/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * 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.
+ *
+ * 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 <http://www.gnu.org/licenses/>.
*/
package jalview.gui;
+import jalview.bin.Cache;
import jalview.io.*;
+
import java.awt.*;
import java.awt.datatransfer.*;
import java.awt.dnd.*;
import java.awt.event.*;
+import java.io.BufferedInputStream;
+import java.io.BufferedOutputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.InputStream;
import java.lang.reflect.Constructor;
+import java.net.URL;
+import java.net.URLConnection;
+import java.nio.channels.ReadableByteChannel;
import java.util.*;
import javax.swing.*;
/**
* 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 jalview.ws.jws1.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();
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);
+ boolean showjconsole = jalview.bin.Cache.getDefault(
+ "SHOW_JAVA_CONSOLE", false);
desktop = new MyDesktopPane(selmemusage);
showMemusage.setSelected(selmemusage);
desktop.setBackground(Color.white);
// 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))
+ Rectangle dims = getLastKnownDimensions("");
+ if (dims != null)
{
- setBounds(Integer.parseInt(x), Integer.parseInt(y),
- Integer.parseInt(width), Integer.parseInt(height));
+ setBounds(dims);
}
else
{
- setBounds( (int) (screenSize.width - 900) / 2,
- (int) (screenSize.height - 650) / 2, 900, 650);
+ 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);
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
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ new SplashScreen();
+ }
+ });
- /////////Add a splashscreen on startup
- /////////Add a splashscreen on startup
- new SplashScreen();
-
+ discoverer = new jalview.ws.jws1.Discoverer(); // Only gets started if gui is
+ // 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();
+ }
- discoverer = new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
+ /**
+ * 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);
+ 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()
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!
+ * Adds and opens the given frame to the desktop
+ *
+ * @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: 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
+
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)
{
Transferable t = evt.getTransferable();
java.util.List files = null;
+ java.util.List protocols = null;
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))
{
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(); )
+ data, "\r\n"); st.hasMoreTokens();)
{
String s = st.nextToken();
if (s.startsWith("#"))
// 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)
+ {
}
- catch (Exception e)
- {}
if (files != null)
{
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"))
}
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)
{
*/
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();
+ }
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!
+ *
+ * @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:"
+ + "\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);
+ 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)
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.
+ * ActionEvent)
*/
protected void garbageCollect_actionPerformed(ActionEvent e)
{
jalview.bin.Cache.log.debug("Finished garbage collection.");
}
- /* (non-Javadoc)
- * @see jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent)
+ /*
+ * (non-Javadoc)
+ *
+ * @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();
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");
if (value == JalviewFileChooser.APPROVE_OPTION)
{
java.io.File choice = chooser.getSelectedFile();
+ JProgressBar progpanel = addProgressPanel("Saving jalview project "
+ + choice.getName());
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+ // TODO catch and handle errors for savestate
new Jalview2XML().SaveState(choice);
+ removeProgressPanel(progpanel);
+
}
}
/**
* 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());
+ setProgressBar("loading jalview project "
+ + chooser.getSelectedFile().getName(), choice.hashCode());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+ .getSelectedFile().getParent());
new Jalview2XML().LoadJalviewAlign(choice);
+ setProgressBar(null, choice.hashCode());
}
}
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)
+ 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)
{
+ 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;
+ 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)
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));
}
}
}
}
+ 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;
+ }
- return count;
+ /**
+ * 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.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());
- } 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 {
- 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.");
}
}
+ /**
+ * 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)
// 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);
vamsasStop.setVisible(false);
vamsasImport.setVisible(true);
- vamsasStart.setText("New Vamsas Session...");
+ vamsasStart.setText("New Vamsas Session");
}
public void vamsasStop_actionPerformed(ActionEvent e)
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)
+ {
+ java.io.File choice = chooser.getSelectedFile();
+ JProgressBar progpanel = addProgressPanel("Saving VAMSAS Document to "
+ + choice.getName());
+ 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);
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ } catch (Exception ex)
{
- 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,
+ warnttl = "Problem saving Vamsas Document.";
+ warnmsg = ex.toString();
+ jalview.bin.Cache.log.warn("Exception Whilst saving document to "
+ + choice, ex);
- warnmsg, warnttl,
- JOptionPane.ERROR_MESSAGE);
- }
}
+ removeProgressPanel(progpanel);
+ 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();
{
try
{
- Thread.sleep(3000);
maxMemory = runtime.maxMemory() / 1048576f;
allocatedMemory = runtime.totalMemory() / 1048576f;
freeMemory = runtime.freeMemory() / 1048576f;
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)
+ // sleep after showing usage
+ Thread.sleep(3000);
+ } catch (Exception ex)
{
ex.printStackTrace();
}
public void paintComponent(Graphics g)
{
- if(showMemoryUsage)
+ if (showMemoryUsage && g != 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());
+ }
}
}
-
-
}
+
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!");
+ 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);
+ 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);
}
- catch (Exception ex)
+ }
+
+ /**
+ * Progress bars managed by the IProgressIndicator method.
+ */
+ private Hashtable progressBars, progressBarHandlers;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
+ */
+ public void setProgressBar(String message, long id)
+ {
+ if (progressBars == null)
+ {
+ progressBars = new Hashtable();
+ progressBarHandlers = new Hashtable();
+ }
+
+ if (progressBars.get(new Long(id)) != null)
+ {
+ JProgressBar progressPanel = (JProgressBar) progressBars
+ .remove(new Long(id));
+ if (progressBarHandlers.contains(new Long(id)))
+ {
+ progressBarHandlers.remove(new Long(id));
+ }
+ removeProgressPanel(progressPanel);
+ }
+ else
+ {
+ 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())
{
- jalview.bin.Cache.log.error("Groovy Shell Creation failed.",ex);
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ 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);
+ }
+ }
- "Couldn't create the groovy Shell. Check the error log for the details of what went wrong.", "Jalview Groovy Support Failed",
- JOptionPane.ERROR_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;
+ }
+
+ public VamsasApplication getVamsasApplication()
+ {
+ return v_client;
+
+ }
+
+ public void startServiceDiscovery()
+ {
+ discoverer.start();
+ new Thread(jalview.ws.jws2.Jws2Discoverer.getDiscoverer()).start();
}
}