Package org.snpeff.snpEffect

Class VariantEffects

java.lang.Object

org.snpeff.snpEffect.VariantEffects

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

Field Summary

Fields

Modifier and Type	Field	Description
static boolean	debug

Constructor Summary

Constructors

Constructor	Description
VariantEffects()

Method Summary

Modifier and Type	Method	Description
void	add(Variant variant, Marker marker, EffectType effectType, java.lang.String message)	Add an effect
void	add(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, java.lang.String message)	Add an effect
void	add(VariantEffect variantEffect)	Add an effect
void	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 ChangeEffect
VariantEffect	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()

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

Field Detail

debug

public static boolean debug

Constructor Detail

VariantEffects

public VariantEffects()

Method Detail

add

public void add(Variant variant,
                Marker marker,
                EffectType effectType,
                VariantEffect.EffectImpact effectImpact,
                java.lang.String message)

Add an effect

add

public void add(Variant variant,
                Marker marker,
                EffectType effectType,
                java.lang.String message)

Add an effect

add

public void add(VariantEffect variantEffect)

Add an effect

addEffectType

public void addEffectType(Variant variant,
                          Marker marker,
                          EffectType effectType)

Add: If possible, only add an effect type (otherwise add the full effect)

addErrorWarning

public void addErrorWarning(Variant variant,
                            ErrorWarningType errwarn)

get

public VariantEffect get()

Get (or create) the latest ChangeEffect

get

public VariantEffect get(int index)

hasMarker

public boolean hasMarker()

highestImpact

public VariantEffect.EffectImpact highestImpact(java.lang.String trId)

Find the highest impact effect for transcript 'trId'

isEmpty

public boolean isEmpty()

iterator

public java.util.Iterator<VariantEffect> iterator()

Specified by:

iterator in interface java.lang.Iterable<VariantEffect>

setMarker

public void setMarker(Marker marker)

size

public int size()

sort

public void sort()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object