Package org.snpeff.interval
Class Upstream
- 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.Upstream
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,TxtSerializable
public class Upstream extends Marker
Interval for a gene, as well as some other information: exons, utrs, cds, etc.- 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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Constructor Summary
Constructors Constructor Description Upstream()
Upstream(Transcript parent, int start, int end, boolean strandMinus, java.lang.String id)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
distanceToTr(Variant variant)
Distance to transcriptprotected boolean
isShowWarningIfParentDoesNotInclude()
Upstream sites are no included in transcript (by definition).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, 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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Upstream
public Upstream()
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Upstream
public Upstream(Transcript parent, int start, int end, boolean strandMinus, java.lang.String id)
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Method Detail
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distanceToTr
public int distanceToTr(Variant variant)
Distance to transcript
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isShowWarningIfParentDoesNotInclude
protected boolean isShowWarningIfParentDoesNotInclude()
Upstream sites are no included in transcript (by definition).- Overrides:
isShowWarningIfParentDoesNotInclude
in classMarker
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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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