Package org.snpeff.interval
Class Custom
- 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.Custom
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,java.lang.Iterable<KeyValue<java.lang.String,java.lang.String>>
,TxtSerializable
- Direct Known Subclasses:
GffMarker
public class Custom extends Marker implements java.lang.Iterable<KeyValue<java.lang.String,java.lang.String>>
This is a custom interval (i.e. intervals provided by the user)- 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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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Custom
cloneShallow()
Perform a shallow clonejava.lang.String
getLabel()
double
getScore()
boolean
hasAnnotations()
Do we have additional annotations?java.util.Iterator<KeyValue<java.lang.String,java.lang.String>>
iterator()
void
setLabel(java.lang.String label)
void
setScore(double score)
java.lang.String
toString()
boolean
variantEffect(Variant variant, VariantEffects changeEffecs)
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, serializeParse, serializeSave, 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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Custom
public Custom()
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Custom
public Custom(Marker parent, int start, int end, boolean strandMinus, java.lang.String id, java.lang.String label)
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Method Detail
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cloneShallow
public Custom cloneShallow()
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classMarker
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getLabel
public java.lang.String getLabel()
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getScore
public double getScore()
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hasAnnotations
public boolean hasAnnotations()
Do we have additional annotations?
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iterator
public java.util.Iterator<KeyValue<java.lang.String,java.lang.String>> iterator()
- Specified by:
iterator
in interfacejava.lang.Iterable<KeyValue<java.lang.String,java.lang.String>>
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setLabel
public void setLabel(java.lang.String label)
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setScore
public void setScore(double score)
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variantEffect
public boolean variantEffect(Variant variant, VariantEffects changeEffecs)
Description copied from class:Marker
Calculate the effect of this variant- Overrides:
variantEffect
in classMarker
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