org.snpeff.interval.codonChange.CodonChangeMnp

public class CodonChangeMnp extends CodonChange

Calculate codon changes produced by a MNP

Field Summary

Fields inherited from class org.snpeff.interval.codonChange.CodonChange
CODON_SIZE, showCodonChange
Constructor Summary

Constructors

Constructor

Description

CodonChangeMnp(Variant variant, Transcript transcript, VariantEffects variantEffects)
Method Summary

Modifier and Type

Method

Description

void

codonChange()

Calculate a list of codon changes

protected void

codonOldNew()

Calculate codons old / codons new

protected String

codonsAlt()

Calculate new codons

protected String

codonsRef()

Calculate old codons

protected String

netCdsChange()

We may have to calculate 'netCdsChange', which is the effect on the CDS Note: A deletion or a MNP might affect several exons

Methods inherited from class org.snpeff.interval.codonChange.CodonChange
additionalEffect, cdsBaseNumber, codonChange, codonsRef, effect, effectNoCodon, effectNoCodon, factory, intersectsExons, toString

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details
- CodonChangeMnp
  
  public CodonChangeMnp(Variant variant, Transcript transcript, VariantEffects variantEffects)
Method Details
- codonChange
  
  public void codonChange()
  
  Calculate a list of codon changes
  
  Overrides:
  
  codonChange in class CodonChange
- codonOldNew
  
  protected void codonOldNew()
  
  Calculate codons old / codons new
- codonsAlt
  
  protected String codonsAlt()
  
  Description copied from class: CodonChange
  
  Calculate new codons
  
  Overrides:
  
  codonsAlt in class CodonChange
- codonsRef
  
  protected String codonsRef()
  
  Calculate old codons
  
  Overrides:
  
  codonsRef in class CodonChange
- netCdsChange
  
  protected String netCdsChange()
  
  We may have to calculate 'netCdsChange', which is the effect on the CDS Note: A deletion or a MNP might affect several exons
  
  Overrides:
  
  netCdsChange in class CodonChange
  
  Returns:

Class CodonChangeMnp

Field Summary