X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=2a72e44c3aeb459d575b9a01f0d40d73a9621a35;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=9a89b0ace54400f22803974d0d88186e353da767;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
old mode 100755
new mode 100644
index 9a89b0a..2a72e44
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,61 +1,153 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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 file is part of Jalview.
*
- * 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.
+ * Jalview 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 3 of the License, or (at your option) any later version.
*
- * 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
+ * Jalview 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 Jalview. If not, see .
*/
package jalview.gui;
-import jalview.io.*;
-
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.dnd.*;
-import java.awt.event.*;
+import jalview.bin.Cache;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.ws.params.ParamManager;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.GridLayout;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.ClipboardOwner;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyVetoException;
+import java.io.BufferedInputStream;
+import java.io.File;
+import java.io.FileOutputStream;
import java.lang.reflect.Constructor;
-import java.util.*;
-
-import javax.swing.*;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.DefaultDesktopManager;
+import javax.swing.DesktopManager;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JComponent;
+import javax.swing.JDesktopPane;
+import javax.swing.JFrame;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.JProgressBar;
+import javax.swing.SwingUtilities;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
/**
- * DOCUMENT ME!
+ * Jalview Desktop
+ *
*
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.155 $
*/
public class Desktop extends jalview.jbgui.GDesktop implements
- DropTargetListener, ClipboardOwner, IProgressIndicator
+ DropTargetListener, ClipboardOwner, IProgressIndicator, jalview.api.StructureSelectionManagerProvider
{
- /** DOCUMENT ME!! */
+
+ private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
+
+ /**
+ * news reader - null if it was never started.
+ */
+ private BlogReader jvnews=null;
+
+ /**
+ * @param listener
+ * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
+ */
+ public void addJalviewPropertyChangeListener(
+ PropertyChangeListener listener)
+ {
+ changeSupport.addJalviewPropertyChangeListener(listener);
+ }
+
+ /**
+ * @param propertyName
+ * @param listener
+ * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String,
+ * java.beans.PropertyChangeListener)
+ */
+ public void addJalviewPropertyChangeListener(String propertyName,
+ PropertyChangeListener listener)
+ {
+ changeSupport.addJalviewPropertyChangeListener(propertyName, listener);
+ }
+
+ /**
+ * @param propertyName
+ * @param listener
+ * @see jalview.gui.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String,
+ * java.beans.PropertyChangeListener)
+ */
+ public void removeJalviewPropertyChangeListener(String propertyName,
+ PropertyChangeListener listener)
+ {
+ changeSupport.removeJalviewPropertyChangeListener(propertyName,
+ listener);
+ }
+
+ /** Singleton Desktop instance */
public static Desktop instance;
- // 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;
- public static jalview.ws.Discoverer discoverer;
+ public static jalview.ws.jws1.Discoverer discoverer;
public static Object[] jalviewClipboard;
@@ -63,6 +155,104 @@ public class Desktop extends jalview.jbgui.GDesktop implements
static int fileLoadingCount = 0;
+ class MyDesktopManager implements DesktopManager
+ {
+
+ private DesktopManager delegate;
+
+ public MyDesktopManager(DesktopManager delegate)
+ {
+ this.delegate = delegate;
+ }
+
+ public void activateFrame(JInternalFrame f)
+ {
+ try
+ {
+ delegate.activateFrame(f);
+ } catch (NullPointerException npe)
+ {
+ Point p = getMousePosition();
+ instance.showPasteMenu(p.x, p.y);
+ }
+ }
+
+ public void beginDraggingFrame(JComponent f)
+ {
+ delegate.beginDraggingFrame(f);
+ }
+
+ public void beginResizingFrame(JComponent f, int direction)
+ {
+ delegate.beginResizingFrame(f, direction);
+ }
+
+ public void closeFrame(JInternalFrame f)
+ {
+ delegate.closeFrame(f);
+ }
+
+ public void deactivateFrame(JInternalFrame f)
+ {
+ delegate.deactivateFrame(f);
+ }
+
+ public void deiconifyFrame(JInternalFrame f)
+ {
+ delegate.deiconifyFrame(f);
+ }
+
+ public void dragFrame(JComponent f, int newX, int newY)
+ {
+ delegate.dragFrame(f, newX, newY);
+ }
+
+ public void endDraggingFrame(JComponent f)
+ {
+ delegate.endDraggingFrame(f);
+ }
+
+ public void endResizingFrame(JComponent f)
+ {
+ delegate.endResizingFrame(f);
+ }
+
+ public void iconifyFrame(JInternalFrame f)
+ {
+ delegate.iconifyFrame(f);
+ }
+
+ public void maximizeFrame(JInternalFrame f)
+ {
+ delegate.maximizeFrame(f);
+ }
+
+ public void minimizeFrame(JInternalFrame f)
+ {
+ delegate.minimizeFrame(f);
+ }
+
+ public void openFrame(JInternalFrame f)
+ {
+ delegate.openFrame(f);
+ }
+
+ public void resizeFrame(JComponent f, int newX, int newY, int newWidth,
+ int newHeight)
+ {
+ delegate.resizeFrame(f, newX, newY, newWidth, newHeight);
+ }
+
+ public void setBoundsForFrame(JComponent f, int newX, int newY,
+ int newWidth, int newHeight)
+ {
+ delegate.setBoundsForFrame(f, newX, newY, newWidth, newHeight);
+ }
+
+ // All other methods, simply delegate
+
+ }
+
/**
* Creates a new Desktop object.
