CINXE.COM

<!DOCTYPE html> <html> <head> <title>Phylo.io</title> <meta charset="UTF-8"> <script src="//peterolson.github.com/BigInteger.js/BigInteger.min.js"></script> <script type="text/javascript" src="js/jquery-2.1.4.min.js"></script> <script type="text/javascript" src="js/treecompare.js"></script> <script type="text/javascript" src="http://underscorejs.org/underscore-min.js"></script> <script type="text/javascript" src="js/spin.min.js"></script> <script type="text/javascript" src="js/d3.min.js"></script> <script type="text/javascript" src="js/bootstrap.min.js"></script> <script type="text/javascript" src="js/circular-json.js"></script> <script type="text/javascript" src="js/canvas-toBlob.js"></script> <script type="text/javascript" src="js/FileSaver.min.js"></script> <link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.0.8/css/solid.css" integrity="sha384-v2Tw72dyUXeU3y4aM2Y0tBJQkGfplr39mxZqlTBDUZAb9BGoC40+rdFCG0m10lXk" crossorigin="anonymous"> <link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.0.8/css/fontawesome.css" integrity="sha384-q3jl8XQu1OpdLgGFvNRnPdj5VIlCvgsDQTQB6owSOHWlAurxul7f+JpUOVdAiJ5P" crossorigin="anonymous"> <link rel="stylesheet" type="text/css" href="css/bootstrap.min.css"> <link rel="stylesheet" type="text/css" href="css/bootstrap-theme.min.css"> <link rel="stylesheet" type="text/css" href="css/simple-sidebar.css"> <link rel="stylesheet" type="text/css" href="css/style.css"> <link rel="stylesheet" type="text/css" href="css/ol.css">  <script> var _paq = window._paq = window._paq || []; /* tracker methods like "setCustomDimension" should be called before "trackPageView" */ _paq.push(["setDocumentTitle", document.domain + "/" + document.title]); _paq.push(["setCookieDomain", "*.phylo.io"]); _paq.push(['trackPageView']); _paq.push(['enableLinkTracking']); (function() { var u="https://matomo.sib.swiss/"; _paq.push(['setTrackerUrl', u+'matomo.php']); _paq.push(['setSiteId', '144']); var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0]; g.async=true; g.src=u+'matomo.js'; s.parentNode.insertBefore(g,s); })(); </script> <noscript><p><img src="https://matomo.sib.swiss/matomo.php?idsite=144&rec=1" style="border:0;" alt="" /></p></noscript>  <style> .extraMargin + span:after { content: "\000A"; white-space: pre; } .modal-container { z-index: 3; right: 50px; top: 75px; position: absolute; padding: 5px 20px 15px 20px; width: 180px; height: 60px; border-radius: 8px; display: none; } </style> </head> <body> <div id="myModal" class="modal fade"> <div class="modal-dialog"> <div class="modal-content"> <div class="modal-header"> <button type="button" class="close" data-dismiss="modal" aria-hidden="true">×</button> <h5 class="modal-title" id="modalTitle">Link to share tree visualisation</h5> </div> <div class="modal-body"> <span id="modalBody"></span> </div> </div> </div> </div> <div id="myErrorModal" class="modal fade"> <div class="modal-dialog"> <div class="modal-content"> <div class="modal-header"> <button type="button" class="close" data-dismiss="modal" aria-hidden="true">×</button> <h5 class="modal-title" id="modalTitleError"></h5> </div> <div class="modal-body"> <span id="modalBodyError" class="text-danger"></span> </div> </div> </div> </div> <nav class="navbar navbar-default navbar-fixed-top"> <div class=""> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false" aria-controls="navbar"> <span class="sr-only"><Toggle> </Toggle> navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <div class="row" style="width: 300px"> <a class="navbar-brand" href="index.html" style="padding-left: 20px;margin-right: 5px; padding-top: 2px">  <span class="navbar-brand" style="font-size:x-large; font-weight: bold; margin-top: -3px"><img src="img/logo.svg" width="130" /></span> </a> </div> </div>  <div id="navbar" class="navbar-collapse collapse list-inline"> <ul class="nav navbar-nav navbar-right list-inline" style="margin-right: 60px"> <li class="dist"> <ul> <li id = "rf"></li> <li id = "eucl"></li> <li id = "spr"></li> </ul> </li> <li class="dropdown" id="action"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Edit <span class="caret"></span></a> <ul class="dropdown-menu"> <li><a href="#" id="cloudShare"><span class="fas fa-cloud-upload-alt" aria-hidden="true"></span> Share</a></li> <li><a href="#" id="svgExport"><span class="glyphicon glyphicon-save" aria-hidden="true"></span> Export both trees</a></li> <li><a href="#" id="distance"><span class="glyphicon glyphicon-share" aria-hidden="true"></span> Calculate distance</a></li> </ul> </li> <li><a href="manual.html" class="homelinks">Help</a></li> <li><a href="about.html" class="homelinks">About</a></li> </ul> </div>  </div> </nav> <div id="wrapper"> <div id="colorScale"></div>  <div id="sidebar-wrapper"> <div id="menu-toggle"> <i class="fas fa-2x fa-arrow-circle-left" id="collapse-sidebar-span" style="color: #e7e7e7; padding-top: 5px; padding-left: 6px;"></i> </div> <div id="sidebar-wrapper-wrapper"> <ul class="sidebar-nav"> <div id="mode-buttons" class="btn-group btn-group-justified" role="group"> <div class="btn-group" role="group"> <button type="button" id="view-btn" class="btn btn-default active" data-condition="haveUndo" data-toggle="modal-confirm" data-message="Changing to view will clear your