Example usage for org.apache.commons.collections15 Transformer Transformer

List of usage examples for org.apache.commons.collections15 Transformer Transformer

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In this page you can find the example usage for org.apache.commons.collections15 Transformer Transformer.

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Usage

From source file:de.bitocean.dspm.examples.Vertex.java

public static void main(String[] args) throws GraphIOException, FileNotFoundException, IOException {

    Reader reader = new FileReader(GRAPHML_ACTIVITY_DEPENDENCY_FILE);

    BufferedReader br = new BufferedReader(reader);
    while (br.ready()) {
        System.out.println(br.readLine());
    }/*from ww  w .  ja  va 2 s. c om*/

    Transformer<NodeMetadata, Vertex> vtrans = new Transformer<NodeMetadata, Vertex>() {
        public Vertex transform(NodeMetadata nmd) {
            Vertex v = new Vertex();
            v.id = nmd.getId();
            v.name = nmd.getProperty("name");
            v.expression = nmd.getProperty("expression");
            return v;
        }
    };

    Transformer<EdgeMetadata, Edge> etrans = new Transformer<EdgeMetadata, Edge>() {
        public Edge transform(EdgeMetadata emd) {
            System.out.println(emd.toString());
            Edge e = new Edge();
            try {
                e.source = emd.getSource();
            } catch (Exception ex) {

            }
            e.target = emd.getTarget();
            e.weight = Double.parseDouble(emd.getProperty("weight"));
            return e;
        }
    };

    Transformer<HyperEdgeMetadata, Edge> hetrans = new Transformer<HyperEdgeMetadata, Edge>() {
        public Edge transform(HyperEdgeMetadata emd) {
            Edge e = new Edge();
            try {
                e.source = emd.getProperty("source");
            } catch (Exception ex) {

            }
            e.target = emd.getProperty("target");
            e.weight = Double.parseDouble(emd.getProperty("weight"));
            return e;
        }
    };
    Transformer<GraphMetadata, DirectedSparseGraph<Vertex, Edge>> gtrans = new Transformer<GraphMetadata, DirectedSparseGraph<Vertex, Edge>>() {
        public DirectedSparseGraph<Vertex, Edge> transform(GraphMetadata gmd) {
            return new DirectedSparseGraph<Vertex, Edge>();
        }
    };

    GraphMLReader2<DirectedSparseGraph<Vertex, Edge>, Vertex, Edge> gmlr =
            //new GraphMLReader2<UndirectedSparseGraph<Vertex,Edge>, Vertex, Edge>(fileReader, graphTransformer, vertexTransformer, edgeTransformer, hyperEdgeTransformer)
            new GraphMLReader2<DirectedSparseGraph<Vertex, Edge>, Vertex, Edge>(reader, gtrans, vtrans, etrans,
                    hetrans);

    DirectedSparseGraph<Vertex, Edge> g = gmlr.readGraph();

    System.out.println("Number of vetex: " + g.getVertexCount());
    System.out.println("Number of edges: " + g.getEdgeCount());

    System.out.println("==========================");
    System.out.println("Vertices");
    System.out.println("==========================");
    for (Vertex v : g.getVertices()) {
        System.out.println(v);
    }

    System.out.println("==========================");
    System.out.println("Edges");
    System.out.println("==========================");
    for (Edge e : g.getEdges()) {
        System.out.println(e);
    }

}

From source file:ega.projekt.graphDraw.DrawGraph.java

/**
 * @param args the command line arguments
 *///from w  w  w  .java 2 s .co  m
public static void main(String[] args) {
    ega.projekt.graph.Graph dataGraph = new ega.projekt.graph.Graph(5, 100, 295, 295);
    if (dataGraph.getEdges().isEmpty())
        System.out.println("Error initializing graph");
    DrawGraph graphView = new DrawGraph(dataGraph); // This builds the graph
    // Layout<V, E>, VisualizationComponent<V,E>
    Layout<Node, Edge> layout = new StaticLayout(graphView.drawGraph);
    for (Node n : graphView.drawGraph.getVertices()) {
        layout.setLocation(n, new java.awt.geom.Point2D.Double(n.getX(), n.getY()));
    }
    layout.setSize(new Dimension(300, 300));
    BasicVisualizationServer<Node, Edge> vv = new BasicVisualizationServer<>(layout);
    vv.setPreferredSize(new Dimension(350, 350));
    // Setup up a new vertex to paint transformer...
    Transformer<Node, Paint> vertexPaint = new Transformer<Node, Paint>() {
        public Paint transform(Node i) {
            return Color.GREEN;
        }
    };

