/**
* Verifica que no hayan partes de red aisladas. Todos los nodos deben estar conectados a una
* misma red.
*/
private void checkIsolatedNetworks() {
Routing routing = SimulationBase.getInstance().getGridSimulatorModel().getRouting();
Boolean foundIsolatedNetworks = false;
if (routing instanceof RoutingViaJung) {
// System.out.println("Entro a:RoutingViaJung");
Graph networkRoutingGraph = ((RoutingViaJung) routing).getHybridNetwork();
GridVertex pivotVertex = null;
Iterator<GridVertex> itVertexes = networkRoutingGraph.getVertices().iterator();
while (itVertexes.hasNext() && !foundIsolatedNetworks) {
GridVertex vertex = itVertexes.next();
if (pivotVertex == null) {
pivotVertex = vertex;
continue;
}
if (pivotVertex.getTheEntity().getHopCount(vertex.getTheEntity()) == -1) {
addError(
SimulationBase.getInstance().getGridSimulatorModel(),
" \n►Contiene redes disconexas.");
foundIsolatedNetworks = true;
}
}
} else if (routing instanceof ShortesPathRouting) {
// System.out.println("Entro a:ShortesPathRouting");
NetworkProxy networkProxy = new NetworkProxy();
networkProxy.setHyrbidNetwork(((ShortesPathRouting) routing).getHyrbidNetwork());
NetworkRouting networkRouting = ((ShortesPathRouting) routing).getHybridNetworkRouting();
String pivotVertexID = null;
Iterator<String> itVertexesID = networkProxy.getNodeIDs().iterator();
while (itVertexesID.hasNext() && !foundIsolatedNetworks) {
String vertexID = itVertexesID.next();
if (pivotVertexID == null) {
pivotVertexID = vertexID;
continue;
}
Iterator<Connection> itConns =
networkRouting.findConnections(pivotVertexID, vertexID).iterator();
while (itConns.hasNext()) {
Connection conn = itConns.next();
if (conn.getRoute() == null) {
addError(
SimulationBase.getInstance().getGridSimulatorModel(),
" \n►Contiene redes disconexas.");
foundIsolatedNetworks = true;
}
}
}
}
}
@Override
public int checkFitness(
Graph<ColorableVertex, ?> graph,
List<ColorableVertex> gVertices,
Colony<ColorableVertex> colony) {
Collections.sort(
colony,
new Comparator<ColorableVertex>() {
@Override
public int compare(ColorableVertex o1, ColorableVertex o2) {
return o1.getId() - o2.getId();
}
});
for (int i = 0; i < gVertices.size(); i++) {
if (gVertices.get(i).getId() != colony.get(i).getId())
throw new IllegalStateException("DUPA");
gVertices.get(i).setColor(colony.get(i).getColor());
}
// Sprawdzenie czy rozwiązanie jest poprawne
int bad = 0;
for (ColorableVertex v : graph.getVertices()) {
for (ColorableVertex c : graph.getNeighbors(v)) {
if ((c.getColor() == v.getColor()) && (c != v)) bad++;
}
}
return bad;
}
public static <V, E> Neo4jTopology loadTopology(Neo4jWorkspaceSettings settings)
throws Exception {
String db = DatabaseConfiguration.readDatabase(settings);
Logger.getLogger(Neo4jWorkspace.class).info("using db " + db);
// Get neo4j stuffs
GraphDatabaseFactory factory = new GraphDatabaseFactory();
GraphDatabaseService database = factory.newEmbeddedDatabase(db);
GlobalGraphOperations operation = GlobalGraphOperations.at(database);
ViewsManager views = new ViewsManager();
views.load(settings);
// Setup graph model
Neo4jGraphModelIO gio = new Neo4jGraphModelIO();
gio.read(SimpleFile.read(settings.getModelPath()));
Neo4jGraphModel typeModel = gio.getGraphModel();
// Build graph
INeo4jGraphReader r = views.getFirst().getFilter();
