package plugin;

import java.awt.event.ActionEvent;
import java.io.File;
import java.io.IOException;
import java.text.DecimalFormat;
import java.text.NumberFormat;

import javax.swing.JOptionPane;
import javax.swing.SwingUtilities;

import cytoscape.CyNetwork;
import cytoscape.Cytoscape;
import cytoscape.CytoscapeInit;
import cytoscape.data.readers.GMLReader;
import cytoscape.data.readers.GraphReader;
import cytoscape.ding.DingNetworkView;
import cytoscape.plugin.CytoscapePlugin;
import cytoscape.task.Task;
import cytoscape.task.TaskMonitor;
import cytoscape.task.ui.JTaskConfig;
import cytoscape.task.util.TaskManager;
import cytoscape.util.CyFileFilter;
import cytoscape.util.CyNetworkNaming;
import cytoscape.util.CytoscapeAction;
import cytoscape.util.FileUtil;
import ding.view.DGraphView;

/**
 * A menu item "Hello World" will appear at Plugins menu. Click on the menu
 * item, a message dialog will show up.
 */
public class FirstPlugin extends CytoscapePlugin {

	public FirstPlugin() {
		LoadNetworkAction menuAction = new LoadNetworkAction(this);
		Cytoscape.getDesktop().getCyMenus().addCytoscapeAction((CytoscapeAction) menuAction);
		((LoadNetworkAction) menuAction).perform();
	}

	class LoadNetworkAction extends CytoscapeAction {

		public LoadNetworkAction(FirstPlugin myPlugin) {
			super("Configure Plugin");
			setPreferredMenu("Plugins");
		}

		@Override
		public void actionPerformed(ActionEvent arg0) {
//			CyFileFilter intFilter = new CyFileFilter();
//	        CyFileFilter gmlFilter = new CyFileFilter();
//	        CyFileFilter graphFilter = new CyFileFilter();

	        // Add accepted File Extensions
//	        gmlFilter.addExtension("gml");
//	        gmlFilter.setDescription("GML files");
//	        intFilter.addExtension("sif");
//	        intFilter.setDescription("Interaction files");
//	        graphFilter.addExtension("sif");
//	        graphFilter.addExtension("gml");
//	        graphFilter.setDescription("All network files");

	        // Get the file name
//	        File  file = FileUtil.getFile("Load Network File",
//	            FileUtil.LOAD, new CyFileFilter[]
//	            {intFilter, gmlFilter, graphFilter});
	        File  file =new File("H:\\Projects\\product_supplier.gml");
	        if (file != null) {
	            int fileType = Cytoscape.FILE_SIF;

	            //  long enough to have a "gml" extension
	            if (file.getName().length() > 4) {
	                String name = file.getName();
	                String extension = name.substring(name.length() - 3);
	                if (extension.equalsIgnoreCase("gml"))
	                    fileType = Cytoscape.FILE_GML;
	            }

	            //  Create LoadNetwork Task
//	            LoadNetworkTask task = new LoadNetworkTask(file, fileType);
	            LoadNetworkTask task = new LoadNetworkTask(file, Cytoscape.FILE_GML);

	            //  Configure JTask Dialog Pop-Up Box
	            JTaskConfig jTaskConfig = new JTaskConfig();
	            jTaskConfig.setOwner(Cytoscape.getDesktop());
	            jTaskConfig.displayCloseButton(true);
	            jTaskConfig.displayStatus(true);
	            jTaskConfig.setAutoDispose(false);

	            //  Execute Task in New Thread;  pops open JTask Dialog Box.
	            TaskManager.executeTask(task, jTaskConfig);
	        }
		}
		public void perform() {
			File  file =new File("H:\\Projects\\product_supplier.gml");
	        if (file != null) {
	            int fileType = Cytoscape.FILE_SIF;

	            //  long enough to have a "gml" extension
	            if (file.getName().length() > 4) {
	                String name = file.getName();
	                String extension = name.substring(name.length() - 3);
	                if (extension.equalsIgnoreCase("gml"))
	                    fileType = Cytoscape.FILE_GML;
	            }

