X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=41cbad850d4adfcb8b9dac42991d6cfb37f3d672;hb=a4da7f0f52e97ebb3fb0c42d6ab3a71762c4b899;hp=e14e99142b500939ca52f162e71c2892a38eb9d7;hpb=2df0e73f2d10339cd837b0aa3f216ff140cd53e7;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index e14e991..41cbad8 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -20,12 +20,11 @@ */ package jalview.gui; -import static jalview.util.UrlConstants.SEQUENCE_ID; - import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; import jalview.bin.Jalview; +import jalview.io.BackupFiles; import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FileFormatException; @@ -38,6 +37,7 @@ import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.jbgui.GSplitFrame; import jalview.jbgui.GStructureViewer; +import jalview.project.Jalview2XML; import jalview.structure.StructureSelectionManager; import jalview.urls.IdOrgSettings; import jalview.util.ImageMaker; @@ -69,6 +69,7 @@ import java.awt.dnd.DropTargetEvent; import java.awt.dnd.DropTargetListener; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; +import java.awt.event.InputEvent; import java.awt.event.KeyEvent; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; @@ -79,9 +80,11 @@ import java.beans.PropertyChangeListener; import java.io.BufferedInputStream; import java.io.File; import java.io.FileOutputStream; +import java.io.FileWriter; import java.io.IOException; import java.net.URL; import java.util.ArrayList; +import java.util.HashMap; import java.util.Hashtable; import java.util.List; import java.util.ListIterator; @@ -92,16 +95,18 @@ import java.util.concurrent.Executors; import java.util.concurrent.Semaphore; import javax.swing.AbstractAction; +import javax.swing.Action; +import javax.swing.ActionMap; import javax.swing.Box; import javax.swing.BoxLayout; import javax.swing.DefaultDesktopManager; import javax.swing.DesktopManager; +import javax.swing.InputMap; import javax.swing.JButton; import javax.swing.JCheckBox; 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; @@ -140,6 +145,10 @@ public class Desktop extends jalview.jbgui.GDesktop private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES"; + protected static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT"; + + public static HashMap savingFiles = new HashMap<>(); + private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); /** @@ -341,14 +350,50 @@ public class Desktop extends jalview.jbgui.GDesktop doConfigureStructurePrefs(); setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION")); - setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); + /* + if (!Platform.isAMac()) + { + // this.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE); + } + else + { + this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE); + } + */ + + try + { + APQHandlers.setAPQHandlers(this); + } catch (Exception e) + { + System.out.println("Exception when trying to set APQHandlers"); + e.printStackTrace(); + } catch (Throwable t) + { + System.out.println("Throwable when trying to set APQHandlers"); + t.printStackTrace(); + } + + + addWindowListener(new WindowAdapter() + { + + @Override + public void windowClosing(WindowEvent ev) + { + quit(); + } + }); + boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE", false); + boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE", false); desktop = new MyDesktopPane(selmemusage); showMemusage.setSelected(selmemusage); desktop.setBackground(Color.white); + getContentPane().setLayout(new BorderLayout()); // alternate config - have scrollbars - see notes in JAL-153 // JScrollPane sp = new JScrollPane(); @@ -359,13 +404,12 @@ public class Desktop extends jalview.jbgui.GDesktop // This line prevents Windows Look&Feel resizing all new windows to maximum // if previous window was maximised - desktop.setDesktopManager( - new MyDesktopManager( - (Platform.isWindows() ? new DefaultDesktopManager() - : Platform.isAMac() - ? new AquaInternalFrameManager( - desktop.getDesktopManager()) - : desktop.getDesktopManager()))); + desktop.setDesktopManager(new MyDesktopManager( + (Platform.isWindows() ? new DefaultDesktopManager() + : Platform.isAMac() + ? new AquaInternalFrameManager( + desktop.getDesktopManager()) + : desktop.getDesktopManager()))); Rectangle dims = getLastKnownDimensions(""); if (dims != null) @@ -391,7 +435,15 @@ public class Desktop extends jalview.jbgui.GDesktop + System.getProperty("java.version") + "\n" + System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " - + System.getProperty("os.version")); + + System.getProperty("os.version") + + (jalview.bin.Cache.getProperty("VERSION").equals("DEVELOPMENT") + ? "\nJava