X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=9e5bbff6372b80145a92a6b7ee94b2855cf77904;hb=a40bbc57a85658544e2e5d7cc2a7596b762566dc;hp=cf89494e72906c97fa8ec6bffe82c59fc967a1a0;hpb=d16a0b70878dd40275ea1316a131da695a94d9b6;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java old mode 100755 new mode 100644 index cf89494..9e5bbff --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -1,44 +1,103 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * 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. - * + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; -import jalview.io.*; +import jalview.io.FileLoader; +import jalview.io.FormatAdapter; +import jalview.io.IdentifyFile; +import jalview.io.JSONFile; +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.viewmodel.AlignmentViewport; import jalview.ws.params.ParamManager; -import java.awt.*; -import java.awt.datatransfer.*; -import java.awt.dnd.*; -import java.awt.event.*; +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.FontMetrics; +import java.awt.Graphics; +import java.awt.GridLayout; +import java.awt.Point; +import java.awt.Rectangle; +import java.awt.Toolkit; +import java.awt.datatransfer.Clipboard; +import java.awt.datatransfer.ClipboardOwner; +import java.awt.datatransfer.DataFlavor; +import java.awt.datatransfer.Transferable; +import java.awt.dnd.DnDConstants; +import java.awt.dnd.DropTargetDragEvent; +import java.awt.dnd.DropTargetDropEvent; +import java.awt.dnd.DropTargetEvent; +import java.awt.dnd.DropTargetListener; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.FocusEvent; +import java.awt.event.FocusListener; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.awt.event.WindowAdapter; +import java.awt.event.WindowEvent; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; +import java.beans.PropertyVetoException; import java.io.BufferedInputStream; -import java.io.BufferedOutputStream; import java.io.File; import java.io.FileOutputStream; -import java.io.InputStream; import java.lang.reflect.Constructor; import java.net.URL; -import java.net.URLConnection; -import java.nio.channels.ReadableByteChannel; -import java.util.*; - -import javax.swing.*; +import 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.DefaultDesktopManager; +import javax.swing.DesktopManager; +import javax.swing.JButton; +import javax.swing.JComboBox; +import javax.swing.JComponent; +import javax.swing.JDesktopPane; +import javax.swing.JFrame; +import javax.swing.JInternalFrame; +import javax.swing.JLabel; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JPanel; +import javax.swing.JPopupMenu; +import javax.swing.JProgressBar; +import javax.swing.SwingUtilities; +import javax.swing.event.HyperlinkEvent; +import javax.swing.event.HyperlinkEvent.EventType; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; @@ -47,84 +106,25 @@ import javax.swing.event.MenuListener; * * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.155 $ */ public class Desktop extends jalview.jbgui.GDesktop implements - DropTargetListener, ClipboardOwner, IProgressIndicator + DropTargetListener, ClipboardOwner, IProgressIndicator, + jalview.api.StructureSelectionManagerProvider { - private class JalviewChangeSupport implements PropertyChangeListener - { - public void propertyChange(PropertyChangeEvent evt) - { - // Handle change events - most are simply routed to other sources - changeSupport.firePropertyChange(evt); - } - - /** - * change listeners are notified of changes to resources so they can update - * their state. E.g. - the 'services' property notifies when the available - * set of web service endpoints have changed. - */ - private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( - this); - - /** - * @param propertyName - * @param listener - * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.lang.String, - * java.beans.PropertyChangeListener) - */ - public void addJalviewPropertyChangeListener(String propertyName, - PropertyChangeListener listener) - { - changeSupport.addPropertyChangeListener(propertyName, listener); - } - - /** - * @param listener - * @see java.beans.PropertyChangeSupport#addPropertyChangeListener( - * java.beans.PropertyChangeListener) - */ - public void addJalviewPropertyChangeListener( - PropertyChangeListener listener) - { - changeSupport.addPropertyChangeListener(listener); - } - - /* - * @param propertyName - * - * @param oldValue - * - * @param newValue - * - * @see - * java.beans.PropertyChangeSupport#firePropertyChange(java.lang.String, - * java.lang.Object, java.lang.Object) public void firePropertyChange(String - * propertyName, Object oldValue, Object newValue) { - * changeSupport.firePropertyChange(propertyName, oldValue, newValue); } - */ - - /** - * @param propertyName - * @param listener - * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.lang.String, - * java.beans.PropertyChangeListener) - */ - public void removeJalviewPropertyChangeListener(String propertyName, - PropertyChangeListener listener) - { - changeSupport.removePropertyChangeListener(propertyName, listener); - } + private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); - } + /** + * news reader - null if it was never started. + */ + private BlogReader jvnews = null; - private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); + private File projectFile; /** * @param listener - * @see jalview.gui.Desktop.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener) + * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener) */ public void addJalviewPropertyChangeListener( PropertyChangeListener listener) @@ -135,7 +135,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements /** * @param propertyName * @param listener - * @see jalview.gui.Desktop.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String, + * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String, * java.beans.PropertyChangeListener) */ public void addJalviewPropertyChangeListener(String propertyName, @@ -147,7 +147,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements /** * @param propertyName * @param listener - * @see jalview.gui.Desktop.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String, + * @see jalview.gui.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String, * java.beans.PropertyChangeListener) */ public void removeJalviewPropertyChangeListener(String propertyName, @@ -168,6 +168,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements static final int yOffset = 30; + private static final int THREE = 3; + + private static AlignFrame currentAlignFrame; + public static jalview.ws.jws1.Discoverer discoverer; public static Object[] jalviewClipboard; @@ -225,6 +229,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void dragFrame(JComponent f, int newX, int newY) { + if (newY < 0) + { + newY = 0; + } delegate.dragFrame(f, newX, newY); } @@ -261,6 +269,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void resizeFrame(JComponent f, int newX, int newY, int newWidth, int newHeight) { + Rectangle b = desktop.getBounds(); + if (newY < 0) + { + newY = 0; + } delegate.resizeFrame(f, newX, newY, newWidth, newHeight); } @@ -287,7 +300,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements instance = this; doVamsasClientCheck(); doGroovyCheck(); - + doConfigureStructurePrefs(); setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION")); setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE", @@ -298,6 +311,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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); @@ -305,6 +322,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements // if previous window was maximised desktop.setDesktopManager(new MyDesktopManager( new DefaultDesktopManager())); + Rectangle dims = getLastKnownDimensions(""); if (dims != null) { @@ -313,14 +331,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements else { Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); - setBounds((int) (screenSize.width - 900) / 2, - (int) (screenSize.height - 650) / 2, 900, 650); + setBounds((screenSize.width - 900) / 2, + (screenSize.height - 650) / 2, 900, 650); } jconsole = new Console(this, showjconsole); // add essential build information - jconsole.setHeader("Jalview Desktop " + jconsole.setHeader("Jalview Version: " + jalview.bin.Cache.getProperty("VERSION") + "\n" - + "Build Date: " + + "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") + " " @@ -329,6 +349,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements showConsole(showjconsole); + showNews.setVisible(false); + this.addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent evt) @@ -337,7 +359,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements } }); - this.addMouseListener(new MouseAdapter() + MouseAdapter ma; + this.addMouseListener(ma = new MouseAdapter() { public void mousePressed(MouseEvent evt) { @@ -347,7 +370,26 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } }); + desktop.addMouseListener(ma); + this.addFocusListener(new FocusListener() + { + + @Override + public void focusLost(FocusEvent e) + { + // TODO Auto-generated method stub + + } + + @Override + public void focusGained(FocusEvent e) + { + Cache.log.debug("Relaying windows after focus gain"); + // make sure that we sort windows properly after we gain focus + instance.relayerWindows(); + } + }); this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this)); // Spawn a thread that shows the splashscreen SwingUtilities.invokeLater(new Runnable() @@ -374,6 +416,90 @@ public class Desktop extends jalview.jbgui.GDesktop implements Cache.log.debug("Filechooser init thread finished."); } }).start(); + // Add the service change listener + changeSupport.addJalviewPropertyChangeListener("services", + new PropertyChangeListener() + { + + @Override + public void propertyChange(PropertyChangeEvent evt) + { + Cache.log.debug("Firing service changed event for " + + evt.getNewValue()); + JalviewServicesChanged(evt); + } + + }); + } + + public void 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 + { + ssm.setAddTempFacAnnot(false); + ssm.setProcessSecondaryStructure(false); + ssm.setSecStructServices(false); + } + } + + public void checkForNews() + { + final Desktop me = this; + // Thread off the news reader, in case there are connection problems. + addDialogThread(new Runnable() + { + @Override + public void run() + { + Cache.log.debug("Starting news thread."); + + jvnews = new BlogReader(me); + showNews.setVisible(true); + Cache.log.debug("Completed news thread."); + } + }); + } + + protected void showNews_actionPerformed(ActionEvent e) + { + showNews(showNews.isSelected()); + } + + void showNews(boolean visible) + { + { + Cache.log.debug((visible ? "Showing" : "Hiding") + " news."); + showNews.setSelected(visible); + if (visible && !jvnews.isVisible()) + { + new Thread(new Runnable() + { + @Override + public void run() + { + long instance = System.currentTimeMillis(); + Desktop.instance.setProgressBar( + MessageManager.getString("status.refreshing_news"), + instance); + jvnews.refreshNews(); + Desktop.instance.setProgressBar(null, instance); + jvnews.showNews(); + } + }).start(); + } + } } /** @@ -414,13 +540,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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 (ix >= screenSize.width) + { + jalview.bin.Cache.log + .debug("Window geometry location recall error: shifting horizontal to within screenbounds."); + ix -= screenSize.width; } - while (iy>=screenSize.height) { - jalview.bin.Cache.log.debug("Window geometry location recall error: shifting vertical to within screenbounds."); - iy-=screenSize.height; + while (iy >= screenSize.height) + { + jalview.bin.Cache.log + .debug("Window geometry location recall error: shifting vertical to within screenbounds."); + iy -= screenSize.height; } jalview.bin.Cache.log.debug("Got last known dimensions for " + windowName + ": x:" + ix + " y:" + iy + " width:" + iw @@ -472,7 +602,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements void showPasteMenu(int x, int y) { JPopupMenu popup = new JPopupMenu(); - JMenuItem item = new JMenuItem("Paste To New Window"); + JMenuItem item = new JMenuItem( + MessageManager.getString("label.paste_new_window")); item.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent evt) @@ -515,38 +646,84 @@ public class Desktop extends jalview.jbgui.GDesktop implements * Adds and opens the given frame to the desktop * * @param frame - * DOCUMENT ME! + * Frame to show * @param title - * DOCUMENT ME! + * Visible Title * @param w - * DOCUMENT ME! + * width * @param h - * DOCUMENT ME! + * height */ public static synchronized void addInternalFrame( final JInternalFrame frame, String title, int w, int h) { - addInternalFrame(frame, title, w, h, true); + addInternalFrame(frame, title, true, w, h, true); } /** - * DOCUMENT ME! + * Add an internal frame to the Jalview desktop * * @param frame - * DOCUMENT ME! + * Frame to show * @param title - * DOCUMENT ME! + * Visible Title + * @param makeVisible + * When true, display frame immediately, otherwise, caller must call + * setVisible themselves. * @param w - * DOCUMENT ME! + * width * @param h - * DOCUMENT ME! + * 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 - * DOCUMENT ME! + * 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). @@ -562,15 +739,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements // 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")) + if (instance == null + || (System.getProperty("java.awt.headless") != null && System + .getProperty("java.awt.headless").equals("true"))) { return; } openFrameCount++; - frame.setVisible(true); + frame.setVisible(makeVisible); frame.setClosable(true); frame.setResizable(resizable); frame.setMaximizable(resizable); @@ -584,34 +762,33 @@ public class Desktop extends jalview.jbgui.GDesktop implements } final JMenuItem menuItem = new JMenuItem(title); - frame - .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() - { - public void internalFrameActivated( - javax.swing.event.InternalFrameEvent evt) - { - JInternalFrame itf = desktop.getSelectedFrame(); - if (itf != null) - { - itf.requestFocus(); - } + frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + { + public void internalFrameActivated( + javax.swing.event.InternalFrameEvent evt) + { + JInternalFrame itf = desktop.getSelectedFrame(); + if (itf != null) + { + itf.requestFocus(); + } - } + } - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - PaintRefresher.RemoveComponent(frame); - openFrameCount--; - windowMenu.remove(menuItem); - JInternalFrame itf = desktop.getSelectedFrame(); - if (itf != null) - { - itf.requestFocus(); - } - System.gc(); - }; - }); + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + PaintRefresher.RemoveComponent(frame); + openFrameCount--; + windowMenu.remove(menuItem); + JInternalFrame itf = desktop.getSelectedFrame(); + if (itf != null) + { + itf.requestFocus(); + } + System.gc(); + }; + }); menuItem.addActionListener(new ActionListener() { @@ -627,6 +804,47 