import {PhylorefWrapper} from '@phyloref/phyx/src/wrappers/PhylorefWrapper.js'PhylorefWrapper
PhylorefWrapper
Static Method Summary
| Static Public Methods | ||
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getStatusCURIEsInEnglish(): {"pso: draft", "pso: final-draft", "pso: under-review", "pso: submitted", "pso: published", "pso: retracted-from-publication"} |
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Constructor Summary
| Public Constructor | ||
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Member Summary
| Public Members | ||
| public |
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| public |
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| public get |
Returns a summarized nomenclatural code for this phyloref. |
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| public get |
Return the external specifiers of this phyloref (if any). |
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| public get |
Return the internal specifiers of this phyloref (if any). |
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| public get |
label: * |
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| public set |
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phyloref: * |
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specifiers: * Return all the specifiers of this phyloref (if any). |
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| public get |
Return a list of all the unique nomenclatural codes used by this phyloreference. |
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Method Summary
| Public Methods | ||
| public |
asJSONLD(fallbackIRI: *): * |
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createClassExpressionsForInternals(jsonld: *, remainingInternals: *, selected: *): * |
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createComponentClass(jsonld: *, internalSpecifiers: *, externalSpecifiers: *, equivClass: *, reusePrevious: boolean, parentClass: *): * Create a component class for the set of internal and external specifiers provided. |
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deleteSpecifier(specifier: *) |
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getCurrentStatus(): {"statusCURIE": string, "statusInEnglish": *} |
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getExpectedNodeLabels(phylogeny: *): * |
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getIncludesRestrictionForTU(tu: *): {"@type": string, "onProperty": string, "someValuesFrom": *} |
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getMRCARestrictionOfTwoTUs(tu1: *, tu2: *): {"@type": string, "onProperty": string, "someValuesFrom": *} Return an OWL restriction for the most recent common ancestor (MRCA) of two taxonomic units. |
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getSpecifierType(specifier: *): string |
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getStatusChanges(): *[] |
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setSpecifierType(specifier: *, specifierType: *) |
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setStatus(status: *) |
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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 Constructors
public constructor() source
Public Members
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 label: * source
public set label source
public phyloref: * source
public phyxDefaultNomenCode: * source
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:
| Name | Type | Attribute | Description |
| fallbackIRI | * |
Return:
| * |
public createClassExpressionsForInternals(jsonld: *, remainingInternals: *, selected: *): * source
Params:
| Name | Type | Attribute | Description |
| 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:
| Name | Type | Attribute | Description |
| jsonld | * | ||
| internalSpecifiers | * | ||
| externalSpecifiers | * | ||
| equivClass | * | ||
| reusePrevious | boolean |
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| parentClass | * |
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Return:
| * |
public deleteSpecifier(specifier: *) source
Params:
| Name | Type | Attribute | Description |
| specifier | * |
public getExpectedNodeLabels(phylogeny: *): * source
Params:
| Name | Type | Attribute | Description |
| phylogeny | * |
Return:
| * |
public getIncludesRestrictionForTU(tu: *): {"@type": string, "onProperty": string, "someValuesFrom": *} source
Params:
| Name | Type | Attribute | Description |
| tu | * |
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:
| Name | Type | Attribute | Description |
| tu1 | * | ||
| tu2 | * |
public getSpecifierType(specifier: *): string source
Params:
| Name | Type | Attribute | Description |
| specifier | * |
public setSpecifierType(specifier: *, specifierType: *) source
Params:
| Name | Type | Attribute | Description |
| specifier | * | ||
| specifierType | * |
public setStatus(status: *) source
Params:
| Name | Type | Attribute | Description |
| status | * |