Graph<IPropertyNode, IPropertyEdge> graph = r.read(operation, typeModel);
Logger.getLogger(Neo4jWorkspace.class)
.info("filtered graph has " + graph.getVertexCount() + " nodes using db " + db);
// Build topology using graph typing model
String topologyName = views.getFirst().getTopologyName();
Neo4jTopologyFactory tfact = new Neo4jTopologyFactory();
Neo4jTopology topology = tfact.newTopology(topologyName, graph, typeModel);
return topology;
}
/**
* Saves a given graph to a dot file, it also creates the file, or overwrites the old one
*
* @param g : The jung graph to save
* @param filename : A string that points to the destination of the save
* @param labeler : A node object -> Node name converter object
* @param graphName : The name of the graph to export (usually this is set the project's name)
* @throws IOException On IO error
*/
public void save(Graph<V, E> g, String filename, Transformer<V, String> labeler, String graphName)
throws IOException {
SortedSet<V> nodes = new TreeSet<V>();
Map<V, SortedSet<V>> successors = new HashMap<V, SortedSet<V>>();
for (V source : g.getVertices()) {
Collection<V> actSuccessors = g.getSuccessors(source);
SortedSet<V> successorTree = new TreeSet<V>();
for (V destination : actSuccessors) {
successorTree.add(destination);
}
nodes.add(source);
successors.put(source, successorTree);
}
BufferedWriter writer =
new BufferedWriter(new OutputStreamWriter(new FileOutputStream(filename), "UTF-8"));
writer.write("digraph \"" + graphName + "\" {\n");
for (V from : nodes) {
Collection<V> actSuccessors = successors.get(from);
for (V to : actSuccessors) {
writer.write(
"\t\"" + labeler.transform(from) + "\" -> \"" + labeler.transform(to) + "\";\n");
}
if (g.getPredecessorCount(from) == 0 && actSuccessors.isEmpty()) {
writer.write("\t\"" + labeler.transform(from) + "\";\n");
}
}
writer.write("}");
writer.close();
}
protected Graph<Cell, CellsLink> getDirectedGraph(Mine mine) {
Graph<Cell, CellsLink> graph = new DirectedSparseGraph<Cell, CellsLink>();
for (CellsLink link : getCellLinks(mine)) {
graph.addEdge(link, link.getSource(), link.getTarget());
}
return graph;
}
/**
* Finds the set of clusters which have the strongest "community structure". The more edges
* removed the smaller and more cohesive the clusters.
*
* @param graph the graph
*/
public Set<Set<V>> transform(Graph<V, E> graph) {
if (mNumEdgesToRemove < 0 || mNumEdgesToRemove > graph.getEdgeCount()) {
throw new IllegalArgumentException("Invalid number of edges passed in.");
}
edges_removed.clear();
for (int k = 0; k < mNumEdgesToRemove; k++) {
BetweennessCentrality<V, E> bc = new BetweennessCentrality<V, E>(graph);
E to_remove = null;
double score = 0;
for (E e : graph.getEdges()) {
Integer weight = mWeight.get(e);
if (bc.getEdgeScore(e) / weight > score) {
to_remove = e;
score = bc.getEdgeScore(e) / weight;
}
}
edges_removed.put(to_remove, graph.getEndpoints(to_remove));
graph.removeEdge(to_remove);
}
WeakComponentClusterer<V, E> wcSearch = new WeakComponentClusterer<V, E>();
Set<Set<V>> clusterSet = wcSearch.transform(graph);
for (Map.Entry<E, Pair<V>> entry : edges_removed.entrySet()) {
Pair<V> endpoints = entry.getValue();
graph.addEdge(entry.getKey(), endpoints.getFirst(), endpoints.getSecond());
}
return clusterSet;
}
/**
* Converts the prefuse graph data into the jung graph data.
