Merge branch 'flask' of http://github.com/zsloan/genenetwork

4 files changed, 1164 insertions, 1183 deletions

diff --git a/web/javascript/header.js b/web/javascript/header.js
index 59fcacd8..65ba1bd6 100755
--- a/web/javascript/header.js
+++ b/web/javascript/header.js
@@ -1,62 +1,62 @@
-ctext = ''

-ctext += '<TD width=30 rowSpan=5>&nbsp;</TD>'

-ctext += '<TD bgColor=#ffffff NOWRAP="yes" width="100%" class="solidBorder">'

-ctext += '	<Table width= "100%" cellSpacing=0 cellPadding=0>'

-ctext += '		<TR>'

-ctext += '			<TD width= "100%" id="smallsize">'

-ctext += '				<a href="/">'

-ctext += '				<IMG src="/images/upload/GeneNet_Banner2009c.png" border="0">'

-ctext += '				</a>'

-ctext += '			</TD>'

-ctext += '			<TD valign="bottom">'

-ctext += '				<A HREF="http://www.touchgraph.com/TGGoogleBrowser.php?start=genenetwork.org&signed=false" target="_blank">'

-ctext += '					<IMG SRC="/images/upload/NetworkLogo.png" width="101" height="73" border="0">'

-ctext += '				</a>'

-ctext += '			</td>'

-ctext += '			<TD valign="bottom">'

-ctext += '				<IMG src="/images/webqtllogo2.gif" alt="WebQTL" border="0">'

-ctext += '			</TD>'

-ctext += '		</TR>'

-ctext += '	</Table>'

-ctext += '</TD>'

-ctext += '<TD width="30" rowSpan=5>&nbsp;</TD>'

-ctext += '</TR>'

-ctext += '<TR>'

-ctext += '<!--Home Help Search News Papers Policies Accounts Links-->'

-ctext += '<TD bgColor=#ddddff NOWRAP="yes" class="solidBorder">'

-ctext += '<table width="100%" cellSpacing=0 cellPadding=0 border=0>'

-ctext += '<tr>'

-ctext += '<td aligh=left NOWRAP="yes">'

-ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'

-ctext += '<Span Id= "menu_grp1" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp1\'])"  onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp1\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'

-ctext += '<Strong>Home</Strong></Span>'

-ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'

-ctext += '<Span Id= "menu_grp2" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp2\'])"  onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp2\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'

-ctext += '<Strong>Search</Strong></Span>'

-ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'

-ctext += '<Span Id= "menu_grp3" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp3\'])"  onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp3\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'

-ctext += '<Strong>Help</Strong></Span>'

-ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'

-ctext += '<Span Id= "menu_grp4" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp4\'])"  onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp4\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'

-ctext += '<A Href="/whats_new.html"  style="font-size:12px;font-family:verdana;color:#0000ae">'

-ctext += '<Strong>News</Strong></A></Span>'

-ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'

-ctext += '<Span Id= "menu_grp5" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp5\'])"  onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp5\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'

-ctext += '<A Href="/reference.html"  style="font-size:12px;font-family:verdana;color:#0000ae">'

-ctext += '<Strong>References</Strong></A></Span>'

-ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'

-ctext += '<Span Id= "menu_grp6" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp6\'])"  onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp6\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'

-ctext += '<Strong>Policies</Strong></Span>'

-ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'

-ctext += '<Span Id= "menu_grp8" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp8\'])"  onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp8\'])"  style="font-size:12px;font-family:verdana;color:#0000ae">'

-ctext += '<A Href="/links.html" style="font-size:12px;font-family:verdana;color:#0000ae">'

-ctext += '<Strong>Links</Strong></A></Span>'

-ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'

-ctext += '</td>'

-ctext += '<td align="right" NOWRAP="yes">'

-ctext += '<!-- %s -->&nbsp;&nbsp;&nbsp;'

-ctext += '</td>'

-ctext += '</tr>'

-ctext += '</table>'

-ctext += '</TD>'

