Package org.snpeff.interval

Class Exon

java.lang.Object

org.snpeff.interval.Interval

org.snpeff.interval.Marker

org.snpeff.interval.MarkerSeq

org.snpeff.interval.Exon

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<Interval>, MarkerWithFrame, TxtSerializable

public class Exon
extends MarkerSeq
implements MarkerWithFrame

Interval for an exon

Author:

pcingola

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	Exon.ExonSpliceType	Characterize exons based on alternative splicing References: "Alternative splicing and evolution - diversification, exon definition and function" (see Box 1)

Field Summary

Fields

Modifier and Type	Field	Description
static int	ToStringVersion

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
Exon()
Exon(Transcript parent, int start, int end, boolean strandMinus, java.lang.String id, int rank)

Method Summary

Modifier and Type	Method	Description
void	add(SpliceSite ss)	Add a splice site to the collection
Exon	apply(Variant variant)	Apply variant to exon WARNING: There might be conditions which change the exon type (e.g.
Exon	cloneShallow()	Perform a shallow clone
SpliceSiteRegion	createSpliceSiteRegionEnd(int size)	Create splice site regions
SpliceSiteRegion	createSpliceSiteRegionStart(int size)	Create splice site regions
boolean	frameCorrection(int frameCorrection)	Correct exons according to frame information Shift the start position one base
int	getAaIdxEnd()
int	getAaIdxStart()
int	getFrame()
int	getRank()
java.util.ArrayList<SpliceSite>	getSpliceSites()
Exon.ExonSpliceType	getSpliceType()
protected boolean	isAdjustIfParentDoesNotInclude(Marker parent)	Adjust parent if it does not include child?
Markers	query(Marker marker)	Query all genomic regions that intersect 'marker'
void	reset()
ErrorWarningType	sanityCheck(Variant variant)	Check that the base in the exon corresponds with the one in the SNP
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	setAaIdx(int aaIdxStart, int aaIdxEnd)
void	setFrame(int frame)	Frame can be {-1, 0, 1, 2}, where '-1' means unknown
void	setRank(int rank)
java.lang.String	toString()
boolean	variantEffect(Variant variant, VariantEffects variantEffects)	Note: This only adds spliceSites effects, for detailed codon changes effects we use 'CodonChange' class

Methods inherited from class org.snpeff.interval.MarkerSeq

applyDel, applyDup, applyIns, applyMnp, applySnp, basesAt, basesAtPos, getSequence, getSequence, hasSequence, setSequence, union

Methods inherited from class org.snpeff.interval.Marker

adjust, applyDel, applyDup, applyIns, applyMixed, clone, codonTable, compareTo, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isDeferredAnalysis, isShowWarningIfParentDoesNotInclude, minus, query, readTxt, shouldApply, 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

Field Detail

ToStringVersion

public static int ToStringVersion

Constructor Detail

Exon

public Exon()

Exon

public Exon(Transcript parent,
            int start,
            int end,
            boolean strandMinus,
            java.lang.String id,
            int rank)

Method Detail

add

public void add(SpliceSite ss)

Add a splice site to the collection

apply

public Exon apply(Variant variant)

Apply variant to exon WARNING: There might be conditions which change the exon type (e.g. an intron is deleted). Nevertheless ExonSpliceType is not updated since it reflects the exon type before a sequence change.

Overrides:

apply in class MarkerSeq

Returns:

The marker result after applying variant

cloneShallow

public Exon cloneShallow()

Description copied from class: Marker

Perform a shallow clone

Overrides:

cloneShallow in class MarkerSeq

createSpliceSiteRegionEnd

public SpliceSiteRegion createSpliceSiteRegionEnd(int size)

Create splice site regions

createSpliceSiteRegionStart

public SpliceSiteRegion createSpliceSiteRegionStart(int size)

Create splice site regions

frameCorrection

public boolean frameCorrection(int frameCorrection)

Correct exons according to frame information Shift the start position one base

getAaIdxEnd

public int getAaIdxEnd()

getAaIdxStart

public int getAaIdxStart()

getFrame

public int getFrame()

Specified by:

getFrame in interface MarkerWithFrame

getRank

public int getRank()

getSpliceSites

public java.util.ArrayList<SpliceSite> getSpliceSites()

getSpliceType

public Exon.ExonSpliceType getSpliceType()

isAdjustIfParentDoesNotInclude

protected boolean isAdjustIfParentDoesNotInclude(Marker parent)

Description copied from class: Marker

Adjust parent if it does not include child?

Overrides:

isAdjustIfParentDoesNotInclude in class Marker

query

public Markers query(Marker marker)

Query all genomic regions that intersect 'marker'

Overrides:

query in class Marker

reset

public void reset()

sanityCheck

public ErrorWarningType sanityCheck(Variant variant)

Check that the base in the exon corresponds with the one in the SNP

serializeParse

public void serializeParse(MarkerSerializer markerSerializer)

Parse a line from a serialized file

Specified by:

serializeParse in interface TxtSerializable

Overrides:

serializeParse in class MarkerSeq

serializeSave

public java.lang.String serializeSave(MarkerSerializer markerSerializer)

Create a string to serialize to a file

Specified by:

serializeSave in interface TxtSerializable

Overrides:

serializeSave in class MarkerSeq

setAaIdx

public void setAaIdx(int aaIdxStart,
                     int aaIdxEnd)

setFrame

public void setFrame(int frame)

Frame can be {-1, 0, 1, 2}, where '-1' means unknown

Specified by:

setFrame in interface MarkerWithFrame

setRank

public void setRank(int rank)

toString

public java.lang.String toString()

Overrides:

toString in class MarkerSeq

variantEffect

public boolean variantEffect(Variant variant,
                             VariantEffects variantEffects)

Note: This only adds spliceSites effects, for detailed codon changes effects we use 'CodonChange' class

Overrides:

variantEffect in class Marker