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AliTV.html
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AliTV.html
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<!DOCTYPE html>
<html>
<head>
<title>AliTV</title>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<link rel="stylesheet" href="lib/jquery-ui.min.css">
<link rel="stylesheet" href="css/AliTV.css">
<link rel="shortcut icon" href="css/ali_logo2.ico" />
<link href="lib/bootstrap.min.css" rel="stylesheet">
<link href="lib/colorpicker/bootstrap-colorpicker.min.css" rel="stylesheet">
<link href="lib/contextMenu/jquery.contextMenu.css" rel="stylesheet">
<link href="lib/jsoneditor.min.css" rel="stylesheet" type="text/css">
<link href="lib/bootstrap-select.min.css" rel="stylesheet">
<script src="lib/d3.v3.min.js"></script>
<script src="lib/jquery.min.js"></script>
<script src="lib/jquery-ui.min.js"></script>
<script src="lib/FileSaver.min.js"></script>
<script src="lib/jsoneditor.min.js"></script>
<script src="lib/contextMenu/jquery.contextMenu.js"></script>
<script src="lib/bootstrap-select.min.js"></script>
<script src="lib/bootbox.min.js"></script>
<script src="lib/underscore-min.js"></script>
<script src="js/AliTV.js"></script>
<script src="lib/bootstrap.min.js"></script>
<script src="lib/colorpicker/bootstrap-colorpicker.min.js"></script>
<script src="lib/textures.min.js"></script>
<script src="lib/d3-legend.min.js"></script>
<!-- Google Analytics -->
<script type="text/javascript">
var gaProperty = 'UA-83792433-5';
// Disable tracking if the opt-out cookie exists.
var disableStr = 'ga-disable-' + gaProperty;
if (document.cookie.indexOf(disableStr + '=true') > -1) {
window[disableStr] = true;
$('document').ready(function() {
$('#google-analytics-info').html('<a href="https://www.google.com/intl/en_en/analytics/">Google Analytics</a> is disabled for you');
});
}
// Opt-out function
function gaOptout() {
document.cookie = disableStr + '=true; expires=Thu, 31 Dec 2099 23:59:59 UTC; path=/';
window[disableStr] = true;
$('#google-analytics-info').html('<a href="https://www.google.com/intl/en_en/analytics/">Google Analytics</a> is disabled for you');
}
function openGADialog() {
var dia = $('#googleAnalyticsDialog');
console.log(dia);
dia.modal();
}
(function(i, s, o, g, r, a, m) {
i['GoogleAnalyticsObject'] = r;
i[r] = i[r] || function() {
(i[r].q = i[r].q || []).push(arguments)
}, i[r].l = 1 * new Date();
a = s.createElement(o),
m = s.getElementsByTagName(o)[0];
a.async = 1;
a.src = g;
m.parentNode.insertBefore(a, m)
})(window, document, 'script', '//www.google-analytics.com/analytics.js', 'ga');
ga('create', 'UA-83792433-5', 'auto', {
anonymizeIp: true
});
ga('send', 'pageview');
</script>
<script type="text/javascript">
var ali;
var editor;
$(document).ready(function() {
$('#version-placeholder').html(AliTV_VERSION);
var svg = $('#wgaCanvas');
ali = new AliTV(svg);
var container = document.getElementById("jsoneditor");
editor = new JSONEditor(container)
ali.startTransaction();
$.getJSON('data/chloroplasts.json', function(data) {
ali.setJSON(data);
initialize();
});
});
// https://learn.jquery.com/using-jquery-core/faq/how-do-i-select-an-element-by-an-id-that-has-characters-used-in-css-notation/
function jq(myid) {
return "#" + myid.replace(/(:|\.|\[|\]|,)/g, "\\$1");
}
function initialize() {
setJSONEditorFromAli();
ali.onDataChange(setJSONEditorFromAli);
addFeatureGroupTemplates();
ali.onDataChange(addFeatureGroupTemplates);
