Uses of Class
org.snpeff.interval.Exon

Packages that use Exon

Package	Description
org.snpeff.interval
org.snpeff.interval.codonChange
org.snpeff.snpEffect
org.snpeff.snpEffect.factory
org.snpeff.stats
org.snpeff.svg

Uses of Exon in org.snpeff.interval

Methods in org.snpeff.interval that return Exon

Modifier and Type	Method	Description
Exon	Exon.apply(Variant variant)	Apply variant to exon WARNING: There might be conditions which change the exon type (e.g.
Exon	Exon.cloneShallow()
Exon	Transcript.findExon(int pos)	Return the an exon that intersects 'pos'
Exon	Transcript.findExon(Marker marker)	Return an exon intersecting 'marker' (first exon found)
Exon	Intron.getExonAfter()
Exon	Intron.getExonBefore()
Exon	Transcript.getFirstCodingExon()	Get first coding exon
Exon	Transcript.queryExon(Marker interval)	Return the first exon that intersects 'interval' (null if not found)

Methods in org.snpeff.interval that return types with arguments of type Exon

Modifier and Type	Method	Description
java.util.Collection<Exon>	Transcript.getExons()	A more intuitive name for 'subintervals'

Methods in org.snpeff.interval with parameters of type Exon

Modifier and Type	Method	Description
Cds	Transcript.findCds(Exon exon)	Find a CDS that matches exactly the exon

Constructors in org.snpeff.interval with parameters of type Exon

Constructor	Description
Intron(Transcript parent, int start, int end, boolean strandMinus, java.lang.String id, Exon exonBefore, Exon exonAfter)
SpliceSite(Exon parent, int start, int end, boolean strandMinus, java.lang.String id)
SpliceSiteRegion(Exon parent, int start, int end, boolean strandMinus, java.lang.String id)
Utr(Exon parent, int start, int end, boolean strandMinus, java.lang.String id)
Utr3prime(Exon parent, int start, int end, boolean strandMinus, java.lang.String id)
Utr5prime(Exon parent, int start, int end, boolean strandMinus, java.lang.String id)

Uses of Exon in org.snpeff.interval.codonChange

Methods in org.snpeff.interval.codonChange with parameters of type Exon

Modifier and Type	Method	Description
protected boolean	CodonChange.codonChange(Exon exon)	Calculate the effect on an exon
protected boolean	CodonChangeDel.codonChange(Exon exon)	Analyze deletions in this transcript.
protected boolean	CodonChangeIns.codonChange(Exon exon)	Analyze insertions in this transcript.
protected boolean	CodonChangeInterval.codonChange(Exon exon)	Interval is not a variant, nothing to do
protected boolean	CodonChangeSnp.codonChange(Exon exon)	Analyze SNPs in this transcript.

Uses of Exon in org.snpeff.snpEffect

Methods in org.snpeff.snpEffect that return Exon

Modifier and Type	Method	Description
Exon	VariantEffect.getExon()	Get exon (if any)

Uses of Exon in org.snpeff.snpEffect.factory

Methods in org.snpeff.snpEffect.factory that return Exon

Modifier and Type	Method	Description
protected Exon	SnpEffPredictorFactory.add(Exon exon)	Add an exon
protected Exon	SnpEffPredictorFactoryGff.addExon(Transcript tr, GffMarker gffMarker, java.lang.String exonId)	Create a new exon
protected Exon	SnpEffPredictorFactoryGff.findOrCreateExon(java.lang.String parentId, GffMarker gffMarker)	Find an exon for a given parentId

Methods in org.snpeff.snpEffect.factory that return types with arguments of type Exon

Modifier and Type	Method	Description
protected java.util.List<Exon>	SnpEffPredictorFactoryGff.addExons(GffMarker gffMarker)	Create and add a new exon

Methods in org.snpeff.snpEffect.factory with parameters of type Exon

Modifier and Type	Method	Description
protected Exon	SnpEffPredictorFactory.add(Exon exon)	Add an exon

Uses of Exon in org.snpeff.stats

Methods in org.snpeff.stats with parameters of type Exon

Modifier and Type	Method	Description
double	ObservedOverExpected.expected(Exon e)	Expected number of sequences (average between plus and minus strand)
int	ObservedOverExpected.observed(Exon e)	Observed sequence (average between plus and minus strand)
double	ObservedOverExpected.oe(Exon e)	Observed over expected ratio

Uses of Exon in org.snpeff.svg

Constructors in org.snpeff.svg with parameters of type Exon

Constructor	Description
SvgExon(Exon ex, Svg svg)