@Override
  public double compare(URI a, URI b, SM_Engine c, SMconf conf) throws SLIB_Ex_Critic {

    GWS weightingScheme = c.getWeightingScheme(conf.getParamAsString("WEIGHTING_SCHEME"));
    URI msa = c.getMSA(a, b, weightingScheme);
    URI root = c.getRoot();

    Map<URI, Double> allSpMsa = c.getAllShortestPath(msa, weightingScheme);

    double sp_mrca_root = allSpMsa.get(root);
    double sp_a_mrca = allSpMsa.get(a);
    double sp_b_mrca = allSpMsa.get(b);

    return sim(sp_mrca_root, sp_a_mrca, sp_b_mrca);
  }
  @Override
  public double compare(
      Set<URI> setA, Set<URI> setB, SM_Engine rc, SMconf groupwiseconf, SMconf conf)
      throws SLIB_Ex_Critic {

    MatrixDouble<URI, URI> results_setA = rc.getMatrixScore(setA, setB, conf);
    return sim(results_setA);
  }
Example #3
0
  @Override
  public Map<URI, Double> compute(IC_Conf_Topo conf, SM_Engine engine) throws SLIB_Ex_Critic {

    setLogBase(conf);

    // The formulation of Seco do not consider inclusive descendants but add + 1 to correct
    return compute(engine.getAllDescendantsInc());
  }