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } }); + menuItem.addMouseListener(new MouseListener() + { + + @Override + public void mouseReleased(MouseEvent e) + { + } + + @Override + public void mousePressed(MouseEvent e) + { + } + + @Override + public void mouseExited(MouseEvent e) + { + try + { + frame.setSelected(false); + } catch (PropertyVetoException e1) + { + } + } + + @Override + public void mouseEntered(MouseEvent e) + { + try + { + frame.setSelected(true); + } catch (PropertyVetoException e1) + { + } + } + + @Override + public void mouseClicked(MouseEvent e) + { + + } + }); windowMenu.add(menuItem); @@ -638,6 +856,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements frame.requestFocus(); } catch (java.beans.PropertyVetoException ve) { + } catch (java.lang.ClassCastException cex) + { + Cache.log + .warn("Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869", + cex); } } @@ -675,6 +898,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ public void drop(DropTargetDropEvent evt) { + boolean success = true; Transferable t = evt.getTransferable(); java.util.List files = null; java.util.List protocols = null; @@ -723,6 +947,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } catch (Exception e) { + success = false; } if (files != null) @@ -751,8 +976,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } catch (Exception ex) { + success = false; } } + evt.dropComplete(success); // need this to ensure input focus is properly + // transfered to any new windows created } /** @@ -763,15 +991,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY"), + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS, jalview.io.AppletFormatAdapter.READABLE_FNAMES, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Open local file"); - chooser.setToolTipText("Open"); + chooser.setDialogTitle(MessageManager + .getString("label.open_local_file")); + chooser.setToolTipText(MessageManager.getString("action.open")); int value = chooser.showOpenDialog(this); @@ -782,7 +1011,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements .getSelectedFile().getParent()); String format = null; - if (chooser.getSelectedFormat().equals("Jalview")) + if (chooser.getSelectedFormat() != null + && chooser.getSelectedFormat().equals("Jalview")) { format = "Jalview"; } @@ -795,6 +1025,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements { new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format); + viewport.setShowSequenceFeatures(JSONFile.isSeqFeaturesEnabled()); + AlignFrame af = viewport.getAlignPanel().alignFrame; + if (af != null) + { + af.changeColour(JSONFile.getColourScheme()); + af.setMenusForViewport(); + } } else { @@ -813,7 +1050,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements { // This construct allows us to have a wider textfield // for viewing - JLabel label = new JLabel("Enter URL of Input File"); + JLabel label = new JLabel( + MessageManager.getString("label.input_file_url")); final JComboBox history = new JComboBox(); JPanel panel = new JPanel(new GridLayout(2, 1)); @@ -838,7 +1076,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements } int reply = JOptionPane.showInternalConfirmDialog(desktop, panel, - "Input Alignment From URL", JOptionPane.OK_CANCEL_OPTION); + MessageManager.getString("label.input_alignment_from_url"), + JOptionPane.OK_CANCEL_OPTION); if (reply != JOptionPane.OK_OPTION) { @@ -866,7 +1105,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (format.equals("URL NOT FOUND")) { JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Couldn't locate " + url, "URL not found", + MessageManager.formatMessage("label.couldnt_locate", + new Object[] + { url }), MessageManager + .getString("label.url_not_found"), JOptionPane.WARNING_MESSAGE); return; @@ -893,7 +1135,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements { CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(viewport); - Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500); + Desktop.addInternalFrame(cap, + MessageManager.getString("label.cut_paste_alignmen_file"), + true, 600, 500); } /* @@ -914,6 +1158,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds()); jconsole.stopConsole(); } + if (jvnews != null) + { + storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds()); + + } + if (dialogExecutor != null) + { + dialogExecutor.shutdownNow(); + } + System.exit(0); } @@ -937,32 +1191,82 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ public void aboutMenuItem_actionPerformed(ActionEvent e) { - StringBuffer message = new StringBuffer("Jalview version " - + jalview.bin.Cache.getProperty("VERSION") + "; last updated: " - + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")); + // StringBuffer message = getAboutMessage(false); + // JOptionPane.showInternalMessageDialog(Desktop.desktop, + // + // message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE); + new Thread(new Runnable() + { + public void run() + { + new SplashScreen(true); + } + }).start(); + } - if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals( - jalview.bin.Cache.getProperty("VERSION"))) + public StringBuffer getAboutMessage(boolean shortv) + { + StringBuffer message = new StringBuffer(); + message.append(""); + if (shortv) { - message - .append("\n\n!! Jalview version " - + jalview.bin.Cache.getProperty("LATEST_VERSION") - + " is available for download from http://www.jalview.org !!\n"); + message.append("

Version: " + + jalview.bin.Cache.getProperty("VERSION") + "

"); + message.append("Last Updated: " + + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + + ""); } - // TODO: update this text for each release or centrally store it for lite - // and application - message - .append("\nAuthors: Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,\n David Martin & Geoff Barton." - + "\nDevelopment managed by The Barton Group, University of Dundee, Scotland, UK.\n" - + "\nFor help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list\n" - + "\nIf you use Jalview, please cite:" - + "\nWaterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)" - + "\nJalview Version 2 - a multiple sequence alignment editor and analysis workbench" - + "\nBioinformatics doi: 10.1093/bioinformatics/btp033"); - JOptionPane.showInternalMessageDialog(Desktop.desktop, + else + { + + message.append("Version " + + jalview.bin.Cache.getProperty("VERSION") + + "; last updated: " + + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")); + } + + if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking").equals( + "Checking")) + { + message.append("
...Checking latest version...
"); + } + else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking") + .equals(jalview.bin.Cache.getProperty("VERSION"))) + { + boolean red = false; + if (jalview.bin.Cache.getProperty("VERSION").toLowerCase() + .indexOf("automated build") == -1) + { + red = true; + // Displayed when code version and jnlp version do not match and code + // version is not a development build + message.append("
"); + } - message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE); + message.append("
!! Version " + + jalview.bin.Cache.getDefault("LATEST_VERSION", + "..Checking..") + + " is available for download from " + + jalview.bin.Cache.getDefault("www.jalview.org", + "http://www.jalview.org") + " !!"); + if (red) + { + message.append("
"); + } + } + message.append("
Authors: " + + jalview.bin.Cache + .getDefault("AUTHORFNAMES", + "The Jalview Authors (See AUTHORS file for current list)") + + "

Development managed by The Barton Group, University of Dundee, Scotland, UK.
