Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'

1 files changed, 0 insertions, 1092 deletions

diff --git a/web/javascript/jqueryFunction.js b/web/javascript/jqueryFunction.js
deleted file mode 100755
index e612098b..00000000
--- a/web/javascript/jqueryFunction.js
+++ /dev/null
@@ -1,1092 +0,0 @@
-/*
- jquery part
-*/
-/*
-used by index (base/indexBody.py)
-*/
-$(document).ready(function () {
-    options_visible = 0; //Whether advanced options are being shown
-    $('tr .advanced_option').hide();
-
-    $('.toggle_advanced').click(function () {
-        $('tr .advanced_option').toggle();
-
-        if (options_visible = 0) {
-            $('.full_search_td').css('display', 'none;');
-            $('.search_td').css('display', 'inline');
-            options_visible = 1;
-        } else {
-            if ($('#type_menu.type_menu').val() = 'Hippocampus') {
-                $('.search_td').css('display', 'none;');
-                $('.full_search_td').css('display', 'inline');
-            }
-            options_visible = 0;
-        }
-    });
-
-    $('#full_search').click(function () {
-        gene_symbol = $('input[name=keyword]').val();
-        scriptable_interface_url = 'http://alexandria.uthsc.edu:89/webqtl/main.py?cmd=sch&gene=' + gene_symbol;
-        window.open(scriptable_interface_url, '_self');
-    });
-});
-
-$('select.type_menu').live('change', function () {
-    var trait_type = $('select.type_menu option:selected').val();
-    $('#tissue').val(trait_type);
-    $('#tissue').trigger('change');
-});
-
-
-/*
-used by CorrelationPage.py, AddToSelectionPage.py, and SearchResultPage.py
-*/
-$(document).ready(function () {
-    $('img[name=addselect], img[name=networkgraph], img[name=corrmatrix], img[name=partialCorr], img[name=comparecorr], img[name=mintmap], img[name=heatmap]').click(function () {
-        if ($('input[name=searchResult]:checked').length < 1) {
-            for (i = 0; i < 10; i++) {
-                $('input[name=searchResult]:eq(' + i + ')').attr('checked', true);
-            }
-        }
-    });
-
-    $('img[name=addselect]').click(function () {
-        addRmvSelection($('input[name=RISet]').val(), document.getElementsByName('showDatabase' + $('input[name=RISet]').val())[0], 'addToSelection');
-    });
-
-    $('.toggleShowHide').click(function () {
-        var className = '.extra_options';
-        if ($(className).css('display') == 'none') {
-            var less = 'less';
-            $('input[name=showHideOptions]').val(less);
-            $(className).show();
-            $('input[name=options]').val('Fewer Options');
-            var display = $('input[name=options]').css('display')
-            $(display).val('block');
-        } else {
-            var more = 'more';
-            $('input[name=showHideOptions]').val(more);
-            $(className).hide();
-            $('input[name=options]').val('More Options');
-            var display = $('input[name=showHideOptions]').css('display')
-            $(display).val('block');
-        }
-    });
-});
-
-/*
-used by AddToSelectionPage.py
-*/
-function validateTraitNumber() {
-    var checkBoxes = $('.checkallbox');
-    if (checkBoxes.filter(":checked").length < 2) {
-        alert("Please select at least two traits.");
-        return false;
-    } else {
-        return true;
-    }
-}
-
-/*
-used by TextSearchPage.py
-*/
-$(document).ready(function () {
-
-    $('.add_traits').click(function () {
-        $('input[name=searchResult]').each(function () {
-            if ($(this).is(':checked')) {
-                groupName = $(this).parents().next().next().children('[href]').text();
-                addORrmv = 'addToSelection';
-                thisForm = $('form[name=showDatabase]');
-                addRmvSelection_allGroups(groupName, thisForm, addORrmv);
-            }
-        });
-    });
-
-    function addRmvSelection_allGroups(groupName, thisForm, addORrmv) {
-        thisForm.attr('target', groupName);
-        thisForm.children('input[name=FormID]:hidden').val(addORrmv);
-        thisForm.children('input[name=RISet]:hidden').val(groupName);
-        var newWindow = open("", thisForm.attr('target'), "menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
-        thisForm.submit();
-    }
-
-    $('.tab_content').hide(); //Hide all tab content
-    $('div.tab_container').each(function () {
-        $(this).parent('td').find('div.tab_container:first').find('div.tab_content:first').show();
-    });
-    $('ul.tabs').each(function () {
-        $(this).find('li:first').addClass('active');
-    });
-    $('ul.tabs:first').find('li:first').show();
-    $('.tab_container:first').find('.tab_content:first').show();
-
-    //On Click Event
-    $('ul.tabs li').click(function () {
-        $('ul.tabs').find('li').removeClass('last_viewed');
-        if ($(this).parent('ul.tabs').next('div.tab_container').attr('id').indexOf('stats') != 1) {
-            $(this).addClass('last_viewed');
-        }
-        $(this).parent('ul.tabs').find('li').removeClass('active');
-        $(this).addClass('active');
-        $(this).parent('ul.tabs').next('div.tab_container').find('.tab_content').hide();
-        var activeTab = $(this).find('a').attr('href');
-        if ($.browser.msie) {
-            $(activeTab).show();
-        } else {
-            $(activeTab).fadeIn();
-        } //Fade in the active ID content
-        return false;
-    });
-
-});
-
-/*
-used by DataEditingPage.py
-*/
-$(document).ready(function () {
-
-    // ZS: This checks the number of columns in order to determine which column to not sort; in this case the plus-minus symbol shouldn't be sortable
-    $('#sortable1,#sortable2').find('th').each(function () {
-        if ($(this).text() == 'SE') {
-            $.tablesorter.defaults.headers = {
-                3: {
-                    sorter: false
-                }
-            };
-            return false;
-        }
-    });
-
-    if ($('#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 segment is called by tablesorter.js; it determines where to get the text used when sorting, based on the type of cell. 
