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empress.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<title>Interactive Tree - Empress</title>
<!-- vendors -->
<link rel="stylesheet" type="text/css" href="pages/empress/vendor/css/slick.grid.css">
<link rel="stylesheet" type="text/css" href="pages/empress/vendor/css/jquery-ui-1.11.3.custom.css">
<link rel="stylesheet" type="text/css" href="pages/empress/vendor/css/slick.grid.format.css">
<script type="text/javascript" src="pages/empress/vendor/js/gl-matrix.min.js"></script>
<script type="text/javascript" src="pages/empress/vendor/js/jquery-2.2.4.min.js"></script>
<script type="text/javascript" src="pages/empress/vendor/js/jquery.event.drag-2.2.min.js"></script>
<script type="text/javascript" src="pages/empress/vendor/js/slick.core.min.js"></script>
<script type="text/javascript" src="pages/empress/vendor/js/slick.editors.min.js"></script>
<script type="text/javascript" src="pages/empress/vendor/js/slick.formatters.min.js"></script>
<script type="text/javascript" src="pages/empress/vendor/js/slick.grid.min.js"></script>
<script type="text/javascript" src="pages/empress/vendor/js/parse.js"></script>
<script type="text/javascript" src="pages/empress/vendor/js/chroma.min.js"></script>
<!-- static -->
<link rel="stylesheet" type="text/css" href="pages/empress/css/tree.css">
<script type="text/javascript" src="pages/empress/js/init_webgl.js"></script>
<script type="text/javascript" src="pages/empress/js/initialize_empress.js"></script>
<script type="text/javascript" src="pages/empress/js/mouse_events.js"></script>
<script type="text/javascript" src="pages/empress/js/callbacks.js"></script>
<script type="text/javascript" src="pages/empress/js/drawing_loop.js"></script>
<script type="text/javascript" src="pages/empress/js/init_webpage.js"></script>
<script type="text/javascript" src="pages/empress/js/tree.js"></script>
</head>
<body>
<!-- The tree -->
<div class="tree-container">
<div class="container">
<canvas class="tree-surface" id="tree-surface">
Your browser does not support HTML5
</canvas>
<div id="tip-label-container"></div>
<div id="node-label-container"></div>
<div class="square"></div>
<div class="selected-tree-menu">
<input id="collapse" type="button" value="collapse" onclick="selectedTreeCollapse()" />
</div>
</div>
<!-- Metadata tabs -->
<div id="side-panel">
<!-- Header bar -->
<p class="side-header">
<input type="text" id="quick-search" placeholder="Search..." title="Enter a taxonomic name to search." style="width: 100%;">
<button title="Help information" style="font-size: 14pt;" onclick="document.getElementById('help-modal').classList.remove('hidden');">?</button>
<button id="hide-ctrl" title="Hide control panel" style="font-size: 14pt; transform: rotate(180deg);">∟</button>
<!-- <button>⚲</button> -->
</p>
<!-- Taxonomy -->
<button class="side-header collapsible">Taxonomy</button>
<div class="side-content control hidden">
<!-- toggle NCBI / GTDB -->
<p>
<label>System</label>
<input type="radio" id="ncbi" name="sys" value="n_" onclick="changeTaxSys()" checked />
<label for="ncbi">NCBI</label>
<input type="radio" id="gtdb" name="sys" value="g_" onclick="changeTaxSys()" />
<label for="gtdb">GTDB</label>
</p>
<p>
<label for="curation">Curation <span class="infomark"></span><span class="tooltip">Choose from original (OFF) or <a href="https://github.com/biocore/tax2tree" target="_blank">tax2tree</a>-curated taxonomy (ON).</span></label>
<label class="switch">
<input type="checkbox" id="curation" onclick="changeTaxSys()" checked><span class="slider"></span>
</label>
</p>
</div>
<button class="side-header collapsible">Labeling</button>
<div class="side-content control hidden">
<p>
<label for="tips">Tip labels</label>
<input type="checkbox" id="tips" title="Enable tip labels" onclick="retrieveTaxonNodes('t')">
<input type="number" id="tips-number" title="Number of tip labels to display" min="1" max="100" value="10" onchange="retrieveTaxonNodes('c')" disabled="true">
<label class="select-container">
<select id="tips-find-level" onchange="retrieveTaxonNodes('c')" disabled="true">
<option value="0" disabled> -- select a rank -- </option>
</select>
</label>
</p>
<p>
<label for="internal-nodes">Node labels</label>
<input type="checkbox" id="internal-nodes" title="Enable node labels" onclick="retrieveTaxonNodes('n')">