*/
@@ -81,34 +271,62 @@ public class Desktop extends jalview.jbgui.GDesktop implements
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
false);
+ boolean showjconsole = jalview.bin.Cache.getDefault(
+ "SHOW_JAVA_CONSOLE", false);
desktop = new MyDesktopPane(selmemusage);
showMemusage.setSelected(selmemusage);
desktop.setBackground(Color.white);
getContentPane().setLayout(new BorderLayout());
+ // alternate config - have scrollbars - see notes in JAL-153
+ //JScrollPane sp = new JScrollPane();
+ //sp.getViewport().setView(desktop);
+ //getContentPane().add(sp, BorderLayout.CENTER);
getContentPane().add(desktop, BorderLayout.CENTER);
- desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
-
+ desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
+
// This line prevents Windows Look&Feel resizing all new windows to maximum
// if previous window was maximised
- desktop.setDesktopManager(new DefaultDesktopManager());
-
- Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
- String x = jalview.bin.Cache.getProperty("SCREEN_X");
- String y = jalview.bin.Cache.getProperty("SCREEN_Y");
- 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))
+ desktop.setDesktopManager(new MyDesktopManager(
+ new DefaultDesktopManager()));
+ Rectangle dims = getLastKnownDimensions("");
+ if (dims != null)
{
- setBounds(Integer.parseInt(x), Integer.parseInt(y), Integer
- .parseInt(width), Integer.parseInt(height));
+ setBounds(dims);
}
else
{
+ Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
setBounds((int) (screenSize.width - 900) / 2,
(int) (screenSize.height - 650) / 2, 900, 650);
}
+ jconsole = new Console(this, showjconsole);
+ // add essential build information
+ jconsole.setHeader("Jalview Desktop "
+ + jalview.bin.Cache.getProperty("VERSION") + "\n"
+ + "Build Date: "
+ + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n"
+ + "Java version: " + System.getProperty("java.version") + "\n"
+ + System.getProperty("os.arch") + " "
+ + System.getProperty("os.name") + " "
+ + System.getProperty("os.version"));
+
+ showConsole(showjconsole);
+
+ showNews.setVisible(false);
+ final Desktop me = this;
+ // Thread off the news reader, in case there are connection problems.
+ new Thread( new Runnable() {
+ @Override
+ public void run()
+ {
+ Cache.log.debug("Starting news thread.");
+ jvnews = new BlogReader(me);
+ showNews.setVisible(true);
+ Cache.log.debug("Completed news thread.");
+ }
+ }).start();
+
this.addWindowListener(new WindowAdapter()
{
public void windowClosing(WindowEvent evt)
@@ -127,13 +345,150 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
}
});
-
+ this.addFocusListener(new FocusListener()
+ {
+
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void focusGained(FocusEvent e)
+ {
+ Cache.log.debug("Relaying windows after focus gain");
+ // make sure that we sort windows properly after we gain focus
+ instance.relayerWindows();
+ }
+ });
this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
// Spawn a thread that shows the splashscreen
- new SplashScreen();
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ new SplashScreen();
+ }
+ });
+
+ // displayed.
+ // Thread off a new instance of the file chooser - this reduces the time it
+ // takes to open it later on.
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+ Cache.log.debug("Filechooser init thread started.");
+ 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"));
+ Cache.log.debug("Filechooser init thread finished.");
+ }
+ }).start();
+ // Add the service change listener
+ changeSupport.addJalviewPropertyChangeListener("services",
+ new PropertyChangeListener()
+ {
+
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ Cache.log.debug("Firing service changed event for "
+ + evt.getNewValue());
+ JalviewServicesChanged(evt);
+ }
- discoverer = new jalview.ws.Discoverer(); // Only gets started if gui is
- // displayed.
