''; // Just to initialize it in case there is no var
+ strainVar = thisRow.find('input:eq(2)').val();
+ otherVars.push(strainVar);
+
+ if (jQuery.inArray(strainName, allStrainNames) == -1) {
+ allStrainNames.push(strainName);
+ allVals.push(strainVal);
+ allVars.push(strainVar);
+ }
+ }
+
+ primaryData = [primaryStrainNames, primaryVals, primaryVars];
+ otherData = [otherStrainNames, otherVals, otherVars];
+ allData = [allStrainNames, allVals, allVars];
+
+ return [primaryData, otherData, allData];
+}
+
+
+/*
+used by networkGraphPageBody.py
+*/
+
+//Default to plain text + symbol for the "Export Graph File" button
+$('input[name=exportGraphFile]').live('click', function() { window.open($('input[name=exportFilename]').val() + "_plain_symbol.txt") });
+
+function changeFormat(graphName){
+ var graphFormat = $('#exportFormat').val();
+ var traitType = $('#traitType').val();
+
+ $('input[name=exportGraphFile]').die('click');
+
+ if (graphFormat=="xgmml"){
+ if (traitType=="symbol"){
+ var graphFile = graphName+ "_xgmml_symbol.txt";
+ $('input[name=exportGraphFile]').live('click', function() { window.open(graphFile) });
+ }
+ else if (traitType=="name"){
+ var graphFile = graphName+ "_xgmml_name.txt";
+ $('input[name=exportGraphFile]').live('click', function() { window.open(graphFile) });
+ }
+ }
+
+ else if (graphFormat=="plain"){
+ if (traitType=="symbol"){
+ var graphFile = graphName+ "_plain_symbol.txt";
+ $('input[name=exportGraphFile]').live('click', function() { window.open(graphFile) });
+ }
+ else if (traitType=="name"){
+ var graphFile = graphName+ "_plain_name.txt";
+ $('input[name=exportGraphFile]').live('click', function() { window.open(graphFile) });
+ }
+ }
+}
+
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 22:29:58 +0000