VariantEffects (SnpEff 5.2 API)

java.lang.Object

org.snpeff.snpEffect.VariantEffects

All Implemented Interfaces:: Iterable<VariantEffect>

public class VariantEffects extends Object implements 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, String message)

Add an effect

void

add(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, 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(String trId)

Find the highest impact effect for transcript 'trId'

boolean

isEmpty()

Iterator<VariantEffect>

iterator()

void

setMarker(Marker marker)

int

size()

void

sort()

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 Details
- debug
  
  public static boolean debug
Constructor Details
- VariantEffects
  
  public VariantEffects()
Method Details
- add
  
  public void add(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, String message)
  
  Add an effect
- add
  
  public void add(Variant variant, Marker marker, EffectType effectType, 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(String trId)
  
  Find the highest impact effect for transcript 'trId'
- isEmpty
  
  public boolean isEmpty()
- iterator
  
  public Iterator<VariantEffect> iterator()
  
  Specified by:
  
  iterator in interface Iterable<VariantEffect>
- setMarker
  
  public void setMarker(Marker marker)
- size
  
  public int size()
- sort
  
  public void sort()
- toString
  
  public String toString()
  
  Overrides:
  
  toString in class Object