+ });
+ }
+
+ protected void showNews_actionPerformed(ActionEvent e)
+ {
+ showNews(showNews.isSelected());
+ }
+ void showNews(boolean visible)
+ {
+ {
+ Cache.log.debug((visible?"Showing":"Hiding")+" news.");
+ showNews.setSelected(visible);
+ if (visible && !jvnews.isVisible())
+ {
+ new Thread(new Runnable() {
+ @Override
+ public void run()
+ {
+ long instance=System.currentTimeMillis();
+ Desktop.instance.setProgressBar("Refreshing news", instance);
+ jvnews.refreshNews();
+ Desktop.instance.setProgressBar(null, instance);
+ jvnews.showNews();
+ }
+ }).start();
+ }
+ }
+ }
+
+ /**
+ * recover the last known dimensions for a jalview window
+ *
+ * @param windowName
+ * - empty string is desktop, all other windows have unique prefix
+ * @return null or last known dimensions scaled to current geometry (if last
+ * window geom was known)
+ */
+ Rectangle getLastKnownDimensions(String windowName)
+ {
+ // TODO: lock aspect ratio for scaling desktop Bug #0058199
+ Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
+ String x = jalview.bin.Cache.getProperty(windowName + "SCREEN_X");
+ String y = jalview.bin.Cache.getProperty(windowName + "SCREEN_Y");
+ String width = jalview.bin.Cache.getProperty(windowName
+ + "SCREEN_WIDTH");
+ String height = jalview.bin.Cache.getProperty(windowName
+ + "SCREEN_HEIGHT");
+ if ((x != null) && (y != null) && (width != null) && (height != null))
+ {
+ int ix = Integer.parseInt(x), iy = Integer.parseInt(y), iw = Integer
+ .parseInt(width), ih = Integer.parseInt(height);
+ if (jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
+ {
+ // attempt #1 - try to cope with change in screen geometry - this
+ // version doesn't preserve original jv aspect ratio.
+ // take ratio of current screen size vs original screen size.
+ double sw = ((1f * screenSize.width) / (1f * Integer
+ .parseInt(jalview.bin.Cache
+ .getProperty("SCREENGEOMETRY_WIDTH"))));
+ double sh = ((1f * screenSize.height) / (1f * Integer
+ .parseInt(jalview.bin.Cache
+ .getProperty("SCREENGEOMETRY_HEIGHT"))));
+ // rescale the bounds depending upon the current screen geometry.
+ ix = (int) (ix * sw);
+ iw = (int) (iw * sw);
+ iy = (int) (iy * sh);
+ ih = (int) (ih * sh);
+ while (ix >= screenSize.width)
+ {
+ jalview.bin.Cache.log
+ .debug("Window geometry location recall error: shifting horizontal to within screenbounds.");
+ ix -= screenSize.width;
+ }
+ while (iy >= screenSize.height)
+ {
+ jalview.bin.Cache.log
+ .debug("Window geometry location recall error: shifting vertical to within screenbounds.");
+ iy -= screenSize.height;
+ }
+ jalview.bin.Cache.log.debug("Got last known dimensions for "
+ + windowName + ": x:" + ix + " y:" + iy + " width:" + iw
+ + " height:" + ih);
+ }
+ // return dimensions for new instance
+ return new Rectangle(ix, iy, iw, ih);
+ }
+ return null;
}
private void doVamsasClientCheck()
@@ -216,16 +571,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
/**
- * DOCUMENT ME!
+ * Adds and opens the given frame to the desktop
*
* @param frame
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param title
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param w
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param h
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public static synchronized void addInternalFrame(
final JInternalFrame frame, String title, int w, int h)
@@ -237,21 +592,23 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* DOCUMENT ME!
*
* @param frame
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param title
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param w
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param h
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param resizable
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public static synchronized void addInternalFrame(
final JInternalFrame frame, String title, int w, int h,
boolean resizable)
{
+ // TODO: allow callers to determine X and Y position of frame (eg. via
+ // bounds object).
// TODO: consider fixing method to update entries in the window submenu with
// the current window title
@@ -286,34 +643,33 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
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()
{
@@ -329,6 +685,47 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
}
});
+ menuItem.addMouseListener(new MouseListener()
+ {
+
+ @Override
+ public void mouseReleased(MouseEvent e)
+ {
+ }
+
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ }
+
+ @Override
+ public void mouseExited(MouseEvent e)
+ {
+ try
+ {
+ frame.setSelected(false);
+ } catch (PropertyVetoException e1)
+ {
+ }
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ try
+ {
+ frame.setSelected(true);
+ } catch (PropertyVetoException e1)
+ {
+ }
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+
+ }
+ });
windowMenu.add(menuItem);
@@ -341,6 +738,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
} catch (java.beans.PropertyVetoException ve)
{
}
+ catch (java.lang.ClassCastException cex)
+ {
+ Cache.log.warn("Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869",cex);
+ }
}
public void lostOwnership(Clipboard clipboard, Transferable contents)
@@ -373,12 +774,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void drop(DropTargetDropEvent evt)
{
Transferable t = evt.getTransferable();
java.util.List files = null;
+ java.util.List protocols = null;
try
{
@@ -397,6 +799,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
String data = (String) t.getTransferData(uriListFlavor);
files = new java.util.ArrayList(1);
+ protocols = new java.util.ArrayList(1);
for (java.util.StringTokenizer st = new java.util.StringTokenizer(
data, "\r\n"); st.hasMoreTokens();)
{
@@ -406,10 +809,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements
// the line is a comment (as per the RFC 2483)
