X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=fe99469528809a36b3cf348605ec6b94fac2fdf5;hb=dd3059c62cd80e712c0f6df866d6d69588e5f3eb;hp=768e1309cae6ea0a9462164202aa6a79cc685c6d;hpb=d053a3c980cf4318b9a19a255f9fc870e74de989;p=jalview.git
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 768e130..fe99469 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
@@ -23,6 +23,7 @@ import jalview.io.FormatAdapter;
import jalview.io.IdentifyFile;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
+import jalview.util.MessageManager;
import jalview.ws.params.ParamManager;
import java.awt.BorderLayout;
@@ -64,6 +65,9 @@ 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;
@@ -80,8 +84,10 @@ import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JProgressBar;
import javax.swing.SwingUtilities;
+import javax.swing.event.HyperlinkEvent;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+import javax.swing.event.HyperlinkEvent.EventType;
/**
* Jalview Desktop
@@ -91,7 +97,8 @@ import javax.swing.event.MenuListener;
* @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();
@@ -99,7 +106,7 @@ 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
@@ -204,6 +211,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
public void dragFrame(JComponent f, int newX, int newY)
{
+ if (newY < 0)
+ {
+ newY = 0;
+ }
delegate.dragFrame(f, newX, newY);
}
@@ -240,6 +251,11 @@ 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)
+ {
+ newY = 0;
+ }
delegate.resizeFrame(f, newX, newY, newWidth, newHeight);
}
@@ -278,16 +294,17 @@ 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);
-
+ 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)
{
@@ -313,20 +330,7 @@ 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)
@@ -335,7 +339,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
});
- this.addMouseListener(new MouseAdapter()
+ MouseAdapter ma;
+ this.addMouseListener(ma = new MouseAdapter()
{
public void mousePressed(MouseEvent evt)
{
@@ -345,16 +350,18 @@ 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)
{
@@ -405,22 +412,42 @@ 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);
@@ -621,8 +648,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
// A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
// IF JALVIEW IS RUNNING HEADLESS
// ///////////////////////////////////////////////
- if (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true"))
+ if (instance == null || (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true")))
{
return;
}
@@ -687,17 +714,17 @@ 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)
{
@@ -708,7 +735,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
}
}
-
+
@Override
public void mouseEntered(MouseEvent e)
{
@@ -719,11 +746,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
}
}
-
+
@Override
public void mouseClicked(MouseEvent e)
{
-
+
}
});
@@ -737,10 +764,11 @@ 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);
}
}
@@ -778,6 +806,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
*/
public void drop(DropTargetDropEvent evt)
{
+ boolean success=true;
Transferable t = evt.getTransferable();
java.util.List files = null;
java.util.List protocols = null;
@@ -826,6 +855,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
} catch (Exception e)
{
+ success=false;
}
if (files != null)
@@ -854,8 +884,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
} catch (Exception ex)
{
+ success=false;
}
}
+ evt.dropComplete(success); // need this to ensure input focus is properly transfered to any new windows created
}
/**
@@ -916,7 +948,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
// This construct allows us to have a wider textfield
// for viewing
- JLabel label = new JLabel("Enter URL of Input File");
+ JLabel label = new JLabel(MessageManager.getString("label.input_file_url"));
final JComboBox history = new JComboBox();
JPanel panel = new JPanel(new GridLayout(2, 1));
@@ -941,7 +973,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
int reply = JOptionPane.showInternalConfirmDialog(desktop, panel,
- "Input Alignment From URL", JOptionPane.OK_CANCEL_OPTION);
+ MessageManager.getString("label.input_alignment_from_url"), JOptionPane.OK_CANCEL_OPTION);
if (reply != JOptionPane.OK_OPTION)
{
@@ -1017,12 +1049,16 @@ 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);
}
@@ -1046,28 +1082,42 @@ 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);
+ // 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)
{
- StringBuffer message=new StringBuffer();
+ StringBuffer message = new StringBuffer();
message.append("");
if (shortv)
- {
- message.append("
Jalview "
- + jalview.bin.Cache.getProperty("VERSION") + "
");
- message.append("Last Updated: "+jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")+"");
-
- } else {
-
- message.append("Jalview version "
- + jalview.bin.Cache.getProperty("VERSION") + "; last updated: "
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
- }
-
+ {
+ message.append("Version: "
+ + jalview.bin.Cache.getProperty("VERSION")
+ + "
");
+ message.append("Last Updated: "
+ + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
+ + "");
+
+ }
+ else
+ {
+
+ message.append("Version "
+ + jalview.bin.Cache.getProperty("VERSION")
+ + "; last updated: "
+ + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+ }
+
if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking").equals(
"Checking"))
{
@@ -1076,27 +1126,34 @@ public class Desktop extends jalview.jbgui.GDesktop implements
else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
.equals(jalview.bin.Cache.getProperty("VERSION")))
{
- boolean red=false;
+ boolean red = false;
if (jalview.bin.Cache.getProperty("VERSION").toLowerCase()
.indexOf("automated build") == -1)
{
- red=true;
+ red = true;
// Displayed when code version and jnlp version do not match and code
// version is not a development build
message.append("");
}
-
- message.append("
!! Jalview version "
- + jalview.bin.Cache.getDefault("LATEST_VERSION",
- "..Checking..")
