X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=b1b913b1871c343f0b43a6067a4cb8670afc5907;hb=55c903147c3642ae7af3b21b9bb274607ca8f496;hp=392bf320b1ad0fa60fab84ec66fd61ae0d5607e2;hpb=fa1a4f7a83e254522451c53b08c9e8e95cdd498d;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 392bf32..b1b913b 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -61,20 +61,16 @@ import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.FocusEvent; import java.awt.event.FocusListener; +import java.awt.event.KeyEvent; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; -import java.awt.event.MouseListener; import java.awt.event.WindowAdapter; import java.awt.event.WindowEvent; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; -import java.beans.PropertyVetoException; import java.io.BufferedInputStream; import java.io.File; import java.io.FileOutputStream; -import java.lang.reflect.Constructor; -import java.lang.reflect.InvocationTargetException; -import java.lang.reflect.Method; import java.net.URL; import java.util.ArrayList; import java.util.Hashtable; @@ -85,9 +81,13 @@ import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.Semaphore; +import javax.swing.AbstractAction; +import javax.swing.Box; +import javax.swing.BoxLayout; import javax.swing.DefaultDesktopManager; import javax.swing.DesktopManager; import javax.swing.JButton; +import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JComponent; import javax.swing.JDesktopPane; @@ -99,9 +99,12 @@ import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.JProgressBar; +import javax.swing.KeyStroke; import javax.swing.SwingUtilities; import javax.swing.event.HyperlinkEvent; import javax.swing.event.HyperlinkEvent.EventType; +import javax.swing.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; @@ -172,8 +175,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements static final int yOffset = 30; - private static AlignFrame currentAlignFrame; - public static jalview.ws.jws1.Discoverer discoverer; public static Object[] jalviewClipboard; @@ -315,7 +316,20 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ instance = this; doVamsasClientCheck(); - doGroovyCheck(); + + groovyShell = new JMenuItem(); + groovyShell.setText(MessageManager.getString("label.groovy_console")); + groovyShell.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + groovyShell_actionPerformed(); + } + }); + toolsMenu.add(groovyShell); + groovyShell.setVisible(true); + doConfigureStructurePrefs(); setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION")); setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); @@ -371,6 +385,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements showNews.setVisible(false); + checkURLLinks(); + this.addWindowListener(new WindowAdapter() { @Override @@ -386,7 +402,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements @Override public void mousePressed(MouseEvent evt) { - if (evt.isPopupTrigger()) + if (evt.isPopupTrigger()) // Mac + { + showPasteMenu(evt.getX(), evt.getY()); + } + } + + @Override + public void mouseReleased(MouseEvent evt) + { + if (evt.isPopupTrigger()) // Windows { showPasteMenu(evt.getX(), evt.getY()); } @@ -794,32 +819,53 @@ public class Desktop extends jalview.jbgui.GDesktop implements * ((openFrameCount - 1) % 10) + yOffset); } + /* + * add an entry for the new frame in the Window menu + * (and remove it when the frame is closed) + */ final JMenuItem menuItem = new JMenuItem(title); - frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + frame.addInternalFrameListener(new InternalFrameAdapter() { @Override - public void internalFrameActivated( - javax.swing.event.InternalFrameEvent evt) + public void internalFrameActivated(InternalFrameEvent evt) { JInternalFrame itf = desktop.getSelectedFrame(); if (itf != null) { itf.requestFocus(); } - } @Override - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) + public void internalFrameClosed(InternalFrameEvent evt) { PaintRefresher.RemoveComponent(frame); - openFrameCount--; + + /* + * defensive check to prevent frames being + * added half off the window + */ + if (openFrameCount > 0) + { + openFrameCount--; + } + + /* + * ensure no reference to alignFrame retained by menu item listener + */ + if (menuItem.getActionListeners().length > 