continue;
}
-
java.net.URI uri = new java.net.URI(s);
- java.io.File file = new java.io.File(uri);
- files.add(file);
+ if (uri.getScheme().toLowerCase().startsWith("http"))
+ {
+ protocols.add(FormatAdapter.URL);
+ files.add(uri.toString());
+ }
+ else
+ {
+ // otherwise preserve old behaviour: catch all for file objects
+ java.io.File file = new java.io.File(uri);
+ protocols.add(FormatAdapter.FILE);
+ files.add(file.toString());
+ }
}
}
} catch (Exception e)
@@ -423,7 +835,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
for (int i = 0; i < files.size(); i++)
{
String file = files.get(i).toString();
- String protocol = FormatAdapter.FILE;
+ String protocol = (protocols == null) ? FormatAdapter.FILE
+ : (String) protocols.get(i);
String format = null;
if (file.endsWith(".jar"))
@@ -449,12 +862,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * 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.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
@@ -497,7 +910,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
{
@@ -577,7 +990,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
{
@@ -591,18 +1004,45 @@ public class Desktop extends jalview.jbgui.GDesktop implements
*/
public void quit()
{
- jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");
- jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");
- jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
- jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
+ Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
+ jalview.bin.Cache
+ .setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
+ jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height
+ + "");
+ storeLastKnownDimensions("", new Rectangle(getBounds().x,
+ getBounds().y, getWidth(), getHeight()));
+
+ if (jconsole != null)
+ {
+ storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds());
+ jconsole.stopConsole();
+ }
+ if (jvnews!=null)
+ {
+ storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds());
+
+ }
+
System.exit(0);
}
+ private void storeLastKnownDimensions(String string, Rectangle jc)
+ {
+ jalview.bin.Cache.log.debug("Storing last known dimensions for "
+ + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
+ + " height:" + jc.height);
+
+ jalview.bin.Cache.setProperty(string + "SCREEN_X", jc.x + "");
+ jalview.bin.Cache.setProperty(string + "SCREEN_Y", jc.y + "");
+ jalview.bin.Cache.setProperty(string + "SCREEN_WIDTH", jc.width + "");
+ jalview.bin.Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + "");
+ }
+
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void aboutMenuItem_actionPerformed(ActionEvent e)
{
@@ -613,22 +1053,20 @@ public class Desktop extends jalview.jbgui.GDesktop implements
if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
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 "+jalview.bin.Cache.getDefault("www.jalview.org","http://www.jalview.org")+" !!\n");
}
// 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.");
-
+ message.append("\nAuthors: Jim Procter, Andrew Waterhouse, 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:"
+ + "\nWaterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+ + "\nJalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+ + "\nBioinformatics doi: 10.1093/bioinformatics/btp033");
JOptionPane.showInternalMessageDialog(Desktop.desktop,
message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
@@ -638,7 +1076,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void documentationMenuItem_actionPerformed(ActionEvent e)
{
@@ -669,7 +1107,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
}
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)
@@ -690,7 +1132,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
/*
* (non-Javadoc)
*
- * @see jalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.ActionEvent)
+ * @seejalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.
+ * ActionEvent)
*/
protected void garbageCollect_actionPerformed(ActionEvent e)
{
@@ -703,13 +1146,43 @@ public class Desktop extends jalview.jbgui.GDesktop implements
/*
* (non-Javadoc)
*
- * @see jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent)
+ * @see
+ * jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent
+ * )
*/
protected void showMemusage_actionPerformed(ActionEvent e)
{
desktop.showMemoryUsage(showMemusage.isSelected());
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GDesktop#showConsole_actionPerformed(java.awt.event.ActionEvent
+ * )
+ */
+ protected void showConsole_actionPerformed(ActionEvent e)
+ {
+ showConsole(showConsole.isSelected());
+ }
+
+ Console jconsole = null;
+
+ /**
+ * control whether the java console is visible or not
+ *
+ * @param selected
+ */
+ void showConsole(boolean selected)
+ {
+ showConsole.setSelected(selected);
+ // TODO: decide if we should update properties file
+ Cache.setProperty("SHOW_JAVA_CONSOLE", Boolean.valueOf(selected)
+ .toString());
+ jconsole.setVisible(selected);
+ }
+
void reorderAssociatedWindows(boolean minimize, boolean close)
{
JInternalFrame[] frames = desktop.getAllFrames();
@@ -791,7 +1264,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void preferences_actionPerformed(ActionEvent e)
{
@@ -802,14 +1275,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * 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");
@@ -818,9 +1291,37 @@ public class Desktop extends jalview.jbgui.GDesktop implements
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- java.io.File choice = chooser.getSelectedFile();
+ final Desktop me = this;
+ final java.io.File choice = chooser.getSelectedFile();
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+
+ setProgressBar("Saving jalview project " + choice.getName(),
+ choice.hashCode());
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
