Package org.snpeff.snpEffect
Class VariantEffects
java.lang.Object
org.snpeff.snpEffect.VariantEffects
- All Implemented Interfaces:
Iterable<VariantEffect>
A sorted collection of variant effects
- Author:
- pcingola
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
add
(Variant variant, Marker marker, EffectType effectType, String message) Add an effectvoid
add
(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, 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) get()
Get (or create) the latest ChangeEffectget
(int index) boolean
highestImpact
(String trId) Find the highest impact effect for transcript 'trId'boolean
isEmpty()
iterator()
void
int
size()
void
sort()
toString()
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Field Details
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debug
public static boolean debug
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Constructor Details
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VariantEffects
public VariantEffects()
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Method Details
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add
public void add(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, String message) Add an effect -
add
Add an effect -
add
Add an effect -
addEffectType
Add: If possible, only add an effect type (otherwise add the full effect) -
addErrorWarning
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get
Get (or create) the latest ChangeEffect -
get
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hasMarker
public boolean hasMarker() -
highestImpact
Find the highest impact effect for transcript 'trId' -
isEmpty
public boolean isEmpty() -
iterator
- Specified by:
iterator
in interfaceIterable<VariantEffect>
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setMarker
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size
public int size() -
sort
public void sort() -
toString
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