phyloio 2.1.1 → 2.2.3

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Files changed (20) hide show
  1. package/Examples/Website/phyloio.html +0 -6
  2. package/dist/phylo.js +278 -245
  3. package/dist/src_worker_bcn_js.phylo.js +226 -226
  4. package/dist/src_worker_distance_js.phylo.js +211 -211
  5. package/{Examples/Website/src_worker_bcn_js.phylo.js → dist-jest/phylo.js} +1150 -234
  6. package/dist-jest/src_utils_js.phylo.js +21 -0
  7. package/dist-jest/src_worker_bcn_js.phylo.js +350 -0
  8. package/dist-jest/src_worker_distance_js.phylo.js +219 -0
  9. package/dist-jest/vendors-node_modules_biojs-io-newick_src_index_js-node_modules_minhashjs_index_js-node_module-7b40e5.phylo.js +1713 -0
  10. package/{Examples/Website/src_worker_distance_js.phylo.js → dist-jest/vendors-node_modules_d3_index_js-node_modules_file-saver_dist_FileSaver_min_js.phylo.js} +212 -310
  11. package/package.json +1 -1
  12. package/rerooting.test.js +297 -0
  13. package/src/container.js +14 -16
  14. package/src/interface.js +7 -6
  15. package/src/model.js +24 -22
  16. package/src/utils.js +9 -2
  17. package/src/viewer.js +6 -2
  18. package/Plot-ai-grant.ipynb +0 -296
  19. package/package-lock.json +0 -19607
  20. package/src/tmp +0 -12
package/dist-jest/src_utils_js.phylo.js ADDED
@@ -0,0 +1,21 @@
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+ /*
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+ * ATTENTION: The "eval" devtool has been used (maybe by default in mode: "development").
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+ * This devtool is neither made for production nor for readable output files.
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+ * It uses "eval()" calls to create a separate source file in the browser devtools.
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+ * If you are trying to read the output file, select a different devtool (https://webpack.js.org/configuration/devtool/)
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+ * or disable the default devtool with "devtool: false".
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+ * If you are looking for production-ready output files, see mode: "production" (https://webpack.js.org/configuration/mode/).
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+ */
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+ (self["webpackChunkPhyloIO"] = self["webpackChunkPhyloIO"] || []).push([["src_utils_js"],{
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+
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+ /***/ "./src/utils.js":
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+ /*!**********************!*\
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+ !*** ./src/utils.js ***!
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+ \**********************/
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+ /***/ ((module, __unused_webpack_exports, __webpack_require__) => {
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+
