public void ungroupCluster(Cluster cluster) {
GraphModel gm = Lookup.getDefault().lookup(GraphController.class).getModel();
if (gm != null) {
HierarchicalGraph graph = gm.getHierarchicalGraphVisible();
graph.ungroupNodes(cluster.getMetaNode());
cluster.setMetaNode(null);
}
}
public void script() {
// Init a project - and therefore a workspace
ProjectController pc = Lookup.getDefault().lookup(ProjectController.class);
pc.newProject();
Workspace workspace = pc.getCurrentWorkspace();
// Get controllers and models
ImportController importController = Lookup.getDefault().lookup(ImportController.class);
// Import file
Container container;
try {
File file =
new File(
getClass().getResource("/org/gephi/toolkit/demos/resources/polblogs.gml").toURI());
container = importController.importFile(file);
container.getLoader().setEdgeDefault(EdgeDefault.DIRECTED); // Force DIRECTED
container.setAllowAutoNode(false); // Don't create missing nodes
} catch (Exception ex) {
ex.printStackTrace();
return;
}
// Append imported data to GraphAPI
importController.process(container, new DefaultProcessor(), workspace);
// List node columns
AttributeController ac = Lookup.getDefault().lookup(AttributeController.class);
AttributeModel model = ac.getModel();
for (AttributeColumn col : model.getNodeTable().getColumns()) {
System.out.println(col);
}
// Add boolean column
AttributeColumn testCol = model.getNodeTable().addColumn("test", AttributeType.BOOLEAN);
// Write values to nodes
GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getModel();
for (Node n : graphModel.getGraph().getNodes()) {
n.getNodeData().getAttributes().setValue(testCol.getIndex(), Boolean.TRUE);
}
// Iterate values - fastest
AttributeColumn sourceCol = model.getNodeTable().getColumn("source");
for (Node n : graphModel.getGraph().getNodes()) {
System.out.println(n.getNodeData().getAttributes().getValue(sourceCol.getIndex()));
}
// Iterate values - normal
for (Node n : graphModel.getGraph().getNodes()) {
System.out.println(n.getNodeData().getAttributes().getValue("source"));
}
}
public void setEnable(boolean enable) {
if (enable) {
if (observer == null) {
observer = graphModel.createGraphObserver(graphModel.getGraph(), false);
}
} else if (observer != null && !observer.isDestroyed()) {
observer.destroy();
observer = null;
}
if (!isAlive()) {
start();
}
}
public boolean execute() {
GraphModel graphModel = workspace.getLookup().lookup(GraphModel.class);
Graph graph = null;
if (exportVisible) {
graph = graphModel.getGraphVisible();
} else {
graph = graphModel.getGraph();
}
try {
exportData(graph);
} catch (Exception e) {
throw new RuntimeException(e);
}
return !cancel;
}
public AppearanceModelImpl(Workspace workspace) {
this.workspace = workspace;
this.graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel(workspace);
this.defaultInterpolator = Interpolator.LINEAR;
this.functionLock = new Object();
this.transformerUIs = initTransformerUIs();
this.nodeTransformers = initNodeTransformers();
this.edgeTransformers = initEdgeTransformers();
this.forcedPartition = new HashSet<String>();
this.forcedRanking = new HashSet<String>();
this.forcedColumnsRefresh = new ArrayList<Column>();
// Functions
functionsMain = new FunctionsModel(graphModel.getGraph());
refreshFunctions(graphModel.getGraph());
}
public boolean requireUpdate() {
if (graph == null) {
// Try to get a graph