changes to current tree!" data-title="Please confirm" data-target="#confirmModal" data-action="view">View</button> </div> <div class="btn-group" role="group"> <button type="button" id="compare-btn" class="btn btn-default" data-condition="haveUndo" data-toggle="modal-confirm" data-message="Changing to compare will clear your changes to current tree!" data-title="Please confirm" data-target="#confirmModal" data-action="compare">Compare</button> </div> </div> <li> <div id="view-tree-params"> <div class="row"> <div class="col-sm-6"> <label>Tree data:</label> </div> <div class="col-sm-6"> <input class="fileIn" id="newickInSingleFile" type="file" style="display:none"> <button class="btn btn-default btn-xs fileIn pull-right" id="newickInSingleButton" type="button"> Upload <i class="fas fa-upload" aria-hidden="true"></i> </button> </div> </div> <div> <textarea class="newickIn singleIn" id="newickInSingle" rows="4" cols="50" placeholder="Newick, NHX formats"></textarea> </div> <div class="row"> <div class="col-sm-12 pull-right"> <div style="font-size: x-small; color: lightgrey;"> <label>Examples:</label> <div class="exampleBtn singleIn" id="simpleSingle" style="display:inline-block;"><a href="#">#1 </a></div> <div class="exampleBtn singleIn" id="bigSingle" style="display:inline-block;"><a href="#">#2</a></div> </div> </div> </div> </div> <div id="cmp-trees-params"> <div class="row"> <div class="col-sm-6"> <label>Left panel:</label> </div> <div class="col-sm-6"> <input class="fileIn" id="newickIn1File" type="file" style="display:none"> <button class="btn btn-default btn-xs fileIn pull-right" id="newickIn1Button" type="button"> Upload <i class="fas fa-upload" aria-hidden="true"></i> </button> </div> </div> <div> <textarea class="newickIn singleIn" id="newickIn1" rows="6" cols="80" placeholder="Newick, NHX formats with one or more trees" style="width: 100%;"></textarea> </div> <div class="row" style="margin-top: 20px;"> <div class="col-sm-6"> <label>Right panel:</label> </div> <div class="col-sm-6"> <input class="fileIn" id="newickIn2File" type="file" style="display:none"> <button class="btn btn-default btn-xs fileIn pull-right" id="newickIn2Button" type="button"> Upload <i class="fas fa-upload" aria-hidden="true"></i> </button> </div> </div> <div> <textarea class="newickIn singleIn" id="newickIn2" rows="6" cols="80" placeholder="Newick, NHX formats with one or more trees"></textarea> </div> <div class="row"> <div class="col-sm-12 pull-right"> <div style="font-size: x-small; color: lightgrey;"> <label>Compare examples:</label> <div class="exampleBtn singleIn" id="simpleDouble" style="display:inline-block;"><a href="#">#1 </a></div> <div class="exampleBtn singleIn" id="bigDouble" style="display:inline-block;"><a href="#">#2</a></div> </div> </div> </div> </div> </li> <li> <div id="renderErrorMessage"></div>  <div> <div style="padding-top: 40px; padding-bottom: 10px; width: 100%; margin: 0 auto;"> <button type="button" id="renderButton" class="btn btn-info" style="width: 200px;" data-condition="haveUndo" data-toggle="modal-confirm" data-message="Rendering will clear your changes to current tree!" data-title="Please confirm" data-target="#confirmModal" data-action="render"> <i class="icon-phyloio-01" aria-hidden="true"></i> Render </button> <a id="clearButton">Clear</a> </div> </div> </li> <li> <a href="#" id="settings" style="line-height: 25px; text-decoration: none;"><i style="vertical-align: middle; text-align: center; margin: 0;" class="fas fa-edit" aria-hidden="true"></i> Settings  </a> <div id="settingsPanel"> <div class="row" style="line-height: 30px;"> <div class="col-sm-7"> <label class="settingsLabel" style="vertical-align: middle;">Auto-Collapse Depth:</label> </div> <div class="col-sm-5 pull-right"> <div id="autoCollapseButtons"> <button type="button" id="collapseDec" class="btn btn-default btn-xs collapseButton"> <i style="margin-left: 2px; vertical-align: middle;" class="fas fa-minus" aria-hidden="true"></i> </button> <span id="collapseAmount" class="collapseElem">3</span> <button type="button" id="collapseInc" class="btn btn-default btn-xs collapseButton"> <i class="fas fa-plus" aria-hidden="true"></i> </button> </div> </div> </div> <label class="settingsLabel">Internal Labels:</label> <form class="internalLabels" id="labelForm" style="padding-bottom: 10px"> <div class="radio"> <label class="settingsCheckboxLabel"> <input type="radio" name="internalLabels" value="none" id="internalLabelsNone" checked>None </label> </div> <div class="radio"> <label class="settingsCheckboxLabel"> <input type="radio" name="internalLabels" value="name">Branch Labels/Support </label> </div> <div class="radio"> <label class="settingsCheckboxLabel"> <input type="radio" name="internalLabels" value="length">Length </label> </div> <div class="radio"> <label class="settingsCheckboxLabel opt"> <input type="radio" name="internalLabels" value="similarity" id="internalLabelsSimilarity">Similarity </label> </div> <div class="radio"> <label class="settingsCheckboxLabel opt"> <input type="radio" name="internalLabels" value="species" id="internalLabelsSpecies">Species </label> </div> <div class="radio"> <label class="settingsCheckboxLabel opt"> <input