	            //  Create LoadNetwork Task
//	            LoadNetworkTask task = new LoadNetworkTask(file, fileType);
	            LoadNetworkTask task = new LoadNetworkTask(file, Cytoscape.FILE_GML);

	            //  Configure JTask Dialog Pop-Up Box
	            JTaskConfig jTaskConfig = new JTaskConfig();
	            jTaskConfig.setOwner(Cytoscape.getDesktop());
	            jTaskConfig.displayCloseButton(true);
	            jTaskConfig.displayStatus(true);
	            jTaskConfig.setAutoDispose(false);

	            //  Execute Task in New Thread;  pops open JTask Dialog Box.
	            TaskManager.executeTask(task, jTaskConfig);
	        }
		}

	}
}
/**
 * Task to Load New Network Data.
 */
class LoadNetworkTask implements Task {
    private File file;
    private int fileType;
    private CyNetwork cyNetwork;
    private TaskMonitor taskMonitor;

    /**
     * Constructor.
     *
     * @param file         File.
     * @param fileType     FileType, e.g. Cytoscape.FILE_SIF or
     *                     Cytoscape.FILE_GML.
     */
    public LoadNetworkTask(File file, int fileType) {
        this.file = file;
        this.fileType = fileType;
    }

    /**
     * Executes Task.
     */
    public void run() {
        taskMonitor.setStatus("Reading in Network Data...");

        try {
            cyNetwork = this.createNetwork(file.getAbsolutePath(), fileType);

            if (cyNetwork != null) {
                informUserOfGraphStats(cyNetwork);
            } else {
                StringBuffer sb = new StringBuffer();
                sb.append("Could not read network from file: " + file.getName());
                sb.append("\nThis file may not be a valid GML or SIF file.");
                taskMonitor.setException(new IOException(sb.toString()),
                        sb.toString());
            }
            taskMonitor.setPercentCompleted(100);
        } catch (IOException e) {
            taskMonitor.setException(e, "Unable to load network file.");
        }
    }

    /**
     * Inform User of Network Stats.
     */
    private void informUserOfGraphStats(CyNetwork newNetwork) {
        NumberFormat formatter = new DecimalFormat("#,###,###");
        StringBuffer sb = new StringBuffer();

        //  Give the user some confirmation
        sb.append("Succesfully loaded network from:  " + file.getName());
        sb.append("\n\nNetwork contains " + formatter.format
                (newNetwork.getNodeCount()));
        sb.append(" nodes and " + formatter.format(newNetwork.getEdgeCount()));
        sb.append(" edges.\n\n");

        if (newNetwork.getNodeCount() < Integer.parseInt(CytoscapeInit.getProperties().getProperty("viewThreshold"))) {
            sb.append("Network is under "
                    + Integer.parseInt(CytoscapeInit.getProperties().getProperty("viewThreshold"))
                    + " nodes.  A view will be automatically created.");
        } else {
            sb.append("Network is over "
                    + Integer.parseInt(CytoscapeInit.getProperties().getProperty("viewThreshold"))
                    + " nodes.  A view will not been created."
                    + "  If you wish to view this network, use "
                    + "\"Create View\" from the \"Edit\" menu.");
        }
        taskMonitor.setStatus(sb.toString());
    }

    /**
     * Halts the Task:  Not Currently Implemented.
     */
    public void halt() {
        //   Task can not currently be halted.
    }

    /**
     * Sets the Task Monitor.
     *
     * @param taskMonitor TaskMonitor Object.
     */
    public void setTaskMonitor(TaskMonitor taskMonitor)
            throws IllegalThreadStateException {
        this.taskMonitor = taskMonitor;
    }

    /**
     * Gets the Task Title.
     *
     * @return Task Title.
     */
    public String getTitle() {
        return new String("Loading Network");
    }

    /**
     * Creates a cytoscape.data.CyNetwork from a file.
     * The passed variable determines the
     * type of file, i.e. GML, SIF, etc.<p>
     * This operation may take a long time to complete.
     *
     * @param location      the location of the file
     * @param file_type     the type of file GML, SIF, SBML, etc.
     * @param biodataserver provides the name conversion service
     * @param species       the species used by the BioDataServer
     */
    private CyNetwork createNetwork(String location, int file_type) throws IOException {