- If a cell has a text input field, it gets the text from its class, which is changed when the user changes the value.
-
- This segment is repeated twice. Ideally this wouldn't be the case, but I can't find a way to reuse the inner textExtraction function.
-*/
-
-    //ZS: Defining these here, so they don't need to be searched for in the DOM for every single node
-    primaryTable = $("#sortable1");
-    otherTable = $("#sortable2");
-
-    primaryValueHeader = primaryTable.find('th:contains("Value"):eq(0)');
-    primarySEHeader = primaryTable.find('th:contains("SE"):eq(0)');
-    otherValueHeader = otherTable.find('th:contains("Value"):eq(1)');
-    otherSEHeader = otherTable.find('th:contains("SE"):eq(1)');
-
-    $("#sortable1").tablesorter({
-        textExtraction: function (node) {
-            if ((node.children[0] == "[object HTMLInputElement]" && node.children[0].type == "text") || (/\S/.test(node.id))) {
-                cellId = node.id;
-                thisCell = $('#' + cellId).children(':eq(0)')
-                valueClassNames = thisCell.attr('class').split(/\s+/);
-                capitalized_column_name = cellId.split('_')[0].charAt(0).toUpperCase() + cellId.split('_')[0].slice(1);
-                value = valueClassNames[valueClassNames.length - 1];
-                newValue = thisCell.val();
-
-                if (newValue == 'x' || value == '9999' || value == '-9999') {
-                    valueType = cellId.split('_')[0];
-                    if (valueType == 'value') {
-                        header = primaryValueHeader;
-                    } else {
-                        header = primarySEHeader;
-                    }
-
-                    if (header.hasClass('headerSortUp')) {
-                        sort_order = 'desc';
-                    } else if (header.hasClass('headerSortDown')) {
-                        sort_order = 'asc';
-                    } else {
-                        sort_order = 'desc';
-                    }
-
-                    if (sort_order == 'desc') {
-                        value = 9999;
-                        thisCell.removeClass(value).addClass('9999');
-                    } else if (sort_order == 'asc') {
-                        value = -9999;
-                        thisCell.removeClass(value).addClass('-9999');
-                    } else {
-                        value = 9999;
-                        thisCell.removeClass(value).addClass('9999');
-                    }
-                }
-
-                text = value;
-            } else {
-                if (node.textContent) {
-                    text = node.textContent;
-                } else {
-                    if (node.childNodes[0] && node.childNodes[0].hasChildNodes()) {
-                        text = node.childNodes[0].innerHTML;
-                    } else {
-                        text = node.innerText;
-                    }
-                }
-            }
-            return text
-        }
-    });
-
-    $("#sortable2").tablesorter({
-        textExtraction: function (node) {
-            if ((node.children[0] == "[object HTMLInputElement]" && node.children[0].type == "text") || (/\S/.test(node.id))) {
-                cellId = node.id;
-                thisCell = $('#' + cellId).children(':eq(0)')
-                valueClassNames = thisCell.attr('class').split(/\s+/);
-                capitalized_column_name = cellId.split('_')[0].charAt(0).toUpperCase() + cellId.split('_')[0].slice(1);
-                value = valueClassNames[valueClassNames.length - 1];
-                newValue = thisCell.val();
-
-                if (newValue == 'x' || value == '9999' || value == '-9999') {
-                    valueType = cellId.split('_')[0];
-                    if (valueType == 'value') {
-                        header = otherValueHeader;
-                    } else {
-                        header = otherSEHeader;
-                    }
-
-                    if (header.hasClass('headerSortUp')) {
-                        sort_order = 'desc';
-                    } else if (header.hasClass('headerSortDown')) {
-                        sort_order = 'asc';
-                    } else {
-                        sort_order = 'desc';
-                    }
-
-                    if (sort_order == 'desc') {
-                        value = 9999;
-                        thisCell.removeClass(value).addClass('9999');
-                    } else if (sort_order == 'asc') {
-                        value = -9999;
-                        thisCell.removeClass(value).addClass('-9999');
-                    } else {
-                        value = 9999;
-                        thisCell.removeClass(value).addClass('9999');
-                    }
-                }
-
-                text = value;
-            } else {
-                if (node.textContent) {
-                    text = node.textContent;