GraphModel graphModel = controller.getModel();
if (graphModel != null) {
graph = graphModel.getHierarchicalGraphVisible();
}
}
// Refresh reader if sight changed
Graph g = graph;
if (g != null) {
if (g.getGraphModel().getVisibleView().getViewId() != graphView) {
reset();
}
return g.getNodeVersion() > nodeVersion || g.getEdgeVersion() > edgeVersion;
}
return false;
}
@Override
public Collection getValues() {
Object[] labels = model.getEdgeTypeLabels();
ArrayList<Object> col = new ArrayList<Object>(labels.length);
for (Object l : labels) {
if (!(l == null && graph.getEdgeCount(0) == 0)) {
col.add(l);
}
}
return col;
}
@Override
public void execute(GraphModel gm, AttributeModel am) {
Graph graph = gm.getUndirectedGraphVisible();
graph.readLock();
// calculate all Euclidean distances between all nodes
double[] distances = geometry.calculateManyEuclideanDistances(graph.getNodes().toArray());
// calculate the variation of coefficient over the distances
result = String.valueOf(math.variationCoefficient(distances));
graph.readUnlockAll();
}
@Override
public void loop(GraphView window, Interval interval) {
Graph graph = graphModel.getGraph(window);
int count = graph.getEdgeCount();
graph.setAttribute(NB_EDGES, count, interval.getLow());
graph.setAttribute(NB_EDGES, count, interval.getHigh());
counts.put(interval.getLow(), count);
counts.put(interval.getHigh(), count);
}
private boolean isRanking(Graph graph, Column column) {
if (column.isDynamic() && column.isNumber()) {
ElementIterable<? extends Element> iterable =
AttributeUtils.isNodeColumn(column) ? graph.getNodes() : graph.getEdges();
for (Element el : iterable) {
if (el.getAttribute(column, graph.getView()) != null) {
iterable.doBreak();
return true;
}
}
} else if (!column.isDynamic() && column.isIndexed() && column.isNumber()) {
Index index;
if (AttributeUtils.isNodeColumn(column)) {
index = localScale ? graphModel.getNodeIndex(graph.getView()) : graphModel.getNodeIndex();
} else {
index = localScale ? graphModel.getEdgeIndex(graph.getView()) : graphModel.getEdgeIndex();
}
if (index.countValues(column) > 0) {
return true;
}
}
return false;
}
private boolean isPartition(Graph graph, Column column) {
if (column.isDynamic()) {
Set<Object> set = new HashSet<Object>();
boolean hasNullValue = false;
int elements = 0;
ElementIterable<? extends Element> iterable =
AttributeUtils.isNodeColumn(column) ? graph.getNodes() : graph.getEdges();
for (Element el : iterable) {
TimeMap val = (TimeMap) el.getAttribute(column);
if (val != null) {
Object[] va = val.toValuesArray();
for (Object v : va) {
if (v != null) {
set.add(v);
} else {
hasNullValue = true;
}
elements++;
}
}
}
double ratio = set.size() / (double) elements;
return ratio <= 0.9;
} else if (column.isIndexed()) {
Index index;
if (AttributeUtils.isNodeColumn(column)) {
index = graphModel.getNodeIndex(graph.getView());
} else {
index = graphModel.getEdgeIndex(graph.getView());
}
int valueCount = index.countValues(column);
int elementCount = index.countElements(column);
double ratio = valueCount / (double) elementCount;
return ratio <= 0.9;
}
return false;
}
public void groupCluster(Cluster cluster) {
GraphModel gm = Lookup.getDefault().lookup(GraphController.class).getModel();
if (gm != null) {
HierarchicalGraph graph = gm.getHierarchicalGraphVisible();
Node[] newGroup = cluster.getNodes();
float centroidX = 0;
float centroidY = 0;
int len = 0;
