Examples of 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
protein.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.

Examples of cbcb.kmulus.util.AlphabetMap

    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 {

View Full Code Here

Examples of cbcb.kmulus.util.AlphabetMap

    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) {

View Full Code Here

Examples of protein.util.AlphabetMap

    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 {

View Full Code Here

Examples of protein.util.AlphabetMap

    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) {

View Full Code Here

TOP

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.