Package org.snpeff.interval
Class Regulation
- 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.Regulation
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,TxtSerializable
public class Regulation extends Marker
Regulatory elements- Author:
- pablocingolani
- 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 Regulation()
Regulation(Marker parent, int start, int end, boolean strandMinus, java.lang.String id, java.lang.String name, java.lang.String regulationType)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Regulation
cloneShallow()
Perform a shallow clonejava.lang.String
getName()
java.lang.String
getRegulationType()
void
serializeParse(MarkerSerializer markerSerializer)
Parse a line from a serialized filejava.lang.String
serializeSave(MarkerSerializer markerSerializer)
Create a string to serialize to a filejava.lang.String
toString()
boolean
variantEffect(Variant variant, VariantEffects variantEffects)
Calculate the effect of this seqChange-
Methods 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, isShowWarningIfParentDoesNotInclude, minus, query, query, readTxt, shouldApply, 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
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Constructor Detail
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Regulation
public Regulation()
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Regulation
public Regulation(Marker parent, int start, int end, boolean strandMinus, java.lang.String id, java.lang.String name, java.lang.String regulationType)
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Method Detail
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cloneShallow
public Regulation cloneShallow()
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classMarker
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getName
public java.lang.String getName()
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getRegulationType
public java.lang.String getRegulationType()
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serializeParse
public void serializeParse(MarkerSerializer markerSerializer)
Parse a line from a serialized file- Specified by:
serializeParse
in interfaceTxtSerializable
- Overrides:
serializeParse
in classMarker
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serializeSave
public java.lang.String serializeSave(MarkerSerializer markerSerializer)
Create a string to serialize to a file- Specified by:
serializeSave
in interfaceTxtSerializable
- Overrides:
serializeSave
in classMarker
- Returns:
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variantEffect
public boolean variantEffect(Variant variant, VariantEffects variantEffects)
Calculate the effect of this seqChange- Overrides:
variantEffect
in classMarker
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