Package org.snpeff.snpEffect
Class VariantEffects
- java.lang.Object
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- org.snpeff.snpEffect.VariantEffects
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- All Implemented Interfaces:
java.lang.Iterable<VariantEffect>
public class VariantEffects extends java.lang.Object implements java.lang.Iterable<VariantEffect>
A sorted collection of variant effects- Author:
- pcingola
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Field Summary
Fields Modifier and Type Field Description static boolean
debug
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Constructor Summary
Constructors Constructor Description VariantEffects()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
add(Variant variant, Marker marker, EffectType effectType, java.lang.String message)
Add an effectvoid
add(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, java.lang.String message)
Add an effectvoid
add(VariantEffect variantEffect)
Add an effectvoid
addEffectType(Variant variant, Marker marker, EffectType effectType)
Add: If possible, only add an effect type (otherwise add the full effect)void
addErrorWarning(Variant variant, ErrorWarningType errwarn)
VariantEffect
get()
Get (or create) the latest ChangeEffectVariantEffect
get(int index)
boolean
hasMarker()
VariantEffect.EffectImpact
highestImpact(java.lang.String trId)
Find the highest impact effect for transcript 'trId'boolean
isEmpty()
java.util.Iterator<VariantEffect>
iterator()
void
setMarker(Marker marker)
int
size()
void
sort()
java.lang.String
toString()
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Method Detail
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add
public void add(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, java.lang.String message)
Add an effect
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add
public void add(Variant variant, Marker marker, EffectType effectType, java.lang.String message)
Add an effect
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add
public void add(VariantEffect variantEffect)
Add an effect
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addEffectType
public void addEffectType(Variant variant, Marker marker, EffectType effectType)
Add: If possible, only add an effect type (otherwise add the full effect)
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addErrorWarning
public void addErrorWarning(Variant variant, ErrorWarningType errwarn)
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get
public VariantEffect get()
Get (or create) the latest ChangeEffect
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get
public VariantEffect get(int index)
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hasMarker
public boolean hasMarker()
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highestImpact
public VariantEffect.EffectImpact highestImpact(java.lang.String trId)
Find the highest impact effect for transcript 'trId'
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isEmpty
public boolean isEmpty()
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iterator
public java.util.Iterator<VariantEffect> iterator()
- Specified by:
iterator
in interfacejava.lang.Iterable<VariantEffect>
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setMarker
public void setMarker(Marker marker)
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size
public int size()
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sort
public void sort()
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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