Package org.snpeff.interval
Class Regulation
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.Regulation
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,TxtSerializable
Regulatory elements
- Author:
- pablocingolani
- 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
ConstructorsConstructorDescriptionRegulation
(Marker parent, int start, int end, boolean strandMinus, String id, String name, String regulationType) -
Method Summary
Modifier and TypeMethodDescriptionPerform a shallow clonegetName()
void
serializeParse
(MarkerSerializer markerSerializer) Parse a line from a serialized fileserializeSave
(MarkerSerializer markerSerializer) Create a string to serialize to a filetoString()
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, codonTable, compareTo, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isAdjustIfParentDoesNotInclude, isDeferredAnalysis, isShowWarningIfParentDoesNotInclude, minus, query, query, readTxt, shouldApply, 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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Regulation
public Regulation() -
Regulation
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Method Details
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cloneShallow
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classMarker
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getName
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getRegulationType
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serializeParse
Parse a line from a serialized file- Specified by:
serializeParse
in interfaceTxtSerializable
- Overrides:
serializeParse
in classMarker
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serializeSave
Create a string to serialize to a file- Specified by:
serializeSave
in interfaceTxtSerializable
- Overrides:
serializeSave
in classMarker
- Returns:
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toString
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variantEffect
Calculate the effect of this variant- Overrides:
variantEffect
in classMarker
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