*
* @param vg the prefuse visual graph
* @return graph the jung graph data
*/
public static edu.uci.ics.jung.graph.Graph<String, String> convertJungGraph(VisualGraph vg) {
edu.uci.ics.jung.graph.Graph<String, String> graph =
new UndirectedSparseGraph<String, String>();
if (vg != null) {
Iterator<?> nodeIter = vg.nodes();
while (nodeIter.hasNext()) {
VisualItem node = (VisualItem) nodeIter.next();
String nodeId = node.getString("id");
// System.out.println("node id == " + nodeId);
graph.addVertex(nodeId);
}
Iterator<?> edgeIter = vg.edges();
while (edgeIter.hasNext()) {
VisualItem edge = (VisualItem) edgeIter.next();
String node1 = edge.getString("node1");
String node2 = edge.getString("node2");
String edgeId = node1 + node2;
// System.out.println("edge id == " + edgeId);
graph.addEdge(edgeId, node1, node2, EdgeType.UNDIRECTED);
}
}
return graph;
}
public void testNoLabels() throws IOException {
String test = "*Vertices 3\n1\n2\n3\n*Edges\n1 2\n2 2";
Reader r = new StringReader(test);
Graph<Number, Number> g = pnr.load(r, undirectedGraphFactory);
assertEquals(g.getVertexCount(), 3);
assertEquals(g.getEdgeCount(), 2);
}
/**
* Connect vertices in the graph. Connects vertices if startVertex and endVertex may be connected
* by a directed edge. Ensures that: * startVertex is a RequiredPort and endVertex is a
* ProvidedPort * the required port has not yet reached the maximal number of connections {@link
* RequiredPort.getMaxDegree() getMaxDegree} * the ports do not belong to the same component * the
* ports are not yet connected
*
* @param startVertex
* @param endVertex
* @param graph
* @return true if the two vertexes were connected
*/
protected boolean connect(NubiSaveVertex startVertex, NubiSaveVertex endVertex) {
boolean shouldNotConnect = shouldNotConnect(startVertex, endVertex);
System.out.println("nubisavecomponentgraphmouseplugin: connect");
if (shouldNotConnect) {
System.out.println("nubisavecomponentgraphmouseplugin: returning false");
return false;
}
AbstractNubisaveComponent start =
(AbstractNubisaveComponent) ((RequiredPort) startVertex).getParentComponent();
AbstractNubisaveComponent end =
(AbstractNubisaveComponent) ((ProvidedPort) endVertex).getParentComponent();
if (!isConnected(startVertex, endVertex)) {
BufferedWriter writer = null;
try {
System.out.println("is not connected");
start.connectToProvidedPort(end);
WeightedNubisaveVertexEdge edge = edgeFactory.create();
edge.setWeight(end.getNrOfFilePartsToStore());
graph.addEdge(edge, startVertex, endVertex, EdgeType.DIRECTED);
File file = new File(storage_directory + "/" + "connections.txt");
if (!file.exists()) {
file.createNewFile();
}
writer = new BufferedWriter(new FileWriter(file, true));
writer.write(start.getUniqueName());
writer.write(" ");
writer.write(end.getUniqueName());
writer.newLine();
writer.close();
} catch (IOException ex) {
Logger.getLogger(AbstractNubisaveComponentEdgeCreator.class.getName())
.log(Level.SEVERE, null, ex);
} finally {
try {
writer.close();
} catch (IOException ex) {
Logger.getLogger(AbstractNubisaveComponentEdgeCreator.class.getName())
.log(Level.SEVERE, null, ex);
}
}
} else {
System.out.println("is connected --> increase weight");
WeightedNubisaveVertexEdge edge =
(WeightedNubisaveVertexEdge) graph.findEdge(startVertex, endVertex);
System.out.println("edge weight: " + edge.getWeight());
int before = end.getNrOfFilePartsToStore();
System.out.println("nroffileparts1: " + before);
end.setNrOfFilePartsToStore(end.getNrOfFilePartsToStore() + 1);
System.out.println("nroffileparts2: " + end.getNrOfFilePartsToStore());
assert (end.getNrOfFilePartsToStore() - 1) == before;
