import {PhyxWrapper} from '@phyloref/phyx/src/wrappers/PhyxWrapper.js'

public class | source

PhyxWrapper

The PhyxWrapper wraps an entire Phyx document.

Constructor Summary

Public Constructor
public	constructor(phyx: Object, newickParser: function(newick: string): {name) Wraps an entire PHYX document.

Member Summary

Public Members
public get	defaultNomenCode: *
public	newickParser: *
public	phyx: *

Method Summary

Public Methods
public	asJSONLD(baseIRI: string): Object Generate an executable ontology from this Phyx document.
public	toRDF(baseIRI: string, filePath: string): Promise[string] Generate an executable ontology from this Phyx document as N-Quads.

Public Constructors

public constructor(phyx: Object, newickParser: function(newick: string): {name) source

Wraps an entire PHYX document.

Params:

Name	Type	Attribute	Description
phyx	Object		The Phyx structure to wrap.
newickParser	function(newick: string): {name	optional default: PhylogenyWrapper.getParsedNewick	A method that accepts a Newick string and returns a list of nodes. Each node should have a 'children' key with its children and optionally a 'name' key with its label. This code previously depended on phylotree.js, whose newick_parser() function works exactly like this. This option allows you to drop in Phylotree's newick_parser() or -- if you prefer -- any other option.

Public Members

public get defaultNomenCode: * source

public newickParser: * source

public phyx: * source

Public Methods

public asJSONLD(baseIRI: string): Object source

Generate an executable ontology from this Phyx document. The document is mostly in JSON-LD already, except for three important things:

We have to convert all phylogenies into a series of statements relating to the nodes inside these phylogenies.
We have to convert phylogenies into OWL restrictions.
Insert all matches between taxonomic units in this file.

Params:

Name	Type	Attribute	Description
baseIRI	string	optional default: ""	The base IRI to use when generating this Phyx document. This should include a trailing '#' or '/'. Use '' to indicate that relative IDs should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a baseIRI is provided, then relative IDs already in the Phyx file (identified by an initial '#') will be turned into absolute IDs by removing the initial `#` and prepending them with the baseIRI.

Return:

Object

This Phyx document as an OWL ontology as a JSON-LD object.

public toRDF(baseIRI: string, filePath: string): Promise[string] source

Generate an executable ontology from this Phyx document as N-Quads. Under the hood, we generate an OWL/JSON-LD representation of this Phyx document, and then convert it into N-Quads so that OWLAPI-supporting tools can directly consume it.

Params:

Name	Type	Attribute	Description
baseIRI	string	optional default: ""	The base IRI to use when generating this Phyx document. This should include a trailing '#' or '/'. Use '' to indicate that relative IDs should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a baseIRI is provided, then relative IDs already in the Phyx file (identified by an initial '#') will be turned into absolute IDs by removing the initial `#` and prepending them with the baseIRI.
filePath	string	optional default: undefined	The path of the Phyx file being converted. Used only if the `@context` of the file is a relative path.

Return:

Promise[string]

A Promise to return this Phyx document as a string that can be written to an N-Quads file.