setParameters();
ali.onDataChange(setParameters);
showHideCircularWarning();
ali.onDataChange(showHideCircularWarning);
setSlider();
ali.drawLinear();
ali.endTransaction();
}
function showHideCircularWarning() {
if (ali.getLayout() === 'circular') {
$('#warn-circular-layout').show();
} else {
$('#warn-circular-layout').hide();
}
}
function setSlider() {
$(function() {
$("#identity-slider").slider({
range: true,
values: [ali.getMinLinkIdentity(), ali.getMaxLinkIdentity()],
min: 0,
max: 100,
slide: function(event, ui) {
$("#identity-label").val(ui.values[0] + " % - " + ui.values[1] + " %");
ali.filters.links.minLinkIdentity = ui.values[0];
ali.filters.links.maxLinkIdentity = ui.values[1];
}
});
$("#identity-label").val($("#identity-slider").slider("values", 0) + " % - " + $("#identity-slider").slider("values", 1) + " %");
$("#length-slider").slider({
range: true,
values: [ali.getMinLinkLength(), ali.getMaxLinkLength()],
min: 0,
max: ali.getMaxChromosomeLength(),
slide: function(event, ui) {
$("#minlength-label").val(ui.values[0] + " bp - " + ui.values[1] + " bp");
ali.filters.links.minLinkLength = ui.values[0];
ali.filters.links.maxLinkLength = ui.values[1];
}
});
$("#minlength-label").val($("#length-slider").slider("values", 0) + " bp - " + $("#length-slider").slider("values", 1) + " bp");
});
}
$(function() {
$('#skipChromosomesWithoutVisibleLinks').change(function() {
if ($('#skipChromosomesWithoutVisibleLinks').is(':checked')) {
ali.filters.skipChromosomesWithoutVisibleLinks = true;
$("#showAllChromosomes").attr("disabled", true);
} else {
ali.filters.skipChromosomesWithoutVisibleLinks = false;
$("#showAllChromosomes").attr("disabled", false);
}
});
});
function getFeatureValues() {
var group = ($("#customGroup").val());
var form;
if ($("#customRect").is(":checked")) {
form = $("#customRect").val();
} else {
form = $("#customArrow").val();
}
var color = ($("#customColor").val());
ali.setNewFeature(group, form, color);
}
$(function() {
$('#showAllChromosomes').change(function() {
if ($('#showAllChromosomes').is(':checked')) {
ali.filters.showAllChromosomes = true;
$("#skipChromosomesWithoutVisibleLinks").attr("disabled", true);
$("#skipChromosomesWithoutLinks").attr("disabled", true);
} else {
ali.filters.showAllChromosomes = false;
$("#skipChromosomesWithoutVisibleLinks").attr("disabled", false);
$("#skipChromosomesWithoutLinks").attr("disabled", false);
}
});
});
$(function() {
$('#skipChromosomesWithoutLinks').change(function() {
if ($('#skipChromosomesWithoutLinks').is(':checked')) {
ali.filters.skipChromosomesWithoutLinks = true;
$("#showAllChromosomes").attr("disabled", true);
} else {
ali.filters.skipChromosomesWithoutLinks = false;
$("#showAllChromosomes").attr("disabled", false);
}
});
});
$(function() {
$('#onlyShowAdjacentLinks').change(function() {
if ($('#onlyShowAdjacentLinks').is(':checked')) {
ali.filters.onlyShowAdjacentLinks = true;
} else {
ali.filters.onlyShowAdjacentLinks = false;
}
});
});
$(function() {
$('#drawTree').change(function() {
if ($('#drawTree').is(':checked')) {
if (ali.hasTree() === false) {
bootbox.alert("there is no tree data");
$("#treeWidth").attr("disabled", true);
$("#treeLeft").attr("disabled", true);
$("#treeRight").attr("disabled", true);
} else {
ali.conf.tree.drawTree = true;
$("#treeWidth").attr("disabled", false);
$("#treeLeft").attr("disabled", false);
$("#treeRight").attr("disabled", false);
}
} else {
ali.conf.tree.drawTree = false;