edge.setWeight(end.getNrOfFilePartsToStore());
assert (edge.getWeight() - 1) == before;
System.out.println("incrreased edge weight: " + edge.getWeight());
}
System.out.println("nubisavecomponentgraphmouseplugin: returning true");
return true;
}
public static void convertGraphToImage(Graph grap) {
try {
Layout layout = new CircleLayout(grap);
Dimension dime = new Dimension(grap.getEdgeCount() * 100, grap.getEdgeCount() * 100);
VisualizationImageServer vv = new VisualizationImageServer(layout, dime);
Transformer<String, Paint> vertexPaint =
new Transformer<String, Paint>() {
@Override
public Paint transform(String i) {
return Color.BLUE;
}
};
Transformer<String, Stroke> edgeStrokeTransformer =
new Transformer<String, Stroke>() {
@Override
public Stroke transform(String s) {
Stroke edgeStroke =
new BasicStroke(1.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER);
return edgeStroke;
}
};
vv.getRenderContext().setVertexFillPaintTransformer(vertexPaint);
vv.getRenderContext().setEdgeStrokeTransformer(edgeStrokeTransformer);
vv.getRenderContext().setVertexLabelTransformer(new ToStringLabeller());
vv.getRenderContext().setEdgeLabelTransformer(new ToStringLabeller());
vv.getRenderContext()
.setVertexLabelRenderer(
new DefaultVertexLabelRenderer(Color.yellow) {
@Override
public Font getFont() {
return new Font(Font.SERIF, 1, 30);
}
@Override
public Color getForeground() {
return Color.YELLOW;
}
});
vv.getRenderer().getVertexLabelRenderer().setPosition(Renderer.VertexLabel.Position.AUTO);
BufferedImage bim = (BufferedImage) vv.getImage(new Point(), dime);
File f =
new File(Util.dateDataToString(new Date(), "dd-MM-yyyy_HH-mm") + "_imagem_teste.png");
ImageIO.write(bim, "png", f);
System.out.println("wrote image for " + f.getAbsolutePath());
} catch (Exception ex) {
ex.printStackTrace();
}
}
// used to construct graph and call graph algorithm used in JUNG
public HashMap Closeness_Centrality_Score(
LinkedList<String> Distinct_nodes,
LinkedList<String> source_vertex,
LinkedList<String> target_vertex,
LinkedList<Double> Edge_Weight) {
// CREATING weighted directed graph
Graph<MyNode, MyLink> g = new DirectedSparseGraph<Graph_Algos.MyNode, Graph_Algos.MyLink>();
// create node objects
Hashtable<String, MyNode> Graph_Nodes = new Hashtable<String, Graph_Algos.MyNode>();
LinkedList<MyNode> Source_Node = new LinkedList<Graph_Algos.MyNode>();
LinkedList<MyNode> Target_Node = new LinkedList<Graph_Algos.MyNode>();
LinkedList<MyNode> Graph_Nodes_Only = new LinkedList<Graph_Algos.MyNode>();
// LinkedList<MyLink> Graph_Links = new LinkedList<Graph_Algos.MyLink>();
// create graph nodes
for (int i = 0; i < Distinct_nodes.size(); i++) {
String node_name = Distinct_nodes.get(i);
MyNode data = new MyNode(node_name);
Graph_Nodes.put(node_name, data);
Graph_Nodes_Only.add(data);
}
// Now convert all source and target nodes into objects
for (int t = 0; t < source_vertex.size(); t++) {
Source_Node.add(Graph_Nodes.get(source_vertex.get(t)));
Target_Node.add(Graph_Nodes.get(target_vertex.get(t)));
}
// Now add nodes and edges to the graph
for (int i = 0; i < Edge_Weight.size(); i++) {
g.addEdge(
new MyLink(Edge_Weight.get(i)),
Source_Node.get(i),
Target_Node.get(i),
EdgeType.DIRECTED);
}
Transformer<MyLink, Double> wtTransformer =
new Transformer<MyLink, Double>() {
public Double transform(MyLink link) {
return link.weight;
}
};
edu.uci.ics.jung.algorithms.scoring.ClosenessCentrality<MyNode, MyLink> CC1 =
new edu.uci.ics.jung.algorithms.scoring.ClosenessCentrality<MyNode, MyLink>(
g, wtTransformer);
// Calculating Closeness Centrality score of nodes
