Package org.snpeff.interval
Class Intron
- 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.Intron
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,TxtSerializable
public class Intron extends Marker
Intron- Author:
- pcingola
- See Also:
- Serialized Form
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Field Summary
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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 Intron()
Intron(Transcript parent, int start, int end, boolean strandMinus, java.lang.String id, Exon exonBefore, Exon exonAfter)
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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 collectionIntron
apply(Variant variant)
Apply a variant to a marker.Intron
cloneShallow()
Perform a shallow cloneSpliceSiteAcceptor
createSpliceSiteAcceptor(int maxSpliceSiteSize)
Create a splice site acceptor of 'size' length Acceptor site: 3' end of the intronSpliceSiteDonor
createSpliceSiteDonor(int maxSpliceSiteSize)
Create a splice site donor of 'maxSize' length Donor site: 5' end of the intronSpliceSiteRegion
createSpliceSiteRegionEnd(int sizeMin, int sizeMax)
Create splice site regionSpliceSiteRegion
createSpliceSiteRegionStart(int sizeMin, int sizeMax)
Create splice site regionExon
getExonAfter()
Exon
getExonBefore()
int
getRank()
java.util.ArrayList<SpliceSite>
getSpliceSites()
java.lang.String
getSpliceType()
Markers
query(Marker marker)
Query all genomic regions that intersect 'marker'void
reset()
void
serializeParse(MarkerSerializer markerSerializer)
Parse a line from a serialized filejava.lang.String
serializeSave(MarkerSerializer markerSerializer)
Create a string to serialize to a filevoid
setRank(int rank)
boolean
variantEffect(Variant variant, VariantEffects variantEffects)
Calculate the effect of this variant-
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, isAdjustIfParentDoesNotInclude, isDeferredAnalysis, isShowWarningIfParentDoesNotInclude, minus, query, readTxt, 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, toStrPos
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Constructor Detail
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Intron
public Intron()
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Intron
public Intron(Transcript parent, int start, int end, boolean strandMinus, java.lang.String id, Exon exonBefore, Exon exonAfter)
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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 Intron apply(Variant variant)
Description copied from class:Marker
Apply a variant to a marker.Calculate a the result of a marker, such that newMarker = marker.apply( variant ) variant = Diff( newMarker , marker ) // Differences in sequence
Note: This method may return: - The same marker (this) when genetic coordinates remain unchanged - 'null' if the whole marker is removed by the variant (e.g. a deletion spanning the whole marker)
For these reasons, the method should never be invoked directly. This is why the method is 'private' and 'final'
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cloneShallow
public Intron cloneShallow()
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classMarker
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createSpliceSiteAcceptor
public SpliceSiteAcceptor createSpliceSiteAcceptor(int maxSpliceSiteSize)
Create a splice site acceptor of 'size' length Acceptor site: 3' end of the intron
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createSpliceSiteDonor
public SpliceSiteDonor createSpliceSiteDonor(int maxSpliceSiteSize)
Create a splice site donor of 'maxSize' length Donor site: 5' end of the intron
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createSpliceSiteRegionEnd
public SpliceSiteRegion createSpliceSiteRegionEnd(int sizeMin, int sizeMax)
Create splice site region
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createSpliceSiteRegionStart
public SpliceSiteRegion createSpliceSiteRegionStart(int sizeMin, int sizeMax)
Create splice site region
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getExonAfter
public Exon getExonAfter()
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getExonBefore
public Exon getExonBefore()
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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 java.lang.String getSpliceType()
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reset
public void reset()
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serializeParse
public void serializeParse(MarkerSerializer markerSerializer)
Description copied from class:Marker
Parse a line from a serialized file- Specified by:
serializeParse
in interfaceTxtSerializable
- Overrides:
serializeParse
in classMarker
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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 classMarker
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setRank
public void setRank(int rank)
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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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