$("#treeWidth").attr("disabled", true);
$("#treeLeft").attr("disabled", true);
$("#treeRight").attr("disabled", true);
}
});
});
$(function() {
$('#treeLeft').change(function() {
if ($('#treeLeft').is(':checked')) {
ali.conf.tree.orientation = "left";
}
});
});
$(function() {
$('#treeRight').change(function() {
if ($('#treeRight').is(':checked')) {
ali.conf.tree.orientation = "right";
}
});
});
$(function() {
$('#showFallback').change(function() {
if ($('#showFallback').is(':checked')) {
ali.conf.features.fallbackStyle.visible = true;
$("#showFeatures").attr("disabled", true);
} else {
ali.conf.features.fallbackStyle.visible = false;
$("#showFeatures").attr("disabled", false);
}
});
});
$(function() {
$('#showGenomeLabels').change(function() {
if ($('#showGenomeLabels').is(':checked')) {
ali.conf.labels.genome.showGenomeLabels = true;
} else {
ali.conf.labels.genome.showGenomeLabels = false;
}
});
});
$(function() {
$('#showTickLabels').change(function() {
if ($('#showTickLabels').is(':checked')) {
ali.conf.labels.ticks.showTickLabels = true;
} else {
ali.conf.labels.ticks.showTickLabels = false;
}
});
});
$(function() {
$('#showFeatureLabels').change(function() {
if ($('#showFeatureLabels').is(':checked')) {
ali.conf.labels.features.showFeatureLabels = true;
} else {
ali.conf.labels.features.showFeatureLabels = false;
}
});
});
$(function() {
$('#showChromosomeLabels').change(function() {
if ($('#showChromosomeLabels').is(':checked')) {
$('#chromosomeLabelDetails').show();
ali.conf.labels.chromosome.show = true;
} else {
$('#chromosomeLabelDetails').hide();
ali.conf.labels.chromosome.show = false;
}
});
});
$(function() {
$("#linear")
.change(function() {
if ($(this).is(":checked")) {
ali.conf.layout = $(this).val();
}
});
});
$(function() {
$("#circular")
.change(function() {
if ($(this).is(":checked")) {
ali.conf.layout = $(this).val();
}
});
});
$(function() {
$('#showGenomeLabels').change(function() {
if ($('#showGenomeLabels').is(':checked')) {
ali.conf.labels.genome.showGenomeLabels = true;
} else {
ali.conf.labels.genome.showGenomeLabels = false;
}
});
});
function changeKaryoSpacer() {
var spacer = $("#karyoSpacer").val();
spacer = Number(spacer);
try {
ali.setKaryoSpacer(spacer);
} catch (err) {
bootbox.alert(err);
$("#karyoSpacer").val(ali.getKaryoSpacer());
}
}
function changeKaryoHeight() {
var height = $("#karyoHeight").val();
try {
ali.setKaryoHeight(height);
} catch (err) {
bootbox.alert(err);
$("#karyoHeight").val(ali.getKaryoHeight());
}
}
function changeCanvasWidth() {
var width = $("#canvasWidth").val();
try {
ali.setCanvasWidth(width);
} catch (err) {
bootbox.alert(err);
$("#canvasWidth").val(ali.getCanvasWidth());
}
}
function changeCanvasHeight() {
var height = $("#canvasHeight").val();
try {
ali.setCanvasHeight(height);
} catch (err) {
bootbox.alert(err);
$("#canvasHeight").val(ali.getCanvasHeight());
}
}
function changeTickDistance() {
var distance = $("#tickDistance").val();
try {
ali.setTickDistance(distance);
} catch (err) {
bootbox.alert(err);
$("#tickDistance").val(ali.getTickDistance());
}
}
function changeTreeWidth() {
var treeWidth = $("#treeWidth").val();
try {
ali.setTreeWidth(treeWidth);
} catch (err) {
bootbox.alert(err);
$("#treeWidth").val(ali.getTreeWidth());
}
}
function changeTickLabelFrequency() {
var frequency = $("#tickLabelFrequency").val();
try {
ali.setTickLabelFrequency(frequency);
} catch (err) {
bootbox.alert(err);
$("#tickLabelFrequency").val(ali.getTickLabelFrequency());