HashMap map = new HashMap();
for (int i = 0; i < Graph_Nodes_Only.size(); i++) {
// System.out.println("Graph Node "+Graph_Nodes_Only.get(i)+" Closeness Centrality"
// +CC1.getVertexScore(Graph_Nodes_Only.get(i)));
String node = Graph_Nodes_Only.get(i) + "";
node = node.substring(1, node.length());
double val = CC1.getVertexScore(Graph_Nodes_Only.get(i));
if (new Double(val).isNaN()) {
val = 0.00001;
}
map.put(node, val);
}
return map;
}
/**
* Build full Neo4jWorkspace involving reading files given by settings:
*
* <ul>
* <li>neo4j database
* <li>view
* <li>graph model
* <li>projection
* </ul>
*
* and build topology & geometrical model according to Neo4j factories
*
* @param settings
* @throws Exception
*/
public Neo4jWorkspace(Neo4jWorkspaceSettings settings) throws Exception {
String db = DatabaseConfiguration.readDatabase(settings);
Logger.getLogger(Neo4jWorkspace.class).info("using db " + db);
// Get neo4j stuffs
GraphDatabaseFactory factory = new GraphDatabaseFactory();
database = factory.newEmbeddedDatabase(db);
operation = GlobalGraphOperations.at(database);
views = new ViewsManager();
views.load(settings);
layoutML = views.getFirst().getLayout();
// Setup graph model
Neo4jGraphModelIO gio = new Neo4jGraphModelIO();
gio.read(SimpleFile.read(settings.getModelPath()));
Neo4jGraphModel typeModel = gio.getGraphModel();
// Build graph
INeo4jGraphReader r = views.getFirst().getFilter();
Graph<IPropertyNode, IPropertyEdge> graph = r.read(operation, typeModel);
Logger.getLogger(Neo4jWorkspace.class)
.info("filtered graph has " + graph.getVertexCount() + " nodes using db " + db);
// Build topology using graph typing model
String topologyName = views.getFirst().getTopologyName();
Neo4jTopologyFactory tfact = new Neo4jTopologyFactory();
topology = tfact.newTopology(topologyName, graph, typeModel);
// Edit topology according to dataprism
Dataprism dp = loadDataprism(settings);
if (dp != null) ((Neo4jTopology) topology).edit().apply(dp);
// Build layout model
modelFactory = new Neo4jModelFactory(gio.getGraphModel());
model = (IHierarchicalNodeModel) modelFactory.getLayoutModel(topology);
edgeModel = model.getEdgeModel();
applyLayoutMLConfiguration(model, layoutML);
// Build layout
layoutFactory = new Neo4jLayoutFactory(typeModel);
if (layoutML != null) {
Map<String, String> mapping = extractModelLayoutMapping(layoutML);
layoutFactory.setModelLayoutMapping(mapping);
}
layout = layoutFactory.getLayout(model);
layout.getEdgeLayout().setEdgePostProcess(null);
// finalize workspace
annotationModel = new AnnotationModel();
metadata = null;
setName(settings.getName());
loadMapIfExist();
this.configuration = new ConfigurationFacade(this);
}
protected void initialize(Graph<V, E> graph) {
this.graph = graph;
this.vertex_scores = new HashMap<V, Double>();
this.edge_scores = new HashMap<E, Double>();
this.vertex_data = new HashMap<V, BetweennessData>();
for (V v : graph.getVertices()) this.vertex_scores.put(v, 0.0);
for (E e : graph.getEdges()) this.edge_scores.put(e, 0.0);
}
/** Creates a new instance of SimpleGraphView */
public InteractiveGraphView3() {
// Graph<V, E> where V is the type of the vertices and E is the type of the edges
g = new SparseMultigraph<Integer, String>();
// Add some vertices and edges
g.addVertex((Integer) 1);
g.addVertex((Integer) 2);
g.addVertex((Integer) 3);
g.addEdge("Edge-A", 1, 2);
g.addEdge("Edge-B", 2, 3);
}
@Test
public void testBacked() {
Cluster<Integer, Integer> c = new BackedClusterImpl<Integer, Integer>(graph);
Graph<Integer, Integer> inducedGraph = c.getInducedGraph();
assertEquals(0, inducedGraph.getEdgeCount());
