Examples of cbcb.kmulus.util.AlphabetMap

cbcb.kmulus.util.AlphabetMap
Supports compressed amino acid alphabets in which several amino acids are represented as a single letter. Along with the obvious mapping of amino acid to alphabet letter, also allows for direct lookup from the DNA triplet to the alphabet letter. @author CH Albach

    public void setup(Context context) throws IOException {
      Configuration conf = context.getConfiguration();
      
      long numSeq = conf.getLong(NUM_SEQ_ATTR, 0);
      int eugID = conf.getInt(EUG_ATTR, EugType.PRIME_ROT.ordinal());
      alphabetMap = new AlphabetMap(conf.getStrings(ALPHABET_ATTR, DEF_ALPHABET)[0]);
      
      if (numSeq < 0) {
        eug = null;
      } else {

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    public void setup(Context context) throws IOException {
      Configuration conf = context.getConfiguration();
      
      long numSeq = conf.getLong(NUM_SEQ_ATTR, 0);
      int eugID = conf.getInt(EUG_ATTR, EugType.PRIME_ROT.ordinal());
      alphabetMap = new AlphabetMap(conf.getStrings(ALPHABET_ATTR, DEF_ALPHABET)[0]);
      
      // To allow for all 6 open reading frames, will generate 6 fold sequences.
      numSeq *= 6;
      
      if (numSeq < 0) {

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