org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData Maven / Gradle / Ivy
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package org.broadinstitute.hellbender.utils.codecs.gtf;
import htsjdk.tribble.annotation.Strand;
import org.broadinstitute.hellbender.utils.SimpleInterval;
import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
/**
* Struct-like container class for the fields in a {@link GencodeGtfFeature}
*
* This is designed to be a basic dummy class to make feature instantiation easier.
*
* Created by jonn on 8/11/17.
*/
final public class GencodeGtfFeatureBaseData {
/**
* The relative order of this Feature.
* Normally it is a line number indicating the position in the original data file of this feature.
*/
public int featureOrderNumber = GencodeGtfFeature.NO_FEATURE_ORDER;
/**
* The source file type from which the data in this {@link GencodeGtfFeatureBaseData} originated.
* This should always correspond to a value returned by {@link AbstractGtfCodec#getGtfFileType()}.
*/
public String gtfSourceFileType;
/**
* Location of this feature on the genome.
*/
public SimpleInterval genomicPosition;
/**
* 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:
* {@link GencodeGtfFeature#ANNOTATION_SOURCE_ENSEMBL}
* {@link GencodeGtfFeature#ANNOTATION_SOURCE_HAVANA}
* {@link GencodeGtfFeature#ANNOTATION_SOURCE_ENA}
*/
public String annotationSource;
/**
* Type of this feature.
*/
public GencodeGtfFeature.FeatureType featureType;
//TODO: Make this a Strand, not a GenomicStrand.
/**
* Which strand this feature is on.
*/
public Strand genomicStrand;
/**
* Frame/phase of this feature.
*/
public GencodeGtfFeature.GenomicPhase genomicPhase;
// "Required" GENCODE GTF Fields:
public String geneId = null;
public String transcriptId = null;
public String geneStatus = null;
/**
* There are no formal definitions for what can be a valid geneType and the
* number of possible values seem to increase as new versions of Gencode are released.
*/
public String geneType = null;
public String geneName = null;
/**
* There are no formal definitions for what can be a valid transcriptType and the
* number of possible values seem to increase as new versions of Gencode are released.
*/
public String transcriptType = null;
public String transcriptStatus = null;
public String transcriptName = null;
public int exonNumber = GencodeGtfFeature.NO_EXON_NUMBER;
public String exonId = null;
public String locusLevel = null;
/**
* Optional GENCODE GTF Fields.
* This also includes unidentified GTF fields that may not be specified in the Gencode GTF specification.
* For details, see the following:
* https://www.gencodegenes.org/data_format.html
* https://www.gencodegenes.org/gencode_tags.html
*/
public List> optionalFields = new ArrayList<>();
public GencodeGtfFeatureBaseData() {}
public GencodeGtfFeatureBaseData(
final String gtfSourceFileType,
final int featureOrderNumber,
final String chromosomeName,
final String annotationSource,
final GencodeGtfFeature.FeatureType featureType,
final int genomicStartLocation,
final int genomicEndLocation,
final Strand genomicStrand,
final GencodeGtfFeature.GenomicPhase genomicPhase,
final String geneId,
final String transcriptId,
final String geneType,
final String geneStatus,
final String geneName,
final String transcriptType,
final String transcriptStatus,
final String transcriptName,
final int exonNumber,
final String exonId,
final String locusLevel,
final List> optionalFields
) {
this.gtfSourceFileType = gtfSourceFileType;
this.featureOrderNumber = featureOrderNumber;
this.genomicPosition = new SimpleInterval(chromosomeName, genomicStartLocation, genomicEndLocation);
this.annotationSource = annotationSource;
this.featureType = featureType;
this.genomicStrand = genomicStrand;
this.genomicPhase = genomicPhase;
this.geneId = geneId;
this.transcriptId = transcriptId;
this.geneType = geneType;
this.geneStatus = geneStatus;
this.geneName = geneName;
this.transcriptType = transcriptType;
this.transcriptStatus = transcriptStatus;
this.transcriptName = transcriptName;
this.exonNumber = exonNumber;
this.exonId = exonId;
this.locusLevel = locusLevel;
if ( optionalFields != null ) {
this.optionalFields = optionalFields;
}
}
@Override
public boolean equals(final Object that) {
if (that == null) {
return false;
}
else if ( this == that ) {
return true;
}
boolean isEqual = that instanceof GencodeGtfFeatureBaseData;
if ( isEqual ) {
final GencodeGtfFeatureBaseData thatBaseData = (GencodeGtfFeatureBaseData) that;
isEqual =
Objects.equals(gtfSourceFileType, thatBaseData.gtfSourceFileType) &&
Objects.equals(featureOrderNumber, thatBaseData.featureOrderNumber) &&
Objects.equals(genomicPosition, thatBaseData.genomicPosition) &&
Objects.equals(annotationSource, thatBaseData.annotationSource) &&
Objects.equals(featureType, thatBaseData.featureType) &&
Objects.equals(genomicStrand, thatBaseData.genomicStrand) &&
Objects.equals(genomicPhase, thatBaseData.genomicPhase) &&
Objects.equals(geneId, thatBaseData.geneId) &&
Objects.equals(transcriptId, thatBaseData.transcriptId) &&
Objects.equals(geneType, thatBaseData.geneType) &&
Objects.equals(geneStatus, thatBaseData.geneStatus) &&
Objects.equals(geneName, thatBaseData.geneName) &&
Objects.equals(transcriptType, thatBaseData.transcriptType) &&
Objects.equals(transcriptStatus, thatBaseData.transcriptStatus) &&
Objects.equals(transcriptName, thatBaseData.transcriptName) &&
Objects.equals(exonNumber, thatBaseData.exonNumber) &&
Objects.equals(exonId, thatBaseData.exonId) &&
Objects.equals(locusLevel, thatBaseData.locusLevel) &&
Objects.equals(optionalFields, thatBaseData.optionalFields); //TODO should equality enforce the order of the optional fields?
}
return isEqual;
}
@Override
public int hashCode() {
int result = featureOrderNumber;
result = 31 * result + (gtfSourceFileType != null ? gtfSourceFileType.hashCode() : 0);
result = 31 * result + (genomicPosition != null ? genomicPosition.hashCode() : 0);
result = 31 * result + (annotationSource != null ? annotationSource.hashCode() : 0);
result = 31 * result + (featureType != null ? featureType.hashCode() : 0);
result = 31 * result + (genomicStrand != null ? genomicStrand.hashCode() : 0);
result = 31 * result + (genomicPhase != null ? genomicPhase.hashCode() : 0);
result = 31 * result + (geneId != null ? geneId.hashCode() : 0);
result = 31 * result + (transcriptId != null ? transcriptId.hashCode() : 0);
result = 31 * result + (geneStatus != null ? geneStatus.hashCode() : 0);
result = 31 * result + (geneType != null ? geneType.hashCode() : 0);
result = 31 * result + (geneName != null ? geneName.hashCode() : 0);
result = 31 * result + (transcriptType != null ? transcriptType.hashCode() : 0);
result = 31 * result + (transcriptStatus != null ? transcriptStatus.hashCode() : 0);
result = 31 * result + (transcriptName != null ? transcriptName.hashCode() : 0);
result = 31 * result + exonNumber;
result = 31 * result + (exonId != null ? exonId.hashCode() : 0);
result = 31 * result + (locusLevel != null ? locusLevel.hashCode() : 0);
result = 31 * result + (optionalFields != null ? optionalFields.hashCode() : 0);
return result;
}
}
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