Package org.snpeff.interval
Class MarkerSeq
- 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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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,TxtSerializable
- Direct Known Subclasses:
Exon
public class MarkerSeq extends Marker
Marker with a DNA sequence- 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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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description MarkerSeq
apply(Variant variant)
Apply variantprotected void
applyDel(Variant variant, MarkerSeq markerSeq)
Apply a change type deletion (update sequence)protected void
applyDup(Variant variant, MarkerSeq markerSeq)
Apply a change type duplication (update sequence)protected void
applyIns(Variant variant, MarkerSeq markerSeq)
Apply a change type insertion (update sequence)protected void
applyMnp(Variant variant, MarkerSeq markerSeq)
Apply a change type MNP (update sequence)protected void
applySnp(Variant variant, MarkerSeq markerSeq)
Apply a change type SNP (update sequence)java.lang.String
basesAt(int index, int len)
Base in this marker at position 'index' (relative to marker start)java.lang.String
basesAtPos(int pos, int len)
Base at position 'pos' (genomic coordinates)MarkerSeq
cloneShallow()
Perform a shallow clonejava.lang.String
getSequence()
Get sequence WARNING: Sequence is always according to coding strand.java.lang.String
getSequence(Marker marker)
Get sequence intersecting 'marker' WARNING: Sequence is always according to coding strand.boolean
hasSequence()
Do we have a sequence for this exon?void
serializeParse(MarkerSerializer markerSerializer)
Parse a line from a serialized filejava.lang.String
serializeSave(MarkerSerializer markerSerializer)
Create a string to serialize to a filevoid
setSequence(java.lang.String sequence)
Set sequence WARNING: Sequence is always according to coding strand.java.lang.String
toString()
Marker
union(Marker m)
Union of two markers-
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, isShowWarningIfParentDoesNotInclude, minus, query, query, readTxt, shouldApply, variantEffect, 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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Method Detail
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applyDel
protected void applyDel(Variant variant, MarkerSeq markerSeq)
Apply a change type deletion (update sequence)
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applyDup
protected void applyDup(Variant variant, MarkerSeq markerSeq)
Apply a change type duplication (update sequence)
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applyIns
protected void applyIns(Variant variant, MarkerSeq markerSeq)
Apply a change type insertion (update sequence)
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applyMnp
protected void applyMnp(Variant variant, MarkerSeq markerSeq)
Apply a change type MNP (update sequence)
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applySnp
protected void applySnp(Variant variant, MarkerSeq markerSeq)
Apply a change type SNP (update sequence)
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basesAt
public java.lang.String basesAt(int index, int len)
Base in this marker at position 'index' (relative to marker start)
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basesAtPos
public java.lang.String basesAtPos(int pos, int len)
Base at position 'pos' (genomic coordinates)
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cloneShallow
public MarkerSeq cloneShallow()
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classMarker
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getSequence
public java.lang.String 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
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getSequence
public java.lang.String getSequence(Marker marker)
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
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hasSequence
public boolean hasSequence()
Do we have a sequence for this exon?
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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 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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setSequence
public void setSequence(java.lang.String sequence)
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.
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