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+ eval("const fs = __webpack_require__(/*! file-saver */ \"./node_modules/file-saver/dist/FileSaver.min.js\")\nconst d3 = __webpack_require__(/*! d3 */ \"./node_modules/d3/index.js\");\n\nfunction 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 = 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\nfunction build_table(hierarchy){\n\n traverse(hierarchy, function(node,children){\n delete node.left_\n delete node.right_\n delete node.weight_\n }, null)\n\n var n = hierarchy.leaves().length\n var X = Array.from(new Array(n), _ => Array(3).fill(null));\n var S2I = {} //Array(n).fill(0)\n var I2S = Array(n).fill(null)\n var n_edges = 0\n\n var nzl = []\n traverse(hierarchy, null, function(node,children){nzl.push(node)})\n nzl.push(hierarchy)\n var nz = nzl.entries()\n\n var n1 = nz.next()\n var n2 = nz.next()\n var i = 0\n\n while (true) {\n\n var node = n1.value[1]\n var node2 = n2.value[1]\n var p = node.parent\n var ii;\n\n // Do work\n if (!(node.hasOwnProperty('children'))) {\n I2S[i] = node.data.name\n S2I[I2S[i]] = i\n node.weight_ = 0\n node.left_ = i\n node.right_ = i\n i += 1\n }\n\n // propagate up\n if (typeof p != \"undefined\"){\n p.left_ = p.hasOwnProperty('left_') ? Math.min(p.left_, node.left_) : node.left_\n p.right_ = p.hasOwnProperty('right_') ? Math.max(p.right_, node.right_) : node.right_\n if (p.hasOwnProperty('weight_')){ p.weight_ = p.weight_ + node.weight_ + 1} else {p.weight_ = node.weight_ +=1}\n }\n\n if (node.hasOwnProperty('children')) {\n\n if( node2.hasOwnProperty('weight_') && node2.weight_ > 0 ){ii = node.left_} else { ii = node.right_}\n X[ii][0] = node.left_\n X[ii][1] = node.right_\n if (node.data.hasOwnProperty('branch_length')){\n X[ii][2] = node.data.branch_length\n }\n else {\n X[ii][2] = 1\n }\n\n\n n_edges += 1\n\n }\n\n n1 = n2\n n2 = nz.next()\n\n if (n2.done){\n\n\n // process seed node, w=0\n ii = hierarchy.leaves().length-1\n X[ii][0] = n1.value[1].left_\n X[ii][1] = n1.value[1].right_\n X[ii][2] = n1.value[1].data.branch_length\n n_edges += 1\n\n break\n }\n\n }\n\n\n\n if (X[0][0] !== null){\n X[0] = Array(3).fill(null)\n\n }\n\n n_edges = 0\n for (const n2Key in X) {\n if (X[n2Key][0] !== null){\n n_edges++\n }\n\n }\n\n var leaf_to_dist = {}\n\n hierarchy.leaves().forEach( e=> { leaf_to_dist[e.data.name] = e.data.branch_length })\n\n\n return {'table': X, 'n_edges': n_edges, 'I2S': I2S, 'S2I': S2I, 'leaf_dict': leaf_to_dist}\n\n\n}\n\nfunction reverse_order(child,parent){\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\nfunction reroot_hierarchy(hierarchy, leaf_name){\n\n\n let leaf = hierarchy.leaves().find(element => element.data.name == leaf_name );\n\n // INVERT PATH TO ROOT\n var ancestors = leaf.ancestors()\n leaf.children = []\n leaf.root = true\n\n\n //leaf.branch_length_before_reverse = leaf.data.branch_length\n\n/*\n for (var j = 0; j < leaf.parent.children.length; j++) {\n\n if (leaf.parent.children[j] != leaf){\n\n leaf.data.branch_length = leaf.parent.children[j].data.branch_length\n break\n\n }\n\n }\n\n */\n\n\n var index\n for (index = 0; index < ancestors.length; index++) {\n\n let child = (index === 0) ? leaf : ancestors[index-1]\n let parent = ancestors[index]\n\n\n /*\n parent.branch_length_before_reverse = parent.data.branch_length\n if (child.branch_length_before_reverse){\n parent.data.branch_length = child.branch_length_before_reverse\n }\n else{\n parent.data.branch_length = child.data.branch_length\n }\n */\n\n\n reverse_order(child,parent)\n }\n\n //DESTROY ROOT\n var old_root_children = ancestors[ancestors.length-1].children\n\n var c = ancestors[ancestors.length-2].children.indexOf(ancestors[ancestors.length-1]);\n if (c > -1) {\n ancestors[ancestors.length-2].children.splice(c, 1);\n }\n for (var j = 0; j < old_root_children.length; j++) {\n\n let parent = old_root_children[j]\n let child = ancestors[ancestors.length-2]\n\n child.children.push(parent)\n parent.parent =child\n }\n\n leaf.parent = null\n leaf.data.branch_length = leaf.children[0].data.branch_length\n\n return leaf\n}\n\nfunction addLogo(svg) {\n // TODO load with ajax\n var logo_xml = '<svg id=\"exportLogo\" x=\"0\" y=\"0\"><g 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style=\"fill:#939598;fill-opacity:1\" /> </g> </g> </g> </g> </svg>';\n\n svg.append(\"g\").html(logo_xml);\n\n}\n\nfunction getSVGString( svgNode ) {\n svgNode.setAttribute('xlink', 'http://www.w3.org/1999/xlink');\n var cssStyleText = getCSSStyles(svgNode);\n cssStyleText += \"* {font-family:Helvetica}\"\n appendCSS( cssStyleText, svgNode );\n\n var serializer = new XMLSerializer();\n var svgString = serializer.serializeToString(svgNode);\n svgString = svgString.replace(/(\\w+)?:?xlink=/g, 'xmlns:xlink='); // Fix root xlink without namespace\n svgString = svgString.replace(/NS\\d+:href/g, 'xlink:href'); // Safari NS namespace fix\n\n return svgString;\n\n function getCSSStyles( parentElement ) {\n var selectorTextArr = [];\n\n // Add Parent element Id and Classes to the list\n selectorTextArr.push( '#'+parentElement.id );\n for (var c = 0; c < parentElement.classList.length; c++)\n if ( !contains('.'+parentElement.classList[c], selectorTextArr) )\n selectorTextArr.push( '.'+parentElement.classList[c] );\n\n // Add Children element Ids and Classes to the list\n var nodes = parentElement.getElementsByTagName(\"*\");\n for (var i = 0; i < nodes.length; i++) {\n var id = nodes[i].id;\n if ( !contains('#'+id, selectorTextArr) )\n selectorTextArr.push( '#'+id );\n\n var classes = nodes[i].classList;\n for (var c = 0; c < classes.length; c++)\n if ( !contains('.'+classes[c], selectorTextArr) )\n selectorTextArr.push( '.'+classes[c] );\n }\n\n // Extract CSS Rules\n var extractedCSSText = \"\";\n for (var i = 0; i < document.styleSheets.length; i++) {\n var s = document.styleSheets[i];\n\n try {\n if(!s.cssRules) continue;\n } catch( e ) {\n if(e.name !== 'SecurityError') throw e; // for Firefox\n continue;\n }\n\n var cssRules = s.cssRules;\n for (var r = 0; r < cssRules.length; r++) {\n if ( contains( cssRules[r].selectorText, selectorTextArr ) )\n extractedCSSText += cssRules[r].cssText;\n }\n }\n\n\n return extractedCSSText;\n\n function contains(str,arr) {\n return arr.indexOf( str ) === -1 ? false : true;\n }\n\n }\n\n function appendCSS( cssText, element ) {\n var styleElement = document.createElement(\"style\");\n styleElement.setAttribute(\"type\",\"text/css\");\n styleElement.innerHTML = cssText;\n var refNode = element.hasChildNodes() ? element.children[0] : null;\n element.insertBefore( styleElement, refNode );\n }\n}\n\nfunction svgString2Image( svgString, width, height, format, callback ) {\n var format = format ? format : 'png';\n\n var imgsrc = 'data:image/svg+xml;base64,'+ btoa( unescape( encodeURIComponent( svgString ) ) ); // Convert SVG string to dataurl\n\n var canvas = document.createElement(\"canvas\");\n var context = canvas.getContext(\"2d\");\n\n canvas.width = width;\n canvas.height = height;\n\n var image = new Image;\n image.onload = function() {\n\n context.clearRect ( 0, 0, width, height );\n context.fillStyle = \"#ffffff\";\n context.fillRect(0, 0, width, height);\n context.drawImage(image, 0, 0, width, height);\n\n canvas.toBlob( function(blob) {\n var filesize = Math.round( blob.length/1024 ) + ' KB';\n if ( callback ) callback( blob, filesize );\n });\n };\n image.src = imgsrc;\n}\n\nfunction screen_shot({ svg1, svg2, format } = {}){\n\n addLogo(svg1);\n var name1 = svg1.attr(\"id\");\n var svgString1 = getSVGString(svg1.node());\n\n var t = \"<svg xmlns=\\\"http://www.w3.org/2000/svg\\\" version=\\\"1.1\\\">\\n\" +\n \"\\n\" +\n \" <g transform=\\\"translate(0,0)\\\">\\n\" +\n svgString1 +\n \" </g>\\n\"\n\n if(svg2){\n\n addLogo(svg2);\n var name2 = svg2.attr(\"id\");\n var svgString2 = getSVGString(svg2.node());\n\n var w = svg2.node().getBoundingClientRect().width\n var h = svg2.node().getBoundingClientRect().height\n\n t += '<line x1=\"' + (w + 5) +'\" y1=\"0\" x2=\"' + (w + 5) +'\" y2=\"' + h+'\" stroke=\"black\" />'\n\n t += \" <g transform=\\\"translate(\" + (w + 10) +\",0)\\\">\\n\" +\n svgString2 +\n \" </g>\\n\"\n\n }\n\n t += \"</svg> \"\n\n if(format === 'svg') {\n\n var blob = new Blob([t], {\"type\": \"image/svg+xml;base64,\"+ btoa(t)});\n fs.saveAs(blob, name1+\".svg\");\n svg1.select(\"#exportLogo\").remove();\n if(svg2){svg2.select(\"#exportLogo\").remove();}\n\n }\n\n else if (format === 'png'){\n\n\n\n var wi = svg1.node().getBoundingClientRect().width\n var he = svg1.node().getBoundingClientRect().height\n\n if(svg2){\n wi = wi*2;\n }\n\n svgString2Image(t, wi, he, 'png', save);\n\n svg1.select(\"#exportLogo\").remove();\n if(svg2){svg2.select(\"#exportLogo\").remove();}\n\n function save(dataBlob, filesize) {\n var filename = (name) ? name+\".\" : \"\";\n fs.saveAs(dataBlob, filename+'phylo.io.png'); // FileSaver.js function\n }\n\n }\n}\n\n//Adapted from Extended Newick format parser in JavaScript.\n//Copyright (c) Miguel Pignatelli 2014 based on Jason Davies\nfunction parse_nhx(s) {\n var ancestors = [];\n var tree = {'data_nhx' : {}};\n // var tokens = s.split(/\\s*(;|\\(|\\)|,|:)\\s*/);\n //[&&NHX:D=N:G=ENSG00000139618:T=9606]\n var tokens = s.split( /\\s*(;|\\(|\\)|\\[|\\]|,|:|=)\\s*/ );\n for (var i=0; i<tokens.length; i++) {\n var token = tokens[i];\n switch (token) {\n case '(': // new children\n var subtree = {'data_nhx' : {}};\n tree.children = [subtree];\n ancestors.push(tree);\n tree = subtree;\n break;\n case ',': // another branch\n var subtree = {'data_nhx' : {}};\n ancestors[ancestors.length-1].children.push(subtree);\n tree = subtree;\n break;\n case ')': // optional name next\n tree = ancestors.pop();\n break;\n case ':': // optional length next\n break;\n default:\n var x = tokens[i-1];\n // var x2 = tokens[i-2];\n if (x == ')' || x == '(' || x == ',') {\n tree.name = token;\n }\n else if (x == ':') {\n var test_type = typeof token;\n if(!isNaN(token)){\n tree.branch_length = parseFloat(token);\n }\n // tree.length = parseFloat(token);\n }\n else if (x == '='){\n tree['data_nhx'][tokens[i-2]] = token\n }\n else {\n var test;\n }\n }\n }\n return tree;\n};\n\nfunction save_file_as(filename, data) {\n const blob = new Blob([data], {type: 'text/csv'});\n if(window.navigator.msSaveOrOpenBlob) {\n window.navigator.msSaveBlob(blob, filename);\n }\n else{\n const elem = window.document.createElement('a');\n elem.href = window.URL.createObjectURL(blob);\n elem.download = filename;\n document.body.appendChild(elem);\n elem.click();\n document.body.removeChild(elem);\n }\n}\n\nfunction compute_RF_Euc(X1,X2){\n\n var n_good = 0\n var euclidian = 0.00\n\n var x2_processed = []\n\n for (var i = 0; i < X1.table.length; i++) {\n var s1 = X1.table[i][0]\n var e1 = X1.table[i][1]\n var w1 = Math.abs(e1-s1)\n\n if (w1 > 0){\n\n var species = X1.I2S.slice(s1,e1+1)\n var index = []\n\n for (const [name, idx] of Object.entries(X2.S2I)) {\n if (species.includes(name)) {index.push(idx)}\n }\n\n if (index.length <= 0) {\n continue\n }\n\n var s2 = Math.min.apply(null,index)\n var e2 = Math.max.apply(null,index)\n var w2 = Math.abs(e2-s2)\n\n if (w1 == w2) {\n\n\n if (X2.table[e2][0] == s2 && X2.table[e2][1] == e2) {\n n_good += 1\n euclidian += Math.abs(parseFloat(X1.table[i][2]) - parseFloat(X2.table[e2][2]) )\n x2_processed.push(e2)\n }\n else if (X2.table[s2][0] == s2 && X2.table[s2][1] == e2){\n\n n_good += 1\n euclidian += Math.abs(parseFloat(X1.table[i][2]) - parseFloat(X2.table[s2][2]) )\n x2_processed.push(s2)\n\n }\n else{\n euclidian += parseFloat(X1.table[i][2])\n\n }\n\n }\n\n\n else{\n euclidian += parseFloat(X1.table[i][2])\n }\n\n\n\n\n\n\n }\n\n }\n\n\n for (var k = 1; k < X2.table.length; k++) {\n if (!x2_processed.includes(k)){\n\n var d = parseFloat(X2.table[k][2])\n\n if(!isNaN(d)) {\n euclidian += d\n x2_processed.push(k)\n }\n\n }\n }\n\n var leaf_dist = 0.00\n for (var key of Object.keys(X1.leaf_dict)) {\n\n leaf_dist += Math.abs(X1.leaf_dict[key] - X2.leaf_dict[key])\n }\n\n var euc = euclidian + leaf_dist\n\n\n return {\n 'E':euc.toFixed(2),\n 'RF': (X1.n_edges + X2.n_edges -2*n_good),\n 'good':n_good,\n 'L':X1.n_edges,\n 'R':X2.n_edges,\n\n }\n}\n\nfunction get_intersection_leaves(h1, h2){\n\n var leaves1 = h1.leaves().map(x => x.data.name);\n var leaves2 = h2.leaves().map(x => x.data.name);\n return Array.from(new Set(leaves1.filter(value => leaves2.includes(value))))\n}\n\nfunction r_child(parent,child){\n let index = parent.children.indexOf(child);\n if (index > -1) {\n parent.children.splice(index, 1);\n }\n}\n\nfunction get_duplicated(array){\n return array.filter((e, i, a) => a.indexOf(e) !== i)\n}\n\nfunction remove_from_array(array, to_remove){\n\n return array.filter(element => !to_remove.includes(element));\n\n}\n\nfunction remove_duplicated_and_unnamed_leaves_hierarchy(h){\n\n var leaf_space = []\n\n h.eachAfter(d => {\n\n if (d.parent && !d.children){\n\n if (d.data.name.length === 0){\n r_child(d.parent,d)\n d= null;\n }\n else {\n leaf_space.push(d.data.name)\n }\n }\n\n\n });\n\n var dup = get_duplicated(leaf_space)\n\n\n var to_keep = remove_from_array(leaf_space, dup)\n\n return filter_leaves_hierarchy(h, to_keep)\n}\n\nfunction filter_leaves_hierarchy(h, leaves_to_keep){\n\n\n h.eachAfter(d => {\n\n if (d.children && d.parent){\n\n if (d.children.length === 0){\n r_child(d.parent, d)\n d = null\n }\n\n else if (d.children.length === 1){\n r_child(d.parent, d)\n d.parent.children.push(d.children[0])\n d.children[0].parent = d.parent\n d = null\n\n }\n }\n\n else if (d.parent){\n\n if (!leaves_to_keep.includes(d.data.name)){\n r_child(d.parent,d)\n d= null;\n }\n }\n\n\n });\n\n if (Array.from(new Set(h.leaves().map(x => x.data.name))).length == leaves_to_keep.length){\n return h\n }\n\n return false\n}\n\nfunction check_whole_hierarchy_labelled(hierarchy ){\n\n\n traverse(hierarchy, function(node,children){\n\n if (typeof node.data['duplication'] === 'undefined' ){\n node.data['duplication'] = false\n }\n\n\n }, null)\n\n return\n}\n\nfunction buildX(hierarchy){\n\n/*\n Define the table X according to (Day 1985) to have contiguous integers for\n each clade, and define a clade by the left-most and right-most identifiers,\n such as [4,7] for the clade [4,5,6,7].