Package org.snpeff.interval
Class SpliceSite
- 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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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,TxtSerializable
- Direct Known Subclasses:
SpliceSiteAcceptor
,SpliceSiteBranch
,SpliceSiteDonor
,SpliceSiteRegion
public abstract class SpliceSite extends Marker
Interval for a splice site Reference: http://en.wikipedia.org/wiki/RNA_splicing Spliceosomal introns often reside in eukaryotic protein-coding genes. Within the intron, a 3' splice site, 5' splice site, and branch site are required for splicing. The 5' splice site or splice donor site includes an almost invariant sequence GU at the 5' end of the intron, within a larger, less highly conserved consensus region. The 3' splice site or splice acceptor site terminates the intron with an almost invariant AG sequence. Upstream (5'-ward) from the AG there is a region high in pyrimidines (C and U), or polypyrimidine tract. Upstream from the polypyrimidine tract is the branch point, which includes an adenine nucleotide.- Author:
- pcingola
- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description static int
CORE_SPLICE_SITE_SIZE
static int
SPLICE_REGION_EXON_SIZE
static int
SPLICE_REGION_INTRON_MAX
static int
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 SpliceSite()
SpliceSite(Exon parent, int start, int end, boolean strandMinus, java.lang.String id)
SpliceSite(Intron parent, int start, int end, boolean strandMinus, java.lang.String id)
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Method Summary
All Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description abstract boolean
intersectsCoreSpliceSite(Marker marker)
Core splice sites are defined as CORE_SPLICE_SITE_SIZE bases after exon end or before exon begins.protected boolean
isShowWarningIfParentDoesNotInclude()
Splice sites are not included in Exons, by definition.boolean
variantEffect(Variant variant, VariantEffects variantEffects)
Calculate the effect of this variant-
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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Field Detail
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CORE_SPLICE_SITE_SIZE
public static final int CORE_SPLICE_SITE_SIZE
- See Also:
- Constant Field Values
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SPLICE_REGION_EXON_SIZE
public static final int SPLICE_REGION_EXON_SIZE
- See Also:
- Constant Field Values
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SPLICE_REGION_INTRON_MIN
public static final int SPLICE_REGION_INTRON_MIN
- See Also:
- Constant Field Values
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SPLICE_REGION_INTRON_MAX
public static final int SPLICE_REGION_INTRON_MAX
- See Also:
- Constant Field Values
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Method Detail
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intersectsCoreSpliceSite
public abstract boolean intersectsCoreSpliceSite(Marker marker)
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".
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isShowWarningIfParentDoesNotInclude
protected boolean isShowWarningIfParentDoesNotInclude()
Splice sites are not included in Exons, by definition.- Overrides:
isShowWarningIfParentDoesNotInclude
in classMarker
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variantEffect
public boolean variantEffect(Variant variant, VariantEffects variantEffects)
Description copied from class:Marker
Calculate the effect of this variant- Overrides:
variantEffect
in classMarker
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