Package org.snpeff.interval

Class NextProt

java.lang.Object

org.snpeff.interval.Interval

org.snpeff.interval.Marker

org.snpeff.interval.NextProt

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

Field Summary

Fields inherited from class org.snpeff.interval.Marker

type

Fields inherited from class org.snpeff.interval.Interval

chromosomeNameOri, end, id, parent, start, strandMinus

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)

Method Summary

Modifier and Type	Method	Description
NextProt	cloneShallow()	Perform a shallow clone
java.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-synonymous
boolean	isHighlyConservedAaSequence()
void	serializeParse(MarkerSerializer markerSerializer)	Parse a line from a serialized file
java.lang.String	serializeSave(MarkerSerializer markerSerializer)	Create a string to serialize to a file
void	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

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

Constructor Detail

NextProt

public NextProt()

NextProt

public NextProt(Transcript transcript,
                int start,
                int end,
                java.lang.String id)

NextProt

public NextProt(Transcript transcript,
                int start,
                int end,
                java.lang.String id,
                java.lang.String name)

Method Detail

cloneShallow

public NextProt cloneShallow()

Description copied from class: Marker

Perform a shallow clone

Overrides:

cloneShallow in class Marker

getName

public java.lang.String getName()

getTranscriptId

public java.lang.String 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 class Marker

isHighlyConservedAaSequence

public boolean isHighlyConservedAaSequence()

setHighlyConservedAaSequence

public void setHighlyConservedAaSequence(boolean highlyConservedAaSequence)

serializeParse

public void serializeParse(MarkerSerializer markerSerializer)

Description copied from class: Marker

Parse a line from a serialized file

Specified by:

serializeParse in interface TxtSerializable

Overrides:

serializeParse in class Marker

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 interface TxtSerializable

Overrides:

serializeSave in class Marker

variantEffect

public boolean variantEffect(Variant variant,
                             VariantEffects variantEffects)

Description copied from class: Marker

Calculate the effect of this variant

Overrides:

variantEffect in class Marker