-                } else {
-                    if (node.childNodes[0] && node.childNodes[0].hasChildNodes()) {
-                        text = node.childNodes[0].innerHTML;
-                    } else {
-                        text = node.innerText;
-                    }
-                }
-            }
-            return text
-        }
-    });
-
-    /*
- ZS: When the user changes the value in the text field, the new value is added as a class. This is because 
- $('input[type=text]').val() gets the value attribute, which is always the default value, instead of the 
- value property (which can be changed)
-*/
-
-    var thisTable = $('#sortable1,#sortable2');
-
-    thisTable.bind("update propertychange keyup input paste", function (e) {
-
-        var target = e.target;
-        $target = $(target);
-
-        if (target.nodeName.toLowerCase() == 'input') {
-            thisClassNames = $target.attr('class').split(/\s+/);
-            valueClass = thisClassNames[thisClassNames.length - 1];
-            newValue = $target.val();
-            thisParent = $target.parent('td');
-            thisParentId = thisParent.attr('id');
-
-            $target.removeClass(valueClass);
-
-            if (newValue == 'x') {
-                thisParent.parent('tr').addClass('blocked');
-            } else {
-                $('#' + thisParentId).children('input.valueField:eq(0)').addClass(newValue);
-            }
-        }
-    });
-
-    ////////////////////////////////////
-    // Initially close tabs
-    ////////////////////////////////////
-    thisForm = $('form[name="dataInput"]');
-
-    $('#sectionbody2').hide();
-    $('#sectionbody3').hide();
-    $('#sectionbody4').hide();
-
-    $('#title1').click(function () {
-        $('#sectionbody1').toggle();
-        return false;
-    });
-    $('#title2').click(function () {
-        $('#sectionbody2').toggle();
-        return false;
-    });
-    $('#title3').click(function () {
-        $('#sectionbody3').toggle();
-        return false;
-    });
-    $('#title4').click(function () {
-        $('#sectionbody4').toggle();
-        return false;
-    });
-    $('#title5').click(function () {
-        $('#sectionbody5').toggle();
-        return false;
-    });
-
-
-
-    //////////////////////////////////////////////////////////////
-    // Switch out + and - icon when you click each section header
-    //////////////////////////////////////////////////////////////
-    var expand_html = "<span class=\"expand_container\">&nbsp;&nbsp;<IMG src=\"/images/Expand.gif\" alt=\"Expand\"></span>";
-    var contract_html = "<span class=\"contract_container\">&nbsp;&nbsp;<IMG src=\"/images/Contract.gif\" alt=\"Contract\"></span>";
-
-    $('#title2, #title3, #title4').prepend(expand_html).addClass('1');
-
-    $('#title1, #title5').prepend(contract_html).addClass('0');
-
-    for (i = 1; i <= 5; i++) {
-        $('#title' + i).click(function () {
-            if ($(this).hasClass('0')) {
-                $(this).find('span').replaceWith(expand_html);
-                $(this).removeClass('0');
-                $(this).addClass('1');
-            } else {
-                $(this).find('span').replaceWith(contract_html);
-                $(this).removeClass('1');
-                $(this).addClass('0');
-            }
-        });
-    }
-
-    // Exclude cases by attributes
-    $('div.attribute_values:first').css('display', 'inline'); //Display the dropdown menu with the first attribute's distinct values
-    $('select[name=exclude_menu]').change(function () {
-        $('div.attribute_values').css('display', 'none'); //clear all other menus when a new attribute is selected
-        attribute = $(this).val();
-        //attribute = $('select[name=exclude_menu]').val();
-        menu = $('div.attribute_values').find('[name=\'' + attribute + '\']');
-        menu.parent().css('display', 'inline');
-    });
-
-    primary_row_count = $('#primary').find('tr').length - 1;
-    other_row_count = $('#other').find('tr').length - 1;
-
-    if (primary_row_count >= other_row_count) {
-        row_count = primary_row_count;
-    } else {
-        row_count = other_row_count;
-    }
-
-    $('div.attribute_values').children('select').change(function () {
-        exclude_value = $(this).val();
-    });
-});
-
-$(window).load(function () {
-
-    //ZS: These are needed in a few places; looping through rows by index is faster than doing a "find" search
-    numPrimaryRows = $('#sortable1').find('tr').length;
-    numOtherRows = $('#sortable2').find('tr').length;
-
-
-    ///////////////////////////////
-    //Basic Statistics
-    ///////////////////////////////
-    /////////////////////////////////////////////////////////////////
-    // Hide unselected Basic Statistics tabs (when just BXD strains
-    // are selected, hide the results for all strains/non-BXD)
-    /////////////////////////////////////////////////////////////////