" + + "

For help, see the FAQ at www.jalview.org/faq and/or join the jalview-discuss@jalview.org mailing list" + + "

If you use Jalview, please cite:" + + "
Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)" + + "
Jalview Version 2 - a multiple sequence alignment editor and analysis workbench" + + "
Bioinformatics doi: 10.1093/bioinformatics/btp033" + + ""); + return message; } /** @@ -975,13 +1279,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { 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); + Help.showHelpWindow(); } catch (Exception ex) { } @@ -1084,7 +1382,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements return; } - AlignViewport source = null, target = null; + AlignmentViewport source = null, target = null; if (frames[0] instanceof AlignFrame) { source = ((AlignFrame) frames[0]).getCurrentView(); @@ -1172,29 +1470,98 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ public void saveState_actionPerformed(ActionEvent e) { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY"), new String[] - { "jar" }, new String[] - { "Jalview Project" }, "Jalview Project"); + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] + { "jvp" }, new String[] + { "Jalview Project" }, "Jalview Project"); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save State"); + chooser.setDialogTitle(MessageManager.getString("label.save_state")); int value = chooser.showSaveDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { - java.io.File choice = chooser.getSelectedFile(); - JProgressBar progpanel = addProgressPanel("Saving jalview project " - + choice.getName()); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); - // TODO catch and handle errors for savestate - new Jalview2XML().SaveState(choice); - removeProgressPanel(progpanel); + final Desktop me = this; + final java.io.File choice = chooser.getSelectedFile(); + setProjectFile(choice); + + // TODO or move inside the new Thread? + saveChimeraSessions(choice.getAbsolutePath()); + + new Thread(new Runnable() + { + public void run() + { + + 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(); + } + } + /** + * Request any open, linked Chimera sessions to save their state. + * + * @param jalviewProjectFilename + * the filename of the Jalview project; Chimera session files should + * be given distinct, but obviously related, names. + */ + public void saveChimeraSessions(String jalviewProjectFilename) + { + int i = 0; + for (JInternalFrame frame : getAllFrames()) + { + if (frame instanceof ChimeraViewFrame) + { + /* + * Construct a filename for the Chimera session by append _chimera.py + * to the Jalview project file name. + */ + String chimeraPath = jalviewProjectFilename + "_chimera_" + i + + ".py"; + ((ChimeraViewFrame) frame).saveSession(chimeraPath); + i++; + } } } + private void setProjectFile(File choice) + { + this.projectFile = choice; + } + + public File getProjectFile() + { + return this.projectFile; + } + /** * DOCUMENT ME! * @@ -1203,24 +1570,51 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ public void loadState_actionPerformed(ActionEvent e) { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY"), new String[] - { "jar" }, new String[] - { "Jalview Project" }, "Jalview Project"); + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] + { "jvp", "jar" }, new String[] + { "Jalview Project", "Jalview Project (old)" }, + "Jalview Project"); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Restore state"); + chooser.setDialogTitle(MessageManager.getString("label.restore_state")); int value = chooser.showOpenDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { - String choice = chooser.getSelectedFile().getAbsolutePath(); - setProgressBar("loading jalview project " - + chooser.getSelectedFile().getName(), choice.hashCode()); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser - .getSelectedFile().getParent()); - new Jalview2XML().LoadJalviewAlign(choice); - setProgressBar(null, choice.hashCode()); + final File selectedFile = chooser.getSelectedFile(); + setProjectFile(selectedFile); + final String choice = selectedFile.getAbsolutePath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", + selectedFile.getParent()); + new Thread(new Runnable() + { + 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(); } } @@ -1231,47 +1625,58 @@ public class Desktop extends jalview.jbgui.GDesktop implements JPanel progressPanel; + ArrayList fileLoadingPanels = new ArrayList(); + public void startLoading(final String fileName) { if (fileLoadingCount == 0) { - addProgressPanel("Loading File: " + fileName + " "); - + fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage( + "label.loading_file", new Object[] + { fileName }))); } fileLoadingCount++; } - private JProgressBar addProgressPanel(String string) + private JPanel addProgressPanel(String string) { if (progressPanel == null) { - progressPanel = new JPanel(new BorderLayout()); + progressPanel = new JPanel(new GridLayout(1, 1)); totalProgressCount = 0; + instance.getContentPane().add(progressPanel, BorderLayout.SOUTH); } + JPanel thisprogress = new JPanel(new BorderLayout(10, 5)); JProgressBar progressBar = new JProgressBar(); progressBar.setIndeterminate(true); - progressPanel.add(new JLabel(string), BorderLayout.WEST); + thisprogress.add(new JLabel(string), BorderLayout.WEST); - progressPanel.add(progressBar, BorderLayout.CENTER); - - instance.getContentPane().add(progressPanel, BorderLayout.SOUTH); - totalProgressCount++; - validate(); - return progressBar; + thisprogress.add(progressBar, BorderLayout.CENTER); + progressPanel.add(thisprogress); + ((GridLayout) progressPanel.getLayout()) + .setRows(((GridLayout) progressPanel.getLayout()).getRows() + 1); + ++totalProgressCount; + instance.validate(); + return thisprogress; } int totalProgressCount = 0; - private void removeProgressPanel(JProgressBar progbar) + private void removeProgressPanel(JPanel progbar) { if (progressPanel != null) { - progressPanel.remove(progbar); - if (--totalProgressCount < 1) + synchronized (progressPanel) { - this.getContentPane().remove(progressPanel); - progressPanel = null; + progressPanel.remove(progbar); + GridLayout gl = (GridLayout) progressPanel.getLayout(); + gl.setRows(gl.getRows() - 1); + if (--totalProgressCount < 1) + { + this.getContentPane().remove(progressPanel); + progressPanel = null; + } } } validate(); @@ -1282,51 +1687,49 @@ public class Desktop extends jalview.jbgui.GDesktop implements fileLoadingCount--; if (fileLoadingCount < 1) { - if (progressPanel != null) + while (fileLoadingPanels.size() > 0) { - this.getContentPane().remove(progressPanel); - progressPanel = null; + removeProgressPanel(fileLoadingPanels.remove(0)); } + fileLoadingPanels.clear(); fileLoadingCount = 0; } validate(); } - public static int getViewCount(String viewId) + public static int getViewCount(String alignmentId) { - AlignViewport[] aps = getViewports(viewId); + AlignmentViewport[] aps = getViewports(alignmentId); return (aps == null) ? 