}
}
function changeGenomeColor() {
var color = [];
color.push($("#startLineColor").val());
color.push($("#endLineColor").val());
try {
ali.setGenomeColor(color);
} catch (err) {
bootbox.alert(err);
var defaultColor = ali.getGenomeColor();
$("#startLineColor").val(defaultColor[0]);
$("#endLineColor").val(defaultColor[1]);
}
}
function changeLinkColor() {
var color = [];
color.push($("#minLinkColor").val());
color.push($("#midLinkColor").val());
color.push($("#maxLinkColor").val());
try {
ali.setLinkColor(color);
} catch (err) {
bootbox.alert(err);
var defaultColor = ali.getLinkColor();
$("#minLinkColor").val(defaultColor[0]);
$("#midLinkColor").val(defaultColor[1]);
$("#maxLinkColor").val(defaultColor[2]);
}
}
function changeLinkOpacity() {
var opacity = $("#linkOpacity").val();
try {
ali.setLinkOpacity(opacity);
} catch (err) {
bootbox.alert(err);
$("#linkOpacity").val(ali.getLinkOpacity());
}
}
function setDrawLinksByIdentity() {
var drawLinksByIdentity = $("#drawLinksByIdentity").is(':checked');
ali.conf.graphicalParameters.drawLinksByIdentity = drawLinksByIdentity;
}
function changeGenomeLabelColor() {
var color = $("#genomeLabelColor").val();
try {
ali.setGenomeLabelColor(color);
} catch (err) {
bootbox.alert(err);
$("#genomeLabelColor").val(this.conf.labels.genome.color);
}
}
function changeGenomeLabelSize() {
var size = $("#genomeLabelSize").val();
try {
ali.setGenomeLabelSize(size);
} catch (err) {
bootbox.alert(err);
$("#genomeLabelSize").val(this.conf.labels.genome.size);
}
}
function changeTickLabelColor() {
var color = $("#tickLabelColor").val();
try {
ali.setTickLabelColor(color);
} catch (err) {
bootbox.alert(err);
$("#tickLabelColor").val(this.conf.labels.ticks.color);
}
}
function changeTickLabelSize() {
var size = $("#tickLabelSize").val();
try {
ali.setTickLabelSize(size);
} catch (err) {
bootbox.alert(err);
$("#tickLabelSize").val(this.conf.labels.ticks.size);
}
}
function changeChromosomeLabelSize() {
var size = $("#chromosomeLabelSize").val();
try {
ali.setChromosomeLabelSize(size)
} catch (err) {
bootbox.alert(err);
$("#chromosomeLabelSize").val(this.conf.labels.chromosome.size);
}
}
function changeChromosomeLabelRotation() {
var rotation = $("#chromosomeLabelRotation").val();
try {
ali.setChromosomeLabelRotation(rotation);
} catch (err) {
bootbox.alert(err);
$("#chromosomeLabelRotation").val(this.conf.labels.chromosome.rotation);
}
}
function changeChromosomeLabelOffset() {
var offset = $("#chromosomeLabelOffset").val();
try {
ali.setChromosomeLabelOffset(offset);
} catch (err) {
bootbox.alert(err);
$("#chromosomeLabelOffset").val(this.conf.labels.chromosome.offset);
}
}
function changeOffset(karyoId) {
var offset = Number($(jq('offset-' + karyoId)).val());
try {
ali.setOffset(offset, karyoId);
$("#offset-" + karyoId).val(ali.getOffset(karyoId));
ali.drawLinear();
} catch (err) {
bootbox.alert(err);
$("#offset-" + karyoId).val(ali.getTickDistance());
}
}
function setParameters() {
$("#karyoSpacer").val(ali.getKaryoSpacer());
$("#karyoHeight").val(ali.getKaryoHeight());
$("#canvasWidth").val(ali.getCanvasWidth());
$("#canvasHeight").val(ali.getCanvasHeight());
$("#tickDistance").val(ali.getTickDistance());
$("#treeWidth").val(ali.getTreeWidth());
$("#startLineColor").val((ali.getGenomeColor()[0]));
$("#endLineColor").val((ali.getGenomeColor()[1]));
$("#minLinkColor").val((ali.getLinkColor()[0]));
$("#midLinkColor").val((ali.getLinkColor()[1]));
