Uses of Class
org.snpeff.snpEffect.VariantEffects
Packages that use VariantEffects
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Uses of VariantEffects in org.snpeff.interval
Methods in org.snpeff.interval with parameters of type VariantEffectsModifier and TypeMethodDescriptionbooleanCustom.variantEffect(Variant variant, VariantEffects changeEffecs) booleanDownstream.variantEffect(Variant variant, VariantEffects variantEffects) booleanExon.variantEffect(Variant variant, VariantEffects variantEffects) Note: This only adds spliceSites effects, for detailed codon changes effects we use 'CodonChange' classbooleanGene.variantEffect(Variant variant, VariantEffects variantEffects) Get some details about the effect on this genebooleanIntron.variantEffect(Variant variant, VariantEffects variantEffects) booleanMarker.variantEffect(Variant variant, VariantEffects variantEffects) Calculate the effect of this variantbooleanMicroRnaBindingSite.variantEffect(Variant variant, VariantEffects changeEffects) booleanMotif.variantEffect(Variant variant, VariantEffects variantEffects) Calculate the effect of this variantbooleanNextProt.variantEffect(Variant variant, VariantEffects variantEffects) booleanProteinInteractionLocus.variantEffect(Variant variant, VariantEffects variantEffects) Calculate the effect of this variantbooleanProteinProteinInteractionLocus.variantEffect(Variant variant, VariantEffects variantEffects) Calculate the effect of this variantbooleanRegulation.variantEffect(Variant variant, VariantEffects variantEffects) Calculate the effect of this variantbooleanSpliceSite.variantEffect(Variant variant, VariantEffects variantEffects) booleanTranscript.variantEffect(Variant variant, VariantEffects variantEffects) Get some details about the effect on this transcriptbooleanUpstream.variantEffect(Variant variant, VariantEffects variantEffects) booleanUtr3prime.variantEffect(Variant variant, VariantEffects variantEffects) booleanUtr5prime.variantEffect(Variant variant, VariantEffects variantEffects) protected voidGene.variantEffectGene(Variant variant, VariantEffects variantEffects) Add gene-specific annotationsbooleanMarker.variantEffectNonRef(Variant variant, VariantEffects variantEffects) Calculate the effect of this variant -
Uses of VariantEffects in org.snpeff.interval.codonChange
Methods in org.snpeff.interval.codonChange with parameters of type VariantEffectsModifier and TypeMethodDescriptionstatic CodonChangeCodonChange.factory(Variant variant, Transcript transcript, VariantEffects variantEffects) Create a specific codon change for a variantConstructors in org.snpeff.interval.codonChange with parameters of type VariantEffectsModifierConstructorDescriptionprotectedCodonChange(Variant variant, Transcript transcript, VariantEffects variantEffects) CodonChangeDel(Variant variant, Transcript transcript, VariantEffects variantEffects) CodonChangeDup(Variant variant, Transcript transcript, VariantEffects variantEffects) CodonChangeIns(Variant variant, Transcript transcript, VariantEffects changeEffects) CodonChangeInterval(Variant variant, Transcript transcript, VariantEffects varEffects) CodonChangeInv(Variant variant, Transcript transcript, VariantEffects variantEffects) CodonChangeMixed(Variant variant, Transcript transcript, VariantEffects variantEffects) CodonChangeMnp(Variant variant, Transcript transcript, VariantEffects variantEffects) CodonChangeSnp(Variant variant, Transcript transcript, VariantEffects variantEffects) CodonChangeStructural(Variant variant, Transcript transcript, VariantEffects variantEffects) -
Uses of VariantEffects in org.snpeff.snpEffect
Methods in org.snpeff.snpEffect that return VariantEffectsModifier and TypeMethodDescriptionSnpEffectPredictor.variantEffect(Variant variant) Predict the effect of a variantMethods in org.snpeff.snpEffect with parameters of type VariantEffectsModifier and TypeMethodDescriptionprotected voidSnpEffectPredictor.variantEffect(Variant variant, VariantEffects variantEffects, Markers intersects) Calculate variant effect for each marker in 'intersect'