/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
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.util.MessageManager;
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.net.URL;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.StringTokenizer;
import java.util.Vector;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Semaphore;
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.HyperlinkEvent;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
import javax.swing.event.HyperlinkEvent.EventType;
/**
* Jalview Desktop
*
*
* @author $author$
* @version $Revision: 1.155 $
*/
public class Desktop extends jalview.jbgui.GDesktop implements
DropTargetListener, ClipboardOwner, IProgressIndicator,
jalview.api.StructureSelectionManagerProvider
{
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;
public static MyDesktopPane desktop;
static int openFrameCount = 0;
static final int xOffset = 30;
static final int yOffset = 30;
public static jalview.ws.jws1.Discoverer discoverer;
public static Object[] jalviewClipboard;
public static boolean internalCopy = false;
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)
{
if (newY < 0)
{
newY = 0;
}
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)
{
Rectangle b = desktop.getBounds();
if (newY < 0)
{
newY = 0;
}
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.
*/
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 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);
// This line prevents Windows Look&Feel resizing all new windows to maximum
// if previous window was maximised
desktop.setDesktopManager(new MyDesktopManager(
new DefaultDesktopManager()));
Rectangle dims = getLastKnownDimensions("");
if (dims != null)
{
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);
this.addWindowListener(new WindowAdapter()
{
public void windowClosing(WindowEvent evt)
{
quit();
}
});
MouseAdapter ma;
this.addMouseListener(ma = new MouseAdapter()
{
public void mousePressed(MouseEvent evt)
{
if (SwingUtilities.isRightMouseButton(evt))
{
showPasteMenu(evt.getX(), evt.getY());
}
}
});
desktop.addMouseListener(ma);
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
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);
}
});
}
public void checkForNews()
{
final Desktop me = this;
// Thread off the news reader, in case there are connection problems.
addDialogThread(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.");
}
});
}
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()
{
if (jalview.bin.Cache.vamsasJarsPresent())
{
setupVamsasDisconnectedGui();
VamsasMenu.setVisible(true);
final Desktop us = this;
VamsasMenu.addMenuListener(new MenuListener()
{
// this listener remembers when the menu was first selected, and
// doesn't rebuild the session list until it has been cleared and
// reselected again.
boolean refresh = true;
public void menuCanceled(MenuEvent e)
{
refresh = true;
}
public void menuDeselected(MenuEvent e)
{
refresh = true;
}
public void menuSelected(MenuEvent e)
{
if (refresh)
{
us.buildVamsasStMenu();
refresh = false;
}
}
});
vamsasStart.setVisible(true);
}
}
void showPasteMenu(int x, int y)
{
JPopupMenu popup = new JPopupMenu();
JMenuItem item = new JMenuItem(
MessageManager.getString("label.paste_new_window"));
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
{
paste();
}
});
popup.add(item);
popup.show(this, x, y);
}
public void paste()
{
try
{
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
Transferable contents = c.getContents(this);
if (contents != null)
{
String file = (String) contents
.getTransferData(DataFlavor.stringFlavor);
String format = new IdentifyFile().Identify(file,
FormatAdapter.PASTE);
new FileLoader().LoadFile(file, FormatAdapter.PASTE, format);
}
} catch (Exception ex)
{
System.out
.println("Unable to paste alignment from system clipboard:\n"
+ ex);
}
}
/**
* 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)
{
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!
*/
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)
{
frame.setSize(w, h);
}
// 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 (instance == null
|| (System.getProperty("java.awt.headless") != null && System
.getProperty("java.awt.headless").equals("true")))
{
return;
}
openFrameCount++;
frame.setVisible(true);
frame.setClosable(true);
frame.setResizable(resizable);
frame.setMaximizable(resizable);
frame.setIconifiable(resizable);
frame.setFrameIcon(null);
if (frame.getX() < 1 && frame.getY() < 1)
{
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();
}
}
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()
{
public void actionPerformed(ActionEvent e)
{
try
{
frame.setSelected(true);
frame.setIcon(false);
} catch (java.beans.PropertyVetoException ex)
{
}
}
});
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);
desktop.add(frame);
frame.toFront();
try
{
frame.setSelected(true);
frame.requestFocus();
} 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)
{
if (!internalCopy)
{
Desktop.jalviewClipboard = null;
}
internalCopy = false;
}
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!