    // Set up a new stroke Transformer for the edges
    //float dash[] = {10.0f};
    final Stroke edgeStroke = new BasicStroke(1.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER);
    Transformer<Edge, Stroke> edgeStrokeTransformer = new Transformer<Edge, Stroke>() {
        public Stroke transform(Edge e) {
            if (e.isMarked()) {
                final Stroke modStroke = new BasicStroke(5.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER);
                return modStroke;
            }
            return edgeStroke;
        }
    };
    Transformer<Edge, Paint> edgePaint = new Transformer<Edge, Paint>() {
        public Paint transform(Edge e) {
            if (e.isMarked()) {
                return Color.RED;
            }
            return Color.BLACK;
        }
    };
    vv.getRenderContext().setVertexFillPaintTransformer(vertexPaint);
    vv.getRenderContext().setEdgeStrokeTransformer(edgeStrokeTransformer);
    vv.getRenderContext().setEdgeShapeTransformer(new EdgeShape.QuadCurve<Node, Edge>());
    vv.getRenderContext().setEdgeLabelTransformer(new Transformer<Edge, String>() {
        public String transform(Edge e) {
            return (e.getFlowString() + "/" + Integer.toString(e.getCapacity()));
        }
    });
    vv.getRenderContext().setVertexLabelTransformer(new Transformer<Node, String>() {
        public String transform(Node n) {
            return (Integer.toString(n.getID()));
        }
    });
    vv.getRenderer().getVertexLabelRenderer().setPosition(Renderer.VertexLabel.Position.CNTR);

    JFrame frame = new JFrame("Simple Graph View 2");
    frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
    frame.getContentPane().add(vv);
    frame.pack();
    frame.setVisible(true);
}

From source file:it.iit.genomics.cru.igb.bundles.mi.view.TestJung.java

public static void main(String[] args) {

    Graph<MoleculeEntry, EdgeInteraction> graph = new SparseMultigraph<>();

    MoleculeEntry v1 = new MoleculeEntry("A");
    v1.addGeneName("A");
    v1.setTaxid("9606");

    MoleculeEntry v2 = new MoleculeEntry("B");
    v2.addGeneName("b");
    v2.setTaxid("9606");

    MoleculeEntry v3 = new MoleculeEntry("DNA");
    v3.addGeneName("DNA");
    v3.setTaxid(MoleculeEntry.TAXID_DNA);

    EdgeInteraction edge = new EdgeInteraction(true, true, true, "e1");
    graph.addEdge(edge, v1, v2, EdgeType.UNDIRECTED);

    EdgeInteraction edge2 = new EdgeInteraction(false, false, true, "e2");
    graph.addEdge(edge2, v1, v3, EdgeType.UNDIRECTED);

    EdgeInteraction edge3 = new EdgeInteraction(false, false, false, "e3");
    graph.addEdge(edge3, v2, v3, EdgeType.UNDIRECTED);

    // The Layout<V, E> is parameterized by the vertex and edge types
    Layout<MoleculeEntry, EdgeInteraction> layout = new ISOMLayout(graph);

    layout.setSize(new Dimension(500, 600)); // sets the initial size of the space
    // The BasicVisualizationServer<V,E> is parameterized by the edge types
    VisualizationViewer<MoleculeEntry, EdgeInteraction> vv = new VisualizationViewer<>(layout);

    vv.setPreferredSize(new Dimension(550, 650)); //Sets the viewing area size
    vv.setBackground(Color.WHITE);
    Transformer<MoleculeEntry, Paint> vertexPaint = new Transformer<MoleculeEntry, Paint>() {
        @Override/*from  w  ww . j a v a 2  s  .c  o  m*/
        public Paint transform(MoleculeEntry molecule) {
            switch (molecule.getTaxid()) {
            case MoleculeEntry.TAXID_DNA:
                ;
            case MoleculeEntry.TAXID_RNA:
                return Color.GREEN;
            case MoleculeEntry.TAXID_LIGAND:
                return Color.MAGENTA;
            default:
                return Color.GREEN;
            }
        }
    };

