Uses of Enum Class
org.snpeff.snpEffect.EffectType
Packages that use EffectType
Package
Description
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Uses of EffectType in org.snpeff.filter
Methods in org.snpeff.filter with parameters of type EffectType -
Uses of EffectType in org.snpeff.interval
Fields in org.snpeff.interval declared as EffectTypeMethods in org.snpeff.interval that return EffectType -
Uses of EffectType in org.snpeff.interval.codonChange
Methods in org.snpeff.interval.codonChange that return EffectTypeModifier and TypeMethodDescriptionprotected EffectTypeCodonChange.additionalEffect(String codonsOld, String codonsNew, int codonNum, int codonIndex, String aaOld, String aaNew) Calculate additional effect due to codon changes E.g.Methods in org.snpeff.interval.codonChange with parameters of type EffectTypeModifier and TypeMethodDescriptionprotected VariantEffectCodonChange.effect(Marker marker, EffectType effectType, boolean allowReplace) Calculate variant effectprotected VariantEffectCodonChange.effectNoCodon(Marker marker, EffectType effectType) protected VariantEffectCodonChange.effectNoCodon(Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact) -
Uses of EffectType in org.snpeff.motif
Methods in org.snpeff.motif with parameters of type EffectTypeModifier and TypeMethodDescriptionMotifLogo.toStringHtml(int width, int maxHeight, EffectType efectType) Return an HTML string that represents the motif. -
Uses of EffectType in org.snpeff.snpEffect
Fields in org.snpeff.snpEffect declared as EffectTypeFields in org.snpeff.snpEffect with type parameters of type EffectTypeMethods in org.snpeff.snpEffect that return EffectTypeModifier and TypeMethodDescriptionprotected EffectTypeVariantEffectStructural.effect()VariantEffect.getEffectType()Highest effect typeEffectType.getGeneRegion()static EffectTypeEffectType.parse(EffFormatVersion formatVersion, String str) Parse a string to an EffectTypestatic EffectTypeReturns the enum constant of this class with the specified name.static EffectType[]EffectType.values()Returns an array containing the constants of this enum class, in the order they are declared.Methods in org.snpeff.snpEffect that return types with arguments of type EffectTypeMethods in org.snpeff.snpEffect with parameters of type EffectTypeModifier and TypeMethodDescriptionvoidVariantEffects.add(Variant variant, Marker marker, EffectType effectType, String message) Add an effectvoidVariantEffects.add(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, String message) Add an effectvoidVariantEffect.addEffect(EffectType effectType) voidVariantEffect.addEffectType(EffectType effectType) voidVariantEffects.addEffectType(Variant variant, Marker marker, EffectType effectType) Add: If possible, only add an effect type (otherwise add the full effect)booleanVariantEffect.hasEffectType(EffectType effectType) voidVariantEffect.set(Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, String message) voidVariantEffect.setEffect(EffectType effectType) Set effect using default impactvoidVariantEffect.setEffectType(EffectType effectType) Constructors in org.snpeff.snpEffect with parameters of type EffectTypeModifierConstructorDescriptionVariantEffect(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, String codonsOld, String codonsNew, int codonNum, int codonIndex, int cDnaPos) -
Uses of EffectType in org.snpeff.vcf
Methods in org.snpeff.vcf that return EffectTypeMethods in org.snpeff.vcf that return types with arguments of type EffectTypeMethods in org.snpeff.vcf with parameters of type EffectTypeModifier and TypeMethodDescriptionvoidVcfEffect.addEffectType(EffectType effectType) booleanVcfEffect.hasEffectType(EffectType effType) Does it have 'effType' ?voidVcfEffect.setEffectType(EffectType effect)