- new Jalview2XML().SaveState(choice);
+ // TODO catch and handle errors for savestate
+ // TODO prevent user from messing with the Desktop whilst we're saving
+ try
+ {
+ new Jalview2XML().SaveState(choice);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning(
+ "Whilst saving current state to " + choice.getName(), oom);
+ } catch (Exception ex)
+ {
+ Cache.log
+ .error("Problems whilst trying to save to "
+ + choice.getName(), ex);
+ JOptionPane.showMessageDialog(me,
+ "Error whilst saving current state to " + choice.getName(),
+ "Couldn't save project", JOptionPane.WARNING_MESSAGE);
+ }
+ setProgressBar(null, choice.hashCode());
+ }
+ }).start();
}
}
@@ -828,14 +1329,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * 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");
@@ -843,10 +1344,32 @@ public class Desktop extends jalview.jbgui.GDesktop implements
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- String choice = chooser.getSelectedFile().getAbsolutePath();
+ final String choice = chooser.getSelectedFile().getAbsolutePath();
jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
.getSelectedFile().getParent());
- new Jalview2XML().LoadJalviewAlign(choice);
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+ setProgressBar("loading jalview project " + choice,
+ choice.hashCode());
+ try
+ {
+ new Jalview2XML().LoadJalviewAlign(choice);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Whilst loading project from " + choice, oom);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Problems whilst loading project from "
+ + choice, ex);
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "Error whilst loading project from " + choice,
+ "Couldn't load project", JOptionPane.WARNING_MESSAGE);
+ }
+ setProgressBar(null, choice.hashCode());
+ }
+ }).start();
}
}
@@ -856,44 +1379,47 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
JPanel progressPanel;
-
+ ArrayList fileLoadingPanels=new ArrayList();
public void startLoading(final String fileName)
{
if (fileLoadingCount == 0)
{
- addProgressPanel("Loading File: " + fileName + " ");
-
+ fileLoadingPanels.add(addProgressPanel("Loading File: " + fileName + " "));
}
fileLoadingCount++;
}
- private JProgressBar addProgressPanel(String string)
+ private JPanel addProgressPanel(String string)
{
if (progressPanel == null)
{
- progressPanel = new JPanel(new BorderLayout());
+ progressPanel = new JPanel(new GridLayout(1,1));
totalProgressCount = 0;
+ instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
}
+ JPanel thisprogress=new JPanel(new BorderLayout(10,5));
JProgressBar progressBar = new JProgressBar();
progressBar.setIndeterminate(true);
- progressPanel.add(new JLabel(string), BorderLayout.WEST);
-
- progressPanel.add(progressBar, BorderLayout.CENTER);
+ thisprogress.add(new JLabel(string), BorderLayout.WEST);
- instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
- totalProgressCount++;
- validate();
- return progressBar;
+ thisprogress.add(progressBar, BorderLayout.CENTER);
+ progressPanel.add(thisprogress);
+ ((GridLayout)progressPanel.getLayout()).setRows(((GridLayout)progressPanel.getLayout()).getRows()+1);
+ ++totalProgressCount;
+ instance.validate();
+ return thisprogress;
}
int totalProgressCount = 0;
- private void removeProgressPanel(JProgressBar progbar)
+ private void removeProgressPanel(JPanel progbar)
{
if (progressPanel != null)
{
progressPanel.remove(progbar);
+ GridLayout gl = (GridLayout) progressPanel.getLayout();
+ gl.setRows(gl.getRows()-1);
if (--totalProgressCount < 1)
{
this.getContentPane().remove(progressPanel);
@@ -908,20 +1434,38 @@ public class Desktop extends jalview.jbgui.GDesktop implements
fileLoadingCount--;
if (fileLoadingCount < 1)
{
- if (progressPanel != null)
+ for (JPanel flp : fileLoadingPanels)
{
- this.getContentPane().remove(progressPanel);
- progressPanel = null;
+ removeProgressPanel(flp);
}
+ fileLoadingPanels.clear();
fileLoadingCount = 0;
}
validate();
}
- public static int getViewCount(String viewId)
+ public static int getViewCount(String alignmentId)
+ {
+ AlignViewport[] aps = getViewports(alignmentId);
+ return (aps == null) ? 0 : aps.length;
+ }
+
+ /**
+ *
+ * @param alignmentId
+ * @return all AlignmentPanels concerning the alignmentId sequence set
+ */
+ public static AlignmentPanel[] getAlignmentPanels(String alignmentId)
{
int count = 0;
+ if (Desktop.desktop == null)
+ {
+ // no frames created and in headless mode
+ // TODO: verify that frames are recoverable when in headless mode
+ return null;
+ }
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ ArrayList aps = new ArrayList();
for (int t = 0; t < frames.length; t++)
{
if (frames[t] instanceof AlignFrame)
@@ -929,17 +1473,75 @@ public class Desktop extends jalview.jbgui.GDesktop implements
AlignFrame af = (AlignFrame) frames[t];
for (int a = 0; a < af.alignPanels.size(); a++)
{
- if (viewId
+ if (alignmentId
.equals(((AlignmentPanel) af.alignPanels.elementAt(a)).av
.getSequenceSetId()))
{
- count++;
+ aps.add(af.alignPanels.elementAt(a));
}
}
}
}
+ 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();
- return count;
+ 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)
@@ -1013,31 +1615,25 @@ public class Desktop extends jalview.jbgui.GDesktop implements
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());
- } catch (Exception ex)
+ String fle = chooser.getSelectedFile().toString();
+ if (!vamsasImport(chooser.getSelectedFile()))
{
- jalview.bin.Cache.log.error(
- "New vamsas session from existing session file failed:",
- ex);
- return;
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Couldn't import '" + fle + "' as a new vamsas session.",
+ "Vamsas Document Import Failed",
+ JOptionPane.ERROR_MESSAGE);
}
- setupVamsasConnectedGui();
- v_client.initial_update(); // TODO: thread ?
