phyloio 2.1.1 → 2.2.3

package/dist-jest/src_worker_bcn_js.phylo.js

@@ -0,0 +1,350 @@
+/*
+ * ATTENTION: The "eval" devtool has been used (maybe by default in mode: "development").
+ * This devtool is neither made for production nor for readable output files.
+ * It uses "eval()" calls to create a separate source file in the browser devtools.
+ * If you are trying to read the output file, select a different devtool (https://webpack.js.org/configuration/devtool/)
+ * or disable the default devtool with "devtool: false".
+ * If you are looking for production-ready output files, see mode: "production" (https://webpack.js.org/configuration/mode/).
+ */
+/******/ (() => { // webpackBootstrap
+/******/ 	var __webpack_modules__ = ({
+
+/***/ "./src/model.js":
+/*!**********************!*\
+  !*** ./src/model.js ***!
+  \**********************/
+/***/ ((__unused_webpack_module, __webpack_exports__, __webpack_require__) => {
+
+"use strict";
+eval("__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpack_require__.d(__webpack_exports__, {\n/* harmony export */   \"default\": () => (/* binding */ Model)\n/* harmony export */ });\n/* harmony import */ var d3__WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__(/*! d3 */ \"./node_modules/d3/index.js\");\n/* harmony import */ var minhashjs__WEBPACK_IMPORTED_MODULE_1__ = __webpack_require__(/*! minhashjs */ \"./node_modules/minhashjs/index.js\");\n/* harmony import */ var biojs_io_newick__WEBPACK_IMPORTED_MODULE_2__ = __webpack_require__(/*! biojs-io-newick */ \"./node_modules/biojs-io-newick/src/index.js\");\n\n\n\n\nvar uid_model = 0\nvar uid_untitle_counter = 0\n;\nconst { parse_nhx } = __webpack_require__(/*! ./utils.js */ \"./src/utils.js\");\nconst { phyloXml } = __webpack_require__(/*! ./phyloxml.js */ \"./src/phyloxml.js\");\n\nclass Model {\n\n    constructor(data, settings, from_raw_data = true) {\n\n        this.zoom;\n        this.settings = {\n            'uid': null,\n            'domain_extended_data' : {},\n            'edge_related_data' : ['Length'],\n            'default_internal_label_is_for_branch': false,\n            'extended_data_type' : {'Topology': 'num'},\n            'labels' : {'leaf' : new Set(), 'node':new Set()},\n            'colorlabels' :{'leaf' : new Set(), 'node':new Set([\"Topology\"])},\n            'display_leaves' : true,\n            'display_nodes_labels' : true,\n            'mirror': false,\n            'name': null,\n            'first_time_render': true,\n            'data_type' : 'newick',\n            'use_branch_lenght' : true,\n            'show_tooltips' : false,\n            'subsample_label' : true,\n            'use_internal_node_name_for_triangles' : true,\n            'display_internal_label' : false,\n            'display_internal_label_left_top' : false,\n            'display_internal_label_left_bottom' : false,\n            'display_leaf_label' : false,\n            'display_leaf_label_left_top' : false,\n            'display_leaf_label_left_bottom' : false,\n            'display_duplication' : false,\n            'has_branch_lenght' : true,\n            'has_duplications' : false,\n            'multiple_search':false,\n            'show_histogram' : false,\n            'align_tip' : false,\n            'use_meta_for_leaf' : true,\n            'use_meta_for_node' : false,\n            'has_histogram_data' : false,\n            'similarity': [],\n            'style': {\n                'font_size_internal' : 14,\n                'color_accessor' : {'leaf' : null, 'node': \"Topology\", 'circle': null},\n                'color_extent_min': {'leaf' : {}, 'node': {\"Topology\":0}, 'circle': {} },\n                'color_extent_max':{'leaf' : {}, 'node': {\"Topology\":1}, 'circle': {}},\n                'number_domain':{ 'Topology': 5, 'Length': 5},\n                'color_domain': {\n                    'Topology' : [\"#a50026\", \"#f46d43\", \"#ffffbf\", \"#74add1\", \"#313695\"],\n                    'Length': ['#253494', '#2C7FB8', '#41B6C4', '#C7E9B4', '#FFFFCC']\n                },\n                'color_domain_default': {\n                    \"Topology\": [\"#a50026\", \"#f46d43\", \"#ffffbf\", \"#74add1\", \"#313695\"],\n                    \"Length\": ['#253494', '#2C7FB8', '#41B6C4', '#C7E9B4', '#FFFFCC'],\n                    \"DEFAULT\": ['#C60101', '#FB6A4A', '#F7F7F7', '#6BAED6', '#253494']\n                }\n\n        },\n            'tree': {\n                'node_vertical_size' : 30,\n                'node_horizontal_size' : 40,\n                'node_radius' : 6, // move to style\n                'line_width' : 3,// move to style\n                'font_size':14, // move to style\n                'max_depth' : 0,\n            },\n            'collapse_level': 0,\n            'stack' : {\n                'type': 'genes',//'events',\n                'showHistogramValues' : false,\n                'showHistogramSummaryValue' : true,\n                'legendTxtSize' : 12,\n                'margin' : 8,\n                'xInitialRightMargin' : 45,\n                'stackHeight' : 120,\n                'stackWidth' : 30,\n                'maxStackHeight': 'max', // ratio -> stack height fixed | max -> largest data = stack height\n                'has_support' : false,\n                'only_support' : false,\n\n            },\n            'sync_coloring': false,\n            'selected_triangle_coloring': 'None',\n            'selected_collapse_uncolored': 'Leaves',\n            'selected_collapse_monocolored': 'Leaves',\n            'colorScale': {'leaf' : null, 'node':null, 'circle': {}},\n            'intercolor': {'leaf' : null, 'node': null, 'circle': {}}\n        }\n\n        if (settings) {\n\n            for(var key in settings) {\n\n                if (key == 'labels_array_leaf'){\n                    var value = settings[key];\n                    this.settings['labels']['leaf'] = new Set(value);\n                }\n                if (key == 'labels_array_node'){\n                    var value = settings[key];\n                    this.settings['labels']['node'] = new Set(value);\n                }\n                if (key == 'colorlabels_array_leaf'){\n                    var value = settings[key];\n                    this.settings['colorlabels']['leaf'] = new Set(value);\n                }\n\n                if (key == 'colorlabels_array_node'){\n                    var value = settings[key];\n                    this.settings['colorlabels']['node'] = new Set(value);\n                }\n\n                else{\n                    var value = settings[key];\n                    this.settings[key] = value;\n                }\n\n\n            }\n\n        }\n\n        this.settings.name = this.settings.name ? this.settings.name : \"Untitled \" + uid_untitle_counter++\n\n        this.uid = null\n        this.input_data = data;\n        this.leaves = []\n\n\n\n        if (from_raw_data){\n            this.uid = uid_model++;\n            this.settings.uid = this.uid;\n            this.data = this.factory(this.parse());\n        }\n        else{\n            this.uid = settings.uid;\n            this.settings.uid = this.uid;\n            this.data = data\n            data.leaves = this.get_leaves(data)\n            this.traverse(data, function(n,c){\n                n.leaves = this.get_leaves(n)\n            })\n            this.set_color_scale('node');\n            this.set_color_scale('leaf');\n        }\n\n        this.data.root = true;\n        this.data.elementS = {}\n        this.data.elementBCN = {}\n        this.rooted = this.data.children.length !== 3\n        this.big_tree = (this.leaves.length > 500)\n\n        // check that histogram data is present and compute\n        if(this.settings.show_histogram && this.data.evolutionaryEvents) {\n            this.settings.has_histogram_data  = true;\n            this.largestGenome =  0;\n            this.largestEvents = 0; // todo\n\n            this.traverse(this.data , function(n,c){\n\n                let g = n.nr_hogs ? n.nr_hogs : n.nr_proteins\n                if (g > this.largestGenome ) {this.largestGenome = g;}\n\n                if (n.evolutionaryEvents){\n\n                    var ga = n.evolutionaryEvents.gained ? n.evolutionaryEvents.gained : 0\n                    var l = n.evolutionaryEvents.lost ? n.evolutionaryEvents.lost : 0\n                    var d = n.evolutionaryEvents.duplications ? n.evolutionaryEvents.duplications : 0\n\n                    let e = ga + l + d\n\n\n                    if (e > this.largestEvents ) {this.largestEvents = e;}\n\n                }\n\n                if (this.settings.stack.has_support){\n\n                    let g_support = n.nr_hogs_support ? n.nr_hogs_support : n.nr_proteins_support\n                    if (g_support > this.largestGenome_support ) {this.largestGenome_support = g_support;}\n\n                    if (n.evolutionaryEvents_support){\n\n\n                        var ga_support = n.evolutionaryEvents_support.gained ? n.evolutionaryEvents_support.gained : 0\n                        var l_support = n.evolutionaryEvents_support.lost ? n.evolutionaryEvents_support.lost : 0\n                        var d_support = n.evolutionaryEvents_support.duplications ? n.evolutionaryEvents_support.duplications : 0\n\n                        let e_support = ga_support + l_support + d_support\n\n                        if (e_support > this.largestEvents_support ) {this.largestEvents_support = e_support;}\n\n                    }\n                }\n\n\n\n            })\n\n\n        }\n\n    }\n\n    set_all_color_scale(){\n        this.set_color_scale('node');\n        this.set_color_scale('leaf');\n        this.set_color_scale('circle');\n    }\n\n    remove_all_color_scale(){\n        this.settings.colorScale ={'leaf' : null, 'node':null, 'circle': {}}\n        this.settings.intercolor ={'leaf' : null, 'node':null, 'circle': {}}\n    }\n\n\n\n    get_name(){\n        return this.settings.name\n    }\n\n    set_name(name){\n        this.settings.name = name\n    }\n\n    traverse(o,func_pre, func_post) {\n\n        if (func_pre){\n            func_pre.apply(this,[o,o[\"children\"]])\n        }\n\n        if(o[\"children\"]){\n\n            for (var c in o[\"children\"] ) {\n\n                var child = o[\"children\"][c]\n\n                child = this.traverse(child, func_pre, func_post)\n\n                if (func_post) {\n                    func_post.apply(this,[child,o])\n                }\n\n\n            }\n\n\n        }\n\n        return o\n\n    }\n\n    set_color_scale(type, api){\n\n\n        var type = (typeof type !== 'undefined') ? type : 'node';\n        var api = (typeof type !== 'undefined') ? api : null;\n\n\n        var colorScaleDomain = false;\n        var colorScaleRange;\n        var number;\n\n\n        if (typeof this != \"undefined\" && this) {\n\n\n            // If categorical do special\n            var acc = this.settings.style.color_accessor[type]\n            var type_acc = this.settings.extended_data_type[acc]\n\n\n            if (acc === null){\n                this.settings.colorScale[type] = null\n                return\n            }\n\n\n            if (type_acc == 'cat'){\n\n                this.settings.colorScale[type] = api.get_color_scale(acc)\n\n\n                //var dom = this.settings.domain_extended_data[acc]\n                //this.settings.colorScale[type] = d3.scaleOrdinal().domain(dom).range(d3.schemePaired);\n                return\n            }\n\n            else if (type_acc == 'color'){\n\n                this.settings.colorScale[type] = null\n                return\n            }\n\n\n\n            number = this.settings.style.number_domain[acc]\n\n\n            if (this.settings.style.color_accessor[type] != null && this.settings.style.color_accessor[type] != 'Topology' ) {\n\n                var ms = this.settings.style;\n\n                var ca = ms.color_accessor[type];\n\n                if (ms.color_extent_max[type][ca] == ms.color_extent_min[type][ca]){\n                    this.settings.intercolor[type] = d3__WEBPACK_IMPORTED_MODULE_0__.interpolate( ms.color_extent_max[type][ca], ms.color_extent_max[type][ca]-1)\n                }else{\n                    this.settings.intercolor[type] = d3__WEBPACK_IMPORTED_MODULE_0__.interpolate( ms.color_extent_max[type][ca], ms.color_extent_min[type][ca])\n                }\n\n\n                colorScaleRange = this.settings.style.color_domain[acc];\n\n            }\n\n            else {\n                this.settings.intercolor[type] = d3__WEBPACK_IMPORTED_MODULE_0__.interpolate(1,0)\n                colorScaleRange = this.settings.style.color_domain[acc];\n            }\n\n\n\n        }\n        else {\n\n            number = 5;\n            colorScaleRange = ['#253494', '#2C7FB8', '#41B6C4', '#C7E9B4', '#FFFFCC']\n            this.settings.intercolor[type] = d3__WEBPACK_IMPORTED_MODULE_0__.interpolate(1, 0);\n        }\n\n\n        switch (number) {\n            case 2:\n                colorScaleDomain = [this.settings.intercolor[type](0),this.settings.intercolor[type](1)]\n                break;\n            case 3:\n                colorScaleDomain = [this.settings.intercolor[type](0),this.settings.intercolor[type](0.5) , this.settings.intercolor[type](1)]\n                break;\n            case 4:\n                colorScaleDomain = [this.settings.intercolor[type](0),this.settings.intercolor[type](0.33),this.settings.intercolor[type](0.66) , this.settings.intercolor[type](1)]\n                break;\n            case 5:\n                colorScaleDomain = [this.settings.intercolor[type](0),this.settings.intercolor[type](0.25) ,this.settings.intercolor[type](0.5) ,this.settings.intercolor[type](0.75) , this.settings.intercolor[type](1)]\n\n        }\n\n\n        this.settings.colorScale[type] = d3__WEBPACK_IMPORTED_MODULE_0__.scaleLinear()\n            .domain(colorScaleDomain)\n            .range(colorScaleRange);\n\n\n\n    }\n\n    traverse_hierarchy(o,func_pre, func_post) {\n\n        var children = o[\"children\"] ? o[\"children\"] : o[\"_children\"]\n\n        if (func_pre){\n            func_pre.apply(this,[o,children])\n        }\n\n        if(children ){\n\n            for (var c in children) {\n\n                var child = children[c]\n\n                child = this.traverse_hierarchy(child, func_pre, func_post)\n\n                if (func_post) {\n                    func_post.apply(this,[child,o])\n                }\n\n\n            }\n\n\n        }\n\n        return o\n\n    }\n\n    set_parent(node,parent){\n        node.parent = parent\n    }\n\n    set_cumulated_length(node, children){\n        if (node.parent) {\n            node.depth = node.parent.depth + 1\n            node.distance_to_root = node.parent.distance_to_root + node.branch_length\n        }\n        else{\n            node.distance_to_root = 