\n\n Note we extend the table to contain the following fields,\n which will be populated later in the algorithm:\n 3: node defining the clade in T1\n 4: node defining the clade in T2\n 5: size of the island rooted in the clade in T1\n 6: size of the island rooted in the clade in T2\n 7: labels in the island rooted in the clade in T1\n 8: labels in the island rooted in the clade in T2\n\n */\n\n var X = []\n var n = hierarchy.leaves().length\n var tax2id = {}\n var n2bip = new Map();\n\n function buildX_r(T){\n if (T.children == null && T._children == null){\n // left right id2taxon nodeT1 nodeT2 sizeIsland1 sizeIsland2 labels1 labels2\n X.push([0,0,T.data.name,0,0,0,0,new Set(),new Set()])\n i = X.length -1\n tax2id[T.data.name] = i\n return [i,i]\n }\n\n else{\n let min_l = n\n let max_r = 0\n\n for (var j = 0; j < T.children.length; j++) {\n var c = T.children[j]\n\n var [l,r] = buildX_r(c)\n min_l = Math.min(l,min_l)\n max_r = Math.max(r,max_r)\n\n }\n\n X[min_l][0]=X[max_r][0]=min_l\n X[min_l][1]=X[max_r][1]=max_r\n X[min_l][3]=X[max_r][3]=T\n n2bip.set(T, [min_l,max_r]);\n\n\n return [min_l,max_r]\n }\n\n }\n\n buildX_r(hierarchy)\n\n return [X, tax2id, n2bip]\n}\n\nfunction findgood(hierarchy,X,tax2id){\n\n\n function findgood_r(T){\n\n if (T.children == null && T._children == null){\n var i = tax2id[T.data.name]\n\n return [i,i,1]\n }\n else {\n var min_l = n\n var max_r=0\n var tot_w=0\n\n for (var j = 0; j < T.children.length; j++) {\n\n var c = T.children[j]\n\n var [l, r, w] = findgood_r(c)\n\n min_l = Math.min(l, min_l)\n max_r = Math.max(r, max_r)\n tot_w += w\n }\n\n if (max_r-min_l+1 == tot_w){\n\n if (X[min_l][0]==min_l && X[min_l][1]==max_r){\n X[min_l][4]= T\n n2bip.set(T, [min_l,max_r]);\n }\n else if (X[max_r][0]==min_l && X[max_r][1]==max_r) {\n X[max_r][4]=T\n n2bip.set(T, [min_l,max_r]);\n }\n }\n\n return [min_l,max_r,tot_w]\n\n\n }\n }\n\n var n2bip = new Map();\n var n = hierarchy.leaves().length\n\n findgood_r(hierarchy)\n\n return(n2bip)\n}\n\nfunction getIslandsDay(t,X,n2bip,isT1){\n\n /*\n An island is separated from the rest of the tree\n by good edges. In the traversal below, we do a preorder\n traversal and create a new island whenever we meet a clade\n defined in X\n ____\n /\n **** x6\n * \\___\n **** x3 ......\n * \\___ ______x7\n ----x1 / ...\n * **** x4 ____\n **** x2 ``-- /\n *********** x5\n \\_____\n\n */\n\n function mytraversal(t,parentIslandId=0){\n\n if (t.children == null && t._children == null){\n return\n }\n\n if (n2bip.has(t)){\n var [l,r] = n2bip.get(t)\n }\n else {\n var l = 0;\n var r = 0;\n }\n\n var row = -1\n\n if (X[l][0]===l && X[l][1]===r && X[l][4]!==0){\n row = l\n }\n\n else if (X[r][0]===l && X[r][1]===r && X[r][4]!==0){\n row = r\n }\n\n // CLADE IS COMMON\n if (row > -1){\n\n // end of previous island, so new island.\n islandId = row\n X[row][off+2].add(t.data.duplication)\n\n\n for (var j = 0; j < t.children.length; j++) {\n var c = t.children[j]\n mytraversal(c,islandId)\n\n }\n\n }\n else {\n // continue previous island\n var islandId = parentIslandId\n\n X[islandId][off+2].add(t.data.duplication)\n X[islandId][off] += 1\n\n for (var j = 0; j < t.children.length; j++) {\n var c = t.children[j]\n\n mytraversal(c,islandId)\n\n }\n\n }\n\n }\n\n\n var off;\n\n if (isT1){\n off = 5\n }\n else{\n off = 6\n }\n\n mytraversal(t)\n\n return\n\n}\n\n// ADAPTED FROM https://github.com/DessimozLab/pylabeledrf\nfunction compute_LRF(t1, t2){\n\n var [ X, tax2id, n12bip ] = buildX(t1)\n\n var n22bip = findgood(t2,X,tax2id)\n\n getIslandsDay(t1,X,n12bip,true)\n getIslandsDay(t2,X,n22bip,false)\n\n\n var rf = 0;\n var subs = 0;\n\n for (var i = 0; i < X.length; i++) {\n\n if (X[i][4] != 0){\n\n rf += X[i][5]+X[i][6]\n\n let intersection = new