Package org.snpeff.interval
Class VariantBnd
- java.lang.Object
-
- org.snpeff.interval.Interval
-
- org.snpeff.interval.Marker
-
- org.snpeff.interval.Variant
-
- org.snpeff.interval.VariantBnd
-
- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,TxtSerializable
public class VariantBnd extends Variant
A 'BND' variant (i.e. translocation) consisting of two endpoints- Author:
- pcingola
- See Also:
- Serialized Form
-
-
Nested Class Summary
-
Nested classes/interfaces inherited from class org.snpeff.interval.Variant
Variant.VariantType
-
-
Field Summary
-
Fields inherited from class org.snpeff.interval.Variant
alt, genotype, HUGE_DELETION_RATIO_THRESHOLD, HUGE_DELETION_SIZE_THRESHOLD, imprecise, NO_VARIANT, ref, variantType
-
Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
-
-
Constructor Summary
Constructors Constructor Description VariantBnd()
VariantBnd(Marker parent, int start, java.lang.String ref, java.lang.String alt, Chromosome chrTr, int startTr, boolean left, boolean before)
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Marker
getEndPoint()
boolean
isBefore()
boolean
isBnd()
boolean
isLeft()
boolean
isStructural()
Markers
query(IntervalForest intervalForest)
Return a collection of intervals that intersect both ends of this variantVariant
realignLeft()
Create a new variant realigning it towards the leftmost positionjava.lang.String
toString()
-
Methods inherited from class org.snpeff.interval.Variant
clone, cloneShallow, compareTo, decompose, factory, getAlt, getGenotype, getReference, getVariantType, hashCode, isDel, isDup, isElongation, isImprecise, isInDel, isIns, isInterval, isInv, isMixed, isMnp, isNonRef, isShowWarningIfParentDoesNotInclude, isSnp, isStructuralHuge, isTruncation, isVariant, lengthChange, netChange, netChange, reverse, setGenotype, setImprecise, setVariantType, toStringEnsembl, toStringOld
-
Methods inherited from class org.snpeff.interval.Marker
adjust, apply, applyDel, applyDup, applyIns, applyMixed, codonTable, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isAdjustIfParentDoesNotInclude, isDeferredAnalysis, minus, query, readTxt, serializeParse, serializeSave, shouldApply, union, variantEffect, variantEffectNonRef
-
Methods inherited from class org.snpeff.interval.Interval
equals, findParent, getChromosome, getChromosomeName, getChromosomeNameOri, getChromosomeNum, getEnd, getGenome, getGenomeName, getId, getStart, getStrand, intersects, intersects, intersects, intersects, intersectSize, isCircular, isSameChromo, isStrandMinus, isStrandPlus, isValid, setChromosomeNameOri, setEnd, setId, setParent, setStart, setStrandMinus, shiftCoordinates, size, toStr, toStringAsciiArt, toStrPos
-
-
-
-
Constructor Detail
-
VariantBnd
public VariantBnd()
-
VariantBnd
public VariantBnd(Marker parent, int start, java.lang.String ref, java.lang.String alt, Chromosome chrTr, int startTr, boolean left, boolean before)
-
-
Method Detail
-
getEndPoint
public Marker getEndPoint()
-
isBefore
public boolean isBefore()
-
isLeft
public boolean isLeft()
-
isStructural
public boolean isStructural()
- Overrides:
isStructural
in classVariant
-
query
public Markers query(IntervalForest intervalForest)
Return a collection of intervals that intersect both ends of this variant
-
realignLeft
public Variant realignLeft()
Description copied from class:Variant
Create a new variant realigning it towards the leftmost position- Overrides:
realignLeft
in classVariant
-
-