}
}
else
@@ -1047,6 +1643,105 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
}
+ /**
+ * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
+ *
+ * @param file
+ * @return true if import was a success and a session was started.
+ */
+ public boolean vamsasImport(URL url)
+ {
+ // TODO: create progress bar
+ if (v_client != null)
+ {
+
+ jalview.bin.Cache.log
+ .error("Implementation error - load session from a running session is not supported.");
+ return false;
+ }
+
+ try
+ {
+ // copy the URL content to a temporary local file
+ // TODO: be a bit cleverer here with nio (?!)
+ File file = File.createTempFile("vdocfromurl", ".vdj");
+ FileOutputStream fos = new FileOutputStream(file);
+ BufferedInputStream bis = new BufferedInputStream(url.openStream());
+ byte[] buffer = new byte[2048];
+ int ln;
+ while ((ln = bis.read(buffer)) > -1)
+ {
+ fos.write(buffer, 0, ln);
+ }
+ bis.close();
+ fos.close();
+ v_client = new jalview.gui.VamsasApplication(this, file,
+ url.toExternalForm());
+ } catch (Exception ex)
+ {
+ jalview.bin.Cache.log.error(
+ "Failed to create new vamsas session from contents of URL "
+ + url, ex);
+ return false;
+ }
+ setupVamsasConnectedGui();
+ v_client.initial_update(); // TODO: thread ?
+ return v_client.inSession();
+ }
+
+ /**
+ * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
+ *
+ * @param file
+ * @return true if import was a success and a session was started.
+ */
+ public boolean vamsasImport(File file)
+ {
+ if (v_client != null)
+ {
+
+ jalview.bin.Cache.log
+ .error("Implementation error - load session from a running session is not supported.");
+ return false;
+ }
+
+ setProgressBar("Importing VAMSAS session from " + file.getName(),
+ file.hashCode());
+ try
+ {
+ v_client = new jalview.gui.VamsasApplication(this, file, null);
+ } catch (Exception ex)
+ {
+ setProgressBar("Importing VAMSAS session from " + file.getName(),
+ file.hashCode());
+ jalview.bin.Cache.log.error(
+ "New vamsas session from existing session file failed:", ex);
+ return false;
+ }
+ setupVamsasConnectedGui();
+ v_client.initial_update(); // TODO: thread ?
+ setProgressBar("Importing VAMSAS session from " + file.getName(),
+ file.hashCode());
+ return v_client.inSession();
+ }
+
+ public boolean joinVamsasSession(String mysesid)
+ {
+ if (v_client != null)
+ {
+ throw new Error(
+ "Trying to join a vamsas session when another is already connected.");
+ }
+ if (mysesid == null)
+ {
+ throw new Error("Invalid vamsas session id.");
+ }
+ v_client = new VamsasApplication(this, mysesid);
+ setupVamsasConnectedGui();
+ v_client.initial_update();
+ return (v_client.inSession());
+ }
+
public void vamsasStart_actionPerformed(ActionEvent e)
{
if (v_client == null)
@@ -1065,7 +1760,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
*
* if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new
* jalview.gui.VamsasApplication(this, chooser.getSelectedFile());
- *
*/
v_client = new VamsasApplication(this);
setupVamsasConnectedGui();
@@ -1084,7 +1778,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
vamsasSave.setVisible(true);
vamsasStop.setVisible(true);
vamsasImport.setVisible(false); // Document import to existing session is
- // not possible for vamsas-client-1.0.
+ // not possible for vamsas-client-1.0.
