Package org.snpeff.interval
Class NextProt
- 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.NextProt
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,TxtSerializable
public class NextProt extends Marker
NextProt annotation marker- 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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Constructor Summary
Constructors Constructor Description NextProt()
NextProt(Transcript transcript, int start, int end, java.lang.String id)
NextProt(Transcript transcript, int start, int end, java.lang.String id, java.lang.String name)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description NextProt
cloneShallow()
Perform a shallow clonejava.lang.String
getName()
java.lang.String
getTranscriptId()
boolean
isDeferredAnalysis()
Deferred analysis markers must be analyzed after 'standard' ones because their impact depends on other results For instance, a NextProt marker's impact would be different if the variant is synonymous or non-synonymousboolean
isHighlyConservedAaSequence()
void
serializeParse(MarkerSerializer markerSerializer)
Parse a line from a serialized filejava.lang.String
serializeSave(MarkerSerializer markerSerializer)
Create a string to serialize to a filevoid
setHighlyConservedAaSequence(boolean highlyConservedAaSequence)
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, toStrPos
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Constructor Detail
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NextProt
public NextProt()
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NextProt
public NextProt(Transcript transcript, int start, int end, java.lang.String id)
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NextProt
public NextProt(Transcript transcript, int start, int end, java.lang.String id, java.lang.String name)
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Method Detail
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cloneShallow
public NextProt 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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getTranscriptId
public java.lang.String getTranscriptId()
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isDeferredAnalysis
public boolean isDeferredAnalysis()
Deferred analysis markers must be analyzed after 'standard' ones because their impact depends on other results For instance, a NextProt marker's impact would be different if the variant is synonymous or non-synonymous- Overrides:
isDeferredAnalysis
in classMarker
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isHighlyConservedAaSequence
public boolean isHighlyConservedAaSequence()
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setHighlyConservedAaSequence
public void setHighlyConservedAaSequence(boolean highlyConservedAaSequence)
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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)
Description copied from class:Marker
Create a string to serialize to a file- Specified by:
serializeSave
in interfaceTxtSerializable
- Overrides:
serializeSave
in classMarker
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variantEffect
public boolean variantEffect(Variant variant, VariantEffects variantEffects)
Description copied from class:Marker
Calculate the effect of this variant- Overrides:
variantEffect
in classMarker
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