Package com.yahoo.labs.taxomo.util

Examples of com.yahoo.labs.taxomo.util.Taxonomy

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    final int nClusters = jsapResult.getInt("clusters");
    final int clusteringIterations = jsapResult.getInt("passes");

    // Load tree
    File taxoFile = new File(jsapResult.getString("taxonomy-file"));
    Taxonomy tree = new Taxonomy(taxoFile);

    // Build initial candidate
    Candidate initialCandidate;
    if (jsapResult.userSpecified("init-explicit")) {
      initialCandidate = new Candidate(tree, Util.split(jsapResult.getString("init-explicit")), null, null);
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    File modelFile = new File(jsapResult.getString("model-file"));
    File taxoFile = new File(jsapResult.getString("taxonomy-file"));
    int numSequences = jsapResult.getInt("num-sequences");
   
    StateSet taxo = new StateSet( modelFile, new Taxonomy(taxoFile) );
    Model hmm = new Model(modelFile, taxo);
   
    for( int i=0; i<numSequences; i++) {
      ArrayList<String> seq = hmm.sequence();
      System.out.println(seq2str(seq));
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      logger.setLevel(Level.DEBUG);
    }

    File modelFile = new File(jsapResult.getString("model-file"));
    File taxoFile = new File(jsapResult.getString("taxonomy-file"));
    StateSet stateSet = new StateSet(modelFile, new Taxonomy(taxoFile));
    Model hmm = new Model(modelFile, stateSet);

    if (jsapResult.userSpecified("input-file")) {
      File inputFile = new File(jsapResult.getString("input-file"));
      BufferedReader br = new BufferedReader(new FileReader(inputFile));
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      logger.setLevel(Level.DEBUG);
    }

    File inputFile = new File(jsapResult.getString("input-file"));
    File taxoFile = new File(jsapResult.getString("taxonomy-file"));
    Taxonomy tree = new Taxonomy(taxoFile);
    Candidate initialCandidate;

    if (jsapResult.userSpecified("init-explicit")) {
      initialCandidate = new Candidate(tree, Util.split(jsapResult.getString("init-explicit")), null, null);
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  Model model1;

  @Before
  public void setUp() throws Exception {
    set1 = new StateSet(UtilTest.class.getResourceAsStream(MODELFILE1), new Taxonomy(TREEFILE1, UtilTest.class.getResourceAsStream(TREEFILE1)));
    model1 = new Model(UtilTest.class.getResourceAsStream(MODELFILE1), set1);

    assertEquals(5, model1.nbStates());
  }
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  Class<SearchStrategy> strategy;

  @Before
  public void setUp() throws Exception {
    taxo1 = new Taxonomy(TAXOFILE1, LearnModelTest.class.getResourceAsStream(TAXOFILE1));
    sym1 = new SymbolTransitionFrequencies(taxo1);
    sym1.processStream(LearnModelTest.class.getResourceAsStream(SEQFILE1));
    LearnModel.logger.setLevel(Level.ERROR);
    strategy = getStrategy(CloserToOrigin.class.getName());
  }
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Related Classes of com.yahoo.labs.taxomo.util.Taxonomy

  • com.yahoo.labs.taxomo.ClusterSequences
  • com.yahoo.labs.taxomo.ComputeProbabilities
  • com.yahoo.labs.taxomo.GenerateSequences
  • com.yahoo.labs.taxomo.learn.LearnModelTest
  • com.yahoo.labs.taxomo.LearnModel
  • com.yahoo.labs.taxomo.ModelTest
  • com.yahoo.labs.taxomo.util.State.Type
  • java.io.InputStreamReader
  • java.io.FileInputStream
  • java.io.BufferedReader
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