/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
package jalview.gui;
import jalview.io.*;
+
import java.awt.*;
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!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class Desktop
- extends jalview.jbgui.GDesktop implements DropTargetListener,
- ClipboardOwner
+public class Desktop extends jalview.jbgui.GDesktop implements
+ DropTargetListener, ClipboardOwner, IProgressIndicator
{
/** DOCUMENT ME!! */
public static Desktop instance;
- //Need to decide if the Memory Usage is to be included in
- //Next release or not.
+ // 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 JDesktopPane desktop;
static int openFrameCount = 0;
+
static final int xOffset = 30;
+
static final int yOffset = 30;
+
public static jalview.ws.Discoverer discoverer;
public static Object[] jalviewClipboard;
+
public static boolean internalCopy = false;
static int fileLoadingCount = 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();
- 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)
- {
- }
+ doGroovyCheck();
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);
String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");
String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");
- if ( (x != null) && (y != null) && (width != null) && (height != null))
+ if ((x != null) && (y != null) && (width != null) && (height != null))
{
- setBounds(Integer.parseInt(x), Integer.parseInt(y),
- Integer.parseInt(width), Integer.parseInt(height));
+ setBounds(Integer.parseInt(x), Integer.parseInt(y), Integer
+ .parseInt(width), Integer.parseInt(height));
}
else
{
- setBounds( (int) (screenSize.width - 900) / 2,
- (int) (screenSize.height - 650) / 2, 900, 650);
+ setBounds((int) (screenSize.width - 900) / 2,
+ (int) (screenSize.height - 650) / 2, 900, 650);
}
this.addWindowListener(new WindowAdapter()
});
this.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent evt)
+ {
+ if (SwingUtilities.isRightMouseButton(evt))
{
- public void mousePressed(MouseEvent evt)
- {
- if(SwingUtilities.isRightMouseButton(evt))
- {
- showPasteMenu(evt.getX(), evt.getY());
- }
- }
- });
-
+ showPasteMenu(evt.getX(), evt.getY());
+ }
+ }
+ });
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.
+ discoverer = new jalview.ws.Discoverer(); // Only gets started if gui is
+ // displayed.
}
private void doVamsasClientCheck()
{
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);
}
}
if (contents != null)
{
String file = (String) contents
- .getTransferData(DataFlavor.stringFlavor);
+ .getTransferData(DataFlavor.stringFlavor);
String format = new IdentifyFile().Identify(file,
- FormatAdapter.PASTE);
+ FormatAdapter.PASTE);
new FileLoader().LoadFile(file, FormatAdapter.PASTE, format);
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
- System.out.println("Unable to paste alignment from system clipboard:\n"
- + ex);
+ System.out
+ .println("Unable to paste alignment from system clipboard:\n"
+ + ex);
}
}
/**
* DOCUMENT ME!
- *
- * @param frame DOCUMENT ME!
- * @param title DOCUMENT ME!
- * @param w DOCUMENT ME!
- * @param h DOCUMENT ME!
+ *
+ * @param frame
+ * DOCUMENT ME!
+ * @param title
+ * DOCUMENT ME!
+ * @param w
+ * DOCUMENT ME!
+ * @param h
+ * DOCUMENT ME!
*/
- public static synchronized void addInternalFrame(final JInternalFrame frame,
- String title, int w, int h)
+ public static synchronized void addInternalFrame(
+ final JInternalFrame frame, String title, int w, int h)
{
addInternalFrame(frame, title, w, h, true);
}
/**
* DOCUMENT ME!
- *
- * @param frame DOCUMENT ME!
- * @param title DOCUMENT ME!
- * @param w DOCUMENT ME!
- * @param h DOCUMENT ME!
- * @param resizable DOCUMENT ME!
+ *
+ * @param frame
+ * DOCUMENT ME!
+ * @param title
+ * DOCUMENT ME!
+ * @param w
+ * DOCUMENT ME!
+ * @param h
+ * DOCUMENT ME!
+ * @param resizable
+ * DOCUMENT ME!
*/
- public static synchronized void addInternalFrame(final JInternalFrame frame,
- String title, int w, int h, boolean resizable)
+ public static synchronized void addInternalFrame(
+ final JInternalFrame frame, String title, int w, int h,
+ boolean resizable)
{
+ // TODO: consider fixing method to update entries in the window submenu with
+ // the current window title
+
frame.setTitle(title);
if (frame.getWidth() < 1 || frame.getHeight() < 1)
{
// THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN
// A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
// IF JALVIEW IS RUNNING HEADLESS
- /////////////////////////////////////////////////
+ // ///////////////////////////////////////////////
if (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true"))
+ && System.getProperty("java.awt.headless").equals("true"))
{
return;
}
if (frame.getX() < 1 && frame.getY() < 1)
{
- frame.setLocation(xOffset * openFrameCount,
- yOffset * ( (openFrameCount - 1) % 10) + yOffset);
+ frame.setLocation(xOffset * openFrameCount, yOffset
+ * ((openFrameCount - 1) % 10) + yOffset);
}
final JMenuItem menuItem = new JMenuItem(title);
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
- {
- public void internalFrameActivated(javax.swing.event.
- InternalFrameEvent evt)
- {
- JInternalFrame itf = desktop.getSelectedFrame();
- if (itf != null)
- {
- itf.requestFocus();
- }
+ frame
+ .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ {
+ public void internalFrameActivated(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ JInternalFrame itf = desktop.getSelectedFrame();
+ if (itf != null)
+ {
+ itf.requestFocus();
+ }
- }
+ }
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- {
- PaintRefresher.RemoveComponent(frame);
- openFrameCount--;
- windowMenu.remove(menuItem);
- JInternalFrame itf = desktop.getSelectedFrame();
- if (itf != null)
- {
- itf.requestFocus();
- }
- System.gc();
- }
- ;
- });
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ PaintRefresher.RemoveComponent(frame);
+ openFrameCount--;
+ windowMenu.remove(menuItem);
+ JInternalFrame itf = desktop.getSelectedFrame();
+ if (itf != null)
+ {
+ itf.requestFocus();
+ }
+ System.gc();
+ };
+ });
menuItem.addActionListener(new ActionListener()
{
{
frame.setSelected(true);
frame.setIcon(false);
- }
- catch (java.beans.PropertyVetoException ex)
+ } catch (java.beans.PropertyVetoException ex)
{
}
{
frame.setSelected(true);
frame.requestFocus();
+ } catch (java.beans.PropertyVetoException ve)
+ {
}
- catch (java.beans.PropertyVetoException ve)
- {}
}
public void lostOwnership(Clipboard clipboard, Transferable contents)
}
public void dragEnter(DropTargetDragEvent evt)
- {}
+ {
+ }
public void dragExit(DropTargetEvent evt)
- {}
+ {
+ }
public void dragOver(DropTargetDragEvent evt)
- {}
+ {
+ }
public void dropActionChanged(DropTargetDragEvent evt)
- {}
+ {
+ }
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void drop(DropTargetDropEvent evt)
{
try
{
DataFlavor uriListFlavor = new DataFlavor(
- "text/uri-list;class=java.lang.String");
+ "text/uri-list;class=java.lang.String");
if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
{
- //Works on Windows and MacOSX
+ // Works on Windows and MacOSX
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
- files = (java.util.List) t.getTransferData(DataFlavor.
- javaFileListFlavor);
+ files = (java.util.List) t
+ .getTransferData(DataFlavor.javaFileListFlavor);
}
else if (t.isDataFlavorSupported(uriListFlavor))
{
String data = (String) t.getTransferData(uriListFlavor);
files = new java.util.ArrayList(1);
for (java.util.StringTokenizer st = new java.util.StringTokenizer(
- data,
- "\r\n");
- st.hasMoreTokens(); )
+ data, "\r\n"); st.hasMoreTokens();)
{
String s = st.nextToken();
if (s.startsWith("#"))
files.add(file);
}
}
+ } catch (Exception e)
+ {
}
- catch (Exception e)
- {}
if (files != null)
{
}
else
{
- format = new IdentifyFile().Identify(file,
- protocol);
+ format = new IdentifyFile().Identify(file, protocol);
}
new FileLoader().LoadFile(file, protocol, format);
}
+ } catch (Exception ex)
+ {
}
- catch (Exception ex)
- {}
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
{
- 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"));
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+ .getProperty("LAST_DIRECTORY"),
+ 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");
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+ .getSelectedFile().getParent());
String format = null;
if (chooser.getSelectedFormat().equals("Jalview"))
if (viewport != null)
{
- new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format);
+ new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE,
+ format);
}
else
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
{
}
}
- int reply = JOptionPane.showInternalConfirmDialog(desktop,
- panel, "Input Alignment From URL",
- JOptionPane.OK_CANCEL_OPTION);
+ int reply = JOptionPane.showInternalConfirmDialog(desktop, panel,
+ "Input Alignment From URL", JOptionPane.OK_CANCEL_OPTION);
if (reply != JOptionPane.OK_OPTION)
{
{
if (viewport != null)
{
- new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, "Jalview");
+ new FileLoader().LoadFile(viewport, url, FormatAdapter.URL,
+ "Jalview");
}
else
{
if (format.equals("URL NOT FOUND"))
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Couldn't locate " + url,
- "URL not found",
- JOptionPane.WARNING_MESSAGE);
+ "Couldn't locate " + url, "URL not found",
+ JOptionPane.WARNING_MESSAGE);
return;
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void aboutMenuItem_actionPerformed(ActionEvent e)
{
- StringBuffer message = new StringBuffer("JalView version " +
- jalview.bin.Cache.getProperty(
- "VERSION") +
- "; last updated: " +
- jalview.bin.
- Cache.getDefault("BUILD_DATE",
- "unknown"));
+ StringBuffer message = new StringBuffer("Jalview version "
+ + jalview.bin.Cache.getProperty("VERSION") + "; last updated: "
+ + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
- jalview.bin.Cache.getProperty("VERSION")))
+ jalview.bin.Cache.getProperty("VERSION")))
{
- message.append("\n\n!! Jalview version "
- + jalview.bin.Cache.getProperty("LATEST_VERSION")
- +
- " is available for download from http://www.jalview.org !!\n");
+ message
+ .append("\n\n!! Jalview version "
+ + jalview.bin.Cache.getProperty("LATEST_VERSION")
+ + " is available for download from http://www.jalview.org !!\n");
}
-
- message.append("\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +
- "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." +
- "\nFor all issues relating to Jalview, email help@jalview.org" +
- "\n\nIf you use JalView, please cite:" +
- "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" +
- "\nBioinformatics, 2004 20;426-7.");
+ // TODO: update this text for each release or centrally store it for lite
+ // and application
+ message
+ .append("\nAuthors: Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,\n David Martin & Geoff Barton."
+ + "\nDevelopment managed by The Barton Group, University of Dundee, Scotland, UK.\n"
+ + "\nFor help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list\n"
+ + "\nIf you use Jalview, please cite:"
+ + "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\""
+ + "\nBioinformatics, 2004 20;426-7.");
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- message.toString(), "About Jalview",
- JOptionPane.INFORMATION_MESSAGE);
+ message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void documentationMenuItem_actionPerformed(ActionEvent e)
{
javax.help.HelpBroker hb = hs.createHelpBroker();
hb.setCurrentID("home");
hb.setDisplayed(true);
+ } catch (Exception ex)
+ {
}
- catch (Exception ex)
- {}
}
public void closeAll_actionPerformed(ActionEvent e)
try
{
frames[i].setClosed(true);
+ } catch (java.beans.PropertyVetoException ex)
+ {
}
- catch (java.beans.PropertyVetoException ex)
- {}
}
System.out.println("ALL CLOSED");
-
+ if (v_client!=null)
+ {
+ // TODO clear binding to vamsas document objects on close_all
+
+ }
}
public void raiseRelated_actionPerformed(ActionEvent e)
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();
AlignViewport source = null, target = null;
if (frames[0] instanceof AlignFrame)
{
- source = ( (AlignFrame) frames[0]).getCurrentView();
+ source = ((AlignFrame) frames[0]).getCurrentView();
}
else if (frames[0] instanceof TreePanel)
{
- source = ( (TreePanel) frames[0]).getViewPort();
+ source = ((TreePanel) frames[0]).getViewPort();
}
else if (frames[0] instanceof PCAPanel)
{
- source = ( (PCAPanel) frames[0]).av;
+ source = ((PCAPanel) frames[0]).av;
}
else if (frames[0].getContentPane() instanceof PairwiseAlignPanel)
{
- source = ( (PairwiseAlignPanel) frames[0].getContentPane()).av;
+ source = ((PairwiseAlignPanel) frames[0].getContentPane()).av;
}
if (source != null)
}
if (frames[i] instanceof AlignFrame)
{
- target = ( (AlignFrame) frames[i]).getCurrentView();
+ target = ((AlignFrame) frames[i]).getCurrentView();
}
else if (frames[i] instanceof TreePanel)
{
- target = ( (TreePanel) frames[i]).getViewPort();
+ target = ((TreePanel) frames[i]).getViewPort();
}
else if (frames[i] instanceof PCAPanel)
{
- target = ( (PCAPanel) frames[i]).av;
+ target = ((PCAPanel) frames[i]).av;
}
else if (frames[i].getContentPane() instanceof PairwiseAlignPanel)
{
- target = ( (PairwiseAlignPanel) frames[i].getContentPane()).av;
+ target = ((PairwiseAlignPanel) frames[i].getContentPane()).av;
}
if (source == target)
}
}
+ } catch (java.beans.PropertyVetoException ex)
+ {
}
- catch (java.beans.PropertyVetoException ex)
- {}
}
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void preferences_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void saveState_actionPerformed(ActionEvent e)
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty(
- "LAST_DIRECTORY"), new String[]
- {"jar"},
- new String[]
- {"Jalview Project"}, "Jalview Project");
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+ .getProperty("LAST_DIRECTORY"), new String[]
+ { "jar" }, new String[]
+ { "Jalview Project" }, "Jalview Project");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save State");
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void loadState_actionPerformed(ActionEvent e)
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty(
- "LAST_DIRECTORY"), new String[]
- {"jar"},
- new String[]
- {"Jalview Project"}, "Jalview Project");
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+ .getProperty("LAST_DIRECTORY"), new String[]
+ { "jar" }, new String[]
+ { "Jalview Project" }, "Jalview Project");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Restore state");
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getAbsolutePath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+ .getSelectedFile().getParent());
new Jalview2XML().LoadJalviewAlign(choice);
}
}
- /* 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);
+ new SequenceFetcher(this);
}
JPanel progressPanel;
{
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 static int getViewCount(String viewId)
{
+ AlignViewport[] aps = getViewports(viewId);
+ return (aps==null) ? 0 : aps.length;
+ }
+ /**
+ *
+ * @param viewId
+ * @return all AlignmentPanels concerning the viewId sequence set
+ */
+ public static AlignmentPanel[] getAlignmentPanels(String viewId)
+ {
int count = 0;
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ ArrayList aps = new ArrayList();
for (int t = 0; t < frames.length; t++)
{
if (frames[t] instanceof AlignFrame)
AlignFrame af = (AlignFrame) frames[t];
for (int a = 0; a < af.alignPanels.size(); a++)
{
- if (viewId.equals(
- ( (AlignmentPanel) af.alignPanels.elementAt(a)).av.
- getSequenceSetId())
- )
+ if (viewId
+ .equals(((AlignmentPanel) af.alignPanels.elementAt(a)).av
+ .getSequenceSetId()))
{
- count++;
+ aps.add(af.alignPanels.elementAt(a));
}
}
}
}
-
- return count;
+ if (aps.size()==0)
+ {
+ return null;
+ }
+ AlignmentPanel[] vap = new AlignmentPanel[aps.size()];
+ for (int t=0;t<vap.length;t++)
+ {
+ vap[t] = (AlignmentPanel) aps.get(t);
+ }
+ return vap;
+ }
+ /**
+ * get all the viewports on an alignment.
+ * @param sequenceSetId unique alignment id
+ * @return all viewports on the alignment bound to sequenceSetId
+ */
+ public static AlignViewport[] getViewports(String sequenceSetId)
+ {
+ Vector viewp = new Vector();
+ if (desktop != null)
+ {
+ javax.swing.JInternalFrame[] frames = instance.getAllFrames();
+
+ for (int t = 0; t < frames.length; t++)
+ {
+ if (frames[t] instanceof AlignFrame)
+ {
+ AlignFrame afr = ((AlignFrame) frames[t]);
+ if (afr.getViewport().getSequenceSetId()
+ .equals(sequenceSetId))
+ {
+ if (afr.alignPanels!=null)
+ {
+ for (int a = 0; a < afr.alignPanels.size(); a++)
+ {
+ if (sequenceSetId
+ .equals(((AlignmentPanel) afr.alignPanels.elementAt(a)).av
+ .getSequenceSetId()))
+ {
+ viewp.addElement(((AlignmentPanel)afr.alignPanels.elementAt(a)).av);
+ }
+ }
+ } else {
+ viewp.addElement(((AlignFrame) frames[t]).getViewport());
+ }
+ }
+ }
+ }
+ if (viewp.size() > 0)
+ {
+ AlignViewport[] vp = new AlignViewport[viewp.size()];
+ viewp.copyInto(vp);
+ return vp;
+ }
+ }
+ return null;
}
public void explodeViews(AlignFrame af)
{
AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(i);
AlignFrame newaf = new AlignFrame(ap);
- if (ap.av.explodedPosition != null &&
- !ap.av.explodedPosition.equals(af.getBounds()))
+ if (ap.av.explodedPosition != null
+ && !ap.av.explodedPosition.equals(af.getBounds()))
{
newaf.setBounds(ap.av.explodedPosition);
}
ap.av.gatherViewsHere = false;
- addInternalFrame(newaf, af.getTitle(),
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
}
af.alignPanels.clear();
}
- 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)
{
- // Start a session.
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty("LAST_DIRECTORY"));
+ // Load and try to start a session.
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+ .getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Load Vamsas file");
- chooser.setToolTipText("Import");
+ 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)
{
- v_client = new jalview.gui.VamsasClient(this,
- chooser.getSelectedFile());
- this.vamsasLoad.setText("Session Update");
- this.vamsasStop.setVisible(true);
- v_client.initial_update();
- v_client.startWatcher();
+ 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"));
+ *
+ * chooser.setFileView(new JalviewFileView());
+ * chooser.setDialogTitle("Load Vamsas file");
+ * chooser.setToolTipText("Import");
+ *
+ * int value = chooser.showOpenDialog(this);
+ *
+ * if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new
+ * jalview.gui.VamsasApplication(this, chooser.getSelectedFile());
+ *
+ */
+ 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
+ *
+ * @param b
+ * true to hide gui, false to reveal gui
*/
public void setVamsasUpdate(boolean b)
{
- jalview.bin.Cache.log.debug("Setting gui for Vamsas update " +
- (b ? "in progress" : "finished"));
- vamsasLoad.setVisible(!b);
- vamsasStop.setVisible(!b);
+ jalview.bin.Cache.log.debug("Setting gui for Vamsas update "
+ + (b ? "in progress" : "finished"));
+ 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()
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.
+ * Checks the given url to see if it gives a response indicating that the user
+ * should be informed of a new questionnaire.
+ *
* @param url
*/
public void checkForQuestionnaire(String url)
{
UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url);
- javax.swing.SwingUtilities.invokeLater(jvq);
+ // javax.swing.SwingUtilities.invokeLater(jvq);
+ new Thread(jvq).start();
}
- 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;
- float maxMemory, allocatedMemory, freeMemory, totalFreeMemory, percentUsage;
+ float maxMemory, allocatedMemory, freeMemory, totalFreeMemory,
+ percentUsage;
public MyDesktopPane(boolean showMemoryUsage)
{
}
}
+ public boolean isShowMemoryUsage()
+ {
+ return showMemoryUsage;
+ }
+
public void run()
{
df = java.text.NumberFormat.getNumberInstance();
percentUsage = (totalFreeMemory / maxMemory) * 100;
- // if (percentUsage < 20)
+ // if (percentUsage < 20)
{
- // border1 = BorderFactory.createMatteBorder(12, 12, 12, 12, Color.red);
- // instance.set.setBorder(border1);
+ // border1 = BorderFactory.createMatteBorder(12, 12, 12, 12,
+ // Color.red);
+ // instance.set.setBorder(border1);
}
repaint();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
public void paintComponent(Graphics g)
{
- if(showMemoryUsage)
+ 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());
+ + "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 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.
+ */
+ public static 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);
+ }
+ }
+
+ /**
+ * Progress bars managed by the IProgressIndicator method.
+ */
+ private Hashtable progressBars;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
+ */
+ public void setProgressBar(String message, long id)
+ {
+ if (progressBars == null)
+ {
+ progressBars = new Hashtable();
+ }
+
+ if (progressBars.get(new Long(id)) != null)
+ {
+ JProgressBar progressPanel = (JProgressBar) progressBars
+ .remove(new Long(id));
+ removeProgressPanel(progressPanel);
+ }
+ else
+ {
+ progressBars.put(new Long(id), addProgressPanel(message));
+ }
+ }
+
+ /**
+ * This will return the first AlignFrame viewing AlignViewport av. It will
+ * break if there are more than one AlignFrames viewing a particular av. This
+ *
+ * @param av
+ * @return alignFrame for av
+ */
+ public static AlignFrame getAlignFrameFor(AlignViewport av)
+ {
+ if (desktop != null)
+ {
+ AlignmentPanel[] aps = getAlignmentPanels(av.getSequenceSetId());
+ for (int panel=0;aps!=null && panel<aps.length;panel++)
+ { if (aps[panel]!=null && aps[panel].av==av) {
+ return aps[panel].alignFrame;
+ }
+ }
+ }
+ return null;
}
+}