    Transformer<EdgeInteraction, Paint> edgePaint = new Transformer<EdgeInteraction, Paint>() {
        @Override
        public Paint transform(EdgeInteraction interaction) {
            return interaction.hasStructure ? Color.BLACK : Color.GRAY;
        }
    };

    final Stroke edgeStroke01 = new BasicStroke();

    final float nodeSize = 20;

    final Stroke edgeStrokeBothContacts = new ShapeStroke(new Shape[] { new Ellipse2D.Float(0, 0, 10, 10) },
            nodeSize, true, true);

    final Stroke edgeStrokeStartContacts = new ShapeStroke(new Shape[] { new Ellipse2D.Float(0, 0, 10, 10) },
            nodeSize, true, false);

    final Stroke edgeStrokeEndContacts = new ShapeStroke(new Shape[] { new Ellipse2D.Float(0, 0, 10, 10) },
            nodeSize, false, true);

    final Stroke edgeStrokeBothContact = new CompoundStroke(edgeStroke01, edgeStrokeBothContacts,
            CompoundStroke.ADD);

    final Stroke edgeStrokeStartContact = new CompoundStroke(edgeStroke01, edgeStrokeStartContacts,
            CompoundStroke.ADD);

    final Stroke edgeStrokeEndContact = new CompoundStroke(edgeStroke01, edgeStrokeEndContacts,
            CompoundStroke.ADD);

    Transformer<EdgeInteraction, Stroke> edgeStrokeTransformer = new Transformer<EdgeInteraction, Stroke>() {
        @Override
        public Stroke transform(EdgeInteraction s) {
            if (s.hasContactsA && s.hasContactsB) {
                return edgeStrokeBothContact;
            }

            if (s.hasContactsA) {
                return edgeStrokeStartContact;
            }

            if (s.hasContactsB) {
                return edgeStrokeEndContact;
            }

            return edgeStroke01;
        }
    };

    Transformer<MoleculeEntry, String> moleculeLabeller = new Transformer<MoleculeEntry, String>() {
        @Override
        public String transform(MoleculeEntry s) {
            return s.getGeneName();
        }
    };

    vv.getRenderContext().setVertexFillPaintTransformer(vertexPaint);
    vv.getRenderContext().setEdgeDrawPaintTransformer(edgePaint);
    vv.getRenderContext().setEdgeStrokeTransformer(edgeStrokeTransformer);

    vv.getRenderContext().setVertexLabelTransformer(moleculeLabeller);

    vv.getRenderer().getVertexLabelRenderer().setPosition(Renderer.VertexLabel.Position.CNTR);

    DefaultModalGraphMouse graphMouse = new DefaultModalGraphMouse();

    graphMouse.setMode(ModalGraphMouse.Mode.PICKING);

    vv.setGraphMouse(graphMouse);

    JFrame frame = new JFrame("Network " + "A");

    frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);

    frame.getContentPane().add(vv);
    frame.pack();

    frame.setVisible(true);
}

From source file:com.googlecode.sarasvati.visual.jung.JungVisualizer.java

@SuppressWarnings("serial")
public static void main(String[] args) throws Exception {
    TestSetup.init();/*from www  .  ja  v a 2 s . c om*/

    Session session = TestSetup.openSession();
    HibEngine engine = new HibEngine(session);

    JFrame frame = new JFrame("Workflow Visualizer");
    frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
    frame.setMinimumSize(new Dimension(800, 600));

    JSplitPane splitPane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT);
    frame.getContentPane().add(splitPane);

    DefaultListModel listModel = new DefaultListModel();
    for (Graph g : engine.getRepository().getGraphs()) {
        listModel.addElement(g);
    }

    ListCellRenderer cellRenderer = new DefaultListCellRenderer() {
        @Override
        public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected,
                boolean cellHasFocus) {
            super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);

