Exemplo n.º 1
0
  /** 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");
  }
Exemplo n.º 2
0
  /** 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();
  }