}
protected void setupVamsasDisconnectedGui()
@@ -1177,9 +1871,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
if (v_client != null)
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"), new String[]
- { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+ 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");
@@ -1191,6 +1885,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
if (value == JalviewFileChooser.APPROVE_OPTION)
{
java.io.File choice = chooser.getSelectedFile();
+ JPanel progpanel = addProgressPanel("Saving VAMSAS Document to "
+ + choice.getName());
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
String warnmsg = null;
String warnttl = null;
@@ -1212,6 +1908,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
+ choice, ex);
}
+ removeProgressPanel(progpanel);
if (warnmsg != null)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
@@ -1222,13 +1919,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
}
- JProgressBar vamUpdate = null;
+ JPanel 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
+ * true to hide gui, false to reveal gui
*/
public void setVamsasUpdate(boolean b)
{
@@ -1315,7 +2012,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
try
{
- Thread.sleep(3000);
maxMemory = runtime.maxMemory() / 1048576f;
allocatedMemory = runtime.totalMemory() / 1048576f;
freeMemory = runtime.freeMemory() / 1048576f;
@@ -1330,7 +2026,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
// instance.set.setBorder(border1);
}
repaint();
-
+ // sleep after showing usage
+ Thread.sleep(3000);
} catch (Exception ex)
{
ex.printStackTrace();
@@ -1340,20 +2037,32 @@ public class Desktop extends jalview.jbgui.GDesktop implements
public void paintComponent(Graphics g)
{
- if (showMemoryUsage)
+ if (showMemoryUsage && g != null && df != null)
{
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());
+ FontMetrics fm = g.getFontMetrics();
+ if (fm != null)
+ {
+ g.drawString(
+ "Total Free Memory: " + df.format(totalFreeMemory)
+ + "MB; Max Memory: " + df.format(maxMemory)
+ + "MB; " + df.format(percentUsage) + "%", 10,
+ getHeight() - fm.getHeight());
+ }
}
}
}
+ /**
+ * fixes stacking order after a modal dialog to ensure windows that should be on top actually are
+ */
+ public void relayerWindows()
+ {
+
+ }
+
protected JMenuItem groovyShell;
public void doGroovyCheck()
@@ -1413,6 +2122,42 @@ public class Desktop extends jalview.jbgui.GDesktop implements
avp.clear();
return afs;
}
+ public AppJmol[] getJmols()
+ {
+ 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 AppJmol)
+ {
+ AppJmol af = (AppJmol) frames[i];
+ avp.addElement(af);
+ }
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ if (avp.size() == 0)
+ {
+ return null;
+ }
+ AppJmol afs[] = new AppJmol[avp.size()];
+ for (int i = 0, j = avp.size(); i < j; i++)
+ {
+ afs[i] = (AppJmol) avp.elementAt(i);
+ }
+ avp.clear();
+ return afs;
+ }
/**
* Add Groovy Support to Jalview
@@ -1454,7 +2199,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
/**
* Progress bars managed by the IProgressIndicator method.
*/
- private Hashtable progressBars;
+ private Hashtable progressBars;
+ private Hashtable progressBarHandlers;
/*
* (non-Javadoc)
@@ -1465,13 +2211,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
if (progressBars == null)
{
- progressBars = new Hashtable();
+ progressBars = new Hashtable();
+ progressBarHandlers = new Hashtable();
}
if (progressBars.get(new Long(id)) != null)
{
- JProgressBar progressPanel = (JProgressBar) progressBars
+ JPanel progressPanel = progressBars
.remove(new Long(id));
+ if (progressBarHandlers.contains(new Long(id)))
+ {
+ progressBarHandlers.remove(new Long(id));
+ }
removeProgressPanel(progressPanel);
}
else
@@ -1479,4 +2230,275 @@ public class Desktop extends jalview.jbgui.GDesktop implements
progressBars.put(new Long(id), addProgressPanel(message));
}
}
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.gui.IProgressIndicator#registerHandler(long,
+ * jalview.gui.IProgressIndicatorHandler)
+ */
+ public void registerHandler(final long id,
+ final IProgressIndicatorHandler handler)
+ {
+ if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
+ {
+ throw new Error(
+ "call setProgressBar before registering the progress bar's handler.");
+ }
+ progressBarHandlers.put(new Long(id), handler);
+ final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+ if (handler.canCancel())
+ {
+ JButton cancel = new JButton("Cancel");
+ final IProgressIndicator us = this;
+ cancel.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ handler.cancelActivity(id);
+ us.setProgressBar(
+ "Cancelled "
+ + ((JLabel) progressPanel.getComponent(0))
+ .getText(), id);
+ }
+ });
+ progressPanel.add(cancel, BorderLayout.EAST);
+ }
+ }
+
+ /**
+ * 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;
+ }
+
+ public VamsasApplication getVamsasApplication()
+ {
+ return v_client;
+
+ }
+
+ /**
+ * flag set if jalview GUI is being operated programmatically
+ */
+ private boolean inBatchMode = false;
+
+ /**
+ * check if jalview GUI is being operated programmatically
+ *
+ * @return inBatchMode
+ */
+ public boolean isInBatchMode()
+ {
+ return inBatchMode;
+ }
+
+ /**
+ * set flag if jalview GUI is being operated programmatically
+ *
+ * @param inBatchMode
+ */
+ public void setInBatchMode(boolean inBatchMode)
+ {
+ this.inBatchMode = inBatchMode;
+ }
+
+ public void startServiceDiscovery()
+ {
+ startServiceDiscovery(false);
+ }
+
+ public void startServiceDiscovery(boolean blocking)
+ {
+ boolean alive = true;
+ Thread t0 = null, t1 = null, t2 = null;
+
+ // todo: changesupport handlers need to be transferred
+ if (discoverer == null)
+ {
+ discoverer = new jalview.ws.jws1.Discoverer();
+ // register PCS handler for desktop.
