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
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Field Summary
FieldsFields inherited from class Interval
chromosomeNameOri, end, id, parent, start, strandMinus -
Constructor Summary
ConstructorsConstructorDescriptionIntergenic(Chromosome parent, int start, int end, boolean strandMinus, String id, String name) -
Method Summary
Modifier and TypeMethodDescriptionPerform a shallow clonestatic IntergeniccreateIntergenic(Gene geneLeft, Gene geneRight) Creates an intergenic marker based on the "space" between two genesgetName()Methods inherited from class 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, variantEffectNonRefMethods inherited from class 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:MarkerPerform a shallow clone- Overrides:
cloneShallowin classMarker
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getName
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