Package org.snpeff.interval
Class SpliceSiteRegion
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.SpliceSite
org.snpeff.interval.SpliceSiteRegion
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,TxtSerializable
Interval for a splice site acceptor
From Sequence Ontology: A sequence variant in which a change has occurred
within the region of the splice site, either within 1-3 bases of the exon
or 3-8 bases of the intron.
- 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
ConstructorsConstructorDescriptionSpliceSiteRegion
(Exon parent, int start, int end, boolean strandMinus, String id) SpliceSiteRegion
(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.boolean
boolean
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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SpliceSiteRegion
public SpliceSiteRegion() -
SpliceSiteRegion
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SpliceSiteRegion
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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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isExonPart
public boolean isExonPart() -
isIntronPart
public boolean isIntronPart()
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