Package org.snpeff.interval
Class Intron
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.Intron
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,TxtSerializable
Intron
- Author:
- pcingola
- See Also:
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Field Summary
Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
add
(SpliceSite ss) Add a splice site to the collectionApply a variant to a marker.Perform a shallow clonecreateSpliceSiteAcceptor
(int maxSpliceSiteSize) Create a splice site acceptor of 'size' length Acceptor site: 3' end of the introncreateSpliceSiteDonor
(int maxSpliceSiteSize) Create a splice site donor of 'maxSize' length Donor site: 5' end of the introncreateSpliceSiteRegionEnd
(int sizeMin, int sizeMax) Create splice site regioncreateSpliceSiteRegionStart
(int sizeMin, int sizeMax) Create splice site regionint
getRank()
Query all genomic regions that intersect 'marker'void
reset()
void
serializeParse
(MarkerSerializer markerSerializer) Parse a line from a serialized fileserializeSave
(MarkerSerializer markerSerializer) Create a string to serialize to a filevoid
setRank
(int rank) boolean
variantEffect
(Variant variant, VariantEffects variantEffects) Calculate the effect of this variantMethods 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
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 Details
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Intron
public Intron() -
Intron
public Intron(Transcript parent, int start, int end, boolean strandMinus, String id, Exon exonBefore, Exon exonAfter)
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Method Details
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add
Add a splice site to the collection -
apply
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
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classMarker
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createSpliceSiteAcceptor
Create a splice site acceptor of 'size' length Acceptor site: 3' end of the intron -
createSpliceSiteDonor
Create a splice site donor of 'maxSize' length Donor site: 5' end of the intron -
createSpliceSiteRegionEnd
Create splice site region -
createSpliceSiteRegionStart
Create splice site region -
getExonAfter
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getExonBefore
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getRank
public int getRank() -
getSpliceSites
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getSpliceType
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query
Query all genomic regions that intersect 'marker' -
reset
public void reset() -
serializeParse
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
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) -
variantEffect
Description copied from class:Marker
Calculate the effect of this variant- Overrides:
variantEffect
in classMarker
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