0\n        node.depth = 0}\n\n    }\n\n    factory(json){ // todo do one traversal with all in one function\n\n        var p;\n\n        //has_branch_lenght\n        this.settings.has_branch_lenght = false;\n\n        json.children.forEach((child) => {\n            if (typeof child.branch_length != 'undefined') { this.settings.has_branch_lenght = true; }\n        })\n\n        if (this.settings.has_branch_lenght) {\n            this.settings.labels['node'].add('Length')\n            this.settings.labels['leaf'].add('Length')\n            this.settings.colorlabels['node'].add('Length')\n            this.settings.colorlabels['leaf'].add('Length')\n            this.settings.extended_data_type['Length'] = 'num'\n\n            this.settings.style.color_extent_max['node']['Length'] = 0;\n            this.settings.style.color_extent_min['node']['Length'] = 1000000000;\n\n            this.settings.style.color_extent_max['leaf']['Length'] = 0;\n            this.settings.style.color_extent_min['leaf']['Length'] = 1000000000;\n        }\n\n\n        // if branch size is not used put 1\n        if (!this.settings.has_branch_lenght) {\n            p = this.traverse(json, function(n,c){n.branch_length=1})\n            p.branch_length = 0 // root\n        }\n        else{ // sanity check\n            p = this.traverse(json, function(n,c){if (typeof n.branch_length == 'undefined') {n.branch_length=1} })\n            if (typeof p.branch_length == 'undefined') {p.branch_length=1}\n        }\n\n        // set parent attribute\n        p = this.traverse(json, null , this.set_parent)\n\n        // compute cumulated  lenght\n        p = this.traverse(p, this.set_cumulated_length , null)\n\n        this.traverse(p, function(n,c){\n\n            n.extended_informations = {}\n            n.elementS = {}\n            n.elementBCN = {}\n            n.force_label_show = null;\n\n            if(n.branch_length){\n                n.extended_informations['Length'] = n.branch_length;\n                if (this.settings.style.color_extent_max['node']['Length'] < n.branch_length){\n                    this.settings.style.color_extent_max['node']['Length'] = n.branch_length\n                    this.settings.style.color_extent_max['leaf']['Length'] = n.branch_length\n                }\n\n                if (this.settings.style.color_extent_min['node']['Length'] > n.branch_length){\n                    this.settings.style.color_extent_min['node']['Length'] = n.branch_length\n                    this.settings.style.color_extent_min['leaf']['Length'] = n.branch_length\n                }\n            }\n\n            if (typeof c !== 'undefined' && typeof n.name !== 'undefined' && n.name !== \"\" ) {\n                n.extended_informations['Data'] = n.name;\n                this.settings.labels['node'].add('Data')\n                this.settings.labels['leaf'].add('Data')\n                this.settings.extended_data_type['Data'] = 'num'\n\n                if (!isNaN(n.name)){\n\n                    if (!this.settings.colorlabels['node'].has('Data')){\n                        this.settings.colorlabels['node'].add('Data');\n                        this.settings.style.color_extent_max['node']['Data'] = 0;\n                        this.settings.style.color_extent_min['node']['Data'] = 1000000000;\n                    }\n\n                    if (this.settings.style.color_extent_max['node']['Data'] <n.name){\n                        this.settings.style.color_extent_max['node']['Data'] = n.name\n                    }\n\n                    if (this.settings.style.color_extent_min['node']['Data'] > n.name){\n                        this.settings.style.color_extent_min['node']['Data'] = n.name\n                    }\n\n                }\n\n                else {this.settings.extended_data_type['Data'] = 'cat'}\n            }\n\n            if(n.data_nhx && Object.keys(n.data_nhx).length > 0){\n\n                Object.entries(n.data_nhx).forEach(([key, value]) => {\n\n                    this.settings.labels['node'].add(key)\n                    this.settings.labels['leaf'].add(key)\n\n                    this.settings.colorlabels['node'].add(key)\n                    this.settings.colorlabels['leaf'].add(key)\n\n\n                    switch(key){\n                        case 'Ev':\n                            if (value == 'duplication') {\n                                n.duplication = true\n                                this.settings.has_duplications = true;\n                            }\n                            n.extended_informations.events = value\n                            n.extended_informations[key] = value\n                            this.settings.extended_data_type['Ev'] = 'cat'\n                            break;\n                        case 'DD':\n                        case 'D':\n                            if (value == 'Y') {\n                                n.duplication = true\n                                this.settings.has_duplications = true;\n\n                            }\n                            else if (value == 'N'){\n                                n.duplication = false\n                                this.settings.has_duplications = true;\n                            }\n                            n.extended_informations.events = value\n                            n.extended_informations[key] = value\n                            this.settings.extended_data_type['D'] = 'cat'\n                            break;\n                        case 'XB':\n                        case 'B':\n                            this.settings.edge_related_data.push(key)\n                            n.extended_informations[key] = value\n                            this.settings.extended_data_type[key] = 'num'\n                        default:\n                            n.extended_informations[key] = value\n                            this.settings.extended_data_type[key] = 'cat'\n                            break;\n                    }\n                });\n\n\n            }\n            // phyloxml specific attributes\n            for (let attr of [\"taxonomies\", \"sequences\"]) {\n                if (n.hasOwnProperty(attr)) {\n                    Object.entries(n[attr][0]).forEach(([key, value]) => {\n                        n.extended_informations[attr + \"_\" + key] = value;\n                        this.settings.extended_data_type[attr + \"_\" + key] = \"cat\";\n                    });\n                    if (n.name === undefined || n.name === \"\") {\n                        if (attr === \"taxonomies\" && n.taxonomies[0].hasOwnProperty(\"scientific_name\")) {\n                            n.name = n.taxonomies[0].scientific_name;\n                        } else if (attr === \"sequences\" && n.sequence.hasOwnProperty(\"name\")) {\n                            n.name = n.sequences[0].name;\n                        }\n                    }\n                }\n            }\n            if (n.hasOwnProperty(\"date\")){\n                n.extended_informations['date'] = n.date;\n                this.settings.extended_data_type['date'] = \"cat\";\n            }\n\n            if (n.depth > this.settings.tree.max_depth){\n                this.settings.tree.max_depth = n.depth\n            }\n            if (!(n.hasOwnProperty('children'))){\n                this.leaves.push(n)\n                n.correspondingLeaf = {}\n\n            }\n\n            n.leaves = this.get_leaves(n)\n\n        })\n\n        // check the type of all extended data\n        this.traverse(p, function(n,c){\n\n            for (var key in n.extended_informations){\n                if (n.extended_informations.hasOwnProperty(key)) {\n\n                    if (this.settings.extended_data_type[key] === 'num'){\n                        continue\n                    }\n\n                    if (!isNaN(n.extended_informations[key])){\n                        this.settings.extended_data_type[key] = 'num'\n                    }\n\n                }\n            }\n\n        })\n\n\n        this.settings.colorlabels['node'].forEach( (value) => {\n            if (this.settings.extended_data_type[value] === 'num' && value !== 'Topology' ) {\n                this.settings.style.color_extent_max['node'][value] = 0\n                this.settings.style.color_extent_min['node'][value] = 1000000000\n            }\n        });\n\n        this.settings.colorlabels['leaf'].forEach( (value) => {\n            if (this.settings.extended_data_type[value] === 'num' ) {\n                this.settings.style.color_extent_max['leaf'][value] = 0\n                this.settings.style.color_extent_min['leaf'][value] = 1000000000\n            }\n        });\n\n\n        this.traverse(p, function(n,c) {\n            for (var key in n.extended_informations) {\n\n                if (n.extended_informations.hasOwnProperty(key)) {\n\n\n\n                    if (this.settings.extended_data_type[key] === 'num') {\n\n                        // check if min and max are set for node and leaf\n\n                        var val = n.extended_informations[key].toString().indexOf('.') != -1 ? parseFloat(n.extended_informations[key]) : parseInt(n.extended_informations[key])\n\n                        if (this.settings.style.color_extent_max['node'][key] < val) {\n                            this.settings.style.color_extent_max['node'][key] = val\n\n                        }\n\n                        if (this.settings.style.color_extent_min['node'][key] > val) {\n                            this.settings.style.color_extent_min['node'][key] = val\n                        }\n\n                        if (this.settings.style.color_extent_max['leaf'][key] < val) {\n                            this.settings.style.color_extent_max['leaf'][key] = val\n                        }\n\n                        if (this.settings.style.color_extent_min['leaf'][key] > val) {\n                            this.settings.style.color_extent_min['leaf'][key] = val\n                        }\n\n                    }\n\n                }\n            }\n\n        })\n\n\n\n        this.settings.suggestions = [] // autocomplete name\n        this.traverse(json, function(n,c){\n\n            if (n.name !== ''){this.settings.suggestions.push(n.name)}}) //todo add id also and ncBI and more + check empty cfucntion\n\n        return p\n    }\n\n    build_hierarchy_mockup(){\n        return d3__WEBPACK_IMPORTED_MODULE_0__.hierarchy(this.data, d => d.children );\n    }\n\n    parse(){\n\n        if (this.settings.data_type === \"newick\") {\n            return biojs_io_newick__WEBPACK_IMPORTED_MODULE_2__.parse_newick(this.input_data);\n        }\n\n        else if (this.settings.data_type === \"nhx\") {\n            return parse_nhx(this.input_data);\n        }\n\n        else if (this.settings.data_type === \"json\") {\n            return this.input_data\n        }\n        else if (this.settings.data_type === \"phyloxml\") {\n            let phylogenies = phyloXml.parse(this.input_data);\n            if (phylogenies === undefined || phylogenies.length === 0){\n                console.error(\"No phylogenies found\");\n                return {};\n            } else if (phylogenies.length > 1) {\n                console.log(\"dataset contains more than one phylogenies: \"+phylogenies.length + \" Will only use the first one\");\n            }\n            return phylogenies[0].children[0];  // return toplevel clade which is returned as children[0].\n        }\n    }\n\n    collapse(data, action){\n        if (!data.children){return}\n        if (action) {data.collapse = true}\n        else if (action == false){data.collapse = false}\n        else{data.collapse ? data.collapse = false : data.collapse = true;}\n\n    }\n\n    toggle_show_label(data){\n        data.force_label_show ||  data.force_label_show == null ? data.force_label_show = false : data.force_label_show = true;\n    }\n\n    collapseAll(data, action){\n        if (action) {\n            this.traverse(data, (n,c) => {\n                this.collapse(n, true)\n                //n.collapse = true\n            } , null)}\n        else if (action == false){\n            this.traverse(data, (n,c) => {\n                this.collapse(n, false)\n                //n.collapse = false\n            } , null)}\n\n\n    }\n\n    get_all_collapse(data){\n\n        var collapsed = []\n\n        this.traverse(data, (n,c) => {if (n.collapse){\n                collapsed.push(n)\n            }}, null)\n\n        return collapsed\n\n    }\n\n    apply_collapse_to_list(collapsed){\n        this.traverse(this.data, (n,c) => {\n            if (collapsed.includes(n)){\n                this.collapse(n, true)\n            }\n            else{\n                this.collapse(n, false)\n            }\n        } , null)\n    }\n\n    swap_subtrees(data){\n         var e = data.children.pop()\n        data.children.unshift(e)\n        data.leaves = this.get_leaves(data)\n    }\n\n    unswap_subtrees(data){\n        var e = data.children.shift()\n        data.children.push(e)\n        data.leaves = this.get_leaves(data)\n\n    }\n\n    reroot(data){\n\n        // extract meta data (zoom)\n        var meta = this.zoom;\n\n        // create new root r\n\n        var root = {\"children\": [], \"name\": \"\", \"branch_length\": 0, \"extended_informations\": {}}\n\n\n        for (var key in data.extended_informations) {\n\n\n            if (this.settings.edge_related_data.includes(key)) {\n                root.extended_informations[key] =  data.extended_informations[key]\n            }\n\n            else{\n                root.extended_informations[key] =  null\n            }\n\n        }\n\n        // source and target node of the clicked edges\n        var parent = data.parent\n        var child = data\n\n        // insert new root node between target and source and connect\n        root.children.push(child)\n        parent.children.push(root)\n        this.set_parent(child, root )\n        this.set_parent(root, parent )\n        const index = parent.children.indexOf(child);\n        if (index > -1) {\n            parent.children.splice(index, 1);\n        }\n\n        // ajust distance now that distance target/source is splitted in two\n        var old_distance = child.branch_length\n\n        child.branch_length = old_distance/2\n        child.extended_informations['Length'] = old_distance/2\n\n        parent.branch_length_before_reverse = parent.branch_length\n        parent.branch_length = old_distance /2\n        parent.extended_informations['Length'] = old_distance/2\n\n        // Until we reach the old root reverse child/parent order\n        var child = root\n        var stack = []\n\n        while (parent.root != true) {\n\n            stack.push([parent,child])\n\n            child = parent\n            parent = parent.parent\n\n            parent.values_before_reverse = {}\n            parent.branch_length_before_reverse = parent.branch_length\n\n            for (var value of this.settings.edge_related_data) {\n\n                parent.values_before_reverse[value] = parent.extended_informations[value]\n\n                if (value=== 'Length'){\n                    parent.branch_length = child.branch_length_before_reverse || child.branch_length;\n                    parent.extended_informations['Length'] = parent.branch_length;\n\n                }\n                else{\n                    if ( child.values_before_reverse && value in child.values_before_reverse){\n                        parent.extended_informations[value] = child.values_before_reverse[value]\n                    }\n                    else{\n                        parent.extended_informations[value] = child.extended_informations[value]\n                        child.extended_informations[value] = null\n                    }\n\n                }\n\n\n\n            }\n\n\n        }\n        stack.push([parent,child])\n        for (var e in stack){\n            var p = stack[e][0]\n            var c = stack[e][1]\n\n            this.reverse_order(p,c)\n\n        }\n\n        // Remove old root\n\n        var old_root = parent\n        var leading_branch = parent.parent\n\n\n\n        if (old_root.children.length == 1){\n\n            const ce = leading_branch.children.indexOf(old_root);\n            if (ce > -1) {\n                leading_branch.children.splice(ce, 1);\n            }\n\n            var i = 0,len = old_root.children.length;\n            while (i < len) {\n                let c = old_root.children[i]\n                c.parent = leading_branch\n                leading_branch.children.push(c)\n                i++\n            }\n\n            old_root = null\n\n\n\n        }\n\n        // For multifurcation we need to keep the root\n        else {\n            old_root.root = false\n            old_root.branch_length = leading_branch.branch_length\n            parent.extended_informations['Length'] = leading_branch.branch_length\n        }\n\n\n        for (var key of this.settings.edge_related_data) {\n\n            for (var childy of root.children) {\n\n                childy.extended_informations[key] =  root.extended_informations[key]\n\n            }\n\n            root.extended_informations[key] =  null\n        }\n\n\n        // configure new root\n        root.zoom = meta\n        this.data = root;\n        this.data.root = true;\n\n        root.leaves = this.get_leaves(root)\n\n\n        this.traverse(root, function(n,c){\n            n.leaves = this.get_leaves(n)\n            n.values_before_reverse = {}\n            n.branch_length_before_reverse = undefined\n        })\n\n\n\n    }\n\n    trim(branch){\n\n        // source and target node of the clicked edges\n        var parent = branch.parent\n        var child = branch\n\n        var untrim_data = {\n            \"parent\" : null,\n            \"floating\" : null,\n            \"untrim_data\" : null,\n            \"index\": null,\n            \"root_mode\": false,\n        }\n\n\n        if (parent.children.length > 2) {\n            untrim_data.index = this.detach_child(parent,child)\n\n            untrim_data.parent = parent;\n            untrim_data.floating = false;\n            untrim_data.child =  child;\n\n            return untrim_data;\n        }\n\n        else{\n\n            if (typeof parent.parent == 'undefined'){ // parent is root\n                untrim_data.root_mode = true;\n\n                var sibling = parent.children[0] == child ? parent.children[1] : parent.children[0]\n                untrim_data.index = this.detach_child(parent, sibling)\n\n                this.data = sibling;\n\n                untrim_data.parent = null;\n                untrim_data.floating = parent;\n                untrim_data.child =  sibling;\n\n                return untrim_data;\n\n            }\n\n            else{\n\n                this.detach_child(parent.parent, parent)\n                var sibling = parent.children[0] == child ? parent.children[1] : parent.children[0]\n                untrim_data.index = this.detach_child(parent, sibling)\n                this.attach_child(parent.parent, sibling)\n\n                untrim_data.parent = parent.parent;\n                untrim_data.floating = parent;\n                untrim_data.child =  sibling;\n\n                return untrim_data;\n\n            }\n\n\n        }\n\n    }\n\n    untrim(parent, floating, child, index, root_mode){\n\n        if (floating != false){\n            if (root_mode){\n                this.data = floating\n                this.attach_child(floating,child, index)\n\n            }else{\n                this.detach_child(parent,child)\n                this.attach_child(parent,floating)\n                this.attach_child(floating,child, index)\n            }\n\n        }\n        else {\n            this.attach_child(parent,child, index)\n        }\n    }\n\n    detach_child(parent, child){\n        var index = parent.children.indexOf(child);\n        if (index > -1) {\n            parent.children.splice(index, 1);\n        }\n        return index\n    }\n\n    attach_child(parent,child_to_adopt, index){\n\n        if (typeof index !== 'undefined') {\n            parent.children.splice( index, 0, child_to_adopt );\n            child_to_adopt.parent = parent;\n\n        } else {\n            parent.children.push(child_to_adopt);\n            child_to_adopt.parent = parent;\n        }\n\n\n    }\n\n    interleave_node(parent, to_insert,child){\n        this.detach_child(parent, child)\n        this.attach_child(parent,to_insert)\n        this.attach_child(to_insert, child)\n    }\n\n    store_zoomTransform(zoom){\n\n        this.zoom = {\n            \"k\":zoom.k,\n            \"x\":zoom.x,\n            \"y\":zoom.y,\n        };\n    }\n\n    /**\n     Description:\n     Creates list of leaves of each node in subtree rooted at v\n\n     Note:\n     Difference between deep leaf list and leaves in:\n     (A:0.1,B:0.2,(C:0.3,D:0.4):0.5);\n     - Root has leaves: A, B, C and D (terminal leaves)\n     - Root has deep leaves: A, B, C, D and CD (terminal leaves + intermediate leaves)\n     */\n    createDeepLeafList(filter) {\n\n        function is_leaf(str) {\n            return !str.includes(\"|__|\");\n        }\n\n         var build_deepLeafList = function(child, node){\n\n             if ( child.hasOwnProperty('children') ){\n                 var dp = child.deepLeafList.filter(is_leaf).sort()\n                 if (!dp.every((e) => e === '')){\n                     child.deepLeafList.push(dp.join('|__|'));\n                 }\n\n             }\n\n             node.deepLeafList = node.deepLeafList.concat(child.deepLeafList)\n        }\n\n        var build_deepLeafLeaves = function(node,children){\n\n             if (!(node.hasOwnProperty('children') )){\n\n                 if (typeof filter != 'undefined') {\n                     if (filter.includes(node.name)){\n                         node.deepLeafList = [node.name]\n                     }\n                     else{\n                         node.deepLeafList = []\n                     }\n\n                 }\n                 else{\n                     node.deepLeafList = [node.name]\n                 }\n\n             }\n             else {\n                 node.deepLeafList = []\n             }\n\n\n        }\n\n        this.traverse(this.data, build_deepLeafLeaves, build_deepLeafList)\n\n    }\n\n    createMinHash(){\n\n        var assign_hash = function(node,children){\n\n            node.min_hash = new minhashjs__WEBPACK_IMPORTED_MODULE_1__.MinHash.MinHash()\n            node.deepLeafList.map(function(w) { node.min_hash.update(w) });\n        }\n\n        this.traverse(this.data, assign_hash, null)\n    }\n\n    removeMinHash(){\n\n        var remove_hash = function(node,children){\n\n            node.min_hash = null\n        }\n\n        this.traverse(this.data, remove_hash, null)\n\n    }\n\n    reverse_order(parent,child) {\n\n        child.children.push(parent)\n        parent.parent =child\n\n        const b = parent.children.indexOf(child);\n        if (b > -1) {\n            parent.children.splice(b, 1);\n        }\n\n    }\n\n    get_leaves(node){\n\n\n        var l = []\n\n        this.traverse(node, function(n,c){\n            if (!(n.hasOwnProperty('children'))){\n                l.push(n)\n            }\n\n\n    })\n        return l\n    }\n\n    remove_circularity(){ // safe my model\n        var data = Object.assign({}, this.data);\n\n        this.traverse(data, function(n,c){\n            n.parent=null;\n            n.leaves=null;\n            n.correspondingLeaf = {}\n            n.elementBCN = null})\n\n        return data\n    }\n\n    remove_circularity_only_parent_and_leaves(){ // safe my model\n        var data = Object.assign({}, this.data);\n\n        this.traverse(data, function(n,c){\n            n.parent=null;\n            n.leaves=null;\n        })\n\n        return data\n    }\n\n    add_circularity_back(){\n\n        this.data.leaves = this.get_leaves(this.data)\n\n        this.traverse(this.data, function(n,c){n.leaves = this.get_leaves(n)}, this.set_parent)\n\n\n    }\n\n    add_meta_leaves(meta, headers, api, reference){\n\n        // headers: column_name -> type\n\n        Object.keys(headers).forEach(item => {\n\n\n            if (item != reference || item != 'Length' ) {\n\n                this.settings.extended_data_type[item] = headers[item]\n                this.settings.domain_extended_data[item] = []\n                this.settings.labels['leaf'].add(item)\n                this.settings.colorlabels['leaf'].add(item)\n\n                if (headers[item] == 'num'){\n                    this.settings.style.color_extent_max['leaf'][item] = 0\n                    this.settings.style.color_extent_min['leaf'][item] = 100000\n                }\n            }\n\n        })\n\n            this.get_leaves(this.data).forEach(d => {\n            if (d.name in meta){\n\n                Object.entries(meta[d.name]).forEach(item => {\n                    if (item[0] != reference){\n\n                        d.extended_informations[item[0]]= item[1]\n\n                        if (this.settings.extended_data_type[item[0]] == 'num' && !isNaN(item[1])) {\n\n                            item[1] = item[1].toString().indexOf('.') != -1 ? parseFloat(item[1]) : parseInt(item[1])\n\n                            if (this.settings.style.color_extent_max['leaf'][item[0]] < item[1]) {\n                                this.settings.style.color_extent_max['leaf'][item[0]] = item[1]\n                            }\n\n                            if (this.settings.style.color_extent_min['leaf'][item[0]] > item[1]) {\n                                this.settings.style.color_extent_min['leaf'][item[0]] = item[1]\n                            }\n\n                        }\n\n                        if (this.settings.extended_data_type[item[0]] == 'cat'){\n\n                            var cs = api.get_color_scale(item[0])\n                            cs.add_value_to_map(item[1])\n\n                            this.settings.domain_extended_data[item[0]].push(item[1])\n                        }\n\n                    }\n\n                })\n\n            }\n\n        })\n\n\n        Object.keys(headers).forEach(item => {\n            if (item != reference || item != 'Length' ) {\n\n\n                if (headers[item] == 'cat'){\n                    api.get_color_scale(item).update()\n\n                }\n            }\n\n        })\n\n\n\n    }\n\n    add_meta_nodes(meta, headers, api, reference){\n\n\n        Object.keys(headers).forEach(item => {\n            if (item != reference|| item != 'Length' ) {\n                this.settings.extended_data_type[item] = headers[item]\n                this.settings.domain_extended_data[item] = []\n                this.settings.labels['node'].add(item)\n                this.settings.colorlabels['node'].add(item)\n\n                if (headers[item] == 'num'){\n                    this.settings.style.color_extent_max['node'][item] = 0\n                    this.settings.style.color_extent_min['node'][item] = 100000\n                }\n            }\n\n        })\n\n        this.traverse(this.data, function(n,c){\n\n            var name_value = n.name in meta ? n.name : n.extended_informations['Data'] in meta ? n.extended_informations['Data'] : false\n\n            if (name_value){\n\n                Object.entries(meta[name_value]).forEach(item => {\n\n                    if (item[0] != reference){\n                        n.extended_informations[item[0]]= item[1]\n\n                        if (this.settings.extended_data_type[item[0]] == 'cat'){\n\n                            var cs = api.get_color_scale(item[0])\n                            cs.add_value_to_map(item[1])\n\n                        }\n\n                        else if (this.settings.extended_data_type[item[0]] == 'num' && !isNaN(item[1]) ) {\n\n                            item[1] = item[1].toString().indexOf('.') != -1 ? parseFloat(item[1]) : parseInt(item[1])\n\n                            if (this.settings.style.color_extent_max['node'][item[0]] < item[1]) {\n                                this.settings.style.color_extent_max['node'][item[0]] = item[1]\n                            }\n\n                            if (this.settings.style.color_extent_min['node'][item[0]] > item[1]) {\n                                this.settings.style.color_extent_min['node'][item[0]] = item[1]\n                            }\n\n                        }\n                    }\n                })\n\n            }\n        })\n\n        Object.keys(headers).forEach(item => {\n\n            if (item != reference || item != 'Length' ) {\n\n\n                if (headers[item] == 'cat'){\n                    api.get_color_scale(item).update()\n\n                }\n            }\n\n        })\n    }\n\n    get_node_by_leafset(lset){\n\n        function setsAreEqual(a, b) {\n            if (a.size !== b.size) {\n                return false;\n            }\n\n            return Array.from(a).every(element => {\n                return b.has(element);\n            });\n        }\n\n        lset = new Set(lset.map(leaf => leaf.toString()))\n\n        var target = false\n\n\n        var check = function(node,children){\n\n            var nl = new Set(node.leaves.map(leaf => leaf.name.replaceAll(\"'\", '').toString()))\n\n            if ( setsAreEqual(nl,lset)){\n                target = node\n            }\n\n        }\n\n        this.traverse(this.data, check, null)\n\n        return target\n    }\n\n};\n\n//# sourceURL=webpack://PhyloIO/./src/model.js?");
+
+/***/ }),
+
+/***/ "./src/phyloxml.js":
+/*!*************************!*\
+  !*** ./src/phyloxml.js ***!
