/** Tests Subgraph. */
public void testSubgraph() {
UndirectedGraph<String, DefaultEdge> g = init(false);
UndirectedSubgraph<String, DefaultEdge> sub =
new UndirectedSubgraph<String, DefaultEdge>(g, null, null);
assertEquals(g.vertexSet(), sub.vertexSet());
assertEquals(g.edgeSet(), sub.edgeSet());
Set<String> vset = new HashSet<String>(g.vertexSet());
g.removeVertex(v1);
assertEquals(vset, sub.vertexSet()); // losing track
g = init(false);
vset = new HashSet<String>();
vset.add(v1);
sub = new UndirectedSubgraph<String, DefaultEdge>(g, vset, null);
assertEquals(vset, sub.vertexSet());
assertEquals(0, sub.degreeOf(v1));
assertEquals(Collections.EMPTY_SET, sub.edgeSet());
vset.add(v2);
vset.add(v3);
sub =
new UndirectedSubgraph<String, DefaultEdge>(
g, vset, new HashSet<DefaultEdge>(g.getAllEdges(v1, v2)));
assertEquals(vset, sub.vertexSet());
assertEquals(1, sub.edgeSet().size());
}
/** {@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));
}
}
}
}
/**
* @param vertexNumber the number which identifies the vertex v in this order.
* @return the identifying numbers of all vertices which are connected to v by an edge incoming to
* v.
*/
public int[] getInEdges(int vertexNumber) {
if (cacheEdges && (incomingEdges[vertexNumber] != null)) {
return incomingEdges[vertexNumber];
}
V v = getVertex(vertexNumber);
Set<E> edgeSet;
if (graph instanceof DirectedGraph<?, ?>) {
edgeSet = ((DirectedGraph<V, E>) graph).incomingEdgesOf(v);
} else {
edgeSet = graph.edgesOf(v);
}
int[] vertexArray = new int[edgeSet.size()];
int i = 0;
for (E edge : edgeSet) {
V source = graph.getEdgeSource(edge), target = graph.getEdgeTarget(edge);
vertexArray[i++] = mapVertexToOrder.get(source.equals(v) ? target : source);
}
if (cacheEdges) {
incomingEdges[vertexNumber] = vertexArray;
}
return vertexArray;
}
/** @see Graph#getAllEdges(Object, Object) */
public Set<E> getAllEdges(V sourceVertex, V targetVertex) {
Set<E> edges = null;
if (containsVertex(sourceVertex) && containsVertex(targetVertex)) {
edges = new ArrayUnenforcedSet<E>();
Iterator<E> iter = getEdgeContainer(sourceVertex).vertexEdges.iterator();
while (iter.hasNext()) {
E e = iter.next();
boolean equalStraight =
sourceVertex.equals(getEdgeSource(e)) && targetVertex.equals(getEdgeTarget(e));
boolean equalInverted =
sourceVertex.equals(getEdgeTarget(e)) && targetVertex.equals(getEdgeSource(e));
if (equalStraight || equalInverted) {
edges.add(e);
}
}
}
return edges;
}
private void init(Graph<V, E> g, Set<V> vertexSet, Set<E> edgeSet) {
// create a map between vertex value to its order(1st,2nd,etc)
// "CAT"=1 "DOG"=2 "RHINO"=3
this.mapVertexToOrder = new HashMap<V, Integer>(vertexSet.size());
int counter = 0;
for (V vertex : vertexSet) {
mapVertexToOrder.put(vertex, new Integer(counter));
counter++;
}
// create a friendlier representation of an edge
// by order, like 2nd->3rd instead of B->A
// use the map to convert vertex to order
// on directed graph, edge A->B must be (A,B)
// on undirected graph, edge A-B can be (A,B) or (B,A)
this.labelsEdgesSet = new HashSet<LabelsEdge>(edgeSet.size());
for (E edge : edgeSet) {
V sourceVertex = g.getEdgeSource(edge);
Integer sourceOrder = mapVertexToOrder.get(sourceVertex);
int sourceLabel = sourceOrder.intValue();
int targetLabel = (mapVertexToOrder.get(g.getEdgeTarget(edge))).intValue();
LabelsEdge lablesEdge = new LabelsEdge(sourceLabel, targetLabel);
this.labelsEdgesSet.add(lablesEdge);
if (g instanceof UndirectedGraph<?, ?>) {
LabelsEdge oppositeEdge = new LabelsEdge(targetLabel, sourceLabel);
this.labelsEdgesSet.add(oppositeEdge);
}
}
}
public Set<String> getIndexedClasses() {
Set<String> classes = newHashSet();
Set<JavaClass> vertexSet = graph.vertexSet();
for (JavaClass each : vertexSet) {
classes.add(each.getName());
}
return classes;
}
private void markPath(V v, V child, V stem, Set<V> blossom) {
while (!contracted.get(v).equals(stem)) {
blossom.add(contracted.get(v));
blossom.add(contracted.get(match.get(v)));
path.put(v, child);
child = match.get(v);
v = path.get(match.get(v));
}
}
public Set<E> getAllEdges(V sourceVertex, V targetVertex) {
Set<E> res = new HashSet<E>();
if (g1.containsVertex(sourceVertex) && g1.containsVertex(targetVertex)) {
res.addAll(g1.getAllEdges(sourceVertex, targetVertex));
}
if (g2.containsVertex(sourceVertex) && g2.containsVertex(targetVertex)) {
