X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=516c33fc28bc18242786a3a7f436256dae795217;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=9e5bbff6372b80145a92a6b7ee94b2855cf77904;hpb=a40bbc57a85658544e2e5d7cc2a7596b762566dc;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 9e5bbff..516c33f 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -23,10 +23,10 @@ package jalview.gui; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; +import jalview.bin.Jalview; import jalview.io.FileLoader; import jalview.io.FormatAdapter; import jalview.io.IdentifyFile; -import jalview.io.JSONFile; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.jbgui.GSplitFrame; @@ -34,6 +34,7 @@ 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; @@ -168,8 +169,6 @@ 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; @@ -266,10 +265,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements delegate.openFrame(f); } + @Override public void resizeFrame(JComponent f, int newX, int newY, int newWidth, int newHeight) { - Rectangle b = desktop.getBounds(); if (newY < 0) { newY = 0; @@ -308,6 +307,10 @@ 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()); @@ -408,7 +411,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void run() { Cache.log.debug("Filechooser init thread started."); - JalviewFileChooser chooser = new JalviewFileChooser( + new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY"), jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS, jalview.io.AppletFormatAdapter.READABLE_FNAMES, @@ -472,6 +475,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements }); } + @Override protected void showNews_actionPerformed(ActionEvent e) { showNews(showNews.isSelected()); @@ -489,12 +493,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements @Override public void run() { - long instance = System.currentTimeMillis(); + long now = System.currentTimeMillis(); Desktop.instance.setProgressBar( - MessageManager.getString("status.refreshing_news"), - instance); + MessageManager.getString("status.refreshing_news"), now); jvnews.refreshNews(); - Desktop.instance.setProgressBar(null, instance); + Desktop.instance.setProgressBar(null, now); jvnews.showNews(); } }).start(); @@ -753,8 +756,13 @@ 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 @@ -886,6 +894,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { } + @Override public void dropActionChanged(DropTargetDragEvent evt) { } @@ -989,6 +998,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) { JalviewFileChooser chooser = new JalviewFileChooser( @@ -1025,13 +1035,13 @@ 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(); - } + // viewport.setShowSequenceFeatures(JSONFile.isSeqFeaturesEnabled()); + // AlignFrame af = viewport.getAlignPanel().alignFrame; + // if (af != null) + // { + // af.changeColour(JSONFile.getColourScheme()); + // af.setMenusForViewport(); + // } } else { @@ -1046,6 +1056,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override public void inputURLMenuItem_actionPerformed(AlignViewport viewport) { // This construct allows us to have a wider textfield @@ -1106,8 +1117,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.formatMessage("label.couldnt_locate", - new Object[] - { url }), MessageManager + new Object[] { url }), MessageManager .getString("label.url_not_found"), JOptionPane.WARNING_MESSAGE); @@ -1126,15 +1136,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements } /** - * DOCUMENT ME! + * Opens the CutAndPaste window for the user to paste an alignment in to * - * @param e - * DOCUMENT ME! + * @param viewPanel + * - if not null, the pasted alignment is added to the current + * alignment; if null, to a new alignment window */ - public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport) + @Override + public void inputTextboxMenuItem_actionPerformed( + AlignmentViewPanel viewPanel) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); - cap.setForInput(viewport); + cap.setForInput(viewPanel); Desktop.addInternalFrame(cap, MessageManager.getString("label.cut_paste_alignmen_file"), true, 600, 500); @@ -1143,6 +1156,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements /* * Exit the program */ + @Override public void quit() { Dimension screen = Toolkit.getDefaultToolkit().getScreenSize(); @@ -1167,7 +1181,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { dialogExecutor.shutdownNow(); } - + closeAll_actionPerformed(null); System.exit(0); } @@ -1189,6 +1203,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override public void aboutMenuItem_actionPerformed(ActionEvent e) { // StringBuffer message = getAboutMessage(false); @@ -1275,6 +1290,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override public void documentationMenuItem_actionPerformed(ActionEvent e) { try @@ -1285,6 +1301,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } + @Override