Package org.snpeff.interval
Class Exon
- 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.MarkerSeq
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- org.snpeff.interval.Exon
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,MarkerWithFrame
,TxtSerializable
public class Exon extends MarkerSeq implements MarkerWithFrame
Interval for an exon- Author:
- pcingola
- See Also:
- Serialized Form
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
Exon.ExonSpliceType
Characterize exons based on alternative splicing References: "Alternative splicing and evolution - diversification, exon definition and function" (see Box 1)
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Field Summary
Fields Modifier and Type Field Description static int
ToStringVersion
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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 Exon()
Exon(Transcript parent, int start, int end, boolean strandMinus, java.lang.String id, int rank)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
add(SpliceSite ss)
Add a splice site to the collectionExon
apply(Variant variant)
Apply variant to exon WARNING: There might be conditions which change the exon type (e.g.Exon
cloneShallow()
Perform a shallow cloneSpliceSiteRegion
createSpliceSiteRegionEnd(int size)
Create splice site regionsSpliceSiteRegion
createSpliceSiteRegionStart(int size)
Create splice site regionsboolean
frameCorrection(int frameCorrection)
Correct exons according to frame information Shift the start position one baseint
getAaIdxEnd()
int
getAaIdxStart()
int
getFrame()
int
getRank()
java.util.ArrayList<SpliceSite>
getSpliceSites()
Exon.ExonSpliceType
getSpliceType()
protected boolean
isAdjustIfParentDoesNotInclude(Marker parent)
Adjust parent if it does not include child?Markers
query(Marker marker)
Query all genomic regions that intersect 'marker'void
reset()
VariantEffect.ErrorWarningType
sanityCheck(Variant variant)
Check that the base in the exon corresponds with the one in the SNPvoid
serializeParse(MarkerSerializer markerSerializer)
Parse a line from a serialized filejava.lang.String
serializeSave(MarkerSerializer markerSerializer)
Create a string to serialize to a filevoid
setAaIdx(int aaIdxStart, int aaIdxEnd)
void
setFrame(int frame)
Frame can be {-1, 0, 1, 2}, where '-1' means unknownvoid
setRank(int rank)
java.lang.String
toString()
boolean
variantEffect(Variant variant, VariantEffects variantEffects)
Note: This only adds spliceSites effects, for detailed codon changes effects we use 'CodonChange' class-
Methods inherited from class org.snpeff.interval.MarkerSeq
applyDel, applyDup, applyIns, applyMnp, applySnp, basesAt, basesAtPos, getSequence, getSequence, hasSequence, setSequence, union
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Methods inherited from class org.snpeff.interval.Marker
adjust, applyDel, applyDup, applyIns, applyMixed, clone, codonTable, compareTo, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isShowWarningIfParentDoesNotInclude, minus, query, readTxt, shouldApply, 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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Constructor Detail
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Exon
public Exon()
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Exon
public Exon(Transcript parent, int start, int end, boolean strandMinus, java.lang.String id, int rank)
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Method Detail
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add
public void add(SpliceSite ss)
Add a splice site to the collection
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apply
public Exon apply(Variant variant)
Apply variant to exon WARNING: There might be conditions which change the exon type (e.g. an intron is deleted). Nevertheless ExonSpliceType is not updated since it reflects the exon type before a sequence change.
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cloneShallow
public Exon cloneShallow()
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classMarkerSeq
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createSpliceSiteRegionEnd
public SpliceSiteRegion createSpliceSiteRegionEnd(int size)
Create splice site regions
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createSpliceSiteRegionStart
public SpliceSiteRegion createSpliceSiteRegionStart(int size)
Create splice site regions
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frameCorrection
public boolean frameCorrection(int frameCorrection)
Correct exons according to frame information Shift the start position one base
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getAaIdxEnd
public int getAaIdxEnd()
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getAaIdxStart
public int getAaIdxStart()
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getFrame
public int getFrame()
- Specified by:
getFrame
in interfaceMarkerWithFrame
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getRank
public int getRank()
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getSpliceSites
public java.util.ArrayList<SpliceSite> getSpliceSites()
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getSpliceType
public Exon.ExonSpliceType getSpliceType()
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isAdjustIfParentDoesNotInclude
protected boolean isAdjustIfParentDoesNotInclude(Marker parent)
Description copied from class:Marker
Adjust parent if it does not include child?- Overrides:
isAdjustIfParentDoesNotInclude
in classMarker
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reset
public void reset()
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sanityCheck
public VariantEffect.ErrorWarningType sanityCheck(Variant variant)
Check that the base in the exon corresponds with the one in the SNP
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serializeParse
public void serializeParse(MarkerSerializer markerSerializer)
Parse a line from a serialized file- Specified by:
serializeParse
in interfaceTxtSerializable
- Overrides:
serializeParse
in classMarkerSeq
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serializeSave
public java.lang.String serializeSave(MarkerSerializer markerSerializer)
Create a string to serialize to a file- Specified by:
serializeSave
in interfaceTxtSerializable
- Overrides:
serializeSave
in classMarkerSeq
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setAaIdx
public void setAaIdx(int aaIdxStart, int aaIdxEnd)
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setFrame
public void setFrame(int frame)
Frame can be {-1, 0, 1, 2}, where '-1' means unknown- Specified by:
setFrame
in interfaceMarkerWithFrame
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setRank
public void setRank(int rank)
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variantEffect
public boolean variantEffect(Variant variant, VariantEffects variantEffects)
Note: This only adds spliceSites effects, for detailed codon changes effects we use 'CodonChange' class- Overrides:
variantEffect
in classMarker
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