res.addAll(g2.getAllEdges(sourceVertex, targetVertex));
}
return Collections.unmodifiableSet(res);
}
public Set<E> edgesOf(V vertex) {
Set<E> res = new HashSet<E>();
if (g1.containsVertex(vertex)) {
res.addAll(g1.edgesOf(vertex));
}
if (g2.containsVertex(vertex)) {
res.addAll(g2.edgesOf(vertex));
}
return Collections.unmodifiableSet(res);
}
public Set<E> outgoingEdgesOf(V vertex) {
Set<E> res = new HashSet<E>();
if (getG1().containsVertex(vertex)) {
res.addAll(getG1().outgoingEdgesOf(vertex));
}
if (getG2().containsVertex(vertex)) {
res.addAll(getG2().outgoingEdgesOf(vertex));
}
return Collections.unmodifiableSet(res);
}
/** . */
public void testStronglyConnected3() {
DirectedGraph<String, DefaultEdge> g =
new DefaultDirectedGraph<String, DefaultEdge>(DefaultEdge.class);
g.addVertex(V1);
g.addVertex(V2);
g.addVertex(V3);
g.addVertex(V4);
g.addEdge(V1, V2);
g.addEdge(V2, V3);
g.addEdge(V3, V1); // strongly connected
g.addEdge(V1, V4);
g.addEdge(V2, V4);
g.addEdge(V3, V4); // weakly connected
StrongConnectivityInspector<String, DefaultEdge> inspector =
new StrongConnectivityInspector<String, DefaultEdge>(g);
// convert from List to Set because we need to ignore order
// during comparison
Set<Set<String>> actualSets = new HashSet<Set<String>>(inspector.stronglyConnectedSets());
// construct the expected answer
Set<Set<String>> expectedSets = new HashSet<Set<String>>();
Set<String> set = new HashSet<String>();
set.add(V1);
set.add(V2);
set.add(V3);
expectedSets.add(set);
set = new HashSet<String>();
set.add(V4);
expectedSets.add(set);
assertEquals(expectedSets, actualSets);
actualSets.clear();
List<DirectedSubgraph<String, DefaultEdge>> subgraphs = inspector.stronglyConnectedSubgraphs();
for (DirectedSubgraph<String, DefaultEdge> sg : subgraphs) {
actualSets.add(sg.vertexSet());
StrongConnectivityInspector<String, DefaultEdge> ci =
new StrongConnectivityInspector<String, DefaultEdge>(sg);
assertTrue(ci.isStronglyConnected());
}
assertEquals(expectedSets, actualSets);
}
/** . */
public void testSubgraphListener() {
UndirectedGraph<String, DefaultEdge> g = init(true);
UndirectedSubgraph<String, DefaultEdge> sub =
new UndirectedSubgraph<String, DefaultEdge>(g, null, null);
assertEquals(g.vertexSet(), sub.vertexSet());
assertEquals(g.edgeSet(), sub.edgeSet());
Set<String> vset = new HashSet<String>(g.vertexSet());
g.removeVertex(v1);
vset.remove(v1);
assertEquals(vset, sub.vertexSet()); // not losing track
assertEquals(g.edgeSet(), sub.edgeSet());
}
private void findParents(JavaClass jclass, Set<JavaClass> changedParents) {
for (JavaClass parent : getParents(jclass)) {
if (changedParents.add(parent)) {
findParents(parent, changedParents);
}
}
}
/*
* The subroutine of DFS. NOTE: the set is used to distinguish between 1st
* and 2nd round of DFS. set == null: finished vertices are stored (1st
* round). set != null: all vertices found will be saved in the set (2nd
* round)
*/
private void dfsVisit(
DirectedGraph<V, E> visitedGraph, VertexData<V> vertexData, Set<V> vertices) {
Deque<VertexData<V>> stack = new ArrayDeque<VertexData<V>>();
stack.add(vertexData);
while (!stack.isEmpty()) {
VertexData<V> data = stack.removeLast();
if (!data.isDiscovered()) {
data.setDiscovered(true);
if (vertices != null) {
vertices.add(data.getVertex());
}
stack.add(new VertexData1<V>(data, true, true));
// follow all edges
for (E edge : visitedGraph.outgoingEdgesOf(data.getVertex())) {
VertexData<V> targetData = vertexToVertexData.get(visitedGraph.getEdgeTarget(edge));
if (!targetData.isDiscovered()) {
// the "recursion"
stack.add(targetData);
}
}
} else if (data.isFinished()) {
if (vertices == null) {
orderedVertices.addFirst(data.getFinishedData());
}
}
}
}
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#getAllEdges(Object, Object) */
public Set<E> getAllEdges(V sourceVertex, V targetVertex) {
Set<E> edges = null;
if (containsVertex(sourceVertex) && containsVertex(targetVertex)) {
edges = new ArrayUnenforcedSet<E>();
DirectedEdgeContainer<V, E> ec = getEdgeContainer(sourceVertex);
Iterator<E> iter = ec.outgoing.iterator();
while (iter.hasNext()) {
E e = iter.next();
if (getEdgeTarget(e).equals(targetVertex)) {
edges.add(e);
}
}
}
return edges;
}
/**
* Finds the vertex set for the subgraph of all cycles.