public void closeAll_actionPerformed(ActionEvent e) { JInternalFrame[] frames = desktop.getAllFrames(); @@ -1301,15 +1318,27 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (v_client != null) { // TODO clear binding to vamsas document objects on close_all + } + /* + * reset state of singleton objects as appropriate (clear down session state + * when all windows are closed) + */ + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(this); + if (ssm != null) + { + ssm.resetAll(); } } + @Override public void raiseRelated_actionPerformed(ActionEvent e) { reorderAssociatedWindows(false, false); } + @Override public void minimizeAssociated_actionPerformed(ActionEvent e) { reorderAssociatedWindows(true, false); @@ -1326,6 +1355,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @seejalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event. * ActionEvent) */ + @Override protected void garbageCollect_actionPerformed(ActionEvent e) { // We simply collect the garbage @@ -1341,6 +1371,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent * ) */ + @Override protected void showMemusage_actionPerformed(ActionEvent e) { desktop.showMemoryUsage(showMemusage.isSelected()); @@ -1353,6 +1384,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * jalview.jbgui.GDesktop#showConsole_actionPerformed(java.awt.event.ActionEvent * ) */ + @Override protected void showConsole_actionPerformed(ActionEvent e) { showConsole(showConsole.isSelected()); @@ -1457,6 +1489,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override protected void preferences_actionPerformed(ActionEvent e) { new Preferences(); @@ -1468,12 +1501,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override public void saveState_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "jvp" }, new String[] - { "Jalview Project" }, "Jalview Project"); + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), + new String[] { "jvp" }, new String[] { "Jalview Project" }, + "Jalview Project"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.save_state")); @@ -1486,17 +1520,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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() { - + // TODO: refactor to Jalview desktop session controller action. setProgressBar(MessageManager.formatMessage( - "label.saving_jalview_project", new Object[] - { choice.getName() }), choice.hashCode()); + "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 @@ -1515,8 +1546,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements ex); JOptionPane.showMessageDialog(me, MessageManager.formatMessage( "label.error_whilst_saving_current_state_to", - new Object[] - { choice.getName() }), MessageManager + new Object[] { choice.getName() }), MessageManager .getString("label.couldnt_save_project"), JOptionPane.WARNING_MESSAGE); } @@ -1526,32 +1556,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } - /** - * 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; @@ -1568,13 +1572,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override public void loadState_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "jvp", "jar" }, new String[] - { "Jalview Project", "Jalview Project (old)" }, - "Jalview Project"); + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] { + "jvp", "jar" }, new String[] { "Jalview Project", + "Jalview Project (old)" }, "Jalview Project"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.restore_state")); @@ -1591,9 +1595,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements { public void run() { - setProgressBar(MessageManager.formatMessage( - "label.loading_jalview_project", new Object[] - { choice }), choice.hashCode()); + setProgressBar( + MessageManager.formatMessage( + "label.loading_jalview_project", + new Object[] { choice }), choice.hashCode()); try { new Jalview2XML().loadJalviewAlign(choice); @@ -1607,8 +1612,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements JOptionPane.showMessageDialog(Desktop.desktop, MessageManager .formatMessage( "label.error_whilst_loading_project_from", - new Object[] - { choice }), MessageManager + new Object[] { choice }), MessageManager .getString("label.couldnt_load_project"), JOptionPane.WARNING_MESSAGE); } @@ -1618,6 +1622,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } + @Override public void inputSequence_actionPerformed(ActionEvent e) { new SequenceFetcher(this); @@ -1632,8 +1637,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (fileLoadingCount == 0) { fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage( - "label.loading_file", new Object[] - { fileName }))); + "label.loading_file", new Object[] { fileName }))); } fileLoadingCount++; } @@ -1727,7 +1731,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements { for (AlignmentPanel ap : af.alignPanels) { - if (alignmentId==null || alignmentId.equals(ap.av.getSequenceSetId())) + if (alignmentId == null + || alignmentId.equals(ap.av.getSequenceSetId())) { aps.add(ap); } @@ -1758,7 +1763,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements for (AlignFrame afr : frames) { - if (sequenceSetId==null || afr.getViewport().getSequenceSetId().equals(sequenceSetId)) + if (sequenceSetId == null + || afr.getViewport().getSequenceSetId() + .equals(sequenceSetId)) { if (afr.alignPanels != null) { @@ -1870,6 +1877,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements jalview.gui.VamsasApplication v_client = null; + @Override public void vamsasImport_actionPerformed(ActionEvent e) { if (v_client == null) @@ -1896,8 +1904,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements Desktop.desktop, MessageManager.formatMessage( "label.couldnt_import_as_vamsas_session", - new Object[] - { fle }), + new Object[] { fle }), MessageManager .getString("label.vamsas_document_import_failed"), JOptionPane.ERROR_MESSAGE); @@ -1974,16 +1981,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements } setProgressBar(MessageManager.formatMessage( - "status.importing_vamsas_session_from", new Object[] - { file.getName() }), file.hashCode()); + "status.importing_vamsas_session_from", + new Object[] { file.getName() }), file.hashCode()); try { v_client = new jalview.gui.VamsasApplication(this, file, null); } catch (Exception ex) { setProgressBar(MessageManager.formatMessage( - "status.importing_vamsas_session_from", new Object[] - { file.getName() }), file.hashCode()); + "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; @@ -1991,8 +1998,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements setupVamsasConnectedGui(); v_client.initial_update(); // TODO: thread ? setProgressBar(MessageManager.formatMessage( - "status.importing_vamsas_session_from", new Object[] - { file.getName() }), file.hashCode()); + "status.importing_vamsas_session_from", + new Object[] { file.getName() }), file.hashCode()); return v_client.inSession(); } @@ -2015,6 +2022,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements return (v_client.inSession()); } + @Override public void vamsasStart_actionPerformed(ActionEvent e) { if (v_client == null) @@ -2063,6 +2071,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements .getString("label.new_vamsas_session")); } + @Override public void vamsasStop_actionPerformed(ActionEvent e) { if (v_client != null) @@ -2097,8 +2106,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements JMenuItem sessit = new JMenuItem(); sessit.setText(sess[i]); sessit.setToolTipText(MessageManager.formatMessage( - "label.connect_to_session", new Object[] - { sess[i] })); + "label.connect_to_session", new Object[] { sess[i] })); final Desktop dsktp = this; final String mysesid = sess[i]; sessit.addActionListener(new ActionListener() @@ -2143,6 +2151,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } + @Override public void vamsasSave_actionPerformed(ActionEvent e) { if (v_client != null) @@ -2150,8 +2159,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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"); + new String[] { "Vamsas Document" }, "Vamsas Document"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager @@ -2163,8 +2171,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements { java.io.File choice = chooser.getSelectedFile(); JPanel progpanel = addProgressPanel(MessageManager.formatMessage( - "label.saving_vamsas_doc", new Object[] - { choice.getName() })); + "label.saving_vamsas_doc", + new Object[] { choice.getName() })); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); String warnmsg = null; String warnttl = null; @@ -2268,10 +2276,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements showMemoryUsage(showMemoryUsage); } - public void showMemoryUsage(boolean showMemoryUsage) + public void showMemoryUsage(boolean showMemory) { - this.showMemoryUsage = showMemoryUsage; - if (showMemoryUsage) + this.showMemoryUsage = showMemory; + if (showMemory) { Thread worker = new Thread(this); worker.start(); @@ -2316,6 +2324,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } + @Override public void paintComponent(Graphics g) { if (showMemoryUsage && g != null && df != null) @@ -2329,9 +2338,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements { g.drawString(MessageManager.formatMessage( "label.memory_stats", - new Object[] - { df.format(totalFreeMemory), df.format(maxMemory), - df.format(percentUsage) }), 10, + new Object[] { df.format(totalFreeMemory), + df.format(maxMemory), df.format(percentUsage) }), 10, getHeight() - fm.getHeight()); } } @@ -2359,7 +2367,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { public void actionPerformed(ActionEvent e) { - groovyShell_actionPerformed(e); + groovyShell_actionPerformed(); } }); toolsMenu.add(groovyShell); @@ -2374,6 +2382,12 @@ 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[] { currentAlignFrame }; + } + JInternalFrame[] frames = Desktop.desktop.getAllFrames(); if (frames == null) @@ -2446,7 +2460,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements /** * Add Groovy Support to Jalview */ - public void groovyShell_actionPerformed(ActionEvent e) + public void groovyShell_actionPerformed() { // use reflection to avoid creating compilation dependency. if (!jalview.bin.Cache.groovyJarsPresent()) @@ -2461,12 +2475,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements "groovy.ui.Console"); Constructor gccons = gcClass.getConstructor(); java.lang.reflect.Method setvar = gcClass.getMethod("setVariable", - new Class[] - { String.class, Object.class }); + 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 }); + setvar.invoke(gc, new Object[] { "Jalview", this }); run.invoke(gc); } catch (Exception ex) { @@ -2501,12 +2513,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (progressBars.get(new Long(id)) != null) { - JPanel progressPanel = progressBars.remove(new Long(id)); + JPanel panel = progressBars.remove(new Long(id)); if (progressBarHandlers.contains(new Long(id))) { progressBarHandlers.remove(new Long(id)); } - removeProgressPanel(progressPanel); + removeProgressPanel(panel); } else { @@ -2523,7 +2535,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void registerHandler(final long id, final IProgressIndicatorHandler handler) { - if (progressBarHandlers == null || !progressBars.contains(new Long(id))) + if (progressBarHandlers == null + || !progressBars.containsKey(new Long(id))) { throw new Error( MessageManager @@ -2543,9 +2556,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements { handler.cancelActivity(id); us.setProgressBar(MessageManager.formatMessage( - "label.cancelled_params", new Object[] - { ((JLabel) progressPanel.getComponent(0)).getText() }), - id); + "label.cancelled_params", + new Object[] { ((JLabel) progressPanel.getComponent(0)) + .getText() }), id); } }); progressPanel.add(cancel, BorderLayout.EAST); @@ -2567,8 +2580,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements } /** - * 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. + * 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 @@ -2577,8 +2591,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (desktop != null) { - AlignmentPanel[] aps = getAlignmentPanels(viewport - .getSequenceSetId()); + AlignmentPanel[] aps = getAlignmentPanels(viewport.getSequenceSetId()); for (int panel = 0; aps != null && panel < aps.length; panel++) { if (aps[panel] != null && aps[panel].av == viewport) @@ -2645,28 +2658,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements (t0 = new Thread(discoverer)).start(); } - // ENFIN services are EOLed as of Jalview 2.8.1 release - if (false) - { - 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) - { - Cache.log - .info("Exception when trying to launch Envision2 workflow discovery.", - e); - Cache.log.info(e.getStackTrace()); - } - } - if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { if (jalview.ws.jws2.Jws2Discoverer.getDiscoverer().isRunning()) @@ -2809,8 +2800,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (progress != null) { progress.setProgressBar(MessageManager.formatMessage( - "status.opening_params", new Object[] - { url }), this.hashCode()); + "status.opening_params", new Object[] { url }), this + .hashCode()); } jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) @@ -2959,7 +2950,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements } /** - * Explode the views in the given frame into separate AlignFrame windows. + * Explode the views in the given SplitFrame into separate SplitFrame windows. + * This respects (remembers) any previous 'exploded geometry' i.e. the size + * and location last time the view was expanded (if any). However it does not + * remember the split pane divider location - this is set to match the + * 'exploding' frame. * * @param sf */ @@ -2988,27 +2983,39 @@ 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(new Dimension(AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT)); + 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(new Dimension(AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT)); + 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); } @@ -3031,15 +3038,23 @@ 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(); String bottomViewId = myBottomFrame.viewport.getSequenceSetId(); - + JInternalFrame[] frames = desktop.getAllFrames(); for (JInternalFrame frame : frames) { @@ -3059,15 +3074,15 @@ 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); } } - + if (gatherThis) { topFrame.getAlignPanels().clear(); @@ -3094,5 +3109,4 @@ public class Desktop extends jalview.jbgui.GDesktop implements Desktop.currentAlignFrame = currentAlignFrame; } - }