Package org.snpeff.interval
Class SpliceSiteDonor
- 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.SpliceSiteDonor
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,TxtSerializable
public class SpliceSiteDonor extends SpliceSite
Interval for a splice site donnor Note: Splice sites donnor are defined as the first 2 bases of an intron Reference: http://en.wikipedia.org/wiki/RNA_splicing- Author:
- pcingola
- 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 SpliceSiteDonor()
SpliceSiteDonor(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)
Core splice sites are defined as CORE_SPLICE_SITE_SIZE bases after exon end or before exon begins.-
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, isDeferredAnalysis, 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, toStrPos
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Constructor Detail
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SpliceSiteDonor
public SpliceSiteDonor()
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SpliceSiteDonor
public SpliceSiteDonor(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)
Description copied from class:SpliceSite
Core splice sites are defined as CORE_SPLICE_SITE_SIZE bases after exon end or before exon begins. Usually CORE_SPLICE_SITE_SIZE is 2 bases. Other spice sites are considered "non-core".- Specified by:
intersectsCoreSpliceSite
in classSpliceSite
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