@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);
}
@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());
}