package plab.prefuseTests; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.WindowAdapter; import java.awt.event.WindowEvent; import java.awt.Font; import java.awt.geom.Point2D; import java.awt.image.BufferedImage; import java.io.File; import java.io.IOException; import java.util.logging.Level; import java.util.logging.Logger; import javax.swing.AbstractAction; import javax.swing.BorderFactory; import javax.swing.Box; import javax.swing.BoxLayout; import javax.swing.JButton; import javax.swing.JFrame; import javax.swing.JMenu; import javax.swing.JMenuBar; import javax.swing.JPanel; import javax.swing.JSplitPane; import javax.swing.KeyStroke; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import javax.swing.JToggleButton; import javax.swing.ButtonGroup; import javax.swing.JRadioButton; import javax.swing.JMenuItem; import prefuse.Display; import prefuse.Visualization; import prefuse.action.ActionList; import prefuse.action.RepaintAction; import prefuse.action.assignment.ColorAction; import prefuse.action.filter.GraphDistanceFilter; import prefuse.action.layout.graph.ForceDirectedLayout; import prefuse.controls.DragControl; import prefuse.controls.NeighborHighlightControl; import prefuse.controls.PanControl; import prefuse.controls.WheelZoomControl; import prefuse.controls.ZoomControl; import prefuse.controls.ZoomToFitControl; import prefuse.data.Graph; import prefuse.data.Tuple; import prefuse.data.event.TupleSetListener; import prefuse.data.io.GraphMLReader; import prefuse.data.tuple.TupleSet; import prefuse.render.DefaultRendererFactory; import prefuse.render.LabelRenderer; import prefuse.util.ColorLib; import prefuse.util.GraphLib; import prefuse.util.force.ForceSimulator; import prefuse.util.io.IOLib; import prefuse.util.ui.JForcePanel; import prefuse.util.ui.JValueSlider; import prefuse.visual.VisualGraph; import prefuse.visual.VisualItem; import prefuse.action.assignment.StrokeAction; import prefuse.util.StrokeLib; import prefuse.action.assignment.DataSizeAction; import prefuse.Constants; import prefuse.data.Node; import java.util.Iterator; import javax.imageio.ImageIO; import javax.swing.ImageIcon; import javax.swing.JLabel; import prefuse.util.ui.UILib; import prefuse.util.force.Force; import prefuse.action.assignment.DataColorAction; import prefuse.render.ShapeRenderer; import prefuse.data.tuple.DefaultTupleSet; import prefuse.render.EdgeRenderer; import prefuse.util.display.ExportDisplayAction; import prefuse.util.ui.JSearchPanel; import prefuse.util.FontLib; import prefuse.data.query.SearchQueryBinding; import prefuse.data.search.KeywordSearchTupleSet; import prefuse.data.search.SearchTupleSet; import prefuse.data.Table; /** * Class to execute MSMExplorer, a visualization module for * protein folding Markov State Models generated with * MSMBuilder. * * Built on GraphView framework by Jeffrey Heer. * * @author Bryce Cronkite-Ratcliff, brycecr@stanford.edu */ public final class MSMExplorer extends JPanel { private static final int SIZE_THRESHOLD = 250; private static final String graph = "graph"; private static final String nodes = "graph.nodes"; private static final String edges = "graph.edges"; private Visualization m_vis; private static JFrame frame; private static final String version = "alpha v0.01"; /** * Constructor * * @param g * @param label */ public MSMExplorer(final Graph g, String label) { super(new BorderLayout()); boolean isBigGraph = (g.getNodeCount() > SIZE_THRESHOLD); // create a new, empty visualization for our data m_vis = new Visualization(); final LabelRenderer tr = new LabelRenderer(); tr.setVerticalAlignment(Constants.BOTTOM); tr.setRoundedCorner(8, 