From 9c74c965d0fb1b2ef6c4c512a62207c4c695a7bd Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 3 Oct 2012 10:48:43 +0100 Subject: [PATCH] formatting --- src/jalview/gui/Desktop.java | 256 +++++++++++++++++++++++++----------------- 1 file changed, 150 insertions(+), 106 deletions(-) diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 294beac..996aad1 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -98,7 +98,8 @@ import javax.swing.event.HyperlinkEvent.EventType; * @version $Revision: 1.155 $ */ public class Desktop extends jalview.jbgui.GDesktop implements - DropTargetListener, ClipboardOwner, IProgressIndicator, jalview.api.StructureSelectionManagerProvider + DropTargetListener, ClipboardOwner, IProgressIndicator, + jalview.api.StructureSelectionManagerProvider { private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); @@ -106,7 +107,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements /** * news reader - null if it was never started. */ - private BlogReader jvnews=null; + private BlogReader jvnews = null; /** * @param listener @@ -211,9 +212,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void dragFrame(JComponent f, int newX, int newY) { - if (newY<0) + if (newY < 0) { - newY=0; + newY = 0; } delegate.dragFrame(f, newX, newY); } @@ -251,10 +252,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void resizeFrame(JComponent f, int newX, int newY, int newWidth, int newHeight) { - Rectangle b=desktop.getBounds(); - if (newY<0) + Rectangle b = desktop.getBounds(); + if (newY < 0) { - newY=0; + newY = 0; } delegate.resizeFrame(f, newX, newY, newWidth, newHeight); } @@ -294,18 +295,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements desktop.setBackground(Color.white); getContentPane().setLayout(new BorderLayout()); // alternate config - have scrollbars - see notes in JAL-153 - //JScrollPane sp = new JScrollPane(); - //sp.getViewport().setView(desktop); - //getContentPane().add(sp, BorderLayout.CENTER); + // JScrollPane sp = new JScrollPane(); + // sp.getViewport().setView(desktop); + // getContentPane().add(sp, BorderLayout.CENTER); getContentPane().add(desktop, BorderLayout.CENTER); desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE); - - + // This line prevents Windows Look&Feel resizing all new windows to maximum // if previous window was maximised desktop.setDesktopManager(new MyDesktopManager( new DefaultDesktopManager())); - + Rectangle dims = getLastKnownDimensions(""); if (dims != null) { @@ -331,7 +331,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements showConsole(showjconsole); showNews.setVisible(false); - + this.addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent evt) @@ -341,7 +341,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements }); MouseAdapter ma; - this.addMouseListener(ma=new MouseAdapter() + this.addMouseListener(ma = new MouseAdapter() { public void mousePressed(MouseEvent evt) { @@ -352,17 +352,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements } }); desktop.addMouseListener(ma); - + this.addFocusListener(new FocusListener() { - + @Override public void focusLost(FocusEvent e) { // TODO Auto-generated method stub - + } - + @Override public void focusGained(FocusEvent e) { @@ -417,7 +417,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements { final Desktop me = this; // Thread off the news reader, in case there are connection problems. - addDialogThread(new Runnable() { + addDialogThread(new Runnable() + { @Override public void run() { @@ -429,22 +430,25 @@ public class Desktop extends jalview.jbgui.GDesktop implements } }); } + protected void showNews_actionPerformed(ActionEvent e) { showNews(showNews.isSelected()); } + void showNews(boolean visible) { { - Cache.log.debug((visible?"Showing":"Hiding")+" news."); + Cache.log.debug((visible ? "Showing" : "Hiding") + " news."); showNews.setSelected(visible); if (visible && !jvnews.isVisible()) { - new Thread(new Runnable() { + new Thread(new Runnable() + { @Override public void run() { - long instance=System.currentTimeMillis(); + long instance = System.currentTimeMillis(); Desktop.instance.setProgressBar("Refreshing news", instance); jvnews.refreshNews(); Desktop.instance.setProgressBar(null, instance); @@ -711,17 +715,17 @@ 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) { @@ -732,7 +736,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { } } - + @Override public void mouseEntered(MouseEvent e) { @@ -743,11 +747,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements { } } - + @Override public void mouseClicked(MouseEvent e) { - + } }); @@ -761,10 +765,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements frame.requestFocus(); } catch (java.beans.PropertyVetoException ve) { - } - catch (java.lang.ClassCastException cex) + } catch (java.lang.ClassCastException cex) { - Cache.log.warn("Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869",cex); + Cache.log + .warn("Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869", + cex); } } @@ -1041,16 +1046,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds()); jconsole.stopConsole(); } - if (jvnews!