<input type="number" id="internal-nodes-number" title="Number of node labels to display" min="1" max="100" value="10" onchange="retrieveTaxonNodes('n')" disabled="=true">
<label class="select-container">
<select id="nodes-find-level" onchange="retrieveTaxonNodes('n')" disabled="true">
<option value="0" disabled> -- select a rank -- </option>
</select>
</label>
</p>
</div>
<!-- Coloring tab -->
<button class="side-header collapsible">Coloring</button>
<div class="side-content control hidden">
<p>
<label for="preset-color">Preset scheme</label>
<label class="switch">
<input type="checkbox" id="preset-color" onclick="userHighlightSelect()"><span class="slider"></span>
</label>
</p>
<p>
<label for="tip-color">Tip color</label>
<input type="checkbox" id="tip-color" onclick="userHighlightSelect()">
<label class="select-container">
<select id="tip-color-options" onchange="userHighlightSelect()" disabled="true"></select>
</label>
</p>
<p>
<label for="branch-color">Node color</label>
<input type="checkbox" id="branch-color" onclick="userHighlightSelect()">
<label class="select-container">
<select id="branch-color-options" onchange="userHighlightSelect()" disabled="true"></select>
</label>
</p>
<p>
<label for="open-file">Upload data <span class="infomark"></span><span class="tooltip">Upload a tab-delimited file with first column as genome/node IDs.</span></label>
<button id="open-file" onclick="document.getElementById('custom-color').click();">Browse...</button>
<input type="file" id="custom-color" class="hidden">
</p>
<!-- <p>
<label for="color-options">Choose Color Map</label>
<select id="color-options">
<option disabled> -- Sequential -- </option>
<option value="viridis" color="red">viridis</option>
<option value="Blues">Blue</option>
<option value="Greens">Green</option>
<option value="Reds">Red</option>
<option value="BuGn">Blue to Green</option>
<option value="cool">Blue to Purple</option>
<option value="YlOrRd">Yellow to Red</option>
<option value="hot">Hot</option>
<option value="winter">Winter</option>
<option disabled>-- Diverging --</option>
<option value="seismic">Blue to Red</option>
<option value=coolwarm>Cool to Warm</option>
<option value="PRGn">Purple to Green</option>
</select>
</p> -->
</div>
<!-- Color Clades -->
<!-- <button class="side-header collapsible">Color Clades</button>
<div class="side-content control">
<p>
<label for="tax-level">Rank</label>
<label class="select-container">
<select id="tax-level">
<option value="0" disabled> -- select an option -- </option>
</select>
</label>
</p>
<p>
<label for="clade-options">Color by</label>
<label class="select-container">
<select id="clade-options">
<option value="0" disabled> -- select an option -- </option>
<option value="0">Default</option>
</select>
</label>
</p>
<p>
<label for="color-options-tax">Color Map</label>
<label class="select-container">
<select id="color-options-tax">
<option disabled> -- Sequential -- </option>
<option value="viridis" color="red">viridis</option>
<option value="Blues">Blue</option>
<option value="Greens">Green</option>
<option value="Reds">Red</option>
<option value="BuGn">Blue to Green</option>
<option value="cool">Blue to Purple</option>
<option value="YlOrRd">Yellow to Red</option>
<option value="hot">Hot</option>
<option value="winter">Winter</option>
<option disabled>-- Diverging --</option>
<option value="seismic">Blue to Red</option>
<option value=coolwarm>Cool to Warm</option>
<option value="PRGn">Purple to Green</option>
</select>
</label>
</p>
<p>
<button onclick="userCladeColor()">Color Clades</button>
</p>
</div> -->
<!-- Collapse -->
<button class="side-header collapsible">Collapse</button>
<div class="side-content control hidden">
<p>
<label for="collapse-cb">Collapse by <span class="infomark"></span><span class="tooltip">Collapse clades at selected rank into triangles, where the long and short edges represent the longest and shortest tips.</span></label>
<input type="checkbox" id="collapse-cb" title="Enable collapsing" onclick="autoCollapseTree()" >
<label class="select-container">
<select id="collapse-level" disabled="true" onchange="autoCollapseTree()">
<option value="0" disabled> -- select a rank -- </option>
</select>
</label>
</p>
</div>
<div class="side-header" style="height: 3px;"></div>
</div>
<!-- show control panel button -->
<button id="show-ctrl" title="Show control panel" style="font-size: 14pt;" class="hidden">∟</button>
</div>
<!-- hover box -->
<div class="hidden" id="hover-box">
