import java.util.*;
import javax.swing.*;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
/**
* DOCUMENT ME!
//Need to decide if the Memory Usage is to be included in
//Next release or not.
- // public static MyDesktopPane desktop;
- public static JDesktopPane desktop;
+ public static MyDesktopPane desktop;
+ // public static JDesktopPane desktop;
static int openFrameCount = 0;
*/
public Desktop()
{
+ /**
+ * A note to implementors. It is ESSENTIAL that any
+ * activities that might block are spawned off as threads rather
+ * than waited for during this constructor.
+ */
instance = this;
doVamsasClientCheck();
doGroovyCheck();
- Image image = null;
- 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 MyDesktopPane(true);
- desktop = new JDesktopPane();
+ boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",false);
+ desktop = new MyDesktopPane(selmemusage);
+ showMemusage.setSelected(selmemusage);
desktop.setBackground(Color.white);
getContentPane().setLayout(new BorderLayout());
getContentPane().add(desktop, BorderLayout.CENTER);
this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
+ // Spawn a thread that shows the splashscreen
+ new SplashScreen();
- /////////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));
- 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);
}
}
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");
reorderAssociatedWindows(false, true);
}
+ /* (non-Javadoc)
+ * @see jalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.ActionEvent)
+ */
+ protected void garbageCollect_actionPerformed(ActionEvent e)
+ {
+ // We simply collect the garbage
+ jalview.bin.Cache.log.debug("Collecting garbage...");
+ System.gc();
+ jalview.bin.Cache.log.debug("Finished garbage collection.");
+ }
+
+ /* (non-Javadoc)
+ * @see jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent)
+ */
+ protected void showMemusage_actionPerformed(ActionEvent e)
+ {
+ desktop.showMemoryUsage(showMemusage.isSelected());
+ }
+
void reorderAssociatedWindows(boolean minimize, boolean close)
{
JInternalFrame[] frames = desktop.getAllFrames();
}
}
}
-
/**
* DOCUMENT ME!
*
}
}
- /* 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);
{
if (fileLoadingCount == 0)
{
+ addProgressPanel("Loading File: " + fileName + " ");
+
+ }
+ fileLoadingCount++;
+ }
+ private JProgressBar addProgressPanel(String string)
+ {
+ if (progressPanel==null)
+ {
progressPanel = new JPanel(new BorderLayout());
- JProgressBar progressBar = new JProgressBar();
- progressBar.setIndeterminate(true);
+ totalProgressCount=0;
+ }
+ JProgressBar progressBar = new JProgressBar();
+ progressBar.setIndeterminate(true);
- progressPanel.add(new JLabel("Loading File: " + fileName + " "),
- BorderLayout.WEST);
+ progressPanel.add(new JLabel(string),
+ BorderLayout.WEST);
- progressPanel.add(progressBar, BorderLayout.CENTER);
+ progressPanel.add(progressBar, BorderLayout.CENTER);
- instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
+ instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
+ totalProgressCount++;
+ validate();
+ return progressBar;
+ }
+ int totalProgressCount=0;
+ private void removeProgressPanel(JProgressBar progbar)
+ {
+ if (progressPanel!=null)
+ {
+ progressPanel.remove(progbar);
+ if (--totalProgressCount<1)
+ {
+ this.getContentPane().remove(progressPanel);
+ progressPanel = null;
+ }
}
- fileLoadingCount++;
validate();
}
-
public void stopLoading()
{
fileLoadingCount--;
}
validate();
}
-
public static int getViewCount(String viewId)
{
int count = 0;
}
- 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)
+ {
+ Thread rthr = new Thread(new Runnable() {
+
+ public void run()
+ {
+ dsktp.v_client = new VamsasApplication(dsktp, mysesid);
+ dsktp.setupVamsasConnectedGui();
+ dsktp.v_client.initial_update();
+ }
+
+ });
+ rthr.start();
+ }
+ };
+ });
+ VamsasStMenu.add(sessit);
+ }
+ // don't show an empty menu.
+ VamsasStMenu.setVisible(sess.length>0);
+
+ }
+ 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);
+ }
+ }
+ }
+ }
+ JProgressBar vamUpdate = null;
/**
* 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);
+
+ if (vamUpdate!=null)
+ {
+ this.removeProgressPanel(vamUpdate);
+ }
+ if (b)
+ {
+ vamUpdate = this.addProgressPanel("Updating vamsas session");
+ }
+ vamsasStart.setVisible(!b);
vamsasStop.setVisible(!b);
-
+ vamsasSave.setVisible(!b);
}
public JInternalFrame[] getAllFrames()
public void checkForQuestionnaire(String url)
{
UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url);
- javax.swing.SwingUtilities.invokeLater(jvq);
+ //javax.swing.SwingUtilities.invokeLater(jvq);
+ new Thread(jvq).start();
}
-
- /*DISABLED
- class MyDesktopPane extends JDesktopPane implements Runnable
+ /**
+ * Proxy class for JDesktopPane which optionally
+ * displays the current memory usage and highlights
+ * the desktop area with a red bar if free memory runs low.
+ * @author AMW
+ */
+ public class MyDesktopPane extends JDesktopPane implements Runnable
{
+
boolean showMemoryUsage = false;
Runtime runtime;
java.text.NumberFormat df;
worker.start();
}
}
-
+ public boolean isShowMemoryUsage()
+ {
+ return showMemoryUsage;
+ }
public void run()
{
df = java.text.NumberFormat.getNumberInstance();
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()
+ groovyShell.setText("Groovy Console...");
+ 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() {
+ * loaded.
+ */
+ public static AlignFrame[] getAlignframes() {
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-
+
if (frames == null)
{
return null;
git://source.jalview.org / jalview.git / blobdiff