+ discoverer.addPropertyChangeListener(changeSupport);
+ }
+ // JAL-940 - disabled JWS1 service configuration - always start discoverer until we phase out completely
+ if (true)
+ {
+ (t0 = new Thread(discoverer)).start();
+ }
+
+ try
+ {
+ if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
+ {
+ // EnfinEnvision web service menu entries are rebuild every time the
+ // menu is shown, so no changeSupport events are needed.
+ jalview.ws.EnfinEnvision2OneWay.getInstance();
+ (t1 = new Thread(jalview.ws.EnfinEnvision2OneWay.getInstance()))
+ .start();
+ }
+ } catch (Exception e)
+ {
+ Cache.log
+ .info("Exception when trying to launch Envision2 workflow discovery.",
+ e);
+ Cache.log.info(e.getStackTrace());
+ }
+ if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ {
+ if (jalview.ws.jws2.Jws2Discoverer.getDiscoverer().isRunning())
+ {
+ jalview.ws.jws2.Jws2Discoverer.getDiscoverer().setAborted(true);
+ }
+ t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer(
+ changeSupport);
+
+ }
+ Thread t3=null;
+ {
+ // TODO: do rest service discovery
+ }
+ if (blocking)
+ {
+ while (alive)
+ {
+ try
+ {
+ Thread.sleep(15);
+ } catch (Exception e)
+ {
+ }
+ alive = (t1 != null && t1.isAlive())
+ || (t2 != null && t2.isAlive())
+ || (t3 != null && t3.isAlive())
+ || (t0 != null && t0.isAlive());
+ }
+ }
+ }
+
+ /**
+ * called to check if the service discovery process completed successfully.
+ *
+ * @param evt
+ */
+ protected void JalviewServicesChanged(PropertyChangeEvent evt)
+ {
+ if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
+ {
+ final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+ .getErrorMessages();
+ if (ermsg != null)
+ {
+ if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true))
+ {
+ if (serviceChangedDialog == null)
+ {
+ // only run if we aren't already displaying one of these.
+ javax.swing.SwingUtilities
+ .invokeLater(serviceChangedDialog = new Runnable()
+ {
+ public void run()
+ {
+
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ ermsg
+ + "It may be that you have invalid JABA URLs\nin your web service preferences.\n\nGo to the Web services tab of the\nTools->Preferences dialog box to change them.\n",
+ "Preferences Problem",
+ JOptionPane.WARNING_MESSAGE);
+ serviceChangedDialog = null;
+
+ }
+ });
+ }
+ }
+ else
+ {
+ Cache.log
+ .error("Errors reported by JABA discovery service. Check web services preferences.\n"
+ + ermsg);
+ }
+ }
+ }
+ }
+
+ private Runnable serviceChangedDialog = null;
+
+ /**
+ * start a thread to open a URL in the configured browser. Pops up a warning
+ * dialog to the user if there is an exception when calling out to the browser
+ * to open the URL.
+ *
+ * @param url
+ */
+ public static void showUrl(final String url)
+ {
+ showUrl(url, Desktop.instance);
+ }
+ /**
+ * Like showUrl but allows progress handler to be specified
+ * @param url
+ * @param progress (null) or object implementing IProgressIndicator
+ */
+ public static void showUrl(final String url, final IProgressIndicator progress)
+ {
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+ try
+ {
+ if (progress!=null) {
+ progress.setProgressBar("Opening "+url, this.hashCode());
+ }
+ jalview.util.BrowserLauncher.openURL(url);
+ } catch (Exception ex)
+ {
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ "Unixers: Couldn't find default web browser."
+ + "\nAdd the full path to your browser in Preferences.",
+ "Web browser not found",
+ JOptionPane.WARNING_MESSAGE);
+
+ ex.printStackTrace();
+ }
+ if (progress!=null) {
+ progress.setProgressBar(null, this.hashCode());
+ }
+ }
+ }).start();
+ }
+
+ public static WsParamSetManager wsparamManager = null;
+
+ public static ParamManager getUserParameterStore()
+ {
+ if (wsparamManager == null)
+ {
+ wsparamManager = new WsParamSetManager();
+ }
+ return wsparamManager;
+ }
+
+
}