            Graph g = (Graph) value;

            setText(g.getName() + "." + g.getVersion() + "  ");
            return this;
        }
    };

    final JList graphList = new JList(listModel);
    graphList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
    graphList.setCellRenderer(cellRenderer);

    JScrollPane listScrollPane = new JScrollPane(graphList);
    listScrollPane.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_AS_NEEDED);
    listScrollPane.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS);

    splitPane.add(listScrollPane);

    //TreeLayout<NodeRef, Arc> layout = new TreeLayout<NodeRef, Arc>();

    DirectedSparseMultigraph<Node, Arc> graph = new DirectedSparseMultigraph<Node, Arc>();

    //final SpringLayout2<HibNodeRef, HibArc> layout = new SpringLayout2<HibNodeRef, HibArc>(graph);
    //final KKLayout<HibNodeRef, HibArc> layout = new KKLayout<HibNodeRef, HibArc>(graph);
    final TreeLayout layout = new TreeLayout(graph);
    final BasicVisualizationServer<Node, Arc> vs = new BasicVisualizationServer<Node, Arc>(layout);
    //vs.getRenderContext().setVertexLabelTransformer( new NodeLabeller() );
    //vs.getRenderContext().setEdgeLabelTransformer( new ArcLabeller() );
    vs.getRenderContext().setVertexShapeTransformer(new NodeShapeTransformer());
    vs.getRenderContext().setVertexFillPaintTransformer(new NodeColorTransformer());
    vs.getRenderContext().setLabelOffset(5);
    vs.getRenderContext().setVertexIconTransformer(new Transformer<Node, Icon>() {
        @Override
        public Icon transform(Node node) {
            return "task".equals(node.getType()) ? new TaskIcon(node) : null;
        }
    });

    Transformer<Arc, Paint> edgeColorTrans = new Transformer<Arc, Paint>() {
        private Color darkRed = new Color(128, 0, 0);

        @Override
        public Paint transform(Arc arc) {
            return "reject".equals(arc.getName()) ? darkRed : Color.black;
        }
    };

    vs.getRenderContext().setEdgeDrawPaintTransformer(edgeColorTrans);
    vs.getRenderContext().setArrowDrawPaintTransformer(edgeColorTrans);

    final JScrollPane scrollPane = new JScrollPane(vs);
    scrollPane.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_AS_NEEDED);
    scrollPane.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED);

    splitPane.add(scrollPane);
    scrollPane.setBackground(Color.white);

    graphList.addListSelectionListener(new ListSelectionListener() {
        @Override
        public void valueChanged(ListSelectionEvent e) {
            if (e.getValueIsAdjusting()) {
                return;
            }

            final Graph g = (Graph) graphList.getSelectedValue();

            if ((g == null && currentGraph == null) || (g != null && g.equals(currentGraph))) {
                return;
            }

            currentGraph = g;

            DirectedSparseMultigraph<Node, Arc> jungGraph = new DirectedSparseMultigraph<Node, Arc>();

            for (Node ref : currentGraph.getNodes()) {
                jungGraph.addVertex(ref);
            }

            for (Arc arc : currentGraph.getArcs()) {
                jungGraph.addEdge(arc, arc.getStartNode(), arc.getEndNode());
            }

            GraphTree graphTree = new GraphTree(g);
            layout.setGraph(jungGraph);
            layout.setInitializer(new NodeLocationTransformer(graphTree));
            scrollPane.repaint();
        }
    });

    frame.setVisible(true);
}

From source file:com.diversityarrays.kdxplore.trials.TrialSelectionDialog.java

static public void main(String[] args) {

    Transformer<BackgroundRunner, TrialSearchOptionsPanel> factory = new Transformer<BackgroundRunner, TrialSearchOptionsPanel>() {
        @Override//from   w  w  w  .j  a v  a2s  .c  o m
        public TrialSearchOptionsPanel transform(BackgroundRunner backgroundRunner) {
            return TrialSelectionSearchOptionsPanel.create(backgroundRunner);
        }
    };

    boolean test = false;
    if (test) {
        @SuppressWarnings("unchecked")
        TrialSelectionDialog tsd = new TrialSelectionDialog(null, "Test Tree", null, Collections.EMPTY_LIST, //$NON-NLS-1$
                factory);
        //         tsd.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
        tsd.setVisible(true);
    } else {