+  \*************************/
+/***/ ((module, __unused_webpack_exports, __webpack_require__) => {
+
+eval("/**\n *  Copyright (C) 2019 Christian M. Zmasek\n *  Copyright (C) 2019 J. Craig Venter Institute\n *  All rights reserved\n *\n *  This library is free software; you can redistribute it and/or\n *  modify it under the terms of the GNU Lesser General Public\n *  License as published by the Free Software Foundation; either\n *  version 2.1 of the License, or (at your option) any later version.\n *\n *  This library is distributed in the hope that it will be useful,\n *  but WITHOUT ANY WARRANTY; without even the implied warranty of\n *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\n *  Lesser General Public License for more details.\n *\n *  You should have received a copy of the GNU Lesser General Public\n *  License along with this library; if not, write to the Free Software\n *  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\n *\n *  Created by czmasek on 7/7/2016.\n */\n\n// v 1.0.0\n// 2019-05-16\n//\n// phyloxml.js is a JavaScript program for reading (SAX style parser)\n// and writing phylogenetic trees in phyloXML format.\n//\n// phyloXML website: http://www.phyloxml.org/\n//\n// Availability:\n//   https://github.com/cmzmasek/phyloxml-js\n//   https://www.npmjs.com/package/phyloxml\n//\n// Dependencies:\n//  sax.js (1.2.4): https://www.npmjs.com/package/sax/v/1.2.4\n//\n//\n// Example:\n// This basic example shows how to parse a phyloXML formatted String into to a\n// object representing a phylogenetic tree. Followed by printing some elements\n// and then converting the object back to a phyloXML formatted String.\n//\n// Change './phyloxml' to 'phyloxml' if you use this code outside of this package\n//\n// var phyloXml = require('./phyloxml').phyloXml;\n//\n// phlyoXmlFormattedString = '<phyloxml xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" ' +\n//     'xmlns=\"http://www.phyloxml.org\" ' +\n//     'xsi:schemaLocation=\"http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd\">' +\n//     '<phylogeny rooted=\"true\" rerootable=\"false\">' +\n//     '<clade><branch_length>0.2</branch_length>' +\n//     '<clade><branch_length>0.4</branch_length><name>A</name></clade>' +\n//     '<clade><branch_length>0.6</branch_length><name>B</name></clade>' +\n//     '</clade>' +\n//     '</phylogeny>' +\n//     '</phyloxml>';\n//\n// var phylogeneticTree = phyloXml.parse(phlyoXmlFormattedString, {trim: true, normalize: true})[0];\n//\n// console.log('Root branch length  : ' + phylogeneticTree.children[0].branch_length);\n// console.log('Node A name         : ' + phylogeneticTree.children[0].children[0].name);\n// console.log('Node A branch length: ' + phylogeneticTree.children[0].children[0].branch_length);\n// console.log('Node B name         : ' + phylogeneticTree.children[0].children[1].name);\n// console.log('Node B branch length: ' + phylogeneticTree.children[0].children[1].branch_length);\n//\n// console.log('Entire tree in phyloXML format:');\n// console.log(phyloXml.toPhyloXML(phylogeneticTree, 4));\n//\n//\n// Synchronous parsing of phyloXML-formatted String:\n//\n// var px = require('./phyloxml').phyloXml;\n// var phys = px.parse(phyloxmlText, {trim: true, normalize: true});\n// console.log(px.toPhyloXML(phys[0], 6));\n//\n//\n// Asynchronous parsing of phyloXML-formatted Stream:\n//\n// var fs = require('fs');\n// var px = require('./phyloxml').phyloXml;\n// var stream = fs.createReadStream(xmlFile, {encoding: 'utf8'});\n// px.parseAsync(stream, {trim: true, normalize: true});\n\n\n(function phyloXml() {\n\n    \"use strict\";\n\n    var sax = null;\n    if ( true && module.exports && !__webpack_require__.g.xmldocAssumeBrowser) {\n        // Being used in a Node-like environment\n        sax = __webpack_require__(/*! sax */ \"./node_modules/sax/lib/sax.js\");\n    }\n    else if (typeof window !== \"undefined\") {\n        // Attached to the Window object in a browser\n        sax = window.sax;\n        if (!sax) {\n            throw new Error(\"Expected sax to be defined. Make sure you are including sax.js before this file.\");\n        }\n    }\n    else {\n        sax = this.sax;\n        if (!sax) {\n            throw new Error(\"Expected sax to be defined. Make sure you are including sax.js before this file.\");\n        }\n    }\n\n    // --------------------------------------------------------------\n    // phyloXML constants\n    // --------------------------------------------------------------\n\n    // Accession\n    var ACCESSION = 'accession';\n    var ACCESSION_SOURCE_ATTR = 'source';\n    var ACCESSION_COMMENT_ATTR = 'comment';\n\n    // Annotation\n    var ANNOTATION = 'annotation';\n    var ANNOTATION_REF_ATTR = 'ref';\n    var ANNOTATION_SOURCE_ATTR = 'source';\n    var ANNOTATION_EVIDENCE_ATTR = 'evidence';\n    var ANNOTATION_TYPE_ATTR = 'type';\n    var ANNOTATION_DESC = 'desc';\n\n    // Clade\n    var CLADE = 'clade';\n    var CLADE_BRANCH_LENGTH = 'branch_length';\n    var CLADE_ID_SOURCE_ATTR = 'id_source';\n    var CLADE_COLLAPSE_ATTR = 'collapse';\n    var CLADE_NAME = 'name';\n    var CLADE_WIDTH = 'width';\n\n    // Clade Relation\n    var CLADE_RELATION = 'clade_relation';\n    var CLADE_RELATION_DISTANCE_ATTR = 'distance';\n    var CLADE_RELATION_ID_REF_0_ATTR = 'id_ref_0';\n    var CLADE_RELATION_ID_REF_1_ATTR = 'id_ref_1';\n    var CLADE_RELATION_TYPE_ATTR = 'type';\n\n    // Sequence Relation\n    var SEQUENCE_RELATION = 'sequence_relation';\n    var SEQUENCE_RELATION_DISTANCE_ATTR = 'distance';\n    var SEQUENCE_RELATION_ID_REF_0_ATTR = 'id_ref_0';\n    var SEQUENCE_RELATION_ID_REF_1_ATTR = 'id_ref_1';\n    var SEQUENCE_RELATION_TYPE_ATTR = 'type';\n\n    // Color\n    var COLOR = 'color';\n    var COLOR_RED = 'red';\n    var COLOR_GREEN = 'green';\n    var COLOR_BLUE = 'blue';\n    var COLOR_ALPHA = 'alpha';\n\n    // Confidence\n    var CONFIDENCE = 'confidence';\n    var CONFIDENCE_TYPE_ATTR = 'type';\n    var CONFIDENCE_STDDEV_ATTR = 'stddev';\n    var CONFIDENCES = 'confidences';\n\n    // Cross References\n    var CROSS_REFERENCES = 'cross_references';\n\n    // Date\n    var DATE = 'date';\n    var DATE_UNIT_ATTR = 'unit';\n    var DATE_DESC = 'desc';\n    var DATE_VALUE = 'value';\n    var DATE_MINIMUM = 'minimum';\n    var DATE_MAXIMUM = 'maximum';\n\n    // Distribution\n    var DISTRIBUTION = 'distribution';\n    var DISTRIBUTION_DESC = 'desc';\n\n    // Domain Architecture\n    var DOMAIN_ARCHITECTURE = 'domain_architecture';\n    var DOMAIN_ARCHITECTURE_LENGTH_ATTR = 'length';\n\n    // Events\n    var EVENTS = 'events';\n    var EVENTS_TYPE = 'type';\n    var EVENTS_DUPLICATIONS = 'duplications';\n    var EVENTS_SPECIATIONS = 'speciations';\n    var EVENTS_LOSSES = 'losses';\n\n    // Id\n    var ID = 'id';\n    var ID_PROVIDER_ATTR = 'provider';\n\n    // Mol Seq\n    var MOLSEQ = 'mol_seq';\n    var MOLSEQ_IS_ALIGNED_ATTR = 'is_aligned';\n\n    // Phylogeny\n    var PHYLOGENY = 'phylogeny';\n\n    // Phyloxml\n    var PHYLOXML = 'phyloxml';\n\n    // Point\n    var POINT = 'point';\n    var POINT_ALT_UNIT_ATTR = 'alt_unit';\n    var POINT_GEODETIC_DATUM_ATTR = 'geodetic_datum';\n    var POINT_LAT = 'lat';\n    var POINT_LONG = 'long';\n    var POINT_ALT = 'alt';\n\n    // Property\n    var PROPERTY = 'property';\n    var PROPERTY_REF_ATTR = 'ref';\n    var PROPERTY_ID_REF_ATTR = 'id_ref';\n    var PROPERTY_UNIT_ATTR = 'unit';\n    var PROPERTY_DATATYPE_ATTR = 'datatype';\n    var PROPERTY_APPLIES_TO_ATTR = 'applies_to';\n    var PROPERTIES = 'properties';\n\n    // Protein Domain\n    var PROTEINDOMAIN = 'domain';\n    var PROTEINDOMAIN_FROM_ATTR = 'from';\n    var PROTEINDOMAIN_TO_ATTR = 'to';\n    var PROTEINDOMAIN_CONFIDENCE_ATTR = 'confidence';\n    var PROTEINDOMAIN_ID_ATTR = 'id';\n\n    // Reference\n    var REFERENCE = 'reference';\n    var REFERENCE_DOI_ATTR = 'doi';\n    var REFERENCE_DESC = 'desc';\n\n    // Sequence\n    var SEQUENCE = 'sequence';\n    var SEQUENCE_ID_SOURCE_ATTR = 'id_source';\n    var SEQUENCE_ID_REF_ATTR = 'id_ref';\n    var SEQUENCE_TYPE_ATTR = 'type';\n    var SEQUENCE_SYMBOL = 'symbol';\n    var SEQUENCE_NAME = 'name';\n    var SEQUENCE_GENE_NAME = 'gene_name';\n    var SEQUENCE_LOCATION = 'location';\n    var SEQUENCES = 'sequences';\n\n    // Taxonomy\n    var TAXONOMY = 'taxonomy';\n    var TAXONOMY_ID_SOURCE_ATTR = 'id_source';\n    var TAXONOMY_CODE = 'code';\n    var TAXONOMY_SCIENTIFIC_NAME = 'scientific_name';\n    var TAXONOMY_AUTHORITY = 'authority';\n    var TAXONOMY_COMMON_NAME = 'common_name';\n    var TAXONOMY_SYNONYM = 'synonym';\n    var TAXONOMY_RANK = 'rank';\n    var TAXONOMIES = 'taxonomies';\n    var TAXONOMY_SYNONYMS = 'synonyms';\n\n    // Uri\n    var URI = 'uri';\n    var URI_TYPE_ATTR = 'type';\n    var URI_DESC_ATTR = 'desc';\n\n    // Phylogeny\n    var PHYLOGENY_ROOTED_ATTR = 'rooted';\n    var PHYLOGENY_REROOTABLE_ATTR = 'rerootable';\n    var PHYLOGENY_BRANCH_LENGTH_UNIT_ATTR = 'branch_length_unit';\n    var PHYLOGENY_TYPE_ATTR = 'type';\n    var PHYLOGENY_NAME = 'name';\n    var PHYLOGENY_DESCRIPTION = 'description';\n    var PHYLOGENY_DATE = 'date';\n\n    // Simple_Characteristics (to be deprecated!)\n    var X_SIMPLE_CHARACTERISTICS = 'Simple_Characteristics';\n    var X_SIMPLE_CHARACTERISTIC_COUNTRY = 'Country';\n    var X_SIMPLE_CHARACTERISTIC_YEAR = 'Year';\n    var X_SIMPLE_CHARACTERISTIC_HOST = 'Host';\n    var X_SIMPLE_CHARACTERISTIC_HA = 'HA';\n    var X_SIMPLE_CHARACTERISTIC_NA = 'NA';\n\n    // appType (special for Virus BRC)\n    var APPTYPE = 'flu_type';\n\n    // Unknown source, id, confidence type:\n    var UNKNOWN = 'unknown';\n\n    // --------------------------------------------------------------\n    // Instance variables\n    // --------------------------------------------------------------\n    var _phylogenies = null;\n    var _phylogeny = null;\n    var _cladeStack = null;\n    var _tagStack = null;\n    var _objectStack = null;\n\n    // --------------------------------------------------------------\n    // Others\n    // --------------------------------------------------------------\n    var PROPERTY_REF_RE = /[a-zA-Z0-9_]+:\\S+/;\n    var PROPERTY_UNIT_RE = /[a-zA-Z0-9_]+:\\S+/;\n    var PROPERTY_DATATYPE_RE = /xsd:\\S+/;\n\n    // --------------------------------------------------------------\n    // Functions for object creation\n    // --------------------------------------------------------------\n    function newAccession(tag) {\n        var parent = _tagStack.get(1);\n        if (!(parent === SEQUENCE || parent === CROSS_REFERENCES)) {\n            throw new PhyloXmlError(\"found accession outside of sequence or cross-references\");\n        }\n        var acc = {};\n        acc.value = null;\n        acc.source = getAttribute(ACCESSION_SOURCE_ATTR, tag.attributes);\n        acc.comment = getAttribute(ACCESSION_COMMENT_ATTR, tag.attributes);\n        if (!acc.source) {\n            acc.source = UNKNOWN;\n        }\n        if (parent === SEQUENCE) {\n            getCurrentObject().accession = acc;\n        }\n        else {\n            addToArrayInCurrentObjectUnnamed(acc);\n        }\n        _objectStack.push(acc);\n    }\n\n    function newAnnotation(tag) {\n        var parent = _tagStack.get(1);\n        if (parent != SEQUENCE) {\n            throw new PhyloXmlError(\"found annotation outside of sequence\");\n        }\n        var ann = {};\n        ann.evidence = getAttribute(ANNOTATION_EVIDENCE_ATTR, tag.attributes);\n        ann.ref = getAttribute(ANNOTATION_REF_ATTR, tag.attributes);\n        ann.source = getAttribute(ANNOTATION_SOURCE_ATTR, tag.attributes);\n        ann.type = getAttribute(ANNOTATION_TYPE_ATTR, tag.attributes);\n        addToArrayInCurrentObject('annotations', ann);\n        _objectStack.push(ann);\n    }\n\n    function newBranchColor() {\n        var parent = _tagStack.get(1);\n        if (parent != CLADE) {\n            throw new PhyloXmlError(\"found branch color outside of clade\");\n        }\n        var col = {};\n        col.red = 0;\n        col.green = 0;\n        col.blue = 0;\n        getCurrentObject().color = col;\n        _objectStack.push(col);\n    }\n\n    function newClade(tag) {\n        var newClade = {};\n        newClade.branch_length = getAttributeAsFloat(CLADE_BRANCH_LENGTH, tag.attributes);\n        newClade.collapse = getAttributeAsBoolean(CLADE_COLLAPSE_ATTR, tag.attributes);\n        if (CLADE_ID_SOURCE_ATTR in tag.attributes) {\n            newClade.id_source = tag.attributes[CLADE_ID_SOURCE_ATTR];\n        }\n        if (_phylogeny === null) {\n            var phylogeny_data = _objectStack.pop();\n            if (!