phylojs/lib/io/writers/newick.js

A simple typescript library for phylogenetic trees

"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
exports.nhxAnnotation = exports.beastAnnotation = exports.newickRecurse = exports.writeNewick = void 0;
/**
 * Writes tree in .newick format. Undefined branch lengths set to 0.
 * @param {tree} tree The tree to write
 * @param {annotationWriter} string Function parsing node annotations to string. Defaults to empty string - no annotation case. Can be user Defined or use in-build beastAnnotations or nhxAnnotations
 * @returns {string}
 */
function writeNewick(tree, annotationWriter = _annotation => '') {
    let newickStr = '';
    if (tree.root !== undefined)
        newickStr += newickRecurse(tree.root, annotationWriter) + ';';
    return newickStr;
}
exports.writeNewick = writeNewick;
/**
 * Recurses through tree, writing building up nwk string as it foes
 * @param {node} Node
 * @param {annotationWriter} string Function parsing Node.annotation to string. Defaults to empty string, not writing annotations. Can be user Defined or use in-build beastAnnotations or nhxAnnotations
 * @returns {string}
 */
function newickRecurse(node, annotationWriter = _annotation => '') {
    let res = '';
    if (!node.isLeaf()) {
        res += '(';
        for (let i = 0; i < node.children.length; i++) {
            if (i > 0)
                res += ',';
            res += newickRecurse(node.children[i], annotationWriter);
        }
        res += ')';
    }
    // TODO: Add hybrid type to node labels - H, LGT, or R
    if (node.label !== undefined && node.hybridID == undefined) {
        res += `"${node.label}"`;
    }
    else if (node.label !== undefined && node.hybridID !== undefined) {
        res += `"${node.label}"#${node.hybridID}`;
    }
    else if (node.label == undefined && node.hybridID !== undefined) {
        res += `#${node.hybridID}`;
    }
    res += annotationWriter(node.annotation);
    if (node.branchLength !== undefined) {
        node.branchLength == 0 ? (res += ':0.0') : (res += `:${node.branchLength}`);
    }
    return res;
}
exports.newickRecurse = newickRecurse;
/**
 * Writes node annotations to a string in the syle of BEAST.
 * Eg: [&Type=A,Cols={Red,Blue}]
 * @param {annotation} typeof Node.prototype.annotation
 * @returns {string}
 */
function beastAnnotation(annotation) {
    let res = '';
    if (annotation !== undefined) {
        const keys = Object.keys(annotation);
        if (keys.length > 0) {
            res += '[&';
            for (let i = 0; i < keys.length; i++) {
                const key = keys[i];
                if (i > 0)
                    res += ',';
                res += `${key}=`;
                const value = annotation[key];
                if (Array.isArray(value)) {
                    res += `{${String(value.join(','))}}`; // Convert the array to a comma-separated string
                }
                else {
                    res += `${String(value)}`; // Explicitly convert the value to a string
                }
            }
            res += ']';
        }
    }
    return res;
}
exports.beastAnnotation = beastAnnotation;
/**
 * Writes node annotations to a string in the syle of NHX.
 * Eg: [&&NHX:Type=A:Col=Red]. NHX does not appear to support
 * array date for annotations. Please get in touch if it does!
 * @param {annotation} typeof Node.prototype.annotation
 * @returns {string}
 */
function nhxAnnotation(annotation) {
    let res = '';
    if (annotation !== undefined) {
        const keys = Object.keys(annotation);
        if (keys.length > 0) {
            res += '[&&NHX:';
            for (let i = 0; i < keys.length; i++) {
                const key = keys[i];
                if (i > 0)
                    res += ':';
                res += `${key}=`;
                const value = annotation[key];
                res += `${String(value)}`; // Explicitly convert the value to a string
            }
            res += ']';
        }
    }
    return res;
}
exports.nhxAnnotation = nhxAnnotation;