0 : aps.length; } /** * - * @param viewId - * @return all AlignmentPanels concerning the viewId sequence set + * @param alignmentId + * - if null, all sets are returned + * @return all AlignmentPanels concerning the alignmentId sequence set */ - public static AlignmentPanel[] getAlignmentPanels(String viewId) + public static AlignmentPanel[] getAlignmentPanels(String alignmentId) { - int count = 0; if (Desktop.desktop == null) { // no frames created and in headless mode // TODO: verify that frames are recoverable when in headless mode return null; } - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - ArrayList aps = new ArrayList(); - for (int t = 0; t < frames.length; t++) + List aps = new ArrayList(); + AlignFrame[] frames = getAlignFrames(); + if (frames == null) + { + return null; + } + for (AlignFrame af : frames) { - if (frames[t] instanceof AlignFrame) + for (AlignmentPanel ap : af.alignPanels) { - AlignFrame af = (AlignFrame) frames[t]; - for (int a = 0; a < af.alignPanels.size(); a++) + if (alignmentId==null || alignmentId.equals(ap.av.getSequenceSetId())) { - if (viewId - .equals(((AlignmentPanel) af.alignPanels.elementAt(a)).av - .getSequenceSetId())) - { - aps.add(af.alignPanels.elementAt(a)); - } + aps.add(ap); } } } @@ -1334,11 +1737,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { return null; } - AlignmentPanel[] vap = new AlignmentPanel[aps.size()]; - for (int t = 0; t < vap.length; t++) - { - vap[t] = (AlignmentPanel) aps.get(t); - } + AlignmentPanel[] vap = aps.toArray(new AlignmentPanel[aps.size()]); return vap; } @@ -1346,52 +1745,51 @@ public class Desktop extends jalview.jbgui.GDesktop implements * get all the viewports on an alignment. * * @param sequenceSetId - * unique alignment id + * unique alignment id (may be null - all viewports returned in that + * case) * @return all viewports on the alignment bound to sequenceSetId */ - public static AlignViewport[] getViewports(String sequenceSetId) + public static AlignmentViewport[] getViewports(String sequenceSetId) { - Vector viewp = new Vector(); + List viewp = new ArrayList(); if (desktop != null) { - javax.swing.JInternalFrame[] frames = instance.getAllFrames(); + AlignFrame[] frames = Desktop.getAlignFrames(); - for (int t = 0; t < frames.length; t++) + for (AlignFrame afr : frames) { - if (frames[t] instanceof AlignFrame) + if (sequenceSetId==null || afr.getViewport().getSequenceSetId().equals(sequenceSetId)) { - AlignFrame afr = ((AlignFrame) frames[t]); - if (afr.getViewport().getSequenceSetId().equals(sequenceSetId)) + if (afr.alignPanels != null) { - if (afr.alignPanels != null) + for (AlignmentPanel ap : afr.alignPanels) { - for (int a = 0; a < afr.alignPanels.size(); a++) + if (sequenceSetId == null + || sequenceSetId.equals(ap.av.getSequenceSetId())) { - if (sequenceSetId.equals(((AlignmentPanel) afr.alignPanels - .elementAt(a)).av.getSequenceSetId())) - { - viewp.addElement(((AlignmentPanel) afr.alignPanels - .elementAt(a)).av); - } + viewp.add(ap.av); } } - else - { - viewp.addElement(((AlignFrame) frames[t]).getViewport()); - } + } + else + { + viewp.add(afr.getViewport()); } } } if (viewp.size() > 0) { - AlignViewport[] vp = new AlignViewport[viewp.size()]; - viewp.copyInto(vp); - return vp; + return viewp.toArray(new AlignmentViewport[viewp.size()]); } } return null; } + /** + * Explode the views in the given frame into separate AlignFrame + * + * @param af + */ public void explodeViews(AlignFrame af) { int size = af.alignPanels.size(); @@ -1402,15 +1800,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements for (int i = 0; i < size; i++) { - AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(i); + AlignmentPanel ap = af.alignPanels.get(i); AlignFrame newaf = new AlignFrame(ap); - if (ap.av.explodedPosition != null - && !ap.av.explodedPosition.equals(af.getBounds())) + + /* + * 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(ap.av.explodedPosition); + newaf.setBounds(geometry); } - ap.av.gatherViewsHere = false; + ap.av.setGatherViewsHere(false); addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); @@ -1421,12 +1825,20 @@ public class Desktop extends jalview.jbgui.GDesktop implements } + /** + * 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.gatherViewsHere = true; - source.viewport.explodedPosition = source.getBounds(); + source.viewport.setGatherViewsHere(true); + source.viewport.setExplodedGeometry(source.getBounds()); JInternalFrame[] frames = desktop.getAllFrames(); - String viewId = source.viewport.sequenceSetID; + String viewId = source.viewport.getSequenceSetId(); for (int t = 0; t < frames.length; t++) { @@ -1436,12 +1848,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements boolean gatherThis = false; for (int a = 0; a < af.alignPanels.size(); a++) { - AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(a); + AlignmentPanel ap = af.alignPanels.get(a); if (viewId.equals(ap.av.getSequenceSetId())) { gatherThis = true; - ap.av.gatherViewsHere = false; - ap.av.explodedPosition = af.getBounds(); + ap.av.setGatherViewsHere(false); + ap.av.setExplodedGeometry(af.getBounds()); source.addAlignmentPanel(ap, false); } } @@ -1463,13 +1875,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (v_client == null) { // Load and try to start a session. - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY")); + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Open a saved VAMSAS session"); - chooser - .setToolTipText("select a vamsas session to be opened as a new vamsas session."); + chooser.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); @@ -1478,10 +1891,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements String fle = chooser.getSelectedFile().toString(); if (!vamsasImport(chooser.getSelectedFile())) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Couldn't import '" + fle + "' as a new vamsas session.", - "Vamsas Document Import Failed", - JOptionPane.ERROR_MESSAGE); + 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); } } } @@ -1524,8 +1943,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements } bis.close(); fos.close(); - v_client = new jalview.gui.VamsasApplication(this, file, url - .toExternalForm()); + v_client = new jalview.gui.VamsasApplication(this, file, + url.toExternalForm()); } catch (Exception ex) { jalview.bin.Cache.log.error( @@ -1554,23 +1973,26 @@ public class Desktop extends jalview.jbgui.GDesktop implements return false; } - setProgressBar("Importing VAMSAS session from " + file.getName(), file - .hashCode()); + 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("Importing VAMSAS session from " + file.getName(), - file.hashCode()); + 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("Importing VAMSAS session from " + file.getName(), file - .hashCode()); + setProgressBar(MessageManager.formatMessage( + "status.importing_vamsas_session_from", new Object[] + { file.getName() }), file.hashCode()); return v_client.inSession(); } @@ -1579,11 +2001,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (v_client != null) { throw new Error( - "Trying to join a vamsas session when another is already connected."); + MessageManager + .getString("error.try_join_vamsas_session_another")); } if (mysesid == null) { - throw new Error("Invalid vamsas session id."); + throw new Error( + MessageManager.getString("error.invalid_vamsas_session_id")); } v_client = new VamsasApplication(this, mysesid); setupVamsasConnectedGui(); @@ -1623,7 +2047,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements protected void setupVamsasConnectedGui() { - vamsasStart.setText("Session Update"); + vamsasStart.setText(MessageManager.getString("label.session_update")); vamsasSave.setVisible(true); vamsasStop.setVisible(true); vamsasImport.setVisible(false); // Document import to existing session is @@ -1635,7 +2059,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements vamsasSave.setVisible(false); vamsasStop.setVisible(false); vamsasImport.setVisible(true); - vamsasStart.setText("New Vamsas Session"); + vamsasStart.setText(MessageManager + .getString("label.new_vamsas_session")); } public void vamsasStop_actionPerformed(ActionEvent e) @@ -1671,7 +2096,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements { JMenuItem sessit = new JMenuItem(); sessit.setText(sess[i]); - sessit.setToolTipText("Connect to session " + 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() @@ -1720,22 +2147,24 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (v_client != null) { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY"), new String[] - { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] + { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ new String[] { "Vamsas Document" }, "Vamsas Document"); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save Vamsas Document Archive"); + chooser.setDialogTitle(MessageManager + .getString("label.save_vamsas_document_archive")); int value = chooser.showSaveDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { java.io.File choice = chooser.getSelectedFile(); - JProgressBar progpanel = addProgressPanel("Saving VAMSAS Document to " - + choice.getName()); + 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; @@ -1768,7 +2197,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } - JProgressBar vamUpdate = null; + JPanel vamUpdate = null; /** * hide vamsas user gui bits when a vamsas document event is being handled. @@ -1787,7 +2216,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements } if (b) { - vamUpdate = this.addProgressPanel("Updating vamsas session"); + vamUpdate = this.addProgressPanel(MessageManager + .getString("label.updating_vamsas_session")); } vamsasStart.setVisible(!b); vamsasStop.setVisible(!b); @@ -1822,6 +2252,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements public class MyDesktopPane extends JDesktopPane implements Runnable { + private static final float ONE_MB = 1048576f; + boolean showMemoryUsage = false; Runtime runtime; @@ -1861,9 +2293,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements { try { - maxMemory = runtime.maxMemory() / 1048576f; - allocatedMemory = runtime.totalMemory() / 1048576f; - freeMemory = runtime.freeMemory() / 1048576f; + maxMemory = runtime.maxMemory() / ONE_MB; + allocatedMemory = runtime.totalMemory() / ONE_MB; + freeMemory = runtime.freeMemory() / ONE_MB; totalFreeMemory = freeMemory + (maxMemory - allocatedMemory); percentUsage = (totalFreeMemory / maxMemory) * 100; @@ -1889,17 +2321,29 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (showMemoryUsage && g != null && df != null) { if (percentUsage < 20) + { g.setColor(Color.red); + } FontMetrics fm = g.getFontMetrics(); if (fm != null) { - g.drawString("Total Free Memory: " + df.format(totalFreeMemory) - + "MB; Max Memory: " + df.format(maxMemory) + "MB; " - + df.format(percentUsage) + "%", 10, getHeight() - - fm.getHeight()); + 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() + { } @@ -1910,7 +2354,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (jalview.bin.Cache.groovyJarsPresent()) { groovyShell = new JMenuItem(); - groovyShell.setText("Groovy Console..."); + groovyShell.setText(MessageManager.getString("label.groovy_console")); groovyShell.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1925,8 +2369,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements /** * Accessor method to quickly get all the AlignmentFrames loaded. + * + * @return an array of AlignFrame, or null if none found */ - public static AlignFrame[] getAlignframes() + public static AlignFrame[] getAlignFrames() { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); @@ -1934,32 +2380,66 @@ public class Desktop extends jalview.jbgui.GDesktop implements { return null; } - Vector avp = new Vector(); - try + List avp = new ArrayList(); + // REVERSE ORDER + for (int i = frames.length - 1; i > -1; i--) { - // REVERSE ORDER - for (int i = frames.length - 1; i > -1; i--) + if (frames[i] instanceof AlignFrame) { - 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) { - AlignFrame af = (AlignFrame) frames[i]; - avp.addElement(af); + avp.add((AlignFrame) sf.getTopFrame()); + } + if (sf.getBottomFrame() instanceof AlignFrame) + { + avp.add((AlignFrame) sf.getBottomFrame()); } } - } catch (Exception ex) - { - ex.printStackTrace(); } if (avp.size() == 0) { return null; } - AlignFrame afs[] = new AlignFrame[avp.size()]; - for (int i = 0, j = avp.size(); i < j; i++) + 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) { - afs[i] = (AlignFrame) avp.elementAt(i); + return null; } - avp.clear(); + List avp = new ArrayList(); + // 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; } @@ -1972,38 +2452,39 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (!jalview.bin.Cache.groovyJarsPresent()) { throw new Error( - "Implementation Error. Cannot create groovyShell without Groovy on the classpath!"); + MessageManager + .getString("error.implementation_error_cannot_create_groovyshell")); } try { - Class gcClass = Desktop.class.getClassLoader().loadClass( + Class gcClass = Desktop.class.getClassLoader().loadClass( "groovy.ui.Console"); - Constructor gccons = gcClass.getConstructor(null); + Constructor gccons = gcClass.getConstructor(); java.lang.reflect.Method setvar = gcClass.getMethod("setVariable", new Class[] { String.class, Object.class }); - java.lang.reflect.Method run = gcClass.getMethod("run", null); - Object gc = gccons.newInstance(null); + java.lang.reflect.Method run = gcClass.getMethod("run"); + Object gc = gccons.newInstance(); setvar.invoke(gc, new Object[] { "Jalview", this }); - run.invoke(gc, null); + run.invoke(gc); } catch (Exception ex) { jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex); - JOptionPane - .showInternalMessageDialog( - Desktop.desktop, + JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Couldn't create the groovy Shell. Check the error log for the details of what went wrong.", - "Jalview Groovy Support Failed", - JOptionPane.ERROR_MESSAGE); + MessageManager.getString("label.couldnt_create_groovy_shell"), + MessageManager.getString("label.groovy_support_failed"), + JOptionPane.ERROR_MESSAGE); } } /** * Progress