assertEquals(0, c.size());
c.add(0);
c.add(1);
assertEquals(2, c.size());
assertEquals(1, inducedGraph.getEdgeCount());
}
/**
* create some vertices
*
* @param count how many to create
* @return the Vertices in an array
*/
private Vertex[] createVertices(int count) {
Vertex[] v = new Vertex[count];
for (int i = 0; i < count; i++) {
v[i] = graph.addVertex(new DirectedSparseVertex());
}
return v;
}
public FSMBuildVisualizer() {
super("Model Visualizer");
graph = new DirectedSparseMultigraph<>();
graph.addVertex(current);
// Layout<FSMTransition, String> layout = new CircleLayout<FSMTransition, String>(graph);
layout = new KKLayout<>(graph);
layout.setSize(new Dimension(800, 600)); // sets the initial size of the space
vv = new VisualizationViewer<>(layout);
vv.setPreferredSize(new Dimension(800, 600)); // Sets the viewing area size
vv.getRenderContext().setVertexLabelTransformer(new ToStringLabeller());
vv.getRenderContext().setEdgeLabelTransformer(new ToStringLabeller());
vv.getRenderer().getVertexLabelRenderer().setPosition(Position.CNTR);
VertexLabelAsShapeRenderer<String, StepCounter> vlasr =
new VertexLabelAsShapeRenderer<>(vv.getRenderContext());
// vv.getRenderContext().setVertexShapeTransformer(vlasr);
vv.getRenderContext().setVertexShapeTransformer(new EllipseVertexTransformer());
// vv.getRenderContext().setVertexLabelRenderer(new
// TransitionVertextLabelRenderer(Color.GREEN));
DefaultModalGraphMouse gm = new DefaultModalGraphMouse();
vv.addKeyListener(gm.getModeKeyListener());
gm.setMode(ModalGraphMouse.Mode.TRANSFORMING);
vv.setGraphMouse(gm);
getContentPane().add(vv);
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
setSize(1024, 768);
pack();
setVisible(true);
}
/**
* Returns <code>true</code> if this edge and its endpoints in this graph are all included in the
* collections of elements to be rendered, and <code>false</code> otherwise.
*
* @param context the edge and graph to be queried
* @return <code>true</code> if this edge and its endpoints are all included in the collections of
* elements to be rendered, <code>false</code> otherwise.
*/
protected boolean isEdgeRendered(Context<Graph<V, E>, E> context) {
Predicate<Context<Graph<V, E>, V>> vertexIncludePredicate =
vv.getRenderContext().getVertexIncludePredicate();
Predicate<Context<Graph<V, E>, E>> edgeIncludePredicate =
vv.getRenderContext().getEdgeIncludePredicate();
Graph<V, E> g = context.graph;
E e = context.element;
boolean edgeTest = edgeIncludePredicate == null || edgeIncludePredicate.apply(context);
Pair<V> endpoints = g.getEndpoints(e);
V v1 = endpoints.getFirst();
V v2 = endpoints.getSecond();
boolean endpointsTest =
vertexIncludePredicate == null
|| (vertexIncludePredicate.apply(Context.<Graph<V, E>, V>getInstance(g, v1))
&& vertexIncludePredicate.apply(Context.<Graph<V, E>, V>getInstance(g, v2)));
return edgeTest && endpointsTest;
}
protected TitledBorder setUpSliderPanel() {
sliderPanel = new JPanel();
sliderPanel.setPreferredSize(new Dimension(210, 50));
int sliderLimit = 50;
if (graph != null) {
final Graph<CallGraphNode, CallGraphLink> jungGraph = graph.getJungGraph();
sliderLimit = jungGraph.getVertexCount();
}
configureIterationSlider(sliderLimit);
sliderPanel.setOpaque(true);
sliderPanel.add(iterationSlider);
iterationSlider.setValue(0);
String eastSize = sliderLabelBase + iterationSlider.getValue();
TitledBorder sliderBorder = BorderFactory.createTitledBorder(eastSize);
sliderPanel.setBorder(sliderBorder);
return sliderBorder;
}
private void addEdge(String step) {
String edge = current + "->" + step;
if (!edges.containsKey(edge)) {
// System.out.println("EDGE+" + edge);