0) + { + menuItem.removeActionListener(menuItem.getActionListeners()[0]); + } windowMenu.remove(menuItem); JInternalFrame itf = desktop.getSelectedFrame(); if (itf != null) { itf.requestFocus(); + if (itf instanceof AlignFrame) + { + Jalview.setCurrentAlignFrame((AlignFrame) itf); + } } System.gc(); }; @@ -840,47 +886,6 @@ 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); @@ -941,54 +946,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void drop(DropTargetDropEvent evt) { boolean success = true; + // JAL-1552 - acceptDrop required before getTransferable call for + // Java's Transferable for native dnd + evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Transferable t = evt.getTransferable(); - java.util.List files = null; - java.util.List protocols = null; + java.util.List files = new ArrayList(); + java.util.List protocols = new ArrayList(); try { - DataFlavor uriListFlavor = new DataFlavor( - "text/uri-list;class=java.lang.String"); - if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) - { - // Works on Windows and MacOSX - evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); - files = (java.util.List) t - .getTransferData(DataFlavor.javaFileListFlavor); - } - else if (t.isDataFlavorSupported(uriListFlavor)) - { - // This is used by Unix drag system - evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); - String data = (String) t.getTransferData(uriListFlavor); - files = new java.util.ArrayList(1); - protocols = new java.util.ArrayList(1); - for (java.util.StringTokenizer st = new java.util.StringTokenizer( - data, "\r\n"); st.hasMoreTokens();) - { - String s = st.nextToken(); - if (s.startsWith("#")) - { - // the line is a comment (as per the RFC 2483) - continue; - } - java.net.URI uri = new java.net.URI(s); - if (uri.getScheme().toLowerCase().startsWith("http")) - { - protocols.add(FormatAdapter.URL); - files.add(uri.toString()); - } - else - { - // otherwise preserve old behaviour: catch all for file objects - java.io.File file = new java.io.File(uri); - protocols.add(FormatAdapter.FILE); - files.add(file.toString()); - } - } - } + Desktop.transferFromDropTarget(files, protocols, evt, t); } catch (Exception e) { + e.printStackTrace(); success = false; } @@ -1208,6 +1178,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements dialogExecutor.shutdownNow(); } closeAll_actionPerformed(null); + + if (groovyConsole != null) + { + // suppress a possible repeat prompt to save script + groovyConsole.setDirty(false); + groovyConsole.exit(); + } System.exit(0); } @@ -1331,6 +1308,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements @Override public void closeAll_actionPerformed(ActionEvent e) { + // TODO show a progress bar while closing? JInternalFrame[] frames = desktop.getAllFrames(); for (int i = 0; i < frames.length; i++) { @@ -1341,6 +1319,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { } } + Jalview.setCurrentAlignFrame(null); System.out.println("ALL CLOSED"); if (v_client != null) { @@ -1357,6 +1336,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { ssm.resetAll(); } + System.gc(); } @Override @@ -1826,7 +1806,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * * @param af */ - public void explodeViews(AlignFrame af) + public static void explodeViews(AlignFrame af) { int size = af.alignPanels.size(); if (size < 2) @@ -2281,6 +2261,55 @@ public class Desktop extends jalview.jbgui.GDesktop implements new Thread(jvq).start(); } + public void checkURLLinks() + { + // Thread off the URL link checker + addDialogThread(new Runnable() + { + @Override + public void run() + { + if (Cache.getDefault("CHECKURLLINKS", true)) + { + // check in case URL links use old style tokens ($SEQUENCE_ID$ for + // sequence id _or_ accession id) + JPanel msgPanel = new JPanel(); + msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS)); + msgPanel.add(Box.createVerticalGlue()); + JLabel msg = new JLabel( + MessageManager + .getString("label.SEQUENCE_ID_for_DB_ACCESSION1")); + JLabel msg2 = new JLabel( + MessageManager + .getString("label.SEQUENCE_ID_for_DB_ACCESSION2")); + msgPanel.add(msg); + msgPanel.add(msg2); + + final JCheckBox jcb = new JCheckBox( + MessageManager.getString("label.do_not_display_again")); + jcb.