Package org.snpeff.interval
Class Utr3prime
- 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.Utr
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- org.snpeff.interval.Utr3prime
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,TxtSerializable
public class Utr3prime extends Utr
Interval for a UTR (5 prime UTR and 3 prime UTR- 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 boolean
isUtr3prime()
boolean
isUtr5prime()
boolean
variantEffect(Variant variant, VariantEffects variantEffects)
Calculate the effect of this variant-
Methods inherited from class org.snpeff.interval.Marker
adjust, apply, applyDel, applyDup, applyIns, applyMixed, clone, cloneShallow, codonTable, compareTo, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isAdjustIfParentDoesNotInclude, isDeferredAnalysis, isShowWarningIfParentDoesNotInclude, minus, query, query, readTxt, serializeParse, serializeSave, shouldApply, toString, union, 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, toStrPos
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Constructor Detail
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Utr3prime
public Utr3prime()
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Utr3prime
public Utr3prime(Exon parent, int start, int end, boolean strandMinus, java.lang.String id)
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Method Detail
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isUtr3prime
public boolean isUtr3prime()
- Specified by:
isUtr3prime
in classUtr
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isUtr5prime
public boolean isUtr5prime()
- Specified by:
isUtr5prime
in classUtr
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variantEffect
public boolean variantEffect(Variant variant, VariantEffects variantEffects)
Description copied from class:Marker
Calculate the effect of this variant- Overrides:
variantEffect
in classMarker
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