X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=2e8644e8c958ef803c836e024a568af971fd5c70;hb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;hp=d03e3f2ee4272b29c23e957b0d6bb3de5c748d4d;hpb=b0842a6ddaef0ceb4de3e1534c3772515d4b103d;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index d03e3f2..2e8644e 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -20,11 +20,18 @@ */ package jalview.gui; +import static jalview.util.UrlConstants.EMBLEBI_STRING; +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.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.FileFormatException; +import jalview.io.FileFormatI; import jalview.io.FileLoader; -import jalview.io.FormatAdapter; import jalview.io.IdentifyFile; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; @@ -33,6 +40,7 @@ import jalview.jbgui.GStructureViewer; import jalview.structure.StructureSelectionManager; import jalview.util.ImageMaker; import jalview.util.MessageManager; +import jalview.util.Platform; import jalview.viewmodel.AlignmentViewport; import jalview.ws.params.ParamManager; @@ -45,6 +53,7 @@ import java.awt.GridLayout; import java.awt.Point; import java.awt.Rectangle; import java.awt.Toolkit; +import java.awt.Window; import java.awt.datatransfer.Clipboard; import java.awt.datatransfer.ClipboardOwner; import java.awt.datatransfer.DataFlavor; @@ -58,31 +67,34 @@ 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.net.URL; import java.util.ArrayList; import java.util.Hashtable; import java.util.List; +import java.util.ListIterator; import java.util.StringTokenizer; import java.util.Vector; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.Semaphore; +import javax.swing.AbstractAction; +import javax.swing.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; @@ -94,9 +106,12 @@ 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; @@ -167,8 +182,6 @@ 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; @@ -187,6 +200,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements this.delegate = delegate; } + @Override public void activateFrame(JInternalFrame f) { try @@ -199,31 +213,37 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } + @Override public void beginDraggingFrame(JComponent f) { delegate.beginDraggingFrame(f); } + @Override public void beginResizingFrame(JComponent f, int direction) { delegate.beginResizingFrame(f, direction); } + @Override public void closeFrame(JInternalFrame f) { delegate.closeFrame(f); } + @Override public void deactivateFrame(JInternalFrame f) { delegate.deactivateFrame(f); } + @Override public void deiconifyFrame(JInternalFrame f) { delegate.deiconifyFrame(f); } + @Override public void dragFrame(JComponent f, int newX, int newY) { if (newY < 0) @@ -233,31 +253,37 @@ public class Desktop extends jalview.jbgui.GDesktop implements delegate.dragFrame(f, newX, newY); } + @Override public void endDraggingFrame(JComponent f) { delegate.endDraggingFrame(f); } + @Override public void endResizingFrame(JComponent f) { delegate.endResizingFrame(f); } + @Override public void iconifyFrame(JInternalFrame f) { delegate.iconifyFrame(f); } + @Override public void maximizeFrame(JInternalFrame f) { delegate.maximizeFrame(f); } + @Override public void minimizeFrame(JInternalFrame f) { delegate.minimizeFrame(f); } + @Override public void openFrame(JInternalFrame f) { delegate.openFrame(f); @@ -274,6 +300,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements delegate.resizeFrame(f, newX, newY, newWidth, newHeight); } + @Override public void setBoundsForFrame(JComponent f, int newX, int newY, int newWidth, int newHeight) { @@ -296,7 +323,20 @@ 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); @@ -305,6 +345,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements boolean showjconsole = jalview.bin.Cache.getDefault( "SHOW_JAVA_CONSOLE", false); desktop = new MyDesktopPane(selmemusage); + if (Platform.isAMac()) + { + desktop.setDoubleBuffered(false); + } showMemusage.setSelected(selmemusage); desktop.setBackground(Color.white); getContentPane().setLayout(new BorderLayout()); @@ -348,8 +392,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements showNews.setVisible(false); + checkURLLinks(); + this.addWindowListener(new WindowAdapter() { + @Override public void windowClosing(WindowEvent evt) { quit(); @@ -359,9 +406,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements MouseAdapter ma; this.addMouseListener(ma = new MouseAdapter() { + @Override public void mousePressed(MouseEvent evt) { - if (SwingUtilities.isRightMouseButton(evt)) + if (evt.isPopupTrigger()) // Mac + { + showPasteMenu(evt.getX(), evt.getY()); + } + } + + @Override + public void mouseReleased(MouseEvent evt) + { + if (evt.isPopupTrigger()) // Windows { showPasteMenu(evt.getX(), evt.getY()); } @@ -391,6 +448,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements // Spawn a thread that shows the splashscreen SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { new SplashScreen(); @@ -402,14 +460,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements // takes to open it later on. new Thread(new Runnable() { + @Override public void run() { Cache.log.debug("Filechooser