Package picard.annotation
Class Gene
- java.lang.Object
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- htsjdk.samtools.util.Interval
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- picard.annotation.Gene
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- All Implemented Interfaces:
htsjdk.samtools.util.Locatable
,htsjdk.tribble.Feature
,Cloneable
,Comparable<htsjdk.samtools.util.Interval>
,Iterable<Gene.Transcript>
public class Gene extends htsjdk.samtools.util.Interval implements Iterable<Gene.Transcript>
Holds annotation of a gene for storage in an OverlapDetector. May hold multiple transcripts for the same gene. The transcripts must all be relative to the same strand.
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Nested Class Summary
Nested Classes Modifier and Type Class Description class
Gene.Transcript
A single transcript of a gene.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Gene.Transcript
addTranscript(String name, int transcriptionStart, int transcriptionEnd, int codingStart, int codingEnd, int numExons)
int
compareTo(Gene that)
boolean
equals(Object other)
Iterator<Gene.Transcript>
iterator()
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Methods inherited from class htsjdk.samtools.util.Interval
abuts, clone, compareTo, countBases, equalsWithStrandAndName, getContig, getEnd, getIntersectionLength, getName, getSequence, getStart, getStrand, hashCode, intersect, intersects, isNegativeStrand, isPositiveStrand, length, pad, toString
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Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait
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Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Method Detail
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addTranscript
public Gene.Transcript addTranscript(String name, int transcriptionStart, int transcriptionEnd, int codingStart, int codingEnd, int numExons)
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iterator
public Iterator<Gene.Transcript> iterator()
- Specified by:
iterator
in interfaceIterable<Gene.Transcript>
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compareTo
public int compareTo(Gene that)
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equals
public boolean equals(Object other)
- Overrides:
equals
in classhtsjdk.samtools.util.Interval
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