Package org.snpeff.interval
Class Motif
- 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.Motif
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,TxtSerializable
public class Motif extends Marker
Regulatory elements- Author:
- pablocingolani
- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description static boolean
debug
static double
SCORE_THRESHOLD
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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 Motif
cloneShallow()
Perform a shallow clonePwm
getPwm()
java.lang.String
getPwmId()
java.lang.String
getPwmName()
void
serializeParse(MarkerSerializer markerSerializer)
Parse a line from a serialized filejava.lang.String
serializeSave(MarkerSerializer markerSerializer)
Create a string to serialize to a filevoid
setPwm(Pwm pwm)
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, codonTable, compareTo, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isAdjustIfParentDoesNotInclude, isShowWarningIfParentDoesNotInclude, minus, query, query, readTxt, 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
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Field Detail
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SCORE_THRESHOLD
public static final double SCORE_THRESHOLD
- See Also:
- Constant Field Values
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debug
public static final boolean debug
- See Also:
- Constant Field Values
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Constructor Detail
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Motif
public Motif()
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Motif
public Motif(Marker parent, int start, int end, boolean strandMinus, java.lang.String id, java.lang.String pwmName, java.lang.String pwmId)
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Method Detail
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cloneShallow
public Motif cloneShallow()
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classMarker
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getPwm
public Pwm getPwm()
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getPwmId
public java.lang.String getPwmId()
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getPwmName
public java.lang.String getPwmName()
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serializeParse
public void serializeParse(MarkerSerializer markerSerializer)
Description copied from class:Marker
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
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setPwm
public void setPwm(Pwm pwm)
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variantEffect
public boolean variantEffect(Variant variant, VariantEffects variantEffects)
Calculate the effect of this variant- Overrides:
variantEffect
in classMarker
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