Add all the source codes into the github.

1 files changed, 1115 insertions, 0 deletions

diff --git a/web/javascript/jqueryFunction.js b/web/javascript/jqueryFunction.js
new file mode 100644
index 00000000..5e6641cd
--- /dev/null
+++ b/web/javascript/jqueryFunction.js
@@ -0,0 +1,1115 @@
+/*
+ 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) });
+                }
+        }
+}
+