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + // update Cache settings if checkbox is selected + if (jcb.isSelected()) + { + Cache.setProperty("CHECKURLLINKS", "false"); + } + } + }); + msgPanel.add(jcb); + + JOptionPane.showMessageDialog(null, msgPanel, MessageManager + .getString("label.SEQUENCE_ID_no_longer_used"), + JOptionPane.WARNING_MESSAGE); + } + } + }); + } + /** * Proxy class for JDesktopPane which optionally displays the current memory * usage and highlights the desktop area with a red bar if free memory runs @@ -2389,25 +2418,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements protected JMenuItem groovyShell; - public void doGroovyCheck() - { - if (jalview.bin.Cache.groovyJarsPresent()) - { - groovyShell = new JMenuItem(); - groovyShell.setText(MessageManager.getString("label.groovy_console")); - groovyShell.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - groovyShell_actionPerformed(); - } - }); - toolsMenu.add(groovyShell); - groovyShell.setVisible(true); - } - } - /** * Accessor method to quickly get all the AlignmentFrames loaded. * @@ -2418,7 +2428,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (Jalview.isHeadlessMode()) { // Desktop.desktop is null in headless mode - return new AlignFrame[] { currentAlignFrame }; + return new AlignFrame[] { Jalview.currentAlignFrame }; } JInternalFrame[] frames = Desktop.desktop.getAllFrames(); @@ -2495,12 +2505,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ public void groovyShell_actionPerformed() { - if (!jalview.bin.Cache.groovyJarsPresent()) - { - throw new Error( - MessageManager - .getString("error.implementation_error_cannot_create_groovyshell")); - } try { openGroovyConsole(); @@ -2516,70 +2520,82 @@ public class Desktop extends jalview.jbgui.GDesktop implements } /** - * Open the Groovy console, using reflection to avoid creating compile-time - * dependency on Groovy libraries - * - * @throws ClassNotFoundException - * @throws NoSuchMethodException - * @throws InstantiationException - * @throws IllegalAccessException - * @throws InvocationTargetException + * Open the Groovy console */ - void openGroovyConsole() throws ClassNotFoundException, - NoSuchMethodException, InstantiationException, - IllegalAccessException, InvocationTargetException + void openGroovyConsole() { - Class gcClass = Desktop.class.getClassLoader().loadClass( - "groovy.ui.Console"); - Constructor gccons = gcClass.getConstructor(); - groovyConsole = gccons.newInstance(); + if (groovyConsole == null) + { + groovyConsole = new groovy.ui.Console(); + groovyConsole.setVariable("Jalview", this); + groovyConsole.run(); - /* - * bind groovy variable 'Jalview' to the Desktop object - */ - Method setvar = gcClass.getMethod("setVariable", new Class[] { - String.class, Object.class }); - setvar.invoke(groovyConsole, new Object[] { "Jalview", this }); + /* + * We allow only one console at a time, so that AlignFrame menu option + * 'Calculate | Run Groovy script' is unambiguous. + * Disable 'Groovy Console', and enable 'Run script', when the console is + * opened, and the reverse when it is closed + */ + Window window = (Window) groovyConsole.getFrame(); + window.addWindowListener(new WindowAdapter() + { + @Override + public void windowClosed(WindowEvent e) + { + /* + * rebind CMD-Q from Groovy Console to Jalview Quit + */ + addQuitHandler(); + enableExecuteGroovy(false); + } + }); + } /* - * start the console + * show Groovy console window (after close and reopen) */ - Method run = gcClass.getMethod("run"); - run.invoke(groovyConsole); + ((Window) groovyConsole.getFrame()).setVisible(true); /* - * Allow only one console at a time, so that the AlignFrame menu option - * 'Calculate | Run Groovy script' is unambiguous. - * Disable 'new console', and enable 'Run script', when the console is - * opened, and the reverse when it is closed + * if we got this far, enable 'Run Groovy' in AlignFrame menus + * and disable opening a second console */ - Method getFrame = gcClass.getMethod("getFrame"); - Window window = (Window) getFrame.invoke(groovyConsole); - window.addWindowListener(new WindowAdapter() + enableExecuteGroovy(true); + } + + /** + * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this + * binding when opened + */ + protected void addQuitHandler() + { + getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( + KeyStroke.getKeyStroke(KeyEvent.VK_Q, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask()), "Quit"); + getRootPane().getActionMap().put("Quit", new