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-rwxr-xr-xweb/javascript/header.js122
-rwxr-xr-x[-rw-r--r--]web/javascript/jqueryFunction.js2041
-rw-r--r--[-rwxr-xr-x]web/javascript/selectDatasetMenu.js0
-rwxr-xr-xweb/javascript/webqtl.js184
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 =''
-
+
}
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-21 15:21:04 +0000