Package org.snpeff.interval
Class Intergenic
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.Intergenic
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,TxtSerializable
Interval for in intergenic region
- Author:
- pcingola
- See Also:
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Field Summary
FieldsFields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Constructor Summary
ConstructorsConstructorDescriptionIntergenic
(Chromosome parent, int start, int end, boolean strandMinus, String id, String name) -
Method Summary
Modifier and TypeMethodDescriptionPerform a shallow clonestatic Intergenic
createIntergenic
(Gene geneLeft, Gene geneRight) Creates an intergenic marker based on the "space" between two genesgetName()
Methods inherited from class org.snpeff.interval.Marker
adjust, apply, applyDel, applyDup, applyIns, applyMixed, clone, codonTable, compareTo, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isAdjustIfParentDoesNotInclude, isDeferredAnalysis, isShowWarningIfParentDoesNotInclude, minus, query, query, readTxt, serializeParse, serializeSave, shouldApply, toString, union, variantEffect, variantEffectNonRef
Methods inherited from class org.snpeff.interval.Interval
equals, findParent, getChromosome, getChromosomeName, getChromosomeNameOri, getChromosomeNum, getEnd, getGenome, getGenomeName, getId, getStart, getStrand, hashCode, intersects, intersects, intersects, intersects, intersectSize, isCircular, isSameChromo, isStrandMinus, isStrandPlus, isValid, setChromosomeNameOri, setEnd, setId, setParent, setStart, setStrandMinus, shiftCoordinates, size, toStr, toStringAsciiArt, toStrPos
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Field Details
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CHROMOSOME_START
- See Also:
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CHROMOSOME_END
- See Also:
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Constructor Details
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Intergenic
public Intergenic() -
Intergenic
public Intergenic(Chromosome parent, int start, int end, boolean strandMinus, String id, String name)
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Method Details
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createIntergenic
Creates an intergenic marker based on the "space" between two genes- Returns:
- null if the marker cannot be created
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cloneShallow
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classMarker
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getName
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