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 exonExon
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 exonConstructors 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 exonprotected 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 doprotected 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 exonprotected Exon
SnpEffPredictorFactoryGff. addExon(Transcript tr, GffMarker gffMarker, java.lang.String exonId)
Create a new exonprotected Exon
SnpEffPredictorFactoryGff. findOrCreateExon(java.lang.String parentId, GffMarker gffMarker)
Find an exon for a given parentIdMethods 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 exonMethods 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)
-