Package org.monarchinitiative.lirical.core.model

Enum Class TranscriptDatabase

java.lang.Object

java.lang.Enum<TranscriptDatabase>

org.monarchinitiative.lirical.core.model.TranscriptDatabase

All Implemented Interfaces:

Serializable, Comparable<TranscriptDatabase>, Constable

public enum TranscriptDatabase
extends Enum<TranscriptDatabase>

Transcript database provides a collection of transcript definitions to use for functional variant annotation.

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Enum

Enum.EnumDesc<E extends Enum<E>>

Enum Constant Summary

Enum Constants

Enum Constant	Description
ENSEMBL	Transcripts sourced from ENSEMBL.
REFSEQ	RefSeq transcripts, including curated transcripts (NM_) as well as the transcripts that are based on gene predictions (XM_).
REFSEQ_CURATED	RefSeq with curated transcripts only (NM_) and excluding the transcripts that are based on gene predictions (XM_).
UCSC	Transcripts sourced from UCSC Genome Browser.

Method Summary

Modifier and Type	Method	Description
static Optional<TranscriptDatabase>	parse(String value)
String	toString()
static TranscriptDatabase	valueOf(String name)	Returns the enum constant of this class with the specified name.
static TranscriptDatabase[]	values()	Returns an array containing the constants of this enum class, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, describeConstable, equals, finalize, getDeclaringClass, hashCode, name, ordinal, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Details

UCSC

public static final TranscriptDatabase UCSC

Transcripts sourced from UCSC Genome Browser.

ENSEMBL

public static final TranscriptDatabase ENSEMBL

Transcripts sourced from ENSEMBL.

REFSEQ

public static final TranscriptDatabase REFSEQ

RefSeq transcripts, including curated transcripts (NM_) as well as the transcripts that are based on gene predictions (XM_).

REFSEQ_CURATED

public static final TranscriptDatabase REFSEQ_CURATED

RefSeq with curated transcripts only (NM_) and excluding the transcripts that are based on gene predictions (XM_).

Method Details

values

public static TranscriptDatabase[] values()

Returns an array containing the constants of this enum class, in the order they are declared.

Returns:

an array containing the constants of this enum class, in the order they are declared

valueOf

public static TranscriptDatabase valueOf(String name)

Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

IllegalArgumentException - if this enum class has no constant with the specified name

NullPointerException - if the argument is null

toString

public String toString()

Overrides:

toString in class Enum<TranscriptDatabase>

parse

public static Optional<TranscriptDatabase> parse(String value)