Class VariantWithScore
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.Variant
org.snpeff.interval.VariantWithScore
- All Implemented Interfaces:
Serializable, Cloneable, Comparable<Interval>, TxtSerializable
A variant that has a numeric score.
- Author:
- pcingola
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from class Variant
Variant.VariantType -
Field Summary
Fields inherited from class Variant
alt, genotype, HUGE_DELETION_RATIO_THRESHOLD, HUGE_DELETION_SIZE_THRESHOLD, imprecise, NO_VARIANT, ref, variantTypeFields inherited from class Interval
chromosomeNameOri, end, id, parent, start, strandMinus -
Constructor Summary
ConstructorsConstructorDescriptionVariantWithScore(Marker parent, int start, int end, String id, double score) -
Method Summary
Methods inherited from class 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, toStringOldMethods inherited from class 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, variantEffectNonRefMethods inherited from class 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 Details
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VariantWithScore
public VariantWithScore() -
VariantWithScore
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Method Details
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cloneShallow
Description copied from class:MarkerPerform a shallow clone- Overrides:
cloneShallowin classVariant
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getScore
public double getScore() -
setScore
public void setScore(double score)
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