phyloio 2.0.0

package/src/utils.js

@@ -0,0 +1,406 @@
+import * as fs from 'file-saver';
+
+function traverse(o,func_pre, func_post) {
+
+    if (func_pre){
+        func_pre.apply(this,[o,o["children"]])
+    }
+
+    if(o["children"]){
+
+        for (var c in o["children"] ) {
+
+            var child = o["children"][c]
+
+            child = traverse(child, func_pre, func_post)
+
+            if (func_post) {
+                func_post.apply(this,[child,o])
+            }
+
+
+        }
+
+
+    }
+
+    return o
+
+}
+
+function build_table(hierarchy){ // build table for RF
+
+    traverse(hierarchy, function(node,children){
+        delete node.left_
+        delete node.right_
+        delete node.weight_
+    }, null)
+
+    var n = hierarchy.leaves().length
+    var X = Array.from(new Array(n), _ => Array(3).fill(0));
+    var S2I = {} //Array(n).fill(0)
+    var I2S = Array(n).fill(0)
+    var n_edges = 0
+
+    var nz = []
+    traverse(hierarchy, null, function(node,children){nz.push(node)})
+    nz = nz.entries()
+
+    var n1 = nz.next()
+    var n2 = nz.next()
+    var i = 0
+
+    while (true) {
+        var node = n1.value[1]
+        var node2 = n2.value[1]
+        var p = node.parent
+        var ii;
+
+        // Do work
+        if (!(node.hasOwnProperty('children'))) {
+            I2S[i] = node.data.name
+            S2I[I2S[i]] = i
+            node.weight_ = 0
+            node.left_ = i
+            node.right_ = i
+            i += 1
+        }
+
+        // propagate up
+        if (typeof p != "undefined"){
+            p.left_ = p.hasOwnProperty('left_') ? Math.min(p.left_, node.left_) : node.left_
+            p.right_ = p.hasOwnProperty('right_') ? Math.max(p.right_, node.right_) : node.right_
+            if (p.hasOwnProperty('weight_')){ p.weight_ = p.weight_ + node.weight_ + 1} else {p.weight_ = node.weight_  +=1}
+        }
+
+        if (node.hasOwnProperty('children')) {
+
+            if( node2.hasOwnProperty('weight_') && node2.weight_ > 0 ){ii = node.left_} else { ii = node.right_}
+
+            X[ii][0] = node.left_
+            X[ii][1] = node.right_
+            if (node.data.hasOwnProperty('branch_length')){
+                X[ii][2] = node.data.branch_length
+            }
+            else {
+                X[ii][2] = 1
+            }
+
+
+            n_edges += 1
+
+        }
+
+        n1 = n2
+        n2 = nz.next()
+
+        if (n2.done){
+            // process seed node, w=0
+            ii = node.right_
+            X[ii][0] = node.left_
+            X[ii][1] = node.right_
+            X[ii][2] = node.data.branch_length
+            n_edges += 1
+            break
+        }
+
+
+
+
+
+
+    }
+
+    return {'table': X, 'n_edges': n_edges, 'I2S': I2S, 'S2I': S2I}
+
+
+}
+
+function reverse_order(child,parent){
+
+    child.children.push(parent)
+    parent.parent =child
+
+    const b = parent.children.indexOf(child);
+    if (b > -1) {
+        parent.children.splice(b, 1);
+    }
+}
+
+function reroot_hierarchy(hierarchy, leaf_name){
+
+
+
+    let leaf = hierarchy.leaves().find(element => element.data.name == leaf_name );
+
+    //  INVERT PATH TO ROOT
+    var ancestors  = leaf.ancestors()
+    leaf.children = []
+    leaf.root = true
+
+    var index
+    for (index = 0; index < ancestors.length; index++) {
+
+        let child = (index === 0) ? leaf : ancestors[index-1]
+        let parent = ancestors[index]
+
+        reverse_order(child,parent)
+    }
+
+    //DESTROY ROOT
+    var old_root_children = ancestors[ancestors.length-1].children
+
+    var c = ancestors[ancestors.length-2].children.indexOf(ancestors[ancestors.length-1]);
+    if (c > -1) {
+        ancestors[ancestors.length-2].children.splice(c, 1);
+    }
+    for (var j = 0; j < old_root_children.length; j++) {
+
+        let parent = old_root_children[j]
+        let child = ancestors[ancestors.length-2]
+
+        child.children.push(parent)
+        parent.parent =child
+    }
+
+    return leaf
+}
+
+function addLogo(svg) {
+    // TODO load with ajax