        GraphReader reader;
        taskMonitor.setPercentCompleted(5);

        //  Set the reader according to what file type was passed.
//        if (file_type == Cytoscape.FILE_SIF) {
//            reader = new InteractionsReader(biodataserver, species, location, taskMonitor);
//        } else
        if (file_type == Cytoscape.FILE_GML) {
            reader = new GMLReader(location, taskMonitor);
        } else {
            throw new IOException("File Type not Supported.");
        }

        // Have the GraphReader read the given file
        reader.read();

        //  Get the RootGraph indices of the nodes and
        //  Edges that were just created
        final int[] nodes = reader.getNodeIndicesArray();
        final int[] edges = reader.getEdgeIndicesArray();

        File file = new File (location);
        final String title = file.getName();

        // Create a new cytoscape.data.CyNetwork from these nodes and edges
        taskMonitor.setStatus("Creating Cytoscape Network...");

        //  Create the CyNetwork
        //  First, set the view threshold to 0.  By doing so, we can disable
        //  the auto-creating of the CyNetworkView.
        int realThreshold = Integer.parseInt(CytoscapeInit.getProperties().getProperty("viewThreshold"));
        CytoscapeInit.getProperties().setProperty("viewThreshold", "0");
        CyNetwork network = Cytoscape.createNetwork(nodes, edges,
            CyNetworkNaming.getSuggestedNetworkTitle (title));

        //  Reset back to the real View Threshold
        CytoscapeInit.getProperties().setProperty("viewThreshold", String.valueOf(realThreshold));

        //  Store GML Data as a Network Attribute
        if (file_type == Cytoscape.FILE_GML) {
            network.putClientData("GML", reader);
        }

        //  Conditionally, Create the CyNetworkView
        if (network.getNodeCount() < Integer.parseInt(CytoscapeInit.getProperties().getProperty("viewThreshold"))  ) {
            createCyNetworkView(network);

            //  Layout Network
            if (Cytoscape.getNetworkView(network.getIdentifier()) != null) {
                ((GMLReader) reader).layout(Cytoscape.getNetworkView(network.getIdentifier()));
            }

            //  Lastly, make the GraphView Canvas Visible.
            SwingUtilities.invokeLater(new Runnable () {
                public void run() {
//                    PGraphView view =(PGraphView)
                    		((DGraphView) Cytoscape.getCurrentNetworkView()).getCanvas().setVisible(true);
//                    PCanvas pCanvas = view.getCanvas();
//                    pCanvas.setVisible(true);
                }
            });
        }
        return network;
    }

    /**
     * Creates the CyNetworkView.
     * Most of this code is copied directly from Cytoscape.createCyNetworkView.
     * However, it requires a bit of a hack to actually hide the network
     * view from the user, and I didn't want to use this hack in the core
     * Cytoscape.java class.
     */
    private void createCyNetworkView (CyNetwork cyNetwork) {
        final DingNetworkView  view = new DingNetworkView (cyNetwork, cyNetwork.getTitle());

      //  Start of Hack:  Hide the View
//      PCanvas pCanvas =
    		  view.getCanvas().setVisible(false);
//      pCanvas.setVisible(false);
      //  End of Hack

      view.setIdentifier(cyNetwork.getIdentifier());
      Cytoscape.getNetworkViewMap().put(cyNetwork.getIdentifier(), view);
      view.setTitle(cyNetwork.getTitle());

      // if Squiggle function enabled, enable squiggling on the created view
//      if (Cytoscape.isSquiggleEnabled()) {
//        view.getSquiggleHandler().beginSquiggling();
//      }

      // set the selection mode on the view
      Cytoscape.setSelectionMode(Cytoscape.getSelectionMode(), view);

      Cytoscape.firePropertyChange
              (cytoscape.view.CytoscapeDesktop.NETWORK_VIEW_CREATED,null, view);

      //  Instead of calling fitContent(), access PGraphView directly.
//      view.getCanvas().getCamera().animateViewToCenterBounds
//                    (view.getCanvas().getLayer().getFullBounds(), true, 0);
    }
}