phylojs/lib/io/readers/nexus.js

A simple typescript library for phylogenetic trees

"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
exports.readTreesFromNexus = exports.readNexus = exports.getTranslateFromNexus = void 0;
const error_1 = require("../../utils/error");
const newick_1 = require("./newick");
// Function to extract the translate mapping
function getTranslateFromNexus(nexus) {
    const tmap = {};
    const lines = nexus.split('\n');
    let fullLine = '';
    for (let i = 1; i < lines.length; i++) {
        fullLine += lines[i].trim();
        // Remove comments
        fullLine = fullLine.replace(/\[[^&][^\]]*\]/g, '').trim();
        // Parse translate line
        if (fullLine.toLowerCase().startsWith('translate')) {
            const tStringArray = fullLine.slice(9, fullLine.length - 1).split(',');
            for (let j = 0; j < tStringArray.length; j++) {
                const tvec = tStringArray[j].trim().split(/\s+/);
                const tkey = tvec[0];
                let tval = tvec.slice(1).join(' ');
                tval = tval.replace(/^"(.*)"$/, '$1').replace(/^'(.*)'$/, '$1');
                tmap[tkey] = tval;
            }
            break;
        }
    }
    return tmap;
}
exports.getTranslateFromNexus = getTranslateFromNexus;
function translateTree(tree, tmap) {
    // traverse nodes
    tree.root.applyPreOrder(node => {
        // If node's identifier exists in tmap, replace it
        if (node.label && tmap[node.label]) {
            node.label = tmap[node.label];
        }
    });
    return tree;
}
function _getTreesFromNexus(nexus, singleTree) {
    const trees = [];
    const lines = nexus.split('\n');
    let inTrees = false;
    let fullLine = '';
    const tmap = getTranslateFromNexus(nexus); // Retrieve the translation mapping
    for (let i = 1; i < lines.length; i++) {
        fullLine += lines[i].trim();
        if (fullLine[fullLine.length - 1] !== ';')
            continue;
        // Remove comments
        fullLine = fullLine.replace(/\[[^&][^\]]*\]/g, '').trim();
        if (!inTrees) {
            if (fullLine.toLowerCase() === 'begin trees;')
                inTrees = true;
            fullLine = '';
            continue;
        }
        if (fullLine.toLowerCase() === 'end;')
            break;
        // Parse tree line
        const matches = /tree (\w|\.)+ *(\[&[^\]]*] *)* *= *(\[&[^\]]*] *)* */.exec(fullLine.toLowerCase());
        if (matches !== null) {
            const eqIdx = matches[0].length;
            try {
                let tree = (0, newick_1.readNewick)(fullLine.slice(eqIdx));
                tree = translateTree(tree, tmap); // Use the translation map here
                trees.push(tree);
                if (singleTree)
                    return trees; // If only one tree is requested, return immediately
            }
            catch (e) {
                if (e instanceof error_1.SkipTreeException) {
                    console.log('Skipping Nexus tree: ' + e.message);
                }
                else {
                    throw e;
                }
            }
        }
        fullLine = '';
    }
    return trees;
}
/**
 * Reads a tree from nexus format. Currently does not support custom annotation parsing.
 * @param {string} nexus
 * @returns {Tree}
 */
function readNexus(nexus) {
    const trees = _getTreesFromNexus(nexus, true);
    if (trees.length === 0) {
        throw new Error('No trees found in Nexus.');
    }
    return trees[0];
}
exports.readNexus = readNexus;
/**
 * Reads trees from from nexus format.
 * @param {string} nexus
 * @returns {Tree[]}
 */
function readTreesFromNexus(nexus) {
    const trees = _getTreesFromNexus(nexus, false);
    return trees;
}
exports.readTreesFromNexus = readTreesFromNexus;