init thread started."); - new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), - jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS, - jalview.io.AppletFormatAdapter.READABLE_FNAMES, - jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT")); + String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); + JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), + // jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS, + // jalview.io.AppletFormatAdapter.READABLE_FNAMES, + fileFormat, true); Cache.log.debug("Filechooser init thread finished."); } }).start(); @@ -573,16 +632,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements // reselected again. boolean refresh = true; + @Override public void menuCanceled(MenuEvent e) { refresh = true; } + @Override public void menuDeselected(MenuEvent e) { refresh = true; } + @Override public void menuSelected(MenuEvent e) { if (refresh) @@ -603,6 +665,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements MessageManager.getString("label.paste_new_window")); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { paste(); @@ -625,10 +688,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements String file = (String) contents .getTransferData(DataFlavor.stringFlavor); - String format = new IdentifyFile().Identify(file, - FormatAdapter.PASTE); + FileFormatI format = new IdentifyFile().identify(file, + DataSourceType.PASTE); - new FileLoader().LoadFile(file, FormatAdapter.PASTE, format); + new FileLoader().LoadFile(file, DataSourceType.PASTE, format); } } catch (Exception ex) @@ -750,38 +813,66 @@ public class Desktop extends jalview.jbgui.GDesktop implements frame.setResizable(resizable); frame.setMaximizable(resizable); frame.setIconifiable(resizable); - frame.setFrameIcon(null); - + if (Platform.isAMac()) + { + frame.setIconifiable(false); + frame.setFrameIcon(null); + // frame.setDesktopIcon(null); + frame.setDoubleBuffered(false); + } if (frame.getX() < 1 && frame.getY() < 1) { frame.setLocation(xOffset * openFrameCount, yOffset * ((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() { - public void internalFrameActivated( - javax.swing.event.InternalFrameEvent evt) + @Override + public void internalFrameActivated(InternalFrameEvent evt) { JInternalFrame itf = desktop.getSelectedFrame(); if (itf != null) { itf.requestFocus(); } - } - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) + @Override + 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(); }; @@ -789,6 +880,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements menuItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { try @@ -801,47 +893,6 @@ 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); @@ -861,6 +912,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } + @Override public void lostOwnership(Clipboard clipboard, Transferable contents) { if (!internalCopy) @@ -871,14 +923,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements internalCopy = false; } + @Override public void dragEnter(DropTargetDragEvent evt) { } + @Override public void dragExit(DropTargetEvent evt) { } + @Override public void dragOver(DropTargetDragEvent evt) { } @@ -894,57 +949,23 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param evt * DOCUMENT ME! */ + @Override public void drop(DropTargetDropEvent evt) { boolean success = true; + // JAL-1552 - acceptDrop required before getTransferable call for + // Java's Transferable for native dnd + evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Transferable t = evt.getTransferable(); - java.util.List files = null; - java.util.List protocols = null; + List files = new ArrayList(); + 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; } @@ -955,18 +976,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements for (int i = 0; i < files.size(); i++) { String file = files.get(i).toString(); - String protocol = (protocols == null) ? FormatAdapter.FILE - : (String) protocols.get(i); - String format = null; + DataSourceType protocol = (protocols == null) ? DataSourceType.FILE + : protocols.get(i); + FileFormatI format = null; if (file.endsWith(".jar")) { - format = "Jalview"; + format = FileFormat.Jalview; } else { - format = new IdentifyFile().Identify(file, protocol); + format = new IdentifyFile().identify(file, protocol); } new FileLoader().LoadFile(file, protocol, format); @@ -990,11 +1011,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements @Override public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) { - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), - jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS, - jalview.io.AppletFormatAdapter.READABLE_FNAMES, - jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT")); + String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); + JalviewFileChooser chooser = JalviewFileChooser.forRead( + Cache.getProperty("LAST_DIRECTORY"), + // AppletFormatAdapter.READABLE_EXTENSIONS, + // AppletFormatAdapter.READABLE_FNAMES, + fileFormat, true); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager @@ -1006,35 +1028,34 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (value == JalviewFileChooser.APPROVE_OPTION) { String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser + Cache.setProperty("LAST_DIRECTORY", chooser .getSelectedFile().getParent()); - String format = null; - if (chooser.getSelectedFormat() != null - && chooser.getSelectedFormat().equals("Jalview")) + FileFormatI format = null; + FileFormatI selectedFormat = chooser.getSelectedFormat(); + if (FileFormat.Jalview.equals(selectedFormat)) { - format = "Jalview"; + format = FileFormat.Jalview; } else { - format = new IdentifyFile().Identify(choice, FormatAdapter.FILE); + try + { + format = new IdentifyFile().identify(choice, DataSourceType.FILE); + } catch (FileFormatException e) + { + // format is null + } } if (viewport != null) { - new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, + new FileLoader().LoadFile(viewport, choice, DataSourceType.FILE, format); - // viewport.setShowSequenceFeatures(JSONFile.isSeqFeaturesEnabled()); - // AlignFrame af = viewport.getAlignPanel().alignFrame; - // if (af != null) - // { - // af.changeColour(JSONFile.getColourScheme()); - // af.setMenusForViewport(); - // } } else { - new FileLoader().LoadFile(choice, FormatAdapter.FILE, format); + new FileLoader().LoadFile(choice, DataSourceType.FILE, format); } } } @@ -1090,19 +1111,28 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (viewport != null) { - new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, - "Jalview"); + new FileLoader().LoadFile(viewport, url, DataSourceType.URL, + FileFormat.Jalview); } else { - new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview"); + new FileLoader().LoadFile(url, DataSourceType.URL, + FileFormat.Jalview); } } else { - String format = new IdentifyFile().Identify(url, FormatAdapter.URL); + FileFormatI format = null; + try + { + format = new IdentifyFile().identify(url, DataSourceType.URL); + } catch (FileFormatException e) + { + // TODO revise error handling, distinguish between + // URL not found and response not valid + } - if (format.equals("URL NOT FOUND")) + if (format == null) { JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.formatMessage("label.couldnt_locate", @@ -1115,11 +1145,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (viewport != null) { - new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format); + new FileLoader() + .LoadFile(viewport, url, DataSourceType.URL, format); } else { - new FileLoader().LoadFile(url, FormatAdapter.URL, format); + new FileLoader().LoadFile(url, DataSourceType.URL, format); } } } @@ -1171,6 +1202,13 @@ 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); } @@ -1201,6 +1239,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements // message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE); new Thread(new Runnable() { + @Override public void run() { new SplashScreen(true); @@ -1293,6 +1332,7 @@ 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++) { @@ -1303,6 +1343,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { } } + Jalview.setCurrentAlignFrame(null); System.out.println("ALL CLOSED"); if (v_client != null) { @@ -1319,6 +1360,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { ssm.resetAll(); } + System.gc(); } @Override @@ -1494,8 +1536,7 @@ 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[] { "jvp" }, new String[] { "Jalview Project" }, + Cache.getProperty("LAST_DIRECTORY"), "jvp", "Jalview Project", "Jalview Project"); chooser.setFileView(new JalviewFileView()); @@ -1511,6 +1552,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements new Thread(new Runnable() { + @Override public void run() { // TODO: refactor to Jalview desktop session controller action. @@ -1565,7 +1607,7 @@ 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[] { + Cache.getProperty("LAST_DIRECTORY"), new String[] { "jvp", "jar" }, new String[] { "Jalview Project", "Jalview Project (old)" }, "Jalview Project"); chooser.setFileView(new JalviewFileView()); @@ -1578,10 +1620,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements final File selectedFile = chooser.getSelectedFile(); setProjectFile(selectedFile); final String choice = selectedFile.getAbsolutePath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", + Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); new Thread(new Runnable() { + @Override public void run() { setProgressBar( @@ -1786,7 +1829,7 @@ 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) @@ -2101,6 +2144,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements sessit.