$("#maxLinkColor").val((ali.getLinkColor()[2]));
$("#genomeLabelColor").val(ali.getGenomeLabelColor());
$("#genomeLabelSize").val(ali.getGenomeLabelSize());
$("#tickLabelColor").val(ali.getTickLabelColor());
$("#tickLabelSize").val(ali.getTickLabelSize());
$("#tickLabelFrequency").val(ali.getTickLabelFrequency());
$.each(ali.getSupportedFeatures(), function(key, value) {
$("#color-" + value).val(ali.getFeatureProperty(value, 'color'));
$("#colorpicker-" + value).colorpicker('setValue', ali.getFeatureProperty(value, 'color'));
$("#" + ali.getFeatureProperty(value, 'form') + "-" + value).prop('checked', true);
if (ali.getFeatureProperty(value, 'visible')) {
$("#show-" + value).prop('checked', true);
}
});
$("#invisibleLinksLabel").val(ali.getInvisibleLinks());
$("#invisibleFeaturesLabel").val(ali.getInvisibleFeatures());
$("#invisibleChromosomesLabel").val(ali.getInvisibleChromosomes());
$("#showChromosomeLabels").attr('checked', ali.conf.labels.chromosome.show);
$("#chromosomeLabelSize").val(ali.conf.labels.chromosome.size);
$("#chromosomeLabelRotation").val(ali.conf.labels.chromosome.rotation);
$("#chromosomeLabelOffset").val(ali.conf.labels.chromosome.offset);
if (ali.conf.labels.chromosome.show) {
$("#chromosomeLabelDetails").show();
} else {
$("#chromosomeLabelDetails").hide();
}
$('#showGenomeLabels').attr('checked', true);
$('#showTickLabels').attr('checked', true);
$('#drawLinksByIdentity').attr('checked', ali.conf.graphicalParameters.drawLinksByIdentity);
$('#drawTree').attr('checked', function() {
return ali.conf.tree.drawTree;
});
$("#linkOpacity").val(ali.getLinkOpacity());
setOffsetGroup();
setSlider();
}
function setFilters() {
var layout = ali.getLayout();
setJSONEditorFromAli();
ali.drawEqualLayout(layout);
setParameters();
}
function setLayoutSettings() {
ali.startTransaction();
var layout = ali.getLayout();
changeCanvasWidth();
changeCanvasHeight();
changeKaryoSpacer();
changeKaryoHeight();
changeTickDistance();
changeGenomeColor();
changeLinkColor();
changeLinkOpacity();
setDrawLinksByIdentity();
changeGenomeLabelColor();
changeGenomeLabelSize();
changeTickLabelColor();
changeTickLabelSize();
changeTickLabelFrequency();
changeChromosomeLabelSize();
changeChromosomeLabelRotation();
changeChromosomeLabelOffset();
setJSONEditorFromAli();
ali.drawEqualLayout(layout);
setParameters();
ali.endTransaction();
}
function setFeatureGroupSettings(groupId) {
ali.startTransaction();
var layout = ali.getLayout();
var color = ($("#colorpicker-" + groupId).colorpicker('getValue'));
var form = $("input[type='radio'][name='shape-" + groupId + "']:checked").val();
var visible = $("#show-" + groupId).is(':checked');
try {
ali.setFeatureProperty(groupId, 'color', color);
ali.setFeatureProperty(groupId, 'form', form);
ali.setFeatureProperty(groupId, 'visible', visible);
} catch (err) {
bootbox.alert(err);
$("#colorpicker-" + groupId).colorpicker('setValue', ali.getFeatureProperty(groupId, 'color'));
$("#" + ali.getFeatureProperty(groupId, 'form') + "-" + groupId).prop('checked', true);
$("#show-" + value).prop('checked', ali.getFeatureProperty(value, 'visible'));
}
ali.drawEqualLayout(ali.getLayout());
ali.endTransaction();
}
function setTreeSettings() {
var layout = ali.getLayout();
changeTreeWidth();
setJSONEditorFromAli();
ali.drawEqualLayout(layout);
setParameters();
}
$(function() {
$('#loadJSON').on('change', function(evt) {
var files = evt.target.files; // FileList object
// files is a FileList of File objects.