+    var logo_xml = '<svg id="exportLogo" x="0" y="0"><g id="g4169"> <path d="m 29.606259,23.679171 1.905511,0 c 0.193778,0.617882 0.290669,1.188505 0.290672,1.711869 0.466506,-0.545171 1.022728,-0.99222 1.668668,-1.341146 0.653108,-0.348904 1.295455,-0.523362 1.927043,-0.523373 0.976073,1.1e-5 1.86603,0.261698 2.669869,0.78506 0.810999,0.523383 1.442581,1.221215 1.894747,2.093495 0.459321,0.865028 0.688986,1.802739 0.688998,2.813134 -1.2e-5,1.010407 -0.229677,1.951752 -0.688998,2.824038 -0.452166,0.865023 -1.083748,1.559219 -1.894747,2.082592 -0.803839,0.516105 -1.693796,0.774156 -2.669869,0.774157 -0.638765,-1e-6 -1.284701,-0.163554 -1.937809,-0.490663 -0.653117,-0.334377 -1.20575,-0.770521 -1.657902,-1.308434 l 0,6.542172 -1.711731,0 0,-12.713622 c -2e-6,-0.552441 -0.04665,-1.170313 -0.139953,-1.853616 -0.08613,-0.683283 -0.20096,-1.148504 -0.344499,-1.395663 m 2.196183,5.539039 c -3e-6,1.133981 0.355261,2.093499 1.065795,2.878557 0.717702,0.777793 1.561006,1.166688 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style="font-size:22.18883514px;font-style:normal;font-variant:normal;font-weight:bold;font-stretch:normal;text-align:start;line-height:125%;letter-spacing:0px;word-spacing:0px;writing-mode:lr-tb;text-anchor:start;fill:#000000;fill-opacity:1;stroke:none;font-family:Sawasdee;-inkscape-font-specification:Sawasdee Bold" id="path4153" /> <path d="m 84.532366,34.0049 c -2e-6,-0.247148 0.08612,-0.457951 0.258374,-0.63241 0.172247,-0.181725 0.380382,-0.272588 0.624405,-0.27259 0.244018,2e-6 0.452152,0.09087 0.624405,0.27259 0.179424,0.174459 0.269137,0.385262 0.269141,0.63241 -4e-6,0.239881 -0.08972,0.454318 -0.269141,0.643314 -0.17943,0.181727 -0.387564,0.27259 -0.624405,0.27259 -0.236846,0 -0.444981,-0.09087 -0.624405,-0.27259 -0.172252,-0.188996 -0.258376,-0.403433 -0.258374,-0.643314" 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+
+    svg.append("g").html(logo_xml);
+
+}
+
+function getSVGString( svgNode ) {
+    svgNode.setAttribute('xlink', 'http://www.w3.org/1999/xlink');
+    var cssStyleText = getCSSStyles(svgNode);
+    cssStyleText += "* {font-family:Helvetica}"
+    appendCSS( cssStyleText, svgNode );
+
+    var serializer = new XMLSerializer();
+    var svgString = serializer.serializeToString(svgNode);
+    svgString = svgString.replace(/(\w+)?:?xlink=/g, 'xmlns:xlink='); // Fix root xlink without namespace
+    svgString = svgString.replace(/NS\d+:href/g, 'xlink:href'); // Safari NS namespace fix
+
+    return svgString;
+
+    function getCSSStyles( parentElement ) {
+        var selectorTextArr = [];
+
+        // Add Parent element Id and Classes to the list
+        selectorTextArr.push( '#'+parentElement.id );
+        for (var c = 0; c < parentElement.classList.length; c++)
+            if ( !contains('.'+parentElement.classList[c], selectorTextArr) )
+                selectorTextArr.push( '.'+parentElement.classList[c] );
+
+        // Add Children element Ids and Classes to the list
+        var nodes = parentElement.getElementsByTagName("*");
+        for (var i = 0; i < nodes.length; i++) {
+            var id = nodes[i].id;
+            if ( !contains('#'+id, selectorTextArr) )
+                selectorTextArr.push( '#'+id );
+
+            var classes = nodes[i].classList;
+            for (var c = 0; c < classes.length; c++)
+                if ( !contains('.'+classes[c], selectorTextArr) )
+                    selectorTextArr.push( '.'+classes[c] );
+        }
+
+        // Extract CSS Rules
+        var extractedCSSText = "";
+        for (var i = 0; i < document.styleSheets.length; i++) {
+            var s = document.styleSheets[i];
+
+            try {
+                if(!s.cssRules) continue;
+            } catch( e ) {
+                if(e.name !== 'SecurityError') throw e; // for Firefox
+                continue;
+            }
+
+            var cssRules = s.cssRules;
+            for (var r = 0; r < cssRules.length; r++) {
+                if ( contains( cssRules[r].selectorText, selectorTextArr ) )
+                    extractedCSSText += cssRules[r].cssText;
+            }
+        }
+
+
+        return extractedCSSText;
+
+        function contains(str,arr) {
+            return arr.indexOf( str ) === -1 ? false : true;
+        }
+
+    }
+
+    function appendCSS( cssText, element ) {
+        var styleElement = document.createElement("style");
+        styleElement.setAttribute("type","text/css");
+        styleElement.innerHTML = cssText;
+        var refNode = element.hasChildNodes() ? element.children[0] : null;
+        element.insertBefore( styleElement, refNode );
+    }
+}
+
+function svgString2Image( svgString, width, height, format, callback ) {
+    var format = format ? format : 'png';
+
+    var imgsrc = 'data:image/svg+xml;base64,'+ btoa( unescape( encodeURIComponent( svgString ) ) ); // Convert SVG string to dataurl
+
+    var canvas = document.createElement("canvas");
+    var context = canvas.getContext("2d");
+
+    canvas.width = width;
+    canvas.height = height;
+
+    var image = new Image;