if (!vertices.contains(step)) {
// System.out.println("VERTEX+" + t);
graph.addVertex(step);
vertices.add(step);
}
StepCounter counter = new StepCounter();
edges.put(edge, counter);
graph.addEdge(counter, current, step);
vv.repaint();
} else {
edges.get(edge).increment();
}
layout.reset();
}
private void initialization() {
dominatingSet = new ArrayList<Integer>();
dominatedMap = new HashMap<Integer, Boolean>();
Collection<Integer> vertices = g.getVertices();
for (Integer v : vertices) {
dominatedMap.put(v, false);
}
}
protected int getIndex(Graph<V, E> graph, E e, V v) {
Collection<E> commonEdgeSet = new HashSet<E>();
for (E another : graph.getIncidentEdges(v)) {
V u = graph.getOpposite(v, another);
if (u.equals(v)) {
commonEdgeSet.add(another);
}
}
int count = 0;
for (E other : commonEdgeSet) {
if (e.equals(other) == false) {
edge_index.put(other, count);
count++;
}
}
edge_index.put(e, count);
return count;
}
private void insertTestData() {
// TODO Auto-generated method stub
trafficDataset.addValue(20, "rx", "1");
trafficDataset.addValue(40, "rx", "2");
trafficDataset.addValue(10, "rx", "3");
trafficDataset.addValue(60, "rx", "4");
trafficDataset.addValue(10, "rx", "5");
trafficDataset.addValue(20, "rx", "6");
trafficDataset.addValue(20, "rx", "7");
trafficDataset.addValue(70, "rx", "8");
trafficDataset.addValue(25, "rx", "9");
trafficDataset.addValue(15, "rx", "10");
trafficDataset.addValue(10, "rx", "11");
trafficDataset.addValue(20, "rx", "12");
trafficDataset.addValue(10, "tx", "1");
trafficDataset.addValue(20, "tx", "2");
trafficDataset.addValue(30, "tx", "3");
trafficDataset.addValue(20, "tx", "4");
trafficDataset.addValue(10, "tx", "5");
trafficDataset.addValue(20, "tx", "6");
trafficDataset.addValue(50, "tx", "7");
trafficDataset.addValue(30, "tx", "8");
trafficDataset.addValue(35, "tx", "9");
trafficDataset.addValue(25, "tx", "10");
trafficDataset.addValue(5, "tx", "11");
trafficDataset.addValue(20, "tx", "12");
trafficChart.setTitle("IP : 124.15.65.76");
nodeTrafficTableModel.addNodeTraffic(new NodeTraffic("148.35.124.7", 80, 66357, 343654, 1));
nodeTrafficTableModel.addNodeTraffic(new NodeTraffic("253.27.64.32", 80, 5757, 3446, 1));
nodeTrafficTableModel.addNodeTraffic(new NodeTraffic("124.15.65.76", 22, 345, 7778, 1));
nodeTrafficTableModel.addNodeTraffic(new NodeTraffic("125.76.43.221", 80, 453, 3456, 1));
nodeTrafficTableModel.addNodeTraffic(new NodeTraffic("57.78.3.11", 80, 765, 26754, 1));
nodeTrafficTableModel.addNodeTraffic(new NodeTraffic("86.34.25.22", 22, 45347, 345346, 1));
graph.addVertex("Internet");
for (int i = 1; i <= 6; i++) {
graph.addVertex("Node" + 1);
graph.addEdge("rx:node" + i, "Internet", "Node" + i, EdgeType.DIRECTED);
graph.addEdge("tx:node" + i, "Node" + i, "Internet", EdgeType.DIRECTED);
}
}
public void init(Functionality.Graph g, int _layout_width, int _layout_height) {
myGraph = g;
layout_width = _layout_width;
layout_height = _layout_height;
qt = new UndirectedSparseGraph();
Iterator<Functionality.Node> nodeIterator = g.getNodes().iterator();
while (nodeIterator.hasNext()) {
qt.addVertex(nodeIterator.next());
}
Iterator<Functionality.Edge> edgeIterator = g.getEdges().iterator();
while (edgeIterator.hasNext()) {
Functionality.Edge currEdge = edgeIterator.next();
qt.addEdge(currEdge, currEdge.getNode1(), currEdge.getNode2());
}
vv = null;
layout = null;
}
/**
* Calculates betweenness scores based on the all-pairs weighted shortest paths in the graph.
*
* <p>NOTE: This version of the algorithm may not work correctly on all graphs; we're still
* working out the bugs. Use at your own risk.