type="radio" name="internalLabels" value="duplication" id="internalLabelsDuplication">Duplication/speciation </label> </div> <div class="radio"> <label class="settingsCheckboxLabel opt"> <input type="radio" name="internalLabels" value="ECNumber" id="internalLabelsECNumber">EC Number </label> </div> <div class="radio"> <label class="settingsCheckboxLabel opt"> <input type="radio" name="internalLabels" value="taxonomyID" id="internalLabelsTaxonomyID">NCBI Taxonomy ID </label> </div> <div class="radio"> <label class="settingsCheckboxLabel opt"> <input type="radio" name="internalLabels" value="likelihood" id="internalLabelsLikelihood">Parent branch log value </label> </div> <div class="radio"> <label class="settingsCheckboxLabel opt"> <input type="radio" name="internalLabels" value="orthologous" id="internalLabelsOrthologous">Display orthology </label> </div> <div class="radio"> <label class="settingsCheckboxLabel opt"> <input type="radio" name="internalLabels" value="superorthologous" id="internalLabelsSuperorthologous">Display super orthology </label> </div> <div class="radio"> <label class="settingsCheckboxLabel opt"> <input type="radio" name="internalLabels" value="subtree" id="internalLabelsSubtree">Subtree </label> </div> <div class="radio"> <label class="settingsCheckboxLabel opt"> <input type="radio" name="internalLabels" value="collapseThis" id="internalLabelsCollapseThis">Collapsed nodes </label> </div> <div class="radio"> <label class="settingsCheckboxLabel opt"> <input type="radio" name="internalLabels" value="color" id="internalLabelsColor">NHX colorscheme </label> </div> </form> <label class="settingsLabel">Adjust Tree Style:</label><br> <label class="settingsCheckboxLabel" style="padding-left: 10px; padding-top: 10px;">Line Thickness</label> <input type="range" class="sizeAdjust" id="lineThickness" min="1" max="10" value="3"> <label class="settingsCheckboxLabel" style="padding-left: 10px; padding-top: 10px;">Node Size</label> <input type="range" class="sizeAdjust" id="nodeSize" min="0" max="10" value="4"> <label class="settingsCheckboxLabel" style="padding-left: 10px; padding-top: 10px;">Font Size</label> <input type="range" class="sizeAdjust" id="fontSize" min="5" max="40" value="15"> <div class="checkbox"> <label class="settingsCheckboxLabel"><input type="checkbox" id="useLengths" checked>Use Lengths</label> </div> <div class="checkbox"> <label class="settingsCheckboxLabel"><input type="checkbox" id="alignTipLabels">Align tip labels </label> </div> <div class="checkbox"> <label class="settingsCheckboxLabel"><input type="checkbox" id="mirrorRightTree">Mirror right tree </label> </div> <div class="checkbox"> <label class="settingsCheckboxLabel"><input type="checkbox" id="moveOnMouseOver" checked>Move To Best Corresponding Node on Highlight Click</label> </div> <div class="checkbox"> <label class="settingsCheckboxLabel"><input type="checkbox" id="selectMultipleSearch">Select multiple search results</label> </div> </div> </li> </ul> <div class="footer" id="footer_div"> </div> </div> </div>   <div class="modal-container" id="spinner-container" style=""><span style="position: relative; margin: 20px 10px 0 0; float: right;">Calculating...</span></div> <div id="page-content-wrapper"> <div id="placeholder"> <div id="arrow"> </div> <div id="text"> <p>1. Choose view for a single tree, Compare for two trees</p> <p>2. Add your trees into the text boxes in newick format</p> <p>3. Click "Render"</p> </div> <div class="alert alert-success alert-dismissible" role="alert" style="margin:25% 10% 0 10% !important; width:80%"> <button type="button" class="close" data-dismiss="alert" aria-label="Close"><span aria-hidden="true">×</span></button> <strong>Good news!</strong> The newest version of phylo.io is now available at <a href="https://beta.phylo.io/" class="alert-link">beta.phylo.io</a>. </div> </div> </div>  </div>   <div class="modal" id="confirmModal" tabindex="-1" role="dialog" aria-labelledby="myModalLabel" aria-hidden="true"> <div class="modal-dialog"> <div class="modal-content"> <div class="modal-header"> <button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">×</span><span class="sr-only">Close</span></button> <h4 class="modal-title"></h4> </div> <div class="modal-body"></div> <div class="modal-footer"> <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button> <button id="confirmok" type="button" data-dismiss="modal" class="btn btn-danger btn-ok" data-target="">Continue</button> </div> </div> </div> </div> <script type="text/javascript"> function haveUndo(){ return $(".undoButton").attr("data-count") > 0; } $(document).ready(function(){ $("#confirmok").on('click', function(event) { if($("#confirmok").data('target')){ var action = $("#confirmok").data('target'); window[action](); } }) $('button[data-toggle="modal-confirm"]').click(function(event) { event.preventDefault(); var self = $(this); var message = self.data('message'); var title = self.data('title'); var target = $(self.data('target')); var condition = self.data('condition'); var action = self.data('action'); if( target.length == 1) { target.find('.modal-title').html(title); target.find('.modal-body').html(message); var showModal = true; var fn = window[condition]; if(typeof fn === 'function') { showModal = fn(condition); } if( showModal ) { $("#confirmok").data('target', action); target.on('shown.bs.modal', function(e) { target.find('button[data-confirm="modal"]').click(function(e){ e.preventDefault(); }); }); target.modal({ show: true }); } else { window[action](); }; }; }); }); </script>  <script> //new ui // Ensures that the acknowledgment footer is correctly placed in the sidebar (function () { var div_footer = $("#footer_div"); var divdiv = $("#sidebar-wrapper-wrapper"); div_footer.width(divdiv.width()); $('#collapse-sidebar-span').attr('data-icon', 'arrow-circle-left'); })(); var spinnerOpts = { lines: 15 // The number of lines to draw , length: 28 // The length of each line , width: 14 // The line thickness , radius: 42 // The radius of the inner circle , scale: 0.20 // Scales overall size of the spinner , corners: 1 // Corner roundness (0..1) , color: '#000' // #rgb or #rrggbb or array of colors , opacity: 0.25 // Opacity of the lines , rotate: 0 // The rotation offset , direction: 1 // 1: clockwise, -1: counterclockwise , speed: 1 // Rounds per second , trail: 50 // Afterglow percentage , fps: 20 // Frames per second when using setTimeout() as a fallback for CSS , zIndex: 2e9 // The z-index (defaults to 2000000000) , className: 'spinner' // The CSS class to assign to the spinner , top: '50%' // Top position relative to parent , left: '10%' // Left position relative to parent , shadow: false // Whether to render a shadow , hwaccel: true // Whether to use hardware acceleration , position: 'relative' // Element positioning }; var spinner = new Spinner(spinnerOpts); //var spinnerTarget = document.getElementById("page-content-wrapper"); var spinnerTarget = document.getElementById("spinner-container"); var gistID = $(location).attr('hash').split(/\s*[#-]\s*/); //get gist id from url var treecomp = TreeCompare().init({ gistSaveServerURL: "http://phylo.io/server/gist.php", scaleColor: "black", loadingCallback: function () { $('#spinner-container').show(); spinner.spin(spinnerTarget); }, loadedCallback: function () { $('#spinner-container').hide(); spinner.stop(); }, enableRerootFixedButtons: $("#rerootFixedButtons").val(), enableSwapFixedButtons: $("#swapFixedButtons").val(), lineThickness: $("#lineThickness").val(), nodeSize: $("#nodeSize").val(), fontSize: $("#fontSize").val(), useLengths: $("#useLengths").is(":checked"), alignTipLabels: $("#alignTipLabels").is(":checked"), ladderizeTree: $("#ladderizeTree").is(":checked"), mirrorRightTree: $("#mirrorRightTree").is(":checked"), selectMultipleSearch: $("#selectMultipleSearch").is(":checked"), comparisonMetric: $("input[name=comparisonMetric]:checked").val(), moveOnClick: $("#moveOnMouseOver").is(":checked"), clickAction: $("input[name=clickAction]:checked").val(), autoCollapse: $("#collapseAmount").html() }); /* Download name */ var update_download_fn = function (canvasId, labelId) { download_fn = document.getElementById(labelId).value; download_fn = (download_fn === '') ? "PhyloIO_Tree" : download_fn; document.getElementById('downloadButtons' + canvasId).getElementsByTagName('a')[0].download = download_fn; }; treecomp.inputTreeFile("newickIn1"); treecomp.inputTreeFile("newickIn2"); treecomp.inputTreeFile("newickInSingle"); // hide optional settings by default $('.opt').parent().hide(); hideOptionalSettings(); var mode = $("#mode-buttons .active").attr('id'); if (mode === "view-btn") { $("#compareIn").removeClass("active"); $("#fileLabel").text("Untitled"); $(".compareIn").css({ "display": "none" }); $("#newickInputs").css({ "padding-bottom": "0px" }); $("#cmp-trees-params").css({ "display": "none" }); $("#view-tree-params").css({ "display": "block" }); $("#action").css( {"display": "none"} ); } /* / / LOAD PAGE FROM GIST / */ if (gistID.length === 2) { //view mode $("#compare-btn").removeClass("active"); $("#view-btn").addClass("active"); $(".compareIn").css({ "display": "none" }); $("#newickInputs").css({ "padding-bottom": "0px" }); var tree1 = treecomp.addTreeGistURL(gistID[1]); if(tree1){ $("#newickInSingle").val(tree1.nwk); $("#page-content-wrapper").empty(); $("#page-content-wrapper").html('<div class="container-fluid vis-container-2" id="vis-container1" style="height: 100%;"></div><div class="vis-scale" id="vis-scale1"></div>'); var tree1 = treecomp.addTree($("#newickInSingle").val(), undefined, "single"); treecomp.viewTree(tree1.name, "vis-container1", "vis-scale1"); $("#colorScale").empty(); $("#action").css({"display": "none"}); } } else if (gistID.length === 3) { //compare mode $("#view-btn").removeClass("active"); $("#compare-btn").addClass("active"); $("#newickInputs").css({ "padding-bottom": "25px" }); $(".compareIn").css({ "display": "block" }); var tree1 = treecomp.addTreeGistURL(gistID[1]); var tree2 = treecomp.addTreeGistURL(gistID[2]); $("#page-content-wrapper").empty(); $("#page-content-wrapper").html('<div class="container-fluid vis-container-2" id="vis-container1"></div><div class="container-fluid vis-container-2" id="vis-container2"></div>'); if(tree1 && tree2) { $("#newickIn1").val(tree1.nwk); $("#newickIn2").val(tree2.nwk); var tree1 = treecomp.addTree($("#newickIn1").val(), undefined, "left"); var tree2 = treecomp.addTree($("#newickIn2").val(), undefined, "right"); treecomp.compareTrees(tree1.name, "vis-container1", tree2.name, "vis-container2", "vis-scale1", "vis-scale2"); $("#colorScale").empty(); treecomp.renderColorScale("colorScale"); $("#action").css({"display": "block"}); } } //end of gist id part $("#menu-toggle").click(function (e) { e.preventDefault(); $("#wrapper").toggleClass("toggled"); var div_footer = $("#footer_div"); var newWidth; var colorScaleWidth = 75; var sidebar_icon = $('#collapse-sidebar-span'); var sb_indicator = sidebar_icon.attr('data-icon'); if (sb_indicator === "arrow-circle-left") { $('#sidebar-nav').hide(); sidebar_icon.attr('data-icon', 'arrow-circle-right'); sidebar_icon.removeClass('fa-arrow-circle-left').addClass('fa-arrow-circle-right'); newWidth = 30; $('#sidebar-wrapper').css("width", "30"); $('#sidebar-wrapper').css("overflow-y", "hidden"); } else { $('#sidebar-nav').show(); sidebar_icon.attr('data-icon', 'arrow-circle-left'); sidebar_icon.removeClass('fa-arrow-circle-right').addClass('fa-arrow-circle-left'); $('#sidebar-wrapper').css("overflow-y", "auto"); if(isScrollBar()){ $('#sidebar-wrapper').css("width", "437"); } else { $('#sidebar-wrapper').css("width", "420"); } } div_footer.width(newWidth); }); /* / / VIEW MODE: active windows in sidebar / */ $("#best_corresponding_tree").hide(); function view() { if ($(window).height() < 550) { $("#sidebar-wrapper").css({ "overflow-y": "scroll" }); } $("#colorScale").empty(); $("#action").css({"display": "none"}); $("#page-content-wrapper").html('<div id="placeholder"><div id="arrow"></div><div id="text"><p>1. Choose view for a single tree, Compare for two trees</p><p>2. Add your trees into the text boxes in newick format</p><p>3. Click "Render"</p></div></div>'); $("#newickInSingle").val(''); $("#compare-btn").removeClass("active"); $("#view-btn").addClass("active"); $(".compareIn").css({ "display": "none" }); $("#best_corresponding_tree").hide(); $("#newickInputs").css({ "padding-bottom": "0px" }); $("#cmp-trees-params").css({ "display": "none" }); $("#view-tree-params").css({ "display": "block" }); $("#renderErrorMessage").empty(); treecomp.changeCanvasSettings({ enableFixedButtons: false }); if (settingsShown) { showHideSettingsPanel("hide"); } if (!$("#rf").is(":empty") || !$("#spr").is(":empty") || !$("#eucl").is(":empty")) { $("#rf").empty(); $("#spr").empty(); $("#eucl").empty(); } } /* / / COMPARE MODE: active windows in sidebar / */ //$("#compare-btn").click(function (e) { function compare() { if ($(window).height() < 750) { $("#sidebar-wrapper").css({ "overflow-y": "scroll" }); } $("#colorScale").empty(); $("#action").css({"display": "block"}); $("#page-content-wrapper").html('<div id="placeholder"><div id="arrow"></div><div id="text"><p>1. Choose view for a single tree, Compare for two trees</p><p>2. Add your trees into the text boxes in newick format</p><p>3. Click "Render"</p></div></div>'); $("#newickIn1").val(''); $("#newickIn2").val(''); $("#view-btn").removeClass("active"); $("#compare-btn").addClass("active"); $("#cmp-trees-params").css({ "display": "block" }); $("#view-tree-params").css({ "display": "none" }); $("#newickInputs").css({ "padding-bottom": "0px" }); $(".compareIn").css({ "display": "block" }); $("#best_corresponding_tree").show(); $("#renderErrorMessage").empty(); treecomp.changeCanvasSettings({ enableFixedButtons: true }); if (settingsShown) { showHideSettingsPanel("hide"); } if(!$("#rf").is(":empty") || !$("#spr").is(":empty") || !$("#eucl").is(":empty")) { $("#rf").empty(); $("#spr").empty(); $("#eucl").empty(); } } /*------------ / / COLLAPSING BY LEVEL BUTTON / ------------*/ $("#collapseInc").click(function (e) { var amountText = $("#collapseAmount").html(); var amount = 0; var maxAmount = treecomp.getMaxAutoCollapse(); if (amountText !== "OFF") { amount = parseInt(amountText); amount += 1; if (amount == maxAmount) { $("#collapseAmount").html("OFF"); } else { $("#collapseAmount").html(amount.toString()); } } else { amount = 0; $("#collapseAmount").html("0"); } treecomp.changeAutoCollapseDepth(amount); }); $("#collapseDec").click(function (e) { var amountText = $("#collapseAmount").html(); var amount = 0; var maxAmount = treecomp.getMaxAutoCollapse(); if (amountText !== "0") { if (amountText === "OFF") { amount = maxAmount; } else { amount = parseInt(amountText); } amount -= 1; if (amount < 0) { amount = null; $("#collapseAmount").html("OFF"); } else { $("#collapseAmount").html(amount.toString()); } } else { amount = null; $("#collapseAmount").html("OFF"); } treecomp.changeAutoCollapseDepth(amount); }); $("#clearButton").click(function (e) { $("#renderErrorMessage").empty(); $("#colorScale").empty(); var mode = $("#mode-buttons .active").attr('id'); if (mode === "compare-btn") { $("#page-content-wrapper").html('<div id="placeholder"><div id="arrow"></div><div id="text"><p>1. Choose view for a single tree, Compare for two trees</p><p>2. Add your trees into the text boxes in newick format</p><p>3. Click "Render"</p></div></div>'); $("#newickIn1").val(''); $("#newickIn2").val(''); } else if (mode === "view-btn") { $("#page-content-wrapper").html('<div id="placeholder"><div id="arrow"></div><div id="text"><p>1. Choose view for a single tree, Compare for two trees</p><p>2. Add your trees into the text boxes in newick format</p><p>3. Click "Render"</p></div></div>'); $("#newickInSingle").val(''); } }); /*------ / / RENDER BUTTON / ------*/ //$("#renderButton").click(function (e) { function render() { $("#renderErrorMessage").empty(); hideOptionalSettings(); $("#menu-toggle").click(); var mode = $("#mode-buttons .active").attr('id'); if (mode === "compare-btn") { if (!