phylojs/lib/io/readers/phyJSON.js

A simple typescript library for phylogenetic trees

"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
exports.readTreesFromPhyJSON = exports.readPhyJSON = void 0;
const __1 = require("../../");
function preprocessTaxa(taxa) {
    const taxaMap = {};
    for (const taxon of taxa) {
        if (taxon.id && taxon.name) {
            taxaMap[taxon.id] = taxon.name;
        }
    }
    return taxaMap;
}
function buildTree(node, taxaMap, currentId) {
    const tree = new __1.Node(currentId);
    tree.label = node.taxon ? taxaMap[node.taxon] || undefined : undefined; // Use taxaMap for label lookup
    tree.branchLength = node.branch_length;
    // Recursively handle children, if any
    if (node.children) {
        node.children.forEach((child, index) => {
            const childNode = buildTree(child, taxaMap, currentId + 1 + index); // Increment ID for each child uniquely
            tree.addChild(childNode);
        });
    }
    return tree; // Return the current tree node and the next available ID
}
function parse(phyNode, taxaMap) {
    const rootNode = buildTree(phyNode, taxaMap, 0);
    const tree = new __1.Tree(rootNode);
    return tree;
}
function readPhyJSON(phyJSONString) {
    const obj = JSON.parse(phyJSONString);
    const taxaMap = preprocessTaxa(obj.taxa);
    const phyRoot = obj.trees[0].root;
    return parse(phyRoot, taxaMap);
}
exports.readPhyJSON = readPhyJSON;
function readTreesFromPhyJSON(phyJSONString) {
    const obj = JSON.parse(phyJSONString);
    const taxaMap = preprocessTaxa(obj.taxa);
    const trees = [];
    for (const treeObj of obj.trees) {
        const tree = parse(treeObj.root, taxaMap);
        trees.push(tree);
    }
    return trees;
}
exports.readTreesFromPhyJSON = readTreesFromPhyJSON;