public void addRedefinedClassWithNativeMethods(@Nonnull String redefinedClassInternalName) {
redefinedClassesWithNativeMethods.add(redefinedClassInternalName.replace('/', '.'));
}
/**
* Compute the minimal triangulation of the graph. Implementation of Algorithm MCS-M+ as described
* in Berry et al. (2010), DOI:10.3390/a3020197 <a href="http://www.mdpi.com/1999-4893/3/2/197">
* http://www.mdpi.com/1999-4893/3/2/197</a>
*/
private void computeMinimalTriangulation() {
// initialize chordGraph with same vertices as graph
chordalGraph = new SimpleGraph<>(graph.getEdgeFactory());
for (V v : graph.vertexSet()) {
chordalGraph.addVertex(v);
}
// initialize g' as subgraph of graph (same vertices and edges)
final UndirectedGraph<V, E> gprime = copyAsSimpleGraph(graph);
int s = -1;
generators = new ArrayList<>();
meo = new LinkedList<>();
final Map<V, Integer> vertexLabels = new HashMap<>();
for (V v : gprime.vertexSet()) {
vertexLabels.put(v, 0);
}
for (int i = 1, n = graph.vertexSet().size(); i <= n; i++) {
V v = getMaxLabelVertex(vertexLabels);
LinkedList<V> Y = new LinkedList<>(Graphs.neighborListOf(gprime, v));
if (vertexLabels.get(v) <= s) {
generators.add(v);
}
s = vertexLabels.get(v);
// Mark x reached and all other vertices of gprime unreached
HashSet<V> reached = new HashSet<>();
reached.add(v);
// mark neighborhood of x reached and add to reach(label(y))
HashMap<Integer, HashSet<V>> reach = new HashMap<>();
// mark y reached and add y to reach
for (V y : Y) {
reached.add(y);
addToReach(vertexLabels.get(y), y, reach);
}
for (int j = 0; j < graph.vertexSet().size(); j++) {
if (!reach.containsKey(j)) {
continue;
}
while (reach.get(j).size() > 0) {
// remove a vertex y from reach(j)
V y = reach.get(j).iterator().next();
reach.get(j).remove(y);
for (V z : Graphs.neighborListOf(gprime, y)) {
if (!reached.contains(z)) {
reached.add(z);
if (vertexLabels.get(z) > j) {
Y.add(z);
E fillEdge = graph.getEdgeFactory().createEdge(v, z);
fillEdges.add(fillEdge);
addToReach(vertexLabels.get(z), z, reach);
} else {
addToReach(j, z, reach);
}
}
}
}
}
for (V y : Y) {
chordalGraph.addEdge(v, y);
vertexLabels.put(y, vertexLabels.get(y) + 1);
}
meo.addLast(v);
gprime.removeVertex(v);
vertexLabels.remove(v);
}
}