Node group = graph.groupNodes(newGroup);
cluster.setMetaNode(group);
group.getNodeData().setLabel("Group");
group.getNodeData().setSize(10f);
for (Node child : newGroup) {
centroidX += child.getNodeData().x();
centroidY += child.getNodeData().y();
len++;
}
centroidX /= len;
centroidY /= len;
group.getNodeData().setX(centroidX);
group.getNodeData().setY(centroidY);
}
}
@Override
public List<? extends ElementDataColumn<Edge>> getFakeDataColumns(
GraphModel graphModel, DataTablesModel dataTablesModel) {
ArrayList<PropertyDataColumn<Edge>> propertiesColumns =
new ArrayList<PropertyDataColumn<Edge>>();
propertiesColumns.add(SOURCE_COLUMN);
propertiesColumns.add(TARGET_COLUMN);
propertiesColumns.add(TYPE_COLUMN);
if (graphModel.isMultiGraph()) {
propertiesColumns.add(KIND_COLUMN);
}
return propertiesColumns;
}
public void script() {
NetworkLayer nl = MultiLayerNetwork.getSelected();
if (pc == null) pc = Lookup.getDefault().lookup(ProjectController.class);
// Init a project - and therefore a workspace
Project pro = pc.getCurrentProject();
if (pro == null) {
pc.newProject();
pro = pc.getCurrentProject();
}
Workspace workspace = pc.newWorkspace(pro);
// Get controllers and models
ImportController importController = Lookup.getDefault().lookup(ImportController.class);
GraphModel graphModel =
Lookup.getDefault().lookup(GraphController.class).getGraphModel(workspace);
// AttributeModel attributeModel =
// Lookup.getDefault().lookup(AttributeController.class).getModel();
// Import database
EdgeListHiveDatabaseImpl db = new EdgeListHiveDatabaseImpl();
db.setDBName("default"); // !!!
db.setHost("127.0.0.1");
// db.setHost( HadoopClusterDefaults.HIVE_SERVER_IP );
db.setPort(10000); // !!!
db.setUsername("kamir");
db.setPasswd("8cwrr");
db.setSQLDriver(new HiveJDBCDriver());
String tab = "edgelist_es_de_erfurt2";
db.setNodeQuery(
"SELECT UNIQUE( " + tab + ".source ) AS id, " + tab + ".source AS label FROM " + tab);
db.setEdgeQuery(
"SELECT "
+ tab
+ ".source AS source, "
+ tab
+ ".target AS target "
+ tab
+ ".q0 AS weight FROM "
+ tab);
ImporterEdgeList edgeListImporter = new ImporterEdgeList();
Container container = null;
String url = SQLUtils.getUrl(db.getSQLDriver(), db.getHost(), db.getPort(), db.getDBName());
System.out.println(url);
javax.swing.JOptionPane.showMessageDialog(null, "Go ... Hive! \n> " + url);
try {
container = importController.importDatabase(db, edgeListImporter);
// container.setAllowAutoNode(false); //Don't create missing nodes
container.getLoader().setEdgeDefault(EdgeDirectionDefault.UNDIRECTED); // Force UNDIRECTED
// Append imported data to GraphAPI
importController.process(container, new DefaultProcessor(), workspace);
} catch (Exception ex) {
ex.printStackTrace();
} finally {
if (container != null) System.out.println(container.getReport().getText());
}
// See if graph is well imported
UndirectedGraph graph = graphModel.getUndirectedGraph();
System.out.println("Nodes: " + graph.getNodeCount());
System.out.println("Edges: " + graph.getEdgeCount());
// Layout - 100 Yifan Hu passes
// YifanHuLayout layout = new YifanHuLayout(null, new StepDisplacement(1f));
// layout.setGraphModel(graphModel);
// layout.resetPropertiesValues();
// layout.initAlgo();
// for (int i = 0; i < 100 && layout.canAlgo(); i++) {
// layout.goAlgo();
// }
// layout.endAlgo();
}
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);
}
