LinkedList<AMEquivalenceClass<CmpVertex,LearnerGraphCachedData>> verticesToMergeInitialMerge = new LinkedList<AMEquivalenceClass<CmpVertex,LearnerGraphCachedData>>();
int scoreInitialMerge = pta.pairscores.computePairCompatibilityScore_general(null, pairsListInitialMerge, verticesToMergeInitialMerge);
assert scoreInitialMerge >= 0;
final LearnerGraph ptaAfterInitialMerge = MergeStates.mergeCollectionOfVertices(pta, null, verticesToMergeInitialMerge);
final CmpVertex vertexWithMostTransitions = MarkovPassivePairSelection.findVertexWithMostTransitions(ptaAfterInitialMerge,MarkovClassifier.computeInverseGraph(pta));
ptaAfterInitialMerge.clearColours();ptaAfterInitialMerge.getInit().setColour(null);vertexWithMostTransitions.setColour(JUConstants.RED);
ptaClassifier = new MarkovClassifier(m,ptaAfterInitialMerge);// rebuild the classifier
LearnerGraphND inverseOfPtaAfterInitialMerge = MarkovClassifier.computeInverseGraph(ptaAfterInitialMerge);
//System.out.println("Centre vertex: "+vertexWithMostTransitions+" "+MarkovPassivePairSelection.countTransitions(ptaAfterInitialMerge, inverseOfPtaAfterInitialMerge, vertexWithMostTransitions));
// These have been recorded, there is no specific reason for the numbers to be as they are. We need them for regression testing.