X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=c9b8de2ba44758bf2412e1be2cf82bad48ecf6d5;hb=59d682209891099d46b960509907c79e3fb276fe;hp=d6ab3ae3ce7a3a04c61270089b363127a04a1794;hpb=3a124a6618aca04d87fa89a76d79cc03c4d45e47;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index d6ab3ae..c9b8de2 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -1,13 +1,13 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR @@ -59,11 +59,15 @@ import java.io.BufferedInputStream; import java.io.File; import java.io.FileOutputStream; import java.lang.reflect.Constructor; +import java.lang.reflect.InvocationTargetException; import java.net.URL; import java.util.ArrayList; import java.util.Hashtable; 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.DefaultDesktopManager; import javax.swing.DesktopManager; @@ -79,6 +83,7 @@ import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.JProgressBar; +import javax.swing.JTextArea; import javax.swing.SwingUtilities; import javax.swing.event.HyperlinkEvent; import javax.swing.event.MenuEvent; @@ -93,7 +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(); @@ -101,7 +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 @@ -206,9 +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); } @@ -246,10 +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); } @@ -289,18 +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) { @@ -326,20 +331,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements showConsole(showjconsole); showNews.setVisible(false); - final Desktop me = this; - // Thread off the news reader, in case there are connection problems. - new Thread( new Runnable() { - @Override - public void run() - { - Cache.log.debug("Starting news thread."); - jvnews = new BlogReader(me); - showNews.setVisible(true); - Cache.log.debug("Completed news thread."); - } - }).start(); - this.addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent evt) @@ -349,7 +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) { @@ -360,17 +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) { @@ -421,22 +413,42 @@ public class Desktop extends jalview.jbgui.GDesktop implements }); } + public void checkForNews() + { + final Desktop me = this; + // Thread off the news reader, in case there are connection problems. + addDialogThread(new Runnable() + { + @Override + public void run() + { + Cache.log.debug("Starting news thread."); + + jvnews = new BlogReader(me); + showNews.setVisible(true); + Cache.log.debug("Completed news thread."); + } + }); + } + 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); @@ -703,17 +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) { @@ -724,7 +736,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { } } - + @Override public void mouseEntered(MouseEvent e) { @@ -735,11 +747,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements { } } - + @Override public void mouseClicked(MouseEvent e) { - + } }); @@ -753,10 +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); } } @@ -1033,12 +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) + { + dialogExecutor.shutdownNow(); + } + System.exit(0); } @@ -1062,11 +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) @@ -1362,28 +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(); } @@ -1443,12 +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++; } @@ -1457,11 +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); @@ -1469,7 +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; @@ -1483,7 +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); @@ -1537,9 +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)); } @@ -2119,11 +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; @@ -2185,6 +2215,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements avp.clear(); return afs; } + public AppJmol[] getJmols() { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); @@ -2262,8 +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) @@ -2274,14 +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)); @@ -2415,7 +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(); @@ -2446,9 +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 } @@ -2485,28 +2517,58 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true)) { - if (serviceChangedDialog == null) - { - // only run if we aren't already displaying one of these. - javax.swing.SwingUtilities - .invokeLater(serviceChangedDialog = new Runnable() - { - public void run() - { - - JOptionPane - .showInternalMessageDialog( - Desktop.desktop, - ermsg - + "It may be that you have invalid JABA URLs\nin your web service preferences.\n\nGo to the Web services tab of the\nTools->Preferences dialog box to change them.\n", - "Preferences Problem", - JOptionPane.WARNING_MESSAGE); - serviceChangedDialog = null; - - } - }); + if (serviceChangedDialog == null) + { + // only run if we aren't already displaying one of these. + addDialogThread(serviceChangedDialog = new Runnable() + { + public void run() + { + + /* + * JalviewDialog jd =new JalviewDialog() { + * + * @Override protected void cancelPressed() { // TODO + * Auto-generated method stub + * + * }@Override protected void okPressed() { // TODO + * Auto-generated method stub + * + * }@Override protected void raiseClosed() { // TODO + * Auto-generated method stub + * + * } }; jd.initDialogFrame(new + * JLabel("
" + ermsg + + * "
It may be that you have invalid JABA URLs in your web service preferences," + * + " or mis-configured HTTP proxy settings.
" + + * "Check the Connections and Web services tab of the" + * + + * " Tools->Preferences dialog box to change them.
" + * ), true, true, "Web Service Configuration Problem", 450, + * 400); + * + * jd.waitForInput(); + */ + JOptionPane + .showConfirmDialog( + Desktop.desktop, + new JLabel( + "
" + + ermsg + + "
" + + "

It may be that you have invalid JABA URLs
in your web service preferences," + + " or mis-configured HTTP proxy settings.

" + + "

Check the Connections and Web services tab
of the" + + " Tools->Preferences dialog box to change them.

"), + "Web Service Configuration Problem", + JOptionPane.DEFAULT_OPTION, + JOptionPane.ERROR_MESSAGE); + serviceChangedDialog = null; + + } + }); + } } - } else { Cache.log @@ -2530,12 +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() { @@ -2543,8 +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) @@ -2559,7 +2626,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements ex.printStackTrace(); } - if (progress!=null) { + if (progress != null) + { progress.setProgressBar(null, this.hashCode()); } } @@ -2578,32 +2646,95 @@ 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(); + + /** + * flag indicating if dialogExecutor should try to acquire a permit + */ + private volatile boolean dialogPause = true; + + /** + * pause the queue + */ + private java.util.concurrent.Semaphore block = new Semaphore(0); + + /** + * add another dialog thread to the queue + * + * @param prompter + */ + public void addDialogThread(final Runnable prompter) + { + dialogExecutor.submit(new Runnable() + { + public void run() + { + if (dialogPause) + { + try + { + block.acquire(); + } catch (InterruptedException x) + { + } + ; + } + if (instance == null) + { + return; + } + try + { + SwingUtilities.invokeAndWait(prompter); + } catch (Exception q) + { + Cache.log.warn("Unexpected Exception in dialog thread.", q); + } + } + }); + } + public void startDialogQueue() + { + // set the flag so we don't pause waiting for another permit and semaphore + // the current task to begin + dialogPause = false; + block.release(); + } }