Ejemplo n.º 1
0
  /** Set values for codons around change. */
  public void setCodonsAround(String codonsLeft, String codonsRight) {
    codonsAroundOld =
        codonsLeft.toLowerCase() + codonsRef.toUpperCase() + codonsRight.toLowerCase();
    codonsAroundNew =
        codonsLeft.toLowerCase() + codonsAlt.toUpperCase() + codonsRight.toLowerCase();

    // Amino acids surrounding the ones changed
    CodonTable codonTable = marker.codonTable();
    String aasLeft = codonTable.aa(codonsLeft);
    String aasRigt = codonTable.aa(codonsRight);
    aasAroundOld = aasLeft.toLowerCase() + aaRef.toUpperCase() + aasRigt.toLowerCase();
    aasAroundNew = aasLeft.toLowerCase() + aaAlt.toUpperCase() + aasRigt.toLowerCase();
  }
Ejemplo n.º 2
0
  /** Return functional class of this effect (i.e. NONSENSE, MISSENSE, SILENT or NONE) */
  public FunctionalClass getFunctionalClass() {
    if (variant.isSnp()) {
      if (!aaAlt.equals(aaRef)) {
        CodonTable codonTable = marker.codonTable();
        if (codonTable.isStop(codonsAlt)) return FunctionalClass.NONSENSE;

        return FunctionalClass.MISSENSE;
      }
      if (!codonsAlt.equals(codonsRef)) return FunctionalClass.SILENT;
    }

    return FunctionalClass.NONE;
  }
Ejemplo n.º 3
0
  /** Set codon change. Calculate effect type based on codon changes (for SNPs & MNPs) */
  public void setCodons(String codonsOld, String codonsNew, int codonNum, int codonIndex) {
    codonsRef = codonsOld;
    codonsAlt = codonsNew;
    this.codonNum = codonNum;
    this.codonIndex = codonIndex;

    CodonTable codonTable = marker.codonTable();

    // Calculate amino acids
    if (codonsOld.isEmpty()) aaRef = "";
    else {
      aaRef = codonTable.aa(codonsOld);
      codonDegeneracy = codonTable.degenerate(codonsOld, codonIndex); // Calculate codon degeneracy
    }

    if (codonsNew.isEmpty()) aaAlt = "";
    else aaAlt = codonTable.aa(codonsNew);
  }