Package org.snpeff.interval
Class Intergenic
- java.lang.Object
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- org.snpeff.interval.Interval
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- org.snpeff.interval.Marker
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- org.snpeff.interval.Intergenic
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,TxtSerializable
public class Intergenic extends Marker
Interval for in intergenic region- Author:
- pcingola
- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
CHROMOSOME_END
static java.lang.String
CHROMOSOME_START
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Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Constructor Summary
Constructors Constructor Description Intergenic()
Intergenic(Chromosome parent, int start, int end, boolean strandMinus, java.lang.String id, java.lang.String name)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description Intergenic
cloneShallow()
Perform a shallow clonestatic Intergenic
createIntergenic(Gene geneLeft, Gene geneRight)
Creates an intergenic marker based on the "space" between two genesjava.lang.String
getName()
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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, isShowWarningIfParentDoesNotInclude, minus, query, query, readTxt, serializeParse, serializeSave, shouldApply, toString, union, variantEffect, variantEffectNonRef
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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
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Field Detail
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CHROMOSOME_START
public static final java.lang.String CHROMOSOME_START
- See Also:
- Constant Field Values
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CHROMOSOME_END
public static final java.lang.String CHROMOSOME_END
- See Also:
- Constant Field Values
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Constructor Detail
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Intergenic
public Intergenic()
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Intergenic
public Intergenic(Chromosome parent, int start, int end, boolean strandMinus, java.lang.String id, java.lang.String name)
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Method Detail
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createIntergenic
public static Intergenic createIntergenic(Gene geneLeft, Gene geneRight)
Creates an intergenic marker based on the "space" between two genes- Returns:
- null if the marker cannot be created
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cloneShallow
public Intergenic cloneShallow()
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classMarker
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getName
public java.lang.String getName()
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