bars managed by the IProgressIndicator method. */ - private Hashtable progressBars, progressBarHandlers; + private Hashtable progressBars; + + private Hashtable progressBarHandlers; /* * (non-Javadoc) @@ -2014,14 +2495,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (progressBars == null) { - progressBars = new Hashtable(); - progressBarHandlers = new Hashtable(); + progressBars = new Hashtable(); + progressBarHandlers = new Hashtable(); } if (progressBars.get(new Long(id)) != null) { - JProgressBar progressPanel = (JProgressBar) progressBars - .remove(new Long(id)); + JPanel progressPanel = progressBars.remove(new Long(id)); if (progressBarHandlers.contains(new Long(id))) { progressBarHandlers.remove(new Long(id)); @@ -2046,13 +2526,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (progressBarHandlers == null || !progressBars.contains(new Long(id))) { throw new Error( - "call setProgressBar before registering the progress bar's handler."); + MessageManager + .getString("error.call_setprogressbar_before_registering_handler")); } progressBarHandlers.put(new Long(id), handler); - final JPanel progressPanel = (JPanel) progressBars.get(new Long(id)); + final JPanel progressPanel = progressBars.get(new Long(id)); if (handler.canCancel()) { - JButton cancel = new JButton("Cancel"); + JButton cancel = new JButton( + MessageManager.getString("action.cancel")); final IProgressIndicator us = this; cancel.addActionListener(new ActionListener() { @@ -2060,8 +2542,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void actionPerformed(ActionEvent e) { handler.cancelActivity(id); - us.setProgressBar("Cancelled " - + ((JLabel) progressPanel.getComponent(0)).getText(), id); + us.setProgressBar(MessageManager.formatMessage( + "label.cancelled_params", new Object[] + { ((JLabel) progressPanel.getComponent(0)).getText() }), + id); } }); progressPanel.add(cancel, BorderLayout.EAST); @@ -2069,20 +2553,35 @@ public class Desktop extends jalview.jbgui.GDesktop implements } /** - * This will return the first AlignFrame viewing AlignViewport av. It will - * break if there are more than one AlignFrames viewing a particular av. This * - * @param av - * @return alignFrame for av + * @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(AlignViewport av) + public static AlignFrame getAlignFrameFor(AlignViewportI viewport) { if (desktop != null) { - AlignmentPanel[] aps = getAlignmentPanels(av.getSequenceSetId()); + AlignmentPanel[] aps = getAlignmentPanels(viewport + .getSequenceSetId()); for (int panel = 0; aps != null && panel < aps.length; panel++) { - if (aps[panel] != null && aps[panel].av == av) + if (aps[panel] != null && aps[panel].av == viewport) { return aps[panel].alignFrame; } @@ -2096,13 +2595,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements return v_client; } + /** * flag set if jalview GUI is being operated programmatically */ - private boolean inBatchMode=false; + private boolean inBatchMode = false; /** * check if jalview GUI is being operated programmatically + * * @return inBatchMode */ public boolean isInBatchMode() @@ -2112,14 +2613,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements /** * set flag if jalview GUI is being operated programmatically - * @param inBatchMode + * + * @param inBatchMode */ public void setInBatchMode(boolean inBatchMode) { this.inBatchMode = inBatchMode; } - public void startServiceDiscovery() { startServiceDiscovery(false); @@ -2129,43 +2630,56 @@ public class Desktop extends jalview.jbgui.GDesktop implements { boolean alive = true; Thread t0 = null, t1 = null, t2 = null; - - // todo: changesupport handlers need to be transferred - if (discoverer == null) - { - discoverer = new jalview.ws.jws1.Discoverer(); - // register PCS handler for desktop. - discoverer.addPropertyChangeListener(changeSupport); - } - if (Cache.getDefault("SHOW_JWS1_SERVICES", true)) + // 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(); } - try + // ENFIN services are EOLed as of Jalview 2.8.1 release + if (false) { - if (Cache.getDefault("SHOW_ENFIN_SERVICES", true)) + try + { + if (Cache.getDefault("SHOW_ENFIN_SERVICES", true)) + { + // EnfinEnvision web service menu entries are rebuild every time the + // menu is shown, so no changeSupport events are needed. + jalview.ws.EnfinEnvision2OneWay.getInstance(); + (t1 = new Thread(jalview.ws.EnfinEnvision2OneWay.getInstance())) + .start(); + } + } catch (Exception e) { - // EnfinEnvision web service menu entries are rebuild every time the - // menu is shown, so no changeSupport events are needed. - jalview.ws.EnfinEnvision2OneWay.getInstance(); - (t1 = new Thread(jalview.ws.EnfinEnvision2OneWay.getInstance())) - .start(); + Cache.log + .info("Exception when trying to launch Envision2 workflow discovery.", + e); + Cache.log.info(e.getStackTrace()); } - } catch (Exception e) - { - Cache.log - .info( - "Exception when trying to launch Envision2 workflow discovery.", - e); - Cache.log.info(e.getStackTrace()); } + if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { - jalview.ws.jws2.Jws2Discoverer.getDiscoverer() - .addPropertyChangeListener(changeSupport); - (t2 = new Thread(jalview.ws.jws2.Jws2Discoverer.getDiscoverer())) - .start(); + if (jalview.ws.jws2.Jws2Discoverer.getDiscoverer().isRunning()) + { + jalview.ws.jws2.Jws2Discoverer.getDiscoverer().setAborted(true); + } + t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer( + changeSupport); + + } + Thread t3 = null; + { + // TODO: do rest service discovery } if (blocking) { @@ -2179,44 +2693,406 @@ public class Desktop extends jalview.jbgui.GDesktop implements } alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive()) + || (t3 != null && t3.isAlive()) || (t0 != null && t0.isAlive()); } } } /** - * start a thread to open a URL in the configured browser. Pops up a warning dialog to the user if there is an exception when calling out to the browser to open the URL. + * called to check if the service discovery process completed successfully. + * + * @param evt + */ + protected void JalviewServicesChanged(PropertyChangeEvent evt) + { + if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector) + { + final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer() + .getErrorMessages(); + if (ermsg != null) + { + if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true)) + { + if (serviceChangedDialog == null) + { + // only run if we aren't already displaying one of these. + addDialogThread(serviceChangedDialog = new Runnable() + { + public void run() + { + + /* + * JalviewDialog jd =new JalviewDialog() { + * + * @Override protected void cancelPressed() { // TODO + * Auto-generated method stub + * + * }@Override protected void okPressed() { // TODO + * Auto-generated method stub + * + * }@Override protected void raiseClosed() { // TODO + * Auto-generated method stub + * + * } }; jd.initDialogFrame(new + * JLabel("
" + ermsg + + * "
It may be that you have invalid JABA URLs in your web service preferences," + * + " or mis-configured HTTP proxy settings.