*
* @param graph the graph for which the scores are to be calculated
* @param edge_weights the edge weights to be used in the path length calculations
*/
public BetweennessCentrality(Graph<V, E> graph, Transformer<E, ? extends Number> edge_weights) {
// reject negative-weight edges up front
for (E e : graph.getEdges()) {
double e_weight = edge_weights.transform(e).doubleValue();
if (e_weight < 0)
throw new IllegalArgumentException("Weight for edge '" + e + "' is < 0: " + e_weight);
}
initialize(graph);
computeBetweenness(new MapBinaryHeap<V>(new BetweennessComparator()), edge_weights);
}
public Graph<String, String> createGraph() {
graph = new UndirectedSparseGraph<String, String>();
Attribute id = exampleSet.getAttributes().getId();
if (id != null) {
for (Example example : exampleSet) {
graph.addVertex(example.getValueAsString(id));
}
addEdges();
}
return graph;
}
/**
* Tests to see whether these two graphs are structurally equivalent, based on the connectivity of
* the vertices with matching indices in each graph. Assumes a 0-based index.
*
* @param g1
* @param g2
*/
private void compareIndexedGraphs(Graph<Number, Number> g1, Graph<Number, Number> g2) {
int n1 = g1.getVertexCount();
int n2 = g2.getVertexCount();
assertEquals(n1, n2);
assertEquals(g1.getEdgeCount(), g2.getEdgeCount());
List<Number> id1 = new ArrayList<Number>(g1.getVertices());
List<Number> id2 = new ArrayList<Number>(g2.getVertices());
for (int i = 0; i < n1; i++) {
Number v1 = id1.get(i);
Number v2 = id2.get(i);
assertNotNull(v1);
assertNotNull(v2);
checkSets(g1.getPredecessors(v1), g2.getPredecessors(v2), id1, id2);
checkSets(g1.getSuccessors(v1), g2.getSuccessors(v2), id1, id2);
}
}
public Data[] execute() {
int numNodes = getInt("numNodes");
Graph graph = (Graph) data[0].getData();
graph = (Graph) graph.copy();
ErrorTolerance et = new ErrorTolerance(graph, numNodes);
boolean isDone = et.testErrorTolerance();
Data[] newdata = null;
if (isDone) {
Data model = new BasicData(et.getGraph(), Graph.class.getName());
Dictionary map = model.getMetaData();
map.put(DataProperty.MODIFIED, new Boolean(true));
map.put(DataProperty.PARENT, data[0]);
map.put(DataProperty.TYPE, DataProperty.NETWORK_TYPE);
map.put(DataProperty.LABEL, "Random Node Deletion (Error Tolerance)");
newdata = new Data[] {model};
}
return newdata;
}
protected int getIndex(Graph<V, E> graph, E e, V u, V v) {
Collection<E> commonEdgeSet = new HashSet<E>(graph.getIncidentEdges(u));
int count = 0;
for (E other : commonEdgeSet) {
if (e.equals(other) == false) {
edge_index.put(other, count);
count++;
}
}
edge_index.put(e, count);
return count;
}
// method for flow graph visualization
public static void visualizeGraph(int[][] matrix, int N, int k) {
Graph<Integer, String> graph = new DirectedSparseGraph<Integer, String>();
for (int i = 0; i < matrix.length; i++) {
graph.addVertex((Integer) i);
}
for (int i = 0; i < matrix.length; i++) {
for (int j = 0; j < matrix[i].length; j++) {
// only select edge that has flow bigger than 0
if (matrix[i][j] > 0) {
graph.addEdge(i + "->" + j, i, j, EdgeType.DIRECTED);
}
}
}
Layout<Integer, String> layout = new CircleLayout<Integer, String>(graph);
layout.setSize(new Dimension(800, 800));
BasicVisualizationServer<Integer, String> vv =
new BasicVisualizationServer<Integer, String>(layout);
Transformer<Integer, Paint> vertexPaint =
new Transformer<Integer, Paint>() {
public Paint transform(Integer i) {
return Color.YELLOW;
}
};
vv.setPreferredSize(new Dimension(800, 800));
vv.getRenderContext().setVertexFillPaintTransformer(vertexPaint);
vv.getRenderContext().setVertexLabelTransformer(new ToStringLabeller<Integer>());
vv.getRenderer().getVertexLabelRenderer().setPosition(Position.CNTR);
JFrame frame = new JFrame("Network Visualization - N = " + N + ", k = " + k);
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
frame.getContentPane().add(vv);
frame.pack();
frame.setVisible(true);
}