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MSTree_holder.html
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MSTree_holder.html
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<!DOCTYPE html>
<html>
<head>
<link rel="stylesheet" href='static/js/jquery-ui-1.11.4/jquery-ui.min.css'>
<link rel="stylesheet" href="static/css/bootstrap.min.css">
<link rel="stylesheet" href="static/css/grapetree.css">
</head>
<body>
<!--metadata div-->
<link rel="stylesheet" href="static/js/SlickGrid/slick.grid.css" type="text/css"/>
<link rel="stylesheet" href="static/js/SlickGrid/examples/examples.css" type="text/css"/>
<script src="static/js/SlickGrid/lib/firebugx.js"></script>
<script src="static/js/SlickGrid/lib/jquery-1.11.2.min.js"></script>
<script src="static/js/SlickGrid/lib/jquery-ui-1.11.3.min.js"></script>
<script src="static/js/SlickGrid/lib/jquery.event.drag-2.3.0.js"></script>
<script src="static/js/SlickGrid/slick.core.js"></script>
<script src="static/js/SlickGrid/plugins/slick.cellrangedecorator.js"></script>
<script src="static/js/SlickGrid/plugins/slick.cellrangeselector.js"></script>
<script src="static/js/SlickGrid/plugins/slick.cellselectionmodel.js"></script>
<script src="static/js/SlickGrid/slick.formatters.js"></script>
<script src="static/js/SlickGrid/slick.editors.js"></script>
<script src="static/js/SlickGrid/slick.grid.js"></script>
<script src="static/js/SlickGrid/slick.dataview.js"></script>
<script src= "static/js/tree/context.js?version={{config['JAVASCRIPT_VERSION']}}"></script>
<script src="static/js/tree/grid.js?version={{config['JAVASCRIPT_VERSION']}}"></script>
<script src="static/js/tree/help.js?version={{config['JAVASCRIPT_VERSION']}}"></script>
<script src="static/js/spectrum/spectrum.min.js"></script>
<link rel="stylesheet" href="static/js/spectrum/spectrum.css" type="text/css"/>
<!--information divs-->
<div id = 'welcome-div' style='background:white;padding:10px'>
<span id= 'welcome-div-close' class="glyphicon glyphicon-remove" style="float:right;margin-right:5px;zoom:1.5;display:none" onclick="$('#welcome-div').hide()"></span>
<div id='welcome-div-text'>
</div>
</div>
<div id ='information-div' class="modal fade" tabindex="-1" role="dialog">
<div class="modal-dialog" role="document">
<div class="modal-content modal-sm">
<div id ="modal-header" class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>
<p align='center'><img id ='waiting-image'style = 'display:none' src= 'static/js/img/ms_failed_1.png'></img></p>
<span id = 'modal-title'></span>
</div>
<div class="modal-body">
<p id ='waiting-information'></p>
<div id ='param-panel' style = 'display:none'>
<label>Method</label>
<select id ='method-select'>
<option class='show-tooltip' title='NINJA is a scalable alternative to Neighbor-Joining algorithm' value='ninja'>NINJA NJ</option>
<option class='show-tooltip' title='MSTreeV2 uses a directed graph to handle missing data' value='MSTreeV2'>MSTreeV2</option>
<option class='show-tooltip' title='A traditional Minimum spanning tree + eBurst weighting' value='MSTree'>MSTree</option>
<option class='show-tooltip' title='A standard Neighbor-Joining algorithm implemented in FastME V2.0' value='NJ'>Standard Neighbour Joining</option>
<option class='show-tooltip' title='Rapid Neighbour Joining for very large datasets' value='RapidNJ'>RapidNJ</option>
</select>
<label><input id ='check-memory' type="checkbox" checked /> Check memory usage</label>
</div>
</div>
<div class="modal-footer">
<button id ="modal-ok-button" type="button" class="btn btn-default" data-dismiss="modal">Close</button>
</div>
</div><!-- /.modal-content -->
</div><!-- /.modal-dialog -->
<script charset="utf-8">
$("#modal-ok-button").click(function(e){
var profile_file = $(this).data("profile_file")
if (profile_file){
processProfileFile(profile_file);
$(this).data("profile_file",null);
$("#modal-ok-button").html("Close");
$("#param-panel").hide();
e.stopImmediatePropagation();
$("#modal-title").hide();
showWaitingDialog("Processing Profiles");
}
});
$("#method-select").change(function(e) {
if ($(this).val() == "MSTree") $("#MST-option").show();
else $("#MST-option").hide();
});
$("#matrix-select").change(function(e) {
if ($(this).val() == "symmetric") $("#symmetric-option").show();
else $("#symmetric-option").hide();
});
</script>
</div><!-- /.modal -->
<div id='sidebar'>
<div>
<a class='show-tooltip' title="EnteroBase" href="https://enterobase.warwick.ac.uk" target = '_blank'><img src="static/js/img/enterobase.png" alt="Enterobase" style="width:40px;height:45px;"></a> |
<a class='show-tooltip' title='GrapeTree GitHub repository' href="https://github.com/achtman-lab/GrapeTree" target = '_blank'><img src="static/js/img/GrapeTree.PNG" alt="GrapeTree" style="width:40px;height:50px;"></a> |
<a class='show-tooltip' title='Help' href="http://enterobase.readthedocs.io/en/latest/grapetree/grapetree-about.html" target = '_blank'><span class="glyphicon glyphicon-question-sign" style="font-size:30px;height:50px;margin-right:5px;top:10px"></span></a>
<h3 id="headertag" style="font-family: times, serif; font-size:12pt; font-style:italic">GrapeTree</h3>
</div>
<br>
<div id='input-output-panel' class='panel panel-default'>
<div class ='panel-heading mst-menu-title' id= 'file-menu'> <b id='input-output-title'>Inputs/Outputs</b><span id = 'file-menu-icon' class='glyphicon glyphicon-menu-down'> </span></div>
<div class = "panel-body" id ='file-menu-panel'>
<div id ='load-panel'>
<button title='Handles trees, profiles and metadata files' id = 'button-files' class = 'show-tooltip'> Load Files</button>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:5px" onclick="getHelpBox('load_files');"></span>
<hr>
</div>
<div id='save-panel'>
<button id ="save-tree-json">Save GrapeTree</button>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:5px" onclick="getHelpBox('save_grapetree');"></span><br>
<button id ="save-tree-nwk">Save as Newick Tree</button><br>
<button id ="mst-download-svg">Download SVG</button><br>
<hr>
<button id ="show-in-microreact">Show in <img src="https://microreact.org/images/logos/microreact.svg" alt="MicroReact" style="width:100px;height:20px"></button>
</div>
</div>
</div>
<div class='panel panel-default'>
<div class ='panel-heading mst-menu-title' id= 'tree-menu'> <b id>Tree Layout</b><span id = 'tree-menu-icon' class='glyphicon glyphicon-menu-right'> </span></div>
<div class = "panel-body" id ='tree-menu-panel' style='padding:0px;' ><br>
<button id = 'button-goback' style='margin-left:15px;' onclick='loadMSTree(tree_raw);if(current_metadata_file) {loadMetadataText(current_metadata_file);}'> Original tree</button>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:15px" onclick="getHelpBox('tree_layout');"></span>
<br>
<button id = 'button-refresh' style='margin-left:15px;' > Static Redraw </button>
<br>
<button id ="center-graph-button" style='margin-left:15px;' >Centre Tree</button>
<br>
<label><input id ='show-node-tooltip' style='margin-left:15px;' type="checkbox" checked /> Show Tooltips</label>
<hr>
<p align = 'center'>
<label> Drag Icon to Rotate: </label>
<span id="rotation-icon" class="glyphicon glyphicon-refresh"></span>
<br>
<label>Zoom: </label>
<span onclick= "javascript:the_tree.setScale(1.1,true)" class=' zoom-icon glyphicon glyphicon-zoom-in'></span>
<span onclick= "javascript:the_tree.setScale(0.9,true)"class='zoom-icon glyphicon glyphicon-zoom-out'></span>
</p>
<div class='panel panel-default sub-panel'>
<div class ='panel-heading mst-menu-title' id= 'mst-node-menu'> <b id>Node Style</b><span id = 'mst-node-menu-icon' class="glyphicon glyphicon-menu-right"></span></div>
<div class = "panel-body" id ='mst-node-menu-panel' >
<label>Colour By:</label>
<br>
<select style="width:160px" id= 'metadata-select'>
<option value='nothing'>No category</option></select>
<hr>
<label><input id ='show-node-labels'type="checkbox" checked /> Show Labels</label>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:5px" onclick="getHelpBox('show_labels');"></span>
<select style='width:160px' id = 'node-label-text'></select>
<br>
<label>Font Size:</label>
<br>
<div id = "slider-node-fontsize" class = "slider-class"></div><input type='text' style='width:20px;height:15px' id ='spinner-node-fontsize' class='spin-group'><br>
<hr>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:5px" onclick="getHelpBox('node_size');"></span>
<div >
<span onclick="$('#spinner-nodesize').spinner('value', 100)" class='glyphicon glyphicon-fast-backward'></span><label> Node Size (%)</label><br>
<div id = "slider-nodesize" class ="slider-class"></div><input type='text' id ='spinner-nodesize' class='spin-group'>
</div>
<div class="show-tooltip" title="Node size relative to number of strains">
<span onclick="$('#spinner-relative-nodesize').spinner('value', 100)" class='glyphicon glyphicon-fast-backward'></span><label> Kurtosis (%)</label><br>
<div id = "slider-relative-nodesize" class ="slider-class"></div><input type='text' id ='spinner-relative-nodesize' class='spin-group'>
</div>
<hr>
<label>Highlight Label</label>
<br>
<input size="11" id ='search-metadata-input'><span id ='search-metadata-icon' class='add-data-icon glyphicon glyphicon-search'></span>
<br>
<label><input id ='show-individual-segments' type="checkbox" /> Show Pie Chart</label>
<br>
</div>
</div>
<div class='panel panel-default sub-panel'>
<div class ='panel-heading mst-menu-title' id= 'mst-link-menu'> <b id>Branch Style</b><span id = 'mst-link-menu-icon' class='glyphicon glyphicon-menu-right'> </span></div>
<div class = "panel-body" id ='mst-link-menu-panel'>
<label><input id ='show-link-labels'type="checkbox" /> Show Labels</label>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:5px" onclick="getHelpBox('branch_labels');"></span>
<br>
<label>Font Size:</label>
<br>
<div id = "slider-linkfontsize" class = "slider-class"></div><input type='text' style='width:20px;height:15px' id ='spinner-linkfontsize' class='spin-group'>
<br>
<div>
<span onclick="$('#spinner-linklength').spinner('value', 100)" class='glyphicon glyphicon-fast-backward'></span><label> Scaling (%)</label><br>
<div id = "slider-linklength" class ="slider-class"> </div><input type='text' id ='spinner-linklength' class='spin-group'>
</div>
<div class="show-tooltip" title="Collapse branches below a certain value">
<span onclick="$('#spinner-collapse-nodes').spinner('value', 0)" class='glyphicon glyphicon-fast-backward'></span><label> Collapse Branches</label><br>
<div id = "slider-collapse-nodes" class ="slider-class"></div><input type='text' id ='spinner-collapse-nodes' class='spin-group'>
</div>
<label><input id ='link-log-scale'type="checkbox" />Log Scale</label>
<hr>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:5px" onclick="getHelpBox('branch_cutoffs');"></span>
<label>For branches <br> longer than:<input type='text' id ='spinner-link-length' class='spin-group'></label>
<table><tbody><tr>
<td>
<div style="opacity: 1;"><input type="radio" id="handle-long-branch-display" name="handle-long-branch" value="display" checked="" style="opacity: 1;">Display</div>
</td>
<td style="padding-left:10px">
<div style="opacity: 1;"><input type="radio" id="handle-long-branch-hide" name="handle-long-branch" value="hide" style="opacity: 1;">Hide</div>
</td>
<td style="padding-left:10px">
<div style="opacity: 1;"><input type="radio" id="handle-long-branch-cap" name="handle-long-branch" value="cap" style="opacity: 1;">Shorten</div>
</td>
</tr></tbody></table>
</div>
</div>
</div>
</div>
<div class='panel panel-default'>
<div class ='panel-heading mst-menu-title' id= 'mst-layout-menu'> <b id>Rendering</b><span id = 'mst-layout-menu-icon' class="glyphicon glyphicon-menu-right"></span></div>
<div class = "panel-body" id ='mst-layout-menu-panel'>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:5px" onclick="getHelpBox('rendering');"></span>
<div><input type='radio' name='render-method' class='render-method' value='automatic'/><b>Dynamic</b></div>
<div style='margin-left:20px;font-size:90%'><input id ='render-selected-only' type="checkbox" checked /> Selected Only</div>
<div style="margin-top:20px"><input type='radio' name='render-method' class='render-method' value='static' checked /><b>Static</b></div>
<div style='margin-left:20px;font-size:90%'><input id ='correct_link_length' type="checkbox" checked /> Real Branch Length</div>
</div>
</div>
<div class='panel panel-default'>
<div class ='panel-heading mst-menu-title' id= 'right-menu'> <b id>Context Menu</b><span id = 'right-menu-icon' class='glyphicon glyphicon-menu-right'> </span></div>
<div class = "panel-body" id ='right-menu-panel'>
<span class="glyphicon glyphicon-question-sign" style="float:right;margin-right:5px" onclick="getHelpBox('context_menu');"></span>
<div class='open-context' id='mst-svg-x' style='font-size:110%;margin:10px'>GrapeTree</div>
<div class='open-context' id='myGrid-x' style='font-size:110%;margin:10px'>Metadata</div>
<div class='open-context' id='legend-svg-x' style='font-size:110%;margin:10px'>Figure Legend</div>
</div>
</div>
</div>
<div id = "graph-div" class="graph-overlay"></div>
<script src ="static/js/main/bootstrap.min.js"></script>
<script charset="utf-8" src="static/js/main/d3.min.js"></script>
<script charset="utf-8" src="static/js/main/spin.min.js"></script>
<script charset="utf-8" src="static/js/tree/base_tree.js?version={{config['JAVASCRIPT_VERSION']}}"></script>
<script charset="utf-8" src="static/js/tree/d3_m_tree.js?version={{config['JAVASCRIPT_VERSION']}}"></script>
<script charset="utf-8" src="static/js/tree/grapetree_fileHandler.js?version={{config['JAVASCRIPT_VERSION']}}"></script>
<script> var tree_id = null</script>
<!--
{% if tree_id%}
{% include 'ms_tree/enterobase_generic_tree.html' %}
{%endif %}
-->
<script charset="utf-8">
var context_menu=null;
var metadata_grid=null;
var the_tree = null;
//getHelpBox('load_files');
var tree_raw = {};
var current_metadata_file = null;
var waiting_spinner= null;
var metadata_categories={};
var cannot_connect=false;
var default_control_panel_values={
max_link_scale:500,
base_node_size:10,
max_link_length:"",
size_power:0.5,
log_link_scale:false,
show_individual_segments:false,
link_font_size:14,
show_link_labels:false,
show_node_labels:false,
node_font_size:12,
hide_link_length:"",
node_collapsed_value:0
};
var tooltip_div =d3.select("body")
.append("div")
.attr("class", "tooltip")
.style("opacity", 0)
.style("z-index", 9)
var legend_colour_chooser = $("<input>").spectrum({
//type: "flat",
togglePaletteOnly: "true",
showInput: "true",
showInitial: "true",
allowEmpty: "false",
showAlpha: "false",
change: function(e) {
var cc = $(this);
the_tree.setColour(cc.data("category"),cc.data("value"),cc.val());
the_tree.changeCategory(cc.data("category"));
}})
.hide();
$("body").append(legend_colour_chooser);
//a map of group to another map of name to label
var metadata_options={};
var file_chooser = new MSFileChooser(".nwk");
//update all the select options
function addMetadataOptions(options){
var fields = Object.keys(options).sort(function(m, n) {return m==='nothing' ? -1 : n === 'nothing' ? 1 : ((m < n) ? -1 : 1)});
for (var fld_id in fields) {
var value = fields[fld_id];
var obj =options[value];
var category = null;
var label = ""
if (typeof obj === 'object'){
label =obj['label'];
category = obj['category'];
}
else{
label=obj;
}
var append_to_1 = $("#metadata-select");
var append_to_2= $("#node-label-text")
if (category){
if (!metadata_categories[category]){
metadata_categories[category]=true;
append_to_1 =$("<optgroup>").attr("label",category);
append_to_2=$("<optgroup>").attr("label",category);
$("#metadata-select").append(append_to_1);
$("#node-label-text").append(append_to_2);
}
else{
var to_find = "[label='"+category+"']";
append_to_1 = $("#metadata-select").find(to_find);
append_to_2 = $("#node-label-text").find(to_find);
}
}
append_to_1.append($("<option>").attr("value",value).text(label));
append_to_2.append($("<option>").attr("value",value).text(label));
}
}
function deleteMetadataCategory(){
var category = $("#add-new-values-select").val();
the_tree.removeCategory(category);
$("#metadata-select option[value='"+category+"']").remove();
$("#node-label-text option[value='"+category+"']").remove();
$("#add-new-values-select option[value='"+category+"']").remove();
delete metadata_options[category];
}
function showToolTip(msg, e){
if (!e) {e=d3.event;}
tooltip_div.transition()
.duration(200)
.style("opacity", .9);
tooltip_div.html(msg)
.style("left", (e.pageX) + "px")
.style("top", (e.pageY - 28) + "px")
.style("height", "auto");
setTimeout(hideToolTip, 2000);
}
function hideToolTip(){
tooltip_div.transition()
