Package org.snpeff.interval.codonChange

Class CodonChange

java.lang.Object
org.snpeff.interval.codonChange.CodonChange
Direct Known Subclasses:
CodonChangeIns, CodonChangeInterval, CodonChangeInv, CodonChangeMnp, CodonChangeSnp, CodonChangeStructural
public class CodonChange extends Object
Analyze codon changes based on a variant and a Transcript
Author:
pcingola

  • Field Details

    • CODON_SIZE

      public static final int CODON_SIZE
      See Also:

    • showCodonChange

      public static boolean showCodonChange

  • Constructor Details

  • Method Details

    • factory

      public static CodonChange factory(Variant variant, Transcript transcript, VariantEffects variantEffects)
      Create a specific codon change for a variant

    • additionalEffect

      protected EffectType additionalEffect(String codonsOld, String codonsNew, int codonNum, int codonIndex, String aaOld, String aaNew)
      Calculate additional effect due to codon changes E.g. A frame-shift that also affects a stop codon

    • cdsBaseNumber

      protected int cdsBaseNumber(int pos)
      Calculate base number in a cds where 'pos' is

    • codonChange

      public void codonChange()
      Calculate a list of codon changes

    • codonChange

      protected boolean codonChange(Exon exon)
      Calculate the effect on an exon

    • codonsAlt

      protected String codonsAlt()
      Calculate new codons

    • codonsRef

      protected String codonsRef()
      Calculate 'reference' codons

    • codonsRef

      protected String codonsRef(int numCodons)
      Calculate 'reference' codons

    • effect

      protected VariantEffect effect(Marker marker, EffectType effectType, boolean allowReplace)
      Calculate variant effect
      Parameters:
      marker - : Genomic marker affected by this variant (e.g. exon, transcript, etc)
      effectType - : Effect type
      allowReplace - : Can another variant effect replace this one?
      Returns:
      A new VariantEffect object

    • effectNoCodon

      protected VariantEffect effectNoCodon(Marker marker, EffectType effectType)

    • effectNoCodon

      protected VariantEffect effectNoCodon(Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact)

    • intersectsExons

      protected boolean intersectsExons()
      Does the variant intersect any exons?

    • 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

    • toString

      public String toString()
      Overrides:
      toString in class Object