var output = [];
for (var i = 0, f; f = files[i]; i++) {
var fr = new FileReader();
fr.onload = function(x) {
ali.setJSON(JSON.parse(x.target.result));
setJSONEditorFromAli();
ali.drawLinear();
}
fr.readAsText(f);
}
});
});
function setInvisibleLinkSelection() {
$('#invisibleLinks').text("");
if (ali.getInvisibleLinks() === 0) {
$('.selectpicker').selectpicker('val', '')
} else {
$.each(ali.filters.links.invisibleLinks, function(key, value) {
$('#invisibleLinks')
.append($("<option></option>")
.attr("value", key)
.text(key))
.selectpicker("refresh");
});
}
}
function restoreLink() {
var selectedLinkID = $('.selectpicker[name=invisibleLinks]').val();
ali.showInvisibleLink(selectedLinkID);
setInvisibleLinkSelection();
$("#invisibleLinksLabel").val(ali.getInvisibleLinks());
}
function setInvisibleFeatureSelection() {
$('#invisibleFeatures').text("");
if (ali.getInvisibleFeatures() === 0) {
$('.selectpicker').selectpicker('val', '')
} else {
$.each(ali.filters.features.invisibleFeatures, function(key, value) {
$('#invisibleFeatures')
.append($("<option></option>")
.attr("value", key)
.text(key))
.selectpicker("refresh");
});
}
}
function restoreFeature() {
var selectedFeatureId = $('.selectpicker[name=invisibleFeatures]').val();
ali.showInvisibleFeature(selectedFeatureId);
setInvisibleFeatureSelection();
$("#invisibleFeaturesLabel").val(ali.getInvisibleFeatures());
}
function setInvisibleChromosomeSelection(chromosomeId) {
$('#invisibleChromosomes').text("");
if (ali.getInvisibleChromosomes() === 0) {
$('.selectpicker').selectpicker('val', '')
} else {
$('#invisibleChromosomes')
.append($("<option></option>")
.attr("value", chromosomeId)
.text(ali.data.karyo.chromosomes[chromosomeId].name))
.selectpicker("refresh");
}
}
function restoreChromosome() {
var selectedChromosomeName = $('.selectpicker[name=invisibleChromosomes]').val();
ali.changeChromosomeVisibility(selectedChromosomeName);
setInvisibleChromosomeSelection();
$("#invisibleChromosomesLabel").val(ali.getInvisibleChromosomes());
ali.drawLinear();
}
function setOffsetGroup() {
$("#offsetGroup").text("");
$.each(ali.data.karyo.chromosomes, function(key, value) {
$('#offsetGroup')
.append($("<option></option>")
.attr("value", key)
.text(value.name))
.selectpicker("refresh");
});
}
function setOffsetButton() {
var karyoId = $('.selectpicker[name=offsetGroup]').val();
addOffsetTemplates(karyoId);
ali.conf.offset.isSet = true;
}
function setAliFromJSONEditor() {
var json = editor.get();
ali.setJSON(json);
ali.drawEqualLayout(ali.getLayout());
}
function setJSONEditorFromAli() {
editor.set(ali.getJSON());
}
function toggleJSONEditor() {
$('#jsoneditor').toggle();
}
function saveSVG() {
if (ali.conf.offset.isSet === true) {
ali.svgD3.selectAll(".buttonGroup").remove();
}
var blob = new Blob([ali.getSvgAsText()], {
type: "image/svg+xml;charset=utf-8"
});
saveAs(blob, "AliTV.svg");
}
function saveJSON() {
var blob = new Blob([JSON.stringify(ali.getJSON())], {
type: "plain/text;charset=utf-8"
});
saveAs(blob, "AliTV.json");
}
function addOffsetTemplates(karyoId) {
$('#menu-' + karyoId).remove();
var templateHTML = $('#templateShiftChromosomes').html();
var templateUS = _.template(templateHTML);
$('#offsetMenu').append(templateUS({
karyoId: karyoId,
karyoName: ali.data.karyo.chromosomes[karyoId].name
}));
$("#offset-" + karyoId).val(ali.getOffset(karyoId));
}
function loadDemo(filename) {
$('#loading-indicator').show();
$.getJSON('data/' + filename, function(data) {
ali.setJSON(data);
setJSONEditorFromAli();
ali.drawLinear();
$('#loading-indicator').hide();
});
}
function addFeatureGroupTemplates() {
var groups = ali.getSupportedFeatures();
var templateHTML = $('#template_feature_group').html();
var templateUS = _.template(templateHTML);
$('.feature-colorpicker').colorpicker('destroy');
$('.feature_template').remove();
$.each(groups, function(key, value) {
$('#featuresMenu').prepend($('<li class="feature_template"><a href="#' + value + '" data-toggle="tab">' + value + '</a></li>'));
$('#interface').append(templateUS({
groupId: value
}));
});
$('.feature-colorpicker').colorpicker();
