final Configuration deepCopy = pta.config.copy();deepCopy.setLearnerCloneGraph(true);
LearnerGraph ptaCopy = new LearnerGraph(deepCopy);LearnerGraph.copyGraphs(pta, ptaCopy);
// now use pathsToMerge to compute which states can/cannot be merged together.
LearnerGraph trimmedReference = MarkovPassivePairSelection.trimUncoveredTransitions(pta,referenceGraph);
final ConsistencyChecker checker = new MarkovClassifier.DifferentPredictionsInconsistencyNoBlacklisting();
//long inconsistencyForTheReferenceGraph = MarkovClassifier.computeInconsistency(trimmedReference, m, checker,false);
//System.out.println("Inconsistency of trimmed reference : "+inconsistencyForTheReferenceGraph);
//if (inconsistencyForTheReferenceGraph != 53)
// break;// ignore automata where we get good results.