_objectStack.isEmpty()) {\n                throw new PhyloXmlError('severe phyloXML format error');\n            }\n            _phylogeny = phylogeny_data;\n            _phylogeny.children = [newClade];\n        }\n        else {\n            var currClade = getCurrentClade();\n            if (currClade.children === undefined) {\n                currClade.children = [newClade];\n            }\n            else {\n                currClade.children.push(newClade);\n            }\n        }\n        _cladeStack.push(newClade);\n        _objectStack.push(newClade);\n    }\n\n    function newCladeRelation(tag) {\n        var cr = {};\n        cr.distance = getAttributeAsFloat(CLADE_RELATION_DISTANCE_ATTR, tag.attributes);\n        cr.id_ref_0 = getAttribute(CLADE_RELATION_ID_REF_0_ATTR, tag.attributes);\n        cr.id_ref_1 = getAttribute(CLADE_RELATION_ID_REF_1_ATTR, tag.attributes);\n        cr.type = getAttribute(CLADE_RELATION_TYPE_ATTR, tag.attributes);\n        addToArrayInCurrentObject('clade_relations', cr);\n        _objectStack.push(cr);\n    }\n\n    function newSequenceRelation(tag) {\n        var sr = {};\n        sr.distance = getAttributeAsFloat(SEQUENCE_RELATION_DISTANCE_ATTR, tag.attributes);\n        sr.id_ref_0 = getAttribute(SEQUENCE_RELATION_ID_REF_0_ATTR, tag.attributes);\n        sr.id_ref_1 = getAttribute(SEQUENCE_RELATION_ID_REF_1_ATTR, tag.attributes);\n        sr.type = getAttribute(SEQUENCE_RELATION_TYPE_ATTR, tag.attributes);\n        addToArrayInCurrentObject('sequence_relations', sr);\n        _objectStack.push(sr);\n    }\n\n    function newConfidence(tag) {\n        var conf = {};\n        conf.value = null;\n        conf.type = getAttribute(CONFIDENCE_TYPE_ATTR, tag.attributes);\n        conf.stddev = getAttributeAsFloat(CONFIDENCE_STDDEV_ATTR, tag.attributes);\n        var parent = _tagStack.get(1);\n        if (parent === CLADE || parent === PHYLOGENY) {\n            addToArrayInCurrentObject(CONFIDENCES, conf);\n        }\n        else if (parent === ANNOTATION || parent === EVENTS || parent === CLADE_RELATION || parent === SEQUENCE_RELATION) {\n            getCurrentObject().confidence = conf;\n        }\n        _objectStack.push(conf);\n    }\n\n    function newCrossReferences() {\n        var parent = _tagStack.get(1);\n        if (parent != SEQUENCE) {\n            throw new PhyloXmlError(\"found cross-reference outside of sequence\");\n        }\n        var xrefs = [];\n        getCurrentObject().cross_references = xrefs;\n        _objectStack.push(xrefs);\n    }\n\n    function newDate(tag) {\n        var date = {};\n        date.unit = getAttribute(DATE_UNIT_ATTR, tag.attributes);\n        getCurrentObject().date = date;\n        _objectStack.push(date);\n    }\n\n    function newDistribution(tag) {\n        var dist = {};\n        dist.desc = null;\n        dist.unit = getAttribute(DATE_UNIT_ATTR, tag.attributes);\n        addToArrayInCurrentObject('distributions', dist);\n        _objectStack.push(dist);\n    }\n\n    function newDomainArchitecture(tag) {\n        var da = {};\n        da.domains = null;\n        da.length = getAttributeAsInt(DOMAIN_ARCHITECTURE_LENGTH_ATTR, tag.attributes);\n        getCurrentObject().domain_architecture = da;\n        _objectStack.push(da);\n    }\n\n    function newEvents() {\n        var events = {};\n        getCurrentObject().events = events;\n        _objectStack.push(events);\n    }\n\n    function newId(tag) {\n        var i = {};\n        i.value = null;\n        i.provider = getAttribute(ID_PROVIDER_ATTR, tag.attributes);\n        getCurrentObject().id = i;\n        _objectStack.push(i);\n    }\n\n    function newMolecularSequence(tag) {\n        var mol_seq = {};\n        mol_seq.is_aligned = getAttributeAsBoolean(MOLSEQ_IS_ALIGNED_ATTR, tag.attributes);\n        getCurrentObject().mol_seq = mol_seq;\n        _objectStack.push(mol_seq);\n    }\n\n    function newPoint(tag) {\n        var p = {};\n        p.alt_unit = getAttribute(POINT_ALT_UNIT_ATTR, tag.attributes);\n        p.geodetic_datum = getAttribute(POINT_GEODETIC_DATUM_ATTR, tag.attributes);\n        var parent = _tagStack.get(1);\n        if (parent === DISTRIBUTION) {\n            addToArrayInCurrentObject('points', p);\n        }\n        _objectStack.push(p);\n    }\n\n    function newProperty(tag) {\n        var prop = {};\n        prop.ref = getAttribute(PROPERTY_REF_ATTR, tag.attributes);\n        prop.unit = getAttribute(PROPERTY_UNIT_ATTR, tag.attributes);\n        prop.datatype = getAttribute(PROPERTY_DATATYPE_ATTR, tag.attributes);\n        prop.applies_to = getAttribute(PROPERTY_APPLIES_TO_ATTR, tag.attributes);\n        prop.id_ref = getAttribute(PROPERTY_ID_REF_ATTR, tag.attributes);\n\n        if (!prop.ref) {\n            throw new PhyloXmlError('property ref is missing');\n        }\n        if (!prop.datatype) {\n            throw new PhyloXmlError('property data-type is missing');\n        }\n        if (!prop.applies_to) {\n            throw new PhyloXmlError('property applies-to is missing');\n        }\n        if (!PROPERTY_REF_RE.test(prop.ref)) {\n            throw new PhyloXmlError('property ref is ill-formatted: ' + prop.ref);\n        }\n        if (!PROPERTY_DATATYPE_RE.test(prop.datatype)) {\n            throw new PhyloXmlError('property data-type is ill-formatted: ' + prop.datatype);\n        }\n        if (prop.unit && !PROPERTY_UNIT_RE.test(prop.unit)) {\n            throw new PhyloXmlError('property unit is ill-formatted: ' + prop.unit);\n        }\n\n        addToArrayInCurrentObject(PROPERTIES, prop);\n        _objectStack.push(prop);\n    }\n\n    function newProteinDomain(tag) {\n        var pd = {};\n        pd.name = null;\n        pd.from = getAttributeAsInt(PROTEINDOMAIN_FROM_ATTR, tag.attributes);\n        pd.to = getAttributeAsInt(PROTEINDOMAIN_TO_ATTR, tag.attributes);\n        pd.confidence = getAttributeAsFloat(PROTEINDOMAIN_CONFIDENCE_ATTR, tag.attributes);\n        pd.id = getAttribute(PROTEINDOMAIN_ID_ATTR, tag.attributes);\n        addToArrayInCurrentObject('domains', pd);\n        _objectStack.push(pd);\n    }\n\n    function newReference(tag) {\n        var reference = {};\n        reference.doi = getAttribute(REFERENCE_DOI_ATTR, tag.attributes);\n        addToArrayInCurrentObject('references', reference);\n        _objectStack.push(reference);\n    }\n\n    function newSequence(tag) {\n        var seq = {};\n        seq.type = getAttribute(SEQUENCE_TYPE_ATTR, tag.attributes);\n        seq.id_source = getAttribute(SEQUENCE_ID_SOURCE_ATTR, tag.attributes);\n        seq.id_ref = getAttribute(SEQUENCE_ID_REF_ATTR, tag.attributes);\n        addToArrayInCurrentObject(SEQUENCES, seq);\n        _objectStack.push(seq);\n    }\n\n    function newTaxonomy(tag) {\n        var tax = {};\n        tax.id_source = getAttribute(TAXONOMY_ID_SOURCE_ATTR, tag.attributes);\n        addToArrayInCurrentObject(TAXONOMIES, tax);\n        _objectStack.push(tax);\n    }\n\n    function newUri(tag) {\n        var uri = {};\n        uri.value = null;\n        uri.desc = getAttribute(URI_DESC_ATTR, tag.attributes);\n        uri.type = getAttribute(URI_TYPE_ATTR, tag.attributes);\n        addToArrayInCurrentObject('uris', uri);\n        _objectStack.push(uri);\n    }\n\n    function newPhylogeny(tag) {\n        var phy = {};\n        phy.rooted = getAttributeAsBoolean(PHYLOGENY_ROOTED_ATTR, tag.attributes);\n        if (phy.rooted === undefined) {\n            phy.rooted = true;\n        }\n        phy.rerootable = getAttributeAsBoolean(PHYLOGENY_REROOTABLE_ATTR, tag.attributes);\n        if (phy.rerootable === undefined) {\n            phy.rerootable = true;\n        }\n        phy.branch_length_unit = getAttribute(PHYLOGENY_BRANCH_LENGTH_UNIT_ATTR, tag.attributes);\n        phy.type = getAttribute(PHYLOGENY_TYPE_ATTR, tag.attributes);\n        _objectStack.push(phy);\n    }\n\n    function newSimpleCharacteristics() {\n        //To be deprecated.\n        var sc = {};\n        getCurrentObject().simple_characteristics = sc;\n        _objectStack.push(sc);\n    }\n\n\n    // --------------------------------------------------------------\n    // Functions for processing text\n    // --------------------------------------------------------------\n\n    function inAccession(text) {\n        getCurrentObject().value = text;\n    }\n\n    function inAnnotation(text) {\n        if (getCurrentTag() === ANNOTATION_DESC) {\n            getCurrentObject().desc = text;\n        }\n    }\n\n    function inAppType(text) {\n        if (getCurrentTag() === APPTYPE) {\n            getCurrentObject().desc = text;\n        }\n    }\n\n    function inBranchColor(text) {\n        if (getCurrentTag() === COLOR_RED) {\n            getCurrentObject().red = parseIntNumber(text);\n        }\n        else if (getCurrentTag() === COLOR_GREEN) {\n            getCurrentObject().green = parseIntNumber(text);\n        }\n        else if (getCurrentTag() === COLOR_BLUE) {\n            getCurrentObject().blue = parseIntNumber(text);\n        }\n        if (getCurrentTag() === COLOR_ALPHA) {\n            getCurrentObject().alpha = parseIntNumber(text);\n        }\n    }\n\n    function inClade(text) {\n        if (getCurrentTag() === CLADE_NAME) {\n            getCurrentClade().name = text;\n        }\n        else if (getCurrentTag() === CLADE_BRANCH_LENGTH) {\n            getCurrentClade().branch_length = parseFloatNumber(text);\n        }\n        else if (getCurrentTag() === CLADE_WIDTH) {\n            getCurrentClade().width = parseFloatNumber(text);\n        }\n    }\n\n    function inConfidence(text) {\n        getCurrentObject().value = parseFloatNumber(text);\n    }\n\n    function inDate(text) {\n        if (getCurrentTag() === DATE_DESC) {\n            getCurrentObject().desc = text;\n        }\n        else if (getCurrentTag() === DATE_VALUE) {\n            getCurrentObject().value = parseFloatNumber(text);\n        }\n        else if (getCurrentTag() === DATE_MINIMUM) {\n            getCurrentObject().minimum = parseFloatNumber(text);\n        }\n        else if (getCurrentTag() === DATE_MAXIMUM) {\n            getCurrentObject().maximum = parseFloatNumber(text);\n        }\n    }\n\n    function inDistribution(text) {\n        if (getCurrentTag() === DISTRIBUTION_DESC) {\n            getCurrentObject().desc = text;\n        }\n    }\n\n    function inEvents(text) {\n        if (getCurrentTag() === EVENTS_TYPE) {\n            getCurrentObject().type = text;\n        }\n        else if (getCurrentTag() === EVENTS_DUPLICATIONS) {\n            getCurrentObject().duplications = parseIntNumber(text);\n        }\n        else if (getCurrentTag() === EVENTS_SPECIATIONS) {\n            getCurrentObject().speciations = parseIntNumber(text);\n        }\n        else if (getCurrentTag() === EVENTS_LOSSES) {\n            getCurrentObject().losses = parseIntNumber(text);\n        }\n    }\n\n    function inId(text) {\n        getCurrentObject().value = text;\n    }\n\n    function inMolecularSequence(text) {\n        getCurrentObject().value = text;\n    }\n\n    function inPoint(text) {\n        if (getCurrentTag() === POINT_LAT) {\n            getCurrentObject().lat = text;\n        }\n        else if (getCurrentTag() === POINT_LONG) {\n            getCurrentObject().long = text;\n        }\n        else if (getCurrentTag() === POINT_ALT) {\n            getCurrentObject().alt = text;\n        }\n    }\n\n    function inProperty(text) {\n        getCurrentObject().value = text;\n    }\n\n    function inProteinDomain(text) {\n        getCurrentObject().name = text;\n    }\n\n    function inPhylogeny(text) {\n        if (getCurrentTag() === PHYLOGENY_NAME) {\n            getCurrentObject().name = text;\n        }\n        else if (getCurrentTag() === PHYLOGENY_DESCRIPTION) {\n            getCurrentObject().description = text;\n        }\n        else if (getCurrentTag() === PHYLOGENY_DATE) {\n            getCurrentObject().date = text;\n        }\n    }\n\n    function inReference(text) {\n        if (getCurrentTag() === REFERENCE_DESC) {\n            getCurrentObject().desc = text;\n        }\n    }\n\n    function inSequence(text) {\n        if (getCurrentTag() === SEQUENCE_SYMBOL) {\n            getCurrentObject().symbol = text;\n        }\n        else if (getCurrentTag() === SEQUENCE_NAME) {\n            getCurrentObject().name = text;\n        }\n        else if (getCurrentTag() === SEQUENCE_GENE_NAME) {\n            getCurrentObject().gene_name = text;\n        }\n        else if (getCurrentTag() === SEQUENCE_LOCATION) {\n            getCurrentObject().location = text;\n        }\n    }\n\n    function inTaxonomy(text) {\n        if (getCurrentTag() === TAXONOMY_CODE) {\n            getCurrentObject().code = text;\n        }\n        else if (getCurrentTag() === TAXONOMY_SCIENTIFIC_NAME) {\n            getCurrentObject().scientific_name = text;\n        }\n        else if (getCurrentTag() === TAXONOMY_AUTHORITY) {\n            getCurrentObject().authority = text;\n        }\n        else if (getCurrentTag() === TAXONOMY_COMMON_NAME) {\n            getCurrentObject().common_name = text;\n        }\n        else if (getCurrentTag() === TAXONOMY_SYNONYM) {\n            addToArrayInCurrentObject(TAXONOMY_SYNONYMS, text);\n        }\n        else if (getCurrentTag() === TAXONOMY_RANK) {\n            getCurrentObject().rank = text;\n        }\n    }\n\n    function inUri(text) {\n        getCurrentObject().value = text;\n    }\n\n    function inSimpleCharacteristics(text) {\n        //To be deprecated.\n        if (getCurrentTag() === X_SIMPLE_CHARACTERISTIC_COUNTRY) {\n            getCurrentObject().country = text;\n        }\n        else if (getCurrentTag() === X_SIMPLE_CHARACTERISTIC_HOST) {\n            getCurrentObject().host = text;\n        }\n        else if (getCurrentTag() === X_SIMPLE_CHARACTERISTIC_YEAR) {\n            getCurrentObject().year = text;\n        }\n        else if (getCurrentTag() === X_SIMPLE_CHARACTERISTIC_HA) {\n            getCurrentObject().ha = text;\n        }\n        else if (getCurrentTag() === X_SIMPLE_CHARACTERISTIC_NA) {\n            getCurrentObject().na = text;\n        }\n    }\n\n    // --------------------------------------------------------------\n    // Functions for SAX parser\n    // --------------------------------------------------------------\n    function phyloxmlOnopentag(tag) {\n        _tagStack.push(tag.name);\n        switch (tag.name) {\n            case CLADE:\n                newClade(tag);\n                break;\n            case ACCESSION:\n                newAccession(tag);\n                break;\n            case ANNOTATION:\n                newAnnotation(tag);\n                break;\n            case CLADE_RELATION:\n                if (_tagStack.get(1) === PHYLOGENY) {\n                    newCladeRelation(tag);\n                }\n                break;\n            case COLOR:\n                newBranchColor();\n                break;\n            case CONFIDENCE:\n                newConfidence(tag);\n                break;\n            case CROSS_REFERENCES:\n                newCrossReferences();\n                break;\n            case DATE:\n                if (_tagStack.get(1) === CLADE) {\n                    newDate(tag);\n                }\n                break;\n            case DISTRIBUTION:\n                newDistribution(tag);\n                break;\n            case DOMAIN_ARCHITECTURE:\n                newDomainArchitecture(tag);\n                break;\n            case EVENTS:\n                newEvents();\n                break;\n            case ID:\n                newId(tag);\n                break;\n            case MOLSEQ:\n                newMolecularSequence(tag);\n                break;\n            case POINT:\n                newPoint(tag);\n                break;\n            case PROTEINDOMAIN:\n                newProteinDomain(tag);\n                break;\n            case PHYLOGENY:\n                newPhylogeny(tag);\n                break;\n            case PROPERTY:\n                newProperty(tag);\n                break;\n            case REFERENCE:\n                newReference(tag);\n                break;\n            case SEQUENCE:\n                newSequence(tag);\n                break;\n            case SEQUENCE_RELATION:\n                if (_tagStack.get(1) === PHYLOGENY) {\n                    newSequenceRelation(tag);\n                }\n                break;\n            case TAXONOMY:\n                newTaxonomy(tag);\n                break;\n            case URI:\n                newUri(tag);\n                break;\n            case X_SIMPLE_CHARACTERISTICS:\n                //To be deprecated.