Package org.snpeff.interval
Class SpliceSiteRegion
- 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.SpliceSiteRegion
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,TxtSerializable
public class SpliceSiteRegion extends SpliceSite
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:
- 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 SpliceSiteRegion()
SpliceSiteRegion(Exon parent, int start, int end, boolean strandMinus, java.lang.String id)
SpliceSiteRegion(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.boolean
isExonPart()
boolean
isIntronPart()
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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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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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isExonPart
public boolean isExonPart()
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isIntronPart
public boolean isIntronPart()
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