+ctext = ''
+ctext += '<TD width=30 rowSpan=5>&nbsp;</TD>'
+ctext += '<TD bgColor=#ffffff NOWRAP="yes" width="100%" class="solidBorder">'
+ctext += '	<Table width= "100%" cellSpacing=0 cellPadding=0>'
+ctext += '		<TR>'
+ctext += '			<TD width= "100%" id="smallsize">'
+ctext += '				<a href="/">'
+ctext += '				<IMG src="/images/upload/GeneNet_Banner2009c.png" border="0">'
+ctext += '				</a>'
+ctext += '			</TD>'
+ctext += '			<TD valign="bottom">'
+ctext += '				<A HREF="http://www.touchgraph.com/TGGoogleBrowser.php?start=genenetwork.org&signed=false" target="_blank">'
+ctext += '					<IMG SRC="/images/upload/NetworkLogo.png" width="101" height="73" border="0">'
+ctext += '				</a>'
+ctext += '			</td>'
+ctext += '			<TD valign="bottom">'
+ctext += '				<IMG src="/images/webqtllogo2.gif" alt="WebQTL" border="0">'
+ctext += '			</TD>'
+ctext += '		</TR>'
+ctext += '	</Table>'
+ctext += '</TD>'
+ctext += '<TD width="30" rowSpan=5>&nbsp;</TD>'
+ctext += '</TR>'
+ctext += '<TR>'
+ctext += '<!--Home Help Search News Papers Policies Accounts Links-->'
+ctext += '<TD bgColor=#ddddff NOWRAP="yes" class="solidBorder">'
+ctext += '<table width="100%" cellSpacing=0 cellPadding=0 border=0>'
+ctext += '<tr>'
+ctext += '<td aligh=left NOWRAP="yes">'
+ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
+ctext += '<Span Id= "menu_grp1" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp1\'])"  onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp1\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'
+ctext += '<Strong>Home</Strong></Span>'
+ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
+ctext += '<Span Id= "menu_grp2" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp2\'])"  onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp2\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'
+ctext += '<Strong>Search</Strong></Span>'
+ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
+ctext += '<Span Id= "menu_grp3" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp3\'])"  onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp3\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'
+ctext += '<Strong>Help</Strong></Span>'
+ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
+ctext += '<Span Id= "menu_grp4" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp4\'])"  onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp4\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'
+ctext += '<A Href="/whats_new.html"  style="font-size:12px;font-family:verdana;color:#0000ae">'
+ctext += '<Strong>News</Strong></A></Span>'
+ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
+ctext += '<Span Id= "menu_grp5" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp5\'])"  onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp5\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'
+ctext += '<A Href="/reference.html"  style="font-size:12px;font-family:verdana;color:#0000ae">'
+ctext += '<Strong>References</Strong></A></Span>'
+ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
+ctext += '<Span Id= "menu_grp6" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp6\'])"  onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp6\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'
+ctext += '<Strong>Policies</Strong></Span>'
+ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
+ctext += '<Span Id= "menu_grp8" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp8\'])"  onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp8\'])"  style="font-size:12px;font-family:verdana;color:#0000ae">'
+ctext += '<A Href="/links.html" style="font-size:12px;font-family:verdana;color:#0000ae">'
+ctext += '<Strong>Links</Strong></A></Span>'
+ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
+ctext += '</td>'
+ctext += '<td align="right" NOWRAP="yes">'
+ctext += '<!-- %s -->&nbsp;&nbsp;&nbsp;'
+ctext += '</td>'
+ctext += '</tr>'
+ctext += '</table>'
+ctext += '</TD>'
 document.write(ctext)
\ No newline at end of file
diff --git a/web/javascript/jqueryFunction.js b/web/javascript/jqueryFunction.js
index 5e6641cd..e612098b 100644..100755
--- a/web/javascript/jqueryFunction.js
+++ b/web/javascript/jqueryFunction.js
@@ -1,80 +1,75 @@
 /*
  jquery part
 */
-
 /*
 used by index (base/indexBody.py)
 */
-
-$(document).ready(function(){
+$(document).ready(function () {
     options_visible = 0; //Whether advanced options are being shown
-    
     $('tr .advanced_option').hide();
 
-    $('.toggle_advanced').click(function(){
+    $('.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;
-	 }
+
+        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(){
+    $('#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');
+        window.open(scriptable_interface_url, '_self');
     });
 });
 
-$('select.type_menu').live('change', function() {
+$('select.type_menu').live('change', function () {
     var trait_type = $('select.type_menu option:selected').val();
-    $('#tissue').val(trait_type);   
-    $('#tissue').trigger('change'); 
+    $('#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++){
-                $('input[name=searchResult]:eq('+i+')').attr('checked',true);
+$(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');
+    $('img[name=addselect]').click(function () {
+        addRmvSelection($('input[name=RISet]').val(), document.getElementsByName('showDatabase' + $('input[name=RISet]').val())[0], 'addToSelection');
     });
 