\n                newSimpleCharacteristics();\n                break;\n            default:\n        }\n    }\n\n    function phyloxmlOnclosetag(tag) {\n        if (tag === CLADE) {\n            _tagStack.pop();\n            _objectStack.pop();\n            _cladeStack.pop();\n        }\n        else if (\n            tag === ACCESSION\n            || tag === ANNOTATION\n            || ( tag === CLADE_RELATION && (_tagStack.get(1) === PHYLOGENY) )\n            || tag === COLOR\n            || tag === CONFIDENCE\n            || tag === CROSS_REFERENCES\n            || ( tag === DATE && (_tagStack.get(1) === CLADE) )\n            || tag === DISTRIBUTION\n            || tag === TAXONOMY\n            || tag === ID\n            || tag === EVENTS\n            || tag === MOLSEQ\n            || tag === REFERENCE\n            || tag === DOMAIN_ARCHITECTURE\n            || tag === PROTEINDOMAIN\n            || tag === SEQUENCE\n            || ( tag === SEQUENCE_RELATION && (_tagStack.get(1) === PHYLOGENY) )\n            || tag === PROPERTY\n            || tag === POINT\n            || tag === URI\n            || tag === X_SIMPLE_CHARACTERISTICS) {\n            _tagStack.pop();\n            _objectStack.pop();\n        }\n        else if (!(tag === PHYLOGENY || tag === PHYLOXML)) {\n            _tagStack.pop();\n        }\n        else if (tag === PHYLOGENY) {\n            phyloxmlOnClosetagSanityCheck();\n            _phylogenies.push(_phylogeny);\n            startNewPhylogeny();\n        }\n    }\n\n    function phyloxmlOntext(text) {\n        var parentTag = _tagStack.get(1);\n        var currentTag = _tagStack.peek();\n        if (parentTag === CLADE) {\n            inClade(text);\n        }\n        else if (parentTag === ANNOTATION) {\n            inAnnotation(text);\n        }\n        else if (parentTag === COLOR) {\n            inBranchColor(text);\n        }\n        else if (parentTag === DATE) {\n            inDate(text);\n        }\n        else if (parentTag === DISTRIBUTION) {\n            inDistribution(text);\n        }\n        else if (parentTag === EVENTS) {\n            inEvents(text);\n        }\n        else if (parentTag === REFERENCE) {\n            inReference(text);\n        }\n        else if (parentTag === PHYLOGENY) {\n            inPhylogeny(text);\n        }\n        else if (parentTag === POINT) {\n            inPoint(text);\n        }\n        else if (parentTag === SEQUENCE) {\n            inSequence(text);\n        }\n        else if (parentTag === TAXONOMY) {\n            inTaxonomy(text);\n        }\n        if (currentTag === ACCESSION) {\n            inAccession(text);\n        }\n        else if (currentTag === APPTYPE) {\n            inAppType(text);\n        }\n        else if (currentTag === CONFIDENCE) {\n            inConfidence(text);\n        }\n        else if (currentTag === ID) {\n            inId(text);\n        }\n        else if (currentTag === MOLSEQ) {\n            inMolecularSequence(text);\n        }\n        else if (currentTag === PROTEINDOMAIN) {\n            inProteinDomain(text);\n        }\n        else if (currentTag === PROPERTY) {\n            inProperty(text);\n        }\n        else if (currentTag === URI) {\n            inUri(text);\n        }\n        else if (parentTag === X_SIMPLE_CHARACTERISTICS) {\n            inSimpleCharacteristics(text);\n        }\n    }\n\n    function phyloxmlOnerror(error) {\n        throw error;\n    }\n\n    function addPhyloxmlParserEvents(sax_parser) {\n        sax_parser.onopentag = phyloxmlOnopentag;\n        sax_parser.onclosetag = phyloxmlOnclosetag;\n        sax_parser.ontext = phyloxmlOntext;\n        sax_parser.onerror = phyloxmlOnerror;\n        // Ignoring: oncdata, oncomment, ondoctype\n    }\n\n    // --------------------------------------------------------------\n    // Helper functions\n    // --------------------------------------------------------------\n    function getCurrentClade() {\n        return _cladeStack.peek();\n    }\n\n    function getCurrentTag() {\n        return _tagStack.peek();\n    }\n\n    function getCurrentObject() {\n        return _objectStack.peek();\n    }\n\n    function getAttribute(attribute_name, attributes) {\n        if (attribute_name in attributes) {\n            return attributes[attribute_name];\n        }\n        return undefined;\n    }\n\n    function getAttributeAsInt(attribute_name, attributes) {\n        if (attribute_name in attributes) {\n            return parseIntNumber(attributes[attribute_name]);\n        }\n        return undefined;\n    }\n\n    function getAttributeAsFloat(attribute_name, attributes) {\n        if (attribute_name in attributes) {\n            return parseFloatNumber(attributes[attribute_name]);\n        }\n        return undefined;\n    }\n\n    function getAttributeAsBoolean(attribute_name, attributes) {\n        if (attribute_name in attributes) {\n            return parseBoolean(attributes[attribute_name]);\n        }\n        return undefined;\n    }\n\n    function addToArrayInCurrentObject(name, value) {\n        var parent = null;\n        if (getCurrentObject()) {\n            parent = getCurrentObject();\n        }\n        else {\n            parent = _phylogeny;\n        }\n        var ary = parent[name];\n        if (ary) {\n            ary.push(value);\n        }\n        else {\n            parent[name] = [value];\n        }\n    }\n\n    function addToArrayInCurrentObjectUnnamed(value) {\n        var obj = getCurrentObject();\n        obj.push(value);\n    }\n\n    function parseFloatNumber(text) {\n        var f = parseFloat(text);\n        if (isNaN(f)) {\n            throw new PhyloXmlError(\"could not parse floating point number from '\" + text + \"'\");\n        }\n        return f;\n    }\n\n    function parseIntNumber(text) {\n        var i = parseInt(text);\n        if (isNaN(i)) {\n            throw new PhyloXmlError(\"could not parse integer number from '\" + text + \"'\");\n        }\n        return i;\n    }\n\n    function parseBoolean(text) {\n        if (text === 'true') {\n            return true;\n        }\n        else if (text === 'false') {\n            return false;\n        }\n        else {\n            throw new PhyloXmlError(\"could not parse boolean from '\" + text + \"'\");\n        }\n    }\n\n    function startNewPhylogeny() {\n        _phylogeny = null;\n        _cladeStack = new Stack();\n        _tagStack = new Stack();\n        _objectStack = new Stack();\n    }\n\n    function phyloxmlOnClosetagSanityCheck() {\n        if (!(_cladeStack.isEmpty() && _objectStack.isEmpty() )) {\n            throw new PhyloXmlError('severe phyloXML format error')\n        }\n    }\n\n    function finalSanityCheck() {\n        if (!_tagStack.isEmpty()) {\n            throw new PhyloXmlError('severe phyloXML format error');\n        }\n    }\n\n    // --------------------------------------------------------------\n    // Stack\n    // --------------------------------------------------------------\n    function Stack() {\n        this._stack = [];\n        this.pop = function () {\n            var p = this._stack.pop();\n            if (p === undefined) {\n                throw new Error('severe phyloXML format error')\n            }\n            return p;\n        };\n        this.push = function (item) {\n            this._stack.push(item);\n        };\n        this.peek = function () {\n            return this._stack[this._stack.length - 1];\n        };\n        this.get = function (i) {\n            return this._stack[this._stack.length - (1 + i)];\n        };\n        this.length = function () {\n            return this._stack.length;\n        };\n        this.isEmpty = function () {\n            return this._stack.length < 1;\n        };\n    }\n\n    // --------------------------------------------------------------\n    // phyloXML error\n    // --------------------------------------------------------------\n    function PhyloXmlError(message) {\n        this.name = 'phyloXmlError';\n        this.message = message || 'phyloXML format error';\n    }\n\n    PhyloXmlError.prototype = Object.create(Error.prototype);\n\n    // --------------------------------------------------------------\n    // To phyloXML\n    // --------------------------------------------------------------\n    phyloXml.toPhyloXML_ = function (phy, dec) {\n        var x = '';\n        var ind = '';\n        openPhyloXml();\n        openPhylogeny(phy, [PHYLOGENY_ROOTED_ATTR, PHYLOGENY_REROOTABLE_ATTR,\n            PHYLOGENY_BRANCH_LENGTH_UNIT_ATTR, PHYLOGENY_TYPE_ATTR]);\n        addSingleElement(PHYLOGENY_NAME, phy.name);\n        addSingleElement(PHYLOGENY_DESCRIPTION, phy.description);\n        addSingleElement(PHYLOGENY_DATE, phy.date);\n        if (phy.children && phy.children.length === 1) {\n            toPhyloXMLhelper(phy.children[0]);\n        }\n        closePhylogeny();\n        closePhyloXml();\n        return x;\n\n        function toPhyloXMLhelper(node) {\n            var l;\n            var i;\n\n            openClade(node, [CLADE_ID_SOURCE_ATTR, CLADE_COLLAPSE_ATTR]);\n\n            addSingleElement(CLADE_NAME, node.name);\n\n            if (node[CLADE_BRANCH_LENGTH]) {\n                addSingleElement(CLADE_BRANCH_LENGTH, (dec && dec > 0) ? roundNumber(node[CLADE_BRANCH_LENGTH], dec) : node[CLADE_BRANCH_LENGTH]);\n            }\n\n            if (node[CONFIDENCES] && node[CONFIDENCES].length > 0) {\n                l = node[CONFIDENCES].length;\n                for (i = 0; i < l; ++i) {\n                    var conf = node[CONFIDENCES][i];\n                    if (!conf[CONFIDENCE_TYPE_ATTR]) {\n                        conf[CONFIDENCE_TYPE_ATTR] = UNKNOWN;\n                    }\n                    addSingleElement(CONFIDENCE, conf.value, conf,\n                        [CONFIDENCE_TYPE_ATTR, CONFIDENCE_STDDEV_ATTR]);\n                }\n            }\n\n            addSingleElement(CLADE_WIDTH, node[CLADE_WIDTH]);\n\n            if (node[COLOR]) {\n                var col = node[COLOR];\n                open(COLOR);\n                addSingleElement(COLOR_RED, col[COLOR_RED]);\n                addSingleElement(COLOR_GREEN, col[COLOR_GREEN]);\n                addSingleElement(COLOR_BLUE, col[COLOR_BLUE]);\n                addSingleElement(COLOR_ALPHA, col[COLOR_ALPHA]);\n                close(COLOR);\n            }\n\n            if (node[TAXONOMIES] && node[TAXONOMIES].length > 0) {\n                l = node[TAXONOMIES].length;\n                for (i = 0; i < l; ++i) {\n                    var tax = node[TAXONOMIES][i];\n                    open(TAXONOMY, tax, [TAXONOMY_ID_SOURCE_ATTR]);\n                    if (tax[ID]) {\n                        if (!tax[ID][ID_PROVIDER_ATTR]) {\n                            tax[ID][ID_PROVIDER_ATTR] = UNKNOWN;\n                        }\n                        addSingleElement(ID, tax[ID].value, tax[ID],\n                            [ID_PROVIDER_ATTR]);\n                    }\n                    addSingleElement(TAXONOMY_CODE, tax[TAXONOMY_CODE]);\n                    addSingleElement(TAXONOMY_SCIENTIFIC_NAME, tax[TAXONOMY_SCIENTIFIC_NAME]);\n                    addSingleElement(TAXONOMY_AUTHORITY, tax[TAXONOMY_AUTHORITY]);\n                    addSingleElement(TAXONOMY_COMMON_NAME, tax[TAXONOMY_COMMON_NAME]);\n                    if (tax[TAXONOMY_SYNONYMS] && tax[TAXONOMY_SYNONYMS].length > 0) {\n                        var ll = tax[TAXONOMY_SYNONYMS].length;\n                        for (var ii = 0; ii < ll; ++ii) {\n                            addSingleElement(TAXONOMY_SYNONYM, tax[TAXONOMY_SYNONYMS][ii]);\n                        }\n                    }\n                    addSingleElement(TAXONOMY_RANK, tax[TAXONOMY_RANK]);\n                    close(TAXONOMY);\n                }\n            }\n\n            if (node[SEQUENCES] && node[SEQUENCES].length > 0) {\n                l = node[SEQUENCES].length;\n                for (i = 0; i < l; ++i) {\n                    var seq = node[SEQUENCES][i];\n                    open(SEQUENCE, seq, [SEQUENCE_TYPE_ATTR, SEQUENCE_ID_SOURCE_ATTR, SEQUENCE_ID_REF_ATTR]);\n                    addSingleElement(SEQUENCE_SYMBOL, seq[SEQUENCE_SYMBOL]);\n                    if (seq[ACCESSION]) {\n                        if (!seq[ACCESSION][ACCESSION_SOURCE_ATTR]) {\n                            seq[ACCESSION][ACCESSION_SOURCE_ATTR] = UNKNOWN;\n                        }\n                        addSingleElement(ACCESSION, seq[ACCESSION].value, seq[ACCESSION],\n                            [ACCESSION_SOURCE_ATTR, ACCESSION_COMMENT_ATTR]);\n                    }\n                    addSingleElement(SEQUENCE_NAME, seq[SEQUENCE_NAME]);\n                    addSingleElement(SEQUENCE_GENE_NAME, seq[SEQUENCE_GENE_NAME]);\n                    addSingleElement(SEQUENCE_LOCATION, seq[SEQUENCE_LOCATION]);\n                    if (seq[MOLSEQ]) {\n                        addSingleElement(MOLSEQ, seq[MOLSEQ].value, seq[MOLSEQ],\n                            [MOLSEQ_IS_ALIGNED_ATTR]);\n                    }\n                    close(SEQUENCE);\n                }\n            }\n\n            if (node[EVENTS]) {\n                var ev = node[EVENTS];\n                open(EVENTS);\n                addSingleElement(EVENTS_TYPE, ev[EVENTS_TYPE]);\n                addSingleElement(EVENTS_DUPLICATIONS, ev[EVENTS_DUPLICATIONS]);\n                addSingleElement(EVENTS_SPECIATIONS, ev[EVENTS_SPECIATIONS]);\n                addSingleElement(EVENTS_LOSSES, ev[EVENTS_LOSSES]);\n                if (ev[CONFIDENCE]) {\n                    var evconf = ev[CONFIDENCE];\n                    addSingleElement(CONFIDENCE, evconf.value, evconf,\n                        [CONFIDENCE_TYPE_ATTR, CONFIDENCE_STDDEV_ATTR]);\n                }\n                close(EVENTS);\n            }\n\n            if (node[PROPERTIES] && node[PROPERTIES].length > 0) {\n                l = node[PROPERTIES].length;\n                for (i = 0; i < l; ++i) {\n                    var prop = node[PROPERTIES][i];\n                    if (!prop[PROPERTY_APPLIES_TO_ATTR]) {\n                        throw new PhyloXmlError(\"property applies-to is missing\");\n                    }\n                    if (!prop[PROPERTY_DATATYPE_ATTR]) {\n                        throw new PhyloXmlError(\"property data-type is missing\");\n                    }\n                    if (!prop[PROPERTY_REF_ATTR]) {\n                        throw new PhyloXmlError(\"property ref is missing\");\n                    }\n                    addSingleElement(PROPERTY, prop.value, prop, [PROPERTY_REF_ATTR,\n                        PROPERTY_UNIT_ATTR, PROPERTY_DATATYPE_ATTR, PROPERTY_APPLIES_TO_ATTR,\n                        PROPERTY_ID_REF_ATTR]);\n                }\n            }\n\n            if (node.children) {\n                l = node.children.length;\n                for (i = 0; i < l; ++i) {\n                    toPhyloXMLhelper(node.children[i]);\n                }\n            }\n            else if (node._children) {\n                l = node._children.length;\n                for (i = 0; i < l; ++i) {\n                    toPhyloXMLhelper(node._children[i]);\n                }\n            }\n\n            closeClade();\n\n        } // toPhyloXMLhelper\n\n        function addSingleElement(elemName, elemValue, object, attributeNames) {\n            if ((elemValue !== null) && (elemValue !== undefined)) {\n                if (typeof elemValue === 'string' || elemValue instanceof String) {\n                    elemValue = elemValue.trim();\n                    if (elemValue.length > 0) {\n                        if ((elemValue.indexOf('&') > -1) || ( elemValue.indexOf('<') > -1) || ( elemValue.indexOf('>') > -1)\n                            || (elemValue.indexOf('\"') > -1) || ( elemValue.indexOf(\"'\") > -1)) {\n                            elemValue = replaceUnsafeChars(elemValue);\n                        }\n                    }\n                    else {\n                        return;\n                    }\n                }\n                x += ( ind + '<' + elemName);\n                if (object && attributeNames && attributeNames.length > 0) {\n                    addAttributes(object, attributeNames);\n                }\n                x += ( '>' + elemValue + '</' + elemName + '>\\n');\n            }\n        }\n\n        function open(elemName, object, attributeNames) {\n            if (object && attributeNames && attributeNames.length > 0) {\n                x += ( ind + '<' + elemName);\n                addAttributes(object, attributeNames);\n                x += '>\\n';\n            }\n            else {\n                x += (ind + '<' + elemName + '>\\n' );\n            }\n            ind = ind + ' ';\n        }\n\n        function close(elemName) {\n            reduceInd();\n            x += ( ind + '</' + elemName + '>\\n' );\n        }\n\n        function openClade(object, attributeNames) {\n            if (object && attributeNames && attributeNames.length > 0) {\n                x += ind + '<clade';\n                addAttributes(object, attributeNames);\n                x += '>\\n';\n            }\n            else {\n                x += ind + '<clade>\\n';\n            }\n            ind = ind + ' ';\n        }\n\n        function closeClade() {\n            reduceInd();\n            x += ind + '</clade>\\n';\n        }\n\n        function openPhylogeny(object, attributeNames) {\n            if (object[PHYLOGENY_ROOTED_ATTR] === undefined ||\n                object[PHYLOGENY_ROOTED_ATTR] === null) {\n                object[PHYLOGENY_ROOTED_ATTR] = true;\n            }\n            if (object[PHYLOGENY_REROOTABLE_ATTR] === undefined ||\n                object[PHYLOGENY_REROOTABLE_ATTR] === null) {\n                object[PHYLOGENY_REROOTABLE_ATTR] = true;\n            }\n            if (object && attributeNames && attributeNames.length > 0) {\n                x += ' <phylogeny';\n                addAttributes(object, attributeNames);\n                x += '>\\n';\n            }\n            else {\n                x += ' <phylogeny>\\n';\n            }\n            ind = '  ';\n        }\n\n        function closePhylogeny() {\n            ind = ' ';\n            x += ' </phylogeny>\\n';\n        }\n\n        function openPhyloXml() {\n            ind = '';\n            x += '<?xml version=\"1.0\" encoding=\"UTF-8\"?>\\n';\n            x += '<phyloxml xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://www.phyloxml.org http://www.phyloxml.org/1.20/phyloxml.xsd\" xmlns=\"http://www.phyloxml.org\">\\n';\n        }\n\n        function closePhyloXml() {\n            x += '</phyloxml>\\n';\n        }\n\n        function addAttributes(object, attributeNames) {\n            var l = attributeNames.length;\n            for (var i = 0; i < l; ++i) {\n                var attributeName = attributeNames[i];\n                if (attributeName && ( object[attributeName] !== undefined && object[attributeName] !== null )) {\n                    x += (' ' + attributeName + '=\"' + object[attributeName] + '\"' );\n                }\n            }\n        }\n\n        function roundNumber(num, dec) {\n            return Math.round(num * Math.pow(10, dec)) / Math.pow(10, dec);\n        }\n\n        function replaceUnsafeChars(str) {\n            return str\n                .replace(/&/g, \"&amp;\")\n                .replace(/</g, \"&lt;\")\n                .replace(/>/g, \"&gt;\")\n                .replace(/\"/g, \"&quot;\")\n                .replace(/'/g, \"&apos;\");\n        }\n\n        function reduceInd() {\n            var l = ind.length;\n            ind = '';\n            for (var i = 0; i <= l - 2; ++i) {\n                ind += ' ';\n            }\n        }\n\n    }; // toPhyloXML_\n\n\n    // --------------------------------------------------------------\n    // Main functions\n    // --------------------------------------------------------------\n\n    /**\n     * To parse phyloXML formatted trees from a stream asynchronously.\n     *\n     * @param stream - The stream to be parsed.\n     * @param parseOptions - Options dict for the SAX parser.\n     *                       (example: {trim: true, normalize: true}).\n     */\n    phyloXml.parseAsync = function (stream, parseOptions) {\n        _phylogenies = [];\n        startNewPhylogeny();\n        var sax_parser = sax.createStream(true, parseOptions);\n        addPhyloxmlParserEvents(sax_parser);\n        stream.pipe(sax_parser);\n\n        sax_parser.on('end', function () {\n            finalSanityCheck();\n            var len = _phylogenies.length;\n            console.log(\"parsed \" + len + \" trees\");\n            // for (var i = 0; i < len; ++i) {\n            //    do something, for example:\n            //    var str = JSON.stringify(_phylogenies[i], null, 2);\n            //}\n        });\n\n        process.stdout.on('drain', function () {\n            stream.resume();\n        });\n    };\n\n    /**\n     * To parse a phyloXML formatted source.\n     *\n     * @param source - The source.\n     * @param parseOptions - Options dict for the SAX parser\n     *                       (example: {trim: true, normalize: true}).\n     * @returns {*} - Array of phylogentic tree objects.\n     */\n    phyloXml.parse = function (source, parseOptions) {\n        source && ( source = source.toString().trim());\n\n        if (!source) {\n            throw new Error('phyloXML source is empty');\n        }\n\n        _phylogenies = [];\n        startNewPhylogeny();\n        var sax_parser = sax.parser(true, parseOptions);\n        addPhyloxmlParserEvents(sax_parser);\n\n        sax_parser.onend = function () {\n            finalSanityCheck();\n        };\n\n        sax_parser.write(source).close();\n        return _phylogenies;\n    };\n\n\n    /**\n     * To convert a phylogentic tree object to a phyloXML formatted string.\n     *\n     * @param phy - A phylogentic tree object.\n     * @param decPointsMax - Maximal number of decimal points for branch lengths (optional).\n     * @returns A phyloXML formatted string.\n     */\n    phyloXml.toPhyloXML = function (phy, decPointsMax) {\n        return phyloXml.toPhyloXML_(phy, decPointsMax);\n    };\n\n    // --------------------------------------------------------------\n    // For exporting\n    // --------------------------------------------------------------\n    if ( true && module.exports && !__webpack_require__.g.xmldocAssumeBrowser)\n        module.exports.phyloXml = phyloXml;\n    else if (typeof window !== \"undefined\")\n        window.phyloXml = phyloXml;\n    else\n        this.phyloXml = phyloXml;\n})();\n\n\n//# sourceURL=webpack://PhyloIO/./src/phyloxml.js?");
+
+/***/ }),
+
+/***/ "./src/worker_bcn.js":
+/*!***************************!*\
+  !*** ./src/worker_bcn.js ***!
+  \***************************/
+/***/ ((__unused_webpack_module, __webpack_exports__, __webpack_require__) => {
+
+"use strict";
+eval("__webpack_require__.r(__webpack_exports__);\n/* harmony import */ var minhashjs__WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__(/*! minhashjs */ \"./node_modules/minhashjs/index.js\");\n/* harmony import */ var _model__WEBPACK_IMPORTED_MODULE_1__ = __webpack_require__(/*! ./model */ \"./src/model.js\");\n\n\n\n\nself.onmessage = (event) => {\n\n    var containers = event.data;\n\n    var processed_tree = compute_similarity_container_pair(containers.tree1,containers.tree2)\n\n    postMessage(processed_tree);\n\n    self.close();\n};\n\n\n\nfunction compute_similarity_container_pair(t1,t2){\n\n    var t1 = new _model__WEBPACK_IMPORTED_MODULE_1__[\"default\"](t1.data, t1.settings, false)\n    var t2 = new _model__WEBPACK_IMPORTED_MODULE_1__[\"default\"](t2.data, t2.settings, false)\n\n\n    console.time(\"similarity\");\n\n    // X = Intersection of T1 & T2 leaves.\n    if (t1.leaves.length <= 0){\n        t1.leaves = t1.get_leaves(t1.data)\n    }\n    if (t2.leaves.length <= 0){\n        t2.leaves = t2.get_leaves(t2.data)\n    }\n    var common_leaves = t1.leaves.map(leaf => leaf.name).filter(value => t2.leaves.map(leaf => leaf.name).includes(value));\n    console.log(\"Intersection\");\n    console.timeLog(\"similarity\");\n\n    // DeepLeaf with filter(X = True)\n    t1.createDeepLeafList(common_leaves)\n    t2.createDeepLeafList(common_leaves)\n    console.log(\"DeepLeaf\");\n    console.timeLog(\"similarity\");\n\n    // MinHash\n    t1.createMinHash()\n    t2.createMinHash()\n    console.log(\"MinHash\");\n    console.timeLog(\"similarity\");\n\n    // For all T1 & T2 Nodes compute the BCN with MinHash\n    var nodes_t1 = []\n    var nodes_t2 = []\n\n    var forest1 = new minhashjs__WEBPACK_IMPORTED_MODULE_0__.MinHashLSHForest.MinHashLSHForest()\n    var forest2 = new minhashjs__WEBPACK_IMPORTED_MODULE_0__.MinHashLSHForest.MinHashLSHForest()\n\n    var cpt =0\n    t1.traverse(t1.data, function(h,children){nodes_t1.push(h);forest1.add(h, h.min_hash);cpt++}, null)\n    t2.traverse(t2.data, function(z,children){nodes_t2.push(z);forest2.add(z, z.min_hash);cpt++}, null)\n\n    forest1.index()\n    forest2.index()\n\n    find_BCN(nodes_t1, forest2, t2.uid)\n    find_BCN(nodes_t2, forest1, t1.uid)\n\n    console.log(\"BCN done\");\n\n    console.timeLog(\"similarity\");\n\n    // Clean non essential datume\n    t1.removeMinHash()\n    t2.removeMinHash()\n\n    console.timeEnd(\"similarity\");\n\n    t1.settings.similarity.push(t2.uid)\n    t2.settings.similarity.push(t1.uid)\n\n    t1.data = t1.remove_circularity_only_parent_and_leaves()\n    t2.data = t2.remove_circularity_only_parent_and_leaves()\n\n    t1.remove_all_color_scale()\n    t2.remove_all_color_scale()\n\n    return [t1,t2]\n\n}\n\nfunction find_BCN(nodes_list, target_forest, target_uid){\n    nodes_list.forEach((node) => {\n\n        function is_leaf(str) {\n            return !str.includes(\"|__|\");\n        }\n\n        var matches = target_forest.query(node.min_hash,10)\n\n        var l = new Set(node.deepLeafList.filter(is_leaf))\n        if (l.size > 0){\n\n            var max_jacc = 0\n            var BCN = null\n\n            matches.forEach(e => {\n                var r =   new Set(e.deepLeafList.filter(is_leaf))\n\n                if (r.size > 0){\n\n\n                    var inter = Array.from(r).filter(x => l.has(x)).length\n                    var union = [...new Set([...l, ...r])].length;\n\n                    var jj = inter/union\n\n\n\n                    if (jj > max_jacc){\n                        max_jacc = jj\n                        BCN = e\n                    }\n\n                }\n\n\n\n\n\n            })\n\n            if (max_jacc > 0) {\n                node.elementS[target_uid] = max_jacc\n                if (!node.elementBCN){\n                    node.elementBCN = {}\n                }\n                node.elementBCN[target_uid] = BCN\n            }\n\n\n        }\n\n\n\n\n    })\n}\n\n//# sourceURL=webpack://PhyloIO/./src/worker_bcn.js?");
+
+/***/ }),
+
+/***/ "?d546":
+/*!************************!*\
+  !*** buffer (ignored) ***!
