import java.awt.datatransfer.*;
import java.awt.dnd.*;
import java.awt.event.*;
+import java.lang.reflect.Constructor;
import java.util.*;
import javax.swing.*;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
/**
* DOCUMENT ME!
{
/** 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.
}
{
if (jalview.bin.Cache.vamsasJarsPresent())
{
+ setupVamsasDisconnectedGui();
VamsasMenu.setVisible(true);
- vamsasLoad.setVisible(true);
+ final Desktop us = this;
+ VamsasMenu.addMenuListener(new MenuListener() {
+ // this listener remembers when the menu was first selected, and
+ // doesn't rebuild the session list until it has been cleared and
+ // reselected again.
+ boolean refresh=true;
+ public void menuCanceled(MenuEvent e)
+ {
+ refresh=true;
+ }
+
+ public void menuDeselected(MenuEvent e)
+ {
+ refresh = true;
+ }
+
+ public void menuSelected(MenuEvent e)
+ {
+ if (refresh)
+ {
+ us.buildVamsasStMenu();
+ refresh=false;
+ }
+ }
+ });
+ vamsasStart.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();
}
;
});
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
getProperty(
"LAST_DIRECTORY"),
- new String[]
- {
- "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
- "jar"
- },
- new String[]
- {
- "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
- }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+ jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
+ jalview.io.AppletFormatAdapter.READABLE_FNAMES,
+ jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Open local file");
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);
}
- jalview.gui.VamsasClient v_client = null;
- public void vamsasLoad_actionPerformed(ActionEvent e)
+ jalview.gui.VamsasApplication v_client = null;
+ public void vamsasImport_actionPerformed(ActionEvent e)
+ {
+ if (v_client==null)
+ {
+ // Load and try to start a session.
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+ getProperty("LAST_DIRECTORY"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Open a saved VAMSAS session");
+ chooser.setToolTipText("select a vamsas session to be opened as a new vamsas session.");
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ try {
+ v_client = new jalview.gui.VamsasApplication(this,
+ chooser.getSelectedFile());
+ } catch (Exception ex)
+ {
+ jalview.bin.Cache.log.error("New vamsas session from existing session file failed:",ex);
+ return;
+ }
+ setupVamsasConnectedGui();
+ v_client.initial_update(); // TODO: thread ?
+ }
+ }else {
+ jalview.bin.Cache.log.error("Implementation error - load session from a running session is not supported.");
+ }
+ }
+
+ public void vamsasStart_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);
+ setupVamsasConnectedGui();
+ v_client.initial_update(); // TODO: thread ?
}
else
{
// store current data in session.
- v_client.push_update();
+ v_client.push_update(); // TODO: thread
}
}
+ protected void setupVamsasConnectedGui()
+ {
+ vamsasStart.setText("Session Update");
+ vamsasSave.setVisible(true);
+ vamsasStop.setVisible(true);
+ vamsasImport.setVisible(false); // Document import to existing session is not possible for vamsas-client-1.0.
+ }
+ protected void setupVamsasDisconnectedGui()
+ {
+ vamsasSave.setVisible(false);
+ vamsasStop.setVisible(false);
+ vamsasImport.setVisible(true);
+ vamsasStart.setText("New Vamsas Session...");
+ }
+
public void vamsasStop_actionPerformed(ActionEvent e)
{
if (v_client != null)
{
v_client.end_session();
v_client = null;
- this.vamsasStop.setVisible(false);
- this.vamsasLoad.setText("Start Vamsas Session...");
+ setupVamsasDisconnectedGui();
+ }
+ }
+ protected void buildVamsasStMenu()
+ {
+ if (v_client == null)
+ {
+ String[] sess = null;
+ try
+ {
+ sess = VamsasApplication.getSessionList();
+ } catch (Exception e)
+ {
+ jalview.bin.Cache.log.warn(
+ "Problem getting current sessions list.", e);
+ sess = null;
+ }
+ if (sess != null)
+ {
+ jalview.bin.Cache.log.debug("Got current sessions list: "
+ + sess.length + " entries.");
+ VamsasStMenu.removeAll();
+ for (int i = 0; i < sess.length; i++)
+ {
+ JMenuItem sessit = new JMenuItem();
+ sessit.setText(sess[i]);
+ sessit.setToolTipText("Connect to session " + sess[i]);
+ final Desktop dsktp = this;
+ final String mysesid = sess[i];
+ sessit.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ if (dsktp.v_client == null)
+ {
+ dsktp.v_client = new VamsasApplication(dsktp, mysesid);
+ dsktp.setupVamsasConnectedGui();
+ dsktp.v_client.initial_update();
+ }
+ };
+ });
+ VamsasStMenu.add(sessit);
+ }
+ VamsasStMenu.setVisible(true);
+ }
+ else
+ {
+ jalview.bin.Cache.log.debug("No current vamsas sessions.");
+ VamsasStMenu.removeAll();
+ VamsasStMenu.setVisible(false);
+ }
+ } else {
+ // Not interested in the content. Just hide ourselves.
+ VamsasStMenu.setVisible(false);
}
}
+ public void vamsasSave_actionPerformed(ActionEvent e)
+ {
+ if (v_client != null)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+ getProperty(
+ "LAST_DIRECTORY"), new String[]
+ {"vdj"}, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+ new String[]
+ {"Vamsas Document"}, "Vamsas Document");
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Save Vamsas Document Archive");
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ java.io.File choice = chooser.getSelectedFile();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+ String warnmsg=null;
+ String warnttl=null;
+ try {
+ v_client.vclient.storeDocument(choice);
+ }
+ catch (Error ex)
+ {
+ warnttl = "Serious Problem saving Vamsas Document";
+ warnmsg = ex.toString();
+ jalview.bin.Cache.log.error("Error Whilst saving document to "+choice,ex);
+
+ }
+ catch (Exception ex)
+ {
+ warnttl = "Problem saving Vamsas Document.";
+ warnmsg = ex.toString();
+ jalview.bin.Cache.log.warn("Exception Whilst saving document to "+choice,ex);
+
+ }
+ if (warnmsg!=null)
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ warnmsg, warnttl,
+ JOptionPane.ERROR_MESSAGE);
+ }
+ }
+ }
+ }
/**
* hide vamsas user gui bits when a vamsas document event is being handled.
* @param b true to hide gui, false to reveal gui
{
jalview.bin.Cache.log.debug("Setting gui for Vamsas update " +
(b ? "in progress" : "finished"));
- vamsasLoad.setVisible(!b);
+ vamsasStart.setVisible(!b);
vamsasStop.setVisible(!b);
+ vamsasSave.setVisible(!b);
+ }
+ 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