" + + * "Check the Connections and Web services tab of the" + * + + * " Tools->Preferences dialog box to change them.
" + * ), true, true, "Web Service Configuration Problem", 450, + * 400); + * + * jd.waitForInput(); + */ + JOptionPane + .showConfirmDialog( + Desktop.desktop, + new JLabel( + "
" + + ermsg + + "
" + + "

It may be that you have invalid JABA URLs
in your web service preferences," + + "
or as a command-line argument, or mis-configured HTTP proxy settings.

" + + "

Check the Connections and Web services tab
of the" + + " Tools->Preferences dialog box to change them.

"), + "Web Service Configuration Problem", + JOptionPane.DEFAULT_OPTION, + JOptionPane.ERROR_MESSAGE); + serviceChangedDialog = null; + + } + }); + } + } + else + { + Cache.log + .error("Errors reported by JABA discovery service. Check web services preferences.\n" + + ermsg); + } + } + } + } + + private Runnable serviceChangedDialog = null; + + /** + * start a thread to open a URL in the configured browser. Pops up a warning + * dialog to the user if there is an exception when calling out to the browser + * to open the URL. + * * @param url */ public static void showUrl(final String url) { - new Thread(new Runnable() { - public void run() { - try { + showUrl(url, Desktop.instance); + } + + /** + * Like showUrl but allows progress handler to be specified + * + * @param url + * @param progress + * (null) or object implementing IProgressIndicator + */ + public static void showUrl(final String url, + final IProgressIndicator progress) + { + new Thread(new Runnable() + { + public void run() + { + try + { + if (progress != null) + { + progress.setProgressBar(MessageManager.formatMessage( + "status.opening_params", new Object[] + { url }), this.hashCode()); + } jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) - { - JOptionPane - .showInternalMessageDialog( - Desktop.desktop, - "Unixers: Couldn't find default web browser." - + "\nAdd the full path to your browser in Preferences.", - "Web browser not found", JOptionPane.WARNING_MESSAGE); + { + 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(); + }).start(); } public static WsParamSetManager wsparamManager = null; + public static ParamManager getUserParameterStore() { - if (wsparamManager==null) + if (wsparamManager == null) { wsparamManager = new WsParamSetManager(); } return wsparamManager; } + /** + * static hyperlink handler proxy method for use by Jalview's internal windows + * + * @param e + */ + public static void hyperlinkUpdate(HyperlinkEvent e) + { + if (e.getEventType() == EventType.ACTIVATED) + { + String url = null; + try + { + url = e.getURL().toString(); + Desktop.showUrl(url); + } catch (Exception x) + { + if (url != null) + { + if (Cache.log != null) + { + Cache.log.error("Couldn't handle string " + url + " as a URL."); + } + else + { + System.err.println("Couldn't handle string " + url + + " as a URL."); + } + } + // ignore any exceptions due to dud links. + } + + } + } + + /** + * single thread that handles display of dialogs to user. + */ + ExecutorService dialogExecutor = Executors.newSingleThreadExecutor(); + + /** + * flag indicating if dialogExecutor should try to acquire a permit + */ + private volatile boolean dialogPause = true; + + /** + * pause the queue + */ + private java.util.concurrent.Semaphore block = new Semaphore(0); + + /** + * add another dialog thread to the queue + * + * @param prompter + */ + public void addDialogThread(final Runnable prompter) + { + dialogExecutor.submit(new Runnable() + { + public void run() + { + if (dialogPause) + { + try + { + block.acquire(); + } catch (InterruptedException x) + { + } + ; + } + if (instance == null) + { + return; + } + try + { + SwingUtilities.invokeAndWait(prompter); + } catch (Exception q) + { + Cache.log.warn("Unexpected Exception in dialog thread.", q); + } + } + }); + } + + public void startDialogQueue() + { + // set the flag so we don't pause waiting for another permit and semaphore + // the current task to begin + dialogPause = false; + block.release(); + } + + @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"); + 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 frame into separate AlignFrame windows. + * + * @param sf + */ + public void explodeViews(SplitFrame sf) + { + AlignFrame oldTopFrame = (AlignFrame) sf.getTopFrame(); + AlignFrame oldBottomFrame = (AlignFrame) sf.getBottomFrame(); + List topPanels = oldTopFrame + .getAlignPanels(); + List bottomPanels = oldBottomFrame + .getAlignPanels(); + int viewCount = topPanels.size(); + if (viewCount < 2) + { + return; + } + + /* + * 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--) + { + /* + * 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. + */ + AlignmentPanel topPanel = (AlignmentPanel) topPanels.get(i); + AlignFrame newTopFrame = new AlignFrame(topPanel); + newTopFrame.setSize(new Dimension(AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT)); + newTopFrame.setVisible(true); + AlignmentPanel bottomPanel = (AlignmentPanel) bottomPanels.get(i); + AlignFrame newBottomFrame = new AlignFrame(bottomPanel); + newBottomFrame.setSize(new Dimension(AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT)); + newBottomFrame.setVisible(true); + topPanel.av.setGatherViewsHere(false); + bottomPanel.av.setGatherViewsHere(false); + JInternalFrame splitFrame = new SplitFrame(newTopFrame, + newBottomFrame); + // either panel may hold previous exploded frame geometry + Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport()) + .getExplodedGeometry(); + if (geometry != null) + { + splitFrame.setBounds(geometry); + } + Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1); + } + + /* + * 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) + { + AlignFrame myTopFrame = (AlignFrame) source.getTopFrame(); + AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame(); + myTopFrame.viewport.setExplodedGeometry(source.getBounds()); + myBottomFrame.viewport.setExplodedGeometry(source.getBounds()); + 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); + // both panels refer to the same split frame geometry + Rectangle position = sf.getBounds(); + topPanel.av.setExplodedGeometry(position); + bottomPanel.av.setExplodedGeometry(position); + myTopFrame.addAlignmentPanel(topPanel, false); + myBottomFrame.addAlignmentPanel(bottomPanel, false); + } + } + + if (gatherThis) + { + topFrame.getAlignPanels().clear(); + bottomFrame.getAlignPanels().clear(); + sf.close(); + } + } + } + + /* + * The dust settles...give focus to the tab we did this from. + */ + myTopFrame.setDisplayedView(myTopFrame.alignPanel); + + } + + public static AlignFrame getCurrentAlignFrame() + { + return currentAlignFrame; + } + + public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) + { + Desktop.currentAlignFrame = currentAlignFrame; + } + + }