@Override
public void execute(GraphModel graphModel, AttributeModel attributeModel) {
// Graph graph = graphModel.getGraphVisible();
HierarchicalGraph graph = null;
// get visible graph
if (directed) {
graph = graphModel.getHierarchicalDirectedGraphVisible();
} else {
graph = graphModel.getHierarchicalUndirectedGraphVisible();
}
// lock graph
graph.readLock();
try {
Progress.start(progressTicket, graph.getNodeCount());
// all coefficients
nodeCoefficients = new double[graph.getNodeCount()];
// attribute column
AttributeTable nodeTable = attributeModel.getNodeTable();
AttributeColumn clusteringColumn = nodeTable.getColumn("newClusteringCoefficient");
if (clusteringColumn == null) {
clusteringColumn =
nodeTable.addColumn(
"newClusteringCoefficient",
"Local Clustering Coefficient",
AttributeType.DOUBLE,
AttributeOrigin.COMPUTED,
0.0);
}
int i = 0;
// for each node
for (Node e : graph.getNodes()) {
// compute coefficient
double coeficient = 0.0;
double denominator = (graph.getDegree(e) * (graph.getDegree(e) - 1));
if (!directed) {
denominator /= 2;
}
double numerator = 0.0;
// get neighbors as list
List<Node> n2 = Arrays.asList(graph.getNeighbors(e).toArray());
List<Node> neighbors2 = new ArrayList<Node>(n2);
for (Node neighbor1 : graph.getNeighbors(e)) {
neighbors2.remove(neighbor1);
// count edges betwwen neighbors
for (Node neighbor2 : neighbors2) {
if (graph.getEdge(neighbor1, neighbor2) != null
|| graph.getEdge(neighbor2, neighbor1) != null) {
numerator++;
}
}
}
// compute coefficient
if (denominator > 0) {
coeficient = numerator / denominator;
} else {
coeficient = 0.0;
}
averageCoefficient += coeficient;
nodeCoefficients[i] = coeficient;
i++;
// set attribute
AttributeRow row = (AttributeRow) e.getNodeData().getAttributes();
row.setValue(clusteringColumn, coeficient);
Progress.progress(progressTicket);
if (cancel) {
break;
}
}
if (graph.getNodeCount() > 0) {
averageCoefficient = averageCoefficient / graph.getNodeCount();
}
graph.readUnlockAll();
} catch (Exception e) {
e.printStackTrace();
// Unlock graph
graph.readUnlockAll();
}
}
public void updateWorld() {
// System.out.println("update world");
cacheMarker++;
GraphModel graphModel = controller.getModel();
if (graphModel == null) {
engine.worldUpdated(cacheMarker);
return;
}
if (gm != null && gm != graphModel) {
reset();
}
gm = graphModel;
HierarchicalGraph graph;
if (graphModel.isDirected()) {
undirected = false;
graph = graphModel.getHierarchicalDirectedGraphVisible();
} else if (graphModel.isUndirected()) {
undirected = true;
graph = graphModel.getHierarchicalUndirectedGraphVisible();
} else if (graphModel.isMixed()) {
undirected = false;
graph = graphModel.getHierarchicalMixedGraphVisible();
} else {
undirected = false;
graph = graphModel.getHierarchicalDirectedGraphVisible();
}
if (dynamicModel == null) {
DynamicController dynamicController = Lookup.getDefault().lookup(DynamicController.class);
dynamicModel = dynamicController.getModel();
}
graphView = graph.getView().getViewId();
ModelClass[] object3dClasses = engine.getModelClasses();
graph.readLock();
ModelClass nodeClass = object3dClasses[AbstractEngine.CLASS_NODE];
if (nodeClass.isEnabled()
&& (graph.getNodeVersion() > nodeVersion || modeManager.requireModeChange())) {
updateNodes(graph);
nodeClass.setCacheMarker(cacheMarker);
}
ModelClass edgeClass = object3dClasses[AbstractEngine.CLASS_EDGE];
if (edgeClass.isEnabled()
&& (graph.getEdgeVersion() > edgeVersion || modeManager.requireModeChange())) {
updateEdges(graph);
updateMetaEdges(graph);
edgeClass.setCacheMarker(cacheMarker);
if (!undirected && vizConfig.isShowArrows()) {
object3dClasses[AbstractEngine.CLASS_ARROW].setCacheMarker(cacheMarker);
}
}
ModelClass potatoClass = object3dClasses[AbstractEngine.CLASS_POTATO];
if (potatoClass.isEnabled()
&& (graph.getNodeVersion() > nodeVersion || modeManager.requireModeChange())) {
updatePotatoes(graph);
potatoClass.setCacheMarker(cacheMarker);
}
nodeVersion = graph.getNodeVersion();
edgeVersion = graph.getEdgeVersion();
graph.readUnlock();
engine.worldUpdated(cacheMarker);
}
public boolean execute() {
attributeModel = workspace.getLookup().lookup(AttributeModel.class);
graphModel = workspace.getLookup().lookup(GraphModel.class);
HierarchicalGraph graph = null;
if (exportVisible) {
graph = graphModel.getHierarchicalGraphVisible();
} else {
graph = graphModel.getHierarchicalGraph();
}
Progress.start(progress);
graph.readLock();
// Options
if (normalize) {
calculateMinMax(graph);
}
// Calculate progress units count
int max = 0;
if (exportHierarchy) {
for (Node n : graph.getNodesTree()) {
max++;
}
for (Edge e : graph.getEdgesTree()) {
max++;
}
} else {
max = graph.getNodeCount();
for (Edge e : graph.getEdgesAndMetaEdges()) {
max++;
}
}
Progress.switchToDeterminate(progress, max);
try {
XMLOutputFactory outputFactory = XMLOutputFactory.newInstance();
outputFactory.setProperty("javax.xml.stream.isRepairingNamespaces", Boolean.FALSE);
XMLStreamWriter xmlWriter = outputFactory.createXMLStreamWriter(writer);
xmlWriter = new IndentingXMLStreamWriter(xmlWriter);
xmlWriter.writeStartDocument("UTF-8", "1.0");
xmlWriter.setPrefix("", GEXF_NAMESPACE);
xmlWriter.writeStartElement(GEXF_NAMESPACE, GEXF);
xmlWriter.writeNamespace("", GEXF_NAMESPACE);
xmlWriter.writeAttribute(GEXF_VERSION, "1.1");
if (exportColors || exportPosition || exportSize) {
xmlWriter.writeNamespace(VIZ, VIZ_NAMESPACE);
}
xmlWriter.writeAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance");
xmlWriter.writeAttribute("xsi:schemaLocation", GEXF_NAMESPACE_LOCATION);
if (exportDynamic) {
DynamicController dynamicController = Lookup.getDefault().lookup(DynamicController.class);
dynamicModel = dynamicController != null ? dynamicController.getModel(workspace) : null;
visibleInterval =
dynamicModel == null
? null
: exportVisible
? dynamicModel.getVisibleInterval()
: new TimeInterval(Double.NEGATIVE_INFINITY, Double.POSITIVE_INFINITY);
}
writeMeta(xmlWriter);
writeGraph(xmlWriter, graph);
xmlWriter.writeEndElement();
xmlWriter.writeEndDocument();
xmlWriter.close();
} catch (Exception e) {
graph.readUnlockAll();
if (e instanceof RuntimeException) {
throw (RuntimeException) e;
}
throw new RuntimeException(e);
}
graph.readUnlock();
Progress.finish(progress);
return !cancel;
}