-    $('.toggleShowHide').click(function(){
+    $('.toggleShowHide').click(function () {
         var className = '.extra_options';
-        if ($(className).css('display') == 'none'){
-	        var less = 'less';
-	        $('input[name=showHideOptions]').val(less);
+        if ($(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');
+            $(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');
         }
     });
 });
@@ -83,82 +78,91 @@ $(document).ready(function(){
 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;
-	}
+    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;
-	});
+$(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
 */
-$(document).ready(function() {
+$(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') {
+            $.tablesorter.defaults.headers = {
+                3: {
+                    sorter: false
+                }
+            };
+            return false;
+        }
+    });
+
+    if ($('#sortable1,#sortable2').find('.outlier').size() > 0) {
+        $('input[name=sample_method]:eq(1)').attr('checked','checked');
+        $('input[name=tissue_method]:eq(1)').attr('checked','checked');
+    }
 
-	// 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. 
@@ -167,949 +171,922 @@ $(document).ready(function() {
  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: 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];
-}
+    var thisTable = $('#sortable1,#sortable2');
 
+    thisTable.bind("update propertychange keyup input paste", function (e) {
 
-/*
-used by networkGraphPageBody.py
-*/
+        var target = e.target;
+        $target = $(target);
 
-//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") });
+        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;
+    });
 
-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) });
+    //////////////////////////////////////////////////////////////
+    // 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;
                 }
-                else if (traitType=="name"){
-                        var graphFile = graphName+ "_xgmml_name.txt";
-                        $('input[name=exportGraphFile]').live('click', function() { window.open(graphFile) });
+            });
+        }
+    });
+
+    $('.update').click(function () {
+        windowName = 'formTarget' + (new Date().getTime());
+        var windowHeight; // windowHeight and windowWidth are used to place the window in the center of the screen
+        var windowWidth;
+        windowHeight = (window.screen.height/2) - (350 + 10)
+        windowWidth = (window.screen.width/2) - (450 + 50)
+        newWindow = open("",windowName,"menubar=1,toolbar=1,resizable=1,left=" + windowWidth + ",top=" + windowHeight + ",screenX=" + windowWidth + ",screenY=" + windowHeight + ",status=1,scrollbars=0,directories=1");
+
+        document.dataInput.target = windowName;
+        document.dataInput.submitID.value = "basicStatistics";
+
+        primaryData = getTraitData()[0];
+        otherData = getTraitData()[1];
+        allData = getTraitData()[2];
+
+        if (otherData[0].length > 0) {
+            if ($('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");
+            }
         }
+    });
 
-        else if (graphFormat=="plain"){
-                if (traitType=="symbol"){
-                        var graphFile = graphName+ "_plain_symbol.txt";
-                        $('input[name=exportGraphFile]').live('click', function() { window.open(graphFile) });
+    $('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');
+                                }
+                            }
+                        }
+                    }
                 }
-                else if (traitType=="name"){
-                        var graphFile = graphName+ "_plain_name.txt";
-                        $('input[name=exportGraphFile]').live('click', function() { window.open(graphFile) });
+                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)
+            });
+        }
+    }
+}
\ No newline at end of file
diff --git a/web/javascript/selectDatasetMenu.js b/web/javascript/selectDatasetMenu.js
index bb910a5b..bb910a5b 100755..100644
--- a/web/javascript/selectDatasetMenu.js
+++ b/web/javascript/selectDatasetMenu.js
diff --git a/web/javascript/webqtl.js b/web/javascript/webqtl.js
index 19ecf3b7..536e7d26 100755
--- a/web/javascript/webqtl.js
+++ b/web/javascript/webqtl.js
@@ -38,16 +38,16 @@ function makeTree(thisForm, nnn){
 			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;
@@ -152,7 +152,11 @@ function showDatabase3(formName, Database,ProbeSetID,CellID){
 	document[formName].database.value = Database;
 	document[formName].ProbeSetID.value = ProbeSetID;
 	document[formName].CellID.value = CellID;
-	document[formName].submit();
+	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();
 }
 
 
@@ -188,10 +192,10 @@ 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)
@@ -205,10 +209,10 @@ 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];
@@ -219,22 +223,22 @@ 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();
-	
+
 }
 