*
* @return set of all vertices which participate in at least one cycle in this graph
*/
public Set<V> findCycles() {
// ProbeIterator can't be used to handle this case,
// so use StrongConnectivityInspector instead.
StrongConnectivityInspector<V, E> inspector = new StrongConnectivityInspector<V, E>(graph);
List<Set<V>> components = inspector.stronglyConnectedSets();
// A vertex participates in a cycle if either of the following is
// true: (a) it is in a component whose size is greater than 1
// or (b) it is a self-loop
Set<V> set = new HashSet<V>();
for (Set<V> component : components) {
if (component.size() > 1) {
// cycle
set.addAll(component);
} else {
V v = component.iterator().next();
if (graph.containsEdge(v, v)) {
// self-loop
set.add(v);
}
}
}
return set;
}
/** @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);
}
public Set<JavaClass> findClasses(Collection<File> changedFiles) {
// First update class index
List<String> changedClassesNames = new ArrayList<String>();
for (File changedFile : changedFiles) {
String changedClassname = builder.classFileChanged(changedFile);
if (changedClassname != null) {
changedClassesNames.add(changedClassname);
}
}
// Then find dependencies
Set<JavaClass> changedClasses = newHashSet();
for (String changedClassesName : changedClassesNames) {
JavaClass javaClass = builder.getClass(changedClassesName);
if (javaClass != null) {
addToIndex(javaClass);
changedClasses.add(javaClass);
}
}
builder.clear();
return changedClasses;
}
/**
* Updates outgoing vertices of the vertex. For each outgoing vertex, the new paths are obtained
* by concatenating the specified edge to the calculated paths of the specified vertex. If the
* weight of a new path is greater than the weight of any path stored so far at the outgoing
* vertex then the path is not added, otherwise it is added to the list of paths in increasing
* order of weight. Complexity =
*
* <ul>
* <li>O(<code>d(v)*k*(m+n)</code>) where <code>d(v)</code> is the outgoing degree of the
* specified vertex, <code>k</code> is the maximum number of shortest paths to compute,
* <code>m</code> is the number of edges of the graph and <code>n</code> is the number of
* vertices of the graph
* </ul>
*
* @param vertex
* @param improvedVertices
*/
private void updateOutgoingVertices(V vertex, Set<V> improvedVertices) {
// try to add new paths for the target vertices of the outgoing edges
// of the vertex in argument.
for (Iterator<E> iter = edgesOfIterator(vertex); iter.hasNext(); ) {
E edge = iter.next();
V vertexReachedByEdge = Graphs.getOppositeVertex(this.graph, edge, vertex);
// check if the path does not loop over the start vertex.
if (!vertexReachedByEdge.equals(this.startVertex)) {
if (this.seenDataContainer.containsKey(vertexReachedByEdge)) {
boolean relaxed = tryToAddNewPaths(vertexReachedByEdge, edge);
if (relaxed) {
improvedVertices.add(vertexReachedByEdge);
}
} else {
boolean relaxed = tryToAddFirstPaths(vertexReachedByEdge, edge);
if (relaxed) {
improvedVertices.add(vertexReachedByEdge);
}
}
}
}
}
/**
* 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()));
}
}
/**
* 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;
}
public int outDegreeOf(V vertex) {
Set<E> res = outgoingEdgesOf(vertex);
return res.size();
}
/**
* .
*
* @param e
*/
public void addIncomingEdge(EE e) {
incoming.add(e);
}
/**
* .
*
* @param e
*/
public void removeEdge(EE e) {
vertexEdges.remove(e);
}
/**
* .
*
* @return
*/
public int edgeCount() {
return vertexEdges.size();
}
/**
* .
*
* @param e
*/
public void addEdge(EE e) {
vertexEdges.add(e);
}
/**
* .
*
* @param e
*/
public void addOutgoingEdge(EE e) {
outgoing.add(e);
}
/**
* .
*
* @param e
*/
public void removeOutgoingEdge(EE e) {
outgoing.remove(e);
}
/**
* .
*
* @param e
*/
public void removeIncomingEdge(EE e) {
incoming.remove(e);
}