*/
public void drop(DropTargetDropEvent evt)
{
boolean success = true;
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");
if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
{
// Works on Windows and MacOSX
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
files = (java.util.List) t
.getTransferData(DataFlavor.javaFileListFlavor);
}
else if (t.isDataFlavorSupported(uriListFlavor))
{
// This is used by Unix drag system
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();)
{
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);
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)
{
success = false;
}
if (files != null)
{
try
{
for (int i = 0; i < files.size(); i++)
{
String file = files.get(i).toString();
String protocol = (protocols == null) ? FormatAdapter.FILE
: (String) protocols.get(i);
String format = null;
if (file.endsWith(".jar"))
{
format = "Jalview";
}
else
{
format = new IdentifyFile().Identify(file, protocol);
}
new FileLoader().LoadFile(file, protocol, format);
}
} catch (Exception ex)
{
success = false;
}
}
evt.dropComplete(success); // need this to ensure input focus is properly
// transfered to any new windows created
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
{
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
jalview.io.AppletFormatAdapter.READABLE_FNAMES,
jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager
.getString("label.open_local_file"));
chooser.setToolTipText(MessageManager.getString("action.open"));
int value = chooser.showOpenDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
.getSelectedFile().getParent());
String format = null;
if (chooser.getSelectedFormat() != null
&& chooser.getSelectedFormat().equals("Jalview"))
{
format = "Jalview";
}
else
{
format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
}
if (viewport != null)
{
new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE,
format);
}
else
{
new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);
}
}
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
{
// This construct allows us to have a wider textfield
// for viewing
JLabel label = new JLabel(
MessageManager.getString("label.input_file_url"));
final JComboBox history = new JComboBox();
JPanel panel = new JPanel(new GridLayout(2, 1));
panel.add(label);
panel.add(history);
history.setPreferredSize(new Dimension(400, 20));
history.setEditable(true);
history.addItem("http://www.");
String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
StringTokenizer st;
if (historyItems != null)
{
st = new StringTokenizer(historyItems, "\t");
while (st.hasMoreTokens())
{
history.addItem(st.nextElement());
}
}
int reply = JOptionPane.showInternalConfirmDialog(desktop, panel,
MessageManager.getString("label.input_alignment_from_url"),
JOptionPane.OK_CANCEL_OPTION);
if (reply != JOptionPane.OK_OPTION)
{
return;
}
String url = history.getSelectedItem().toString();
if (url.toLowerCase().endsWith(".jar"))
{
if (viewport != null)
{
new FileLoader().LoadFile(viewport, url, FormatAdapter.URL,
"Jalview");
}
else
{
new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");
}
}
else
{
String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
if (format.equals("URL NOT FOUND"))
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
"Couldn't locate " + url, "URL not found",
JOptionPane.WARNING_MESSAGE);
return;
}
if (viewport != null)
{
new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);
}
else
{
new FileLoader().LoadFile(url, FormatAdapter.URL, format);
}
}
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(viewport);
Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
}
/*
* Exit the program
*/
public void quit()
{
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());
}
if (dialogExecutor != null)
{
dialogExecutor.shutdownNow();
}
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!