        File propertiesFile = new File(System.getProperty("user.home"), //$NON-NLS-1$
                "LoginDialog.properties"); //$NON-NLS-1$
        //.getBundle("LoginDialog"); //, Locale.getDefault());

        ResourceBundle bundle = null;

        if (propertiesFile.exists()) {
            try {
                bundle = new PropertyResourceBundle(new FileReader(propertiesFile));
            } catch (FileNotFoundException e) {
                e.printStackTrace();
                System.exit(1);
            } catch (IOException e) {
                e.printStackTrace();
                System.exit(1);
            }
        }

        Preferences loginPreferences = KdxplorePreferences.getInstance().getPreferences();
        //         Preferences loginPreferences = Preferences.userNodeForPackage(KdxConstants.class);

        LoginDialog ld = new LoginDialog(null, "Login Please", loginPreferences, bundle); //$NON-NLS-1$
        ld.setVisible(true);
        DALClient client = ld.getDALClient();
        if (client != null) {
            @SuppressWarnings("unchecked")
            TrialSelectionDialog tsd = new TrialSelectionDialog(null, "Test Tree", client, //$NON-NLS-1$
                    Collections.EMPTY_LIST, factory);
            //            tsd.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
            tsd.setVisible(true);
            if (tsd.trialRecords == null) {
                System.out.println("Cancelled !"); //$NON-NLS-1$
            } else {
                System.out.println(tsd.trialRecords.length + " chosen: "); //$NON-NLS-1$
                for (TrialPlus tr : tsd.trialRecords) {
                    System.out.println("\t" + tr.getTrialId() + ": " + tr.getTrialName()); //$NON-NLS-1$ //$NON-NLS-2$
                }
                System.out.println("- - -"); //$NON-NLS-1$
            }
        }
    }
    System.exit(0);
}

From source file:SequentialPersonalizedPageRank.java

@SuppressWarnings({ "static-access" })
public static void main(String[] args) throws IOException {
    Options options = new Options();

    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("input path").create(INPUT));
    options.addOption(/*w  w  w  . j av  a 2s .  c  o m*/
            OptionBuilder.withArgName("val").hasArg().withDescription("random jump factor").create(JUMP));
    options.addOption(OptionBuilder.withArgName("node").hasArg()
            .withDescription("source node (i.e., destination of the random jump)").create(SOURCE));

    CommandLine cmdline = null;
    CommandLineParser parser = new GnuParser();

    try {
        cmdline = parser.parse(options, args);
    } catch (ParseException exp) {
        System.err.println("Error parsing command line: " + exp.getMessage());
        System.exit(-1);
    }

    if (!cmdline.hasOption(INPUT) || !cmdline.hasOption(SOURCE)) {
        System.out.println("args: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.setWidth(120);
        formatter.printHelp(SequentialPersonalizedPageRank.class.getName(), options);
        ToolRunner.printGenericCommandUsage(System.out);
        System.exit(-1);
    }

    String infile = cmdline.getOptionValue(INPUT);
    final String source = cmdline.getOptionValue(SOURCE);
    float alpha = cmdline.hasOption(JUMP) ? Float.parseFloat(cmdline.getOptionValue(JUMP)) : 0.15f;

    int edgeCnt = 0;
    DirectedSparseGraph<String, Integer> graph = new DirectedSparseGraph<String, Integer>();

    BufferedReader data = new BufferedReader(new InputStreamReader(new FileInputStream(infile)));

    String line;
    while ((line = data.readLine()) != null) {
        line.trim();
        String[] arr = line.split("\\t");

        for (int i = 1; i < arr.length; i++) {
            graph.addEdge(new Integer(edgeCnt++), arr[0], arr[i]);
        }
    }

    data.close();

    if (!graph.containsVertex(source)) {
        System.err.println("Error: source node not found in the graph!");
        System.exit(-1);
    }

    WeakComponentClusterer<String, Integer> clusterer = new WeakComponentClusterer<String, Integer>();

    Set<Set<String>> components = clusterer.transform(graph);
    int numComponents = components.size();
    System.out.println("Number of components: " + numComponents);
    System.out.println("Number of edges: " + graph.getEdgeCount());
    System.out.println("Number of nodes: " + graph.getVertexCount());
    System.out.println("Random jump factor: " + alpha);

