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import {PhylorefWrapper} from '@phyloref/phyx/src/wrappers/PhylorefWrapper.js'
public class | source

PhylorefWrapper

PhylorefWrapper

Static Method Summary

Static Public Methods
public static

getStatusCURIEsInEnglish(): {"pso: draft", "pso: final-draft", "pso: under-review", "pso: submitted", "pso: published", "pso: retracted-from-publication"}

public static

normalize(phyloref: *): *

Normalize a phyloreference.

Constructor Summary

Public Constructor
public

Member Summary

Public Members
public
public
public get

Returns a summarized nomenclatural code for this phyloref.
public get

Return the external specifiers of this phyloref (if any).
public get

Return the internal specifiers of this phyloref (if any).
public get

label: *

public set
public
public
public get

Return all the specifiers of this phyloref (if any).
public get

Return a list of all the unique nomenclatural codes used by this phyloreference.

Method Summary

Public Methods
public

asJSONLD(fallbackIRI: *): *

public

createClassExpressionsForInternals(jsonld: *, remainingInternals: *, selected: *): *

public

createComponentClass(jsonld: *, internalSpecifiers: *, externalSpecifiers: *, equivClass: *, reusePrevious: boolean, parentClass: *): *

Create a component class for the set of internal and external specifiers provided.
public

deleteSpecifier(specifier: *)

public

getCurrentStatus(): {"statusCURIE": string, "statusInEnglish": *}

public

getExpectedNodeLabels(phylogeny: *): *

public

getIncludesRestrictionForTU(tu: *): {"@type": string, "onProperty": string, "someValuesFrom": *}

public

getMRCARestrictionOfTwoTUs(tu1: *, tu2: *): {"@type": string, "onProperty": string, "someValuesFrom": *}

Return an OWL restriction for the most recent common ancestor (MRCA) of two taxonomic units.
public

getSpecifierType(specifier: *): string

public
public

setSpecifierType(specifier: *, specifierType: *)

public

setStatus(status: *)

Static Public Methods

public static getStatusCURIEsInEnglish(): {"pso: draft", "pso: final-draft", "pso: under-review", "pso: submitted", "pso: published", "pso: retracted-from-publication"} source

Return:

{"pso: draft", "pso: final-draft", "pso: under-review", "pso: submitted", "pso: published", "pso: retracted-from-publication"}

public static normalize(phyloref: *): * source

Normalize a phyloreference.

Params:

NameTypeAttributeDescription
phyloref *

Return:

*

Public Constructors

public constructor() source

Public Members

public componentClassCount: number source

public componentClassesByLabel: {} source

public get defaultNomenCode: * source

Returns a summarized nomenclatural code for this phyloref. If all of the specifiers have either the same nomenclatural code or undefined, this getter will return that nomenclatural code. Otherwise, this method will return owlterms.UNKNOWN_CODE.

public get externalSpecifiers: * source

Return the external specifiers of this phyloref (if any).

public get internalSpecifiers: * source

Return the internal specifiers of this phyloref (if any).

public get label: * source

public set label source

public phyloref: * source

public phyxDefaultNomenCode: * source

public get specifiers: * source

Return all the specifiers of this phyloref (if any).

public get uniqNomenCodes: * source

Return a list of all the unique nomenclatural codes used by this phyloreference. The default nomenclatural code used in creating the PhylorefWrapper will be used for any taxonomic units that don't have any nomenclatural code set. If any specifiers are not taxon concepts, they will be represented in the returned list as owlterms.UNKNOWN_CODE.

Public Methods

public asJSONLD(fallbackIRI: *): * source

Params:

NameTypeAttributeDescription
fallbackIRI *

Return:

*

public createClassExpressionsForInternals(jsonld: *, remainingInternals: *, selected: *): * source

Params:

NameTypeAttributeDescription
jsonld *
remainingInternals *
selected *

Return:

*

public createComponentClass(jsonld: *, internalSpecifiers: *, externalSpecifiers: *, equivClass: *, reusePrevious: boolean, parentClass: *): * source

Create a component class for the set of internal and external specifiers provided. We turn this into a label (in the form A & B ~ C V D), which we use to ensure that we don't create more than one class for a particular set of internal and external specifiers.

  • jsonld: The JSON-LD representation of the Phyloreference this is an component class for. We mainly use this to retrieve its '@id'.
  • internalSpecifiers: The set of internal specifiers for this component class.
  • externalSpecifiers: The set of external specifiers for this component class.
  • equivClass: The equivalent class expression for this component class as a function that returns the expression as a string.
  • reusePrevious (default: true): If true, we reuse previous expressions with the same set of included and excluded specifiers. If false, we always generate a new component class for this expression.
  • parentClass: If not undefined, provides a JSON-LD definition of the class to set as the parent class of this component class. We only use the ['@id'].

Params:

NameTypeAttributeDescription
jsonld *
internalSpecifiers *
externalSpecifiers *
equivClass *
reusePrevious boolean
  • optional
  • default: true
parentClass *
  • optional
  • default: undefined

Return:

*

public deleteSpecifier(specifier: *) source

Params:

NameTypeAttributeDescription
specifier *

public getCurrentStatus(): {"statusCURIE": string, "statusInEnglish": *} source

Return:

{"statusCURIE": string, "statusInEnglish": *}

public getExpectedNodeLabels(phylogeny: *): * source

Params:

NameTypeAttributeDescription
phylogeny *

Return:

*

public getIncludesRestrictionForTU(tu: *): {"@type": string, "onProperty": string, "someValuesFrom": *} source

Params:

NameTypeAttributeDescription
tu *

Return:

{"@type": string, "onProperty": string, "someValuesFrom": *}

public getMRCARestrictionOfTwoTUs(tu1: *, tu2: *): {"@type": string, "onProperty": string, "someValuesFrom": *} source

Return an OWL restriction for the most recent common ancestor (MRCA) of two taxonomic units.

Params:

NameTypeAttributeDescription
tu1 *
tu2 *

Return:

{"@type": string, "onProperty": string, "someValuesFrom": *}

public getSpecifierType(specifier: *): string source

Params:

NameTypeAttributeDescription
specifier *

Return:

string

public getStatusChanges(): *[] source

Return:

*[]

public setSpecifierType(specifier: *, specifierType: *) source

Params:

NameTypeAttributeDescription
specifier *
specifierType *

public setStatus(status: *) source

Params:

NameTypeAttributeDescription
status *