private void executeDynamic(DynamicStatistics statistics, DynamicLongTask dynamicLongTask) {
GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
GraphModel graphModel = graphController.getGraphModel();
double window = statistics.getWindow();
double tick = statistics.getTick();
GraphView currentView = graphModel.getVisibleView();
Interval bounds = statistics.getBounds();
if (bounds == null) {
if (currentView.isMainView()) {
bounds = graphModel.getTimeBounds();
} else {
bounds = currentView.getTimeInterval();
}
statistics.setBounds(bounds);
}
if (dynamicLongTask != null) {
// Count
int c = (int) ((bounds.getHigh() - window - bounds.getLow()) / tick);
dynamicLongTask.start(c);
}
// Init
statistics.execute(graphModel);
// Loop
for (double low = bounds.getLow(); low <= bounds.getHigh() - window; low += tick) {
double high = low + window;
Graph graph = graphModel.getGraphVisible();
graph.writeLock();
GraphView view = graphModel.createView();
Subgraph g = graphModel.getGraph(view);
TimeIndex<Node> nodeIndex = graphModel.getNodeTimeIndex(currentView);
if (Double.isInfinite(nodeIndex.getMinTimestamp())
&& Double.isInfinite(nodeIndex.getMaxTimestamp())) {
for (Node node : graph.getNodes()) {
g.addNode(node);
}
} else {
for (Node node : nodeIndex.get(new Interval(low, high))) {
g.addNode(node);
}
}
TimeIndex<Edge> edgeIndex = graphModel.getEdgeTimeIndex(currentView);
if (Double.isInfinite(edgeIndex.getMinTimestamp())
&& Double.isInfinite(edgeIndex.getMaxTimestamp())) {
for (Edge edge : graph.getEdges()) {
if (g.contains(edge.getSource()) && g.contains(edge.getTarget())) {
g.addEdge(edge);
}
}
} else {
for (Edge edge : edgeIndex.get(new Interval(low, high))) {
if (g.contains(edge.getSource()) && g.contains(edge.getTarget())) {
g.addEdge(edge);
}
}
}
graph.writeUnlock();
statistics.loop(g.getView(), new Interval(low, high));
// Cancelled?
if (dynamicLongTask != null && dynamicLongTask.isCancelled()) {
return;
} else if (dynamicLongTask != null) {
dynamicLongTask.progress();
}
}
statistics.end();
model.addReport(statistics);
}
@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 PreviewUIControllerImpl() {
listeners = new ArrayList<PropertyChangeListener>();
ProjectController pc = Lookup.getDefault().lookup(ProjectController.class);
graphController = Lookup.getDefault().lookup(GraphController.class);
pc.addWorkspaceListener(
new WorkspaceListener() {
public void initialize(Workspace workspace) {
workspace.add(new PreviewUIModelImpl());
enableRefresh();
}
public void select(Workspace workspace) {
// Make sure AttributeModel is created before graph model:
Lookup.getDefault().lookup(AttributeController.class).getModel();
graphModel = graphController.getModel();
graphModel.addGraphListener(PreviewUIControllerImpl.this);
model = workspace.getLookup().lookup(PreviewUIModelImpl.class);
if (model == null) {
model = new PreviewUIModelImpl();
workspace.add(model);
}
fireEvent(SELECT, model);
}
public void unselect(Workspace workspace) {
if (graphModel != null) {
graphModel.removeGraphListener(PreviewUIControllerImpl.this);
graphModel = null;
}
fireEvent(UNSELECT, model);
}
public void close(Workspace workspace) {}
public void disable() {
if (graphModel != null) {
graphModel.removeGraphListener(PreviewUIControllerImpl.this);
graphModel = null;
}
fireEvent(SELECT, null);
model = null;
}
});
if (pc.getCurrentWorkspace() != null) {
