phylojs/lib/io/readers/phyloXML.js

A simple typescript library for phylogenetic trees

"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
exports.PhyloXML = exports.readTreesFromPhyloXML = exports.readPhyloXML = void 0;
const __1 = require("../../");
const error_1 = require("../../utils/error");
function parse(phyloxml) {
    const parser = new DOMParser();
    const doc = parser.parseFromString(phyloxml, 'application/xml');
    return doc.getElementsByTagName('phylogeny');
}
/**
 * Read a tree from phyloXML format. If a list of trees is
 * @param {string} phyloxml
 * @returns {Tree}
 */
function readPhyloXML(phyloxml) {
    const phylogenyElements = parse(phyloxml);
    if (phylogenyElements.length === 0) {
        throw new Error('No phylogeny element found in phyloXML.');
    }
    const phylogenyElement = phylogenyElements[0];
    const phyloXML = new PhyloXML(phylogenyElement);
    if (!phyloXML.root) {
        throw new Error('Failed to parse the phyloXML data correctly.');
    }
    return new __1.Tree(phyloXML.root);
}
exports.readPhyloXML = readPhyloXML;
/**
 * Reads multiple trees from phyloXML format.
 * @param {string} phyloxml
 * @returns {Tree[]}
 */
function readTreesFromPhyloXML(phyloxml) {
    const trees = [];
    const phylogenyElements = parse(phyloxml);
    for (let i = 0; i < phylogenyElements.length; i++) {
        const phylogenyElement = phylogenyElements[i];
        try {
            const phyloXML = new PhyloXML(phylogenyElement);
            trees.push(new __1.Tree(phyloXML.root));
        }
        catch (SkipTreeException) {
            console.log(`Skipping phyloXML tree ${i}: Unrooted tree.`);
        }
    }
    return trees;
}
exports.readTreesFromPhyloXML = readTreesFromPhyloXML;
// TreeFromPhyloXML constructor
class PhyloXML {
    constructor(phylogenyElement) {
        this.thisNodeID = 0;
        this.root = this.walkDom(undefined, phylogenyElement);
        // Zero root edge length means undefined
        if (this.root.branchLength === 0.0)
            this.root.branchLength = undefined;
    }
    annotateNode(node, prefix, elements) {
        for (let j = 0; j < elements.length; j++) {
            const tname = elements[j].tagName;
            const tval = elements[j].textContent;
            node.annotation[prefix + '_' + tname] = tval;
        }
    }
    walkDom(parent, cladeElement) {
        const node = new __1.Node(this.thisNodeID++);
        if (parent !== undefined)
            parent.addChild(node);
        for (let i = 0; i < cladeElement.children.length; i++) {
            const childEl = cladeElement.children[i];
            const tagName = childEl.tagName;
            switch (tagName) {
                case 'clade':
                    this.walkDom(node, childEl);
                    break;
                case 'name':
                    if (childEl.textContent) {
                        node.label = childEl.textContent;
                    }
                    break;
                case 'taxonomy':
                    this.annotateNode(node, 'taxonomy', childEl.children);
                    break;
                case 'sequence':
                    this.annotateNode(node, 'sequence', childEl.children);
                    break;
                case 'confidence':
                    node.annotation[`confidence_${childEl.getAttribute('type') || ''}`] =
                        childEl.textContent;
                    break;
                case 'branch_length':
                    node.branchLength = Number(childEl.textContent);
                    break;
                case 'property': {
                    const refAttribute = childEl.getAttribute('ref');
                    if (refAttribute) {
                        // this checks both for null and empty string
                        node.annotation[refAttribute] = childEl.textContent;
                    }
                    break;
                }
                default:
                    break;
            }
        }
        const rootedAttribute = cladeElement.getAttribute('rooted');
        if (rootedAttribute && rootedAttribute.toLowerCase() === 'false')
            throw new error_1.SkipTreeException('Unrooted tree.');
        if (cladeElement.hasAttribute('branch_length'))
            node.branchLength = Number(cladeElement.getAttribute('branch_length'));
        return node;
    }
}
exports.PhyloXML = PhyloXML;