*/
public void aboutMenuItem_actionPerformed(ActionEvent e)
{
// StringBuffer message = getAboutMessage(false);
// JOptionPane.showInternalMessageDialog(Desktop.desktop,
//
// message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
new Thread(new Runnable()
{
public void run()
{
new SplashScreen(true);
}
}).start();
}
public StringBuffer getAboutMessage(boolean shortv)
{
StringBuffer message = new StringBuffer();
message.append("");
if (shortv)
{
message.append("Version: "
+ jalview.bin.Cache.getProperty("VERSION")
+ "
");
message.append("Last Updated: "
+ jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
+ "");
}
else
{
message.append("Version "
+ jalview.bin.Cache.getProperty("VERSION")
+ "; last updated: "
+ jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
}
if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking").equals(
"Checking"))
{
message.append("
...Checking latest version...");
}
else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
.equals(jalview.bin.Cache.getProperty("VERSION")))
{
boolean red = false;
if (jalview.bin.Cache.getProperty("VERSION").toLowerCase()
.indexOf("automated build") == -1)
{
red = true;
// Displayed when code version and jnlp version do not match and code
// version is not a development build
message.append("");
}
message.append("
!! Version "
+ jalview.bin.Cache.getDefault("LATEST_VERSION",
"..Checking..")
+ " is available for download from "
+ jalview.bin.Cache.getDefault("www.jalview.org",
"http://www.jalview.org") + " !!");
if (red)
{
message.append("
");
}
}
message.append("
Authors: "
+ jalview.bin.Cache
.getDefault(
"AUTHORFNAMES",
"The Jalview Authors (See AUTHORS file for current list)")
+ "
Development managed by The Barton Group, University of Dundee, Scotland, UK.
"
+ "
For help, see the FAQ at www.jalview.org/faq and/or join the jalview-discuss@jalview.org mailing list"
+ "
If you use Jalview, please cite:"
+ "
Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+ "
Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+ "
Bioinformatics doi: 10.1093/bioinformatics/btp033"
+ "");
return message;
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
public void documentationMenuItem_actionPerformed(ActionEvent e)
{
try
{
ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
javax.help.HelpBroker hb = hs.createHelpBroker();
hb.setCurrentID("home");
hb.setDisplayed(true);
} catch (Exception ex)
{
}
}
public void closeAll_actionPerformed(ActionEvent e)
{
JInternalFrame[] frames = desktop.getAllFrames();
for (int i = 0; i < frames.length; i++)
{
try
{
frames[i].setClosed(true);
} 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, false);
}
public void minimizeAssociated_actionPerformed(ActionEvent e)
{
reorderAssociatedWindows(true, false);
}
void closeAssociatedWindows()
{
reorderAssociatedWindows(false, true);
}
/*
* (non-Javadoc)
*
* @seejalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.
* ActionEvent)
*/
protected void garbageCollect_actionPerformed(ActionEvent e)
{
// We simply collect the garbage
jalview.bin.Cache.log.debug("Collecting garbage...");
System.gc();
jalview.bin.Cache.log.debug("Finished garbage collection.");
}
/*
* (non-Javadoc)
*
* @see
* jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent
* )
*/
protected void showMemusage_actionPerformed(ActionEvent e)
{
desktop.showMemoryUsage(showMemusage.isSelected());
}
/*
* (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();
if (frames == null || frames.length < 1)
{
return;
}
AlignViewport source = null, target = null;
if (frames[0] instanceof AlignFrame)
{
source = ((AlignFrame) frames[0]).getCurrentView();
}
else if (frames[0] instanceof TreePanel)
{
source = ((TreePanel) frames[0]).getViewPort();
}
else if (frames[0] instanceof PCAPanel)
{
source = ((PCAPanel) frames[0]).av;
}
else if (frames[0].getContentPane() instanceof PairwiseAlignPanel)
{
source = ((PairwiseAlignPanel) frames[0].getContentPane()).av;
}
if (source != null)
{
for (int i = 0; i < frames.length; i++)
{
target = null;
if (frames[i] == null)
{
continue;
}
if (frames[i] instanceof AlignFrame)
{
target = ((AlignFrame) frames[i]).getCurrentView();
}
else if (frames[i] instanceof TreePanel)
{
target = ((TreePanel) frames[i]).getViewPort();
}
else if (frames[i] instanceof PCAPanel)
{
target = ((PCAPanel) frames[i]).av;
