public void testUndirected() {
UndirectedGraph<String, DefaultEdge> g =
new SimpleGraph<String, DefaultEdge>(DefaultEdge.class);
g.addVertex(V1);
g.addVertex(V2);
g.addEdge(V1, V2);
g.addVertex(V3);
g.addEdge(V3, V1);
StringWriter w = new StringWriter();
exporter.export(w, g);
assertEquals(UNDIRECTED, w.toString());
}
public void testAdjacencyUndirected() {
UndirectedGraph<String, DefaultEdge> g =
new Pseudograph<String, DefaultEdge>(DefaultEdge.class);
g.addVertex(V1);
g.addVertex(V2);
g.addEdge(V1, V2);
g.addVertex(V3);
g.addEdge(V3, V1);
g.addEdge(V1, V1);
StringWriter w = new StringWriter();
exporter.exportAdjacencyMatrix(w, g);
assertEquals(UNDIRECTED_ADJACENCY, w.toString());
}
public void testLaplacian() {
UndirectedGraph<String, DefaultEdge> g =
new SimpleGraph<String, DefaultEdge>(DefaultEdge.class);
g.addVertex(V1);
g.addVertex(V2);
g.addEdge(V1, V2);
g.addVertex(V3);
g.addEdge(V3, V1);
StringWriter w = new StringWriter();
exporter.exportLaplacianMatrix(w, g);
assertEquals(LAPLACIAN, w.toString());
w = new StringWriter();
exporter.exportNormalizedLaplacianMatrix(w, g);
assertEquals(NORMALIZED_LAPLACIAN, w.toString());
}
public void testUndirectedEdgeList() {
UndirectedGraph<Integer, DefaultEdge> g = new SimpleGraph<>(DefaultEdge.class);
g.addVertex(1);
g.addVertex(2);
g.addVertex(3);
g.addVertex(4);
g.addVertex(5);
g.addEdge(1, 2);
g.addEdge(1, 3);
g.addEdge(3, 1);
g.addEdge(3, 4);
g.addEdge(4, 5);
g.addEdge(5, 1);
CSVExporter<Integer, DefaultEdge> exporter =
new CSVExporter<>(nameProvider, CSVFormat.EDGE_LIST, ';');
StringWriter w = new StringWriter();
exporter.exportGraph(g, w);
assertEquals(UNDIRECTED_EDGE_LIST, w.toString());
}
/**
* Create a copy of a graph for internal use.
*
* @param graph the graph to copy.
* @return A copy of the graph projected to a SimpleGraph.
*/
private static <V, E> UndirectedGraph<V, E> copyAsSimpleGraph(UndirectedGraph<V, E> graph) {
UndirectedGraph<V, E> copy = new SimpleGraph<>(graph.getEdgeFactory());
if (graph instanceof SimpleGraph) {
Graphs.addGraph(copy, graph);
} else {
// project graph to SimpleGraph
Graphs.addAllVertices(copy, graph.vertexSet());
for (E e : graph.edgeSet()) {
V v1 = graph.getEdgeSource(e);
V v2 = graph.getEdgeTarget(e);
if ((v1 != v2) && !copy.containsEdge(e)) {
copy.addEdge(v1, v2);
}
}
}
return copy;
}
/**
* 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);
}
}