<table id="hover-table"></table>
</div>
<!-- color keys -->
<div id="legend-panel">
<div id="tip-color-key" class="legend hidden" disabled="true"></div>
<div id="node-color-key" class="legend hidden" disabled="true"></div>
<div id="preset-color-key" class="legend hidden" disabled="true"></div>
</div>
<!-- about modal -->
<div class="modal hidden" id="help-modal">
<div class="modal-body">
<div class="modal-header"><label>About</label></div>
<div class="modal-content">
<table style="border-collapse: separate;">
<tr>
<td rowspan="4" style="padding-right: 25px;"><a href="https://biocore.github.io/wol/"><img src="gallery/logo/logo_s.png" alt="Empress" width="200" height="176"></a></td>
<td>Interactive view of the reference <a href="data/trees/astral/branch_length/cons/collapsed/astral.cons.nid.e5p50.nwk">phylogeney</a>, powered by:</td>
</tr>
<tr><td><span style="font-weight: bold; font-size: 150%">Empress</span></a>, a very fast and scalable tree viewer.</td></tr>
<tr><td style="padding-left: 20px;"><a href="https://github.com/biocore/empress" target="_blank">https://github.com/biocore/empress</a></td></tr>
<tr><td>For questions and suggestions contact the main developers:<br>
<ul style="margin-left: 20px; margin-bottom: 5px;"><li>Kalen Cantrell (<a href="mailto:[email protected]">[email protected]</a>)</li><li>Yimeng Yang (<a href="mailto:[email protected]">[email protected]</a>)</li></ul></td></tr>
</table>
<br>
<div style="margin: 10px; padding: 10px 20px; border: 1px solid gray; background-color: white;">
<p style="font-size: 120%; font-weight: 500; padding-left: 10px;">Quick tips</p>
<hr style="text-align: left; margin-left: 10px; width: 100px; border: 0; height: 1px; background-color: darkgray;">
<ul style="margin-left: 20px; margin-bottom: 5px; line-height: 150%;">
<li>Mouse drag to move, mouse scroll to zoom.</li>
<li>Mouse over a node to show taxonomy and download.</li>
<li>Taxonomic annotation by NCBI and GTDB, original and curated.</li>
<li>Dynamic labeling and collapsing by taxonomic rank.</li>
<li>Coloring by metadata and user upload.</li>
</ul>
<br>
</div>
</div>
</div>
</div>
<!-- export modal -->
<div class="modal hidden" id="export-modal">
<div class="modal-body">
<div class="modal-header"><label>Export</label></div>
<div class="modal-content control">
<p>
<label>Export target</label>
<input type="radio" id="rad-ids" name="exp-content" checked />
<label for="rad-ids">Identifiers</label>
<input type="radio" id="rad-links" name="exp-content" />
<label for="rad-links">Download links <span class="infomark"></span><span class="tooltip">URLs to genome data at NCBI FTP server, which can be batch-downloaded using this <a href="data/genomes/batch_down.sh">script</a>.</span></label>
<input type="radio" id="rad-subtree" name="exp-content" />
<label for="rad-subtree">Subtree</label>
</p>
<p id="p-links" class="hidden">
<label>Download target</label>
<label class="select-container">
<select id="downfile-options">
<option disabled> -- select an option -- </option>
<option value="genomic.fna" selected="selected">Genome sequences</option>
<option value="genomic.gbff">Genome annotations (GenBank)</option>
<option value="genomic.gff">Genome annotations (GFF3)</option>
<option value="protein.faa">Protein sequences</option>
<option value="protein.gpff">Protein annotations (GenPept)</option>
<option value="rna_from_genomic.fna">RNA sequences</option>
<option value="cds_from_genomic.fna">CDS sequences</option>
<option value="feature_table.txt">Feature tables</option>
<option value="feature_count.txt">Feature counts</option>
</select>
</label>
</p>
<hr>
<p><button id="btn-export">Export</button></p>
</div>
</div>
</div>
<div class="metadata-container"></div>
<div id="scrolltable"></div>
<!-- toast -->
<div id="toast" class="hidden"></div>
<!-- loading screen -->
<div id="loading-screen">
<div id="loading-animation"></div>
<div id="loading-text">Loading...</div>
</div>
</body>
<!-- main data file, which is big, so load after DOMs -->
<script type="text/javascript" src="pages/empress/js/wol_tree.js"></script>
<script type="text/javascript">
// global constants
const ranks = ["kingdom", "phylum", "class", "order", "family", "genus", "species"];
// window load
window.addEventListener("load", function () {
"use strict";
// initialize interface
// document.querySelectorAll(".side-content").forEach(function(div) {
// div.classList.add("hidden");
// });
