org.broadinstitute.hellbender.utils.codecs.gtf

Class GencodeGtfTranscriptFeature

java.lang.Object

org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature

org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfTranscriptFeature

All Implemented Interfaces:

htsjdk.samtools.util.Locatable, htsjdk.tribble.Feature, java.lang.Comparable<GencodeGtfFeature>

public final class GencodeGtfTranscriptFeature
extends GencodeGtfFeature

A Gencode GTF Feature representing a transcript. A GTF Feature represents one row of a GTF File. The specification of a GTF file is defined here: http://mblab.wustl.edu/GTF22.html Created by jonn on 7/25/17.

Nested Class Summary

Nested classes/interfaces inherited from class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature

GencodeGtfFeature.AnnotationSource, GencodeGtfFeature.FeatureTag, GencodeGtfFeature.FeatureType, GencodeGtfFeature.GeneTranscriptStatus, GencodeGtfFeature.GenomicPhase, GencodeGtfFeature.KnownGeneBiotype, GencodeGtfFeature.LocusLevel, GencodeGtfFeature.OptionalField<T>, GencodeGtfFeature.RemapStatus, GencodeGtfFeature.RemapTargetStatus, GencodeGtfFeature.TranscriptSupportLevel

Field Summary

Fields inherited from class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature

ANNOTATION_SOURCE_ENA, ANNOTATION_SOURCE_ENSEMBL, ANNOTATION_SOURCE_HAVANA, EXTRA_FIELD_KEY_VALUE_SPLITTER, NO_EXON_NUMBER, NO_FEATURE_ORDER

Method Summary

Modifier and Type	Method and Description
void	addExon(GencodeGtfExonFeature exon)
void	addSelenocysteine(GencodeGtfSelenocysteineFeature selenocysteine)
void	addUtr(GencodeGtfUTRFeature utr)
static GencodeGtfFeature	create(GencodeGtfFeatureBaseData baseData)
static GencodeGtfFeature	create(java.lang.String[] gtfFields, java.lang.String gtfFileType)
boolean	equals(java.lang.Object other)
protected java.util.List<GencodeGtfFeature>	getAllFeatures() Get all the features from this GencodeGtfFeature itself.
java.util.List<GencodeGtfExonFeature>	getExons()
java.util.List<GencodeGtfSelenocysteineFeature>	getSelenocysteines()
java.util.List<GencodeGtfUTRFeature>	getUtrs()
int	hashCode()

Methods inherited from class org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature

compareTo, contains, create, getAnnotationSource, getAnonymousOptionalFields, getChromosomeName, getContig, getEnd, getExonId, getExonNumber, getFeatureOrderNumber, getFeatureType, getGeneId, getGeneName, getGeneStatus, getGeneType, getGenomicEndLocation, getGenomicPhase, getGenomicPosition, getGenomicStartLocation, getGenomicStrand, getGtfSourceFileType, getLocusLevel, getOptionalField, getOptionalFields, getStart, getTranscriptId, getTranscriptName, getTranscriptStatus, getTranscriptType, getUcscGenomeVersion, overlaps, serializeToString, setFeatureOrderNumber, setUcscGenomeVersion, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface htsjdk.tribble.Feature

getChr

Methods inherited from interface htsjdk.samtools.util.Locatable

contigsMatch, getLengthOnReference, withinDistanceOf

Method Detail

create

public static GencodeGtfFeature create(java.lang.String[] gtfFields,
                                       java.lang.String gtfFileType)

create

public static GencodeGtfFeature create(GencodeGtfFeatureBaseData baseData)

getExons

public java.util.List<GencodeGtfExonFeature> getExons()

addExon

public void addExon(GencodeGtfExonFeature exon)

getSelenocysteines

public java.util.List<GencodeGtfSelenocysteineFeature> getSelenocysteines()

addSelenocysteine

public void addSelenocysteine(GencodeGtfSelenocysteineFeature selenocysteine)

getUtrs

public java.util.List<GencodeGtfUTRFeature> getUtrs()

addUtr

public void addUtr(GencodeGtfUTRFeature utr)

getAllFeatures

protected java.util.List<GencodeGtfFeature> getAllFeatures()

Description copied from class: GencodeGtfFeature

Get all the features from this GencodeGtfFeature itself. This is useful to get any subfeatures included in this GencodeGtfFeature.

Returns:

A List of the features represented in this GencodeGtfFeature.

equals

public boolean equals(java.lang.Object other)

Overrides:

equals in class GencodeGtfFeature

hashCode

public int hashCode()

Overrides:

hashCode in class GencodeGtfFeature