-    $('#stats_tabs1').hide();
-    $('#stats_tabs2').hide();
-
-    $('#sectionbody2').find('select[name=stats_mdp]').change(function () {
-        selected = $('#sectionbody2').find('select[name=stats_mdp] option:selected').val();
-        for (i = 0; i <= 2; i++) {
-            $('#stats_tabs' + i).hide();
-        }
-        $('#stats_tabs' + selected).show();
-    });
-
-    ////////////////////////////////////////////////////////////////////////
-    // Select the same tab across each sample group (when a Box Plot is 
-    // selected for BXD, switching to Non-BXD will also display a Box Plot)
-    ////////////.///////////////////////////////////////////////////////////
-    var $tabs1 = $('#stats_tabs0').tabs();
-    var $tabs2 = $('#stats_tabs1').tabs();
-    var $tabs3 = $('#stats_tabs2').tabs();
-
-    $tabs1.tabs({
-        show: function (event, ui) {
-            var selected = $tabs1.tabs('option', 'selected');
-            $tabs2.tabs('select', selected);
-            $tabs3.tabs('select', selected);
-        }
-    });
-    $tabs2.tabs({
-        show: function (event, ui) {
-            var selected = $tabs2.tabs('option', 'selected');
-            $tabs1.tabs('select', selected);
-            $tabs3.tabs('select', selected);
-        }
-    });
-    $tabs3.tabs({
-        show: function (event, ui) {
-            var selected = $tabs3.tabs('option', 'selected');
-            $tabs1.tabs('select', selected);
-            $tabs2.tabs('select', selected);
-        }
-    });
-
-
-    ///////////////////////////////
-    //Calculate Correlations
-    ///////////////////////////////
-    $('#sectionbody3').find('input[name="sample_corr"]').click(function () {
-        dbValue = $('select[name=database1] option:selected').val();
-        $('input[name=database]').val(dbValue);
-        criteriaValue = $('select[name=criteria1] option:selected').val();
-        $('input[name=criteria]').val(criteriaValue);
-        MDPValue = $('select[name=MDPChoice1] option:selected').val();
-        $('input[name=MDPChoice]').val(MDPValue);
-
-        methodValue = $('input[name=sample_method]:checked').val();
-
-        //This simple method can be used now that 'method' is defaulted to None instead of ''
-        if (methodValue == "1") {
-            $('input[name=method]').val('1');
-        } else {
-            $('input[name=method]').val('2');
-        }
-
-        dataEditingFunc(this.form, 'correlation');
-    });
-
-    $('#sectionbody3').find('input[name="lit_corr"]').click(function () {
-        dbValue = $('select[name=database2] option:selected').val();
-        $('input[name=database]').val(dbValue);
-        criteriaValue = $('select[name=criteria2] option:selected').val();
-        $('input[name=criteria]').val(criteriaValue);
-        MDPValue = $('select[name=MDPChoice2] option:selected').val();
-        $('input[name=MDPChoice]').val(MDPValue);
-
-        $('input[name=method]').val('3');
-
-        dataEditingFunc(this.form, 'correlation');
-    });
-
-    $('#sectionbody3').find('input[name="tiss_corr"]').click(function () {
-        dbValue = $('select[name=database3] option:selected').val();
-        $('input[name=database]').val(dbValue);
-        criteriaValue = $('select[name=criteria3] option:selected').val();
-        $('input[name=criteria]').val(criteriaValue);
-        MDPValue = $('select[name=MDPChoice3] option:selected').val();
-        $('input[name=MDPChoice]').val(MDPValue);
-
-        methodValue = $('input[name=tissue_method]:checked').val();
-
-        if (methodValue == "4") {
-            $('input[name=method]').val('4');
-        } else {
-            $('input[name=method]').val('5');
-        }
-        dataEditingFunc(this.form, 'correlation');
-    });
-
-    ///////////////////////////////
-    //Mapping Tools
-    ///////////////////////////////
-    $('#sectionbody4').find('input[name=interval]').click(function () {
-        chrValue = $('select[name=chromosomes1] option:selected').val();
-        $('input[name=chromosomes]').val(chrValue);
-        scaleValue = $('select[name=scale1] option:selected').val();
-        $('input[name=scale]').val(scaleValue);
-        $('input[name=controlLocus]').val('');
-
-        //Changed the way permValue, bootValue, and parentsValue are acquired; before it was $(____).is(':checked');
-        permValue = $('input[name=permCheck1]:checked').val();
-        $('input[name=permCheck]').val(permValue);
-
-        bootValue = $('input[name=bootCheck1]:checked').val();
-        $('input[name=bootCheck]').val(bootValue);
-
-        if ($('input[name=parentsf14regression1]:checked').length > 0) {
-            $('input[name=parentsf14regression]').val('on');
-        } else {
-            $('input[name=parentsf14regression]').val('off');
-        }
-
-        varValue = $('input[name=applyVarianceSE1]:checked').val();
-        $('input[name=applyVarianceSE]').val(varValue);