$("#rf").is(":empty") || !$("#spr").is(":empty") || !$("#eucl").is(":empty")) { $("#rf").empty(); $("#spr").empty(); $("#eucl").empty(); } try { //$("#page-content-wrapper").empty(); $("#page-content-wrapper").html('<div class="container-fluid vis-container-2" id="vis-container1"></div><div class="container-fluid vis-container-2" id="vis-container2"></div>'); var tree1 = treecomp.addTree($("#newickIn1").val(), undefined, "left"); var tree2 = treecomp.addTree($("#newickIn2").val(), undefined, "right"); treecomp.changeCanvasSettings({ autoCollapse: tree1.data.autoCollapseDepth }) var collapseText = tree1.data.autoCollapseDepth === null ? "OFF" : tree1.data.autoCollapseDepth.toString(); $("#collapseAmount").html(collapseText); //TODO: change this treecomp.compareTrees(tree1.name, "vis-container1", tree2.name, "vis-container2", "vis-scale1", "vis-scale2"); treecomp.undo("undoBtn"); $("#colorScale").empty(); treecomp.renderColorScale("colorScale"); $("#action").css({"display": "block"}); } catch (e) { if (e === "TooLittle)") { $("#renderErrorMessage").append($('<div style="width: 100%" class="alert alert-danger" role="alert">Tree file not correct: too little ")"</div>')).hide().slideDown(300); } else if (e === "TooLittle(") { $("#renderErrorMessage").append($('<div style="width: 100%" class="alert alert-danger" role="alert">Tree file not correct: too little "("</div>')).hide().slideDown(300); } else if (e === "NoTree") { $("#renderErrorMessage").append($('<div style="width: 100%" class="alert alert-danger" role="alert">Please add tree</div>')).hide().slideDown(300); } else if (e === "") { $("#renderErrorMessage").append($('<div style="width: 100%" class="alert alert-danger" role="alert">Empty</div>')).hide().slideDown(300); } } // if // $("#distancesList").style.display="none"; } else if (mode === "view-btn") { // init & enable undo //$("#undoBtn").data('undoIdx', undoIndex); try { // var tree1 = treecomp.addTree($("#newickInSingle").val(), undefined, "single"); treecomp.changeCanvasSettings({ autoCollapse: tree1.data.autoCollapseDepth }); var collapseText = tree1.data.autoCollapseDepth === null ? "OFF" : tree1.data.autoCollapseDepth.toString(); $("#collapseAmount").html(collapseText); //$("#page-content-wrapper").empty(); $("#page-content-wrapper").html('<div class="container-fluid vis-container" id="vis-container1"></div>'); treecomp.viewTree(tree1.name, "vis-container1", "vis-scale1"); treecomp.undo("undoBtn"); $("#colorScale").empty(); $("#action").css({"display": "none"}); } catch (e) { if (e === "TooLittle)") { $("#renderErrorMessage").append($('<div style="width: 100%" class="alert alert-danger" role="alert">Tree file not correct: too little ")"</div>')).hide().slideDown(300); } else if (e === "TooLittle(") { $("#renderErrorMessage").append($('<div style="width: 100%" class="alert alert-danger" role="alert">Tree file not correct: too little "("</div>')).hide().slideDown(300); } else if (e === "NoTree") { $("#renderErrorMessage").append($('<div style="width: 100%" class="alert alert-danger" role="alert">Please add tree</div>')).hide().slideDown(300); } else if (e === "") { $("#renderErrorMessage").append($('<div style="width: 100%" class="alert alert-danger" role="alert">Empty</div>')).hide().slideDown(300); } } } // }); } /*------ / / EXPORT BOTH TREES / ------*/ $("#svgExport").click(function (e) { treecomp.exportBothTrees("vis-container1", "vis-container2"); }); /*------ / / Calculate Distance / ------*/ $("#distance").click(function(e){ var distances = treecomp.calcDist(); if(distances) { var rf = distances[0][0]; var rf_norm = distances[0][1]; var eucl = distances[1]; var spr = distances[2]; d3.select("#rf").text("Robinson-Foulds: "+rf+"/"+rf_norm); d3.select("#eucl").text("Euclidean: " + eucl); d3.select("#spr").text("SPR: " + spr); } }); /*------ / / SETTINGS / ------*/ function hideOptionalSettings() { var v = $("label.opt"); $(v).each(function (i) { ($(this).hide().next().hide()) }); } var settingsShown = false; $("#settings").click(function (e) { if (settingsShown) { showHideSettingsPanel("hide"); } else { showHideSettingsPanel("show"); } }); function isScrollBar(){ // sidebarheight taller than document height - nav bar height -> scroll bar is visible if($("ul.sidebar-nav").height() > ($(document).height() - 50)){ return true; } else { return false; } } function showHideSettingsPanel(mode) { if (mode == "show") { $("#settingsPanel").slideDown(200, function() { settingsShown = true; $("#sidebar-wrapper").css({ "overflow-y": "auto" }); // hardcode the value, it's close enough if(isScrollBar()) { $('#sidebar-wrapper').width(437); } else { $('#sidebar-wrapper').width(420); } }); } else if (mode == "hide") { $("#settingsPanel").slideUp(100, function () { settingsShown = false; $(this).css({ "display": "none" }); // hardcode the value, it's close enough if(isScrollBar()) { $('#sidebar-wrapper').width(437); } else { $('#sidebar-wrapper').width(420); } }); } else { console.log("You