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { if (dsktp.v_client == null) @@ -2108,6 +2152,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements Thread rthr = new Thread(new Runnable() { + @Override public void run() { dsktp.v_client = new VamsasApplication(dsktp, mysesid); @@ -2146,9 +2191,8 @@ 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 - new String[] { "Vamsas Document" }, "Vamsas Document"); + Cache.getProperty("LAST_DIRECTORY"), "vdj",// TODO: VAMSAS DOCUMENT EXTENSION is VDJ + "Vamsas Document", "Vamsas Document"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager @@ -2162,7 +2206,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements JPanel progpanel = addProgressPanel(MessageManager.formatMessage( "label.saving_vamsas_doc", new Object[] { choice.getName() })); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); + Cache.setProperty("LAST_DIRECTORY", choice.getParent()); String warnmsg = null; String warnttl = null; try @@ -2204,7 +2248,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ public void setVamsasUpdate(boolean b) { - jalview.bin.Cache.log.debug("Setting gui for Vamsas update " + Cache.log.debug("Setting gui for Vamsas update " + (b ? "in progress" : "finished")); if (vamUpdate != null) @@ -2239,6 +2283,84 @@ 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 what the actual links are - if it's just the default don't + // bother with the warning + Vector links = Preferences.sequenceURLLinks; + + // only need to check links if there is one with a + // SEQUENCE_ID which is not the default EMBL_EBI link + ListIterator li = links.listIterator(); + boolean check = false; + List urls = new ArrayList(); + while (li.hasNext()) + { + String link = li.next(); + if (link.contains(SEQUENCE_ID) && !link.equals(EMBLEBI_STRING)) + { + check = true; + int barPos = link.indexOf("|"); + String urlMsg = barPos == -1 ? link : link.substring(0, + barPos) + ": " + link.substring(barPos + 1); + urls.add(new JLabel(urlMsg)); + } + } + if (!check) + { + return; + } + + // ask user to 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); + for (JLabel url : urls) + { + msgPanel.add(url); + } + 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 for "don't show this again" + boolean showWarningAgain = !jcb.isSelected(); + Cache.setProperty("CHECKURLLINKS", + Boolean.valueOf(showWarningAgain).toString()); + } + }); + msgPanel.add(jcb); + + JOptionPane.showMessageDialog(Desktop.desktop, 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 @@ -2280,6 +2402,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements return showMemoryUsage; } + @Override public void run() { df = java.text.NumberFormat.getNumberInstance(); @@ -2346,24 +2469,6 @@ 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() - { - public void actionPerformed(ActionEvent e) - { - groovyShell_actionPerformed(); - } - }); - toolsMenu.add(groovyShell); - groovyShell.setVisible(true); - } - } - /** * Accessor method to quickly get all the AlignmentFrames loaded. * @@ -2371,6 +2476,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ public static AlignFrame[] getAlignFrames() { + if (Jalview.isHeadlessMode()) + { + // Desktop.desktop is null in headless mode + return new AlignFrame[] { Jalview.currentAlignFrame }; + } + JInternalFrame[] frames = Desktop.desktop.getAllFrames(); if (frames == null) @@ -2445,24 +2556,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ public void groovyShell_actionPerformed() { - // use reflection to avoid creating compilation dependency. - if (!jalview.bin.Cache.groovyJarsPresent()) - { - throw new Error( - MessageManager - .getString("error.implementation_error_cannot_create_groovyshell")); - } try { - Class gcClass = Desktop.class.getClassLoader().loadClass( - "groovy.ui.Console"); - 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"); - Object gc = gccons.newInstance(); - setvar.invoke(gc, new Object[] { "Jalview", this }); - run.invoke(gc); + openGroovyConsole(); } catch (Exception ex) { jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex); @@ -2475,6 +2571,93 @@ public class Desktop extends jalview.jbgui.GDesktop implements } /** + * Open the Groovy console + */ + void openGroovyConsole() + { + if (groovyConsole == null) + { + groovyConsole = new groovy.ui.Console(); + groovyConsole.setVariable("Jalview", this); + groovyConsole.run(); + + /* + * We allow only one console at a time, so that AlignFrame menu option + * 'Calculate | Run Groovy script' is unambiguous. + * Disable 'Groovy Console', and enable 'Run script', when the console is + * opened, and the reverse when it is closed + */ + Window window = (Window) groovyConsole.getFrame(); + window.addWindowListener(new WindowAdapter() + { + @Override + public void windowClosed(WindowEvent e) + { + /* + * rebind CMD-Q from Groovy Console to Jalview Quit + */ + addQuitHandler(); + enableExecuteGroovy(false); + } + }); + } + + /* + * show Groovy console window (after close and reopen) + */ + ((Window) groovyConsole.getFrame()).setVisible(true); + + /* + * if we got this far, enable 'Run Groovy' in AlignFrame menus + * and disable opening a second console + */ + enableExecuteGroovy(true); + } + + /** + * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this + * binding when opened + */ + protected void addQuitHandler() + { + getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( + KeyStroke.getKeyStroke(KeyEvent.VK_Q, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask()), "Quit"); + getRootPane().getActionMap().put("Quit", new AbstractAction() + { + @Override + public void actionPerformed(ActionEvent e) + { + quit(); + } + }); + } + + /** + * Enable or disable 'Run Groovy script' in AlignFrame calculate menus + * + * @param enabled + * true if Groovy console is open + */ + public void enableExecuteGroovy(boolean