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 TypeMethodDescriptionboolean
Custom.variantEffect
(Variant variant, VariantEffects changeEffecs) boolean
Downstream.variantEffect
(Variant variant, VariantEffects variantEffects) boolean
Exon.variantEffect
(Variant variant, VariantEffects variantEffects) Note: This only adds spliceSites effects, for detailed codon changes effects we use 'CodonChange' classboolean
Gene.variantEffect
(Variant variant, VariantEffects variantEffects) Get some details about the effect on this geneboolean
Intron.variantEffect
(Variant variant, VariantEffects variantEffects) boolean
Marker.variantEffect
(Variant variant, VariantEffects variantEffects) Calculate the effect of this variantboolean
MicroRnaBindingSite.variantEffect
(Variant variant, VariantEffects changeEffects) boolean
Motif.variantEffect
(Variant variant, VariantEffects variantEffects) Calculate the effect of this variantboolean
NextProt.variantEffect
(Variant variant, VariantEffects variantEffects) boolean
ProteinInteractionLocus.variantEffect
(Variant variant, VariantEffects variantEffects) Calculate the effect of this variantboolean
ProteinProteinInteractionLocus.variantEffect
(Variant variant, VariantEffects variantEffects) Calculate the effect of this variantboolean
Regulation.variantEffect
(Variant variant, VariantEffects variantEffects) Calculate the effect of this variantboolean
SpliceSite.variantEffect
(Variant variant, VariantEffects variantEffects) boolean
Transcript.variantEffect
(Variant variant, VariantEffects variantEffects) Get some details about the effect on this transcriptboolean
Upstream.variantEffect
(Variant variant, VariantEffects variantEffects) boolean
Utr3prime.variantEffect
(Variant variant, VariantEffects variantEffects) boolean
Utr5prime.variantEffect
(Variant variant, VariantEffects variantEffects) protected void
Gene.variantEffectGene
(Variant variant, VariantEffects variantEffects) Add gene-specific annotationsboolean
Marker.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 CodonChange
CodonChange.factory
(Variant variant, Transcript transcript, VariantEffects variantEffects) Create a specific codon change for a variantConstructors in org.snpeff.interval.codonChange with parameters of type VariantEffectsModifierConstructorDescriptionprotected
CodonChange
(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 void
SnpEffectPredictor.variantEffect
(Variant variant, VariantEffects variantEffects, Markers intersects) Calculate variant effect for each marker in 'intersect'void
ProteinFastaWriter.write
(Variant var, VariantEffects variantEffects) Append ALT protein sequence to fasta protein file