Package org.snpeff.interval
Class NextProt
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.NextProt
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,TxtSerializable
NextProt annotation marker
- Author:
- pcingola
- See Also:
-
Field Summary
Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
-
Constructor Summary
ConstructorsConstructorDescriptionNextProt()
NextProt
(Transcript transcript, int start, int end, String id) NextProt
(Transcript transcript, int start, int end, String id, String name) -
Method Summary
Modifier and TypeMethodDescriptionPerform a shallow clonegetName()
boolean
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
void
serializeParse
(MarkerSerializer markerSerializer) Parse a line from a serialized fileserializeSave
(MarkerSerializer markerSerializer) Create a string to serialize to a filevoid
setHighlyConservedAaSequence
(boolean highlyConservedAaSequence) boolean
variantEffect
(Variant variant, VariantEffects variantEffects) 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, isShowWarningIfParentDoesNotInclude, minus, query, query, readTxt, shouldApply, toString, 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
-
Constructor Details
-
NextProt
public NextProt() -
NextProt
-
NextProt
-
-
Method Details
-
cloneShallow
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classMarker
-
getName
-
getTranscriptId
-
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
-
isHighlyConservedAaSequence
public boolean isHighlyConservedAaSequence() -
setHighlyConservedAaSequence
public void setHighlyConservedAaSequence(boolean highlyConservedAaSequence) -
serializeParse
Description copied from class:Marker
Parse a line from a serialized file- Specified by:
serializeParse
in interfaceTxtSerializable
- Overrides:
serializeParse
in classMarker
-
serializeSave
Description copied from class:Marker
Create a string to serialize to a file- Specified by:
serializeSave
in interfaceTxtSerializable
- Overrides:
serializeSave
in classMarker
-
variantEffect
Description copied from class:Marker
Calculate the effect of this variant- Overrides:
variantEffect
in classMarker
-