}
else if (frames[i].getContentPane() instanceof PairwiseAlignPanel)
{
target = ((PairwiseAlignPanel) frames[i].getContentPane()).av;
}
if (source == target)
{
try
{
if (close)
{
frames[i].setClosed(true);
}
else
{
frames[i].setIcon(minimize);
if (!minimize)
{
frames[i].toFront();
}
}
} catch (java.beans.PropertyVetoException ex)
{
}
}
}
}
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
protected void preferences_actionPerformed(ActionEvent e)
{
new Preferences();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
public void saveState_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
{ "jvp" }, new String[]
{ "Jalview Project" }, "Jalview Project");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save State");
int value = chooser.showSaveDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
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());
// 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();
}
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
public void loadState_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
{ "jvp", "jar" }, new String[]
{ "Jalview Project", "Jalview Project (old)" },
"Jalview Project");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Restore state");
int value = chooser.showOpenDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
final String choice = chooser.getSelectedFile().getAbsolutePath();
jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
.getSelectedFile().getParent());
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();
}
}
public void inputSequence_actionPerformed(ActionEvent e)
{
new SequenceFetcher(this);
}
JPanel progressPanel;
ArrayList fileLoadingPanels = new ArrayList();
public void startLoading(final String fileName)
{
if (fileLoadingCount == 0)
{
fileLoadingPanels.add(addProgressPanel("Loading File: " + fileName
+ " "));
}
fileLoadingCount++;
}
private JPanel addProgressPanel(String string)
{
if (progressPanel == null)
{
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);
thisprogress.add(new JLabel(string), BorderLayout.WEST);
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(JPanel progbar)
{
if (progressPanel != null)
{
synchronized (progressPanel)
{
progressPanel.remove(progbar);
GridLayout gl = (GridLayout) progressPanel.getLayout();
gl.setRows(gl.getRows() - 1);
if (--totalProgressCount < 1)
{
this.getContentPane().remove(progressPanel);
progressPanel = null;
}
}
}
validate();
}
public void stopLoading()
{
fileLoadingCount--;
if (fileLoadingCount < 1)
{
while (fileLoadingPanels.size() > 0)
{
removeProgressPanel(fileLoadingPanels.remove(0));
}
fileLoadingPanels.clear();
fileLoadingCount = 0;
}
validate();
}
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)
{
AlignFrame af = (AlignFrame) frames[t];
for (int a = 0; a < af.alignPanels.size(); a++)
{
if (alignmentId.equals(((AlignmentPanel) af.alignPanels
.elementAt(a)).av.getSequenceSetId()))
{
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();
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)
{
int size = af.alignPanels.size();
if (size < 2)
{
return;
}
for (int i = 0; i < size; i++)
{
AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(i);
AlignFrame newaf = new AlignFrame(ap);
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);
}
af.alignPanels.clear();
af.closeMenuItem_actionPerformed(true);
}
public void gatherViews(AlignFrame source)
{
source.viewport.gatherViewsHere = true;
source.viewport.explodedPosition = source.getBounds();
JInternalFrame[] frames = desktop.getAllFrames();
String viewId = source.viewport.getSequenceSetId();
for (int t = 0; t < frames.length; t++)
{
if (frames[t] instanceof AlignFrame && frames[t] != source)
{
AlignFrame af = (AlignFrame) frames[t];
boolean gatherThis = false;
for (int a = 0; a < af.alignPanels.size(); a++)
{
AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(a);
if (viewId.equals(ap.av.getSequenceSetId()))
{
gatherThis = true;
ap.av.gatherViewsHere = false;
ap.av.explodedPosition = af.getBounds();
source.addAlignmentPanel(ap, false);
}
}
if (gatherThis)
{
af.alignPanels.clear();
af.closeMenuItem_actionPerformed(true);
}
}
}
}
jalview.gui.VamsasApplication v_client = null;
public void vamsasImport_actionPerformed(ActionEvent e)
{
if (v_client == null)
{
// Load and try to start a session.
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Open a saved VAMSAS session");
chooser.setToolTipText(MessageManager
.getString("label.select_vamsas_session_opened_as_new_vamsas_session"));
int value = chooser.showOpenDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String fle = chooser.getSelectedFile().toString();
if (!vamsasImport(chooser.getSelectedFile()))
{
JOptionPane
.showInternalMessageDialog(
Desktop.desktop,
MessageManager.formatMessage(
"label.couldnt_import_as_vamsas_session",
new String[]
{ fle }),
MessageManager
.getString("label.vamsas_document_import_failed"),
JOptionPane.ERROR_MESSAGE);
}
}
}
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());
*/
v_client = new VamsasApplication(this);
setupVamsasConnectedGui();
v_client.initial_update(); // TODO: thread ?
}
else
{
// store current data in session.
v_client.push_update(); // TODO: thread
}
}
protected void setupVamsasConnectedGui()
{
vamsasStart.setText(MessageManager.getString("label.session_update"));
vamsasSave.setVisible(true);
vamsasStop.setVisible(true);
vamsasImport.setVisible(false); // Document import to existing session is
// not possible for vamsas-client-1.0.
}
protected void setupVamsasDisconnectedGui()
{
vamsasSave.setVisible(false);
vamsasStop.setVisible(false);
vamsasImport.setVisible(true);
vamsasStart.setText(MessageManager
.getString("label.new_vamsas_session"));
}
public void vamsasStop_actionPerformed(ActionEvent e)
{
if (v_client != null)
{
v_client.end_session();
v_client = null;
setupVamsasDisconnectedGui();
}
}
protected void buildVamsasStMenu()
{
if (v_client == null)
{
String[] sess = null;
try
{
sess = VamsasApplication.getSessionList();
} catch (Exception e)
{
jalview.bin.Cache.log.warn(
"Problem getting current sessions list.", e);
sess = null;
}
if (sess != null)
{
jalview.bin.Cache.log.debug("Got current sessions list: "
+ sess.length + " entries.");
VamsasStMenu.removeAll();
for (int i = 0; i < sess.length; i++)
{
JMenuItem sessit = new JMenuItem();
sessit.setText(sess[i]);
sessit.setToolTipText(MessageManager.formatMessage(
"label.connect_to_session", new String[]
{ sess[i] }));
final Desktop dsktp = this;
final String mysesid = sess[i];
sessit.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
if (dsktp.v_client == null)
{
Thread rthr = new Thread(new Runnable()
{
public void run()
{
dsktp.v_client = new VamsasApplication(dsktp, mysesid);
dsktp.setupVamsasConnectedGui();
dsktp.v_client.initial_update();
}
});
rthr.start();
}
};
});
VamsasStMenu.add(sessit);
}
// don't show an empty menu.
VamsasStMenu.setVisible(sess.length > 0);
}
else
{
jalview.bin.Cache.log.debug("No current vamsas sessions.");
VamsasStMenu.removeAll();
VamsasStMenu.setVisible(false);
}
}
else
{
// Not interested in the content. Just hide ourselves.
VamsasStMenu.setVisible(false);
}
}
public void vamsasSave_actionPerformed(ActionEvent e)
{
if (v_client != null)
{
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
{ "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
new String[]
{ "Vamsas Document" }, "Vamsas Document");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save Vamsas Document Archive");
int value = chooser.showSaveDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
java.io.File choice = chooser.getSelectedFile();
JPanel 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);
} catch (Exception ex)
{
warnttl = "Problem saving Vamsas Document.";
warnmsg = ex.toString();
jalview.bin.Cache.log.warn("Exception Whilst saving document to "
+ choice, ex);
}
removeProgressPanel(progpanel);
if (warnmsg != null)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
warnmsg, warnttl, JOptionPane.ERROR_MESSAGE);
}
}
}
}
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
*/
public void setVamsasUpdate(boolean b)
{
jalview.bin.Cache.log.debug("Setting gui for Vamsas update "
+ (b ? "in progress" : "finished"));
if (vamUpdate != null)
{
this.removeProgressPanel(vamUpdate);
}
if (b)
{
vamUpdate = this.addProgressPanel("Updating vamsas session");
}
vamsasStart.setVisible(!b);
vamsasStop.setVisible(!b);
vamsasSave.setVisible(!b);
}
public JInternalFrame[] getAllFrames()
{
return desktop.getAllFrames();
}
/**
* Checks the given url to see if it gives a response indicating that the user
* should be informed of a new questionnaire.
