Examples with ONDEXJUNGGraph net.sourceforge.ondex.ovtk2.graph.ONDEXJUNGGraph used on opensource projects

Example 1 with ONDEXJUNGGraph

use of net.sourceforge.ondex.ovtk2.graph.ONDEXJUNGGraph in project knetbuilder by Rothamsted.

the class OVTK2DefaultModalGraphMouse method actionPerformed.

@Override
public void actionPerformed(ActionEvent e) {
    String cmd = e.getActionCommand();
    // current graph
    ONDEXJUNGGraph graph = this.viewer.getONDEXJUNGGraph();
    // gain access to current plugin
    OVTK2AnnotatingGraphMousePlugin plugin = (OVTK2AnnotatingGraphMousePlugin) this.annotatingPlugin;
    // keeps track of annotations
    AnnotationManager manager = plugin.getAnnotationMananger();
    // pass annotations to AnnotationControls
    if (cmd.equals("load") && graph.getAnnotations() != null && graph.getAnnotations().containsKey(KEY)) {
        // get current annotation from graph
        String xml = graph.getAnnotations().get(KEY);
        if (xml == null || xml.trim().length() == 0)
            return;
        // will contain de-serialised annotations
        Set<Annotation> annos = new HashSet<Annotation>();
        // configure XML input
        System.setProperty("ondex.javax.xml.stream.XMLInputFactory", "com.ctc.wstx.stax.WstxInputFactory");
        XMLInputFactory2 xmlInput = (XMLInputFactory2) XMLInputFactory2.newFactory("ondex.javax.xml.stream.XMLInputFactory", this.getClass().getClassLoader());
        xmlInput.configureForSpeed();
        // parse from a String
        final ByteArrayInputStream inStream = new ByteArrayInputStream(xml.getBytes());
        try {
            // configure Parser
            XMLStreamReader2 xmlReadStream = (XMLStreamReader2) xmlInput.createXMLStreamReader(inStream, CharsetNames.CS_UTF8);
            // de-serialise annotations from XML
            AnnotationXMLReader.read(xmlReadStream, annos);
            xmlReadStream.close();
        } catch (XMLStreamException e1) {
            ErrorDialog.show(e1);
        }
        // add all annotations to manager
        for (Annotation anno : annos) {
            manager.add(anno.getLayer(), anno);
        }
        // update visualisation
        viewer.getVisualizationViewer().fireStateChanged();
        viewer.getVisualizationViewer().repaint();
    } else // get annotations from AnnotationControls
    if (cmd.equals("save")) {
        // annotations of lower layer
        AnnotationPaintable lower = manager.getAnnotationPaintable(Annotation.Layer.LOWER);
        // annotations of upper layer
        AnnotationPaintable upper = manager.getAnnotationPaintable(Annotation.Layer.UPPER);
        // all annotations of lower layer
        Set<Annotation> annos = new HashSet<Annotation>(lower.getAnnotations());
        // all annotations of upper layer
        annos.addAll(upper.getAnnotations());
        // configure XML output
        System.setProperty("ondex.javax.xml.stream.XMLOutputFactory", "com.ctc.wstx.stax.WstxOutputFactory");
        XMLOutputFactory2 xmlOutput = (XMLOutputFactory2) XMLOutputFactory2.newFactory("ondex.javax.xml.stream.XMLOutputFactory", this.getClass().getClassLoader());
        xmlOutput.configureForSpeed();
        xmlOutput.setProperty(XMLOutputFactory2.IS_REPAIRING_NAMESPACES, false);
        // output goes into a String
        final ByteArrayOutputStream outStream = new ByteArrayOutputStream();
        try {
            // configure writer
            XMLStreamWriter2 xmlWriteStream = (XMLStreamWriter2) xmlOutput.createXMLStreamWriter(outStream, CharsetNames.CS_UTF8);
            // serialise Annotations to XML
            AnnotationXMLWriter.write(xmlWriteStream, annos);
            xmlWriteStream.flush();
            xmlWriteStream.close();
            // set annotation data to graph
            graph.getAnnotations().put(KEY, outStream.toString());
        } catch (XMLStreamException e1) {
            ErrorDialog.show(e1);
        }
    }
}

Example 2 with ONDEXJUNGGraph

use of net.sourceforge.ondex.ovtk2.graph.ONDEXJUNGGraph in project knetbuilder by Rothamsted.

the class VisualisationExtension method showContextMembers.