    // Compute personalized PageRank.
    PageRankWithPriors<String, Integer> ranker = new PageRankWithPriors<String, Integer>(graph,
            new Transformer<String, Double>() {
                @Override
                public Double transform(String vertex) {
                    return vertex.equals(source) ? 1.0 : 0;
                }
            }, alpha);

    ranker.evaluate();

    // Use priority queue to sort vertices by PageRank values.
    PriorityQueue<Ranking<String>> q = new PriorityQueue<Ranking<String>>();
    int i = 0;
    for (String pmid : graph.getVertices()) {
        q.add(new Ranking<String>(i++, ranker.getVertexScore(pmid), pmid));
    }

    // Print PageRank values.
    System.out.println("\nPageRank of nodes, in descending order:");
    Ranking<String> r = null;
    while ((r = q.poll()) != null) {
        System.out.println(r.rankScore + "\t" + r.getRanked());
    }
}

From source file:edu.umd.shrawanraina.SequentialPersonalizedPageRank.java

@SuppressWarnings({ "static-access" })
public static void main(String[] args) throws IOException {
    Options options = new Options();

    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("input path").create(INPUT));
    options.addOption(//from   w w w  .  jav a2 s. c om
            OptionBuilder.withArgName("val").hasArg().withDescription("random jump factor").create(JUMP));
    options.addOption(OptionBuilder.withArgName("node").hasArg()
            .withDescription("source node (i.e., destination of the random jump)").create(SOURCE));

    CommandLine cmdline = null;
    CommandLineParser parser = new GnuParser();

    try {
        cmdline = parser.parse(options, args);
    } catch (ParseException exp) {
        System.err.println("Error parsing command line: " + exp.getMessage());
        System.exit(-1);
    }

    if (!cmdline.hasOption(INPUT) || !cmdline.hasOption(SOURCE)) {
        System.out.println("args: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.setWidth(120);
        formatter.printHelp(SequentialPersonalizedPageRank.class.getName(), options);
        ToolRunner.printGenericCommandUsage(System.out);
        System.exit(-1);
    }

    String infile = cmdline.getOptionValue(INPUT);
    final String source = cmdline.getOptionValue(SOURCE);
    float alpha = cmdline.hasOption(JUMP) ? Float.parseFloat(cmdline.getOptionValue(JUMP)) : 0.15f;

    int edgeCnt = 0;
    DirectedSparseGraph<String, Integer> graph = new DirectedSparseGraph<String, Integer>();

    BufferedReader data = new BufferedReader(new InputStreamReader(new FileInputStream(infile)));

    String line;
    while ((line = data.readLine()) != null) {
        line.trim();
        String[] arr = line.split("\\t");

        for (int i = 1; i < arr.length; i++) {
            graph.addEdge(new Integer(edgeCnt++), arr[0], arr[i]);
        }
    }

    data.close();

    if (!graph.containsVertex(source)) {
        System.err.println("Error: source node not found in the graph!");
        System.exit(-1);
    }

    WeakComponentClusterer<String, Integer> clusterer = new WeakComponentClusterer<String, Integer>();

    Set<Set<String>> components = clusterer.transform(graph);
    int numComponents = components.size();
    System.out.println("Number of components: " + numComponents);
    System.out.println("Number of edges: " + graph.getEdgeCount());
    System.out.println("Number of nodes: " + graph.getVertexCount());
    System.out.println("Random jump factor: " + alpha);

    // Compute personalized PageRank.
    PageRankWithPriors<String, Integer> ranker = new PageRankWithPriors<String, Integer>(graph,
            new Transformer<String, Double>() {
                public Double transform(String vertex) {
                    return vertex.equals(source) ? 1.0 : 0;
                }
            }, alpha);

    ranker.evaluate();

    // Use priority queue to sort vertices by PageRank values.
    PriorityQueue<Ranking<String>> q = new PriorityQueue<Ranking<String>>();
    int i = 0;
    for (String pmid : graph.getVertices()) {
        q.add(new Ranking<String>(i++, ranker.getVertexScore(pmid), pmid));
    }