path:" + + System.getProperty( + "java.home") + + File.separator + "bin" + + File.separator + "java" + : "") + ); showConsole(showjconsole); @@ -515,7 +567,7 @@ public class Desktop extends jalview.jbgui.GDesktop { final Desktop me = this; // Thread off the news reader, in case there are connection problems. - addDialogThread(new Runnable() + new Thread(new Runnable() { @Override public void run() @@ -526,13 +578,13 @@ public class Desktop extends jalview.jbgui.GDesktop showNews.setVisible(true); Cache.log.debug("Completed news thread."); } - }); + }).start(); } public void getIdentifiersOrgData() { // Thread off the identifiers fetcher - addDialogThread(new Runnable() + new Thread(new Runnable() { @Override public void run() @@ -549,7 +601,8 @@ public class Desktop extends jalview.jbgui.GDesktop + e.getMessage()); } } - }); + }).start(); + ; } @Override @@ -903,8 +956,6 @@ public class Desktop extends jalview.jbgui.GDesktop menuItem.removeActionListener(menuItem.getActionListeners()[0]); } windowMenu.remove(menuItem); - - System.gc(); }; }); @@ -924,6 +975,8 @@ public class Desktop extends jalview.jbgui.GDesktop } }); + setKeyBindings(frame); + desktop.add(frame); windowMenu.add(menuItem); @@ -943,6 +996,42 @@ public class Desktop extends jalview.jbgui.GDesktop } } + /** + * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close + * the window + * + * @param frame + */ + private static void setKeyBindings(JInternalFrame frame) + { + @SuppressWarnings("serial") + final Action closeAction = new AbstractAction() + { + @Override + public void actionPerformed(ActionEvent e) + { + frame.dispose(); + } + }; + + /* + * set up key bindings for Ctrl-W and Cmd-W, with the same (Close) action + */ + KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, + InputEvent.CTRL_DOWN_MASK); + KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()); + + InputMap inputMap = frame + .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW); + String ctrlW = ctrlWKey.toString(); + inputMap.put(ctrlWKey, ctrlW); + inputMap.put(cmdWKey, ctrlW); + + ActionMap actionMap = frame.getActionMap(); + actionMap.put(ctrlW, closeAction); + } + @Override public void lostOwnership(Clipboard clipboard, Transferable contents) { @@ -1045,7 +1134,7 @@ public class Desktop extends jalview.jbgui.GDesktop { String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); JalviewFileChooser chooser = JalviewFileChooser - .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat); + .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, true); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( @@ -1210,6 +1299,8 @@ public class Desktop extends jalview.jbgui.GDesktop @Override public void quit() { + //System.out.println("********** Desktop.quit()"); + //System.out.println(savingFiles.toString()); Dimension screen = Toolkit.getDefaultToolkit().getScreenSize(); jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + ""); @@ -1392,7 +1483,6 @@ public class Desktop extends jalview.jbgui.GDesktop { ssm.resetAll(); } - System.gc(); } @Override @@ -1559,28 +1649,49 @@ public class Desktop extends jalview.jbgui.GDesktop } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Shows a file chooser dialog and writes out the current session as a Jalview + * project file */ @Override - public void saveState_actionPerformed(ActionEvent e) + public void saveState_actionPerformed() { - JalviewFileChooser chooser = new JalviewFileChooser("jvp", - "Jalview Project"); + saveState_actionPerformed(false); + } - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager.getString("label.save_state")); + public void saveState_actionPerformed(boolean saveAs) + { + java.io.File projectFile = getProjectFile(); + // autoSave indicates we already have a file and don't need to ask + boolean autoSave = projectFile != null && !saveAs + && BackupFiles.getEnabled(); - int value = chooser.showSaveDialog(this); + // System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"', + // saveAs="+saveAs+", Backups + // "+(BackupFiles.getEnabled()?"enabled":"disabled")); - if (value == JalviewFileChooser.APPROVE_OPTION) + boolean approveSave = false; + if (!autoSave) { - final Desktop me = this; - final java.io.File choice = chooser.getSelectedFile(); - setProjectFile(choice); + JalviewFileChooser chooser = new JalviewFileChooser("jvp", + "Jalview Project"); + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle(MessageManager.getString("label.save_state")); + + int value = chooser.showSaveDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + projectFile = chooser.getSelectedFile(); + setProjectFile(projectFile); + approveSave = true; + } + } + + if (approveSave || autoSave) + { + final Desktop me = this; + final java.io.File chosenFile = projectFile; new Thread(new Runnable() { @Override @@ -1589,38 +1700,47 @@ public class Desktop extends jalview.jbgui.GDesktop // TODO: refactor to Jalview desktop session controller action. setProgressBar(MessageManager.formatMessage( "label.saving_jalview_project", new Object[] - { choice.getName() }), choice.hashCode()); + { chosenFile.getName() }), chosenFile.hashCode()); jalview.bin.Cache.setProperty("LAST_DIRECTORY", - choice.getParent()); + chosenFile.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); + BackupFiles backupfiles = new BackupFiles(chosenFile); + + new Jalview2XML().saveState(backupfiles.getTempFile()); + + backupfiles.setWriteSuccess(true); + backupfiles.rollBackupsAndRenameTempFile(); } catch (OutOfMemoryError oom) { - new OOMWarning( - "Whilst saving current state to " + choice.getName(), - oom); + new OOMWarning("Whilst saving current state to " + + chosenFile.getName(), oom); } catch (Exception ex) { - Cache.log.error( - "Problems whilst trying to save to " + choice.getName(), - ex); + Cache.log.error("Problems whilst trying to save to " + + chosenFile.getName(), ex); JvOptionPane.showMessageDialog(me, MessageManager.formatMessage( "label.error_whilst_saving_current_state_to", new Object[] - { choice.getName() }), + { chosenFile.getName() }), MessageManager.getString("label.couldnt_save_project"), JvOptionPane.WARNING_MESSAGE); } - setProgressBar(null, choice.hashCode()); + setProgressBar(null, chosenFile.hashCode()); } }).start(); } } + @Override + public void saveAsState_actionPerformed(ActionEvent e) + { + saveState_actionPerformed(true); + } + private void setProjectFile(File choice) { this.projectFile = choice; @@ -1632,20 +1752,19 @@ public class Desktop extends jalview.jbgui.GDesktop } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Shows a file chooser dialog and tries to read in the selected file as a + * Jalview project */ @Override - public void loadState_actionPerformed(ActionEvent e) + public void loadState_actionPerformed() { + final String[] suffix = new String[] { "jvp", "jar" }; + final String[] desc = new String[] { "Jalview Project", + "Jalview Project (old)" }; JalviewFileChooser chooser = new JalviewFileChooser( - Cache.getProperty("LAST_DIRECTORY"), new String[] - { "jvp", "jar" }, - new String[] - { "Jalview Project", "Jalview Project (old)" }, - "Jalview Project"); + Cache.getProperty("LAST_DIRECTORY"), suffix, desc, + "Jalview Project", true, true); // last two booleans: allFiles, + // allowBackupFiles chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.restore_state")); @@ -2341,7 +2460,7 @@ public class Desktop extends jalview.jbgui.GDesktop while (li.hasNext()) { String link = li.next(); - if (link.contains(SEQUENCE_ID) + if (link.contains(jalview.util.UrlConstants.SEQUENCE_ID) && !UrlConstants.isDefaultString(link)) { check = true; @@ -2495,7 +2614,6 @@ public class Desktop extends jalview.jbgui.GDesktop } } - /** * Accessor method to quickly get all the AlignmentFrames loaded. * @@ -2650,7 +2768,7 @@ public class Desktop extends jalview.jbgui.GDesktop { getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW) .put(KeyStroke.getKeyStroke(KeyEvent.VK_Q, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()), + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()), "Quit"); getRootPane().getActionMap().put("Quit", new AbstractAction() { @@ -2707,18 +2825,18 @@ public class Desktop extends jalview.jbgui.GDesktop progressBarHandlers = new Hashtable<>(); } - if (progressBars.get(new Long(id)) != null) + if (progressBars.get(Long.valueOf(id)) != null) { - JPanel panel = progressBars.remove(new Long(id)); - if (progressBarHandlers.contains(new Long(id))) + JPanel panel = progressBars.remove(Long.valueOf(id)); + if (progressBarHandlers.contains(Long.valueOf(id))) { - progressBarHandlers.remove(new Long(id)); + progressBarHandlers.remove(Long.valueOf(id)); } removeProgressPanel(panel); } else { - progressBars.put(new Long(id), addProgressPanel(message)); + progressBars.put(Long.valueOf(id), addProgressPanel(message)); } } @@ -2733,13 +2851,13 @@ public class Desktop extends jalview.jbgui.GDesktop final IProgressIndicatorHandler handler) { if (progressBarHandlers == null - || !progressBars.containsKey(new Long(id))) + || !progressBars.containsKey(Long.valueOf(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)); + progressBarHandlers.put(Long.valueOf(id), handler); + final JPanel progressPanel = progressBars.get(Long.valueOf(id)); if (handler.canCancel()) { JButton cancel = new JButton( @@ -3297,6 +3415,21 @@ public class Desktop extends jalview.jbgui.GDesktop return groovyConsole; } + /** + * handles the payload of a drag and drop event. + * + * TODO refactor to desktop utilities class + * + * @param files + * - Data source strings extracted from the drop event + * @param protocols + * - protocol for each data source extracted from the drop event + * @param evt + * - the drop event + * @param t + * - the payload from the drop event + * @throws Exception + */ public static void transferFromDropTarget(List files, List protocols, DropTargetDropEvent evt, Transferable t) throws Exception @@ -3318,15 +3451,15 @@ public class Desktop extends jalview.jbgui.GDesktop try { - java.net.URL url = (URL) t.getTransferData(urlFlavour); + java.net.URL url = (URL) t.getTransferData(urlFlavour); // nb: java 8 osx bug https://bugs.openjdk.java.net/browse/JDK-8156099 // means url may be null. - if (url != null) - { - protocols.add(DataSourceType.URL); - files.add(url.toString()); - Cache.log.debug("Drop handled as URL dataflavor " - + files.get(files.size() - 1)); + if (url != null) + { + protocols.add(DataSourceType.URL); + files.add(url.toString()); + Cache.log.debug("Drop handled as URL dataflavor " + + files.get(files.size() - 1)); return; } else @@ -3337,7 +3470,7 @@ public class Desktop extends jalview.jbgui.GDesktop "Please ignore plist error - occurs due to problem with java 8 on OSX"); } ; - } + } } catch (Throwable ex) { Cache.log.debug("URL drop handler failed.", ex); @@ -3370,85 +3503,114 @@ public class Desktop extends jalview.jbgui.GDesktop // 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()) + DataFlavor textDf = new DataFlavor( + "text/plain;class=java.lang.String"); + if (t.isDataFlavorSupported(textDf)) { - Cache.log.debug("Plain text drop content returned " + data); + data = (String) t.getTransferData(textDf); } + + Cache.log.debug("Plain text drop content returned " + + (data == null ? "Null - failed" : data)); + } - while (protocols.size() < files.size()) - { - Cache.log.debug("Adding missing FILE protocol for " - + files.get(protocols.size())); - protocols.add(DataSourceType.FILE); - } - for (java.util.StringTokenizer st = new java.util.StringTokenizer( - data, "\r\n"); st.hasMoreTokens();) + if (data != null) { - 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(DataSourceType.URL); - files.add(uri.toString()); - } - else + while (protocols.size() < files.size()) { - // otherwise preserve old behaviour: catch all for file objects - java.io.File file = new java.io.File(uri); + Cache.log.debug("Adding missing FILE protocol for " + + files.get(protocols.size())); protocols.add(DataSourceType.FILE); - files.add(file.toString()); } - } - if (Platform.isWindows()) - { - Cache.log.debug("Scanning dropped content for Windows Link Files"); - - // resolve any .lnk files in the file drop - for (int f=0;f 0) { Cache.log.debug( - "Supported transfer dataflavor: " + fl.toString()); - Object df = t.getTransferData(fl); - if (df != null) - { - Cache.log.debug("Retrieves: " + df); - } - else + "Couldn't resolve drop data. Here are the supported flavors:"); + for (DataFlavor fl : t.getTransferDataFlavors()) { - Cache.log.debug("Retrieved nothing"); + 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"); + } } } + else + { + Cache.log.debug("Couldn't resolve dataflavor for drop: " + + t.toString()); + } + } + } + } + if (Platform.isWindows()) + + { + Cache.log.debug("Scanning dropped content for Windows Link Files"); + + // resolve any .lnk files in the file drop + for (int f = 0; f < files.size(); f++) + { + String source = files.get(f).toLowerCase(); + if (protocols.get(f).equals(DataSourceType.FILE) + && (source.endsWith(".lnk") || source.endsWith(".url") + || source.endsWith(".site"))) + { + try + { + File lf = new File(files.get(f)); + // process link file to get a URL + Cache.log.debug("Found potential link file: " + lf); + WindowsShortcut wscfile = new WindowsShortcut(lf); + String fullname = wscfile.getRealFilename(); + protocols.set(f, FormatAdapter.checkProtocol(fullname)); + files.set(f, fullname); + Cache.log.debug("Parsed real filename " + fullname + + " to extract protocol: " + protocols.get(f)); + } catch (Exception ex) + { + Cache.log.error( + "Couldn't parse " + files.get(f) + " as a link file.", + ex); + } } } }