1. Modified the way <hmmgen.pl> parses out stop codons
     * In Stop Codon section of "Generate Emissions State Counts"
     * Needed to take into account last exons that were
       equal to the size of stop codon + order
2. Changed how Taxa abbrev. was determined in
   <test_train_sets.pl> in order to name test and training
   sets
     * Uses the first two characters of the first ID
3. Changed Translation Function in <genesmith.cpp>
     * Now uses hard coded char vector, rather than parsing
       through trans table "gencode.txt", to identify AAs