    // Print PageRank values.
    System.out.println("\nPageRank of nodes, in descending order:");
    Ranking<String> r = null;
    while ((r = q.poll()) != null) {
        System.out.println(r.rankScore + "\t" + r.getRanked());
    }
}

From source file:de.unisb.cs.st.javaslicer.jung.ShowJungGraph.java

public static void main(String[] args) throws InterruptedException {
    Options options = createOptions();//from   ww  w .j  ava2  s.co m
    CommandLineParser parser = new GnuParser();
    CommandLine cmdLine;

    try {
        cmdLine = parser.parse(options, args, true);
    } catch (ParseException e) {
        System.err.println("Error parsing the command line arguments: " + e.getMessage());
        return;
    }

    if (cmdLine.hasOption('h')) {
        printHelp(options, System.out);
        System.exit(0);
    }

    String[] additionalArgs = cmdLine.getArgs();
    if (additionalArgs.length != 2) {
        printHelp(options, System.err);
        System.exit(-1);
    }
    File traceFile = new File(additionalArgs[0]);
    String slicingCriterionString = additionalArgs[1];

    Long threadId = null;
    if (cmdLine.hasOption('t')) {
        try {
            threadId = Long.parseLong(cmdLine.getOptionValue('t'));
        } catch (NumberFormatException e) {
            System.err.println("Illegal thread id: " + cmdLine.getOptionValue('t'));
            System.exit(-1);
        }
    }

    TraceResult trace;
    try {
        trace = TraceResult.readFrom(traceFile);
    } catch (IOException e) {
        System.err.format("Could not read the trace file \"%s\": %s%n", traceFile, e);
        System.exit(-1);
        return;
    }

    List<SlicingCriterion> sc = null;
    try {
        sc = StaticSlicingCriterion.parseAll(slicingCriterionString, trace.getReadClasses());
    } catch (IllegalArgumentException e) {
        System.err.println("Error parsing slicing criterion: " + e.getMessage());
        System.exit(-1);
        return;
    }

    List<ThreadId> threads = trace.getThreads();
    if (threads.size() == 0) {
        System.err.println("The trace file contains no tracing information.");
        System.exit(-1);
    }

    ThreadId tracing = null;
    for (ThreadId t : threads) {
        if (threadId == null) {
            if ("main".equals(t.getThreadName())
                    && (tracing == null || t.getJavaThreadId() < tracing.getJavaThreadId()))
                tracing = t;
        } else if (t.getJavaThreadId() == threadId.longValue()) {
            tracing = t;
        }
    }

    if (tracing == null) {
        System.err.println(threadId == null ? "Couldn't find the main thread."
                : "The thread you specified was not found.");
        System.exit(-1);
        return;
    }

    Transformer<InstructionInstance, Object> transformer;
    Transformer<Object, String> vertexLabelTransformer;
    Transformer<Object, String> vertexTooltipTransformer;

    String granularity = cmdLine.getOptionValue("granularity");
    if (granularity == null || "instance".equals(granularity)) {
        transformer = new Transformer<InstructionInstance, Object>() {
            @Override
            public InstructionInstance transform(InstructionInstance inst) {
                return inst;
            }
        };
        vertexLabelTransformer = new Transformer<Object, String>() {
            @Override
            public String transform(Object inst) {
                return getShortInstructionText(((InstructionInstance) inst).getInstruction());
            }
        };
        vertexTooltipTransformer = new Transformer<Object, String>() {
            @Override
            public String transform(Object inst) {
                return getInstructionTooltip(((InstructionInstance) inst).getInstruction());
            }
        };
    } else if ("instruction".equals(granularity)) {
        transformer = new Transformer<InstructionInstance, Object>() {
            @Override
            public Instruction transform(InstructionInstance inst) {
                return inst.getInstruction();
            }
        };
        vertexLabelTransformer = new Transformer<Object, String>() {
            @Override
            public String transform(Object inst) {
                return getShortInstructionText(((Instruction) inst));
            }
        };
        vertexTooltipTransformer = new Transformer<Object, String>() {
            @Override
            public String transform(Object inst) {
                return getInstructionTooltip(((Instruction) inst));
            }
        };
    } else if ("line".equals(granularity)) {
        transformer = new Transformer<InstructionInstance, Object>() {
            @Override
            public Line transform(InstructionInstance inst) {
                return new Line(inst.getInstruction().getMethod(), inst.getInstruction().getLineNumber());
            }
        };
        vertexLabelTransformer = new Transformer<Object, String>() {
            @Override
            public String transform(Object inst) {
                Line line = (Line) inst;
                return line.getMethod().getName() + ":" + line.getLineNr();
            }
        };
        vertexTooltipTransformer = new Transformer<Object, String>() {
            @Override
            public String transform(Object inst) {
                Line line = (Line) inst;
                return "Line " + line.getLineNr() + " in method " + line.getMethod().getReadClass().getName()
                        + "." + line.getMethod();
            }
        };
    } else {
        System.err.println("Illegal granularity specification: " + granularity);
        System.exit(-1);
        return;
    }

