/*
- * 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
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class Desktop
- extends jalview.jbgui.GDesktop implements DropTargetListener,
- ClipboardOwner, IProgressIndicator
+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.
+ * 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();
-
setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
- boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",false);
+ boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
+ false);
desktop = new MyDesktopPane(selmemusage);
showMemusage.setSelected(selmemusage);
desktop.setBackground(Color.white);
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();
-
+ new SplashScreen();
-
- 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()
setupVamsasDisconnectedGui();
VamsasMenu.setVisible(true);
final Desktop us = this;
- VamsasMenu.addMenuListener(new MenuListener() {
+ 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;
+ boolean refresh = true;
+
public void menuCanceled(MenuEvent e)
{
- refresh=true;
+ refresh = true;
}
public void menuDeselected(MenuEvent e)
if (refresh)
{
us.buildVamsasStMenu();
- refresh=false;
+ refresh = false;
}
}
});
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
+ // 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"),
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+ .getProperty("LAST_DIRECTORY"),
jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
- jalview.io.AppletFormatAdapter.READABLE_FNAMES,
+ jalview.io.AppletFormatAdapter.READABLE_FNAMES,
jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
chooser.setFileView(new JalviewFileView());
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." +
- "\nDevelopment managed by The Barton Group, University of Dundee.\n"+
- "\nFor specific issues relating to Jalview, email help@jalview.org\n"+
- " 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.");
+ // 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");
reorderAssociatedWindows(false, true);
}
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.ActionEvent)
*/
protected void garbageCollect_actionPerformed(ActionEvent e)
jalview.bin.Cache.log.debug("Finished garbage collection.");
}
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent)
*/
protected void showMemusage_actionPerformed(ActionEvent e)
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);
}
}
if (fileLoadingCount == 0)
{
addProgressPanel("Loading File: " + fileName + " ");
-
+
}
fileLoadingCount++;
}
+
private JProgressBar addProgressPanel(String string)
{
- if (progressPanel==null)
+ if (progressPanel == null)
{
progressPanel = new JPanel(new BorderLayout());
- totalProgressCount=0;
+ totalProgressCount = 0;
}
JProgressBar progressBar = new JProgressBar();
progressBar.setIndeterminate(true);
- progressPanel.add(new JLabel(string),
- BorderLayout.WEST);
+ progressPanel.add(new JLabel(string), BorderLayout.WEST);
progressPanel.add(progressBar, BorderLayout.CENTER);
validate();
return progressBar;
}
- int totalProgressCount=0;
+
+ int totalProgressCount = 0;
+
private void removeProgressPanel(JProgressBar progbar)
{
- if (progressPanel!=null)
+ if (progressPanel != null)
{
progressPanel.remove(progbar);
- if (--totalProgressCount<1)
+ if (--totalProgressCount < 1)
{
this.getContentPane().remove(progressPanel);
progressPanel = null;
}
validate();
}
+
public void stopLoading()
{
fileLoadingCount--;
}
validate();
}
+
public static int getViewCount(String viewId)
{
int count = 0;
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++;
}
{
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.VamsasApplication v_client = null;
+
public void vamsasImport_actionPerformed(ActionEvent e)
{
- if (v_client==null)
+ if (v_client == null)
{
// Load and try to start a session.
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty("LAST_DIRECTORY"));
+ 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.");
+ 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());
+ 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);
+ 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.");
+ }
+ else
+ {
+ jalview.bin.Cache.log
+ .error("Implementation error - load session from a running session is not supported.");
}
}
// 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());
- *
- */
+ * 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 ?
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.
+ vamsasImport.setVisible(false); // Document import to existing session is
+ // not possible for vamsas-client-1.0.
}
+
protected void setupVamsasDisconnectedGui()
{
vamsasSave.setVisible(false);
setupVamsasDisconnectedGui();
}
}
+
protected void buildVamsasStMenu()
{
if (v_client == null)
{
if (dsktp.v_client == null)
{
- Thread rthr = new Thread(new Runnable() {
+ Thread rthr = new Thread(new Runnable()
+ {
public void run()
{
dsktp.setupVamsasConnectedGui();
dsktp.v_client.initial_update();
}
-
+
});
rthr.start();
}
VamsasStMenu.add(sessit);
}
// don't show an empty menu.
- VamsasStMenu.setVisible(sess.length>0);
-
+ VamsasStMenu.setVisible(sess.length > 0);
+
}
else
{
VamsasStMenu.removeAll();
VamsasStMenu.setVisible(false);
}
- } else {
+ }
+ 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");
+ 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");
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Save Vamsas Document Archive");
- int value = chooser.showSaveDialog(this);
+ int value = chooser.showSaveDialog(this);
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ 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
{
- 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,
+ 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);
- warnmsg, warnttl,
- JOptionPane.ERROR_MESSAGE);
- }
+ } 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"));
-
- if (vamUpdate!=null)
+ jalview.bin.Cache.log.debug("Setting gui for Vamsas update "
+ + (b ? "in progress" : "finished"));
+
+ if (vamUpdate != null)
{
this.removeProgressPanel(vamUpdate);
}
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();
}
+
/**
- * 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.
+ * 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
+ 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)
{
worker.start();
}
}
+
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() {
+
+ 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);
- }
+ public void actionPerformed(ActionEvent e)
+ {
+ groovyShell_actionPerformed(e);
+ }
});
toolsMenu.add(groovyShell);
groovyShell.setVisible(true);
}
}
+
/**
- * Accessor method to quickly get all the AlignmentFrames
- * loaded.
+ * Accessor method to quickly get all the AlignmentFrames loaded.
*/
- public static AlignFrame[] getAlignframes() {
+ 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)
+ }
+ Vector avp = new Vector();
+ try
+ {
+ // REVERSE ORDER
+ for (int i = frames.length - 1; i > -1; i--)
{
- return null;
- }
- AlignFrame afs[] = new AlignFrame[avp.size()];
- for (int i=0,j=avp.size(); i<j; i++) {
- afs[i] = (AlignFrame) avp.elementAt(i);
+ if (frames[i] instanceof AlignFrame)
+ {
+ AlignFrame af = (AlignFrame) frames[i];
+ avp.addElement(af);
+ }
}
- avp.clear();
- return afs;
+ } 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) {
+ * 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);
+ throw new Error(
+ "Implementation Error. Cannot create groovyShell without Groovy on the classpath!");
}
- catch (Exception ex)
+ try
{
- 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);
+ 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.
+ * Progress bars managed by the IProgressIndicator method.
*/
private Hashtable progressBars;
- /* (non-Javadoc)
+
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
*/
public void setProgressBar(String message, long id)
{
- if(progressBars == null)
+ if (progressBars == null)
{
progressBars = new Hashtable();
}
- if(progressBars.get( new Long(id) )!=null)
+ if (progressBars.get(new Long(id)) != null)
+ {
+ JProgressBar progressPanel = (JProgressBar) progressBars
+ .remove(new Long(id));
+ removeProgressPanel(progressPanel);
+ }
+ else
{
- JProgressBar progressPanel = (JProgressBar)progressBars.remove( new Long(id) );
- removeProgressPanel(progressPanel);
- } else {
progressBars.put(new Long(id), addProgressPanel(message));
}
}
git://source.jalview.org / jalview.git / blobdiff