/**
* Constructs a new JGraph model adapter for the specified JGraphT graph.
*
* @param jGraphTGraph the JGraphT graph for which JGraph model adapter to be created. <code>null
* </code> is NOT permitted.
* @param defaultVertexAttributes a default map of JGraph attributes to format vertices. <code>
* null</code> is NOT permitted.
* @param defaultEdgeAttributes a default map of JGraph attributes to format edges. <code>null
* </code> is NOT permitted.
* @param cellFactory a {@link CellFactory} to be used to create the JGraph cells. <code>null
* </code> is NOT permitted.
* @throws IllegalArgumentException
*/
public JGraphModelAdapter(
Graph<V, E> jGraphTGraph,
AttributeMap defaultVertexAttributes,
AttributeMap defaultEdgeAttributes,
CellFactory<V, E> cellFactory) {
super();
if ((jGraphTGraph == null)
|| (defaultVertexAttributes == null)
|| (defaultEdgeAttributes == null)
|| (cellFactory == null)) {
throw new IllegalArgumentException("null is NOT permitted");
}
jtGraph = new ShieldedGraph(jGraphTGraph);
setDefaultVertexAttributes(defaultVertexAttributes);
setDefaultEdgeAttributes(defaultEdgeAttributes);
this.cellFactory = cellFactory;
if (jGraphTGraph instanceof ListenableGraph<?, ?>) {
ListenableGraph<V, E> g = (ListenableGraph<V, E>) jGraphTGraph;
g.addGraphListener(new JGraphTListener());
}
for (Iterator<V> i = jGraphTGraph.vertexSet().iterator(); i.hasNext(); ) {
handleJGraphTAddedVertex(i.next());
}
for (Iterator<E> i = jGraphTGraph.edgeSet().iterator(); i.hasNext(); ) {
handleJGraphTAddedEdge(i.next());
}
this.addGraphModelListener(new JGraphListener());
}
E addEdge(V jtSource, V jtTarget) {
E jtEdge = graph.getEdgeFactory().createEdge(jtSource, jtTarget);
jtElementsBeingAdded.add(jtEdge);
boolean added = graph.addEdge(jtSource, jtTarget, jtEdge);
jtElementsBeingAdded.remove(jtEdge);
return added ? jtEdge : null;
}
private void calcStats() {
// Graph resultGraph = getAlgorithmRunner().getResultGraph();
IGesRunner runner = (IGesRunner) getAlgorithmRunner();
if (runner.getTopGraphs().isEmpty()) {
throw new IllegalArgumentException(
"No patterns were recorded. Please adjust the number of " + "patterns to store.");
}
Graph resultGraph = runner.getTopGraphs().get(runner.getIndex()).getGraph();
if (getAlgorithmRunner().getDataModel() instanceof DataSet) {
// resultGraph may be the output of a PC search.
// Such graphs sometimes contain doubly directed edges.
// /We converte such edges to directed edges here.
// For the time being an orientation is arbitrarily selected.
Set<Edge> allEdges = resultGraph.getEdges();
for (Edge edge : allEdges) {
if (edge.getEndpoint1() == Endpoint.ARROW && edge.getEndpoint2() == Endpoint.ARROW) {
// Option 1 orient it from node1 to node2
resultGraph.setEndpoint(edge.getNode1(), edge.getNode2(), Endpoint.ARROW);
// Option 2 remove such edges:
resultGraph.removeEdge(edge);
}
}
Pattern pattern = new Pattern(resultGraph);
PatternToDag ptd = new PatternToDag(pattern);
Graph dag = ptd.patternToDagMeekRules();
DataSet dataSet = (DataSet) getAlgorithmRunner().getDataModel();
String report;
if (dataSet.isContinuous()) {
report = reportIfContinuous(dag, dataSet);
} else if (dataSet.isDiscrete()) {
report = reportIfDiscrete(dag, dataSet);
} else {
throw new IllegalArgumentException("");
}
JScrollPane dagWorkbenchScroll = dagWorkbenchScroll(dag);
modelStatsText.setLineWrap(true);
modelStatsText.setWrapStyleWord(true);
modelStatsText.setText(report);
removeStatsTabs();
tabbedPane.addTab("DAG in pattern", dagWorkbenchScroll);
tabbedPane.addTab("DAG Model Statistics", modelStatsText);
}
}
private void uncorrelationExogenousVariables() {
Graph graph = getWorkbench().getGraph();
Set<Edge> edges = graph.getEdges();
for (Edge edge : edges) {
if (Edges.isBidirectedEdge(edge)) {
try {
graph.removeEdge(edge);
} catch (Exception e) {
// Ignore.
