/** {@inheritDoc} */
protected void encounterVertexAgain(V vertex, E edge) {
super.encounterVertexAgain(vertex, edge);
int i;
if (root != null) {
// For rooted detection, the path must either
// double back to the root, or to a node of a cycle
// which has already been detected.
if (vertex.equals(root)) {
i = 0;
} else if ((cycleSet != null) && cycleSet.contains(vertex)) {
i = 0;
} else {
return;
}
} else {
i = path.indexOf(vertex);
}
if (i > -1) {
if (cycleSet == null) {
// we're doing yes/no cycle detection
throw new CycleDetectedException();
} else {
for (; i < path.size(); ++i) {
cycleSet.add(path.get(i));
}
}
}
}
/**
* Compute the unique decomposition of the input graph G (atoms of G). Implementation of algorithm
* Atoms 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 computeAtoms() {
if (chordalGraph == null) {
computeMinimalTriangulation();
}
separators = new HashSet<>();
// initialize g' as subgraph of graph (same vertices and edges)
UndirectedGraph<V, E> gprime = copyAsSimpleGraph(graph);
// initialize h' as subgraph of chordalGraph (same vertices and edges)
UndirectedGraph<V, E> hprime = copyAsSimpleGraph(chordalGraph);
atoms = new HashSet<>();
Iterator<V> iterator = meo.descendingIterator();
while (iterator.hasNext()) {
V v = iterator.next();
if (generators.contains(v)) {
Set<V> separator = new HashSet<>(Graphs.neighborListOf(hprime, v));
if (isClique(graph, separator)) {
if (separator.size() > 0) {
if (separators.contains(separator)) {
fullComponentCount.put(separator, fullComponentCount.get(separator) + 1);
} else {
fullComponentCount.put(separator, 2);
separators.add(separator);
}
}
UndirectedGraph<V, E> tmpGraph = copyAsSimpleGraph(gprime);
tmpGraph.removeAllVertices(separator);
ConnectivityInspector<V, E> con = new ConnectivityInspector<>(tmpGraph);
if (con.isGraphConnected()) {
throw new RuntimeException("separator did not separate the graph");
}
for (Set<V> component : con.connectedSets()) {
if (component.contains(v)) {
gprime.removeAllVertices(component);
component.addAll(separator);
atoms.add(new HashSet<>(component));
assert (component.size() > 0);
break;
}
}
}
}
hprime.removeVertex(v);
}
if (gprime.vertexSet().size() > 0) {
atoms.add(new HashSet<>(gprime.vertexSet()));
}
}
private V lowestCommonAncestor(V a, V b) {
Set<V> seen = new HashSet<>();
for (; ; ) {
a = contracted.get(a);
seen.add(a);
if (!match.containsKey(a)) {
break;
}
a = path.get(match.get(a));
}
for (; ; ) {
b = contracted.get(b);
if (seen.contains(b)) {
return b;
}
b = path.get(match.get(b));
}
}
/** @see Graph#edgesOf(Object) */
public Set<E> edgesOf(V vertex) {
ArrayUnenforcedSet<E> inAndOut = new ArrayUnenforcedSet<E>(getEdgeContainer(vertex).incoming);
inAndOut.addAll(getEdgeContainer(vertex).outgoing);
// we have two copies for each self-loop - remove one of them.
if (allowingLoops) {
Set<E> loops = getAllEdges(vertex, vertex);
for (int i = 0; i < inAndOut.size(); ) {
Object e = inAndOut.get(i);
if (loops.contains(e)) {
inAndOut.remove(i);
loops.remove(e); // so we remove it only once
} else {
i++;
}
}
}
return Collections.unmodifiableSet(inAndOut);
}
/**
* Runs the algorithm on the input graph and returns the match edge set.
*
* @return set of Edges
*/
private Set<E> findMatch() {
Set<E> result = new ArrayUnenforcedSet<>();
match = new HashMap<>();
path = new HashMap<>();
contracted = new HashMap<>();
for (V i : graph.vertexSet()) {
// Any augmenting path should start with _exposed_ vertex
// (vertex may not escape match-set being added once)
if (!match.containsKey(i)) {
// Match is maximal iff graph G contains no more augmenting paths
V v = findPath(i);
while (v != null) {
V pv = path.get(v);
V ppv = match.get(pv);
match.put(v, pv);
match.put(pv, v);
v = ppv;
}
}
}
Set<V> seen = new HashSet<>();
graph
.vertexSet()
.stream()
.filter(v -> !seen.contains(v) && match.containsKey(v))
.forEach(
v -> {
seen.add(v);
seen.add(match.get(v));
result.add(graph.getEdge(v, match.get(v)));
});
return result;
}
private V findPath(V root) {
Set<V> used = new HashSet<>();
Queue<V> q = new ArrayDeque<>();
// Expand graph back from its contracted state
path.clear();
contracted.clear();
graph.vertexSet().forEach(vertex -> contracted.put(vertex, vertex));
used.add(root);
q.add(root);
while (!q.isEmpty()) {
V v = q.remove();
for (E e : graph.edgesOf(v)) {
V to = graph.getEdgeSource(e);
if (to.equals(v)) {
to = graph.getEdgeTarget(e);
}
if ((contracted.get(v).equals(contracted.get(to))) || to.equals(match.get(v))) {
continue;
}
// Check whether we've hit a 'blossom'
if ((to.equals(root)) || ((match.containsKey(to)) && (path.containsKey(match.get(to))))) {
V stem = lowestCommonAncestor(v, to);
Set<V> blossom = new HashSet<>();
markPath(v, to, stem, blossom);
markPath(to, v, stem, blossom);
graph
.vertexSet()
.stream()
.filter(i -> contracted.containsKey(i) && blossom.contains(contracted.get(i)))
.forEach(
i -> {
contracted.put(i, stem);
if (!used.contains(i)) {
used.add(i);
q.add(i);
}
});
// Check whether we've had hit a loop (of even length (!) presumably)
} else if (!path.containsKey(to)) {
path.put(to, v);
if (!match.containsKey(to)) {
return to;
}
to = match.get(to);
used.add(to);
q.add(to);
}
}
}
return null;
}