*
* @param url
*/
public void checkForQuestionnaire(String url)
{
UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url);
// 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.
*
* @author AMW
*/
public class MyDesktopPane extends JDesktopPane implements Runnable
{
boolean showMemoryUsage = false;
Runtime runtime;
java.text.NumberFormat df;
float maxMemory, allocatedMemory, freeMemory, totalFreeMemory,
percentUsage;
public MyDesktopPane(boolean showMemoryUsage)
{
showMemoryUsage(showMemoryUsage);
}
public void showMemoryUsage(boolean showMemoryUsage)
{
this.showMemoryUsage = showMemoryUsage;
if (showMemoryUsage)
{
Thread worker = new Thread(this);
worker.start();
}
}
public boolean isShowMemoryUsage()
{
return showMemoryUsage;
}
public void run()
{
df = java.text.NumberFormat.getNumberInstance();
df.setMaximumFractionDigits(2);
runtime = Runtime.getRuntime();
while (showMemoryUsage)
{
try
{
maxMemory = runtime.maxMemory() / 1048576f;
allocatedMemory = runtime.totalMemory() / 1048576f;
freeMemory = runtime.freeMemory() / 1048576f;
totalFreeMemory = freeMemory + (maxMemory - allocatedMemory);
percentUsage = (totalFreeMemory / maxMemory) * 100;
// if (percentUsage < 20)
{
// border1 = BorderFactory.createMatteBorder(12, 12, 12, 12,
// Color.red);
// instance.set.setBorder(border1);
}
repaint();
// sleep after showing usage
Thread.sleep(3000);
} catch (Exception ex)
{
ex.printStackTrace();
}
}
}
public void paintComponent(Graphics g)
{
if (showMemoryUsage && g != null && df != null)
{
if (percentUsage < 20)
g.setColor(Color.red);
FontMetrics fm = g.getFontMetrics();
if (fm != null)
{
g.drawString(MessageManager.formatMessage(
"label.memory_stats",
new String[]
{ df.format(totalFreeMemory), df.format(maxMemory),
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()
{
if (jalview.bin.Cache.groovyJarsPresent())
{
groovyShell = new JMenuItem();
groovyShell.setText(MessageManager.getString("label.groovy_console"));
groovyShell.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
groovyShell_actionPerformed(e);
}
});
toolsMenu.add(groovyShell);
groovyShell.setVisible(true);
}
}
/**
* Accessor method to quickly get all the AlignmentFrames loaded.
*/
public static AlignFrame[] getAlignframes()
{
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
if (frames == null)
{
return null;
}
Vector avp = new Vector();
try
{
// REVERSE ORDER
for (int i = frames.length - 1; i > -1; i--)
{
if (frames[i] instanceof AlignFrame)
{
AlignFrame af = (AlignFrame) frames[i];
avp.addElement(af);
}
}
} catch (Exception ex)
{
ex.printStackTrace();
}
if (avp.size() == 0)
{
return null;
}
AlignFrame afs[] = new AlignFrame[avp.size()];
for (int i = 0, j = avp.size(); i < j; i++)
{
afs[i] = (AlignFrame) avp.elementAt(i);
}
avp.clear();
return afs;
}
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
*/
public void groovyShell_actionPerformed(ActionEvent e)
{
// use reflection to avoid creating compilation dependency.
if (!jalview.bin.Cache.groovyJarsPresent())
{
throw new Error(
"Implementation Error. Cannot create groovyShell without Groovy on the classpath!");
}
try
{
Class gcClass = Desktop.class.getClassLoader().loadClass(
"groovy.ui.Console");
Constructor gccons = gcClass.getConstructor(null);
java.lang.reflect.Method setvar = gcClass.getMethod("setVariable",
new Class[]
{ String.class, Object.class });
java.lang.reflect.Method run = gcClass.getMethod("run", null);
Object gc = gccons.newInstance(null);
setvar.invoke(gc, new Object[]
{ "Jalview", this });
run.invoke(gc, null);
} catch (Exception ex)
{
jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
JOptionPane
.showInternalMessageDialog(
Desktop.desktop,
"Couldn't create the groovy Shell. Check the error log for the details of what went wrong.",
"Jalview Groovy Support Failed",
JOptionPane.ERROR_MESSAGE);
}
}
/**
* Progress bars managed by the IProgressIndicator method.
*/
private Hashtable progressBars;
private Hashtable 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)
{
JPanel progressPanel = 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())
{
JButton cancel = new JButton(
MessageManager.getString("action.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);
}
}
/**
*
* @return true if any progress bars are still active
*/
@Override
public boolean operationInProgress()
{
if (progressBars != null && progressBars.size() > 0)
{
return true;
}
return false;
}
/**
* 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;
// JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
if (true)
{
// 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
(t0 = new Thread(discoverer)).start();
}
// ENFIN services are EOLed as of Jalview 2.8.1 release
if (false)
{
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.
addDialogThread(serviceChangedDialog = new Runnable()
{
public void run()
{
/*
* JalviewDialog jd =new JalviewDialog() {
*
* @Override protected void cancelPressed() { // TODO
* Auto-generated method stub
*
* }@Override protected void okPressed() { // TODO
* Auto-generated method stub
*
* }@Override protected void raiseClosed() { // TODO
* Auto-generated method stub
*
* } }; jd.initDialogFrame(new
* JLabel("" + ermsg +
* "
It may be that you have invalid JABA URLs in your web service preferences,"
* + " or mis-configured HTTP proxy settings.
" +
* "Check the Connections and Web services tab of the"
* +
* " Tools->Preferences dialog box to change them. |
"
* ), true, true, "Web Service Configuration Problem", 450,
* 400);
*
* jd.waitForInput();
*/
JOptionPane
.showConfirmDialog(
Desktop.desktop,
new JLabel(
""
+ "It may be that you have invalid JABA URLs
in your web service preferences,"
+ " or mis-configured HTTP proxy settings.
"
+ "Check the Connections and Web services tab
of the"
+ " Tools->Preferences dialog box to change them.
"),
"Web Service Configuration Problem",
JOptionPane.DEFAULT_OPTION,
JOptionPane.ERROR_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;
}
/**
* static hyperlink handler proxy method for use by Jalview's internal windows
*
* @param e
*/
public static void hyperlinkUpdate(HyperlinkEvent e)
{
if (e.getEventType() == EventType.ACTIVATED)
{
String url = null;
try
{
url = e.getURL().toString();
Desktop.showUrl(url);
} catch (Exception x)
{
if (url != null)
{
if (Cache.log != null)
{
Cache.log.error("Couldn't handle string " + url + " as a URL.");
}
else
{
System.err.println("Couldn't handle string " + url
+ " as a URL.");
}
}
// ignore any exceptions due to dud links.
}
}
}
/**
* single thread that handles display of dialogs to user.
*/
ExecutorService dialogExecutor = Executors.newSingleThreadExecutor();
/**
* flag indicating if dialogExecutor should try to acquire a permit
*/
private volatile boolean dialogPause = true;
/**
* pause the queue
*/
private java.util.concurrent.Semaphore block = new Semaphore(0);
/**
* add another dialog thread to the queue
*
* @param prompter
*/
public void addDialogThread(final Runnable prompter)
{
dialogExecutor.submit(new Runnable()
{
public void run()
{
if (dialogPause)
{
try
{
block.acquire();
} catch (InterruptedException x)
{
}
;
}
if (instance == null)
{
return;
}
try
{
SwingUtilities.invokeAndWait(prompter);
} catch (Exception q)
{
Cache.log.warn("Unexpected Exception in dialog thread.", q);
}
}
});
}
public void startDialogQueue()
{
// set the flag so we don't pause waiting for another permit and semaphore
// the current task to begin
dialogPause = false;
block.release();
}
}