8); // selfref renderer is for self-transitions. However, at this point, // it does not respond to probability color adjustments. m_vis.setRendererFactory( new DefaultRendererFactory(tr/*, new SelfRefEdgeRenderer()*/)); // These tis line will create curved transition edges. This is useful // because it separates the two edges of bidirectional transitions, // thus making both colors more visible. However, this also makes // rendering substantially slower and makes the graph more dense. // ((EdgeRenderer)((DefaultRendererFactory)m_vis.getRendererFactory()).getDefaultEdgeRenderer()).setEdgeType(Constants.EDGE_TYPE_CURVE); // -------------------------------------------------------------------- // register the data with a visualization // adds graph to visualization and sets renderer label field setGraph(g, label); // fix selected focus nodes final TupleSet focusGroup = m_vis.getGroup(Visualization.FOCUS_ITEMS); focusGroup.addTupleSetListener(new TupleSetListener() { public void tupleSetChanged(TupleSet ts, Tuple[] add, Tuple[] rem) { for (int i = 0; i < rem.length; ++i) { ((VisualItem) rem[i]).setFixed(false); Iterator focusEdges = ((Node) rem[i]).edges(); while (focusEdges.hasNext()) { VisualItem currEdge = (VisualItem) focusEdges.next(); currEdge.setHover(false); } } for (int i = 0; i < add.length; ++i) { ((VisualItem) add[i]).setFixed(false); Iterator focusEdges = ((Node) add[i]).edges(); while (focusEdges.hasNext()) { VisualItem currEdge = (VisualItem) focusEdges.next(); currEdge.setHover(false); } ((VisualItem) add[i]).setFixed(true); Iterator focusEdges2 = ((Node) add[i]).edges(); while (focusEdges2.hasNext()) { VisualItem currEdge = (VisualItem) focusEdges2.next(); currEdge.setHover(true); } } if (ts.getTupleCount() == 0) { ts.addTuple(rem[0]); ((VisualItem) rem[0]).setFixed(false); Iterator focusEdges2 = ((Node) rem[0]).edges(); while (focusEdges2.hasNext()) { VisualItem currEdge = (VisualItem) focusEdges2.next(); currEdge.setHover(false); } } if (ts.getTupleCount() > 1) { Iterator tuples = ts.tuples(); //TODO: enable selection of sets of points for target/source DefaultTupleSet A = new DefaultTupleSet(); A.addTuple((Tuple) tuples.next()); DefaultTupleSet B = new DefaultTupleSet(); B.addTuple((Tuple) tuples.next()); TPTWindow tptw = new TPTWindow(g, A, B); focusGroup.clear(); } m_vis.run("draw"); } }); initGraph(g, m_vis); if (g.getNodeCount() < SIZE_THRESHOLD) { tr.getImageFactory().preloadImages(g.nodes(), "image"); } // -------------------------------------------------------------------- // set up a display to show the visualization final Display display = new Display(m_vis); display.setSize(700, 700); display.pan(350, 350); display.setForeground(Color.GRAY); display.setBackground(Color.WHITE); // main display controls display.addControlListener(new FocusControlWithDeselect(1)); display.addControlListener(new DragControl()); display.addControlListener(new PanControl()); display.addControlListener(new ZoomControl()); display.addControlListener(new WheelZoomControl()); display.addControlListener(new ZoomToFitControl()); display.addControlListener(new NeighborHighlightControl()); display.setForeground(Color.GRAY); display.setBackground(Color.WHITE); display.setHighQuality(true); JPanel fpanel = new JPanel(); fpanel.setLayout(new BoxLayout(fpanel, BoxLayout.Y_AXIS)); fpanel.setBackground(Color.WHITE); final JValueSlider slider = new JValueSlider("Distance", 0, 40, 37); slider.