model = pc.getCurrentWorkspace().getLookup().lookup(PreviewUIModelImpl.class);
if (model == null) {
model = new PreviewUIModelImpl();
pc.getCurrentWorkspace().add(model);
}
graphModel = graphController.getModel();
graphModel.addGraphListener(this);
}
previewController = Lookup.getDefault().lookup(PreviewController.class);
// Register editors
// Overriding default Preview API basic editors that don't support CustomEditor
PropertyEditorManager.registerEditor(EdgeColor.class, EdgeColorPropertyEditor.class);
PropertyEditorManager.registerEditor(
DependantOriginalColor.class, DependantOriginalColorPropertyEditor.class);
PropertyEditorManager.registerEditor(DependantColor.class, DependantColorPropertyEditor.class);
}
public Graph retrieveGraph(GraphModel graphModel, boolean isFilterGraph) {
Graph graph = graphModel.getGraph();
graph.clear();
Map<Integer, JsonObject> nMap;
Map<Integer, JsonObject> eMap;
if (!isFilterGraph) {
nMap = nodesMap;
eMap = edgesMap;
} else {
nMap = nodesMapFilter;
eMap = edgesMapFilter;
}
for (Entry<Integer, JsonObject> enSet : nMap.entrySet()) {
Map<String, Object> map = enSet.getValue().getMap();
Node node = graphModel.factory().newNode(enSet.getValue().getValue("id"));
for (Entry<String, Object> attSet : map.entrySet()) {
if (!attSet.getKey().equalsIgnoreCase("id")
&& !attSet.getKey().equalsIgnoreCase("x")
&& !attSet.getKey().equalsIgnoreCase("y")
&& !attSet.getKey().equalsIgnoreCase("cR")
&& !attSet.getKey().equalsIgnoreCase("size")
&& !attSet.getKey().equalsIgnoreCase("cG")
&& !attSet.getKey().equalsIgnoreCase("cB")) {
node.setAttribute(attSet.getKey(), attSet.getValue());
}
if (attSet.getKey().equalsIgnoreCase("x")) {
node.setX((float) attSet.getValue());
}
if (attSet.getKey().equalsIgnoreCase("y")) {
node.setY((float) attSet.getValue());
}
}
node.setSize((float) Double.parseDouble(map.get("size").toString()));
node.setColor(
new Color(
(float) Double.parseDouble(map.get("cR").toString()),
(float) Double.parseDouble(map.get("cG").toString()),
(float) Double.parseDouble(map.get("cB").toString())));
graph.addNode(node);
}
for (Entry<Integer, JsonObject> enSet : eMap.entrySet()) {
Map<String, Object> map = enSet.getValue().getMap();
Edge edge =
graphModel
.factory()
.newEdge(
map.get("id"),
graph.getNode(map.get("source")),
graph.getNode(map.get("target")),
1,
Double.parseDouble(map.get("weight").toString()),
true);
for (Entry<String, Object> attSet : map.entrySet()) {
if (!attSet.getKey().equalsIgnoreCase("id")
&& !attSet.getKey().equalsIgnoreCase("source")
&& !attSet.getKey().equalsIgnoreCase("target")
&& !attSet.getKey().equalsIgnoreCase("size")
&& !attSet.getKey().equalsIgnoreCase("cR")
&& !attSet.getKey().equalsIgnoreCase("cG")
&& !attSet.getKey().equalsIgnoreCase("cB")) {
edge.setAttribute(attSet.getKey(), attSet.getValue());
}
}
edge.setWeight(Double.parseDouble(map.get("size").toString()));
edge.setColor(
new Color(
(float) Double.parseDouble(map.get("cR").toString()),
(float) Double.parseDouble(map.get("cG").toString()),
(float) Double.parseDouble(map.get("cB").toString())));
graph.addEdge(edge);
}
return graph;
}
@Override
public int count(Object value) {
return graph.getEdgeCount(model.getEdgeType(value));
}
private void writeEdges(XMLStreamWriter xmlWriter, HierarchicalGraph graph) throws Exception {
if (cancel) {
return;
}
xmlWriter.writeStartElement(EDGES);
AttributeColumn dynamicCol =