.duration(500)
.style("opacity", 0);
}
function treeLoaded(tree){
//add the extra functionality
metadata_grid = new D3MSMetadataTable(tree);
if (tree_id){
metadata_grid.setAddColumnFunction(function(name){
addCustomColumn(name);
})
}
context_menu= new D3MSTreeContextMenu(tree,metadata_grid);
metadata_grid.updateMetadataTable();
//add the ability to show/hide grid,
//update the dropdowns if new options added
tree.addTreeChangedListener(function(type,data){
if (type === 'metadata_options_altered'){
addMetadataOptions(data);
}
else if (type === 'nodes_collapased'){
$( "#spinner-collapse-nodes" ).val(data);
$( "#spinner-collapse-nodes" ).spinner('value', data);
var v = parseFloat(data);
$("#slider-collapse-nodes").slider('value', Math.log(v)*1000);
}
});
tree.addDisplayChangedListener(function(type,data){
if (type==='category_changed'){
$("#metadata-select").val(data);
}
});
tree.legendItemClicked = function(data){
legend_colour_chooser.spectrum("set", data.colour);
//.css({"left":0,"top":0})
//.val(data.colour)
legend_colour_chooser.data({"value":data.value.split(" [")[0],"category":data.category});
//legend_colour_chooser.spectrum("show");
setTimeout(function(){legend_colour_chooser.spectrum("show");}, 50);
};
$("#spinner-link-length").spinner({
min: 0,
max: tree.max_link_distance,
step:Math.max(1e-6, (tree.max_link_distance/1000.0).toPrecision(1)),
});
$( "#spinner-collapse-nodes" ).data('branches', $.unique(tree.original_links.map(function(d) {return d.distance}).sort(function(d1, d2) {return d1-d2})));
$( "#spinner-collapse-nodes" ).spinner({
min: 0,
max: tree.max_link_distance,
value: tree.node_collapsed_value,
step: 1e-6,
});
$( "#slider-collapse-nodes" ).slider({
min:Math.log(1e-7)*1000,
max: Math.log(tree.max_link_distance+0.01)*1000,
value: Math.log(tree.node_collapsed_value)*1000,
});
tree.centerGraph();
$(waiting_spinner.el).hide();
$("#waiting-information").text("Complete. Tree has "+tree.force_nodes.length+" nodes");
$("#waiting-image").attr("src","static/js/img/ms_complete_1.png").show();
// legend_colour_chooser.hide();
$("#information-div").modal("hide");
}
function setControlPanel(data){
$("#slider-linklength").slider("value",Math.log(data['max_link_scale']/5.)*1000.0);
$("#spinner-linklength").val(data['max_link_scale']/5.);
$("#slider-nodesize").slider("value",data['base_node_size']*10);
$("#spinner-nodesize").val(data['base_node_size']*10);
if (data['max_link_length']){
$("#spinner-link-length").val(data['max_link_length']);
$("#handle-long-branch-hide").prop("checked", true);
} else if (data['hide_link_length']){
$("#spinner-link-length").val(data['hide-link-length']);
$("#handle-long-branch-cap").prop("checked", true);
}
if (data['size_power']){
$("#slider-relative-nodesize").slider("value",data['size_power']*200.0);
$("#spinner-relative-nodesize").val(data['size_power']*200.0);
}
if (data['log_link_scale']){
$('#link-log-scale').prop('checked', true);
}
if (data['show_individual_segments']){
$("#show-individual-segments").prop("checked",true);
}
if (data['link_font_size']){
$("#slider-linkfontsize").slider("value",data['link_font_size']);
$("#spinner-linkfontsize").spinner("value",data['link_font_size']);
}
var sll =true;
if (data['show_link_labels']===false){
sll= false;
}
$("#show-link-labels").prop("checked",sll);
$("#show-node-labels").prop("checked",data['show_node_labels']);
if (data['node_font_size']){
$("#slider-node-fontsize").slider("value",data['node_font_size']);
$("#spinner-node-fontsize").spinner("value",data['node_font_size']);
}
var col_value = data['node_collapsed_value']?data['node_collapsed_value']:0;
$( "#slider-collapse-nodes" ).slider("value",Math.log(col_value)*1000);
$("#spinner-collapse-nodes").val(col_value);
}
function loadMSTree(data){
metadata_options = {};
if (the_tree) {
the_tree.svg.remove();
the_tree.legend_div[0].remove();
$("#metadata-select").find("option").remove();
$("#node-label-text").find("option").remove();
$("#metadata-div").remove();
$("#context-menu").remove();
}
$("#waiting-information").text("Loading Data");
function treeLoading(tree,msg){
if (msg==='complete'){
treeLoaded(tree);
} else {
$("#waiting-information").text(msg);
