Uses of Class
org.snpeff.interval.Exon
Packages that use Exon
Package
Description
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Uses of Exon in org.snpeff.interval
Methods in org.snpeff.interval that return ExonModifier and TypeMethodDescriptionApply variant to exon WARNING: There might be conditions which change the exon type (e.g.Exon.cloneShallow()Transcript.findExon(int pos) Return the an exon that intersects 'pos'Return an exon intersecting 'marker' (first exon found)Intron.getExonAfter()Intron.getExonBefore()Transcript.getFirstCodingExon()Get first coding exonReturn the first exon that intersects 'interval' (null if not found)Methods in org.snpeff.interval that return types with arguments of type ExonMethods in org.snpeff.interval with parameters of type ExonModifier and TypeMethodDescriptionFind a CDS that matches exactly the exonConstructors in org.snpeff.interval with parameters of type ExonModifierConstructorDescriptionIntron(Transcript parent, int start, int end, boolean strandMinus, String id, Exon exonBefore, Exon exonAfter) SpliceSite(Exon parent, int start, int end, boolean strandMinus, String id) SpliceSiteRegion(Exon parent, int start, int end, boolean strandMinus, String id) -
Uses of Exon in org.snpeff.interval.codonChange
Methods in org.snpeff.interval.codonChange with parameters of type ExonModifier and TypeMethodDescriptionprotected booleanCodonChange.codonChange(Exon exon) Calculate the effect on an exonprotected booleanCodonChangeDel.codonChange(Exon exon) Analyze deletions in this transcript.protected booleanCodonChangeIns.codonChange(Exon exon) Analyze insertions in this transcript.protected booleanCodonChangeInterval.codonChange(Exon exon) Interval is not a variant, nothing to doprotected booleanCodonChangeSnp.codonChange(Exon exon) Analyze SNPs in this transcript. -
Uses of Exon in org.snpeff.snpEffect
Methods in org.snpeff.snpEffect that return Exon -
Uses of Exon in org.snpeff.snpEffect.factory
Methods in org.snpeff.snpEffect.factory that return ExonModifier and TypeMethodDescriptionprotected ExonAdd an exonprotected ExonSnpEffPredictorFactoryGff.addExon(Transcript tr, GffMarker gffMarker, String exonId) Create a new exonprotected ExonSnpEffPredictorFactoryGff.findOrCreateExon(String parentId, GffMarker gffMarker) Find an exon for a given parentIdMethods in org.snpeff.snpEffect.factory that return types with arguments of type ExonModifier and TypeMethodDescriptionCreate and add a new exonMethods in org.snpeff.snpEffect.factory with parameters of type Exon -
Uses of Exon in org.snpeff.stats
Methods in org.snpeff.stats with parameters of type ExonModifier and TypeMethodDescriptiondoubleExpected number of sequences (average between plus and minus strand)intObserved sequence (average between plus and minus strand)doubleObserved over expected ratio -
Uses of Exon in org.snpeff.svg
Constructors in org.snpeff.svg with parameters of type Exon
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