-
-        dataEditingFunc(this.form, 'intervalMap');
-    });
-
-    var tiptext = "e.g., rs12345";
-    controlLocus = $('#sectionbody4').find('input[name=controlLocus]');
-
-    if (controlLocus.val() == '' || controlLocus == tiptext) {
-        controlLocus.addClass('searchtip').val(tiptext);
-    }
-
-    controlLocus.focus(function (e) {
-        if (controlLocus.val() == tiptext) {
-            controlLocus.val('');
-        }
-        controlLocus.removeClass('searchtip');
-    });
-
-    controlLocus.blur(function (e) {
-        if (controlLocus.val() == '') {
-            controlLocus.addClass('searchtip').val(tiptext);
-        } else if (controlLocus.val() == tiptext) {
-            controlLocus.addClass('searchtip');
-        } else {
-            controlLocus.removeClass('searchtip');
-        }
-    });
-
-    $('#sectionbody4').find('input[name=composite]').click(function () {
-        chrValue = $('select[name=chromosomes2] option:selected').val();
-        $('input[name=chromosomes]').val(chrValue);
-        scaleValue = $('select[name=scale2] option:selected').val();
-        $('input[name=scale]').val(scaleValue);
-        controlValue = controlLocus.val();
-        if (controlValue != tiptext) {
-            controlLocus.val(controlValue);
-        } else {
-            controlLocus.val('');
-        }
-
-        //Changed the way permValue, bootValue, and parentsValue are acquired; before it was $(____).is(':checked');
-        permValue = $('input[name=permCheck2]:checked').val();
-        $('input[name=permCheck]').val(permValue);
-
-        bootValue = $('input[name=bootCheck2]:checked').val();
-        $('input[name=bootCheck]').val(bootValue);
-
-        if ($('input[name=parentsf14regression3]:checked').length > 0) {
-            $('input[name=parentsf14regression]').val('on');
-        } else {
-            $('input[name=parentsf14regression]').val('off');
-        }
-
-        dataEditingFunc(this.form, 'intervalMap');
-
-    });
-
-    $('#sectionbody4').find('input[name=marker]').click(function () {
-        //Changed the way parentsValue is acquired; before it was $(____).is(':checked');
-        if ($('input[name=parentsf14regression2]:checked').length > 0) {
-            $('input[name=parentsf14regression]').val('on');
-        } else {
-            $('input[name=parentsf14regression]').val('off');
-        }
-
-        varValue = $('input[name=applyVarianceSE2]:checked').val();
-        $('input[name=applyVarianceSE]').val(varValue);
-
-        dataEditingFunc(this.form, 'markerRegression');
-    });
-
-    ///////////////////////////////
-    //Review and Edit Data
-    ///////////////////////////////
-    $('input[name=excludeGroup]').click(function () {
-        for (i = 1; i <= Math.max(primary_row_count, other_row_count) - 1; i++) {
-            valueExists = 0;
-            $('#Primary_' + i + ',#Other_' + i).children().each(function () {
-                if ($(this).text() == exclude_value) {
-                    $('#Primary_' + i + ',#Other_' + i).addClass('blocked').find('input[type=text]').val('x');
-                    valueExists = 1;
-                    return false;
-                }
-            });
-        }
-    });
-
-    $('.update').click(function () {
-        windowName = 'formTarget' + (new Date().getTime());
-        var windowHeight; // windowHeight and windowWidth are used to place the window in the center of the screen
-        var windowWidth;
-        windowHeight = (window.screen.height/2) - (350 + 10)
-        windowWidth = (window.screen.width/2) - (450 + 50)
-        newWindow = open("",windowName,"menubar=1,toolbar=1,resizable=1,left=" + windowWidth + ",top=" + windowHeight + ",screenX=" + windowWidth + ",screenY=" + windowHeight + ",status=1,scrollbars=0,directories=1");
-
-        document.dataInput.target = windowName;
-        document.dataInput.submitID.value = "basicStatistics";
-
-        primaryData = getTraitData()[0];
-        otherData = getTraitData()[1];
-        allData = getTraitData()[2];
-
-        if (otherData[0].length > 0) {
-            if ($('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");
-            }
-        }
-    });
-
-    $('input[name=resetButton]').click(function () {
-
-        //ZS: Reset "hide no value" and "hide outliers"
-        $('#showHideOptions').find('input[name=showHideNoValue]').val(' Hide No Value ');
-        $('#showHideOptions').find('input[name=showHideOutliers]').val(' Hide Outliers ');
-        noValShown = 1;
-        outliersShown = 1;
-
-        for (i = 1; i <= numPrimaryRows - 1; i++) {
-            var thisRow = $('#Primary_' + i);
-            if (thisRow.is('.invisible')) {
-                thisRow.removeClass('invisible');
-            }
-            if (thisRow.is('.blocked')) {
-                thisRow.removeClass('blocked');
-            }
-            if (thisRow.is(':not(.outlier)')) {