}
}
the_tree = null;
the_tree = new D3MSTree(
"graph-div",JSON.parse(JSON.stringify(data)), function(tree,msg){
treeLoading(tree,msg);
});
the_tree.addSegmentOverListener(function(d){
if ($("#show-node-tooltip").prop("checked")){
if (the_tree.display_category === 'nothing') {
var node_ids = the_tree.grouped_nodes[d.data.idx];
var value = $.map(node_ids, function(idx) {return the_tree.metadata[idx].Name ? the_tree.metadata[idx].Name : the_tree.metadata[idx].ID}).join('<br>');
showToolTip(value);
} else {
var display = d.data.type;
showToolTip(display+"("+d.data.value+")");
}
}
});
the_tree.addSegmentOutListener(function(d){
hideToolTip();
});
the_tree.addLinkOverListener(function(d){
if ($("#show-node-tooltip").prop("checked")){
showToolTip("length:"+d.value);
}
});
the_tree.addLinkOutListener(function(d){
hideToolTip();
});
//the_tree.resize();
if (the_tree.metadata_info){
addMetadataOptions(the_tree.metadata_info);
}
$("#node-label-text").val('ID');
if (data['initial_category']){
$("#metadata-select").val(data['initial_category']);
} else {
$("#metadata-select").val('nothing');
}
if (data['layout_data'] && data['layout_data']['nodes_links']){
setControlPanel(data['layout_data']['nodes_links'])
} else {
setControlPanel(default_control_panel_values);
}
if (current_metadata_file) {
loadMetadataText(current_metadata_file);
}
$('.panel-default').find('input, textarea, button, select, div, span').css("opacity", 1.0).prop('disabled',false);
}
function initiateLoading(msg){
$("#welcome-div-close").show();
$("#welcome-div").draggable().css({position:'relative', border:'1px solid black', margin:'10px', 'z-index':9999}).hide();
$("#graph-div").empty();
$("#metadata-select").empty();
$("#add-new-values-select").empty();
metadata_options={};
showWaitingDialog(msg);
};
function showWaitingDialog(msg){
$("#information-div").modal("show");
$("#waiting-image").hide();
$(waiting_spinner.el).show();
$("#waiting-information").text(msg).show();
};
window.onload = function (){
$(".open-context").on('click', function(e, ui) {
var id = e.target.id;
context_menu._trigger_context(id.substring(0, id.length-2), e);
});
$(".show-tooltip").on('mouseenter', function(e){
showToolTip($(this).attr('title'), {
pageX: $(this).offset().left + $(this).width() + 10,
pageY: $(this).offset().top + $(this).height()/2+10
});
}).on('mouseleave', function(e) {
setTimeout(hideToolTip, 200);
});
//allow dragging and dropping files
dropFiles($("#graph-div"));
$(".render-method").on("change", function(e) {
if (this.value == 'static') {
the_tree.fixAllNodes( document.getElementById("correct_link_length").checked );
} else if (this.value == 'automatic') {
the_tree.unfixSelectedNodes(! $("#render-selected-only").is(":checked"));
}
});
$("#handle-long-branch-display, #handle-long-branch-hide, #handle-long-branch-cap").on("change", function(e) {
var max = $("#spinner-link-length").val();
if (!max) {
max = the_tree.max_link_distance+1;
}
if (this.value == 'hide') {
the_tree.setMaxLinkLength(the_tree.max_link_distance+1);
the_tree.setHideLinkLength(max);
} else if (this.value == 'cap') {
the_tree.setHideLinkLength(the_tree.max_link_distance+1);
the_tree.setMaxLinkLength(max);
} else {
the_tree.setMaxLinkLength(the_tree.max_link_distance+1);
the_tree.setHideLinkLength(the_tree.max_link_distance+1);
}
});
$("#spinner-link-length").on('change', function(e, ui) {
var max = $("#spinner-link-length").val();
if (!max) {
max = the_tree.max_link_distance+1;
}
var method = null;
if ($("#handle-long-branch-hide").prop("checked")) {
method = 'hide';
} else if ($("#handle-long-branch-cap").prop("checked")) {
method = 'cap';
}
if (method == 'hide') {
the_tree.setMaxLinkLength(the_tree.max_link_distance+1);
the_tree.setHideLinkLength(max);
} else if (method == 'cap') {
the_tree.setHideLinkLength(the_tree.max_link_distance+1);
the_tree.setMaxLinkLength(max);
}
});
$("#metadata-select").on("change",function(e){
the_tree.changeCategory($(this).val());
});
$("#node-label-text").change(function(e){
the_tree.setNodeText($(this).val());
});
$("#mst-download-svg").click(function(e){
saveTextAsFile(the_tree.getSVG(), "MSTree.svg");
});
$(".panel-body").hide();
// all slider spinners
$(function sliderSpinners() {
$(".slider-class").slider({
slide: function(e) {
$(this).trigger('change');
},
change: function(e) {
if (e.originalEvent) {
$(this).trigger('change');
}
}
});
$(".spin-group").spinner({
spin: function(e, ui) {
$(this).spinner("value", ui.value);
},
change: function(e) {
$(this).trigger('change', e);
}
}).keypress(function(e){
if (e.which === 13) {
$(this).trigger('change', e);
}
});
$( "#slider-linklength" ).on("change", function(e) {
var brlen = Math.exp($(this).slider("value")/1000.0);
$("#spinner-linklength").spinner('value', brlen);
})
.slider({
orientation: "horizontal",
min: 1609,
max: 9903,
value: 4605,
});
$("#spinner-linklength").on("change", function (e){
var brlen = parseInt($(this).val());
$( "#slider-linklength" ).slider('value', Math.log(brlen)*1000.0);
the_tree.setLinkLength(brlen*5.0);
})
.spinner({
min: 5,
max: 20000,
value: 100,
step: 1,
});
$( "#slider-nodesize" ).on("change", function(e) {
$( "#spinner-nodesize" ).spinner("value", $(this).slider("value"));
})
.slider({
orientation: "horizontal",
min:20,
max:500,
value: 100,
});
$( "#spinner-nodesize" ).on('change', function(){
the_tree.setNodeSize(parseInt($(this).val())/10.);
$( "#slider-nodesize" ).slider("value", parseInt($(this).val()));
})
.spinner({
min:20,
max:500,
value: 100,
});
$( "#slider-relative-nodesize" ).on("change", function(e) {
$( "#spinner-relative-nodesize" ).spinner("value", $(this).slider("value"));
})
.slider({
orientation: "horizontal",
min:30,
max:150,
value: 100,
step:1,
})
$( "#spinner-relative-nodesize" ).on("change", function(e){
the_tree.setRelativeNodeSize(parseInt($(this).val())/200.0);
$( "#slider-relative-nodesize" ).slider("value", parseInt($(this).val()));
})
.spinner({
min:30,
max:150,
value: 100,
step:1,
});
$( "#slider-node-fontsize" ).on("change", function(e) {
$("#spinner-node-fontsize").spinner('value', $(this).slider("value"));
})
.slider({
orientation: "horizontal",
min:6,
max: 30,
value: 12,
});
$("#spinner-node-fontsize").on("change", function(e) {
$( "#slider-node-fontsize" ).slider('value', parseInt($(this).val()));
the_tree.setNodeFontSize(parseInt($(this).val()));
})
.spinner({
min: 6,
max: 30,
value: 12,
});
$( "#slider-linkfontsize" ).on("change", function(e) {
$("#spinner-linkfontsize").spinner('value', $("#slider-linkfontsize").slider("value"));
})
.slider({
orientation: "horizontal",
min:6,
max: 30,
value: 14,
});
$("#spinner-linkfontsize").on("change", function(e) {
$( "#slider-linkfontsize" ).slider('value', parseInt($(this).val()));
the_tree.setLinkFontSize(parseInt($(this).val()));
})
.spinner({
min: 6,
max: 30,
value: 14,
});
$( "#slider-charge" ).on("change", function(e) {
the_tree.alterCharge($("#slider-charge").slider("value"));
$(this).prop("title", $(this).slider("value"));
})
.slider({
orientation: "horizontal",
min:0,
max: 30,
});
$( "#slider-collapse-nodes" ).on("change", function(e) {
var val = Math.exp($(this).slider('value')/1000);
$("#spinner-collapse-nodes").spinner('value', val);
})
.slider({
orientation: "horizontal",
min:0,
max: 100,
value: 0,
});
$( "#spinner-collapse-nodes" ).on("change", function(e, ui) {
var v = parseFloat($("#spinner-collapse-nodes").val());
if (v != $(this).data.v) {
$(this).data.v = v;
$("#slider-collapse-nodes").slider('value', Math.log(v)*1000);
the_tree.collapseNodes(v);
}
})
.spinner({
min:0,
value: 0
});
});
$("#node-label-text").change(function(e){
var val = $(this).val();
if (val ==="cat"){
val = the_tree.display_category;
}
the_tree.setNodeText(val);
});
$("#show-link-labels").click(function(e){
the_tree.showLinkLabels($(this).is(":checked"))
});
$("#show-node-labels").click(function(e){
the_tree.showNodeLabels($(this).is(":checked"));
});
$("#show-individual-segments").click(function(e){
the_tree.showIndividualSegments($(this).is(":checked"));
});
$("#show-node-tooltip").click(function(e){
show_node_tooltips = $(this).is(":checked");
});
$("#link-log-scale").click(function(e){
the_tree.setLogLinkScale($(this).is(":checked"));
});
$("#button-files").click(function(e) {
var diag = $('<div id="read-text" title="Paste or read files"></div>').appendTo($('body'))
.append("<p><label>Paste a tree, profile or metadata here: </label></p>")
.append("<textarea id='paste-text' rows='10' cols='100'>")
.append("<p><label>Or load the files directly: </label></p>")
.append("<button title='Handles trees, profiles and metadata files' id = 'button-load-nwk' class = 'show-tooltip'> Load Files</button>");
$("#button-load-nwk").click(function(e){
file_chooser.setFilter("");
file_chooser.showOpenDialog(function(files){
filesDropped(files);
diag.dialog("close");
});
});
diag.dialog({
width: "auto",
resizable: false,
height: "auto",
modal: false,
close: function() {
$("#read-text").dialog('destroy').remove();
},
buttons: {
Confirm: function(){
distributeFile($("#paste-text").val(), '');
$(this).dialog("close");
},
Cancel: function() {
$(this).dialog("close");
}
}
});
});
$("#save-tree-json").click(function(e){
saveTextAsFile(JSON.stringify(the_tree.getTreeAsObject()),"ms_tree.json");
});
$("#save-tree-nwk").click(function(e){
saveTextAsFile(the_tree.getTreeAsNewick(),"ms_tree.nwk");
});
$("#show-in-microreact").click(function(e) {
showWaitingDialog("Sending tree and metadata to MicroReact");
metadata_grid.sendToMicroReact(function() {
$("#information-div").modal("hide");
}, ! cannot_connect);
});
$("#center-graph-button").click(function(e){
the_tree.centerGraph();
});
$("#button-refresh").click(function(){
showWaitingDialog("Refreshing The Tree");
setTimeout(function(){
the_tree.refreshGraph();
$("#information-div").modal("hide");
},500);
});
$("#rotation-icon").draggable({
containment: "#sidebar",
scroll: false,
start: function(e) {
the_tree._dragStarted(the_tree.force_nodes[0], [$("#rotation-icon").position().left, $("#rotation-icon").position().top]);
},
drag: function(e) {
the_tree._dragging(the_tree.force_nodes[0], [e.clientX, e.clientY]);
},
stop: function(e) {
the_tree._dragEnded(the_tree.force_nodes[0], [e.clientX, e.clientY]);
},
revert: true,
revertDuration: 10,
helper: function() {return $("<div style='cursor:none'><label id='angle-text'></label></div>")},
});
$("#rotation-icon").on("drag", function(event, ui) {
var x_dif = ui.helper.position().left - $("#rotation-icon").position().left;
var y_dif = $("#rotation-icon").position().top - ui.helper.position().top;
var angle = y_dif !== 0 ? Math.atan(x_dif/y_dif)/Math.PI * 180 : (x_dif === 0 ? 0 : (x_dif > 0 ? 90 : -90));
if (y_dif < 0 ) {
angle = 180 + angle;
} else if (x_dif < 0) {
angle = 360 + angle;
}
ui.helper.select('.angle-text').text(Math.round(angle) + '\xB0').css({
'font-size':'1.2em',
'font-style':'bold',
}) ;
});
$("#search-metadata-icon").click(function(e){
var keyword= $("#search-metadata-input").val();
if (keyword){
var ids = the_tree.searchMetadata(keyword, $("#node-label-text").val());
the_tree.highlightNodes(ids);
}
});
$("#graph-div").on('dblclick', function(e){
if (the_tree) the_tree.clearSelection();
});
var target = document.getElementById('modal-header');
waiting_spinner= new Spinner({color:'black', lines: 12,top:"13%"}).spin(target);
$('.panel-default').find('input, textarea, button, select, span, div').css("opacity", 0.3).prop('disabled',true);
window.addEventListener("beforeunload", function (e) {
if (the_tree) {
var confirmationMessage = 'All the modifications will lost if you have not saved the GrapeTree as a local file.';
(e || window.event).returnValue = confirmationMessage;
return confirmationMessage;
}
});
if (tree_id){
setupEnterobasePanel();
initiateLoading("Waiting");
getRemoteData();
} else {
$("#file-menu-panel").css("opacity", 1.0).addClass("open-menu-panel").show();
$("#button-files").parent().css('opacity', 1.0);
$("#button-files").css("opacity", 1.0).prop("disabled", false).trigger('mouseenter');
}
$(".mst-menu-title").click(function(e){
if($(this).prop("disabled") === true) {
return;
}
var id = $(this).attr("id");
var this_panel = $("#"+id+"-panel");
var icon = $("#"+id+"-icon");
if (this_panel.hasClass("open-menu-panel")){
this_panel.toggle("50");
this_panel.removeClass("open-menu-panel");
icon.attr("class", "glyphicon glyphicon-menu-right");
}
else{
this_panel.toggle("50");
this_panel.addClass("open-menu-panel");
icon.attr("class","glyphicon glyphicon-menu-down");
}