    int maxLevel = Integer.MAX_VALUE;
    if (cmdLine.hasOption("maxlevel")) {
        try {
            maxLevel = Integer.parseInt(cmdLine.getOptionValue("maxlevel"));
        } catch (NumberFormatException e) {
            System.err.println("Argument to \"maxlevel\" must be an integer.");
            System.exit(-1);
            return;
        }
    }

    long startTime = System.nanoTime();
    ShowJungGraph<Object> showGraph = new ShowJungGraph<Object>(trace, transformer);
    showGraph.setMaxLevel(maxLevel);
    showGraph.setVertexLabelTransformer(vertexLabelTransformer);
    showGraph.setVertexTooltipTransformer(vertexTooltipTransformer);
    if (cmdLine.hasOption("progress"))
        showGraph.addProgressMonitor(new ConsoleProgressMonitor());
    boolean multithreaded;
    if (cmdLine.hasOption("multithreaded")) {
        String multithreadedStr = cmdLine.getOptionValue("multithreaded");
        multithreaded = ("1".equals(multithreadedStr) || "true".equals(multithreadedStr));
    } else {
        multithreaded = Runtime.getRuntime().availableProcessors() > 1;
    }

    DirectedGraph<Object, SliceEdge<Object>> graph = showGraph.getGraph(tracing, sc, multithreaded);
    long endTime = System.nanoTime();

    System.out.format((Locale) null, "%nSlice graph consists of %d nodes.%n", graph.getVertexCount());
    System.out.format((Locale) null, "Computation took %.2f seconds.%n", 1e-9 * (endTime - startTime));

    showGraph.displayGraph(graph);
}

From source file:edu.uci.ics.jung.algorithms.scoring.util.ScoringUtils.java

/**
 * Assigns a probability of 1/<code>roots.size()</code> to each of the elements of <code>roots</code>.
 * @param <V> the vertex type/*from   w  ww  . j av  a 2 s.c  o m*/
 * @param roots the vertices to be assigned nonzero prior probabilities
 * @return
 */
public static <V> Transformer<V, Double> getUniformRootPrior(Collection<V> roots) {
    final Collection<V> inner_roots = roots;
    Transformer<V, Double> distribution = new Transformer<V, Double>() {
        public Double transform(V input) {
            if (inner_roots.contains(input))
                return new Double(1.0 / inner_roots.size());
            else
                return 0.0;
        }
    };

    return distribution;
}

From source file:JGraphLoader.GraphSaver.java

public static void saveG(String filename, Graph g) {

    final AbstractLayout layout = new StaticLayout(g);

    GraphMLWriter<node, edge> graphWriter = new GraphMLWriter<node, edge>();
    try {//from   ww w  .java  2  s  . c o m
        PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(filename)));

        graphWriter.addEdgeData("id", null, "0", new Transformer<edge, String>() {
            @Override
            public String transform(edge i) {
                return i.getValue();
            }
        });
        /*
         graphWriter.addVertexData("y", null, "0",
         new Transformer<node, String>() {
         public String transform(node v) {
         return Double.toString(layout.getY(v));
         }
         }
         );*/

        graphWriter.save(g, out);
    } catch (IOException ex) {
        Logger.getLogger(GraphSaver.class.getName()).log(Level.SEVERE, null, ex);
    }

}