Uses of Class
org.snpeff.snpEffect.VariantEffect.EffectImpact
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Packages that use VariantEffect.EffectImpact Package Description org.snpeff.interval.codonChange org.snpeff.snpEffect org.snpeff.snpEffect.testCases.unity org.snpeff.vcf -
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Uses of VariantEffect.EffectImpact in org.snpeff.interval.codonChange
Methods in org.snpeff.interval.codonChange with parameters of type VariantEffect.EffectImpact Modifier and Type Method Description protected VariantEffect
CodonChange. effectNoCodon(Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact)
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Uses of VariantEffect.EffectImpact in org.snpeff.snpEffect
Fields in org.snpeff.snpEffect declared as VariantEffect.EffectImpact Modifier and Type Field Description protected VariantEffect.EffectImpact
VariantEffect. effectImpact
Fields in org.snpeff.snpEffect with type parameters of type VariantEffect.EffectImpact Modifier and Type Field Description protected java.util.List<VariantEffect.EffectImpact>
VariantEffect. effectImpacts
Methods in org.snpeff.snpEffect that return VariantEffect.EffectImpact Modifier and Type Method Description VariantEffect.EffectImpact
EffectType. effectImpact()
Return effect impactVariantEffect.EffectImpact
VariantEffect. getEffectImpact()
Return impact of this effectVariantEffect.EffectImpact
VariantEffects. highestImpact(java.lang.String trId)
Find the highest impact effect for transcript 'trId'static VariantEffect.EffectImpact
VariantEffect.EffectImpact. valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.static VariantEffect.EffectImpact[]
VariantEffect.EffectImpact. values()
Returns an array containing the constants of this enum type, in the order they are declared.Methods in org.snpeff.snpEffect with parameters of type VariantEffect.EffectImpact Modifier and Type Method Description void
VariantEffects. add(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, java.lang.String message)
Add an effectvoid
VariantEffect. addEffectImpact(VariantEffect.EffectImpact effectImpact)
boolean
VariantEffect. hasEffectImpact(VariantEffect.EffectImpact effectImpact)
void
VariantEffect. set(Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, java.lang.String message)
void
VariantEffect. setEffectImpact(VariantEffect.EffectImpact effectImpact)
Constructors in org.snpeff.snpEffect with parameters of type VariantEffect.EffectImpact 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 VariantEffect.EffectImpact in org.snpeff.snpEffect.testCases.unity
Methods in org.snpeff.snpEffect.testCases.unity with parameters of type VariantEffect.EffectImpact Modifier and Type Method Description 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, 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[] expHgvsc, VariantEffect.EffectImpact expectedImpact, java.lang.String[] expAnns)
protected void
TestCasesStructuralInv. checkEffects(Variant variant, EffectType[] expEffs, 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)
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Uses of VariantEffect.EffectImpact in org.snpeff.vcf
Methods in org.snpeff.vcf that return VariantEffect.EffectImpact Modifier and Type Method Description VariantEffect.EffectImpact
VcfEffect. getImpact()
Methods in org.snpeff.vcf with parameters of type VariantEffect.EffectImpact Modifier and Type Method Description void
VcfEffect. setImpact(VariantEffect.EffectImpact impact)
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