org.broadinstitute.hellbender.utils.codecs.gtf

Class GencodeGtfFeatureBaseData

java.lang.Object

org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData

public final class GencodeGtfFeatureBaseData
extends java.lang.Object

Struct-like container class for the fields in a GencodeGtfFeature This is designed to be a basic dummy class to make feature instantiation easier. Created by jonn on 8/11/17.

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.String	annotationSource Keyword identifying the source of this feature.
java.lang.String	anonymousOptionalFields Additional optional GTF fields.
java.lang.String	exonId
int	exonNumber
int	featureOrderNumber The relative order of this Feature.
GencodeGtfFeature.FeatureType	featureType Type of this feature.
java.lang.String	geneId
java.lang.String	geneName
GencodeGtfFeature.GeneTranscriptStatus	geneStatus
GencodeGtfFeature.GeneTranscriptType	geneType
GencodeGtfFeature.GenomicPhase	genomicPhase Frame/phase of this feature.
SimpleInterval	genomicPosition Location of this feature on the genome.
htsjdk.tribble.annotation.Strand	genomicStrand Which strand this feature is on.
java.lang.String	gtfSourceFileType The source file type from which the data in this GencodeGtfFeatureBaseData originated.
GencodeGtfFeature.LocusLevel	locusLevel
java.util.List<GencodeGtfFeature.OptionalField<?>>	optionalFields Optional GENCODE GTF Fields.
java.lang.String	transcriptId
java.lang.String	transcriptName
GencodeGtfFeature.GeneTranscriptStatus	transcriptStatus
GencodeGtfFeature.GeneTranscriptType	transcriptType

Constructor Summary

Constructors

Constructor and Description
GencodeGtfFeatureBaseData()
GencodeGtfFeatureBaseData(java.lang.String gtfSourceFileType, int featureOrderNumber, java.lang.String chromosomeName, java.lang.String annotationSource, GencodeGtfFeature.FeatureType featureType, int genomicStartLocation, int genomicEndLocation, htsjdk.tribble.annotation.Strand genomicStrand, GencodeGtfFeature.GenomicPhase genomicPhase, java.lang.String geneId, java.lang.String transcriptId, GencodeGtfFeature.GeneTranscriptType geneType, GencodeGtfFeature.GeneTranscriptStatus geneStatus, java.lang.String geneName, GencodeGtfFeature.GeneTranscriptType transcriptType, GencodeGtfFeature.GeneTranscriptStatus transcriptStatus, java.lang.String transcriptName, int exonNumber, java.lang.String exonId, GencodeGtfFeature.LocusLevel locusLevel, java.util.List<GencodeGtfFeature.OptionalField<?>> optionalFields, java.lang.String anonymousOptionalFields)

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object that)
int	hashCode()

Methods inherited from class java.lang.Object

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

Field Detail

featureOrderNumber

public int featureOrderNumber

The relative order of this Feature. Normally it is a line number indicating the position in the original data file of this feature.

gtfSourceFileType

public java.lang.String gtfSourceFileType

The source file type from which the data in this GencodeGtfFeatureBaseData originated. This should always correspond to a value returned by AbstractGtfCodec.getGtfFileType().

genomicPosition

public SimpleInterval genomicPosition

Location of this feature on the genome.

annotationSource

public java.lang.String annotationSource

Keyword identifying the source of this feature. There is no restriction on which keywords can be used here, but some known annotation sources are defined in their GTF parent objects: GencodeGtfCodec#GENCODE_ANNOTATION_SOURCE_ENSEMBL GencodeGtfCodec#GENCODE_ANNOTATION_SOURCE_HAVANA EnsemblGtfCodec#ENSEMBL_ANNOTATION_SOURCE_ENA

featureType

public GencodeGtfFeature.FeatureType featureType

Type of this feature.

genomicStrand

public htsjdk.tribble.annotation.Strand genomicStrand

Which strand this feature is on.

genomicPhase

public GencodeGtfFeature.GenomicPhase genomicPhase

Frame/phase of this feature.

geneId

public java.lang.String geneId

transcriptId

public java.lang.String transcriptId

geneStatus

public GencodeGtfFeature.GeneTranscriptStatus geneStatus

geneType

public GencodeGtfFeature.GeneTranscriptType geneType

geneName

public java.lang.String geneName

transcriptType

public GencodeGtfFeature.GeneTranscriptType transcriptType

transcriptStatus

public GencodeGtfFeature.GeneTranscriptStatus transcriptStatus

transcriptName

public java.lang.String transcriptName

exonNumber

public int exonNumber

exonId

public java.lang.String exonId

locusLevel

public GencodeGtfFeature.LocusLevel locusLevel

optionalFields

public java.util.List<GencodeGtfFeature.OptionalField<?>> optionalFields

Optional GENCODE GTF Fields. For details, see the following: https://www.gencodegenes.org/data_format.html https://www.gencodegenes.org/gencode_tags.html

anonymousOptionalFields

public java.lang.String anonymousOptionalFields

Additional optional GTF fields.

Constructor Detail

GencodeGtfFeatureBaseData

public GencodeGtfFeatureBaseData()

GencodeGtfFeatureBaseData

public GencodeGtfFeatureBaseData(java.lang.String gtfSourceFileType,
                                 int featureOrderNumber,
                                 java.lang.String chromosomeName,
                                 java.lang.String annotationSource,
                                 GencodeGtfFeature.FeatureType featureType,
                                 int genomicStartLocation,
                                 int genomicEndLocation,
                                 htsjdk.tribble.annotation.Strand genomicStrand,
                                 GencodeGtfFeature.GenomicPhase genomicPhase,
                                 java.lang.String geneId,
                                 java.lang.String transcriptId,
                                 GencodeGtfFeature.GeneTranscriptType geneType,
                                 GencodeGtfFeature.GeneTranscriptStatus geneStatus,
                                 java.lang.String geneName,
                                 GencodeGtfFeature.GeneTranscriptType transcriptType,
                                 GencodeGtfFeature.GeneTranscriptStatus transcriptStatus,
                                 java.lang.String transcriptName,
                                 int exonNumber,
                                 java.lang.String exonId,
                                 GencodeGtfFeature.LocusLevel locusLevel,
                                 java.util.List<GencodeGtfFeature.OptionalField<?>> optionalFields,
                                 java.lang.String anonymousOptionalFields)

Method Detail

equals

public boolean equals(java.lang.Object that)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object