enabled) + { + /* + * disable opening a second Groovy console + * (or re-enable when the console is closed) + */ + groovyShell.setEnabled(!enabled); + + AlignFrame[] alignFrames = getAlignFrames(); + if (alignFrames != null) + { + for (AlignFrame af : alignFrames) + { + af.setGroovyEnabled(enabled); + } + } + } + + /** * Progress bars managed by the IProgressIndicator method. */ private Hashtable progressBars; @@ -2486,6 +2669,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) */ + @Override public void setProgressBar(String message, long id) { if (progressBars == null) @@ -2515,6 +2699,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @see jalview.gui.IProgressIndicator#registerHandler(long, * jalview.gui.IProgressIndicatorHandler) */ + @Override public void registerHandler(final long id, final IProgressIndicatorHandler handler) { @@ -2535,6 +2720,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements cancel.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { handler.cancelActivity(id); @@ -2693,6 +2879,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements // only run if we aren't already displaying one of these. addDialogThread(serviceChangedDialog = new Runnable() { + @Override public void run() { @@ -2776,6 +2963,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { new Thread(new Runnable() { + @Override public void run() { try @@ -2865,6 +3053,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ private java.util.concurrent.Semaphore block = new Semaphore(0); + private static groovy.ui.Console groovyConsole; + /** * add another dialog thread to the queue * @@ -2874,6 +3064,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { dialogExecutor.submit(new Runnable() { + @Override public void run() { if (dialogPause) @@ -2917,7 +3108,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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"); + + ".eps"), "View of desktop", null, 0, false); try { paintAll(im.getGraphics()); @@ -2966,25 +3157,39 @@ public class Desktop extends jalview.jbgui.GDesktop implements * AlignmentPanel objects, including their AlignmentViewports, so the * cdna/protein relationships between the viewports is carried over to the * new split frames. + * + * explodedGeometry holds the (x, y) position of the previously exploded + * SplitFrame, and the (width, height) of the AlignFrame component */ AlignmentPanel topPanel = (AlignmentPanel) topPanels.get(i); AlignFrame newTopFrame = new AlignFrame(topPanel); newTopFrame.setSize(oldTopFrame.getSize()); newTopFrame.setVisible(true); + Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport()) + .getExplodedGeometry(); + if (geometry != null) + { + newTopFrame.setSize(geometry.getSize()); + } + AlignmentPanel bottomPanel = (AlignmentPanel) bottomPanels.get(i); AlignFrame newBottomFrame = new AlignFrame(bottomPanel); newBottomFrame.setSize(oldBottomFrame.getSize()); newBottomFrame.setVisible(true); + geometry = ((AlignViewport) bottomPanel.getAlignViewport()) + .getExplodedGeometry(); + if (geometry != null) + { + newBottomFrame.setSize(geometry.getSize()); + } + 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); + splitFrame.setLocation(geometry.getLocation()); } Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1); } @@ -3007,10 +3212,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ public void gatherViews(GSplitFrame source) { + /* + * special handling of explodedGeometry for a view within a SplitFrame: - it + * holds the (x, y) position of the enclosing SplitFrame, and the (width, + * height) of the AlignFrame component + */ AlignFrame myTopFrame = (AlignFrame) source.getTopFrame(); AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame(); - myTopFrame.viewport.setExplodedGeometry(source.getBounds()); - myBottomFrame.viewport.setExplodedGeometry(source.getBounds()); + myTopFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(), + source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight())); + myBottomFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(), + source.getY(), myBottomFrame.getWidth(), myBottomFrame + .getHeight())); myTopFrame.viewport.setGatherViewsHere(true); myBottomFrame.viewport.setGatherViewsHere(true); String topViewId = myTopFrame.viewport.getSequenceSetId(); @@ -3035,10 +3248,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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); + topPanel.av.setExplodedGeometry(new Rectangle(sf.getLocation(), + topFrame.getSize())); + bottomPanel.av.setExplodedGeometry(new Rectangle(sf + .getLocation(), bottomFrame.getSize())); myTopFrame.addAlignmentPanel(topPanel, false); myBottomFrame.addAlignmentPanel(bottomPanel, false); } @@ -3057,17 +3270,107 @@ 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; - } + 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(DataSourceType.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(DataSourceType.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(DataSourceType.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(DataSourceType.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"); + } + } + } + } + } + } }