-                thisRow.css("background-color", "white");
-            }
-
-            var thisValueField = thisRow.find('.valueField');
-
-            var originalValue = thisValueField[0].defaultValue;
-            var thisClassNames = thisRow.find('input:eq(1)').attr('class').split(/\s+/);
-            var valueClass = thisClassNames[thisClassNames.length - 1];
-            thisRow.find('input:eq(1)').removeClass(valueClass).addClass(originalValue).val(originalValue);
-
-            if (thisValueField.length > 1) {
-                var originalValue = thisValueField[1].defaultValue;
-                var thisClassNames = thisRow.find('input:eq(2)').attr('class').split(/\s+/);
-                var valueClass = thisClassNames[thisClassNames.length - 1];
-                thisRow.find('input:eq(2)').removeClass(valueClass).addClass(originalValue).val(originalValue);
-            }
-        }
-        for (i = 1; i <= numOtherRows - 1; i++) {
-            var thisRow = $('#Other_' + i);
-            if (thisRow.is('.invisible')) {
-                thisRow.removeClass('invisible')
-            }
-            if (thisRow.is('.blocked')) {
-                thisRow.removeClass('blocked');
-            }
-            if (thisRow.is(':not(.outlier)')) {
-                thisRow.css("background-color", "white");
-            }
-
-            var thisValueField = thisRow.find('.valueField');
-
-            var originalValue = thisValueField[0].defaultValue;
-            var thisClassNames = thisRow.find('input:eq(1)').attr('class').split(/\s+/);
-            var valueClass = thisClassNames[thisClassNames.length - 1];
-            thisRow.find('input:eq(1)').removeClass(valueClass).addClass(originalValue).val(originalValue);
-
-            if (thisValueField.length > 1) {
-                var originalValue = thisValueField[1].defaultValue;
-                var thisClassNames = thisRow.find('input:eq(2)').attr('class').split(/\s+/);
-                var valueClass = thisClassNames[thisClassNames.length - 1];
-                thisRow.find('input:eq(2)').removeClass(valueClass).addClass(originalValue).val(originalValue);
-            }
-        }
-    });
-
-    var tiptext2 = "e.g., 4, 6-30, 43";
-    var blockField = $('#showHideOptions').find('input[name=removeField]'); //ZS: Field where user inputs the index of the samples he/she wants to block; created variable because it's used often
-    if (blockField.val() == '' || blockField.val() == tiptext2) {
-        blockField.addClass('searchtip');
-        blockField.val(tiptext2);
-    }
-
-    blockField.focus(function (e) {
-        if (blockField.val() == tiptext2) {
-            blockField.val('');
-        }
-        blockField.removeClass('searchtip');
-    });
-
-    blockField.blur(function (e) {
-        if (blockField.val() == '') {
-            blockField.addClass('searchtip');
-            blockField.val(tiptext2);
-        } else if (blockField.val() == tiptext2) {
-            blockField.addClass('searchtip');
-        } else {
-            blockField.removeClass('searchtip');
-        }
-    });
-
-    var noValShown = new Boolean(1);
-    var outliersShown = new Boolean(1);
-
-    $('#showHideOptions').bind('click', function (e) {
-        var target = e.target;
-        $target = $(target);
-
-        if (target.name === 'blockSamples') {
-            if (blockField.val() == tiptext2) {
-                blockField.val('')
-            }
-            blockedText = blockField.val();
-            blockedTextSplit = new Array();
-            blockedItems = new Array();
-
-            blockedTextSplit = blockedText.split(/\,/);
-
-            for (i = 0; i <= blockedTextSplit.length - 1; i++) {
-                var item = blockedTextSplit[i];
-                if (item.indexOf('-') != -1) {
-                    subArray = new Array();
-                    subArray = item.split('-');
-                    num1 = parseInt(subArray[0]);
-                    num2 = parseInt(subArray[1]);
-                    for (j = num1; j <= num2; j = j + 1) {
-                        blockedItems.push(j);
-                    }
-                } else if (!(isNaN(item))) {
-                    blockedItems.push(item);
-                }
-            }
-
-            for (i = 0; i <= blockedItems.length - 1; i++) {
-                item = blockedItems[i];
-                if ($('select[name=block_method]').val() == '0') {
-                    var thisRow = $('#Other_' + item);
-                } else {
-                    var thisRow = $('#Primary_' + item);
-                }
-
-                if (thisRow.is('.novalue')) {
-                    continue;
-                } else {
-                    thisRow.addClass('blocked').find('input.valueField').val('x');
-                }
-
-                //First look at value cell
-                var thisCell = thisRow.find('input:eq(1)');