}
function removeOffsetButton(karyoId) {
$("#menu-" + karyoId).remove();
}
$('#myTabs a').click(function(e) {
e.preventDefault()
e.stopPropagation();
$(this).tab('show')
});
$('.dropdown-toggle').dropdown()
$(function() {
$('.demo2').colorpicker();
});
jQuery(document).ready(function($) {
$('#tabs').tab();
});
$(function() {
$.contextMenu({
selector: '.karyoGroup',
build: function($trigger, e) {
var selectedChromosome = ($(e.target).attr("id"));
var split = selectedChromosome.split(", ");
var genome_name = split[0];
var chromosomeId = split[1];
var name = ali.data.karyo.chromosomes[chromosomeId].name;
//Remove selection rect if exists
ali.svgD3.selectAll("rect.selection").remove();
return {
items: {
"info": {
name: "Name: " + name
},
"sep1": "---------",
"Visible": {
name: "Hide",
callback: function(key, options) {
ali.changeChromosomeVisibility(chromosomeId);
ali.getInvisibleChromosomes();
setInvisibleChromosomeSelection(chromosomeId);
ali.drawLinear();
$("#invisibleChromosomesLabel").val(ali.getInvisibleChromosomes());
}
},
"Change orientation": {
name: "Change orientation",
callback: function(key, options) {
ali.changeChromosomeOrientation(chromosomeId);
ali.drawLinear();
}
},
"scrollUp": {
name: "Move up",
callback: function(key, options) {
ali.changeGenomeOrder(genome_name, +1);
ali.drawLinear();
}
},
"scrollDown": {
name: "Move down",
callback: function(key, options) {
ali.changeGenomeOrder(genome_name, -1);
ali.drawLinear();
}
},
"left": {
name: "Move left",
callback: function(key, options) {
ali.changeChromosomeOrder(chromosomeId, -1);
ali.drawLinear();
}
},
"right": {
name: "Move right",
callback: function(key, options) {
ali.changeChromosomeOrder(chromosomeId, 1);
ali.drawLinear();
}
},
"Reset genome zoom/pan": {
name: "Reset genome zoom/pan",
callback: function(key, options) {
ali.resetGenomeRegion(ali.data.karyo.chromosomes[chromosomeId].genome_id);
ali.drawLinear();
}
},
"Quit": {
name: "Quit",
callback: $.noop
}
}
};
}
});
});
$(function() {
$.contextMenu({
selector: '.linkGroup',
build: function($trigger, e) {
var name = ($(e.target).attr("id"));
var identity = ali.visibleLinks[name].identity;
//Remove selection rect if exists
ali.svgD3.selectAll("rect.selection").remove();
return {
items: {
"name": {
name: "Link: " + name
},
"identity": {
name: "Identity: " + identity + "%"
},
"sep1": "---------",
"Visible": {
name: "Hide",
callback: function() {
var selectedLinkID = $(e.target).attr("id");
ali.setLinkInvisible(selectedLinkID);
setInvisibleLinkSelection();
$("#invisibleLinksLabel").val(ali.getInvisibleLinks());
}
},
"Quit": {
name: "Quit",
callback: $.noop
}
}
};
}
});
});
$(function() {
$.contextMenu({
selector: '.featureGroup',
build: function($trigger, e) {
var feature = $(e.target).attr("id");
var split = feature.split("_");
var group = split[1];
var id = split[0];
//Remove selection rect if exists
ali.svgD3.selectAll("rect.selection").remove();
return {
items: {
"name": {
name: "Name: " + ali.data.features[group][id].name
},
"group": {
name: "Group: " + group
},
"sep1": "---------",
"Visible": {
name: "Hide",
callback: function(key, options) {
ali.setFeatureInvisible(feature);
setInvisibleFeatureSelection();
$("#invisibleFeaturesLabel").val(ali.getInvisibleFeatures());
}
},
"Quit": {
name: "Quit",
callback: $.noop
}
}
};
}
});
});
</script>
</head>
<body>
<div class="page-header">
<h1><img src="css/AliTV_logo.png" alt="logo" width="200" height="160" style="margin:0px 20px" /><b>AliTV <sup id="version-placeholder"></sup></b><small> Visualize multiple whole genome alignments as linear
maps</small></h1>
<div>
<ul class="nav nav-tabs" role="tablist">
<li role="presentation"><a href="#about" aria-controls="about" role="tab" data-toggle="tab"><b>About
AliTV</b></a></li>
<li role="presentation"><a href="#filter" aria-controls="about" role="tab" data-toggle="tab"><b>Filtering</b></a></li>
<li class="dropdown"><a id="dLabel" data-toggle="dropdown"><b>Show/Hide Annotations</b> <span class="caret"></span></a>
<ul class="dropdown-menu" role="menu" id="featuresMenu">
<li role="separator" class="divider"></li>