should not be able to see this!!!!"); } } $(".sizeAdjust").change(function () { treecomp.changeTreeSettings({ lineThickness: $("#lineThickness").val(), nodeSize: $("#nodeSize").val(), fontSize: $("#fontSize").val() }); }); $("#useLengths").on("click", function () { treecomp.changeTreeSettings({ useLengths: $("#useLengths").is(":checked") }); }); $("#alignTipLabels").on("click", function () { treecomp.changeTreeSettings({ alignTipLabels: $("#alignTipLabels").is(":checked") }); }); $("#ladderizeTree").on("click", function () { treecomp.changeTreeSettings({ ladderizeTree: $("#ladderizeTree").is(":checked") }); }); $("#mirrorRightTree").on("click", function () { treecomp.changeTreeSettings({ mirrorRightTree: $("#mirrorRightTree").is(":checked") }); }); $("input[name=comparisonMetric]:radio").on("change", function () { treecomp.changeTreeSettings({ comparisonMetric: $("input[name=comparisonMetric]:checked").val() }) }); $("#moveOnMouseOver").on("click", function () { treecomp.changeTreeSettings({ moveOnClick: $("#moveOnMouseOver").is(":checked") }) }); $("#selectMultipleSearch").on("click", function () { treecomp.changeTreeSettings({ selectMultipleSearch: $("#selectMultipleSearch").is(":checked") }) }); $("input[name=internalLabels]:radio").on("change", function () { treecomp.changeTreeSettings({ internalLabels: $("input[name=internalLabels]:checked").val() }); }); //TODO: code to sync version number with tag in git-repo /*var gitHubPath = 'phylo-io'; // example repo var url = 'https://gitolite@lab.dessimoz.org:2222/' + gitHubPath + '/tags'; $.get(url).done(function (data) { var versions = data.sort(function (v1, v2) { return semver.compare(v2.name, v1.name) }); $('#git-tag').html(versions[0].name); console.log($('#git-tag').html(versions[0].name)); });*/ $('#git-tag').html("1.0.0"); $("#last-modif").html(document.lastModified); /*var enableAutomation = true; if (enableAutomation) { $("#demoTrees").trigger("click"); $("#view-btn").trigger("click"); setTimeout(function() { $("#renderCheckbox1").trigger("click"); $("#renderButton").trigger("click"); }, 800); }*/ //$("#simpleSingle").click(function() {$("#newickInSingle").val("(A:0.01,((C:0.02,D:0.05)51:0.06,E:0.09)94:0.05,B:0.06);");}); $("#simpleSingle").click(function () { $("#newickInSingle").val("((sba:0.03984952076326608861,(sca:0.24212307199678842484,(cgl:0.29957965624763355228,(((kla:0.32829009627835226137,ago:0.35217085340006204497):0.05741546733669361524,(skl:0.15813405639248145906,kwa:0.25658337062111585825):0.04348414441988464330):0.03689776646512240438,(yli:1.00856143917930674014,(((lel:0.28806785996189482324,(cal:0.11643570498932501178,ctr:0.12746420698315982789):0.08774131940069260227):0.12449843844102517765,pst:0.20187483296288805112):0.04951181210826986756,(pgu:0.32083506939774530942,dha:0.19121342958249643029):0.04448806563879210280):0.37619889625745939199):0.45090563411571948915):0.08921537612721808230):0.03625000527459597971):0.17548658899657892940):0.01414267170946369515,((sce:0.02228625922028022385,spa:0.01687593406907536564):0.01282179619059338992,smi:0.03661027033511007195):0.01331228080676675335,sku:0.04268512407808848497):0.0;"); }); $("#bigSingle").click(function () { 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}); $("#simpleDouble").click(function () { //$("#newickIn1").val("(AFIL.CDS.id62578.tr68301:0.525368,Afi-Ppxl:0.483887,(Spu-Phb1:1.23315,Sko-Phb1:1.3481,(Smi-gi|313475154|dbj|BAJ41032.1:0.472375,((((Lva-pmar1I:0.001563,Lva-pmar1H:0.001597,Lva-pmar1G:0.008937)1:0.011037,Lva-pmar1F:0.002403)0.65:0.008459,(Lva-pmar1E:0.003557,((Lva-pmar1D:0.005373,Lva-pmar1C:0.006285)0.99:0.015518,Lva-pmar1B:0.009016)0.54:0.003857)0.89:0.008241,Lva-pmar1A:0.018191)0.96:0.172247,((Pli-pmar1F:0.053952,(Pli-pmar1C:0.05325,(Pli-pmar1E:0.02152,(Pli-pmar1D:0.025287,Pli-pmar1A:0.019942)1:0.013265)0.98:0.00928)0.51:0.005035)0.99:0.081252,((Spu-Pmar1d:0.037692,Spu-Pmar1c:0.017113)0.9:0.024698,(Spu-Pmar1a:0.071715,Hpu-micro1-gi:0.038382)0.96:0.018524)0.87:0.04667)0.81:0.04896)0.59:0.100861)1:1.43733,(Pmi-Phb1:0.873401,Afi-Phb1:0.44691)0.79:0.22189,(((Pmi-Otx:0.264476,(Spu-Otx:0.01093,Lva-Otx:0.062025)0.99:0.281342)0.7:0.093593,Cin-gi|74136734|ref|NM_001032490.2:0.477395,Afi-Otx:0.268409)1:1.21583,(Pmi-Gsc:0.38765,(Spu-GsC:0.015565,Lva-Gsc:0.208362)0.97:0.29216,Bfl-gi|260831451|ref|XM_002610627.1:0.818611,Afi-Gsc:0.496737)1:0.824482,(Cin-gi|198429586|ref|XM_002119104.1:1.73942,Bfl-gi|260831719|ref|XM_002610760.1:0.976953,(Bfl-gi|260801388|ref|XM_002595532.1:0.526166,Bfl-gi|260801382|ref|XM_002595529.1:0.946938)0.98:0.316371,(Bfl-gi|260791955|ref|XM_002590947.1:0.050132,Bfl-gi|260791951|ref|XM_002590945.1:0.288184)0.98:0.431474,Bfl-gi|260790761|ref|XM_002590364.1:1.12817,(Bfl-gi|260802229|ref|XM_002595949.1:0.524083,Ame-Phb1:0.86344)0.85:0.438539,((Spu-alx-unknown:0.406992,Cin-gi|118343664|ref|NM_001078186.1:1.00838)0.51:0.174577,Bfl-gi|260796220|ref|XM_002593057.1:0.264691,(Spu-Chx10:0.343706,Afi-Chx10:0.166438)0.99:1.1707)0.69:0.313216,(Spu-Arxl:0.523774,Pmi-Arxl:1.12284,Afi-Arxl:0.369079)0.87:0.400322)0.61:0.315159)0.99:0.7752)0.93:0.319184);"); //$("#newickIn2").val("((Pli-pmar1C:0.04982971476216899176,((Pli-pmar1A:0.01853490272383020998,Pli-pmar1D:0.02271900137434858594)92:0.01115161265327409452,Pli-pmar1E:0.01