Package org.snpeff.interval
Class Exon
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.MarkerSeq
org.snpeff.interval.Exon
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,MarkerWithFrame
,TxtSerializable
Interval for an exon
- Author:
- pcingola
- See Also:
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic enum
Characterize exons based on alternative splicing References: "Alternative splicing and evolution - diversification, exon definition and function" (see Box 1) -
Field Summary
FieldsFields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Constructor Summary
ConstructorsConstructorDescriptionExon()
Exon
(Transcript parent, int start, int end, boolean strandMinus, String id, int rank) -
Method Summary
Modifier and TypeMethodDescriptionvoid
add
(SpliceSite ss) Add a splice site to the collectionApply variant to exon WARNING: There might be conditions which change the exon type (e.g.Perform a shallow clonecreateSpliceSiteRegionEnd
(int size) Create splice site regionscreateSpliceSiteRegionStart
(int size) Create splice site regionsboolean
frameCorrection
(int frameCorrection) Correct exons according to frame information Shift the start position one baseint
int
int
getFrame()
int
getRank()
protected boolean
isAdjustIfParentDoesNotInclude
(Marker parent) Adjust parent if it does not include child?Query all genomic regions that intersect 'marker'void
reset()
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 fileserializeSave
(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) toString()
boolean
variantEffect
(Variant variant, VariantEffects variantEffects) Note: This only adds spliceSites effects, for detailed codon changes effects we use 'CodonChange' classMethods inherited from class org.snpeff.interval.MarkerSeq
applyDel, applyDup, applyIns, applyMnp, applySnp, basesAt, basesAtPos, getSequence, getSequence, hasSequence, setSequence, union
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, isDeferredAnalysis, isShowWarningIfParentDoesNotInclude, minus, query, readTxt, shouldApply, 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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Field Details
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ToStringVersion
public static int ToStringVersion
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Constructor Details
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Exon
public Exon() -
Exon
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Method Details
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add
Add a splice site to the collection -
apply
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. -
cloneShallow
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classMarkerSeq
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createSpliceSiteRegionEnd
Create splice site regions -
createSpliceSiteRegionStart
Create splice site regions -
frameCorrection
public boolean frameCorrection(int frameCorrection) Correct exons according to frame information Shift the start position one base -
getAaIdxEnd
public int getAaIdxEnd() -
getAaIdxStart
public int getAaIdxStart() -
getFrame
public int getFrame()- Specified by:
getFrame
in interfaceMarkerWithFrame
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getRank
public int getRank() -
getSpliceSites
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getSpliceType
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isAdjustIfParentDoesNotInclude
Description copied from class:Marker
Adjust parent if it does not include child?- Overrides:
isAdjustIfParentDoesNotInclude
in classMarker
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query
Query all genomic regions that intersect 'marker' -
reset
public void reset() -
sanityCheck
Check that the base in the exon corresponds with the one in the SNP -
serializeParse
Parse a line from a serialized file- Specified by:
serializeParse
in interfaceTxtSerializable
- Overrides:
serializeParse
in classMarkerSeq
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serializeSave
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) -
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) -
toString
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variantEffect
Note: This only adds spliceSites effects, for detailed codon changes effects we use 'CodonChange' class- Overrides:
variantEffect
in classMarker
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