Uses of Class
org.snpeff.snpEffect.EffectType
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Packages that use EffectType Package Description org.snpeff.filter org.snpeff.interval org.snpeff.interval.codonChange org.snpeff.motif org.snpeff.snpEffect org.snpeff.snpEffect.testCases.unity org.snpeff.vcf -
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Uses of EffectType in org.snpeff.filter
Methods in org.snpeff.filter with parameters of type EffectType Modifier and Type Method Description void
VariantEffectFilter. add(EffectType effType)
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Uses of EffectType in org.snpeff.interval
Fields in org.snpeff.interval declared as EffectType Modifier and Type Field Description protected EffectType
Marker. type
Methods in org.snpeff.interval that return EffectType Modifier and Type Method Description EffectType
Marker. getType()
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Uses of EffectType in org.snpeff.interval.codonChange
Methods in org.snpeff.interval.codonChange that return EffectType Modifier and Type Method Description protected EffectType
CodonChange. additionalEffect(java.lang.String codonsOld, java.lang.String codonsNew, int codonNum, int codonIndex, java.lang.String aaOld, java.lang.String aaNew)
Calculate additional effect due to codon changes E.g.Methods in org.snpeff.interval.codonChange with parameters of type EffectType Modifier and Type Method Description protected VariantEffect
CodonChange. effect(Marker marker, EffectType effectType, boolean allowReplace)
protected VariantEffect
CodonChange. effectNoCodon(Marker marker, EffectType effectType)
protected VariantEffect
CodonChange. effectNoCodon(Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact)
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Uses of EffectType in org.snpeff.motif
Methods in org.snpeff.motif with parameters of type EffectType Modifier and Type Method Description java.lang.String
MotifLogo. 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 EffectType Modifier and Type Field Description protected EffectType
VariantEffect. effectType
Fields in org.snpeff.snpEffect with type parameters of type EffectType Modifier and Type Field Description protected java.util.List<EffectType>
VariantEffect. effectTypes
Methods in org.snpeff.snpEffect that return EffectType Modifier and Type Method Description protected EffectType
VariantEffectStructural. effect()
EffectType
VariantEffect. getEffectType()
Highest effect typeEffectType
EffectType. getGeneRegion()
static EffectType
EffectType. parse(EffFormatVersion formatVersion, java.lang.String str)
Parse a string to an EffectTypestatic EffectType
EffectType. valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.static EffectType[]
EffectType. values()
Returns an array containing the constants of this enum type, in the order they are declared.Methods in org.snpeff.snpEffect that return types with arguments of type EffectType Modifier and Type Method Description java.util.List<EffectType>
VariantEffect. getEffectTypes()
Highest effect typeMethods in org.snpeff.snpEffect with parameters of type EffectType Modifier and Type Method Description void
VariantEffects. add(Variant variant, Marker marker, EffectType effectType, java.lang.String message)
Add an effectvoid
VariantEffects. add(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, java.lang.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, java.lang.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 EffectType Constructor Description VariantEffect(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, java.lang.String codonsOld, java.lang.String codonsNew, int codonNum, int codonIndex, int cDnaPos)
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Uses of EffectType in org.snpeff.snpEffect.testCases.unity
Methods in org.snpeff.snpEffect.testCases.unity with parameters of type EffectType Modifier and Type Method Description protected void
TestCasesBase. checkEffect(Variant variant, EffectType effectExpected)
protected void
TestCasesBase. checkEffect(Variant variant, EffectType effectExpected, EffectType effectNotExpected, VariantEffect.EffectImpact impact)
protected void
TestCasesStructuralDel. checkEffects(Variant variant, EffectType[] expEffs, java.lang.String[] expHgvsp, java.lang.String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, java.lang.String[] expAnns)
protected void
TestCasesStructuralDup. checkEffects(Variant variant, EffectType[] expEffs, java.lang.String[] expHgvsp, java.lang.String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, java.lang.String[] expAnns)
protected void
TestCasesStructuralInv. checkEffects(Variant variant, EffectType[] expEffs, java.lang.String[] expHgvsp, java.lang.String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, java.lang.String[] expAnns)
protected void
TestCasesStructuralInv. checkEffects(Variant variant, EffectType[] expEffs, java.lang.String[] expHgvsp, java.lang.String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, java.lang.String[] expAnns, Gene[] genesToAdd)
protected void
TestCasesStructuralTranslocations. checkEffects(Variant variant, EffectType[] expEffs, EffectType[] notExpEffs, java.lang.String[] expHgvsp, java.lang.String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, java.lang.String[] expAnns)
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Uses of EffectType in org.snpeff.vcf
Methods in org.snpeff.vcf that return EffectType Modifier and Type Method Description EffectType
VcfEffect. getEffectType()
Methods in org.snpeff.vcf that return types with arguments of type EffectType Modifier and Type Method Description java.util.List<EffectType>
VcfEffect. getEffectTypes()
Methods in org.snpeff.vcf with parameters of type EffectType Modifier and Type Method Description void
VcfEffect. addEffectType(EffectType effectType)
boolean
VcfEffect. hasEffectType(EffectType effType)
Does it have 'effType' ?void
VcfEffect. setEffectType(EffectType effect)
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