Package org.snpeff.interval
Class Custom
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.Custom
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,Iterable<KeyValue<String,
,String>> TxtSerializable
- Direct Known Subclasses:
GffMarker
This is a custom interval (i.e. intervals provided by the user)
- Author:
- pcingola
- 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
Constructors -
Method Summary
Modifier and TypeMethodDescriptionPerform a shallow clonegetLabel()
double
getScore()
boolean
Do we have additional annotations?iterator()
void
void
setScore
(double score) toString()
boolean
variantEffect
(Variant variant, VariantEffects changeEffecs) 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, serializeParse, serializeSave, 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
Methods inherited from class java.lang.Object
equals, finalize, getClass, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Constructor Details
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Custom
public Custom() -
Custom
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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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getLabel
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getScore
public double getScore() -
hasAnnotations
public boolean hasAnnotations()Do we have additional annotations? -
iterator
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setLabel
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setScore
public void setScore(double score) -
toString
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variantEffect
Description copied from class:Marker
Calculate the effect of this variant- Overrides:
variantEffect
in classMarker
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