 
@@ -242,12 +246,12 @@ 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];
@@ -284,15 +288,15 @@ function ODE(thisForm, script){
 	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){	
+	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();
@@ -302,14 +306,14 @@ function ODE(thisForm, script){
 		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;
@@ -318,13 +322,13 @@ function ODE(thisForm, script){
 	}
 }
 */
-// 02/12/2009 
+// 02/12/2009
 // Lei Yan
 
 /*scripts in the Dataediting form*/
 
 function dataEditingFunc(thisForm,submitIdValue){
-	
+
 	windowName = 'formTarget' + (new Date().getTime());
 
 	if (thisForm.FormID.value!='secondRegression'){
@@ -336,7 +340,7 @@ function dataEditingFunc(thisForm,submitIdValue){
 	}
 
 	else if (submitIdValue == "addRecord"){
-		windowName = thisForm.RISet.value;	
+		windowName = thisForm.RISet.value;
 		var name = thisForm.identification.value;
 		if (name != ""){
 		}
@@ -352,7 +356,7 @@ function dataEditingFunc(thisForm,submitIdValue){
 
 	newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
 	thisForm.target = windowName;
-	newWindow.focus();		
+	newWindow.focus();
 	thisForm.submitID.value = submitIdValue;
 	thisForm.submit();
 }
@@ -394,7 +398,7 @@ function addRmvSelection(windowName, thisForm, addORrmv){
 	thisForm.target = windowName;
 	thisForm.FormID.value = addORrmv;
 	thisForm.submit();
-	newWindow.focus();	
+	newWindow.focus();
 }
 
 function batchSelection(thisForm){
@@ -424,7 +428,7 @@ function showTop10(formName, submitIdValue){
 	if ((submitIdValue == "markerRegression")||(submitIdValue == "compositeRegression")){
 		thisForm.topten.value = "topten";
 	}
-		
+
 	thisForm.submitID.value = submitIdValue;
 	thisForm.submit();
 }
@@ -441,12 +445,12 @@ function showIndividualChromosome(formName, submitIdValue, ii){
 	}
 	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;
 	}
@@ -529,10 +533,10 @@ function dataWindow(form){
 }
 
 
-function xchange() {  
+function xchange() {
   var select = document.crossChoice.RISet;
   var value = select.options[select.selectedIndex].value;
-  
+
   if (value !="BDAI") return;
   document.crossChoice.variance.checked = false;
 }
@@ -580,97 +584,97 @@ function crossinfo2(){
 
 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){ 
+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){ 
+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){ 
+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){ 
+function checkTraits2(thisForm){
 	var length = thisForm.searchResult.length;
 	var category = thisForm.selectmenu.value;
 	for(var i = 0; i < length; i++)
@@ -720,18 +724,18 @@ function checkTraits2(thisForm){
 		else
 			{}
 	}
-} 
+}
 
 
 function checkNumeric(field,limit,resetvalue,compares,fdname)
 	{
-		pattern = /^-?[0-9]*\.?[0-9]*$/; 
+		pattern = /^-?[0-9]*\.?[0-9]*$/;
 		if(pattern.test(field.value)==false)
 		{
 			alert("Not numeric in " + fdname);
 			field.value = resetvalue;
 		}
-		else 
+		else
 		{
 			if (compares == 'gthan') {
 			if(field.value > limit)
@@ -748,7 +752,7 @@ function checkNumeric(field,limit,resetvalue,compares,fdname)
 		}
 	}
 
-function checkTraits(thisForm){ 
+function checkTraits(thisForm){
 	var length = thisForm.searchResult.length;
 	var andor = thisForm.selectandor.value;
 	var gthan = parseFloat(thisForm.selectgt.value);
@@ -780,7 +784,7 @@ function checkTraits(thisForm){
 }
 