=null) + if (jvnews != null) { storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds()); - + } - if (dialogExecutor!=null) + if (dialogExecutor != null) { dialogExecutor.shutdownNow(); } - + System.exit(0); } @@ -1074,11 +1079,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ public void aboutMenuItem_actionPerformed(ActionEvent e) { -// StringBuffer message = getAboutMessage(false); -// JOptionPane.showInternalMessageDialog(Desktop.desktop, -// -// message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE); - new Thread(new Runnable() { public void run() {new SplashScreen(true);}}).start(); + // StringBuffer message = getAboutMessage(false); + // JOptionPane.showInternalMessageDialog(Desktop.desktop, + // + // message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE); + new Thread(new Runnable() + { + public void run() + { + new SplashScreen(true); + } + }).start(); } public StringBuffer getAboutMessage(boolean shortv) @@ -1374,28 +1385,31 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void run() { - setProgressBar("Saving jalview project " + choice.getName(), - choice.hashCode()); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); - // TODO catch and handle errors for savestate - // TODO prevent user from messing with the Desktop whilst we're saving - try - { - new Jalview2XML().SaveState(choice); - } catch (OutOfMemoryError oom) - { - new OOMWarning( - "Whilst saving current state to " + choice.getName(), oom); - } catch (Exception ex) - { - Cache.log - .error("Problems whilst trying to save to " - + choice.getName(), ex); - JOptionPane.showMessageDialog(me, - "Error whilst saving current state to " + choice.getName(), - "Couldn't save project", JOptionPane.WARNING_MESSAGE); - } - setProgressBar(null, choice.hashCode()); + setProgressBar("Saving jalview project " + choice.getName(), + choice.hashCode()); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", + choice.getParent()); + // TODO catch and handle errors for savestate + // TODO prevent user from messing with the Desktop whilst we're saving + try + { + new Jalview2XML().SaveState(choice); + } catch (OutOfMemoryError oom) + { + new OOMWarning("Whilst saving current state to " + + choice.getName(), oom); + } catch (Exception ex) + { + Cache.log.error( + "Problems whilst trying to save to " + choice.getName(), + ex); + JOptionPane.showMessageDialog( + me, + "Error whilst saving current state to " + + choice.getName(), "Couldn't save project", + JOptionPane.WARNING_MESSAGE); + } + setProgressBar(null, choice.hashCode()); } }).start(); } @@ -1455,12 +1469,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements } JPanel progressPanel; - ArrayList fileLoadingPanels=new ArrayList(); + + ArrayList fileLoadingPanels = new ArrayList(); + public void startLoading(final String fileName) { if (fileLoadingCount == 0) { - fileLoadingPanels.add(addProgressPanel("Loading File: " + fileName + " ")); + fileLoadingPanels.add(addProgressPanel("Loading File: " + fileName + + " ")); } fileLoadingCount++; } @@ -1469,11 +1486,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (progressPanel == null) { - progressPanel = new JPanel(new GridLayout(1,1)); + progressPanel = new JPanel(new GridLayout(1, 1)); totalProgressCount = 0; instance.getContentPane().add(progressPanel, BorderLayout.SOUTH); } - JPanel thisprogress=new JPanel(new BorderLayout(10,5)); + JPanel thisprogress = new JPanel(new BorderLayout(10, 5)); JProgressBar progressBar = new JProgressBar(); progressBar.setIndeterminate(true); @@ -1481,7 +1498,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements thisprogress.add(progressBar, BorderLayout.CENTER); progressPanel.add(thisprogress); - ((GridLayout)progressPanel.getLayout()).setRows(((GridLayout)progressPanel.getLayout()).getRows()+1); + ((GridLayout) progressPanel.getLayout()) + .setRows(((GridLayout) progressPanel.getLayout()).getRows() + 1); ++totalProgressCount; instance.validate(); return thisprogress; @@ -1495,7 +1513,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { progressPanel.remove(progbar); GridLayout gl = (GridLayout) progressPanel.getLayout(); - gl.setRows(gl.getRows()-1); + gl.setRows(gl.getRows() - 1); if (--totalProgressCount < 1) { this.getContentPane().remove(progressPanel); @@ -1549,9 +1567,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements AlignFrame af = (AlignFrame) frames[t]; for (int a = 0; a < af.alignPanels.size(); a++) { - if (alignmentId - .equals(((AlignmentPanel) af.alignPanels.elementAt(a)).av - .getSequenceSetId())) + if (alignmentId.equals(((AlignmentPanel) af.alignPanels + .elementAt(a)).av.getSequenceSetId())) { aps.add(af.alignPanels.elementAt(a)); } @@ -2131,11 +2148,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements } /** - * fixes stacking order after a modal dialog to ensure windows that should be on top actually are + * fixes stacking order after a modal dialog to ensure windows that should be + * on top actually are */ public void relayerWindows() { - + } protected JMenuItem groovyShell; @@ -2197,6 +2215,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements avp.clear(); return afs; } + public AppJmol[] getJmols() { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); @@ -2274,8 +2293,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements /** * Progress bars managed by the IProgressIndicator method. */ - private Hashtable progressBars; - private Hashtable progressBarHandlers; + private Hashtable progressBars; + + private Hashtable progressBarHandlers; /* * (non-Javadoc) @@ -2286,14 +2306,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (progressBars == null) { - progressBars = new Hashtable(); - progressBarHandlers = new Hashtable(); + progressBars = new Hashtable(); + progressBarHandlers = new Hashtable(); } if (progressBars.get(new Long(id)) != null) { - JPanel progressPanel = progressBars - .remove(new Long(id)); + JPanel progressPanel = progressBars.remove(new Long(id)); if (progressBarHandlers.contains(new Long(id))) { progressBarHandlers.remove(new Long(id)); @@ -2427,7 +2446,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements // register PCS handler for desktop. discoverer.addPropertyChangeListener(changeSupport); } - // JAL-940 - disabled JWS1 service configuration - always start discoverer until we phase out completely + // JAL-940 - disabled JWS1 service configuration - always start discoverer + // until we phase out completely if (true) { (t0 = new Thread(discoverer)).start(); @@ -2458,9 +2478,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements } t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer( changeSupport); - + } - Thread t3=null; + Thread t3 = null; { // TODO: do rest service discovery } @@ -2572,12 +2592,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements { showUrl(url, Desktop.instance); } + /** * Like showUrl but allows progress handler to be specified + * * @param url - * @param progress (null) or object implementing IProgressIndicator + * @param progress + * (null) or object implementing IProgressIndicator */ - public static void showUrl(final String url, final IProgressIndicator progress) + public static void showUrl(final String url, + final IProgressIndicator progress) { new Thread(new Runnable() { @@ -2585,8 +2609,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements { try { - if (progress!=null) { - progress.setProgressBar("Opening "+url, this.hashCode()); + if (progress != null) + { + progress.setProgressBar("Opening " + url, this.hashCode()); } jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) @@ -2601,7 +2626,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements ex.printStackTrace(); } - if (progress!=null) { + if (progress != null) + { progress.setProgressBar(null, this.hashCode()); } } @@ -2620,47 +2646,57 @@ public class Desktop extends jalview.jbgui.GDesktop implements } /** - * static hyperlink handler proxy method for use by Jalview's internal windows + * static hyperlink handler proxy method for use by Jalview's internal windows + * * @param e */ public static void hyperlinkUpdate(HyperlinkEvent e) { if (e.getEventType() == EventType.ACTIVATED) { - String url=null; + String url = null; try { url = e.getURL().toString(); Desktop.showUrl(url); } catch (Exception x) { - if (url!=null) { - if (Cache.log!=null) { - Cache.log.error("Couldn't handle string "+url+" as a URL."); - } else { - System.err.println("Couldn't handle string "+url+" as a URL."); + if (url != null) + { + if (Cache.log != null) + { + Cache.log.error("Couldn't handle string " + url + " as a URL."); + } + else + { + System.err.println("Couldn't handle string " + url + + " as a URL."); } } // ignore any exceptions due to dud links. } - } + } } + /** * single thread that handles display of dialogs to user. */ - ExecutorService dialogExecutor=Executors.newSingleThreadExecutor(); + ExecutorService dialogExecutor = Executors.newSingleThreadExecutor(); + /** * flag indicating if dialogExecutor should try to acquire a permit */ - private volatile boolean dialogPause=true; + private volatile boolean dialogPause = true; + /** - * pause the queue + * pause the queue */ - private java.util.concurrent.Semaphore block=new Semaphore(0); - + private java.util.concurrent.Semaphore block = new Semaphore(0); + /** * add another dialog thread to the queue + * * @param prompter */ public void addDialogThread(final Runnable prompter) @@ -2669,10 +2705,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements { public void run() { - if (dialogPause) { - try { block.acquire(); } catch (InterruptedException x){}; + if (dialogPause) + { + try + { + block.acquire(); + } catch (InterruptedException x) + { + } + ; } - if (instance==null) + if (instance == null) { return; } @@ -2689,8 +2732,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void startDialogQueue() { - // set the flag so we don't pause waiting for another permit and semaphore the current task to begin - dialogPause=false; + // set the flag so we don't pause waiting for another permit and semaphore + // the current task to begin + dialogPause = false; block.release(); } } -- 1.7.10.2