/** 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();
}
/** 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;
}
/** 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);
}