Set( [...X[i][7]].filter(x => X[i][8].has(x)));\n\n if ( intersection.size == 0){\n subs +=1\n }\n }\n }\n\n return rf+subs\n\n}\n\nfunction prepare_and_run_distance(m1,m2){\n\n var distance = {\n 'no_distance_message': true,\n 'clade': false,\n 'Cl_good': false,\n 'Cl_left': false,\n 'Cl_right': false,\n 'RF': false,\n 'RF_good': false,\n 'RF_left': false,\n 'RF_right': false,\n 'Euc': false,\n 'LRF':false\n }\n\n // CHECK INTERSECTING LEAVES\n var h1_raw = d3.hierarchy(m1.data, d => d.children );\n var h2_raw = d3.hierarchy(m2.data, d => d.children );\n\n var h1 = remove_duplicated_and_unnamed_leaves_hierarchy(h1_raw)\n var h2 = remove_duplicated_and_unnamed_leaves_hierarchy(h2_raw)\n\n var intersection = get_intersection_leaves(h1,h2)\n\n if (intersection.length == 0){\n distance.no_distance_message = 'No leaves in common to compute distance.'\n return distance\n }\n\n // FILTER TREE TO KEEP ONLY INTERSECTING LEAVES\n var hierachy1 = filter_leaves_hierarchy(h1, intersection )\n var table1 = build_table(hierachy1 )\n\n var hierachy2 = filter_leaves_hierarchy(h2, intersection )\n var table2 = build_table(hierachy2 )\n\n // CLADISTIC DISTANCE & EUCLIDIAN\n var r = compute_RF_Euc(table1,table2)\n distance.clade = r.RF\n distance.Cl_good = r.good\n distance.Cl_left = r.L\n distance.Cl_right = r.R\n distance.Euc = r.E\n\n // RF\n var hierarchy_mockup_rerooted1 = reroot_hierarchy(hierachy1, intersection[0])\n var hierarchy_mockup_rerooted2 = reroot_hierarchy(hierachy2, intersection[0])\n\n // build tables\n var X1 = build_table(hierarchy_mockup_rerooted1)\n var X2 = build_table(hierarchy_mockup_rerooted2)\n\n var r2 = compute_RF_Euc(X1,X2)\n distance.RF = r2.RF\n distance.RF_good = r2.good\n distance.RF_left = r2.L\n distance.RF_right = r2.R\n\n\n // LRF\n if ( m1.settings.has_duplications && m2.settings.has_duplications) {\n check_whole_hierarchy_labelled(hierarchy_mockup_rerooted1)\n check_whole_hierarchy_labelled(hierarchy_mockup_rerooted2)\n\n distance.LRF = compute_LRF(hierarchy_mockup_rerooted1, hierarchy_mockup_rerooted2,'duplication' )\n }\n\n return distance\n}\n\nfunction check_if_color(query){\n var accepted_spelling = ['color', 'colour'];\n\n if (accepted_spelling.includes(query.toLowerCase())){\n return true;\n }\n else {\n return false;\n }\n}\n\nfunction hexToRgb(hex){\n if (typeof hex === 'object' && hex.r !== undefined) {\n return hex;\n }\n if (typeof hex === 'string' && hex.startsWith('rgb')) {\n const values = hex.match(/\\d+/g).map(Number);\n return { r: values[0], g: values[1], b: values[2] };\n }\n const bigint = parseInt(hex.slice(1), 16);\n const r = (bigint >> 16) & 255;\n const g = (bigint >> 8) & 255;\n const b = bigint & 255;\n return { r, g, b };\n}\n\nfunction colorDifference(hex1, hex2) {\n const color1 = hexToRgb(hex1);\n const color2 = hexToRgb(hex2);\n const rDiff = color1.r - color2.r;\n const gDiff = color1.g - color2.g;\n const bDiff = color1.b - color2.b;\n const distance = Math.sqrt(rDiff * rDiff + gDiff * gDiff + bDiff * bDiff);\n const maxDistance = Math.sqrt(255 * 255 * 3);\n return (distance / maxDistance);\n}\n\nmodule.exports = {colorDifference, check_if_color, prepare_and_run_distance, build_table, reroot_hierarchy, screen_shot, parse_nhx, save_file_as, compute_RF_Euc, get_intersection_leaves, filter_leaves_hierarchy, remove_duplicated_and_unnamed_leaves_hierarchy};\n\n\n\n\n//# sourceURL=webpack://PhyloIO/./src/utils.js?");
18
+
19
+ /***/ })
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+
21
+ }]);