Package picard.annotation
Class Gene
java.lang.Object
htsjdk.samtools.util.Interval
picard.annotation.Gene
- All Implemented Interfaces:
htsjdk.samtools.util.Locatable
,htsjdk.tribble.Feature
,htsjdk.tribble.NamedFeature
,Cloneable
,Comparable<htsjdk.samtools.util.Interval>
,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 -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionaddTranscript
(String name, int transcriptionStart, int transcriptionEnd, int codingStart, int codingEnd, int numExons) int
boolean
iterator()
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
Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait
Methods inherited from interface htsjdk.tribble.Feature
getChr
Methods inherited from interface java.lang.Iterable
forEach, spliterator
Methods inherited from interface htsjdk.samtools.util.Locatable
contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf
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Constructor Details
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Gene
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Method Details
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addTranscript
public Gene.Transcript addTranscript(String name, int transcriptionStart, int transcriptionEnd, int codingStart, int codingEnd, int numExons) -
iterator
- Specified by:
iterator
in interfaceIterable<Gene.Transcript>
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compareTo
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equals
- Overrides:
equals
in classhtsjdk.samtools.util.Interval
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