901859200836115635)80:0.00746600508734124660)78:0.00432473905358994951,(((((((AFIL.CDS.id62578.tr68301:0.40380291681391977665,Afi-Ppxl:0.41444967698110529719)91:0.30219956781642881571,(Pmi-Phb1:0.79440690097898281063,Afi-Phb1:0.37365336412740352001)61:0.13333362861261538468)30:0.10460860532948103307,(((Bfl-gi|260831451|ref|XM_002610627.1:0.64866922307940477754,((Pmi-Gsc:0.36937144741360378175,Afi-Gsc:0.42935749187216976086)58:0.08633761177527859987,(Lva-Gsc:0.17953091125256040450,Spu-GsC:0.03107504551201345500)96:0.27592232106501696220)46:0.04252309223538374566)98:0.38683078306470125574,(((Pmi-Otx:0.23517153357868259000,(Lva-Otx:0.05330603384273001344,Spu-Otx:0.01712736457236331208)100:0.26570980742971184174)66:0.00000141211799157180,(Afi-Otx:0.29013852965796421701,Cin-gi|74136734|ref|NM_001032490.2:0.41883746565520973970)59:0.12151122598965137522)100:0.78549225904186681380,((Ame-Phb1:0.64271362422831646022,Bfl-gi|260802229|ref|XM_002595949.1:0.49846147581683269978)76:0.35918126374909170595,((Bfl-gi|260831719|ref|XM_002610760.1:0.88228939367580017095,(Pmi-Arxl:1.08556158371680866459,(Afi-Arxl:0.41504207554468192098,Spu-Arxl:0.49283900206322062143)67:0.04919942871689284014)58:0.21399781399059111808)14:0.06903856430662934363,((Bfl-gi|260801388|ref|XM_002595532.1:0.51405593866218979304,Bfl-gi|260801382|ref|XM_002595529.1:0.76984758160539545901)87:0.29649541025870662647,(((Cin-gi|198429586|ref|XM_002119104.1:1.43610537881052957587,(Spu-Chx10:0.24420417056054768978,Afi-Chx10:0.26225439305605835472)99:0.64093362693240918393)15:0.23912230371659187744,(Bfl-gi|260790761|ref|XM_002590364.1:0.95608583358528032026,(Bfl-gi|260791951|ref|XM_002590945.1:0.25792428231570035946,Bfl-gi|260791955|ref|XM_002590947.1:0.05799404890873638418)96:0.31798011001876452797)24:0.08940147506755243001)5:0.16190722027514037329,(Bfl-gi|260796220|ref|XM_002593057.1:0.30272766867709932637,(Spu-alx-unknown:0.37130565399142828609,Cin-gi|118343664|ref|NM_001078186.1:0.89719169779980556534)74:0.22061118421743999840)52:0.23995848824645796271)2:0.06459336747582460070)4:0.10101472788404428083)6:0.07762265306208614157)27:0.15411980739446087818)36:0.09037448430284705791)83:0.40528173888583468587,Sko-Phb1:1.05782545759954982323)19:0.02028210416908014097)38:0.31235639607643039817,Spu-Phb1:0.84061576812303639983)100:0.82771628908512673295,Smi-gi|313475154|dbj|BAJ41032.1:0.35703831029590410440)65:0.09799446838093080203,((Lva-pmar1F:0.00000141211799157180,(Lva-pmar1G:0.00735701973928339081,(Lva-pmar1H:0.00000141211799157180,Lva-pmar1I:0.00000141211799157180)82:0.00000141211799157180)88:0.01102050389863199961)45:0.00737236097464944937,((((Lva-pmar1D:0.00371996294401328838,Lva-pmar1C:0.00461751230557235545)99:0.01410591393923983639,Lva-pmar1B:0.00739046843003031678)39:0.00000141211799157180,Lva-pmar1E:0.00368582124942792204)54:0.00740036229075003750,Lva-pmar1A:0.01487109144681754251)13:0.00000141211799157180)99:0.15085147990969502430)65:0.06455208511189490517,((Spu-Pmar1d:0.03446135590923457559,Spu-Pmar1c:0.01730548753707577408)57:0.02399889489544585267,(Spu-Pmar1a:0.06914585039397486144,Hpu-micro1-gi:0.03842890940433322383)65:0.01341633040145582753)73:0.04976798798075844632)93:0.06987675919317459794,Pli-pmar1F:0.04929361396699290243);"); //$("#newickIn1").val("((((A,B),C),D),(E,F));"); //$("#newickIn2").val("(((F,E),(D,(B,A))),C);"); //$("#newickIn2").val("((sba:0.04645932805874481569,(smi:0.03315550229946162553,(spa:0.01466907419174275952,sce:0.02383733069302066895):0.01620853054082276729):0 $("#newickIn1").val("((yli:1.0085614391793067,(((lel:0.2880678599618948,(cal:0.11643570498932501,ctr:0.12746420698315983):0.0877413194006926):0.12449843844102518,pst:0.20187483296288805):0.04951181210826987,(pgu:0.3208350693977453,dha:0.19121342958249643):0.0444880656387921):0.3761988962574594):0.22545281705785974,(((kla:0.32829009627835226,ago:0.35217085340006204):0.057415467336693615,(skl:0.15813405639248146,kwa:0.25658337062111586):0.04348414441988464):0.036897766465122404,(cgl:0.29957965624763355,(sca:0.24212307199678842,(sba:0.03984952076326609,(((sce:0.022286259220280224,spa:0.016875934069075366):0.01282179619059339,smi:0.03661027033511007):0.013312280806766753,sku:0.042685124078088485):0.014142671709463695):0.17548658899657893):0.03625000527459598):0.08921537612721808):0.22545281705785974):0;"); $("#newickIn2").val("((sba:0.04645932805874481569,(smi:0.03315550229946162553,(spa:0.01466907419174275952,sce:0.02383733069302066895):0.01620853054082276729):0.01834962617511207497):0.06496501071301066799,(sca:0.21928497146352055047,((((ago:0.34529718349701971070,kla:0.26611733077459831520):0.04460721000595434249,(kwa:0.23458417353426505580,skl:0.38245746198409408256):0.02217438839159899949):0.02847427462232336726,(((pst:0.21220493191897629726,((cal:0.09792303271040220247,ctr:0.11778282966461572911):0.07993742108354510989,lel:0.23757786374413303321):0.09896075353236584438):0.04667831716440219020,(pgu:0.28475663985974825065,dha:0.17797706546403241346):0.04249479494672471491):0.29326816910580705278,yli:0.72911704942210797675):0.31199925135971823265):0.06946141605430436461,cgl:0.27125751484306920291):0.03678319509837457008):0.09011350505801994648,sku:3.28511106679567399524):0.0;"); 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