+    image.onload = function() {
+
+        context.clearRect ( 0, 0, width, height );
+        context.fillStyle = "#ffffff";
+        context.fillRect(0, 0, width, height);
+        context.drawImage(image, 0, 0, width, height);
+
+        canvas.toBlob( function(blob) {
+            var filesize = Math.round( blob.length/1024 ) + ' KB';
+            if ( callback ) callback( blob, filesize );
+        });
+    };
+    image.src = imgsrc;
+}
+
+function screen_shot({ svg1, svg2, format } = {}){
+
+    addLogo(svg1);
+    var name1 = svg1.attr("id");
+    var svgString1 = getSVGString(svg1.node());
+
+    var t = "<svg xmlns=\"http://www.w3.org/2000/svg\" version=\"1.1\">\n" +
+        "\n" +
+        "  <g transform=\"translate(0,0)\">\n" +
+        svgString1 +
+        "  </g>\n"
+
+    if(svg2){
+
+        addLogo(svg2);
+        var name2 = svg2.attr("id");
+        var svgString2 = getSVGString(svg2.node());
+
+        var w = svg2.node().getBoundingClientRect().width
+        var h = svg2.node().getBoundingClientRect().height
+
+        t += '<line x1="' + (w + 5) +'" y1="0" x2="' + (w + 5) +'" y2="' + h+'" stroke="black" />'
+
+        t += "  <g transform=\"translate(" + (w + 10)  +",0)\">\n" +
+            svgString2 +
+            "  </g>\n"
+
+    }
+
+    t += "</svg> "
+
+    if(format === 'svg') {
+
+        var blob = new Blob([t], {"type": "image/svg+xml;base64,"+ btoa(t)});
+        fs.saveAs(blob, name1+".svg");
+        svg1.select("#exportLogo").remove();
+        if(svg2){svg2.select("#exportLogo").remove();}
+
+    }
+
+    else if (format === 'png'){
+
+
+
+        var wi = svg1.node().getBoundingClientRect().width
+        var he = svg1.node().getBoundingClientRect().height
+
+        if(svg2){
+            wi = wi*2;
+        }
+
+        svgString2Image(t,  wi, he, 'png', save);
+
+        svg1.select("#exportLogo").remove();
+        if(svg2){svg2.select("#exportLogo").remove();}
+
+        function save(dataBlob, filesize) {
+            var filename = (name) ? name+"." : "";
+            fs.saveAs(dataBlob, filename+'phylo.io.png'); // FileSaver.js function
+        }
+
+    }
+}
+
+//Adapted from Extended Newick format parser in JavaScript.
+//Copyright (c) Miguel Pignatelli 2014 based on Jason Davies
+function parse_nhx(s) {
+    var ancestors = [];
+    var tree = {'data_nhx' : {}};
+    // var tokens = s.split(/\s*(;|\(|\)|,|:)\s*/);
+    //[&&NHX:D=N:G=ENSG00000139618:T=9606]
+    var tokens = s.split( /\s*(;|\(|\)|\[|\]|,|:|=)\s*/ );
+    for (var i=0; i<tokens.length; i++) {
+        var token = tokens[i];
+        switch (token) {
+            case '(': // new children
+                var subtree = {'data_nhx' : {}};
+                tree.children = [subtree];
+                ancestors.push(tree);
+                tree = subtree;
+                break;
+            case ',': // another branch
+                var subtree = {'data_nhx' : {}};
+                ancestors[ancestors.length-1].children.push(subtree);
+                tree = subtree;
+                break;
+            case ')': // optional name next
+                tree = ancestors.pop();
+                break;
+            case ':': // optional length next
+                break;
+            default:
+                var x = tokens[i-1];
+                // var x2 = tokens[i-2];
+                if (x == ')' || x == '(' || x == ',') {
+                    tree.name = token;
+                }
+                else if (x == ':') {
+                    var test_type = typeof token;
+                    if(!isNaN(token)){
+                        tree.branch_length = parseFloat(token);
+                    }
+                    // tree.length = parseFloat(token);
+                }
+                else if (x == '='){
+                    tree['data_nhx'][tokens[i-2]] = token
+                }
+                else {
+                    var test;
+                }
+        }
+    }
+    return tree;
+};
+
+function save_file_as(filename, data) {
+    const blob = new Blob([data], {type: 'text/csv'});
+    if(window.navigator.msSaveOrOpenBlob) {
+        window.navigator.msSaveBlob(blob, filename);
+    }
+    else{
+        const elem = window.document.createElement('a');
+        elem.href = window.URL.createObjectURL(blob);
+        elem.download = filename;
+        document.body.appendChild(elem);
+        elem.click();
+        document.body.removeChild(elem);
+    }
+}
+
+export {build_table, reroot_hierarchy, screen_shot, parse_nhx, save_file_as};