X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=5c45232b6deac2361b75512773ec8dd24eacab21;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=1228965ca4010379f5049e7d5ab6b6b90d4fb048;hpb=e2d6753e8cf3c5eaf8bccf34f4f5e9d651e9cb8e;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 1228965..5c45232 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) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -167,8 +167,6 @@ 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; @@ -265,10 +263,10 @@ 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; @@ -407,7 +405,7 @@ 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, @@ -471,6 +469,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements }); } + @Override protected void showNews_actionPerformed(ActionEvent e) { showNews(showNews.isSelected()); @@ -488,12 +487,11 @@ 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(); @@ -885,6 +883,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { } + @Override public void dropActionChanged(DropTargetDragEvent evt) { } @@ -988,6 +987,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) { JalviewFileChooser chooser = new JalviewFileChooser( @@ -1045,6 +1045,7 @@ 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 @@ -1105,8 +1106,7 @@ 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); @@ -1125,15 +1125,18 @@ 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); @@ -1142,6 +1145,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements /* * Exit the program */ + @Override public void quit() { Dimension screen = Toolkit.getDefaultToolkit().getScreenSize(); @@ -1166,7 +1170,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { dialogExecutor.shutdownNow(); } - + closeAll_actionPerformed(null); System.exit(0); } @@ -1188,6 +1192,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override public void aboutMenuItem_actionPerformed(ActionEvent e) { // StringBuffer message = getAboutMessage(false); @@ -1274,6 +1279,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override public void documentationMenuItem_actionPerformed(ActionEvent e) { try @@ -1284,6 +1290,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } + @Override public void closeAll_actionPerformed(ActionEvent e) { JInternalFrame[] frames = desktop.getAllFrames(); @@ -1300,15 +1307,27 @@ 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); @@ -1325,6 +1344,7 @@ 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 @@ -1340,6 +1360,7 @@ 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()); @@ -1352,6 +1373,7 @@ 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()); @@ -1456,6 +1478,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override protected void preferences_actionPerformed(ActionEvent e) { new Preferences(); @@ -1467,12 +1490,13 @@ 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")); @@ -1485,17 +1509,14 @@ 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 @@ -1514,8 +1535,7 @@ 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); } @@ -1525,32 +1545,6 @@ 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; @@ -1567,13 +1561,13 @@ 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")); @@ -1590,9 +1584,10 @@ 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); @@ -1606,8 +1601,7 @@ 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); } @@ -1617,6 +1611,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } + @Override public void inputSequence_actionPerformed(ActionEvent e) { new SequenceFetcher(this); @@ -1631,8 +1626,7 @@ 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++; } @@ -1726,7 +1720,8 @@ 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); } @@ -1757,7 +1752,9 @@ 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) { @@ -1869,6 +1866,7 @@ 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) @@ -1895,8 +1893,7 @@ 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); @@ -1973,16 +1970,16 @@ 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; @@ -1990,8 +1987,8 @@ 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(); } @@ -2014,6 +2011,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements return (v_client.inSession()); } + @Override public void vamsasStart_actionPerformed(ActionEvent e) { if (v_client == null) @@ -2062,6 +2060,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements .getString("label.new_vamsas_session")); } + @Override public void vamsasStop_actionPerformed(ActionEvent e) { if (v_client != null) @@ -2096,8 +2095,7 @@ 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() @@ -2142,6 +2140,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } + @Override public void vamsasSave_actionPerformed(ActionEvent e) { if (v_client != null) @@ -2149,8 +2148,7 @@ 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 @@ -2162,8 +2160,8 @@ 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; @@ -2267,10 +2265,10 @@ 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(); @@ -2315,6 +2313,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } + @Override public void paintComponent(Graphics g) { if (showMemoryUsage && g != null && df != null) @@ -2328,9 +2327,8 @@ 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()); } } @@ -2358,7 +2356,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { public void actionPerformed(ActionEvent e) { - groovyShell_actionPerformed(e); + groovyShell_actionPerformed(); } }); toolsMenu.add(groovyShell); @@ -2445,7 +2443,7 @@ 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()) @@ -2460,12 +2458,10 @@ 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) { @@ -2500,12 +2496,12 @@ 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 { @@ -2522,7 +2518,8 @@ 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 @@ -2542,9 +2539,9 @@ 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); @@ -2566,8 +2563,9 @@ 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 @@ -2576,8 +2574,7 @@ 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) @@ -2644,28 +2641,6 @@ 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()) @@ -2808,8 +2783,8 @@ 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) @@ -3038,7 +3013,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements myBottomFrame.viewport.setGatherViewsHere(true); String topViewId = myTopFrame.viewport.getSequenceSetId(); String bottomViewId = myBottomFrame.viewport.getSequenceSetId(); - + JInternalFrame[] frames = desktop.getAllFrames(); for (JInternalFrame frame : frames) { @@ -3066,7 +3041,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements myBottomFrame.addAlignmentPanel(bottomPanel, false); } } - + if (gatherThis) { topFrame.getAlignPanels().clear(); @@ -3083,15 +3058,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements } - // public static AlignFrame getCurrentAlignFrame() - // { - // return currentAlignFrame; - // } - // - // public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) - // { - // Desktop.currentAlignFrame = currentAlignFrame; - // } + public static AlignFrame getCurrentAlignFrame() + { + return currentAlignFrame; + } + public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) + { + Desktop.currentAlignFrame = currentAlignFrame; + } }