 
-function checkPM(thisForm){ 
+function checkPM(thisForm){
 	var length = thisForm.searchResult.length;
 	for(var i = 0; i < length; i++)
 	{
@@ -792,8 +796,8 @@ function checkPM(thisForm){
 			{thisForm.searchResult[i].checked = false;}
 		highlight(thisForm.searchResult[i]);
 	}
-} 
-function checkMM(thisForm){ 
+}
+function checkMM(thisForm){
 	var length = thisForm.searchResult.length;
 	for(var i = 0; i < length; i++)
 	{
@@ -804,14 +808,14 @@ function checkMM(thisForm){
 			{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 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';
@@ -869,7 +873,7 @@ function snpbrowser_function_refresh() {
       for (var i=1; i<document.newSNPPadding.exonfunction.length; i++) {
           document.newSNPPadding.exonfunction.options[i].selected=false;
       }
-   } 
+   }
 }
 
 function snpbrowser_domain_refresh() {
@@ -889,7 +893,7 @@ 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";
@@ -898,22 +902,22 @@ function showHideOptions() {
 		showOptions.value = '0';
 		optionsButton.value = "Show Options";
 	}
-	
-	options.style.display = (options.style.display != 'none' ? 'none' : '' );	
+
+	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);
 		}
@@ -921,13 +925,13 @@ function editPCAName(thisForm) {
 			nameArray.push(editName);
 		}
 	}
-	
+
 	var newNames = nameArray.join(",");
-	
+
 	thisForm.newNames.value = newNames;
 	thisForm.searchResult = thisForm.oldSearchResult;
 	thisForm.FormID.value = "corMatrix";
-	
+
 	thisForm.submit();
 }
 
@@ -950,7 +954,7 @@ function unknownChipError(chipName){
 }
 
 /*
-Used by PartialCorrInputPage.py, 
+Used by PartialCorrInputPage.py,
 */
 function validateTrait(thisForm, inputRadioNames, type, method)
 {
@@ -1029,7 +1033,7 @@ function validateTrait(thisForm, inputRadioNames, type, method)
         }
 
     }
-    
+
 }
 
 /*
@@ -1044,7 +1048,7 @@ function changeView(i, Chr_Mb_list){
 	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.startMb.value = '0.000000';
 	document.changeViewForm.endMb.value = Chr_Mb_list[i];
 	document.changeViewForm.graphWidth.value = 1280;
 	document.changeViewForm.submit();
@@ -1076,7 +1080,7 @@ 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";
@@ -1087,7 +1091,7 @@ function changeFormat(graphName){
 			document.getElementById('exportGraphFile').onclick = function() { window.open(graphname) };
 		}
 	}
-	
+
 	else if (graphFormat=="plain")
 	{
 		if (traitType=="symbol")
@@ -1102,7 +1106,7 @@ function changeFormat(graphName){
 		}
 	}
 
-} 
+}
 
 
 /*
@@ -1126,13 +1130,13 @@ function set_customStrains_cookie() {
 }
 
 /*
-* moved from beta2.js 
-*/	
+* 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;
@@ -1145,12 +1149,12 @@ function centerIntervalMapOnRange2(chr, start, stop, form) {
 	form.chromosomes.selectedIndex = oldindex;
 	form.startMb.value = oldstart;
 	form.endMb.value = oldend;
-	
+
 }
 
 /*
-* moved from index3.html 
-*/	
+* moved from index3.html
+*/
 
 String.prototype.trim = function(){
 	return this.replace(/(^\s*)|(\s*$)/g, "");
@@ -1282,13 +1286,13 @@ 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;
 
@@ -1302,7 +1306,7 @@ function showTissueCorrPlot(fmName,geneSymbol1, geneSymbol2,rank){
     if(typeof(thisForm.ProbeSetID2) !== 'undefined'){
     	thisForm.ProbeSetID2.value = 'none';
     }
-    thisForm.submit();	
+    thisForm.submit();
 }
 
 /* Used by MarkerRegressionPage.py */
@@ -1317,7 +1321,7 @@ function validatePvalue(thisForm){
 	{
 		alert("Please enter numeric value.");
 		thisForm.pValue.focus();
-	}	
+	}
 	else if (pValue <0){
 		alert("Please enter the valid P-Value.");
 		thisForm.pValue.focus();
@@ -1327,7 +1331,7 @@ function validatePvalue(thisForm){
 
 	}
 
-	
+
 
 }
 
@@ -1338,9 +1342,9 @@ function showTissueAbbr(fmName,shortname, fullname){
     thisForm.FormID.value = 'tissueAbbreviation';
     thisForm.shortTissueName.value=shortname;
     thisForm.fullTissueName.value=fullname;
-	
+
     thisForm.submit();
     thisForm.FormID.value = 'showCorrelationPlot';
     thisForm.target =''
-	
+
 }