/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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 2.6)
+ * 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 jalview.ws.params.ParamManager;
import java.awt.*;
import java.awt.datatransfer.*;
import java.awt.dnd.*;
import java.awt.event.*;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+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.*;
-
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
/**
- * DOCUMENT ME!
- *
+ * Jalview Desktop
+ *
+ *
* @author $author$
* @version $Revision$
*/
-public class Desktop extends jalview.jbgui.GDesktop
- implements DropTargetListener
+public class Desktop extends jalview.jbgui.GDesktop implements
+ DropTargetListener, ClipboardOwner, IProgressIndicator
{
- /** DOCUMENT ME!! */
- public static JDesktopPane desktop;
- static int openFrameCount = 0;
- static final int xOffset = 30;
- static final int yOffset = 30;
- public static jalview.ws.Discoverer discoverer;
+
+ private class JalviewChangeSupport implements PropertyChangeListener
+ {
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ // Handle change events - most are simply routed to other sources
+ changeSupport.firePropertyChange(evt);
+ }
+
+ /**
+ * change listeners are notified of changes to resources so they can update
+ * their state. E.g. - the 'services' property notifies when the available
+ * set of web service endpoints have changed.
+ */
+ private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+ this);
+
/**
- * Creates a new Desktop object.
+ * @param propertyName
+ * @param listener
+ * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.lang.String,
+ * java.beans.PropertyChangeListener)
*/
- public Desktop()
+ public void addJalviewPropertyChangeListener(String propertyName,
+ PropertyChangeListener listener)
{
- Image image = null;
+ changeSupport.addPropertyChangeListener(propertyName, listener);
+ }
- try
- {
- java.net.URL url = getClass().getResource("/images/logo.gif");
+ /**
+ * @param listener
+ * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(
+ * java.beans.PropertyChangeListener)
+ */
+ public void addJalviewPropertyChangeListener(
+ PropertyChangeListener listener)
+ {
+ changeSupport.addPropertyChangeListener(listener);
+ }
- if (url != null)
- {
- image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+ /*
+ * @param propertyName
+ *
+ * @param oldValue
+ *
+ * @param newValue
+ *
+ * @see
+ * java.beans.PropertyChangeSupport#firePropertyChange(java.lang.String,
+ * java.lang.Object, java.lang.Object) public void firePropertyChange(String
+ * propertyName, Object oldValue, Object newValue) {
+ * changeSupport.firePropertyChange(propertyName, oldValue, newValue); }
+ */
- MediaTracker mt = new MediaTracker(this);
- mt.addImage(image, 0);
- mt.waitForID(0);
- setIconImage(image);
- }
- }
- catch (Exception ex)
- {
- }
+ /**
+ * @param propertyName
+ * @param listener
+ * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.lang.String,
+ * java.beans.PropertyChangeListener)
+ */
+ public void removeJalviewPropertyChangeListener(String propertyName,
+ PropertyChangeListener listener)
+ {
+ changeSupport.removePropertyChangeListener(propertyName, listener);
+ }
- setTitle("Jalview 2005");
- setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
- desktop = new JDesktopPane();
- desktop.setBackground(Color.white);
- setContentPane(desktop);
- desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
+ }
- // This line prevents Windows Look&Feel resizing all new windows to maximum
- // if previous window was maximised
- desktop.setDesktopManager(new DefaultDesktopManager());
+ private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
- 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");
+ /**
+ * @param listener
+ * @see jalview.gui.Desktop.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
+ */
+ public void addJalviewPropertyChangeListener(
+ PropertyChangeListener listener)
+ {
+ changeSupport.addJalviewPropertyChangeListener(listener);
+ }
- if ((x != null) && (y != null) && (width != null) && (height != null))
- {
- setBounds(Integer.parseInt(x), Integer.parseInt(y),
- Integer.parseInt(width), Integer.parseInt(height));
- }
- else
- {
- setBounds((int) (screenSize.width - 900) / 2,
- (int) (screenSize.height - 650) / 2, 900, 650);
- }
+ /**
+ * @param propertyName
+ * @param listener
+ * @see jalview.gui.Desktop.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String,
+ * java.beans.PropertyChangeListener)
+ */
+ public void addJalviewPropertyChangeListener(String propertyName,
+ PropertyChangeListener listener)
+ {
+ changeSupport.addJalviewPropertyChangeListener(propertyName, listener);
+ }
- this.addWindowListener(new WindowAdapter()
- {
- public void windowClosing(WindowEvent evt)
- {
- quit();
- }
- });
+ /**
+ * @param propertyName
+ * @param listener
+ * @see jalview.gui.Desktop.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String,
+ * java.beans.PropertyChangeListener)
+ */
+ public void removeJalviewPropertyChangeListener(String propertyName,
+ PropertyChangeListener listener)
+ {
+ changeSupport.removeJalviewPropertyChangeListener(propertyName,
+ listener);
+ }
- this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
+ /** Singleton Desktop instance */
+ public static Desktop instance;
- /////////Add a splashscreen on startup
- /////////Add a splashscreen on startup
- JInternalFrame frame = new JInternalFrame();
+ public static MyDesktopPane desktop;
- SplashScreen splash = new SplashScreen(frame, image);
- frame.setContentPane(splash);
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
- frame.setLocation((int) ((getWidth() - 750) / 2),
- (int) ((getHeight() - 160) / 2));
+ static int openFrameCount = 0;
- addInternalFrame(frame, "", 750, 160, false);
+ static final int xOffset = 30;
- discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
+ static final int yOffset = 30;
- }
+ public static jalview.ws.jws1.Discoverer discoverer;
- /**
- * DOCUMENT ME!
- *
- * @param frame DOCUMENT ME!
- * @param title DOCUMENT ME!
- * @param w DOCUMENT ME!
- * @param h DOCUMENT ME!
- */
- public static synchronized void addInternalFrame(final JInternalFrame frame,
- String title, int w, int h)
+ public static Object[] jalviewClipboard;
+
+ public static boolean internalCopy = false;
+
+ static int fileLoadingCount = 0;
+
+ class MyDesktopManager implements DesktopManager
+ {
+
+ private DesktopManager delegate;
+
+ public MyDesktopManager(DesktopManager delegate)
{
- addInternalFrame(frame, title, w, h, true);
+ this.delegate = delegate;
}
- /**
- * 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 void activateFrame(JInternalFrame f)
{
-
- frame.setTitle(title);
- if(frame.getWidth()<1 || frame.getHeight()<1)
+ try
{
- 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 (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true"))
+ delegate.activateFrame(f);
+ } catch (NullPointerException npe)
{
- return;
+ Point p = getMousePosition();
+ instance.showPasteMenu(p.x, p.y);
}
+ }
+ public void beginDraggingFrame(JComponent f)
+ {
+ delegate.beginDraggingFrame(f);
+ }
- 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 internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- {
- openFrameCount--;
- windowMenu.remove(menuItem);
- }
- ;
- });
+ public void beginResizingFrame(JComponent f, int direction)
+ {
+ delegate.beginResizingFrame(f, direction);
+ }
- menuItem.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- try
- {
- frame.setSelected(true);
- frame.setIcon(false);
- }
- catch (java.beans.PropertyVetoException ex)
- {
-
- }
- }
- });
+ public void closeFrame(JInternalFrame f)
+ {
+ delegate.closeFrame(f);
+ }
- windowMenu.add(menuItem);
+ public void deactivateFrame(JInternalFrame f)
+ {
+ delegate.deactivateFrame(f);
+ }
- desktop.add(frame);
- frame.toFront();
- try{
- frame.setSelected(true);
- }catch(java.beans.PropertyVetoException ve)
- {}
+ public void deiconifyFrame(JInternalFrame f)
+ {
+ delegate.deiconifyFrame(f);
}
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void dragEnter(DropTargetDragEvent evt)
+ public void dragFrame(JComponent f, int newX, int newY)
{
+ delegate.dragFrame(f, newX, newY);
}
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void dragExit(DropTargetEvent evt)
+ public void endDraggingFrame(JComponent f)
{
+ delegate.endDraggingFrame(f);
}
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void dragOver(DropTargetDragEvent evt)
+ public void endResizingFrame(JComponent f)
{
+ delegate.endResizingFrame(f);
}
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void dropActionChanged(DropTargetDragEvent evt)
+ public void iconifyFrame(JInternalFrame f)
{
+ delegate.iconifyFrame(f);
}
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void drop(DropTargetDropEvent evt)
+ public void maximizeFrame(JInternalFrame f)
{
- Transferable t = evt.getTransferable();
+ delegate.maximizeFrame(f);
+ }
- if (!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
- {
- return;
- }
+ public void minimizeFrame(JInternalFrame f)
+ {
+ delegate.minimizeFrame(f);
+ }
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+ public void openFrame(JInternalFrame f)
+ {
+ delegate.openFrame(f);
+ }
- try
- {
- java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
+ public void resizeFrame(JComponent f, int newX, int newY, int newWidth,
+ int newHeight)
+ {
+ delegate.resizeFrame(f, newX, newY, newWidth, newHeight);
+ }
- for (int i = 0; i < files.size(); i++)
- {
- String file = files.get(i).toString();
- String protocol = "File";
- String format = null;
+ public void setBoundsForFrame(JComponent f, int newX, int newY,
+ int newWidth, int newHeight)
+ {
+ delegate.setBoundsForFrame(f, newX, newY, newWidth, newHeight);
+ }
- if (file.endsWith(".jar"))
- {
- format = "Jalview";
+ // All other methods, simply delegate
- }
- else
- {
- format = jalview.io.IdentifyFile.Identify(file,
- protocol);
- }
- LoadFile(file, protocol, format);
- }
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
+ }
+ /**
+ * Creates a new Desktop object.
+ */
+ public Desktop()
+ {
/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ * 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.
*/
- public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
+ 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());
+ 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)
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"),
- new String[]
- {
- "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
- "jar"
- },
- new String[]
- {
- "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
- }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Open local file");
- chooser.setToolTipText("Open");
-
- int value = chooser.showOpenDialog(this);
+ 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);
+
+ this.addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent evt)
+ {
+ quit();
+ }
+ });
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ this.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent evt)
+ {
+ if (SwingUtilities.isRightMouseButton(evt))
{
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
-
- String format = null;
- if (chooser.getSelectedFormat().equals("Jalview"))
- {
- format = "Jalview";
- }
- else
- {
- format = IdentifyFile.Identify(choice, "File");
- }
-
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
- LoadFile(choice, "File", format);
+ showPasteMenu(evt.getX(), evt.getY());
}
- }
+ }
+ });
- /**
- * DOCUMENT ME!
- *
- * @param file DOCUMENT ME!
- * @param protocol DOCUMENT ME!
- * @param format DOCUMENT ME!
- */
- public void LoadFile(String file, String protocol, String format)
+ 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();
+ }
+
+ /**
+ * 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))
{
- FileLoader fileLoader = new FileLoader();
- fileLoader.LoadFile(file, protocol, format);
+ 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;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void inputURLMenuItem_actionPerformed(ActionEvent e)
+ private void doVamsasClientCheck()
+ {
+ if (jalview.bin.Cache.vamsasJarsPresent())
{
- String url = JOptionPane.showInternalInputDialog(Desktop.desktop,
- "Enter url of input file", "Input alignment from URL",
- JOptionPane.QUESTION_MESSAGE, null, null, "http://www.")
- .toString();
+ 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;
- if (url == null)
+ public void menuCanceled(MenuEvent e)
{
- return;
+ refresh = true;
}
- if (url.trim().toLowerCase().endsWith(".jar"))
+ public void menuDeselected(MenuEvent e)
{
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview");
- Jalview2XML.LoadJalviewAlign(url);
+ refresh = true;
}
- else
- {
-
- String format = IdentifyFile.Identify(url, "URL");
- if (format.equals("URL NOT FOUND"))
+ public void menuSelected(MenuEvent e)
+ {
+ if (refresh)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Couldn't locate " + url,
- "URL not found",
- JOptionPane.WARNING_MESSAGE);
-
- return;
+ us.buildVamsasStMenu();
+ refresh = false;
}
-
- LoadFile(url, "URL", format);
}
+ });
+ vamsasStart.setVisible(true);
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
+ void showPasteMenu(int x, int y)
+ {
+ JPopupMenu popup = new JPopupMenu();
+ JMenuItem item = new JMenuItem("Paste To New Window");
+ item.addActionListener(new ActionListener()
{
- CutAndPasteTransfer cap = new CutAndPasteTransfer();
- cap.setForInput();
- Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
- }
+ public void actionPerformed(ActionEvent evt)
+ {
+ paste();
+ }
+ });
- /*
- * Exit the program
- */
- 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() + "");
- System.exit(0);
- }
+ popup.add(item);
+ popup.show(this, x, y);
+ }
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void aboutMenuItem_actionPerformed(ActionEvent e)
+ public void paste()
+ {
+ try
{
- StringBuffer message = new StringBuffer("JalView 2005 version " +
- jalview.bin.Cache.getProperty(
- "VERSION") +
- "; last updated: " +
- jalview.bin.
- Cache.getDefault("BUILD_DATE", "unknown"));
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+ Transferable contents = c.getContents(this);
- if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
- jalview.bin.Cache.getProperty("VERSION")))
+ if (contents != null)
{
- message.append("\n\n!! Jalview version "
- + jalview.bin.Cache.getProperty("LATEST_VERSION")
- + " is available for download from http://www.jalview.org !!\n");
+ 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 (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true"))
+ {
+ return;
+ }
- 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 12;426-7.");
+ openFrameCount++;
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ frame.setVisible(true);
+ frame.setClosable(true);
+ frame.setResizable(resizable);
+ frame.setMaximizable(resizable);
+ frame.setIconifiable(resizable);
+ frame.setFrameIcon(null);
- message.toString(), "About Jalview",
- JOptionPane.INFORMATION_MESSAGE);
+ if (frame.getX() < 1 && frame.getY() < 1)
+ {
+ frame.setLocation(xOffset * openFrameCount, yOffset
+ * ((openFrameCount - 1) % 10) + yOffset);
}
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void documentationMenuItem_actionPerformed(ActionEvent e)
+ 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
{
- 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)
+ frame.setSelected(true);
+ frame.setIcon(false);
+ } catch (java.beans.PropertyVetoException ex)
{
- ex.printStackTrace();
+
}
+ }
+ });
+
+ windowMenu.add(menuItem);
+
+ desktop.add(frame);
+ frame.toFront();
+ try
+ {
+ frame.setSelected(true);
+ frame.requestFocus();
+ } catch (java.beans.PropertyVetoException ve)
+ {
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- protected void preferences_actionPerformed(ActionEvent e)
+ public void lostOwnership(Clipboard clipboard, Transferable contents)
+ {
+ if (!internalCopy)
{
- new Preferences();
+ Desktop.jalviewClipboard = null;
}
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void saveState_actionPerformed(ActionEvent e)
+ 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)
+ {
+ 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)
+ {
+ }
+
+ if (files != null)
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"), new String[] { "jar" },
- new String[] { "Jalview Project" }, "Jalview Project");
+ 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;
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save State");
+ if (file.endsWith(".jar"))
+ {
+ format = "Jalview";
- int value = chooser.showSaveDialog(this);
+ }
+ else
+ {
+ format = new IdentifyFile().Identify(file, protocol);
+ }
+
+ new FileLoader().LoadFile(file, protocol, format);
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- java.io.File choice = chooser.getSelectedFile();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
- Jalview2XML.SaveState(choice);
}
+ } catch (Exception ex)
+ {
+ }
}
+ }
+
+ /**
+ * 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("Open local file");
+ chooser.setToolTipText("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());
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void loadState_actionPerformed(ActionEvent e)
+ String format = null;
+ if (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("Enter URL of Input File");
+ 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)
{
- 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");
+ st = new StringTokenizer(historyItems, "\t");
- int value = chooser.showOpenDialog(this);
+ while (st.hasMoreTokens())
+ {
+ history.addItem(st.nextElement());
+ }
+ }
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- String choice = chooser.getSelectedFile().getAbsolutePath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
- Jalview2XML.LoadJalviewAlign(choice);
- }
+ int reply = JOptionPane.showInternalConfirmDialog(desktop, panel,
+ "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();
+ }
+ 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 = 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")))
+ {
+ message
+ .append("\n\n!! Jalview version "
+ + jalview.bin.Cache.getProperty("LATEST_VERSION")
+ + " is available for download from http://www.jalview.org !!\n");
+
+ }
+ // TODO: update this text for each release or centrally store it for lite
+ // and application
+ message
+ .append("\nAuthors: Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,\n David Martin & Geoff Barton."
+ + "\nDevelopment managed by The Barton Group, University of Dundee, Scotland, UK.\n"
+ + "\nFor help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list\n"
+ + "\nIf you use Jalview, please cite:"
+ + "\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);
+ }
+
+ /**
+ * 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[]
+ { "jar" }, new String[]
+ { "Jalview Project" }, "Jalview Project");
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Save State");
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ java.io.File choice = chooser.getSelectedFile();
+ setProgressBar("Saving jalview project "
+ + choice.getName(), choice.hashCode());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+ // TODO catch and handle errors for savestate
+ 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(this, "Error whilst saving current state to "+choice.getName(), "Couldn't save project", JOptionPane.WARNING_MESSAGE);
+ }
+ setProgressBar(null, choice.hashCode());
+
+ }
+ }
+
+ /**
+ * 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");
+ 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;
+
+ public void startLoading(final String fileName)
+ {
+ if (fileLoadingCount == 0)
+ {
+ addProgressPanel("Loading File: " + fileName + " ");
+
+ }
+ fileLoadingCount++;
+ }
+
+ private JProgressBar addProgressPanel(String string)
+ {
+ if (progressPanel == null)
+ {
+ progressPanel = new JPanel(new BorderLayout());
+ totalProgressCount = 0;
+ }
+ JProgressBar progressBar = new JProgressBar();
+ progressBar.setIndeterminate(true);
+
+ progressPanel.add(new JLabel(string), BorderLayout.WEST);
+
+ progressPanel.add(progressBar, BorderLayout.CENTER);
+
+ instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
+ totalProgressCount++;
+ validate();
+ return progressBar;
+ }
+
+ int totalProgressCount = 0;
+
+ private void removeProgressPanel(JProgressBar progbar)
+ {
+ if (progressPanel != null)
+ {
+ progressPanel.remove(progbar);
+ if (--totalProgressCount < 1)
+ {
+ this.getContentPane().remove(progressPanel);
+ progressPanel = null;
+ }
+ }
+ validate();
+ }
+
+ public void stopLoading()
+ {
+ fileLoadingCount--;
+ if (fileLoadingCount < 1)
+ {
+ if (progressPanel != null)
+ {
+ this.getContentPane().remove(progressPanel);
+ progressPanel = null;
+ }
+ fileLoadingCount = 0;
+ }
+ 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()))
+ {
+ 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.sequenceSetID;
+
+ 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("select a vamsas session to be opened as a 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,
+ "Couldn't import '" + fle + "' as a new vamsas session.",
+ "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("Session Update");
+ vamsasSave.setVisible(true);
+ vamsasStop.setVisible(true);
+ vamsasImport.setVisible(false); // Document import to existing session is
+ // not possible for vamsas-client-1.0.
+ }
+
+ protected void setupVamsasDisconnectedGui()
+ {
+ vamsasSave.setVisible(false);
+ vamsasStop.setVisible(false);
+ vamsasImport.setVisible(true);
+ vamsasStart.setText("New Vamsas Session");
+ }
+
+ public void vamsasStop_actionPerformed(ActionEvent e)
+ {
+ if (v_client != null)
+ {
+ v_client.end_session();
+ v_client = null;
+ setupVamsasDisconnectedGui();
+ }
+ }
+
+ protected void buildVamsasStMenu()
+ {
+ if (v_client == null)
+ {
+ String[] sess = null;
+ try
+ {
+ sess = VamsasApplication.getSessionList();
+ } catch (Exception e)
+ {
+ jalview.bin.Cache.log.warn(
+ "Problem getting current sessions list.", e);
+ sess = null;
+ }
+ if (sess != null)
+ {
+ jalview.bin.Cache.log.debug("Got current sessions list: "
+ + sess.length + " entries.");
+ VamsasStMenu.removeAll();
+ for (int i = 0; i < sess.length; i++)
+ {
+ JMenuItem sessit = new JMenuItem();
+ sessit.setText(sess[i]);
+ sessit.setToolTipText("Connect to session " + sess[i]);
+ final Desktop dsktp = this;
+ final String mysesid = sess[i];
+ sessit.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ if (dsktp.v_client == null)
+ {
+ Thread rthr = new Thread(new Runnable()
+ {
+
+ public void run()
+ {
+ dsktp.v_client = new VamsasApplication(dsktp, mysesid);
+ dsktp.setupVamsasConnectedGui();
+ dsktp.v_client.initial_update();
+ }
+
+ });
+ rthr.start();
+ }
+ };
+ });
+ VamsasStMenu.add(sessit);
+ }
+ // don't show an empty menu.
