/** Check proteins using all possible codon tables */
void checkCodonTables() {
if (verbose) Timer.showStdErr("Comparing Proteins...");
createTrByChromo(); // Create lists of transcripts by chromosome
// For each chromosome...
for (Chromosome chromo : genome) {
String chr = chromo.getId();
// Check against each codon table
for (CodonTable codonTable : CodonTables.getInstance()) {
setCodonTable(chromo, codonTable);
proteinCompare(chr, false, false);
}
}
if (verbose) Timer.showStdErr("done");
}
/** Set codon table for a given chromosome */
void setCodonTable(Chromosome chromo, CodonTable codonTable) {
CodonTables.getInstance().set(genome, chromo, codonTable); // Set codon tables
// Reset all protein translations for this chromosome
for (Transcript tr : trByChromo.get(chromo.getId())) tr.resetCache();
}