//if (inconsistencyForTheReferenceGraph != 53)
// break;// ignore automata where we get good results.
MarkovClassifier ptaClassifier = new MarkovClassifier(m,pta);
final List<List<Label>> pathsToMerge=ptaClassifier.identifyPathsToMerge(checker);
final Collection<Set<CmpVertex>> verticesToMergeBasedOnInitialPTA=ptaClassifier.buildVerticesToMergeForPaths(pathsToMerge);
List<StatePair> pairsListInitialMerge = ptaClassifier.buildVerticesToMergeForPath(pathsToMerge);
LinkedList<AMEquivalenceClass<CmpVertex,LearnerGraphCachedData>> verticesToMergeInitialMerge = new LinkedList<AMEquivalenceClass<CmpVertex,LearnerGraphCachedData>>();
int scoreInitialMerge = pta.pairscores.computePairCompatibilityScore_general(null, pairsListInitialMerge, verticesToMergeInitialMerge);