BioKotlin/biokotlin.featureTree/TypeSchema

TypeSchema

Defines ids, names, synonym, isA, and partOf relationships for types. Each genome will have a type schema, that may be modified from the base type schema defined by the sequence ontology to be more permissive.

Types

TypeDecorator

inner class TypeDecorator : Type

Wraps around an existing type to give it additional properties or defines a user-created type

Functions

addIsA

fun addIsA(subType: String, superType: String)

Adds subType as a subtype of superType

addPartOf

fun addPartOf(child: String, parent: String)

Adds child as a part of parent

addRoughSynonym

fun addRoughSynonym(type: String, vararg synonym: String)

Adds all synonym as rough synonyms of type

addSynonym

fun addSynonym(type: String, vararg synonym: String)

Adds all synonym as exact synonyms of type

containsID

fun containsID(id: String): Boolean

Returns true if id is associated with a type in the schema

containsName

fun containsName(name: String): <Error class: unknown class>

Returns true if name is associated with at least one type in the schema

copy

fun copy(): TypeSchema

defineType

fun defineType(id: String, exactSynonyms: Set<String>, roughSynonyms: Set<String>, isA: Set<String>, partOf: Set<String>)

isA

fun isA(subType: String, superType: String): Boolean

Returns true iff subType is a subtype of superType.

isRoughSynonym

fun isRoughSynonym(name: String, vararg names: String): Boolean

Returns true iff all names are rough synonyms, exact synonyms, or ids of any type associated with name

isSynonym

fun isSynonym(name: String, vararg names: String): Boolean

Returns true iff all names are exact synonyms or ids of any type associated with name

partOf

fun partOf(child: String, parent: String): Boolean

Returns true if child is part of parent, meaning that they can have a parent/child relationship

roughSynonyms

fun roughSynonyms(name: String): Set<String>

The id, name, exact synonyms, and rough synonyms of all types associated with name

synonyms

fun synonyms(name: String): Set<String>

visualize

fun visualize(): String

Outputs DOT format visualization of this schema