import java.awt.datatransfer.*;
import java.awt.dnd.*;
import java.awt.event.*;
+import java.lang.reflect.Constructor;
import java.util.*;
import javax.swing.*;
{
/** DOCUMENT ME!! */
public static Desktop instance;
- public static JDesktopPane desktop;
+
+ //Need to decide if the Memory Usage is to be included in
+ //Next release or not.
+ // public static MyDesktopPane desktop;
+ public static JDesktopPane desktop;
+
+
static int openFrameCount = 0;
static final int xOffset = 30;
static final int yOffset = 30;
{
instance = this;
doVamsasClientCheck();
- Image image = null;
+ doGroovyCheck();
- try
- {
- java.net.URL url = getClass().getResource("/images/logo.gif");
-
- if (url != null)
- {
- image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-
- MediaTracker mt = new MediaTracker(this);
- mt.addImage(image, 0);
- mt.waitForID(0);
- setIconImage(image);
- }
- }
- catch (Exception ex)
- {
- }
setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+
desktop = new JDesktopPane();
desktop.setBackground(Color.white);
getContentPane().setLayout(new BorderLayout());
}
});
+ this.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent evt)
+ {
+ if(SwingUtilities.isRightMouseButton(evt))
+ {
+ showPasteMenu(evt.getX(), evt.getY());
+ }
+ }
+ });
+
+
this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
/////////Add a splashscreen on startup
/////////Add a splashscreen on startup
- JInternalFrame frame = new JInternalFrame();
-
- SplashScreen splash = new SplashScreen(frame, image);
- frame.setContentPane(splash);
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
- frame.setLocation( (int) ( (getWidth() - 750) / 2),
- (int) ( (getHeight() - 160) / 2));
+ new SplashScreen();
- addInternalFrame(frame, "", 750, 160, false);
discoverer = new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
}
VamsasMenu.setVisible(true);
vamsasLoad.setVisible(true);
}
+ }
+ void showPasteMenu(int x, int y)
+ {
+ JPopupMenu popup = new JPopupMenu();
+ JMenuItem item = new JMenuItem("Paste To New Window");
+ item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ paste();
+ }
+ });
+
+ popup.add(item);
+ popup.show(this, x, y);
+ }
+
+ public void paste()
+ {
+ try
+ {
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+ Transferable contents = c.getContents(this);
+
+ if (contents != null)
+ {
+ String file = (String) contents
+ .getTransferData(DataFlavor.stringFlavor);
+
+ String format = new IdentifyFile().Identify(file,
+ FormatAdapter.PASTE);
+
+ new FileLoader().LoadFile(file, FormatAdapter.PASTE, format);
+
+ }
+ }
+ catch (Exception ex)
+ {
+ System.out.println("Unable to paste alignment from system clipboard:\n"
+ + ex);
+ }
}
/**
{
itf.requestFocus();
}
+ System.gc();
}
;
});
catch (java.beans.PropertyVetoException ex)
{}
}
+ System.out.println("ALL CLOSED");
+
}
public void raiseRelated_actionPerformed(ActionEvent e)
}
}
- /* public void vamsasLoad_actionPerformed(ActionEvent e)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Load Vamsas file");
- chooser.setToolTipText("Import");
-
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null);
- vs.load(
- chooser.getSelectedFile().getAbsolutePath()
- );
- }
-
- }*/
-
-
public void inputSequence_actionPerformed(ActionEvent e)
{
new SequenceFetcher(null);
{
AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(i);
AlignFrame newaf = new AlignFrame(ap);
- if (ap.av.explodedPosition != null)
+ if (ap.av.explodedPosition != null &&
+ !ap.av.explodedPosition.equals(af.getBounds()))
{
newaf.setBounds(ap.av.explodedPosition);
}
}
- jalview.gui.VamsasClient v_client = null;
+ jalview.gui.VamsasApplication v_client = null;
public void vamsasLoad_actionPerformed(ActionEvent e)
{
if (v_client == null)
{
// Start a session.
+ // we just start a default session for moment.
+ /*
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
getProperty("LAST_DIRECTORY"));
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- v_client = new jalview.gui.VamsasClient(this,
+ v_client = new jalview.gui.VamsasApplication(this,
chooser.getSelectedFile());
- this.vamsasLoad.setText("Session Update");
- this.vamsasStop.setVisible(true);
- v_client.initial_update();
- v_client.startWatcher();
- }
+ *
+ */
+ v_client = new VamsasApplication(this);
+ vamsasLoad.setText("Session Update");
+ vamsasStop.setVisible(true);
+ v_client.initial_update();
}
else
{
}
+ public JInternalFrame[] getAllFrames()
+ {
+ return desktop.getAllFrames();
+ }
+
+
/**
* Checks the given url to see if it gives a response indicating that
* the user should be informed of a new questionnaire.