dynamicCol = attributeModel.getEdgeTable().getColumn(DynamicModel.TIMEINTERVAL_COLUMN);
EdgeIterable edgeIterable =
exportHierarchy ? graph.getEdgesTree() : graph.getEdgesAndMetaEdges();
for (Edge edge : edgeIterable) {
xmlWriter.writeStartElement(EDGE);
if (edge.getEdgeData().getId() != null
&& !edge.getEdgeData().getId().equals(Integer.toString(edge.getId()))) {
xmlWriter.writeAttribute(EDGE_ID, edge.getEdgeData().getId());
}
xmlWriter.writeAttribute(EDGE_SOURCE, edge.getSource().getNodeData().getId());
xmlWriter.writeAttribute(EDGE_TARGET, edge.getTarget().getNodeData().getId());
if (edge.isDirected() && graphModel.isMixed()) {
xmlWriter.writeAttribute(EDGE_TYPE, "directed");
} else if (!edge.isDirected() && graphModel.isMixed()) {
xmlWriter.writeAttribute(EDGE_TYPE, "undirected");
}
String label = edge.getEdgeData().getLabel();
if (label != null && !label.isEmpty()) {
xmlWriter.writeAttribute(EDGE_LABEL, label);
}
float weight = edge.getWeight();
if (weight != 1f) {
xmlWriter.writeAttribute(EDGE_WEIGHT, "" + weight);
}
if (exportDynamic && dynamicCol != null && visibleInterval != null) {
TimeInterval timeInterval =
(TimeInterval) edge.getEdgeData().getAttributes().getValue(dynamicCol.getIndex());
if (timeInterval != null) {
writeTimeInterval(xmlWriter, timeInterval);
}
}
if (exportColors) {
writeEdgeColor(xmlWriter, edge);
}
if (exportAttributes && edge.getEdgeData().getAttributes() != null) {
AttributeRow attributeRow = (AttributeRow) edge.getEdgeData().getAttributes();
writeAttValues(xmlWriter, attributeRow, visibleInterval);
}
xmlWriter.writeEndElement();
Progress.progress(progress);
if (cancel) {
break;
}
}
xmlWriter.writeEndElement();
}
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;
}
public void process() {
// Workspace
ProjectController pc = Lookup.getDefault().lookup(ProjectController.class);
if (workspace == null) {
workspace = pc.newWorkspace(pc.getCurrentProject());
pc.openWorkspace(workspace);
}
if (container.getSource() != null) {
pc.setSource(workspace, container.getSource());
}
// Architecture
GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getModel(workspace);
HierarchicalGraph graph = null;
switch (container.getEdgeDefault()) {
case DIRECTED:
graph = graphModel.getHierarchicalDirectedGraph();
break;
case UNDIRECTED:
graph = graphModel.getHierarchicalUndirectedGraph();
break;
case MIXED:
graph = graphModel.getHierarchicalMixedGraph();
break;
default:
graph = graphModel.getHierarchicalMixedGraph();
break;
}
GraphFactory factory = graphModel.factory();
// Attributes - Creates columns for properties
attributeModel = Lookup.getDefault().lookup(AttributeController.class).getModel(workspace);
attributeModel.mergeModel(container.getAttributeModel());
// Dynamic
if (container.getTimeFormat() != null) {
DynamicController dynamicController = Lookup.getDefault().lookup(DynamicController.class);
if (dynamicController != null) {
dynamicController.setTimeFormat(container.getTimeFormat());
}
}
int nodeCount = 0;
// Create all nodes
for (NodeDraftGetter draftNode : container.getNodes()) {
Node n = factory.newNode(draftNode.isAutoId() ? null : draftNode.getId());
flushToNode(draftNode, n);
draftNode.setNode(n);
nodeCount++;
}
// Push nodes in data structure
for (NodeDraftGetter draftNode : container.getNodes()) {
Node n = draftNode.getNode();
NodeDraftGetter[] parents = draftNode.getParents();
if (parents != null) {