/**
 * Shows all of the members of context(s) selected in the viewer
 *
 * @param viewer
 */
public static void showContextMembers(OVTK2PropertiesAggregator viewer) {
    ONDEXJUNGGraph graph = viewer.getONDEXJUNGGraph();
    for (ONDEXConcept contextConcept : viewer.getPickedNodes().toArray(new ONDEXConcept[0])) {
        graph.setVisibility(graph.getConceptsOfTag(contextConcept), true);
        graph.setVisibility(graph.getRelationsOfTag(contextConcept), true);
    }
}

Example 3 with ONDEXJUNGGraph

use of net.sourceforge.ondex.ovtk2.graph.ONDEXJUNGGraph in project knetbuilder by Rothamsted.

the class VisualisationExtension method showConnectingRelations.

/**
 * Makes all of the relations visible, if their target and source are
 * currently visible
 */
public static void showConnectingRelations(OVTK2PropertiesAggregator viewer) {
    ONDEXJUNGGraph graph = viewer.getONDEXJUNGGraph();
    for (ONDEXRelation r : graph.getRelations()) {
        ONDEXConcept c1 = r.getFromConcept();
        ONDEXConcept c2 = r.getToConcept();
        if (graph.isVisible(c1) && graph.isVisible(c2)) {
            graph.setVisibility(r, true);
        }
    }
    viewer.updateViewer(null);
}

Example 4 with ONDEXJUNGGraph

use of net.sourceforge.ondex.ovtk2.graph.ONDEXJUNGGraph in project knetbuilder by Rothamsted.

the class VisualizationHandler method processingFinished.

/*
	 * (non-Javadoc)
	 * 
	 * @see net.sourceforge.ondex.ovtk2.ui.scripting.ProcessingCheckpoint#
	 * processingFinished()
	 */
public synchronized void processingFinished() {
    try {
        for (Entry<OVTK2PropertiesAggregator, ONDEXJUNGGraph> ent : graphs.entrySet()) {
            OVTK2ResourceAssesor resources = OVTK2Desktop.getDesktopResources();
            // put graph into viewer
            // OVTK2PropertiesAggregator viewer =
            // DesktopUtils.initViewer(ent.getValue());
            OVTK2PropertiesAggregator viewer = ent.getKey();
            // set viewer as active viewer
            resources.setSelectedViewer(viewer);
            // decide when to display viewer immediately
            if (Math.max(ent.getValue().getConcepts().size(), ent.getValue().getRelations().size()) < 2000) {
                // we can display everything here
                viewer.getONDEXJUNGGraph().setEverythingVisible();
            // make sure layout is set
            // VisualisationUtils.relayout(viewer);
            }
            // update all visual attributes of graph
            viewer.updateViewer(null);
            if (viewer instanceof OVTK2Viewer) {
                ((OVTK2Viewer) viewer).getMetaGraph().updateMetaData();
                try {
                    ((OVTK2Viewer) viewer).setSelected(true);
                } catch (PropertyVetoException e) {
                    ErrorDialog.show(e);
                }
            }
            // update UI
            viewer.getVisualizationViewer().fireStateChanged();
            viewer.getVisualizationViewer().repaint();
        // hack to show meta graph
        // JCheckBoxMenuItem item = new JCheckBoxMenuItem();
        // item.setSelected(true);
        // desktop.actionPerformed(new ActionEvent(item,
        // ActionEvent.ACTION_PERFORMED, "metagraph"));
        // ((ActionListener)v).actionPerformed(new
        // ActionEvent(this,0,"refresh"));
        // v.getJUNGGraph().addActionListener((ActionListener)v);
        }
        graphs.clear();
    // OVTK2PropertiesAggregator v =
    // OVTK2Desktop.getInstance().getDesktopResources().getSelectedViewer();
    // v.setMaximizable(true);
    // v.setIconifiable(true);
    // if(state.containsKey(v))
    // v.setIcon(state.remove(v));
    // OVTK-206
    // VisualisationUtils.relayout(v);
    // v.center();
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 5 with ONDEXJUNGGraph

use of net.sourceforge.ondex.ovtk2.graph.ONDEXJUNGGraph in project knetbuilder by Rothamsted.

the class ONDEXMetaGraphPanel method initVisviewer.