javax.swing.SwingUtilities.invokeLater(jvq);
}
+ /*DISABLED
+ class MyDesktopPane extends JDesktopPane implements Runnable
+ {
+ boolean showMemoryUsage = false;
+ Runtime runtime;
+ java.text.NumberFormat df;
+
+ float maxMemory, allocatedMemory, freeMemory, totalFreeMemory, percentUsage;
+
+ public MyDesktopPane(boolean showMemoryUsage)
+ {
+ showMemoryUsage(showMemoryUsage);
+ }
+
+ public void showMemoryUsage(boolean showMemoryUsage)
+ {
+ this.showMemoryUsage = showMemoryUsage;
+ if (showMemoryUsage)
+ {
+ Thread worker = new Thread(this);
+ worker.start();
+ }
+ }
+
+ public void run()
+ {
+ df = java.text.NumberFormat.getNumberInstance();
+ df.setMaximumFractionDigits(2);
+ runtime = Runtime.getRuntime();
+
+ while (showMemoryUsage)
+ {
+ try
+ {
+ Thread.sleep(3000);
+ maxMemory = runtime.maxMemory() / 1048576f;
+ allocatedMemory = runtime.totalMemory() / 1048576f;
+ freeMemory = runtime.freeMemory() / 1048576f;
+ totalFreeMemory = freeMemory + (maxMemory - allocatedMemory);
+
+ percentUsage = (totalFreeMemory / maxMemory) * 100;
+
+ // if (percentUsage < 20)
+ {
+ // border1 = BorderFactory.createMatteBorder(12, 12, 12, 12, Color.red);
+ // instance.set.setBorder(border1);
+ }
+ repaint();
+
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ }
+
+ public void paintComponent(Graphics g)
+ {
+ if(showMemoryUsage)
+ {
+ if (percentUsage < 20)
+ g.setColor(Color.red);
+
+ g.drawString("Total Free Memory: " + df.format(totalFreeMemory)
+ + "MB; Max Memory: " + df.format(maxMemory)
+ + "MB; " + df.format(percentUsage) + "%", 10,
+ getHeight() - g.getFontMetrics().getHeight());
+ }
+ }
+ }*/
+ protected JMenuItem groovyShell;
+ public void doGroovyCheck() {
+ if (jalview.bin.Cache.groovyJarsPresent())
+ {
+ groovyShell = new JMenuItem();
+ groovyShell.setText("Groovy Shell...");
+ groovyShell.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e) {
+ groovyShell_actionPerformed(e);
+ }
+ });
+ toolsMenu.add(groovyShell);
+ groovyShell.setVisible(true);
+ }
+ }
+ /**
+ * Accessor method to quickly get all the AlignmentFrames
+ * loaded.
+ */
+ protected AlignFrame[] getAlignframes() {
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+
+ if (frames == null)
+ {
+ return null;
+ }
+ Vector avp=new Vector();
+ try
+ {
+ //REVERSE ORDER
+ for (int i = frames.length - 1; i > -1; i--)
+ {
+ if (frames[i] instanceof AlignFrame)
+ {
+ AlignFrame af = (AlignFrame) frames[i];
+ avp.addElement(af);
+ }
+ }
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ if (avp.size()==0)
+ {
+ return null;
+ }
+ AlignFrame afs[] = new AlignFrame[avp.size()];
+ for (int i=0,j=avp.size(); i<j; i++) {
+ afs[i] = (AlignFrame) avp.elementAt(i);
+ }
+ avp.clear();
+ return afs;
+ }
+
+ /**
+ * Add Groovy Support to Jalview
+ */
+ public void groovyShell_actionPerformed(ActionEvent e) {
+ // use reflection to avoid creating compilation dependency.
+ if (!jalview.bin.Cache.groovyJarsPresent())
+ {
+ throw new Error("Implementation Error. Cannot create groovyShell without Groovy on the classpath!");
+ }
+ try {
+ Class gcClass = Desktop.class.getClassLoader().loadClass("groovy.ui.Console");
+ Constructor gccons = gcClass.getConstructor(null);
+ java.lang.reflect.Method setvar = gcClass.getMethod("setVariable", new Class[] { String.class, Object.class} );
+ java.lang.reflect.Method run = gcClass.getMethod("run", null);
+ Object gc = gccons.newInstance(null);
+ setvar.invoke(gc, new Object[] { "Jalview", this});
+ run.invoke(gc, null);
+ }
+ catch (Exception ex)
+ {
+ jalview.bin.Cache.log.error("Groovy Shell Creation failed.",ex);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+
+ "Couldn't create the groovy Shell. Check the error log for the details of what went wrong.", "Jalview Groovy Support Failed",
+ JOptionPane.ERROR_MESSAGE);
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff