/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
+ *
+ * Jalview is 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
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import jalview.io.*;
-
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.dnd.*;
-import java.awt.event.*;
-import java.util.*;
-
-import javax.swing.*;
-
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GSplitFrame;
+import jalview.jbgui.GStructureViewer;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.AlignmentViewport;
+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.Window;
+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.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.BufferedInputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+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.AbstractAction;
+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.KeyStroke;
+import javax.swing.SwingUtilities;
+import javax.swing.event.HyperlinkEvent;
+import javax.swing.event.HyperlinkEvent.EventType;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
/**
- * DOCUMENT ME!
- *
+ * Jalview Desktop
+ *
+ *
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.155 $
*/
-public class Desktop extends jalview.jbgui.GDesktop
- implements DropTargetListener, ClipboardOwner
+public class Desktop extends jalview.jbgui.GDesktop implements
+ DropTargetListener, ClipboardOwner, IProgressIndicator,
+ jalview.api.StructureSelectionManagerProvider
{
- /** DOCUMENT ME!! */
- public static Desktop instance;
- public static JDesktopPane desktop;
- static int openFrameCount = 0;
- static final int xOffset = 30;
- static final int yOffset = 30;
- public static jalview.ws.Discoverer discoverer;
-
- public static Object [] jalviewClipboard;
- public static boolean internalCopy = false;
- static int fileLoadingCount= 0;
+ private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
- /**
- * Creates a new Desktop object.
- */
- public Desktop()
- {
- instance = this;
- doVamsasClientCheck();
- Image image = null;
+ /**
+ * news reader - null if it was never started.
+ */
+ private BlogReader jvnews = null;
- try
- {
- java.net.URL url = getClass().getResource("/images/logo.gif");
+ private File projectFile;
- if (url != null)
- {
- image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+ /**
+ * @param listener
+ * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
+ */
+ public void addJalviewPropertyChangeListener(
+ PropertyChangeListener listener)
+ {
+ changeSupport.addJalviewPropertyChangeListener(listener);
+ }
- MediaTracker mt = new MediaTracker(this);
- mt.addImage(image, 0);
- mt.waitForID(0);
- setIconImage(image);
- }
- }
- catch (Exception ex)
- {
- }
+ /**
+ * @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);
+ }
- setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION"));
- setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
- desktop = new JDesktopPane();
- desktop.setBackground(Color.white);
- getContentPane().setLayout(new BorderLayout());
- getContentPane().add(desktop, BorderLayout.CENTER);
- desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
+ /**
+ * @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);
+ }
- // This line prevents Windows Look&Feel resizing all new windows to maximum
- // if previous window was maximised
- desktop.setDesktopManager(new DefaultDesktopManager());
+ /** Singleton Desktop instance */
+ public static Desktop instance;
- 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");
+ public static MyDesktopPane desktop;
- 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);
- }
+ static int openFrameCount = 0;
- this.addWindowListener(new WindowAdapter()
- {
- public void windowClosing(WindowEvent evt)
- {
- quit();
- }
- });
+ static final int xOffset = 30;
- this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
+ static final int yOffset = 30;
- /////////Add a splashscreen on startup
- /////////Add a splashscreen on startup
- JInternalFrame frame = new JInternalFrame();
+ public static jalview.ws.jws1.Discoverer discoverer;
- SplashScreen splash = new SplashScreen(frame, image);
- frame.setContentPane(splash);
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
- frame.setLocation((int) ((getWidth() - 750) / 2),
- (int) ((getHeight() - 160) / 2));
+ public static Object[] jalviewClipboard;
- addInternalFrame(frame, "", 750, 160, false);
+ public static boolean internalCopy = false;
- discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
- }
+ static int fileLoadingCount = 0;
- private void doVamsasClientCheck() {
- if (jalview.bin.Cache.vamsasJarsPresent()) {
- VamsasMenu.setVisible(true);
- vamsasLoad.setVisible(true);
- }
+ class MyDesktopManager implements DesktopManager
+ {
- }
+ private DesktopManager delegate;
- /**
- * 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 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)
+ @Override
+ 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);
}
+ }
+ @Override
+ 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);
+ @Override
+ public void beginResizingFrame(JComponent f, int direction)
+ {
+ delegate.beginResizingFrame(f, direction);
+ }
- if (frame.getX()<1 && frame.getY()<1)
- {
- frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount-1)%10)+yOffset);
- }
+ @Override
+ public void closeFrame(JInternalFrame f)
+ {
+ delegate.closeFrame(f);
+ }
- 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();
+ @Override
+ public void deactivateFrame(JInternalFrame f)
+ {
+ delegate.deactivateFrame(f);
+ }
- }
+ @Override
+ public void deiconifyFrame(JInternalFrame f)
+ {
+ delegate.deiconifyFrame(f);
+ }
+ @Override
+ public void dragFrame(JComponent f, int newX, int newY)
+ {
+ if (newY < 0)
+ {
+ newY = 0;
+ }
+ delegate.dragFrame(f, newX, newY);
+ }
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- {
- PaintRefresher.RemoveComponent(frame);
- openFrameCount--;
- windowMenu.remove(menuItem);
- JInternalFrame itf = desktop.getSelectedFrame();
- if (itf != null)
- itf.requestFocus();
- }
- ;
- });
+ @Override
+ public void endDraggingFrame(JComponent f)
+ {
+ delegate.endDraggingFrame(f);
+ }
- menuItem.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- try
- {
- frame.setSelected(true);
- frame.setIcon(false);
- }
- catch (java.beans.PropertyVetoException ex)
- {
-
- }
- }
- });
+ @Override
+ public void endResizingFrame(JComponent f)
+ {
+ delegate.endResizingFrame(f);
+ }
- windowMenu.add(menuItem);
+ @Override
+ public void iconifyFrame(JInternalFrame f)
+ {
+ delegate.iconifyFrame(f);
+ }
- desktop.add(frame);
- frame.toFront();
- try{
- frame.setSelected(true);
- frame.requestFocus();
- }catch(java.beans.PropertyVetoException ve)
- { }
+ @Override
+ public void maximizeFrame(JInternalFrame f)
+ {
+ delegate.maximizeFrame(f);
}
- public void lostOwnership(Clipboard clipboard, Transferable contents)
+ @Override
+ public void minimizeFrame(JInternalFrame f)
{
- if (!internalCopy)
- Desktop.jalviewClipboard = null;
+ delegate.minimizeFrame(f);
+ }
- internalCopy = false;
+ @Override
+ public void openFrame(JInternalFrame f)
+ {
+ delegate.openFrame(f);
}
- public void dragEnter(DropTargetDragEvent evt)
- {}
+ @Override
+ public void resizeFrame(JComponent f, int newX, int newY, int newWidth,
+ int newHeight)
+ {
+ if (newY < 0)
+ {
+ newY = 0;
+ }
+ delegate.resizeFrame(f, newX, newY, newWidth, newHeight);
+ }
- public void dragExit(DropTargetEvent evt)
- {}
+ @Override
+ public void setBoundsForFrame(JComponent f, int newX, int newY,
+ int newWidth, int newHeight)
+ {
+ delegate.setBoundsForFrame(f, newX, newY, newWidth, newHeight);
+ }
- public void dragOver(DropTargetDragEvent evt)
- {}
+ // All other methods, simply delegate
- public void dropActionChanged(DropTargetDragEvent evt)
- {}
+ }
+ /**
+ * Creates a new Desktop object.
+ */
+ public Desktop()
+ {
/**
- * DOCUMENT ME!
- *
- * @param evt 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 drop(DropTargetDropEvent evt)
+ instance = this;
+ doVamsasClientCheck();
+
+ groovyShell = new JMenuItem();
+ groovyShell.setText(MessageManager.getString("label.groovy_console"));
+ groovyShell.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ groovyShell_actionPerformed();
+ }
+ });
+ toolsMenu.add(groovyShell);
+ groovyShell.setVisible(true);
+
+ doConfigureStructurePrefs();
+ 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);
+ if (Platform.isAMac())
+ {
+ desktop.setDoubleBuffered(false);
+ }
+ 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
{
- Transferable t = evt.getTransferable();
- java.util.List files = null;
+ Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
+ setBounds((screenSize.width - 900) / 2,
+ (screenSize.height - 650) / 2, 900, 650);
+ }
+ jconsole = new Console(this, showjconsole);
+ // add essential build information
+ jconsole.setHeader("Jalview Version: "
+ + jalview.bin.Cache.getProperty("VERSION") + "\n"
+ + "Jalview Installation: "
+ + jalview.bin.Cache.getDefault("INSTALLATION", "unknown")
+ + "\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()
+ {
+ @Override
+ public void windowClosing(WindowEvent evt)
+ {
+ quit();
+ }
+ });
- try
+ MouseAdapter ma;
+ this.addMouseListener(ma = new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger()) // Mac
{
- 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);
- 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);
- java.io.File file = new java.io.File(uri);
- files.add(file);
- }
- }
+ showPasteMenu(evt.getX(), evt.getY());
}
- catch (Exception e)
- { }
+ }
- if (files != null)
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger()) // Windows
{
- try
- {
- for (int i = 0; i < files.size(); i++)
- {
- String file = files.get(i).toString();
- String protocol = FormatAdapter.FILE;
- 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)
- { }
+ showPasteMenu(evt.getX(), evt.getY());
}
- }
+ }
+ });
+ desktop.addMouseListener(ma);
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
+ this.addFocusListener(new FocusListener()
{
- 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");
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ // TODO Auto-generated method stub
- int value = chooser.showOpenDialog(this);
+ }
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
+ @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()
+ {
+ @Override
+ public void run()
+ {
+ new SplashScreen();
+ }
+ });
- String format = null;
- if (chooser.getSelectedFormat().equals("Jalview"))
- {
- format = "Jalview";
- }
- else
+ // 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()
+ {
+ @Override
+ public void run()
+ {
+ Cache.log.debug("Filechooser init thread started.");
+ 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()
{
- 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);
- }
- }
-
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ Cache.log.debug("Firing service changed event for "
+ + evt.getNewValue());
+ JalviewServicesChanged(evt);
+ }
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
+ });
+ }
+
+ public void doConfigureStructurePrefs()
+ {
+ // configure services
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(this);
+ if (jalview.bin.Cache.getDefault(Preferences.ADD_SS_ANN, true))
+ {
+ ssm.setAddTempFacAnnot(jalview.bin.Cache.getDefault(
+ Preferences.ADD_TEMPFACT_ANN, true));
+ ssm.setProcessSecondaryStructure(jalview.bin.Cache.getDefault(
+ Preferences.STRUCT_FROM_PDB, true));
+ ssm.setSecStructServices(jalview.bin.Cache.getDefault(
+ Preferences.USE_RNAVIEW, true));
+ }
+ else
{
- // 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();
+ ssm.setAddTempFacAnnot(false);
+ ssm.setProcessSecondaryStructure(false);
+ ssm.setSecStructServices(false);
+ }
+ }
- 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.");
+ 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.");
- String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
+ jvnews = new BlogReader(me);
+ showNews.setVisible(true);
+ Cache.log.debug("Completed news thread.");
+ }
+ });
+ }
- StringTokenizer st;
+ @Override
+ protected void showNews_actionPerformed(ActionEvent e)
+ {
+ showNews(showNews.isSelected());
+ }
- if (historyItems != null)
+ void showNews(boolean visible)
+ {
+ {
+ Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
+ showNews.setSelected(visible);
+ if (visible && !jvnews.isVisible())
{
- st = new StringTokenizer(historyItems, "\t");
-
- while (st.hasMoreTokens())
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ long now = System.currentTimeMillis();
+ Desktop.instance.setProgressBar(
+ MessageManager.getString("status.refreshing_news"), now);
+ jvnews.refreshNews();
+ Desktop.instance.setProgressBar(null, now);
+ 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)
{
- history.addItem(st.nextElement());
+ 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;
+ }
- int reply = JOptionPane.showInternalConfirmDialog(desktop,
- panel, "Input Alignment From URL",
- JOptionPane.OK_CANCEL_OPTION );
-
+ 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;
- if (reply != JOptionPane.OK_OPTION )
+ @Override
+ public void menuCanceled(MenuEvent e)
{
- return;
+ refresh = true;
}
- String url = history.getSelectedItem().toString();
-
- if (url.toLowerCase().endsWith(".jar"))
+ @Override
+ public void menuDeselected(MenuEvent e)
{
- if (viewport != null)
- new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, "Jalview");
- else
- new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");
+ refresh = true;
}
- else
- {
- String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
- if (format.equals("URL NOT FOUND"))
+ @Override
+ 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;
}
-
- if (viewport != null)
- new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);
- else
- new FileLoader().LoadFile(url, FormatAdapter.URL, format);
}
+ });
+ vamsasStart.setVisible(true);
}
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
+ }
+
+ void showPasteMenu(int x, int y)
+ {
+ JPopupMenu popup = new JPopupMenu();
+ JMenuItem item = new JMenuItem(
+ MessageManager.getString("label.paste_new_window"));
+ item.addActionListener(new ActionListener()
{
- CutAndPasteTransfer cap = new CutAndPasteTransfer();
- cap.setForInput(viewport);
- Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
- }
+ @Override
+ 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 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);
- }
-
- message.append( "\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +
- "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." +
- "\nFor all issues relating to Jalview, email help@jalview.org" +
- "\n\nIf you use JalView, please cite:" +
- "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" +
- "\nBioinformatics, 2004 20;426-7.");
-
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ String format = new IdentifyFile().identify(file,
+ FormatAdapter.PASTE);
- message.toString(), "About Jalview",
- JOptionPane.INFORMATION_MESSAGE);
- }
+ new FileLoader().LoadFile(file, FormatAdapter.PASTE, format);
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void documentationMenuItem_actionPerformed(ActionEvent e)
+ }
+ } catch (Exception ex)
{
- 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)
- { }
+ System.out
+ .println("Unable to paste alignment from system clipboard:\n"
+ + ex);
}
-
- public void closeAll_actionPerformed(ActionEvent e)
+ }
+
+ /**
+ * Adds and opens the given frame to the desktop
+ *
+ * @param frame
+ * Frame to show
+ * @param title
+ * Visible Title
+ * @param w
+ * width
+ * @param h
+ * height
+ */
+ public static synchronized void addInternalFrame(
+ final JInternalFrame frame, String title, int w, int h)
+ {
+ addInternalFrame(frame, title, true, w, h, true);
+ }
+
+ /**
+ * Add an internal frame to the Jalview desktop
+ *
+ * @param frame
+ * Frame to show
+ * @param title
+ * Visible Title
+ * @param makeVisible
+ * When true, display frame immediately, otherwise, caller must call
+ * setVisible themselves.
+ * @param w
+ * width
+ * @param h
+ * height
+ */
+ public static synchronized void addInternalFrame(
+ final JInternalFrame frame, String title, boolean makeVisible,
+ int w, int h)
+ {
+ addInternalFrame(frame, title, makeVisible, w, h, true);
+ }
+
+ /**
+ * Add an internal frame to the Jalview desktop and make it visible
+ *
+ * @param frame
+ * Frame to show
+ * @param title
+ * Visible Title
+ * @param w
+ * width
+ * @param h
+ * height
+ * @param resizable
+ * Allow resize
+ */
+ public static synchronized void addInternalFrame(
+ final JInternalFrame frame, String title, int w, int h,
+ boolean resizable)
+ {
+ addInternalFrame(frame, title, true, w, h, resizable);
+ }
+
+ /**
+ * Add an internal frame to the Jalview desktop
+ *
+ * @param frame
+ * Frame to show
+ * @param title
+ * Visible Title
+ * @param makeVisible
+ * When true, display frame immediately, otherwise, caller must call
+ * setVisible themselves.
+ * @param w
+ * width
+ * @param h
+ * height
+ * @param resizable
+ * Allow resize
+ */
+ public static synchronized void addInternalFrame(
+ final JInternalFrame frame, String title, boolean makeVisible,
+ 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)
{
- JInternalFrame [] frames = desktop.getAllFrames();
- for(int i=0; i<frames.length; i++)
- {
- try{
- frames[i].setClosed(true);
- }catch(java.beans.PropertyVetoException ex){}
- }
+ frame.setSize(w, h);
}
-
- public void raiseRelated_actionPerformed(ActionEvent e)
+ // 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")))
{
- reorderAssociatedWindows(false, false);
+ return;
}
- public void minimizeAssociated_actionPerformed(ActionEvent e)
+ openFrameCount++;
+
+ frame.setVisible(makeVisible);
+ frame.setClosable(true);
+ frame.setResizable(resizable);
+ frame.setMaximizable(resizable);
+ frame.setIconifiable(resizable);
+ if (Platform.isAMac())
{
- reorderAssociatedWindows(true, false);
+ frame.setIconifiable(false);
+ frame.setFrameIcon(null);
+ // frame.setDesktopIcon(null);
+ frame.setDoubleBuffered(false);
}
-
- void closeAssociatedWindows()
+ if (frame.getX() < 1 && frame.getY() < 1)
{
- reorderAssociatedWindows(false, true);
+ frame.setLocation(xOffset * openFrameCount, yOffset
+ * ((openFrameCount - 1) % 10) + yOffset);
}
- void reorderAssociatedWindows(boolean minimize, boolean close)
+ /*
+ * add an entry for the new frame in the Window menu
+ * (and remove it when the frame is closed)
+ */
+ final JMenuItem menuItem = new JMenuItem(title);
+ frame.addInternalFrameListener(new InternalFrameAdapter()
{
- JInternalFrame[] frames = desktop.getAllFrames();
- if (frames == null || frames.length<1)
- return;
+ @Override
+ public void internalFrameActivated(InternalFrameEvent evt)
+ {
+ JInternalFrame itf = desktop.getSelectedFrame();
+ if (itf != null)
+ {
+ itf.requestFocus();
+ }
+ }
- 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;
+ @Override
+ public void internalFrameClosed(InternalFrameEvent evt)
+ {
+ PaintRefresher.RemoveComponent(frame);
+ /*
+ * defensive check to prevent frames being
+ * added half off the window
+ */
+ if (openFrameCount > 0)
+ {
+ openFrameCount--;
+ }
- if (source != null)
- for (int i = 0; i < frames.length; i++)
+ /*
+ * ensure no reference to alignFrame retained by menu item listener
+ */
+ if (menuItem.getActionListeners().length > 0)
{
- 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)
+ menuItem.removeActionListener(menuItem.getActionListeners()[0]);
+ }
+ windowMenu.remove(menuItem);
+ JInternalFrame itf = desktop.getSelectedFrame();
+ if (itf != null)
+ {
+ itf.requestFocus();
+ if (itf instanceof AlignFrame)
{
- try
- {
- if (close)
- frames[i].setClosed(true);
- else
- {
- frames[i].setIcon(minimize);
- if (!minimize)
- {
- frames[i].toFront();
- }
- }
-
- }
- catch (java.beans.PropertyVetoException ex)
- { }
+ Jalview.setCurrentAlignFrame((AlignFrame) itf);
}
}
- }
+ System.gc();
+ };
+ });
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ frame.setSelected(true);
+ frame.setIcon(false);
+ } catch (java.beans.PropertyVetoException ex)
+ {
+
+ }
+ }
+ });
+ windowMenu.add(menuItem);
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- protected void preferences_actionPerformed(ActionEvent e)
+ desktop.add(frame);
+ frame.toFront();
+ try
+ {
+ frame.setSelected(true);
+ frame.requestFocus();
+ } catch (java.beans.PropertyVetoException ve)
{
- new Preferences();
+ } 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);
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void saveState_actionPerformed(ActionEvent e)
+ @Override
+ public void lostOwnership(Clipboard clipboard, Transferable contents)
+ {
+ if (!internalCopy)
{
- 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();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
- new Jalview2XML().SaveState(choice);
- }
+ Desktop.jalviewClipboard = null;
}
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void loadState_actionPerformed(ActionEvent e)
+ internalCopy = false;
+ }
+
+ @Override
+ public void dragEnter(DropTargetDragEvent evt)
+ {
+ }
+
+ @Override
+ public void dragExit(DropTargetEvent evt)
+ {
+ }
+
+ @Override
+ public void dragOver(DropTargetDragEvent evt)
+ {
+ }
+
+ @Override
+ public void dropActionChanged(DropTargetDragEvent evt)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void drop(DropTargetDropEvent evt)
+ {
+ boolean success = true;
+ // JAL-1552 - acceptDrop required before getTransferable call for
+ // Java's Transferable for native dnd
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+ Transferable t = evt.getTransferable();
+ java.util.List<String> files = new ArrayList<String>();
+ java.util.List<String> protocols = new ArrayList<String>();
+
+ try
{
- 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)
- {
- String choice = chooser.getSelectedFile().getAbsolutePath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
- new Jalview2XML().LoadJalviewAlign(choice);
- }
+ Desktop.transferFromDropTarget(files, protocols, evt, t);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ success = false;
}
- /* public void vamsasLoad_actionPerformed(ActionEvent e)
+ if (files != null)
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty("LAST_DIRECTORY"));
+ 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("Load Vamsas file");
- chooser.setToolTipText("Import");
+ if (file.endsWith(".jar"))
+ {
+ format = "Jalview";
- int value = chooser.showOpenDialog(this);
+ }
+ 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!
+ */
+ @Override
+ 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!
+ */
+ @Override
+ 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,
+ MessageManager.formatMessage("label.couldnt_locate",
+ new Object[] { url }), MessageManager
+ .getString("label.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);
+ }
+ }
+ }
+
+ /**
+ * Opens the CutAndPaste window for the user to paste an alignment in to
+ *
+ * @param viewPanel
+ * - if not null, the pasted alignment is added to the current
+ * alignment; if null, to a new alignment window
+ */
+ @Override
+ public void inputTextboxMenuItem_actionPerformed(
+ AlignmentViewPanel viewPanel)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ cap.setForInput(viewPanel);
+ Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.cut_paste_alignmen_file"),
+ true, 600, 500);
+ }
+
+ /*
+ * Exit the program
+ */
+ @Override
+ 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();
+ }
+ closeAll_actionPerformed(null);
+
+ if (groovyConsole != null)
+ {
+ // suppress a possible repeat prompt to save script
+ groovyConsole.setDirty(false);
+ groovyConsole.exit();
+ }
+ 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!
+ */
+ @Override
+ 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()
+ {
+ @Override
+ public void run()
+ {
+ new SplashScreen(true);
+ }
+ }).start();
+ }
+
+ public StringBuffer getAboutMessage(boolean shortv)
+ {
+ StringBuffer message = new StringBuffer();
+ message.append("<html>");
+ if (shortv)
+ {
+ message.append("<h1><strong>Version: "
+ + jalview.bin.Cache.getProperty("VERSION") + "</strong></h1>");
+ message.append("<strong>Last Updated: <em>"
+ + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
+ + "</em></strong>");
+
+ }
+ else
+ {
+
+ message.append("<strong>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("<br>...Checking latest version...</br>");
+ }
+ 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("<div style=\"color: #FF0000;font-style: bold;\">");
+ }
+
+ message.append("<br>!! 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("</div>");
+ }
+ }
+ message.append("<br>Authors: "
+ + jalview.bin.Cache
+ .getDefault("AUTHORFNAMES",
+ "The Jalview Authors (See AUTHORS file for current list)")
+ + "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
+ + "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
+ + "<br><br>If you use Jalview, please cite:"
+ + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+ + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+ + "<br>Bioinformatics doi: 10.1093/bioinformatics/btp033"
+ + "</html>");
+ return message;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void documentationMenuItem_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ Help.showHelpWindow();
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ @Override
+ public void closeAll_actionPerformed(ActionEvent e)
+ {
+ // TODO show a progress bar while closing?
+ JInternalFrame[] frames = desktop.getAllFrames();
+ for (int i = 0; i < frames.length; i++)
+ {
+ try
+ {
+ frames[i].setClosed(true);
+ } catch (java.beans.PropertyVetoException ex)
+ {
+ }
+ }
+ Jalview.setCurrentAlignFrame(null);
+ System.out.println("ALL CLOSED");
+ if (v_client != null)
+ {
+ // TODO clear binding to vamsas document objects on close_all
+ }
+
+ /*
+ * reset state of singleton objects as appropriate (clear down session state
+ * when all windows are closed)
+ */
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(this);
+ if (ssm != null)
+ {
+ ssm.resetAll();
+ }
+ System.gc();
+ }
+
+ @Override
+ public void raiseRelated_actionPerformed(ActionEvent e)
+ {
+ reorderAssociatedWindows(false, false);
+ }
+
+ @Override
+ 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)
+ */
+ @Override
+ 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
+ * )
+ */
+ @Override
+ protected void showMemusage_actionPerformed(ActionEvent e)
+ {
+ desktop.showMemoryUsage(showMemusage.isSelected());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GDesktop#showConsole_actionPerformed(java.awt.event.ActionEvent
+ * )
+ */
+ @Override
+ 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;
+ }
+
+ AlignmentViewport 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!
+ */
+ @Override
+ protected void preferences_actionPerformed(ActionEvent e)
+ {
+ new Preferences();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ 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(MessageManager.getString("label.save_state"));
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ final Desktop me = this;
+ final java.io.File choice = chooser.getSelectedFile();
+ setProjectFile(choice);
+
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ // TODO: refactor to Jalview desktop session controller action.
+ setProgressBar(MessageManager.formatMessage(
+ "label.saving_jalview_project",
+ new Object[] { 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, MessageManager.formatMessage(
+ "label.error_whilst_saving_current_state_to",
+ new Object[] { choice.getName() }), MessageManager
+ .getString("label.couldnt_save_project"),
+ JOptionPane.WARNING_MESSAGE);
+ }
+ setProgressBar(null, choice.hashCode());
+ }
+ }).start();
+ }
+ }
+
+ private void setProjectFile(File choice)
+ {
+ this.projectFile = choice;
+ }
+
+ public File getProjectFile()
+ {
+ return this.projectFile;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ 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(MessageManager.getString("label.restore_state"));
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ final File selectedFile = chooser.getSelectedFile();
+ setProjectFile(selectedFile);
+ final String choice = selectedFile.getAbsolutePath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ selectedFile.getParent());
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ setProgressBar(
+ MessageManager.formatMessage(
+ "label.loading_jalview_project",
+ new Object[] { 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, MessageManager
+ .formatMessage(
+ "label.error_whilst_loading_project_from",
+ new Object[] { choice }), MessageManager
+ .getString("label.couldnt_load_project"),
+ JOptionPane.WARNING_MESSAGE);
+ }
+ setProgressBar(null, choice.hashCode());
+ }
+ }).start();
+ }
+ }
+
+ @Override
+ public void inputSequence_actionPerformed(ActionEvent e)
+ {
+ new SequenceFetcher(this);
+ }
+
+ JPanel progressPanel;
+
+ ArrayList<JPanel> fileLoadingPanels = new ArrayList<JPanel>();
+
+ public void startLoading(final String fileName)
+ {
+ if (fileLoadingCount == 0)
+ {
+ fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage(
+ "label.loading_file", new Object[] { 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)
+ {
+ AlignmentViewport[] aps = getViewports(alignmentId);
+ return (aps == null) ? 0 : aps.length;
+ }
+
+ /**
+ *
+ * @param alignmentId
+ * - if null, all sets are returned
+ * @return all AlignmentPanels concerning the alignmentId sequence set
+ */
+ public static AlignmentPanel[] getAlignmentPanels(String alignmentId)
+ {
+ if (Desktop.desktop == null)
+ {
+ // no frames created and in headless mode
+ // TODO: verify that frames are recoverable when in headless mode
+ return null;
+ }
+ List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>();
+ AlignFrame[] frames = getAlignFrames();
+ if (frames == null)
+ {
+ return null;
+ }
+ for (AlignFrame af : frames)
+ {
+ for (AlignmentPanel ap : af.alignPanels)
+ {
+ if (alignmentId == null
+ || alignmentId.equals(ap.av.getSequenceSetId()))
+ {
+ aps.add(ap);
+ }
+ }
+ }
+ if (aps.size() == 0)
+ {
+ return null;
+ }
+ AlignmentPanel[] vap = aps.toArray(new AlignmentPanel[aps.size()]);
+ return vap;
+ }
+
+ /**
+ * get all the viewports on an alignment.
+ *
+ * @param sequenceSetId
+ * unique alignment id (may be null - all viewports returned in that
+ * case)
+ * @return all viewports on the alignment bound to sequenceSetId
+ */
+ public static AlignmentViewport[] getViewports(String sequenceSetId)
+ {
+ List<AlignmentViewport> viewp = new ArrayList<AlignmentViewport>();
+ if (desktop != null)
+ {
+ AlignFrame[] frames = Desktop.getAlignFrames();
+
+ for (AlignFrame afr : frames)
+ {
+ if (sequenceSetId == null
+ || afr.getViewport().getSequenceSetId()
+ .equals(sequenceSetId))
+ {
+ if (afr.alignPanels != null)
+ {
+ for (AlignmentPanel ap : afr.alignPanels)
+ {
+ if (sequenceSetId == null
+ || sequenceSetId.equals(ap.av.getSequenceSetId()))
+ {
+ viewp.add(ap.av);
+ }
+ }
+ }
+ else
+ {
+ viewp.add(afr.getViewport());
+ }
+ }
+ }
+ if (viewp.size() > 0)
+ {
+ return viewp.toArray(new AlignmentViewport[viewp.size()]);
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Explode the views in the given frame into separate AlignFrame
+ *
+ * @param af
+ */
+ public static void explodeViews(AlignFrame af)
+ {
+ int size = af.alignPanels.size();
+ if (size < 2)
+ {
+ return;
+ }
+
+ for (int i = 0; i < size; i++)
+ {
+ AlignmentPanel ap = af.alignPanels.get(i);
+ AlignFrame newaf = new AlignFrame(ap);
+
+ /*
+ * Restore the view's last exploded frame geometry if known. Multiple
+ * views from one exploded frame share and restore the same (frame)
+ * position and size.
+ */
+ Rectangle geometry = ap.av.getExplodedGeometry();
+ if (geometry != null)
+ {
+ newaf.setBounds(geometry);
+ }
+
+ ap.av.setGatherViewsHere(false);
+
+ addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+
+ af.alignPanels.clear();
+ af.closeMenuItem_actionPerformed(true);
+
+ }
+
+ /**
+ * Gather expanded views (separate AlignFrame's) with the same sequence set
+ * identifier back in to this frame as additional views, and close the
+ * expanded views. Note the expanded frames may themselves have multiple
+ * views. We take the lot.
+ *
+ * @param source
+ */
+ public void gatherViews(AlignFrame source)
+ {
+ source.viewport.setGatherViewsHere(true);
+ source.viewport.setExplodedGeometry(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 = af.alignPanels.get(a);
+ if (viewId.equals(ap.av.getSequenceSetId()))
+ {
+ gatherThis = true;
+ ap.av.setGatherViewsHere(false);
+ ap.av.setExplodedGeometry(af.getBounds());
+ source.addAlignmentPanel(ap, false);
+ }
+ }
+
+ if (gatherThis)
+ {
+ af.alignPanels.clear();
+ af.closeMenuItem_actionPerformed(true);
+ }
+ }
+ }
+
+ }
+
+ jalview.gui.VamsasApplication v_client = null;
+
+ @Override
+ 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(MessageManager
+ .getString("label.open_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 Object[] { 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(MessageManager.formatMessage(
+ "status.importing_vamsas_session_from",
+ new Object[] { file.getName() }), file.hashCode());
+ try
+ {
+ v_client = new jalview.gui.VamsasApplication(this, file, null);
+ } catch (Exception ex)
+ {
+ setProgressBar(MessageManager.formatMessage(
+ "status.importing_vamsas_session_from",
+ new Object[] { 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(MessageManager.formatMessage(
+ "status.importing_vamsas_session_from",
+ new Object[] { file.getName() }), file.hashCode());
+ return v_client.inSession();
+ }
+
+ public boolean joinVamsasSession(String mysesid)
+ {
+ if (v_client != null)
+ {
+ throw new Error(
+ MessageManager
+ .getString("error.try_join_vamsas_session_another"));
+ }
+ if (mysesid == null)
+ {
+ throw new Error(
+ MessageManager.getString("error.invalid_vamsas_session_id"));
+ }
+ v_client = new VamsasApplication(this, mysesid);
+ setupVamsasConnectedGui();
+ v_client.initial_update();
+ return (v_client.inSession());
+ }
+
+ @Override
+ 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"));
+ }
+
+ @Override
+ public void vamsasStop_actionPerformed(ActionEvent e)
+ {
+ if (v_client != null)
+ {
+ v_client.end_session();
+ v_client = null;
+ setupVamsasDisconnectedGui();
+ }
+ }
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ protected void buildVamsasStMenu()
+ {
+ if (v_client == null)
+ {
+ String[] sess = null;
+ try
+ {
+ sess = VamsasApplication.getSessionList();
+ } catch (Exception e)
{
- jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null);
- vs.load(
- chooser.getSelectedFile().getAbsolutePath()
- );
+ 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 Object[] { sess[i] }));
+ final Desktop dsktp = this;
+ final String mysesid = sess[i];
+ sessit.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (dsktp.v_client == null)
+ {
+ Thread rthr = new Thread(new Runnable()
+ {
- }*/
+ @Override
+ 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);
- public void inputSequence_actionPerformed(ActionEvent e)
+ }
+ else
+ {
+ jalview.bin.Cache.log.debug("No current vamsas sessions.");
+ VamsasStMenu.removeAll();
+ VamsasStMenu.setVisible(false);
+ }
+ }
+ else
{
- new SequenceFetcher(null);
+ // Not interested in the content. Just hide ourselves.
+ VamsasStMenu.setVisible(false);
}
+ }
- JPanel progressPanel;
-
- public void startLoading(final String fileName)
+ @Override
+ public void vamsasSave_actionPerformed(ActionEvent e)
+ {
+ if (v_client != null)
{
- if (fileLoadingCount == 0)
+ 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(MessageManager
+ .getString("label.save_vamsas_document_archive"));
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
{
- progressPanel = new JPanel(new BorderLayout());
- JProgressBar progressBar = new JProgressBar();
- progressBar.setIndeterminate(true);
+ java.io.File choice = chooser.getSelectedFile();
+ JPanel progpanel = addProgressPanel(MessageManager.formatMessage(
+ "label.saving_vamsas_doc",
+ new Object[] { 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);
- progressPanel.add(new JLabel("Loading File: " + fileName + " "),
- BorderLayout.WEST);
+ } catch (Exception ex)
+ {
+ warnttl = "Problem saving Vamsas Document.";
+ warnmsg = ex.toString();
+ jalview.bin.Cache.log.warn("Exception Whilst saving document to "
+ + choice, ex);
- progressPanel.add(progressBar, BorderLayout.CENTER);
+ }
+ removeProgressPanel(progpanel);
+ if (warnmsg != null)
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
- instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
+ warnmsg, warnttl, JOptionPane.ERROR_MESSAGE);
+ }
}
- fileLoadingCount++;
- validate();
+ }
+ }
+
+ 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(MessageManager
+ .getString("label.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
+ {
+
+ private static final float ONE_MB = 1048576f;
+
+ boolean showMemoryUsage = false;
+
+ Runtime runtime;
+
+ java.text.NumberFormat df;
+
+ float maxMemory, allocatedMemory, freeMemory, totalFreeMemory,
+ percentUsage;
+
+ public MyDesktopPane(boolean showMemoryUsage)
+ {
+ showMemoryUsage(showMemoryUsage);
}
- public void stopLoading()
+ public void showMemoryUsage(boolean showMemory)
{
- fileLoadingCount--;
- if (fileLoadingCount < 1)
+ this.showMemoryUsage = showMemory;
+ if (showMemory)
{
- if(progressPanel!=null)
- {
- this.getContentPane().remove(progressPanel);
- progressPanel = null;
- }
- fileLoadingCount = 0;
+ Thread worker = new Thread(this);
+ worker.start();
}
- validate();
}
- public static int getViewCount(String viewId)
+ public boolean isShowMemoryUsage()
+ {
+ return showMemoryUsage;
+ }
+
+ @Override
+ public void run()
{
- int count = 0;
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- for (int t = 0; t < frames.length; t++)
+ df = java.text.NumberFormat.getNumberInstance();
+ df.setMaximumFractionDigits(2);
+ runtime = Runtime.getRuntime();
+
+ while (showMemoryUsage)
{
- if (frames[t] instanceof AlignFrame)
+ try
{
- AlignFrame af = (AlignFrame) frames[t];
- for(int a=0; a<af.alignPanels.size(); a++)
+ maxMemory = runtime.maxMemory() / ONE_MB;
+ allocatedMemory = runtime.totalMemory() / ONE_MB;
+ freeMemory = runtime.freeMemory() / ONE_MB;
+ totalFreeMemory = freeMemory + (maxMemory - allocatedMemory);
+
+ percentUsage = (totalFreeMemory / maxMemory) * 100;
+
+ // if (percentUsage < 20)
{
- if(viewId.equals(
- ((AlignmentPanel)af.alignPanels.elementAt(a)).av.getSequenceSetId() )
- )
- count ++;
+ // 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();
}
}
+ }
- return count;
+ @Override
+ 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 Object[] { 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;
+
+ /**
+ * Accessor method to quickly get all the AlignmentFrames loaded.
+ *
+ * @return an array of AlignFrame, or null if none found
+ */
+ public static AlignFrame[] getAlignFrames()
+ {
+ if (Jalview.isHeadlessMode())
+ {
+ // Desktop.desktop is null in headless mode
+ return new AlignFrame[] { Jalview.currentAlignFrame };
}
- public void explodeViews(AlignFrame af)
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+
+ if (frames == null)
{
- int size = af.alignPanels.size();
- if(size<2)
- return;
+ return null;
+ }
+ List<AlignFrame> avp = new ArrayList<AlignFrame>();
+ // REVERSE ORDER
+ for (int i = frames.length - 1; i > -1; i--)
+ {
+ if (frames[i] instanceof AlignFrame)
+ {
+ avp.add((AlignFrame) frames[i]);
+ }
+ else if (frames[i] instanceof SplitFrame)
+ {
+ /*
+ * Also check for a split frame containing an AlignFrame
+ */
+ GSplitFrame sf = (GSplitFrame) frames[i];
+ if (sf.getTopFrame() instanceof AlignFrame)
+ {
+ avp.add((AlignFrame) sf.getTopFrame());
+ }
+ if (sf.getBottomFrame() instanceof AlignFrame)
+ {
+ avp.add((AlignFrame) sf.getBottomFrame());
+ }
+ }
+ }
+ if (avp.size() == 0)
+ {
+ return null;
+ }
+ AlignFrame afs[] = avp.toArray(new AlignFrame[avp.size()]);
+ return afs;
+ }
+
+ /**
+ * Returns an array of any AppJmol frames in the Desktop (or null if none).
+ *
+ * @return
+ */
+ public GStructureViewer[] getJmols()
+ {
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+
+ if (frames == null)
+ {
+ return null;
+ }
+ List<GStructureViewer> avp = new ArrayList<GStructureViewer>();
+ // REVERSE ORDER
+ for (int i = frames.length - 1; i > -1; i--)
+ {
+ if (frames[i] instanceof AppJmol)
+ {
+ GStructureViewer af = (GStructureViewer) frames[i];
+ avp.add(af);
+ }
+ }
+ if (avp.size() == 0)
+ {
+ return null;
+ }
+ GStructureViewer afs[] = avp.toArray(new GStructureViewer[avp.size()]);
+ return afs;
+ }
+
+ /**
+ * Add Groovy Support to Jalview
+ */
+ public void groovyShell_actionPerformed()
+ {
+ try
+ {
+ openGroovyConsole();
+ } catch (Exception ex)
+ {
+ jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
- for(int i=0; i<size; i++)
+ MessageManager.getString("label.couldnt_create_groovy_shell"),
+ MessageManager.getString("label.groovy_support_failed"),
+ JOptionPane.ERROR_MESSAGE);
+ }
+ }
+
+ /**
+ * Open the Groovy console
+ */
+ void openGroovyConsole()
+ {
+ if (groovyConsole == null)
+ {
+ groovyConsole = new groovy.ui.Console();
+ groovyConsole.setVariable("Jalview", this);
+ groovyConsole.run();
+
+ /*
+ * We allow only one console at a time, so that AlignFrame menu option
+ * 'Calculate | Run Groovy script' is unambiguous.
+ * Disable 'Groovy Console', and enable 'Run script', when the console is
+ * opened, and the reverse when it is closed
+ */
+ Window window = (Window) groovyConsole.getFrame();
+ window.addWindowListener(new WindowAdapter()
{
- AlignmentPanel ap = (AlignmentPanel)af.alignPanels.elementAt(i);
- AlignFrame newaf = new AlignFrame(ap);
- if(ap.av.explodedPosition!=null)
- newaf.setBounds(ap.av.explodedPosition);
+ @Override
+ public void windowClosed(WindowEvent e)
+ {
+ /*
+ * rebind CMD-Q from Groovy Console to Jalview Quit
+ */
+ addQuitHandler();
+ enableExecuteGroovy(false);
+ }
+ });
+ }
+
+ /*
+ * show Groovy console window (after close and reopen)
+ */
+ ((Window) groovyConsole.getFrame()).setVisible(true);
- ap.av.gatherViewsHere = false;
+ /*
+ * if we got this far, enable 'Run Groovy' in AlignFrame menus
+ * and disable opening a second console
+ */
+ enableExecuteGroovy(true);
+ }
+
+ /**
+ * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this
+ * binding when opened
+ */
+ protected void addQuitHandler()
+ {
+ getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
+ KeyStroke.getKeyStroke(KeyEvent.VK_Q, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()), "Quit");
+ getRootPane().getActionMap().put("Quit", new AbstractAction()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ quit();
+ }
+ });
+ }
+
+ /**
+ * Enable or disable 'Run Groovy script' in AlignFrame calculate menus
+ *
+ * @param enabled
+ * true if Groovy console is open
+ */
+ public void enableExecuteGroovy(boolean enabled)
+ {
+ /*
+ * disable opening a second Groovy console
+ * (or re-enable when the console is closed)
+ */
+ groovyShell.setEnabled(!enabled);
- addInternalFrame(newaf, af.getTitle(),
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame[] alignFrames = getAlignFrames();
+ if (alignFrames != null)
+ {
+ for (AlignFrame af : alignFrames)
+ {
+ af.setGroovyEnabled(enabled);
}
+ }
+ }
+
+ /**
+ * Progress bars managed by the IProgressIndicator method.
+ */
+ private Hashtable<Long, JPanel> progressBars;
+
+ private Hashtable<Long, IProgressIndicatorHandler> progressBarHandlers;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
+ */
+ @Override
+ public void setProgressBar(String message, long id)
+ {
+ if (progressBars == null)
+ {
+ progressBars = new Hashtable<Long, JPanel>();
+ progressBarHandlers = new Hashtable<Long, IProgressIndicatorHandler>();
+ }
- af.alignPanels.clear();
- af.closeMenuItem_actionPerformed(true);
+ if (progressBars.get(new Long(id)) != null)
+ {
+ JPanel panel = progressBars.remove(new Long(id));
+ if (progressBarHandlers.contains(new Long(id)))
+ {
+ progressBarHandlers.remove(new Long(id));
+ }
+ removeProgressPanel(panel);
+ }
+ else
+ {
+ progressBars.put(new Long(id), addProgressPanel(message));
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.gui.IProgressIndicator#registerHandler(long,
+ * jalview.gui.IProgressIndicatorHandler)
+ */
+ @Override
+ public void registerHandler(final long id,
+ final IProgressIndicatorHandler handler)
+ {
+ if (progressBarHandlers == null
+ || !progressBars.containsKey(new Long(id)))
+ {
+ throw new Error(
+ MessageManager
+ .getString("error.call_setprogressbar_before_registering_handler"));
+ }
+ progressBarHandlers.put(new Long(id), handler);
+ final JPanel progressPanel = progressBars.get(new Long(id));
+ if (handler.canCancel())
+ {
+ JButton cancel = new JButton(
+ MessageManager.getString("action.cancel"));
+ final IProgressIndicator us = this;
+ cancel.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ handler.cancelActivity(id);
+ us.setProgressBar(MessageManager.formatMessage(
+ "label.cancelled_params",
+ new Object[] { ((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 holding the given viewport instance.
+ * It will break if there are more than one AlignFrames viewing a particular
+ * av.
+ *
+ * @param viewport
+ * @return alignFrame for viewport
+ */
+ public static AlignFrame getAlignFrameFor(AlignViewportI viewport)
+ {
+ if (desktop != null)
+ {
+ AlignmentPanel[] aps = getAlignmentPanels(viewport.getSequenceSetId());
+ for (int panel = 0; aps != null && panel < aps.length; panel++)
+ {
+ if (aps[panel] != null && aps[panel].av == viewport)
+ {
+ 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();
}
- public void gatherViews(AlignFrame source)
+ if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
- source.viewport.gatherViewsHere = true;
- source.viewport.explodedPosition = source.getBounds();
- JInternalFrame[] frames = desktop.getAllFrames();
- String viewId = source.viewport.sequenceSetID;
+ if (jalview.ws.jws2.Jws2Discoverer.getDiscoverer().isRunning())
+ {
+ jalview.ws.jws2.Jws2Discoverer.getDiscoverer().setAborted(true);
+ }
+ t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer(
+ changeSupport);
- for (int t = 0; t < frames.length; t++)
+ }
+ 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 (frames[t] instanceof AlignFrame && frames[t] != source)
+ if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true))
{
- AlignFrame af = (AlignFrame) frames[t];
- boolean gatherThis = false;
- for (int a = 0; a < af.alignPanels.size(); a++)
+ if (serviceChangedDialog == null)
{
- AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(a);
- if (viewId.equals(ap.av.getSequenceSetId()))
+ // only run if we aren't already displaying one of these.
+ addDialogThread(serviceChangedDialog = new Runnable()
{
- gatherThis = true;
- ap.av.gatherViewsHere = false;
- ap.av.explodedPosition = af.getBounds();
- source.addAlignmentPanel(ap, false);
- }
+ @Override
+ 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("<html><table width=\"450\"><tr><td>" + ermsg +
+ * "<br/>It may be that you have invalid JABA URLs in your web service preferences,"
+ * + " or mis-configured HTTP proxy settings.<br/>" +
+ * "Check the <em>Connections</em> and <em>Web services</em> tab of the"
+ * +
+ * " Tools->Preferences dialog box to change them.</td></tr></table></html>"
+ * ), true, true, "Web Service Configuration Problem", 450,
+ * 400);
+ *
+ * jd.waitForInput();
+ */
+ JOptionPane
+ .showConfirmDialog(
+ Desktop.desktop,
+ new JLabel(
+ "<html><table width=\"450\"><tr><td>"
+ + ermsg
+ + "</td></tr></table>"
+ + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
+ + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>"
+ + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
+ + " Tools->Preferences dialog box to change them.</p></html>"),
+ "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()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ if (progress != null)
+ {
+ progress.setProgressBar(MessageManager.formatMessage(
+ "status.opening_params", new Object[] { url }), this
+ .hashCode());
}
+ jalview.util.BrowserLauncher.openURL(url);
+ } catch (Exception ex)
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager
+ .getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"),
+ JOptionPane.WARNING_MESSAGE);
+
+ ex.printStackTrace();
+ }
+ if (progress != null)
+ {
+ progress.setProgressBar(null, this.hashCode());
+ }
+ }
+ }).start();
+ }
+
+ public static WsParamSetManager wsparamManager = null;
- if (gatherThis)
+ 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
{
- af.alignPanels.clear();
- af.closeMenuItem_actionPerformed(true);
+ 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);
+
+ private static groovy.ui.Console groovyConsole;
+
+ /**
+ * add another dialog thread to the queue
+ *
+ * @param prompter
+ */
+ public void addDialogThread(final Runnable prompter)
+ {
+ dialogExecutor.submit(new Runnable()
+ {
+ @Override
+ 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();
+ }
+
+ @Override
+ protected void snapShotWindow_actionPerformed(ActionEvent e)
+ {
+ invalidate();
+ File of;
+ ImageMaker im = new jalview.util.ImageMaker(this, ImageMaker.TYPE.EPS,
+ "View of Desktop", getWidth(), getHeight(), of = new File(
+ "Jalview_snapshot" + System.currentTimeMillis()
+ + ".eps"), "View of desktop", null, 0, false);
+ try
+ {
+ paintAll(im.getGraphics());
+ im.writeImage();
+ } catch (Exception q)
+ {
+ Cache.log.error("Couldn't write snapshot to " + of.getAbsolutePath(),
+ q);
+ return;
+ }
+ Cache.log.info("Successfully written snapshot to file "
+ + of.getAbsolutePath());
+ }
+
+ /**
+ * Explode the views in the given SplitFrame into separate SplitFrame windows.
+ * This respects (remembers) any previous 'exploded geometry' i.e. the size
+ * and location last time the view was expanded (if any). However it does not
+ * remember the split pane divider location - this is set to match the
+ * 'exploding' frame.
+ *
+ * @param sf
+ */
+ public void explodeViews(SplitFrame sf)
+ {
+ AlignFrame oldTopFrame = (AlignFrame) sf.getTopFrame();
+ AlignFrame oldBottomFrame = (AlignFrame) sf.getBottomFrame();
+ List<? extends AlignmentViewPanel> topPanels = oldTopFrame
+ .getAlignPanels();
+ List<? extends AlignmentViewPanel> bottomPanels = oldBottomFrame
+ .getAlignPanels();
+ int viewCount = topPanels.size();
+ if (viewCount < 2)
+ {
+ return;
+ }
- jalview.gui.VamsasClient v_client=null;
- public void vamsasLoad_actionPerformed(ActionEvent e)
+ /*
+ * Processing in reverse order works, forwards order leaves the first panels
+ * not visible. I don't know why!
+ */
+ for (int i = viewCount - 1; i >= 0; i--)
{
- if (v_client==null) {
- // Start a session.
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty("LAST_DIRECTORY"));
+ /*
+ * Make new top and bottom frames. These take over the respective
+ * AlignmentPanel objects, including their AlignmentViewports, so the
+ * cdna/protein relationships between the viewports is carried over to the
+ * new split frames.
+ *
+ * explodedGeometry holds the (x, y) position of the previously exploded
+ * SplitFrame, and the (width, height) of the AlignFrame component
+ */
+ AlignmentPanel topPanel = (AlignmentPanel) topPanels.get(i);
+ AlignFrame newTopFrame = new AlignFrame(topPanel);
+ newTopFrame.setSize(oldTopFrame.getSize());
+ newTopFrame.setVisible(true);
+ Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport())
+ .getExplodedGeometry();
+ if (geometry != null)
+ {
+ newTopFrame.setSize(geometry.getSize());
+ }
+
+ AlignmentPanel bottomPanel = (AlignmentPanel) bottomPanels.get(i);
+ AlignFrame newBottomFrame = new AlignFrame(bottomPanel);
+ newBottomFrame.setSize(oldBottomFrame.getSize());
+ newBottomFrame.setVisible(true);
+ geometry = ((AlignViewport) bottomPanel.getAlignViewport())
+ .getExplodedGeometry();
+ if (geometry != null)
+ {
+ newBottomFrame.setSize(geometry.getSize());
+ }
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Load Vamsas file");
- chooser.setToolTipText("Import");
+ topPanel.av.setGatherViewsHere(false);
+ bottomPanel.av.setGatherViewsHere(false);
+ JInternalFrame splitFrame = new SplitFrame(newTopFrame,
+ newBottomFrame);
+ if (geometry != null)
+ {
+ splitFrame.setLocation(geometry.getLocation());
+ }
+ Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1);
+ }
- int value = chooser.showOpenDialog(this);
+ /*
+ * Clear references to the panels (now relocated in the new SplitFrames)
+ * before closing the old SplitFrame.
+ */
+ topPanels.clear();
+ bottomPanels.clear();
+ sf.close();
+ }
+
+ /**
+ * Gather expanded split frames, sharing the same pairs of sequence set ids,
+ * back into the given SplitFrame as additional views. Note that the gathered
+ * frames may themselves have multiple views.
+ *
+ * @param source
+ */
+ public void gatherViews(GSplitFrame source)
+ {
+ /*
+ * special handling of explodedGeometry for a view within a SplitFrame: - it
+ * holds the (x, y) position of the enclosing SplitFrame, and the (width,
+ * height) of the AlignFrame component
+ */
+ AlignFrame myTopFrame = (AlignFrame) source.getTopFrame();
+ AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame();
+ myTopFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
+ source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight()));
+ myBottomFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
+ source.getY(), myBottomFrame.getWidth(), myBottomFrame
+ .getHeight()));
+ myTopFrame.viewport.setGatherViewsHere(true);
+ myBottomFrame.viewport.setGatherViewsHere(true);
+ String topViewId = myTopFrame.viewport.getSequenceSetId();
+ String bottomViewId = myBottomFrame.viewport.getSequenceSetId();
+
+ JInternalFrame[] frames = desktop.getAllFrames();
+ for (JInternalFrame frame : frames)
+ {
+ if (frame instanceof SplitFrame && frame != source)
+ {
+ SplitFrame sf = (SplitFrame) frame;
+ AlignFrame topFrame = (AlignFrame) sf.getTopFrame();
+ AlignFrame bottomFrame = (AlignFrame) sf.getBottomFrame();
+ boolean gatherThis = false;
+ for (int a = 0; a < topFrame.alignPanels.size(); a++)
+ {
+ AlignmentPanel topPanel = topFrame.alignPanels.get(a);
+ AlignmentPanel bottomPanel = bottomFrame.alignPanels.get(a);
+ if (topViewId.equals(topPanel.av.getSequenceSetId())
+ && bottomViewId.equals(bottomPanel.av.getSequenceSetId()))
+ {
+ gatherThis = true;
+ topPanel.av.setGatherViewsHere(false);
+ bottomPanel.av.setGatherViewsHere(false);
+ topPanel.av.setExplodedGeometry(new Rectangle(sf.getLocation(),
+ topFrame.getSize()));
+ bottomPanel.av.setExplodedGeometry(new Rectangle(sf
+ .getLocation(), bottomFrame.getSize()));
+ myTopFrame.addAlignmentPanel(topPanel, false);
+ myBottomFrame.addAlignmentPanel(bottomPanel, false);
+ }
+ }
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ if (gatherThis)
{
- v_client = new jalview.gui.VamsasClient(this,
- chooser.getSelectedFile());
- this.vamsasLoad.setText("Session Update");
- this.vamsasStop.setVisible(true);
- v_client.initial_update();
- v_client.startWatcher();
+ topFrame.getAlignPanels().clear();
+ bottomFrame.getAlignPanels().clear();
+ sf.close();
}
- } else {
- // store current data in session.
- v_client.push_update();
}
}
- public void vamsasStop_actionPerformed(ActionEvent e) {
- if (v_client!=null) {
- v_client.end_session();
- v_client=null;
- this.vamsasStop.setVisible(false);
- this.vamsasLoad.setText("Start Vamsas Session...");
+
+ /*
+ * The dust settles...give focus to the tab we did this from.
+ */
+ myTopFrame.setDisplayedView(myTopFrame.alignPanel);
+ }
+
+ public static groovy.ui.Console getGroovyConsole()
+ {
+ return groovyConsole;
+ }
+
+ public static void transferFromDropTarget(List<String> files,
+ List<String> protocols, DropTargetDropEvent evt, Transferable t)
+ throws Exception
+ {
+
+ DataFlavor uriListFlavor = new DataFlavor(
+ "text/uri-list;class=java.lang.String");
+ if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+ {
+ // Works on Windows and MacOSX
+ Cache.log.debug("Drop handled as javaFileListFlavor");
+ for (Object file : (List) t
+ .getTransferData(DataFlavor.javaFileListFlavor))
+ {
+ files.add(((File) file).toString());
+ protocols.add(FormatAdapter.FILE);
}
}
- /**
- * 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"));
- vamsasLoad.setVisible(!b);
- vamsasStop.setVisible(!b);
-
+ else
+ {
+ // Unix like behaviour
+ boolean added = false;
+ String data = null;
+ if (t.isDataFlavorSupported(uriListFlavor))
+ {
+ Cache.log.debug("Drop handled as uriListFlavor");
+ // This is used by Unix drag system
+ data = (String) t.getTransferData(uriListFlavor);
+ }
+ if (data == null)
+ {
+ // fallback to text: workaround - on OSX where there's a JVM bug
+ Cache.log.debug("standard URIListFlavor failed. Trying text");
+ // try text fallback
+ data = (String) t.getTransferData(new DataFlavor(
+ "text/plain;class=java.lang.String"));
+ if (Cache.log.isDebugEnabled())
+ {
+ Cache.log.debug("fallback returned " + data);
+ }
+ }
+ while (protocols.size() < files.size())
+ {
+ Cache.log.debug("Adding missing FILE protocol for "
+ + files.get(protocols.size()));
+ protocols.add(FormatAdapter.FILE);
+ }
+ for (java.util.StringTokenizer st = new java.util.StringTokenizer(
+ data, "\r\n"); st.hasMoreTokens();)
+ {
+ added = true;
+ 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());
+ }
+ }
+ if (Cache.log.isDebugEnabled())
+ {
+ if (data == null || !added)
+ {
+ Cache.log
+ .debug("Couldn't resolve drop data. Here are the supported flavors:");
+ for (DataFlavor fl : t.getTransferDataFlavors())
+ {
+ Cache.log.debug("Supported transfer dataflavor: "
+ + fl.toString());
+ Object df = t.getTransferData(fl);
+ if (df != null)
+ {
+ Cache.log.debug("Retrieves: " + df);
+ }
+ else
+ {
+ Cache.log.debug("Retrieved nothing");
+ }
+ }
+ }
+ }
}
-
+ }
}
-
git://source.jalview.org / jalview.git / blobdiff