-                var thisClassNames = thisCell.attr('class').split(/\s+/);
-                var valueClass = thisClassNames[thisClassNames.length - 1];
-                var header = thisRow.parents('table.tablesorter').find('th.header:contains("Value"):eq(0)');
-                if (header.hasClass('headerSortUp')) {
-                    thisCell.removeClass(valueClass).addClass('-9999');
-                } else if (header.hasClass('headerSortDown')) {
-                    thisCell.removeClass(valueClass).addClass('9999');
-                } else {
-                    thisCell.removeClass(valueClass).addClass('-9999');
-                }
-
-                //Check if there is an SE column			
-                if (thisRow.find('input.valueField').length > 1) {
-                    var thisCell = thisRow.find('input:eq(2)');
-                    var thisClassNames = thisCell.attr('class').split(/\s+/);
-                    var valueClass = thisClassNames[thisClassNames.length - 1];
-                    var header = thisRow.parents('table.tablesorter').find('th.header:contains("SE"):eq(0)');
-                    if (header.hasClass('headerSortUp')) {
-                        thisCell.removeClass(valueClass).addClass('-9999');
-                    } else if (header.hasClass('headerSortDown')) {
-                        thisCell.removeClass(valueClass).addClass('9999');
-                    } else {
-                        thisCell.removeClass(valueClass).addClass('-9999');
-                    }
-                }
-            }
-        } else if (target.name === 'showHideNoValue') {
-            if (noValShown) {
-                $('#showHideOptions').find('input[name=showHideNoValue]').val(' Show No Value ');
-                for (i = 1; i <= Math.max(numPrimaryRows, numOtherRows) - 1; i++) {
-                    if (i <= numPrimaryRows - 1) {
-                        var thisRow = $('#Primary_' + i);
-                        if (thisRow.is('.novalue:visible') || thisRow.is('.blocked:visible')) {
-                            jQuery(thisRow).addClass('invisible');
-                        }
-                    }
-                    if (i <= numOtherRows - 1) {
-                        var thisOtherRow = $('#Other_' + i);
-                        if (thisOtherRow.is('.novalue:visible') || thisOtherRow.is('.blocked:visible')) {
-                            if (thisOtherRow.is(':visible')) {
-                                jQuery(thisOtherRow).addClass('invisible');
-                            }
-                        }
-                    }
-                }
-                noValShown = 0;
-            } else {
-                $('#showHideOptions').find('input[name=showHideNoValue]').val(' Hide No Value ');
-                for (i = 1; i <= Math.max(numPrimaryRows, numOtherRows) - 1; i++) {
-                    if (i <= numPrimaryRows - 1) {
-                        var thisRow = $('#Primary_' + i);
-                        if (thisRow.is('.novalue') || thisRow.is('.blocked')) {
-                            jQuery(thisRow).removeClass('invisible');
-                            if (!(outliersShown)) {
-                                if (thisRow.is('.outlier:visible')) {
-                                    jQuery(thisRow).addClass('invisible');
-                                }
-                            }
-                        }
-                    }
-                    if (i <= numOtherRows - 1) {
-                        var thisOtherRow = $('#Other_' + i);
-                        if (thisOtherRow.is('.novalue') || thisOtherRow.is('.blocked')) {
-                            jQuery(thisOtherRow).removeClass('invisible');
-                            if (!(outliersShown)) {
-                                if (thisOtherRow.is('.outlier:visible')) {
-                                    jQuery(thisOtherRow).addClass('invisible');
-                                }
-                            }
-                        }
-                    }
-                }
-                noValShown = 1;
-            }
-        } else if (target.name === 'showHideOutliers') {
-            if (outliersShown) {
-                $('#showHideOptions').find('input[name=showHideOutliers]').val(' Show Outliers ');
-                for (i = 1; i <= Math.max(numPrimaryRows, numOtherRows) - 1; i++) {
-                    if (i <= numPrimaryRows - 1) {
-                        thisRow = $('#Primary_' + i);
-                        if (thisRow.is('.outlier:visible') && (!(thisRow.is('.invisible')))) {
-                            thisRow.addClass('invisible')
-                        }
-                    }
-                    if (i <= numOtherRows - 1) {
-                        thisOtherRow = $('#Other_' + i);
-                        if (thisOtherRow.is('.outlier:visible') && (!(thisOtherRow.is('.invisible')))) {
-                            thisOtherRow.addClass('invisible')
-                        }
-                    }
-                }
-                outliersShown = 0;
-            } else {
-                $('#showHideOptions').find('input[name=showHideOutliers]').val(' Hide Outliers ');
-                for (i = 1; i <= Math.max(numPrimaryRows, numOtherRows) - 1; i++) {
-                    if (i <= numPrimaryRows - 1) {
-                        thisRow = $('#Primary_' + i);
-                        if (thisRow.is('.outlier') && (!(thisRow.is(':visible')))) {
-                            if (!(noValShown)) {
-                                if (thisRow.is('.blocked')) {
-                                    continue;
-                                }
-                            }
-                            jQuery(thisRow).removeClass('invisible')
-                        }
-                    }
-                    if (i <= numOtherRows - 1) {
-                        thisOtherRow = $('#Other_' + i);
-                        if (thisOtherRow.is('.outlier') && (!(thisOtherRow.is(':visible')))) {
-                            if (!(noValShown)) {
-                                if (thisOtherRow.is('.blocked')) {
-                                    continue;
-                                }
-                            }
-                            jQuery(thisOtherRow).removeClass('invisible')
-                        }
-                    }
-                }
-                outliersShown = 1;
-            }
-        }
-        return false;
-    });
-});
-
-function getTraitData() {
-    primary_row_count = $('#sortable1').find('tr').length - 1;
-    other_row_count = $('#sortable2').find('tr').length - 1;
-
-    primaryStrainNames = new Array();
-    primaryVals = new Array();
-    primaryVars = new Array();
-
-    allStrainNames = new Array();
-    allVals = new Array();
-    allVars = new Array();
-
-    for (i = 1; i <= primary_row_count; i++) {
-        thisRow = $('#Primary_' + i);
-        strainName = thisRow.find('span:first').text();
-        primaryStrainNames.push(strainName);
-        allStrainNames.push(strainName);
-        strainVal = thisRow.find('input:eq(1)').val();
-        primaryVals.push(strainVal);
-        allVals.push(strainVal);
-        strainVar = ''; // Just to initialize it in case there is no var
-        strainVar = thisRow.find('input:eq(2)').val();
-        primaryVars.push(strainVar);
-        allVars.push(strainVar);
-    }
-
-    otherStrainNames = new Array();
-    otherVals = new Array();
-    otherVars = new Array();
-
-    for (j = 1; j <= other_row_count; j++) {
-        thisRow = $('#Other_' + j)
-        strainName = thisRow.find('span:first').text();
-        otherStrainNames.push(strainName);
-        strainVal = thisRow.find('input:eq(1)').val();
-        otherVals.push(strainVal);
-        strainVar = ''; // Just to initialize it in case there is no var
-        strainVar = thisRow.find('input:eq(2)').val();
-        otherVars.push(strainVar);
-
-        if (jQuery.inArray(strainName, allStrainNames) == -1) {
-            allStrainNames.push(strainName);
-            allVals.push(strainVal);
-            allVars.push(strainVar);
-        }
-    }
-
-    primaryData = [primaryStrainNames, primaryVals, primaryVars];
-    otherData = [otherStrainNames, otherVals, otherVars];
-    allData = [allStrainNames, allVals, allVars];
-
-    return [primaryData, otherData, allData];
-}
-
-/*
-used by networkGraphPageBody.py
-*/
-
-//Default to plain text + symbol for the "Export Graph File" button
-$('input[name=exportGraphFile]').live('click', function () {
-    window.open($('input[name=exportFilename]').val() + "_plain_symbol.txt")
-});
-
-function changeFormat(graphName) {
-    var graphFormat = $('#exportFormat').val();
-    var traitType = $('#traitType').val();
-
-    $('input[name=exportGraphFile]').die('click');
-
-    if (graphFormat == "xgmml") {
-        if (traitType == "symbol") {
-            var graphFile = graphName + "_xgmml_symbol.txt";
-            $('input[name=exportGraphFile]').live('click', function () {
-                window.open(graphFile)
-            });
-        } else if (traitType == "name") {
-            var graphFile = graphName + "_xgmml_name.txt";
-            $('input[name=exportGraphFile]').live('click', function () {
-                window.open(graphFile)
-            });
-        }
-    } else if (graphFormat == "plain") {
-        if (traitType == "symbol") {
-            var graphFile = graphName + "_plain_symbol.txt";
-            $('input[name=exportGraphFile]').live('click', function () {
-                window.open(graphFile)
-            });
-        } else if (traitType == "name") {
-            var graphFile = graphName + "_plain_name.txt";
-            $('input[name=exportGraphFile]').live('click', function () {
-                window.open(graphFile)
-            });
-        }
-    }
-}
\ No newline at end of file