+  \************************/
+/***/ (() => {
+
+eval("/* (ignored) */\n\n//# sourceURL=webpack://PhyloIO/buffer_(ignored)?");
+
+/***/ }),
+
+/***/ "?8131":
+/*!************************!*\
+  !*** buffer (ignored) ***!
+  \************************/
+/***/ (() => {
+
+eval("/* (ignored) */\n\n//# sourceURL=webpack://PhyloIO/buffer_(ignored)?");
+
+/***/ }),
+
+/***/ "?3fc0":
+/*!************************!*\
+  !*** crypto (ignored) ***!
+  \************************/
+/***/ (() => {
+
+eval("/* (ignored) */\n\n//# sourceURL=webpack://PhyloIO/crypto_(ignored)?");
+
+/***/ }),
+
+/***/ "?4068":
+/*!************************!*\
+  !*** buffer (ignored) ***!
+  \************************/
+/***/ (() => {
+
+eval("/* (ignored) */\n\n//# sourceURL=webpack://PhyloIO/buffer_(ignored)?");
+
+/***/ }),
+
+/***/ "?e7e4":
+/*!************************!*\
+  !*** buffer (ignored) ***!
+  \************************/
+/***/ (() => {
+
+eval("/* (ignored) */\n\n//# sourceURL=webpack://PhyloIO/buffer_(ignored)?");
+
+/***/ }),
+
+/***/ "?7bec":
+/*!************************!*\
+  !*** buffer (ignored) ***!
+  \************************/
+/***/ (() => {
+
+eval("/* (ignored) */\n\n//# sourceURL=webpack://PhyloIO/buffer_(ignored)?");
+
+/***/ }),
+
+/***/ "?0aec":
+/*!************************!*\
+  !*** buffer (ignored) ***!
+  \************************/
+/***/ (() => {
+
+eval("/* (ignored) */\n\n//# sourceURL=webpack://PhyloIO/buffer_(ignored)?");
+
+/***/ }),
+
+/***/ "?fbf1":
+/*!************************!*\
+  !*** buffer (ignored) ***!
+  \************************/
+/***/ (() => {
+
+eval("/* (ignored) */\n\n//# sourceURL=webpack://PhyloIO/buffer_(ignored)?");
+
+/***/ }),
+
+/***/ "?ed1b":
+/*!**********************!*\
+  !*** util (ignored) ***!
+  \**********************/
+/***/ (() => {
+
+eval("/* (ignored) */\n\n//# sourceURL=webpack://PhyloIO/util_(ignored)?");
+
+/***/ }),
+
+/***/ "?d17e":
+/*!**********************!*\
+  !*** util (ignored) ***!
+  \**********************/
+/***/ (() => {
+
+eval("/* (ignored) */\n\n//# sourceURL=webpack://PhyloIO/util_(ignored)?");
+
+/***/ })
+
+/******/ 	});
+/************************************************************************/
+/******/ 	// The module cache
+/******/ 	var __webpack_module_cache__ = {};
+/******/ 	
+/******/ 	// The require function
+/******/ 	function __webpack_require__(moduleId) {
+/******/ 		// Check if module is in cache
+/******/ 		var cachedModule = __webpack_module_cache__[moduleId];
+/******/ 		if (cachedModule !== undefined) {
+/******/ 			return cachedModule.exports;
+/******/ 		}
+/******/ 		// Create a new module (and put it into the cache)
+/******/ 		var module = __webpack_module_cache__[moduleId] = {
+/******/ 			id: moduleId,
+/******/ 			loaded: false,
+/******/ 			exports: {}
+/******/ 		};
+/******/ 	
+/******/ 		// Execute the module function
+/******/ 		__webpack_modules__[moduleId].call(module.exports, module, module.exports, __webpack_require__);
+/******/ 	
+/******/ 		// Flag the module as loaded
+/******/ 		module.loaded = true;
+/******/ 	
+/******/ 		// Return the exports of the module
+/******/ 		return module.exports;
+/******/ 	}
+/******/ 	
+/******/ 	// expose the modules object (__webpack_modules__)
+/******/ 	__webpack_require__.m = __webpack_modules__;
+/******/ 	
+/******/ 	// the startup function
+/******/ 	__webpack_require__.x = () => {
+/******/ 		// Load entry module and return exports
+/******/ 		// This entry module depends on other loaded chunks and execution need to be delayed
+/******/ 		var __webpack_exports__ = __webpack_require__.O(undefined, ["vendors-node_modules_d3_index_js-node_modules_file-saver_dist_FileSaver_min_js","vendors-node_modules_biojs-io-newick_src_index_js-node_modules_minhashjs_index_js-node_module-7b40e5","src_utils_js"], () => (__webpack_require__("./src/worker_bcn.js")))
+/******/ 		__webpack_exports__ = __webpack_require__.O(__webpack_exports__);
+/******/ 		return __webpack_exports__;
+/******/ 	};
+/******/ 	
+/************************************************************************/
+/******/ 	/* webpack/runtime/chunk loaded */
+/******/ 	(() => {
+/******/ 		var deferred = [];
+/******/ 		__webpack_require__.O = (result, chunkIds, fn, priority) => {
+/******/ 			if(chunkIds) {
+/******/ 				priority = priority || 0;
+/******/ 				for(var i = deferred.length; i > 0 && deferred[i - 1][2] > priority; i--) deferred[i] = deferred[i - 1];
+/******/ 				deferred[i] = [chunkIds, fn, priority];
+/******/ 				return;
+/******/ 			}
+/******/ 			var notFulfilled = Infinity;
+/******/ 			for (var i = 0; i < deferred.length; i++) {
+/******/ 				var [chunkIds, fn, priority] = deferred[i];
+/******/ 				var fulfilled = true;
+/******/ 				for (var j = 0; j < chunkIds.length; j++) {
+/******/ 					if ((priority & 1 === 0 || notFulfilled >= priority) && Object.keys(__webpack_require__.O).every((key) => (__webpack_require__.O[key](chunkIds[j])))) {
+/******/ 						chunkIds.splice(j--, 1);
+/******/ 					} else {
+/******/ 						fulfilled = false;
+/******/ 						if(priority < notFulfilled) notFulfilled = priority;
+/******/ 					}
+/******/ 				}
+/******/ 				if(fulfilled) {
+/******/ 					deferred.splice(i--, 1)
+/******/ 					var r = fn();
+/******/ 					if (r !== undefined) result = r;
+/******/ 				}
+/******/ 			}
+/******/ 			return result;
+/******/ 		};
+/******/ 	})();
+/******/ 	
+/******/ 	/* webpack/runtime/define property getters */
+/******/ 	(() => {
+/******/ 		// define getter functions for harmony exports
+/******/ 		__webpack_require__.d = (exports, definition) => {
+/******/ 			for(var key in definition) {
+/******/ 				if(__webpack_require__.o(definition, key) && !__webpack_require__.o(exports, key)) {
+/******/ 					Object.defineProperty(exports, key, { enumerable: true, get: definition[key] });
+/******/ 				}
+/******/ 			}
+/******/ 		};
+/******/ 	})();
+/******/ 	
+/******/ 	/* webpack/runtime/ensure chunk */
+/******/ 	(() => {
+/******/ 		__webpack_require__.f = {};
+/******/ 		// This file contains only the entry chunk.
+/******/ 		// The chunk loading function for additional chunks
+/******/ 		__webpack_require__.e = (chunkId) => {
+/******/ 			return Promise.all(Object.keys(__webpack_require__.f).reduce((promises, key) => {
+/******/ 				__webpack_require__.f[key](chunkId, promises);
+/******/ 				return promises;
+/******/ 			}, []));
+/******/ 		};
+/******/ 	})();
+/******/ 	
+/******/ 	/* webpack/runtime/get javascript chunk filename */
+/******/ 	(() => {
+/******/ 		// This function allow to reference async chunks and sibling chunks for the entrypoint
+/******/ 		__webpack_require__.u = (chunkId) => {
+/******/ 			// return url for filenames based on template
+/******/ 			return "" + chunkId + ".phylo.js";
+/******/ 		};
+/******/ 	})();
+/******/ 	
+/******/ 	/* webpack/runtime/global */
+/******/ 	(() => {
+/******/ 		__webpack_require__.g = (function() {
+/******/ 			if (typeof globalThis === 'object') return globalThis;
+/******/ 			try {
+/******/ 				return this || new Function('return this')();
+/******/ 			} catch (e) {
+/******/ 				if (typeof window === 'object') return window;
+/******/ 			}
+/******/ 		})();
+/******/ 	})();
+/******/ 	
+/******/ 	/* webpack/runtime/hasOwnProperty shorthand */
+/******/ 	(() => {
+/******/ 		__webpack_require__.o = (obj, prop) => (Object.prototype.hasOwnProperty.call(obj, prop))
+/******/ 	})();
+/******/ 	
+/******/ 	/* webpack/runtime/make namespace object */
+/******/ 	(() => {
+/******/ 		// define __esModule on exports
+/******/ 		__webpack_require__.r = (exports) => {
+/******/ 			if(typeof Symbol !== 'undefined' && Symbol.toStringTag) {
+/******/ 				Object.defineProperty(exports, Symbol.toStringTag, { value: 'Module' });
+/******/ 			}
+/******/ 			Object.defineProperty(exports, '__esModule', { value: true });
+/******/ 		};
+/******/ 	})();
+/******/ 	
+/******/ 	/* webpack/runtime/node module decorator */
+/******/ 	(() => {
+/******/ 		__webpack_require__.nmd = (module) => {
+/******/ 			module.paths = [];
+/******/ 			if (!module.children) module.children = [];
+/******/ 			return module;
+/******/ 		};
+/******/ 	})();
+/******/ 	
+/******/ 	/* webpack/runtime/publicPath */
+/******/ 	(() => {
+/******/ 		__webpack_require__.p = "";
+/******/ 	})();
+/******/ 	
+/******/ 	/* webpack/runtime/importScripts chunk loading */
+/******/ 	(() => {
+/******/ 		// no baseURI
+/******/ 		
+/******/ 		// object to store loaded chunks
+/******/ 		// "1" means "already loaded"
+/******/ 		var installedChunks = {
+/******/ 			"src_worker_bcn_js": 1
+/******/ 		};
+/******/ 		
+/******/ 		// importScripts chunk loading
+/******/ 		var installChunk = (data) => {
+/******/ 			var [chunkIds, moreModules, runtime] = data;
+/******/ 			for(var moduleId in moreModules) {
+/******/ 				if(__webpack_require__.o(moreModules, moduleId)) {
+/******/ 					__webpack_require__.m[moduleId] = moreModules[moduleId];
+/******/ 				}
+/******/ 			}
+/******/ 			if(runtime) runtime(__webpack_require__);
+/******/ 			while(chunkIds.length)
+/******/ 				installedChunks[chunkIds.pop()] = 1;
+/******/ 			parentChunkLoadingFunction(data);
+/******/ 		};
+/******/ 		__webpack_require__.f.i = (chunkId, promises) => {
+/******/ 			// "1" is the signal for "already loaded"
+/******/ 			if(!installedChunks[chunkId]) {
+/******/ 				if(true) { // all chunks have JS
+/******/ 					importScripts(__webpack_require__.p + __webpack_require__.u(chunkId));
+/******/ 				}
+/******/ 			}
+/******/ 		};
+/******/ 		
+/******/ 		var chunkLoadingGlobal = self["webpackChunkPhyloIO"] = self["webpackChunkPhyloIO"] || [];
+/******/ 		var parentChunkLoadingFunction = chunkLoadingGlobal.push.bind(chunkLoadingGlobal);
+/******/ 		chunkLoadingGlobal.push = installChunk;
+/******/ 		
+/******/ 		// no HMR
+/******/ 		
+/******/ 		// no HMR manifest
+/******/ 	})();
+/******/ 	
+/******/ 	/* webpack/runtime/startup chunk dependencies */
+/******/ 	(() => {
+/******/ 		var next = __webpack_require__.x;
+/******/ 		__webpack_require__.x = () => {
+/******/ 			return Promise.all(["vendors-node_modules_d3_index_js-node_modules_file-saver_dist_FileSaver_min_js","vendors-node_modules_biojs-io-newick_src_index_js-node_modules_minhashjs_index_js-node_module-7b40e5","src_utils_js"].map(__webpack_require__.e, __webpack_require__)).then(next);
+/******/ 		};
+/******/ 	})();
+/******/ 	
+/************************************************************************/
+/******/ 	
+/******/ 	// run startup
+/******/ 	var __webpack_exports__ = __webpack_require__.x();
+/******/ 	module.exports.PhyloIO = __webpack_exports__;
+/******/ 	
+/******/ })()
+;