}
}
}
}
protected void fileOpen() {
JFileChooser chooser = null;
if (currentFile == null) {
chooser = new JFileChooser(startDirectory);
} else {
chooser = new JFileChooser(currentFile);
}
int returnVal = chooser.showOpenDialog(gw);
if (returnVal == JFileChooser.APPROVE_OPTION) {
graph.clear();
currentFile = chooser.getSelectedFile();
graph.loadAll(currentFile);
gp.update(gp.getGraphics());
}
}
public void init() {
// setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
for (Iterator<Arc> itr = graph.findArcs().iterator(); itr.hasNext(); ) {
arcListModel.addElement(itr.next());
}
panel = new DrawViewPanel();
this.getContentPane().add(panel);
}
protected void fileNew() {
if (currentFile != null) {
if (!currentFile.isDirectory()) {
currentFile = currentFile.getParentFile();
}
}
graph.clear();
gp.update(gp.getGraphics());
}
public static void main(String[] args) {
if (args.length != 1) {
System.out.println("Usage: java Msp <filename>");
System.exit(2);
}
Graph g = new Graph();
loadFile(g, args[0]);
// Calculate locations of nodes
g.prepareNodes();
// Perform kruskal algorithm
g.kruskal();
// Show results in JFrame
MainWindow f = new MainWindow(g);
f.setSize(800, 600);
f.setVisible(true);
f.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
}
protected void fileSave() {
if (currentFile == null) {
fileSaveAs();
} else {
if (currentFile.isDirectory()) {
fileSaveAs();
} else {
graph.saveAll(currentFile);
gp.update(gp.getGraphics());
}
}
}
private void correlateExogenousVariables() {
Graph graph = getWorkbench().getGraph();
if (graph instanceof Dag) {
JOptionPane.showMessageDialog(
JOptionUtils.centeringComp(), "Cannot add bidirected edges to DAG's.");
return;
}
List<Node> nodes = graph.getNodes();
List<Node> exoNodes = new LinkedList<Node>();
for (int i = 0; i < nodes.size(); i++) {
Node node = nodes.get(i);
if (graph.isExogenous(node)) {
exoNodes.add(node);
}
}
for (int i = 0; i < exoNodes.size(); i++) {
loop:
for (int j = i + 1; j < exoNodes.size(); j++) {
Node node1 = exoNodes.get(i);
Node node2 = exoNodes.get(j);
List<Edge> edges = graph.getEdges(node1, node2);
for (int k = 0; k < edges.size(); k++) {
Edge edge = edges.get(k);
if (Edges.isBidirectedEdge(edge)) {
continue loop;
}
}
graph.addBidirectedEdge(node1, node2);
}
}
}
public static void loadFile(Graph g, String fileName) {
System.out.println("Reading date from " + fileName);
try {
BufferedReader input = new BufferedReader(new FileReader(fileName));
try {
String line = null;
int index = 0;
System.out.println("Graph...");
while ((line = input.readLine()) != null) {
if (line.trim().equals("#EDGES")) break;
String[] arr = line.split(" ");
System.out.println("Graph Line " + index + ": " + line);
Vertex n = null;
Vertex node = null;
for (int j = 0; j < arr.length; j++) {
n = new Vertex(arr[j]);
node = g.findNode(n);
if (node == null) g.addNode(n, index);
}
index++;
}
System.out.println("Edges...");
while ((line = input.readLine()) != null) {
String[] arr = line.split(" ");
System.out.println("[" + arr[0] + " - " + arr[1] + "] - Cost: " + arr[2]);
Vertex n = new Vertex(arr[0]);
Vertex left = g.findNode(n);
n = new Vertex(arr[1]);
Vertex right = g.findNode(n);
g.addEdge(left, right, Integer.parseInt(arr[2]));
}
} finally {
input.close();
}
} catch (Exception e) {
}
}
protected void fileSaveSimple() {
JFileChooser chooser = null;
if (currentFile == null) {
chooser = new JFileChooser(startDirectory);
} else {
chooser = new JFileChooser(currentFile);
if (!currentFile.isDirectory()) {
chooser.setSelectedFile(currentFile);
}
}
int returnVal = chooser.showSaveDialog(gw);
if (returnVal == JFileChooser.APPROVE_OPTION) {
currentFile = chooser.getSelectedFile();
graph.saveSimple(currentFile);
}
}
public GraphViewer(Graph g, int options) {
graph = g;
graph.addListener(this);
nodeListModel = new DefaultListModel<Node>();
setViewOptions(options);
layouter = new GraphLayouter(graph, new Point2D.Double());
layouter.makeLayout();
if (hasOption(VIEW_3D | VIEW_WF)) {
layouterWF3D = new GraphLayouter3D(graph);
layouterWF3D.makeLayout();
}
// addNodes();
// layouter.makeLayout();
// layouterWF3D.makeLayout();
init();
// remove adding nodes, read them from file instead
// addNodes();
}
V getEdgeSource(E e) {
return graph.getEdgeSource(e);
}
void removeVertex(V jtVertex) {
jtElementsBeingRemoved.add(jtVertex);
graph.removeVertex(jtVertex);
jtElementsBeingRemoved.remove(jtVertex);
}
void removeEdge(E jtEdge) {
jtElementsBeingRemoved.add(jtEdge);
graph.removeEdge(jtEdge);
jtElementsBeingRemoved.remove(jtEdge);
}
boolean removeAllEdges(Collection<E> edges) {
return graph.removeAllEdges(edges);
}
Set<E> edgesOf(V vertex) {
return graph.edgesOf(vertex);
}
void addVertex(V jtVertex) {
jtElementsBeingAdded.add(jtVertex);
graph.addVertex(jtVertex);
jtElementsBeingAdded.remove(jtVertex);
}
V getEdgeTarget(E e) {
return graph.getEdgeTarget(e);
}
protected void editSelectAll() {
gp.getSelection().addNodes(graph.getNodes());
gp.getSelection().addEdges(graph.getEdges());
gp.repaint();
}
