Package org.snpeff.interval
Class SpliceSiteBranch
- 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.SpliceSite
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- org.snpeff.interval.SpliceSiteBranch
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,TxtSerializable
- Direct Known Subclasses:
SpliceSiteBranchU12
public class SpliceSiteBranch extends SpliceSite
A (putative) branch site.- Author:
- pablocingolani
- See Also:
- Serialized Form
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Field Summary
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Fields inherited from class org.snpeff.interval.SpliceSite
CORE_SPLICE_SITE_SIZE, SPLICE_REGION_EXON_SIZE, SPLICE_REGION_INTRON_MAX, SPLICE_REGION_INTRON_MIN
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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 SpliceSiteBranch()
SpliceSiteBranch(Intron parent, int start, int end, boolean strandMinus, java.lang.String id)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
intersectsCoreSpliceSite(Marker marker)
These are NOT core splice sites-
Methods inherited from class org.snpeff.interval.SpliceSite
isShowWarningIfParentDoesNotInclude, variantEffect
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Methods inherited from class org.snpeff.interval.Marker
adjust, apply, applyDel, applyDup, applyIns, applyMixed, clone, cloneShallow, codonTable, compareTo, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isAdjustIfParentDoesNotInclude, minus, query, query, readTxt, serializeParse, serializeSave, shouldApply, toString, union, 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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Constructor Detail
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SpliceSiteBranch
public SpliceSiteBranch()
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SpliceSiteBranch
public SpliceSiteBranch(Intron parent, int start, int end, boolean strandMinus, java.lang.String id)
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Method Detail
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intersectsCoreSpliceSite
public boolean intersectsCoreSpliceSite(Marker marker)
These are NOT core splice sites- Specified by:
intersectsCoreSpliceSite
in classSpliceSite
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