Package org.snpeff.interval
Class Upstream
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.Upstream
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,TxtSerializable
Interval for a gene, as well as some other information: exons, utrs, cds, etc.
- Author:
- pcingola
- See Also:
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Field Summary
Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Constructor Summary
ConstructorsConstructorDescriptionUpstream()
Upstream
(Transcript parent, int start, int end, boolean strandMinus, String id) -
Method Summary
Modifier and TypeMethodDescriptionint
distanceToTr
(Variant variant) Distance to transcriptprotected boolean
Upstream sites are no included in transcript (by definition).boolean
variantEffect
(Variant variant, VariantEffects variantEffects) Calculate the effect of this variantMethods 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, minus, query, query, readTxt, serializeParse, serializeSave, shouldApply, toString, union, variantEffectNonRef
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 Details
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Upstream
public Upstream() -
Upstream
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Method Details
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distanceToTr
Distance to transcript -
isShowWarningIfParentDoesNotInclude
protected boolean isShowWarningIfParentDoesNotInclude()Upstream sites are no included in transcript (by definition).- Overrides:
isShowWarningIfParentDoesNotInclude
in classMarker
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variantEffect
Description copied from class:Marker
Calculate the effect of this variant- Overrides:
variantEffect
in classMarker
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