AbstractAction() { @Override - public void windowClosed(WindowEvent e) + public void actionPerformed(ActionEvent e) { - groovyShell.setEnabled(true); - enableExecuteGroovy(false); + quit(); } }); - - /* - * if we got this far, enable 'Run Groovy' in AlignFrame menus - * and disable opening a second console - */ - groovyShell.setEnabled(false); - enableExecuteGroovy(true); } /** * Enable or disable 'Run Groovy script' in AlignFrame calculate menus * * @param enabled + * true if Groovy console is open */ public void enableExecuteGroovy(boolean enabled) { + /* + * disable opening a second Groovy console + * (or re-enable when the console is closed) + */ + groovyShell.setEnabled(!enabled); + AlignFrame[] alignFrames = getAlignFrames(); if (alignFrames != null) { @@ -2986,12 +3002,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ private java.util.concurrent.Semaphore block = new Semaphore(0); - /* - * groovy.ui.Console object - if Groovy jars are present and the - * user has activated the Groovy console. Use via reflection to - * avoid compile-time dependency on Groovy libraries. - */ - private static Object groovyConsole; + private static groovy.ui.Console groovyConsole; /** * add another dialog thread to the queue @@ -3208,22 +3219,106 @@ public class Desktop extends jalview.jbgui.GDesktop implements * The dust settles...give focus to the tab we did this from. */ myTopFrame.setDisplayedView(myTopFrame.alignPanel); - } - public static AlignFrame getCurrentAlignFrame() + public static groovy.ui.Console getGroovyConsole() { - return currentAlignFrame; + return groovyConsole; } - public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) + public static void transferFromDropTarget(List files, + List protocols, DropTargetDropEvent evt, Transferable t) + throws Exception { - Desktop.currentAlignFrame = currentAlignFrame; - } - public static Object getGroovyConsole() - { - return groovyConsole; + DataFlavor uriListFlavor = new DataFlavor( + "text/uri-list;class=java.lang.String"); + if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) + { + // Works on Windows and MacOSX + Cache.log.debug("Drop handled as javaFileListFlavor"); + for (Object file : (List) t + .getTransferData(DataFlavor.javaFileListFlavor)) + { + files.add(((File) file).toString()); + protocols.add(FormatAdapter.FILE); + } + } + else + { + // Unix like behaviour + boolean added = false; + String data = null; + if (t.isDataFlavorSupported(uriListFlavor)) + { + Cache.log.debug("Drop handled as uriListFlavor"); + // This is used by Unix drag system + data = (String) t.getTransferData(uriListFlavor); + } + if (data == null) + { + // fallback to text: workaround - on OSX where there's a JVM bug + Cache.log.debug("standard URIListFlavor failed. Trying text"); + // try text fallback + data = (String) t.getTransferData(new DataFlavor( + "text/plain;class=java.lang.String")); + if (Cache.log.isDebugEnabled()) + { + Cache.log.debug("fallback returned " + data); + } + } + while (protocols.size() < files.size()) + { + Cache.log.debug("Adding missing FILE protocol for " + + files.get(protocols.size())); + protocols.add(FormatAdapter.FILE); + } + for (java.util.StringTokenizer st = new java.util.StringTokenizer( + data, "\r\n"); st.hasMoreTokens();) + { + added = true; + String s = st.nextToken(); + if (s.startsWith("#")) + { + // the line is a comment (as per the RFC 2483) + continue; + } + java.net.URI uri = new java.net.URI(s); + if (uri.getScheme().toLowerCase().startsWith("http")) + { + protocols.add(FormatAdapter.URL); + files.add(uri.toString()); + } + else + { + // otherwise preserve old behaviour: catch all for file objects + java.io.File file = new java.io.File(uri); + protocols.add(FormatAdapter.FILE); + files.add(file.toString()); + } + } + if (Cache.log.isDebugEnabled()) + { + if (data == null || !added) + { + Cache.log + .debug("Couldn't resolve drop data. Here are the supported flavors:"); + for (DataFlavor fl : t.getTransferDataFlavors()) + { + Cache.log.debug("Supported transfer dataflavor: " + + fl.toString()); + Object df = t.getTransferData(fl); + if (df != null) + { + Cache.log.debug("Retrieves: " + df); + } + else + { + Cache.log.debug("Retrieved nothing"); + } + } + } + } + } } - }