Package org.snpeff.interval
Class VariantWithScore
- 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.Variant
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- org.snpeff.interval.VariantWithScore
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,TxtSerializable
public class VariantWithScore extends Variant
A variant that has a numeric score.- Author:
- pcingola
- See Also:
- Serialized Form
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Nested Class Summary
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Nested classes/interfaces inherited from class org.snpeff.interval.Variant
Variant.VariantType
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Field Summary
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Fields inherited from class org.snpeff.interval.Variant
alt, genotype, HUGE_DELETION_RATIO_THRESHOLD, HUGE_DELETION_SIZE_THRESHOLD, imprecise, NO_VARIANT, ref, variantType
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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 VariantWithScore()
VariantWithScore(Marker parent, int start, int end, java.lang.String id, double score)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description VariantWithScore
cloneShallow()
Perform a shallow clonedouble
getScore()
void
setScore(double score)
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Methods inherited from class org.snpeff.interval.Variant
clone, compareTo, decompose, factory, getAlt, getGenotype, getReference, getVariantType, hashCode, isBnd, isDel, isDup, isElongation, isImprecise, isInDel, isIns, isInterval, isInv, isMixed, isMnp, isNonRef, isShowWarningIfParentDoesNotInclude, isSnp, isStructural, isStructuralHuge, isTruncation, isVariant, lengthChange, netChange, netChange, realignLeft, reverse, setGenotype, setImprecise, setVariantType, toString, toStringEnsembl, toStringOld
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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, query, readTxt, serializeParse, serializeSave, shouldApply, union, 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, 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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VariantWithScore
public VariantWithScore()
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VariantWithScore
public VariantWithScore(Marker parent, int start, int end, java.lang.String id, double score)
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Method Detail
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cloneShallow
public VariantWithScore cloneShallow()
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classVariant
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getScore
public double getScore()
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setScore
public void setScore(double score)
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