Uses of Class
org.snpeff.snpEffect.EffectType

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

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)

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()

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)	Calculate variant effect
protected 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 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 type
EffectType	EffectType.getGeneRegion()
static EffectType	EffectType.parse(EffFormatVersion formatVersion, java.lang.String str)	Parse a string to an EffectType
static 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 type

Methods 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 effect
void	VariantEffects.add(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, java.lang.String message)	Add an effect
void	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 impact
void	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)

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)
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 found
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[] 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)

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)