import {PhylogenyWrapper} from '@phyloref/phyx/src/wrappers/PhylogenyWrapper.js'PhylogenyWrapper
Static Method Summary
| Static Public Methods | ||
| public static |
getErrorsInNewickString(newick: *): * |
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| public static |
getParsedNewick(newick: *): {"json": *} |
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| public static |
normalize(phylogeny: *): * Return a normalized form of the phylogeny. |
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| public static |
recurseNodes(node: *, func: *, nodeCount: number, parentCount: *): * |
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Constructor Summary
| Public Constructor | ||
| public |
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Member Summary
| Public Members | ||
| public |
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| public |
phylogeny: * |
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Method Summary
| Public Methods | ||
| public |
asJSONLD(fallbackIRI: *, newickParser: *): * |
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| public |
getNodeLabels(nodeType: string): * |
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| public |
getNodeLabelsMatchedBySpecifier(specifier: *): * |
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| public |
getNodesAsJSONLD(baseIRI: *, newickParser: *): * |
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| public |
getParsedNewickWithIRIs(baseIRI: *, newickParser: *): * |
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| public |
getTaxonomicUnits(nodeType: string): * |
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| public |
getTaxonomicUnitsForNodeLabel(nodeLabel: *): *[] Return a list of taxonomic units for a node label. |
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Static Public Methods
public static getErrorsInNewickString(newick: *): * source
Params:
| Name | Type | Attribute | Description |
| newick | * |
Return:
| * |
public static getParsedNewick(newick: *): {"json": *} source
Params:
| Name | Type | Attribute | Description |
| newick | * |
Return:
| {"json": *} |
public static normalize(phylogeny: *): * source
Return a normalized form of the phylogeny.
Params:
| Name | Type | Attribute | Description |
| phylogeny | * |
Return:
| * |
Public Constructors
public constructor() source
Public Methods
public asJSONLD(fallbackIRI: *, newickParser: *): * source
Params:
| Name | Type | Attribute | Description |
| fallbackIRI | * | ||
| newickParser | * |
Return:
| * |
public getNodeLabels(nodeType: string): * source
Params:
| Name | Type | Attribute | Description |
| nodeType | string |
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Return:
| * |
public getNodeLabelsMatchedBySpecifier(specifier: *): * source
Params:
| Name | Type | Attribute | Description |
| specifier | * |
Return:
| * |
public getNodesAsJSONLD(baseIRI: *, newickParser: *): * source
Params:
| Name | Type | Attribute | Description |
| baseIRI | * | ||
| newickParser | * |
Return:
| * |
public getParsedNewickWithIRIs(baseIRI: *, newickParser: *): * source
Params:
| Name | Type | Attribute | Description |
| baseIRI | * | ||
| newickParser | * |
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Return:
| * |
public getTaxonomicUnits(nodeType: string): * source
Params:
| Name | Type | Attribute | Description |
| nodeType | string |
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Return:
| * |
public getTaxonomicUnitsForNodeLabel(nodeLabel: *): *[] source
Return a list of taxonomic units for a node label.
If the additionalNodeProperties for this node label includes taxonomic units
(using representsTaxonomicUnits = obo:CDAO_0000187), then those taxonomic
units are used. Otherwise, one will be constructed using the default
nomenclatural code set up when this PhylogenyWrapper was set up.
Params:
| Name | Type | Attribute | Description |
| nodeLabel | * |
Return:
| *[] |