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent e) { ((GraphDistanceFilter) ((ActionList) m_vis.getAction("draw")).get(0)).setDistance(slider.getValue().intValue()); m_vis.run("draw"); } }); slider.setBackground(Color.WHITE); slider.setPreferredSize(new Dimension(300, 30)); slider.setMaximumSize(new Dimension(300, 30)); Box cf = new Box(BoxLayout.Y_AXIS); cf.add(slider); cf.setBorder(BorderFactory.createTitledBorder("Connectivity Filter")); fpanel.add(cf); JToggleButton togglePM = new JToggleButton("Picture Mode", false); togglePM.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ae) { display.setHighQuality(((JToggleButton)ae.getSource()).isSelected()); } }); togglePM.setSelected(true); JToggleButton curveBtn = new JToggleButton("Edge Type", false); curveBtn.addActionListener( new ActionListener () { public void actionPerformed( ActionEvent ae ) { if (((JToggleButton)ae.getSource()).isSelected()) ((EdgeRenderer)((DefaultRendererFactory) m_vis.getRendererFactory()). getDefaultEdgeRenderer()). setEdgeType(Constants.EDGE_TYPE_CURVE); else ((EdgeRenderer)((DefaultRendererFactory) m_vis.getRendererFactory()). getDefaultEdgeRenderer()). setEdgeType(Constants.EDGE_TYPE_LINE); m_vis.run("draw"); } }); Box rendBox = new Box(BoxLayout.X_AXIS); rendBox.setBorder(BorderFactory.createTitledBorder("Gen. Renderer")); rendBox.add(togglePM); rendBox.add(curveBtn); fpanel.add(rendBox); ButtonGroup nodeRenderers = new ButtonGroup(); JRadioButton circleRB = new JRadioButton("Circle", false); circleRB.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ae) { JRadioButton circleRB = (JRadioButton) ae.getSource(); if (circleRB.isSelected()) { m_vis.setRendererFactory(new DefaultRendererFactory(new ShapeRenderer()/*, new SelfRefEdgeRenderer()*/)); m_vis.setValue(nodes, null, VisualItem.SHAPE, Constants.SHAPE_ELLIPSE); } } }); nodeRenderers.add(circleRB); JRadioButton labelRB = new JRadioButton("Label", false); labelRB.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ae) { JRadioButton labelRB = (JRadioButton) ae.getSource(); if (labelRB.isSelected()) { m_vis.setRendererFactory(new DefaultRendererFactory(tr/*, new SelfRefEdgeRenderer()*/)); } } }); nodeRenderers.add(labelRB); Box nrBox = new Box(BoxLayout.X_AXIS); nrBox.setBorder(BorderFactory.createTitledBorder("Node Renderer")); nrBox.add(circleRB); nrBox.add(labelRB); labelRB.setSelected(true); fpanel.add(nrBox); JButton pause = new JButton("Stop Layout"); pause.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { //if (((ActionList)m_vis.getAction("lll")).isRunning()) ((ActionList) m_vis.getAction("lll")).cancel(); } }); if (g.getNodeCount() > SIZE_THRESHOLD) //HERE { pause.setEnabled(false); } JButton start = new JButton("Run Layout"); start.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { //if (!lll.isScheduled()) ((ActionList) m_vis.getAction("lll")).run(); } }); if (g.getNodeCount() > SIZE_THRESHOLD) //HERE { start.setEnabled(false); } Box runControls = new Box(BoxLayout.X_AXIS); runControls.add(start); runControls.add(pause); runControls.setBorder( BorderFactory.createTitledBorder("Run Control")); fpanel.add(runControls); JButton openImg = new JButton("Open Image"); openImg.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ae) { Tuple focus = (Tuple) m_vis.getGroup(Visualization.FOCUS_ITEMS).tuples().next(); Picture imgFrame = new Picture((String) focus.get("image")); imgFrame.show(); } }); JButton exportDisplay = new JButton("Save Image"); exportDisplay.addActionListener(new ExportDisplayAction(display)); Box imgControls = new Box(BoxLayout.X_AXIS); imgControls.setBorder(BorderFactory.createTitledBorder("Image Controls")); imgControls.add(openImg); imgControls.add(exportDisplay); fpanel.add(imgControls); JToggleButton togglePics = new JToggleButton("Show Images", false); togglePics.