Examples of LikelihoodAlgorithm

Examples of org.cipres.treebase.domain.study.LikelihoodAlgorithm

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  public AnalysisStepCommand() {
    algorithmMap.put(Constants.ALGORITHM_Bayesian, new BayesianAlgorithm());
    algorithmMap.put(Constants.ALGORITHM_Evolution, new EvolutionAlgorithm());
    algorithmMap.put(Constants.ALGORITHM_Joining, new JoiningAlgorithm());
    algorithmMap.put(Constants.ALGORITHM_UPGMA, new UPGMAAlgorithm());
    algorithmMap.put(Constants.ALGORITHM_LIKELIHOOD, new LikelihoodAlgorithm());
    algorithmMap.put(Constants.ALGORITHM_OTHER, new OtherAlgorithm());
    // ParsimonyAlgorithm parsimonyAlgorithm = new ParsimonyAlgorithm();
    // parsimonyAlgorithm.setGapMode(new GapMode());
    // parsimonyAlgorithm.setPolyTCount(new PolyTCount());
    algorithmMap.put(Constants.ALGORITHM_PARSIMONY, new ParsimonyAlgorithm());
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Examples of org.cipres.treebase.domain.study.LikelihoodAlgorithm

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      } else if (tb1Algorithm.equalsIgnoreCase("joining")) {
        theAlgorithm = new JoiningAlgorithm();
      } else if (tb1Algorithm.equalsIgnoreCase("UPGMA")) {
        theAlgorithm = new UPGMAAlgorithm();
      } else if (tb1Algorithm.equalsIgnoreCase("likelihood")) {
        theAlgorithm = new LikelihoodAlgorithm();
      } else {
        theAlgorithm = new OtherAlgorithm(); 
      }
      theAlgorithm.setDescription(tb1Algorithm);
      ContextManager.getAlgorithmHome().save(theAlgorithm);
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