Package org.snpeff.interval
Class MarkerSeq
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.MarkerSeq
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,TxtSerializable
- Direct Known Subclasses:
Exon
Marker with a DNA sequence
- 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 TypeMethodDescriptionApply variantprotected void
Apply a change type deletion (update sequence)protected void
Apply a change type duplication (update sequence)protected void
Apply a change type insertion (update sequence)protected void
Apply a change type MNP (update sequence)protected void
Apply a change type SNP (update sequence)basesAt
(int index, int len) Base in this marker at position 'index' (relative to marker start)basesAtPos
(int pos, int len) Base at position 'pos' (genomic coordinates)Perform a shallow cloneGet sequence WARNING: Sequence is always according to coding strand.getSequence
(Marker marker) Get sequence intersecting 'marker' WARNING: Sequence is always according to coding strand.boolean
Do we have a sequence for this exon?void
serializeParse
(MarkerSerializer markerSerializer) Parse a line from a serialized fileserializeSave
(MarkerSerializer markerSerializer) Create a string to serialize to a filevoid
setSequence
(String sequence) Set sequence WARNING: Sequence is always according to coding strand.toString()
Union of two markersMethods 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, query, readTxt, shouldApply, variantEffect, 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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MarkerSeq
public MarkerSeq() -
MarkerSeq
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MarkerSeq
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Method Details
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apply
Apply variant -
applyDel
Apply a change type deletion (update sequence) -
applyDup
Apply a change type duplication (update sequence) -
applyIns
Apply a change type insertion (update sequence) -
applyMnp
Apply a change type MNP (update sequence) -
applySnp
Apply a change type SNP (update sequence) -
basesAt
Base in this marker at position 'index' (relative to marker start) -
basesAtPos
Base at position 'pos' (genomic coordinates) -
cloneShallow
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classMarker
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getSequence
Get sequence WARNING: Sequence is always according to coding strand. E.g. if the strand is negative, the sequence returned by this method is the reverse-WC that you see in the reference genome -
getSequence
Get sequence intersecting 'marker' WARNING: Sequence is always according to coding strand. E.g. if the strand is negative, the sequence returned by this method is the reverse-WC that you see in the reference genome -
hasSequence
public boolean hasSequence()Do we have a sequence for this exon? -
serializeParse
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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setSequence
Set sequence WARNING: Sequence is always according to coding strand. So use you should use setSequence( GprSeq.reverseWc( seq ) ) if the marker is in negative strand. -
toString
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union
Union of two markers
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