org.snpeff.interval.VariantWithScore

All Implemented Interfaces:: Serializable, Cloneable, Comparable<Interval>, TxtSerializable

public class VariantWithScore extends Variant

A variant that has a numeric score.

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.Marker
type

Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
Constructor Summary

Constructors

Constructor

Description

VariantWithScore()

VariantWithScore(Marker parent, int start, int end, String id, double score)
Method Summary

Modifier and Type

Method

Description

VariantWithScore

cloneShallow()

Perform a shallow clone

double

getScore()

void

setScore(double score)

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

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

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

Methods inherited from class java.lang.Object
equals, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Details
- VariantWithScore
  
  public VariantWithScore()
- VariantWithScore
  
  public VariantWithScore(Marker parent, int start, int end, String id, double score)
Method Details
- cloneShallow
  
  public VariantWithScore cloneShallow()
  
  Description copied from class: Marker
  
  Perform a shallow clone
  
  Overrides:
  
  cloneShallow in class Variant
- getScore
  
  public double getScore()
- setScore
  
  public void setScore(double score)

Class VariantWithScore

Nested Class Summary

Nested classes/interfaces inherited from class org.snpeff.interval.Variant

Field Summary

Fields inherited from class org.snpeff.interval.Variant

Fields inherited from class org.snpeff.interval.Marker

Fields inherited from class org.snpeff.interval.Interval

Constructor Summary

Method Summary

Methods inherited from class org.snpeff.interval.Variant

Methods inherited from class org.snpeff.interval.Marker

Methods inherited from class org.snpeff.interval.Interval

Methods inherited from class java.lang.Object

Constructor Details

VariantWithScore

VariantWithScore

Method Details

cloneShallow

getScore

setScore