for (int i = 0; i < parents.length; i++) {
Node parent = parents[i].getNode();
graph.addNode(n, parent);
}
} else {
graph.addNode(n);
}
}
// Create all edges and push to data structure
int edgeCount = 0;
for (EdgeDraftGetter edge : container.getEdges()) {
Node source = edge.getSource().getNode();
Node target = edge.getTarget().getNode();
Edge e = null;
switch (container.getEdgeDefault()) {
case DIRECTED:
e =
factory.newEdge(
edge.isAutoId() ? null : edge.getId(), source, target, edge.getWeight(), true);
break;
case UNDIRECTED:
e =
factory.newEdge(
edge.isAutoId() ? null : edge.getId(), source, target, edge.getWeight(), false);
break;
case MIXED:
e =
factory.newEdge(
edge.isAutoId() ? null : edge.getId(),
source,
target,
edge.getWeight(),
edge.getType().equals(EdgeType.UNDIRECTED) ? false : true);
break;
}
flushToEdge(edge, e);
edgeCount++;
graph.addEdge(e);
}
workspace = null;
}
@Override
public int size() {
int size = model.getEdgeTypeCount();
return graph.getEdgeCount(0) == 0 ? size - 1 : size;
}
private void doPoetGraph(String path, String poet) {
System.out.println(poet);
ProjectController pc = Lookup.getDefault().lookup(ProjectController.class);
pc.newProject();
Workspace workspace = pc.getCurrentWorkspace();
GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getModel();
UndirectedGraph directedGraph = graphModel.getUndirectedGraph();
ExportController ec = Lookup.getDefault().lookup(ExportController.class);
ArrayList<String> queue = new ArrayList<String>();
ArrayList<Integer> depthqueue = new ArrayList<Integer>();
queue.add(poet);
depthqueue.add(0);
int depth = 0;
int nodecount = 0;
while (queue.size() != 0 && depth < 3 && nodecount < 20) {
String name = queue.remove(0);
depth = depthqueue.remove(0);
Node n = directedGraph.getNode(name);
if (n == null) {
n = graphModel.factory().newNode(name);
n.getNodeData().setLabel(name);
directedGraph.addNode(n);
nodecount++;
}
Iterator<String> it = edges.get(poet).keySet().iterator();
while (it.hasNext()) {
String to = it.next();
Node slave = directedGraph.getNode(to);
if (slave == null) {
slave = graphModel.factory().newNode(to);
slave.getNodeData().setLabel(to);
directedGraph.addNode(slave);
}
Edge e = graphModel.factory().newEdge(n, slave, edges.get(poet).get(to) * 15, false);
directedGraph.addEdge(e);
queue.add(to);
depthqueue.add(depth + 1);
}
}
// Preview
PreviewModel previewModel = Lookup.getDefault().lookup(PreviewController.class).getModel();
previewModel.getProperties().putValue(PreviewProperty.SHOW_NODE_LABELS, Boolean.TRUE);
previewModel.getProperties().putValue(PreviewProperty.EDGE_COLOR, new EdgeColor(Color.BLUE));
previewModel.getProperties().putValue(PreviewProperty.EDGE_THICKNESS, new Float(0.005f));
previewModel
.getProperties()
.putValue(PreviewProperty.NODE_LABEL_COLOR, new DependantOriginalColor(Color.RED));
previewModel
.getProperties()
.putValue(
PreviewProperty.NODE_LABEL_FONT,
previewModel
.getProperties()
.getFontValue(PreviewProperty.NODE_LABEL_FONT)
.deriveFont(12));
YifanHuLayout layout = new YifanHuLayout(null, new StepDisplacement(1f));
layout.setGraphModel(graphModel);
layout.resetPropertiesValues();
layout.setOptimalDistance(120f);
layout.initAlgo();
for (int i = 0; i < 100 && layout.canAlgo(); i++) {
layout.goAlgo();
}
try {
ec.exportFile(new File(path + poet + ".svg"));
} catch (IOException ex) {
ex.printStackTrace();
return;
}
}
