Package org.snpeff.interval
Class SpliceSiteDonor
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.SpliceSite
org.snpeff.interval.SpliceSiteDonor
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,TxtSerializable
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:
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Field Summary
Fields inherited from class org.snpeff.interval.SpliceSite
CORE_SPLICE_SITE_SIZE, SPLICE_REGION_EXON_SIZE, SPLICE_REGION_INTRON_MAX, SPLICE_REGION_INTRON_MIN
Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Constructor Summary
ConstructorsConstructorDescriptionSpliceSiteDonor
(Intron parent, int start, int end, boolean strandMinus, String id) -
Method Summary
Modifier and TypeMethodDescriptionboolean
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
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
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 Details
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SpliceSiteDonor
public SpliceSiteDonor() -
SpliceSiteDonor
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Method Details
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intersectsCoreSpliceSite
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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