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ae) { JToggleButton tp = (JToggleButton) ae.getSource(); if (!tp.isSelected()) { tr.setImageField(null); ((DataSizeAction) m_vis.getAction("nodeSize")).setMaximumSize(50.0); m_vis.run("nodeSize"); } else { ((DataSizeAction) m_vis.getAction("nodeSize")).setMaximumSize(1.0); m_vis.run("nodeSize"); tr.setImageField("image"); tr.setImagePosition(Constants.TOP); tr.getImageFactory().setMaxImageDimensions(100, 100); } m_vis.run("draw"); } }); JButton runTPT = new JButton("TPT Selector"); runTPT.addActionListener( new ActionListener () { public void actionPerformed( ActionEvent ae ) { TPTSetupBox tsb = new TPTSetupBox(g, true, m_vis); } }); Box renderControls = new Box(BoxLayout.X_AXIS); renderControls.setBorder(BorderFactory.createTitledBorder("Function Control")); renderControls.add(togglePics); renderControls.add(runTPT); fpanel.add(renderControls); SearchTupleSet searchGroup = new KeywordSearchTupleSet(); m_vis.addFocusGroup(Visualization.SEARCH_ITEMS, searchGroup); searchGroup.addTupleSetListener( new TupleSetListener() { public void tupleSetChanged(TupleSet ts, Tuple[] add, Tuple[] rem) { if ( add.length > 0 ) { Point2D p = new Point2D.Double(); p.setLocation(((VisualItem)add[0]).getX(), ((VisualItem)add[0]).getY()); display.animatePanToAbs(p, 1000); } } }); SearchQueryBinding sq = new SearchQueryBinding((Table)m_vis.getGroup(nodes), "label", (SearchTupleSet)m_vis.getGroup(Visualization.SEARCH_ITEMS)); JSearchPanel search = sq.createSearchPanel(false); // JSearchPanel search = new JSearchPanel(m_vis, nodes, Visualization.SEARCH_ITEMS, "label", true, false); search.setShowResultCount(true); search.setBorder(BorderFactory.createEmptyBorder(5, 5, 4, 0)); Box searchBox = new Box(BoxLayout.X_AXIS); searchBox.setBorder(BorderFactory.createTitledBorder("Search")); searchBox.add(search); fpanel.add(searchBox); Display overview = new Display(m_vis); overview.setSize(290, 290); overview.addItemBoundsListener(new FitOverviewListener()); overview.setHighQuality(true); JPanel opanel = new JPanel(); opanel.setBorder(BorderFactory.createTitledBorder("Overview")); opanel.setBackground(Color.WHITE); opanel.add(overview); fpanel.add(opanel); fpanel.add(Box.createVerticalGlue()); // create a new JSplitPane to present the interface JSplitPane split = new JSplitPane(); split.setLeftComponent(display); split.setRightComponent(fpanel); split.setOneTouchExpandable(true); split.setContinuousLayout(false); split.setDividerLocation(700); // now we run our action list m_vis.run("draw"); m_vis.run("lll"); //HERE m_vis.run("nodeSize"); add(split); } public void setGraph(Graph g, String label) { // update labeling DefaultRendererFactory drf = (DefaultRendererFactory) m_vis.getRendererFactory(); //((LabelRenderer)drf.getDefaultRenderer()).setTextField(label); // update graph m_vis.removeGroup(graph); VisualGraph vg = m_vis.addGraph(graph, g); m_vis.setValue(edges, null, VisualItem.INTERACTIVE, Boolean.FALSE); VisualItem f = (VisualItem) vg.getNode(0); m_vis.getGroup(Visualization.FOCUS_ITEMS).setTuple(f); f.setFixed(false); } public void initGraph(Graph g, Visualization vis) { ColorAction fill = new NodeColorAction(nodes); /*ColorAction fill = new ColorAction(nodes, VisualItem.FILLCOLOR, ColorLib.rgb(179, 255, 156)); fill.add(VisualItem.FIXED, ColorLib.rgb(255, 100, 100)); fill.add(VisualItem.HIGHLIGHT, ColorLib.rgb(255, 200, 125));*/ DataColorAction edgeColor = new DataColorAction(edges, "probability", Constants.NOMINAL, VisualItem.STROKECOLOR, ColorLib.getGrayscalePalette()); edgeColor.add(VisualItem.HOVER, ColorLib.rgb(200, 40, 60)); edgeColor.add(VisualItem.HIGHLIGHT, ColorLib.rgb(255, 150, 68)); DataColorAction