+ VamsasStMenu.setVisible(sess.length > 0);
+
+ }
+ else
+ {
+ jalview.bin.Cache.log.debug("No current vamsas sessions.");
+ VamsasStMenu.removeAll();
+ VamsasStMenu.setVisible(false);
+ }
+ }
+ else
+ {
+ // Not interested in the content. Just hide ourselves.
+ VamsasStMenu.setVisible(false);
+ }
+ }
+
+ public void vamsasSave_actionPerformed(ActionEvent e)
+ {
+ if (v_client != null)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+ .getProperty("LAST_DIRECTORY"), new String[]
+ { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+ new String[]
+ { "Vamsas Document" }, "Vamsas Document");
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Save Vamsas Document Archive");
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ java.io.File choice = chooser.getSelectedFile();
+ 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);
+
+ } 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);
+ }
+ }
+ }
+ }
+
+ 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
+ */
+ 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("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()
+ {
+ if (jalview.bin.Cache.groovyJarsPresent())
+ {
+ groovyShell = new JMenuItem();
+ groovyShell.setText("Groovy Console...");
+ groovyShell.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ groovyShell_actionPerformed(e);
+ }
+ });
+ toolsMenu.add(groovyShell);
+ groovyShell.setVisible(true);
+ }
+ }
+
+ /**
+ * Accessor method to quickly get all the AlignmentFrames loaded.
+ */
+ public static AlignFrame[] getAlignframes()
+ {
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+
+ if (frames == null)
+ {
+ return null;
+ }
+ Vector avp = new Vector();
+ try
+ {
+ // REVERSE ORDER
+ for (int i = frames.length - 1; i > -1; i--)
+ {
+ if (frames[i] instanceof AlignFrame)
+ {
+ AlignFrame af = (AlignFrame) frames[i];
+ avp.addElement(af);
+ }
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ if (avp.size() == 0)
+ {
+ return null;
+ }
+ AlignFrame afs[] = new AlignFrame[avp.size()];
+ for (int i = 0, j = avp.size(); i < j; i++)
+ {
+ afs[i] = (AlignFrame) avp.elementAt(i);
+ }
+ avp.clear();
+ return afs;
+ }
+
+ /**
+ * Add Groovy Support to Jalview
+ */
+ public void groovyShell_actionPerformed(ActionEvent e)
+ {
+ // use reflection to avoid creating compilation dependency.
+ if (!jalview.bin.Cache.groovyJarsPresent())
+ {
+ throw new Error(
+ "Implementation Error. Cannot create groovyShell without Groovy on the classpath!");
+ }
+ try
+ {
+ Class gcClass = Desktop.class.getClassLoader().loadClass(
+ "groovy.ui.Console");
+ Constructor gccons = gcClass.getConstructor(null);
+ java.lang.reflect.Method setvar = gcClass.getMethod("setVariable",
+ new Class[]
+ { String.class, Object.class });
+ java.lang.reflect.Method run = gcClass.getMethod("run", null);
+ Object gc = gccons.newInstance(null);
+ setvar.invoke(gc, new Object[]
+ { "Jalview", this });
+ run.invoke(gc, null);
+ } catch (Exception ex)
+ {
+ jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+
+ "Couldn't create the groovy Shell. Check the error log for the details of what went wrong.",
+ "Jalview Groovy Support Failed",
+ JOptionPane.ERROR_MESSAGE);
+ }
+ }
+
+ /**
+ * Progress bars managed by the IProgressIndicator method.
+ */
+ private Hashtable progressBars, 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())
+ {
+ JButton cancel = new JButton("Cancel");
+ final IProgressIndicator us = this;
+ cancel.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ handler.cancelActivity(id);
+ us.setProgressBar("Cancelled "
+ + ((JLabel) progressPanel.getComponent(0)).getText(), id);
+ }
+ });
+ progressPanel.add(cancel, BorderLayout.EAST);
+ }
+ }
+
+ /**
+ * This will return the first AlignFrame viewing AlignViewport av. It will
+ * break if there are more than one AlignFrames viewing a particular av. This
+ *
+ * @param av
+ * @return alignFrame for av
+ */
+ public static AlignFrame getAlignFrameFor(AlignViewport av)
+ {
+ if (desktop != null)
+ {
+ AlignmentPanel[] aps = getAlignmentPanels(av.getSequenceSetId());
+ for (int panel = 0; aps != null && panel < aps.length; panel++)
+ {
+ if (aps[panel] != null && aps[panel].av == av)
+ {
+ return aps[panel].alignFrame;
+ }
+ }
+ }
+ return null;
+ }
+
+ public VamsasApplication getVamsasApplication()
+ {
+ return v_client;
+
+ }
+ /**
+ * flag set if jalview GUI is being operated programmatically
+ */
+ private boolean inBatchMode=false;
+
+ /**
+ * check if jalview GUI is being operated programmatically
+ * @return inBatchMode
+ */
+ public boolean isInBatchMode()
+ {
+ return inBatchMode;
+ }
+
+ /**
+ * set flag if jalview GUI is being operated programmatically
+ * @param inBatchMode
+ */
+ public void setInBatchMode(boolean inBatchMode)
+ {
+ this.inBatchMode = inBatchMode;
+ }
+
+
+ public void startServiceDiscovery()
+ {
+ startServiceDiscovery(false);
+ }
+
+ public void startServiceDiscovery(boolean blocking)
+ {
+ boolean alive = true;
+ Thread t0 = null, t1 = null, t2 = null;
+
+ // todo: changesupport handlers need to be transferred
+ if (discoverer == null)
+ {
+ discoverer = new jalview.ws.jws1.Discoverer();
+ // register PCS handler for desktop.
+ discoverer.addPropertyChangeListener(changeSupport);
+ }
+ if (Cache.getDefault("SHOW_JWS1_SERVICES", true))
+ {
+ (t0 = new Thread(discoverer)).start();
+ }
+
+ try
+ {
+ if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
+ {
+ // EnfinEnvision web service menu entries are rebuild every time the
+ // menu is shown, so no changeSupport events are needed.
+ jalview.ws.EnfinEnvision2OneWay.getInstance();
+ (t1 = new Thread(jalview.ws.EnfinEnvision2OneWay.getInstance()))
+ .start();
+ }
+ } catch (Exception e)
+ {
+ Cache.log
+ .info(
+ "Exception when trying to launch Envision2 workflow discovery.",
+ e);
+ Cache.log.info(e.getStackTrace());
+ }
+ if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ {
+ jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+ .addPropertyChangeListener(changeSupport);
+ (t2 = new Thread(jalview.ws.jws2.Jws2Discoverer.getDiscoverer()))
+ .start();
+ }
+ if (blocking)
+ {
+ while (alive)
+ {
+ try
+ {
+ Thread.sleep(15);
+ } catch (Exception e)
+ {
+ }
+ alive = (t1 != null && t1.isAlive())
+ || (t2 != null && t2.isAlive())
+ || (t0 != null && t0.isAlive());
+ }
+ }
+ }
+
+ /**
+ * 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)
+ {
+ new Thread(new Runnable() {
+ public void run() {
+ try {
+ 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();
+ }
+ }
+ }).start();
+ }
+
+ public static WsParamSetManager wsparamManager = null;
+ public static ParamManager getUserParameterStore()
+ {
+ if (wsparamManager==null)
+ {
+ wsparamManager = new WsParamSetManager();
+ }
+ return wsparamManager;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff