phylojs/lib/io/writers/newick.d.ts

A simple typescript library for phylogenetic trees

import { Node, Tree } from '../../';
/**
 * 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}
 */
export declare function writeNewick(tree: Tree, annotationWriter?: (annotation: typeof Node.prototype.annotation) => string): string;
/**
 * 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}
 */
export declare function newickRecurse(node: Node, annotationWriter?: (annotation: typeof Node.prototype.annotation) => string): string;
/**
 * 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}
 */
export declare function beastAnnotation(annotation: typeof Node.prototype.annotation): string;
/**
 * 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}
 */
export declare function nhxAnnotation(annotation: typeof Node.prototype.annotation): string;