/**
 * Creates JUNG visualization of metagraph.
 */
private void initVisviewer() {
    ONDEXJUNGGraph jung = viewer.getONDEXJUNGGraph();
    // new metagraph viewer
    layout = new KKLayout<ONDEXMetaConcept, ONDEXMetaRelation>(meta);
    visviewer = new VisualizationViewer<ONDEXMetaConcept, ONDEXMetaRelation>(layout, preferredSize);
    visviewer.setDoubleBuffered(true);
    visviewer.setBackground(Color.white);
    // set label position and label transformer
    visviewer.getRenderer().getVertexLabelRenderer().setPosition(Position.AUTO);
    visviewer.getRenderContext().setVertexLabelTransformer(new ONDEXMetaConceptLabels(jung));
    visviewer.getRenderContext().setEdgeLabelTransformer(new ONDEXMetaRelationLabels(jung));
    // set visible attribute renderer
    visviewer.getRenderContext().setEdgeDrawPaintTransformer(new ONDEXMetaRelationColors(jung, visviewer.getPickedEdgeState()));
    visviewer.getRenderContext().setVertexShapeTransformer(new ONDEXMetaConceptShapes(jung));
    // visviewer.getRenderContext().setVertexDrawPaintTransformer(
    // new ONDEXMetaConceptColors( aog));
    visviewer.getRenderContext().setVertexFillPaintTransformer(new ONDEXMetaConceptColors(jung, visviewer.getPickedVertexState()));
    visviewer.getRenderContext().setEdgeArrowPredicate(new ONDEXMetaRelationArrows(jung));
    visviewer.getRenderContext().setEdgeStrokeTransformer(new ONDEXMetaRelationStrokes(jung));
    // set antialiasing painting on
    Map<?, ?> temp = visviewer.getRenderingHints();
    // copying necessary because of typesafety
    Iterator<?> it = temp.keySet().iterator();
    while (it.hasNext()) {
        RenderingHints.Key key = (RenderingHints.Key) it.next();
        hints.put(key, temp.get(key));
    }
    hints.put(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
    visviewer.setRenderingHints(hints);
    // standard mouse support
    DefaultModalGraphMouse<ONDEXMetaConcept, ONDEXMetaRelation> graphMouse = new DefaultModalGraphMouse<ONDEXMetaConcept, ONDEXMetaRelation>();
    // Trying out our new popup menu mouse producer...
    PopupVertexEdgeMenuMousePlugin<ONDEXMetaConcept, ONDEXMetaRelation> myPlugin = new PopupVertexEdgeMenuMousePlugin<ONDEXMetaConcept, ONDEXMetaRelation>();
    // Add some popup menus for the edges and vertices to our mouse
    // producer.
    JPopupMenu edgeMenu = new MetaRelationMenu(viewer);
    JPopupMenu vertexMenu = new MetaConceptMenu(viewer);
    myPlugin.setEdgePopup(edgeMenu);
    myPlugin.setVertexPopup(vertexMenu);
    // Add our new producer to the mouse
    graphMouse.add(myPlugin);
    visviewer.setGraphMouse(graphMouse);
    visviewer.addKeyListener(graphMouse.getModeKeyListener());
    // zoom pane and mouse menu in the corner
    GraphZoomScrollPane scrollPane = new GraphZoomScrollPane(visviewer);
    JMenuBar menu = new JMenuBar();
    menu.add(graphMouse.getModeMenu());
    scrollPane.setCorner(menu);
    // set graph mode to picking
    graphMouse.setMode(Mode.PICKING);
    // button panel
    JPanel buttons = new JPanel();
    BoxLayout buttons_layout = new BoxLayout(buttons, BoxLayout.LINE_AXIS);
    buttons.setLayout(buttons_layout);
    // metadata legend button
    JButton legend = new JButton(Config.language.getProperty("MetaGraph.MetaDataLegend"));
    legend.addActionListener(this);
    legend.setActionCommand("legend");
    buttons.add(legend);
    // metadata legend button
    JButton mainGraph = new JButton(Config.language.getProperty("MetaGraph.ShowMainGraph"));
    mainGraph.addActionListener(this);
    mainGraph.setActionCommand("mainGraph");
    buttons.add(mainGraph);
    // make sure that the layout has actually finished
    while (!layout.done()) {
        layout.step();
    }
    // add to content pane
    this.add(scrollPane, BorderLayout.CENTER);
    this.add(buttons, BorderLayout.SOUTH);
    this.revalidate();
    this.scaleToFit();
    this.addComponentListener(this);
}