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 EffectType
CodonChange.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 VariantEffect
CodonChange.effect
(Marker marker, EffectType effectType, boolean allowReplace) Calculate variant effectprotected VariantEffect
CodonChange.effectNoCodon
(Marker marker, EffectType effectType) protected VariantEffect
CodonChange.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 EffectType
VariantEffectStructural.effect()
VariantEffect.getEffectType()
Highest effect typeEffectType.getGeneRegion()
static EffectType
EffectType.parse
(EffFormatVersion formatVersion, String str) Parse a string to an EffectTypestatic EffectType
Returns 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 TypeMethodDescriptionvoid
VariantEffects.add
(Variant variant, Marker marker, EffectType effectType, String message) Add an effectvoid
VariantEffects.add
(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, String message) Add an effectvoid
VariantEffect.addEffect
(EffectType effectType) void
VariantEffect.addEffectType
(EffectType effectType) void
VariantEffects.addEffectType
(Variant variant, Marker marker, EffectType effectType) Add: If possible, only add an effect type (otherwise add the full effect)boolean
VariantEffect.hasEffectType
(EffectType effectType) void
VariantEffect.set
(Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, String message) void
VariantEffect.setEffect
(EffectType effectType) Set effect using default impactvoid
VariantEffect.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.snpEffect.testCases.unity
Methods in org.snpeff.snpEffect.testCases.unity with parameters of type EffectTypeModifier and TypeMethodDescriptionprotected void
TestCasesBase.checkEffect
(Variant variant, EffectType effectExpected) protected void
TestCasesBase.checkEffect
(Variant variant, EffectType effectExpected, EffectType effectNotExpected, VariantEffect.EffectImpact impact) void
TestGenome.checkEffect
(Variant variant, EffectType effectTypeExpected, VariantEffect.EffectImpact effectImpactExpected, int countMatchExpected) Apply a predictor to a variant and check whether the expected number of matches are foundprotected void
TestCasesStructuralDel.checkEffects
(Variant variant, EffectType[] expEffs, String[] expHgvsp, String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, String[] expAnns) protected void
TestCasesStructuralDup.checkEffects
(Variant variant, EffectType[] expEffs, String[] expHgvsp, String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, String[] expAnns) protected void
TestCasesStructuralInv.checkEffects
(Variant variant, EffectType[] expEffs, String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, String[] expAnns) protected void
TestCasesStructuralInv.checkEffects
(Variant variant, EffectType[] expEffs, String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, String[] expAnns, Gene[] genesToAdd) protected void
TestCasesStructuralTranslocations.checkEffects
(Variant variant, EffectType[] expEffs, EffectType[] notExpEffs, String[] expHgvsp, String[] expHgvsc, VariantEffect.EffectImpact expectedImpact) -
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 TypeMethodDescriptionvoid
VcfEffect.addEffectType
(EffectType effectType) boolean
VcfEffect.hasEffectType
(EffectType effType) Does it have 'effType' ?void
VcfEffect.setEffectType
(EffectType effect)