edgeFill = new DataColorAction(edges, "probability", Constants.NOMINAL, VisualItem.FILLCOLOR, ColorLib.getGrayscalePalette()); edgeFill.add(VisualItem.HIGHLIGHT, ColorLib.rgb(200, 0, 0)); StrokeAction edgeWeight = new StrokeAction(edges, StrokeLib.getStroke(1.0f)); edgeWeight.add(VisualItem.HIGHLIGHT, StrokeLib.getStroke(2.0f)); StrokeAction nodeWeight = new StrokeAction(nodes, StrokeLib.getStroke(1.0f)); edgeWeight.add(VisualItem.HIGHLIGHT, StrokeLib.getStroke(2.0f)); DataSizeAction nodeSize = new DataSizeAction(nodes, "eqProb", 50, Constants.LOG_SCALE); nodeSize.setMaximumSize(50.0); g.getNodes().addColumn("image", "CONCAT('/images/macro',label,'.png')"); int hops = 5; final GraphDistanceFilter filter = new GraphDistanceFilter(graph, 40); final ActionList draw = new ActionList(); draw.add(filter); draw.add(edgeFill); draw.add(new ColorAction(nodes, VisualItem.TEXTCOLOR, ColorLib.rgb(0, 0, 0))); draw.add(new ColorAction(nodes, VisualItem.STROKECOLOR, ColorLib.gray(50))); ActionList animate = new ActionList(ActionList.INFINITY); animate.add(edgeWeight); animate.add(edgeColor); animate.add(fill); animate.add(new RepaintAction()); final ActionList lll = new ActionList(); if (g.getNodeCount() > SIZE_THRESHOLD) //If graph is large { lll.add(new ForceDirectedLayout(graph, false, true)); //Then run-once } else { lll.setDuration(ActionList.INFINITY); lll.add(new ForceDirectedLayout(graph)); //Else, continually animate } // finally, we register our ActionList with the Visualization. // we can later execute our Actions by invoking a method on our // Visualization, using the name we've chosen below. m_vis.putAction("draw", draw); m_vis.putAction("lll", lll); m_vis.putAction("nodeSize", nodeSize); m_vis.putAction("layout", animate); m_vis.runAfter("draw", "layout"); ForceSimulator fsim = ((ForceDirectedLayout) ((ActionList) m_vis.getAction("lll")).get(0)).getForceSimulator(); //HERE Force[] forces = fsim.getForces(); final Force NBodyForce = forces[0]; //final Force DragForce = forces[1]; final Force SpringForce = forces[2]; SetForces: { NBodyForce.setMinValue(0, -40.0f); NBodyForce.setParameter(0, -40.0f); NBodyForce.setParameter(1, -1); SpringForce.setParameter(0, .000001f); SpringForce.setParameter(1, 200f); } } private static void preemptiveTPT(JFrame selector) { Graph g = IOLib.getGraphFile(null); if (g == null) return; selector.dispose(); TPTSetupBox setup = new TPTSetupBox(g, false); } // ------------------------------------------------------------------------ // Main and demo methods // ------------------------------------------------------------------------ public static void main(String[] args) { UILib.setPlatformLookAndFeel(); final JFrame selector = new JFrame("Start Screen"); selector.setLayout(new BorderLayout()); JButton graphButton = new JButton("Whole Graph"); graphButton.addActionListener( new ActionListener() { public void actionPerformed( ActionEvent ae ) { selector.dispose(); frame = demo("5macro.xml", "label"); //HERE frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); } }); JButton tptButton = new JButton("Just TPT"); tptButton.addActionListener( new ActionListener() { public void actionPerformed( ActionEvent ae ) { preemptiveTPT(selector); } }); Box container = new Box(BoxLayout.X_AXIS); container.add(Box.createHorizontalStrut(130)); container.add(graphButton); container.add(tptButton); container.add(Box.createHorizontalGlue()); JLabel versionLabel = new JLabel(version + " "); versionLabel.setFont(FontLib.getFont("Tahoma", 10)); container.add(versionLabel); container.setBackground(Color.WHITE); BufferedImage image; try { String curDir = System.getProperty("user.dir"); System.out.println(curDir); image = ImageIO.read(new File(curDir + "/splash.jpg")); } catch (IOException ex) { System.err.println("Could not find splash image"); image = new BufferedImage(500,300,BufferedImage.TYPE_INT_RGB); } ImageIcon splash = new ImageIcon(image); selector.add(new JLabel(splash), BorderLayout.CENTER); selector.add(container, BorderLayout.SOUTH); selector.setBackground(Color.WHITE); selector.pack(); selector.setSize(500, 380); selector.setLocationRelativeTo(null); selector.setVisible(true); } // end of main public static JFrame demo(String datafile, String label) { Graph g = null; if (datafile == null) { g = GraphLib.getGrid(15, 15); label = "label"; } else { try { g = new GraphMLReader().readGraph(datafile); } catch (Exception e) { System.err.println(e.getMessage()); System.err.println(e.getCause()); System.err.println("fuck. =["); System.exit(1); } } return demo(g, label); } // end of class demo(String, String) public static JFrame demo(final Graph g, String label) { final MSMExplorer view = new MSMExplorer(g, label); JMenuItem openAdj = new JMenuItem("Adjustment Panel"); openAdj.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ae) { JFrame forceFrame = new JFrame("Force Adjustment"); ForceSimulator fsim = ((ForceDirectedLayout) ((ActionList) view.m_vis.getAction("lll")).get(0)).getForceSimulator(); JForcePanel fPanel = new JForcePanel(fsim); forceFrame.add(fPanel); forceFrame.pack(); forceFrame.setVisible(true); } }); JMenuItem makeMovie = new JMenuItem("Create PDB Movie"); makeMovie.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent ae) { PDBFrame pdbf = new PDBFrame(g, view.m_vis); } }); // set up menu JMenu dataMenu = new JMenu("Data"); dataMenu.add(openAdj); dataMenu.add(makeMovie); dataMenu.add(new OpenGraphAction(view)); JMenuBar menubar = new JMenuBar(); menubar.add(dataMenu); // launch window JFrame frame = new JFrame("p r e f u s e | g r a p h v i e w"); frame.setJMenuBar(menubar); frame.setContentPane(view); frame.pack(); frame.setVisible(true); frame.addWindowListener(new WindowAdapter() { @Override public void windowActivated(WindowEvent e) { view.m_vis.run("layout"); } @Override public void windowDeactivated(WindowEvent e) { if ((((JFrame) e.getWindow()).getTitle()).equals("Force Adjustment")) { view.m_vis.cancel("layout"); } } }); return frame; } //end of class demo(Graph, String) // ------------------------------------------------------------------------ // Utility classes // ------------------------------------------------------------------------ /** * Really awfully messy method to open a new graph from * the menu "Open Graph" option. TODO: fix this shit. * */ public static class OpenGraphAction extends AbstractAction { private MSMExplorer m_view; public OpenGraphAction(MSMExplorer view) { m_view = view; this.putValue(AbstractAction.NAME, "Open File..."); this.putValue(AbstractAction.ACCELERATOR_KEY, KeyStroke.getKeyStroke("ctrl O")); } public void actionPerformed(ActionEvent e) { Graph g = IOLib.getGraphFile(m_view); if (g != null) { frame.dispose(); frame = demo(g, "label"); } } } // end of class OpenGraphAction public static class NodeColorAction extends ColorAction { public NodeColorAction(String group) { super(group, VisualItem.FILLCOLOR); } @Override public int getColor(VisualItem item) { if (m_vis.isInGroup(item, Visualization.SEARCH_ITEMS)) { return ColorLib.rgb(255, 120, 120); } else if (item.isFixed()) { return ColorLib.rgb(245, 150, 50); } else if (item.isHighlighted()) { return ColorLib.rgb(245, 200, 100); } else { return ColorLib.rgb(245, 230, 210); } } } // end of inner class NodeColorAction } // end of class GraphView