// add rank names
["collapse-level", "tips-find-level", "nodes-find-level"]
.forEach(function(id) {
const sel = document.getElementById(id);
ranks.forEach(function(rank) {
const opt = document.createElement("option");
opt.text = rank;
if (rank === "phylum") {
opt.selected = "selected";
}
sel.add(opt);
});
});
// quick search box
document.getElementById("quick-search").addEventListener("keyup", function(e) {
e.preventDefault();
if (e.keyCode === 13) {
quickSearch();
}
});
// file upload button
document.getElementById("custom-color").addEventListener("change",
function (e) {
uploadFile(e.target.files[0]);
});
// toggle download links
document.getElementsByName("exp-content").forEach(function(rad) {
rad.addEventListener("click", function() {
document.getElementById("p-links").classList
.toggle("hidden", !document.getElementById("rad-links").checked);
});
});
// activate control panel
document.querySelectorAll(".collapsible").forEach(function(btn) {
btn.addEventListener("click", function() {
this.classList.toggle("active");
this.nextElementSibling.classList.toggle("hidden");
document.getElementById("side-panel").classList.toggle("panel-active",
document.querySelector(".side-content:not(.hidden)"));
});
});
document.getElementById("quick-search").addEventListener("focus", function() {
document.getElementById("side-panel").classList.add("panel-active");
});
document.getElementById("quick-search").addEventListener("blur", function() {
document.getElementById("side-panel").classList.toggle("panel-active",
document.querySelector(".side-content:not(.hidden)"));
});
// fold control panel
document.getElementById("hide-ctrl").addEventListener("click", function() {
document.getElementById("side-panel").classList.add("hidden");
document.getElementById("show-ctrl").classList.remove("hidden");
});
document.getElementById("show-ctrl").addEventListener("click", function() {
this.classList.add("hidden");
document.getElementById("side-panel").classList.remove("hidden");
});
// modals
document.querySelectorAll(".modal-header").forEach(function(bar) {
let btn = document.createElement("button");
btn.innerHTML = "×";
btn.classList.add("close");
btn.title = "Close the " + bar.textContent
.toLowerCase() + " window";
bar.appendChild(btn);
btn.addEventListener("click", function () {
this.parentElement.parentElement.parentElement.classList.add("hidden");
});
let div = document.createElement("div");
div.classList.add("modal-footer");
bar.parentElement.appendChild(div);
});
// export clade
document.getElementById("btn-export").addEventListener("click", function() {
let clsID = document.getElementById("export-modal").dataset.clsID;
if(document.getElementById("rad-ids").checked){
downloadGenomeIds(clsID);
}
else if (document.getElementById("rad-links").checked) {
downloadLinks(clsID);
}
else if (document.getElementById("rad-subtree").checked) {
downloadSubtree(clsID);
}
});
document.getElementById("loading-screen").classList.add("hidden");
});
</script>
<script type="text/javascript">
// fields to extract from metadata, used in extractInfo()
let field = {
edgeFields: ["px", "py", "branch_color", "x", "y", "branch_color"],
nodeFields: ["x", "y", "color"],
triangleFields: ["cx", "cy", "color", "lx", "ly", "color", "rx", "ry", "color"]
};
// stores matrices, and buffers that webgl will uses
let shaderProgram = {};
let c_shaderProgram = {};
// the complied vertex/fragment shaders
let gl = {}; // webgl context - used to call webgl functions
// stores info need to draw such as vertex data
let drawingData = {
isMouseDown: false,
lastMouseX: null,
lastMouseY: null,
zoomAmount: 50,
currentZoom: 0,
maxZoom: 30,
hoveredNode: [],
coloredClades: [],
selectTree: [],
triangles: [],
numBranches: 0
};
let numAttr = 0;
let attrItem = {};
let grid = {};
let tipLabels = [];
let nodeLabels = [];
let labelPos = 0;
let gridInfo = {
initData: [],
data: [],
columns: [],
options: {},
grid: {}
};
const TRI_PER_ARC = 100;
const ELEMENTS_PER_VERT = 5;
const VERT_PER_TRI = 3;
let numUserSelects = 0;
const CLEAR_COLOR_HEX = "FFFFFF";
const CLEAR_COLOR = 1;
let camera = {};
let shftPress = false;
let showLabels = false;
let taxonNodes = [];
let highToLow = function (dataRow1, dataRow2) {
return dataRow1[3] < dataRow2[3] ? 1 : -1;
};
let random = function(dataRow1, dataRow2) {
return Math.round(Math.random()) > 0 ? 1 : -1;
}
</script>
<script type="text/javascript">
{
initialize();
}
</script>
</html>