- + " is available for download from "+jalview.bin.Cache.getDefault("www.jalview.org","http://www.jalview.org")+" !!");
- if (red) {
+
+ message.append("
!! Version "
+ + jalview.bin.Cache.getDefault("LATEST_VERSION",
+ "..Checking..")
+ + " is available for download from "
+ + jalview.bin.Cache.getDefault("www.jalview.org",
+ "http://www.jalview.org") + " !!");
+ if (red)
+ {
message.append("
");
}
- }
- message.append("
Authors: "+jalview.bin.Cache.getDefault("AUTHORNAMES","Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton")
+ }
+ message.append("
Authors: "
+ + jalview.bin.Cache
+ .getDefault(
+ "AUTHORNAMES",
+ "Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton")
+ "
Development managed by The Barton Group, University of Dundee, Scotland, UK.
"
- + "
For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list"
+ + "
For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list"
+ "
If you use Jalview, please cite:"
+ "
Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+ "
Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
@@ -1331,28 +1388,31 @@ 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();
}
@@ -1412,12 +1472,15 @@ 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++;
}
@@ -1426,11 +1489,11 @@ 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);
@@ -1438,7 +1501,8 @@ 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;
@@ -1452,7 +1516,7 @@ 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);
@@ -1506,9 +1570,8 @@ 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));
}
@@ -1663,8 +1726,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
if (!vamsasImport(chooser.getSelectedFile()))
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Couldn't import '" + fle + "' as a new vamsas session.",
- "Vamsas Document Import Failed",
+ MessageManager.formatMessage("label.couldnt_import_as_vamsas_session", new String[]{fle}),
+ MessageManager.getString("label.vamsas_document_import_failed"),
JOptionPane.ERROR_MESSAGE);
}
}
@@ -1807,7 +1870,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
protected void setupVamsasConnectedGui()
{
- vamsasStart.setText("Session Update");
+ vamsasStart.setText(MessageManager.getString("label.session_update"));
vamsasSave.setVisible(true);
vamsasStop.setVisible(true);
vamsasImport.setVisible(false); // Document import to existing session is
@@ -1819,7 +1882,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
vamsasSave.setVisible(false);
vamsasStop.setVisible(false);
vamsasImport.setVisible(true);
- vamsasStart.setText("New Vamsas Session");
+ vamsasStart.setText(MessageManager.getString("label.new_vamsas_session"));
}
public void vamsasStop_actionPerformed(ActionEvent e)
@@ -2078,22 +2141,20 @@ public class Desktop extends jalview.jbgui.GDesktop implements
if (fm != null)
{
g.drawString(
- "Total Free Memory: " + df.format(totalFreeMemory)
- + "MB; Max Memory: " + df.format(maxMemory)
- + "MB; " + df.format(percentUsage) + "%", 10,
+ MessageManager.formatMessage("label.memory_stats", new String[]{df.format(totalFreeMemory),df.format(maxMemory),df.format(percentUsage)}), 10,
getHeight() - fm.getHeight());
}
}
}
-
}
/**
- * 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;
@@ -2103,7 +2164,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
if (jalview.bin.Cache.groovyJarsPresent())
{
groovyShell = new JMenuItem();
- groovyShell.setText("Groovy Console...");
+ groovyShell.setText(MessageManager.getString("label.groovy_console"));
groovyShell.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -2155,6 +2216,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
avp.clear();
return afs;
}
+
public AppJmol[] getJmols()
{
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
@@ -2232,8 +2294,9 @@ 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)
@@ -2244,14 +2307,13 @@ 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));
@@ -2282,7 +2344,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
if (handler.canCancel())
{
- JButton cancel = new JButton("Cancel");
+ JButton cancel = new JButton(MessageManager.getString("action.cancel"));
final IProgressIndicator us = this;
cancel.addActionListener(new ActionListener()
{
@@ -2301,6 +2363,20 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
/**
+ *
+ * @return true if any progress bars are still active
+ */
+ @Override
+ public boolean operationInProgress()
+ {
+ if (progressBars != null && progressBars.size() > 0)
+ {
+ return true;
+ }
+ return false;
+ }
+
+ /**
* This will return the first AlignFrame viewing AlignViewport av. It will
* break if there are more than one AlignFrames viewing a particular av. This
*
@@ -2363,7 +2439,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
boolean alive = true;
Thread t0 = null, t1 = null, t2 = null;
-
+ // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
+ if (true)
+ {
// todo: changesupport handlers need to be transferred
if (discoverer == null)
{
@@ -2371,29 +2449,33 @@ 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
- if (true)
- {
+ // JAL-940 - disabled JWS1 service configuration - always start discoverer
+ // until we phase out completely
(t0 = new Thread(discoverer)).start();
}
- try
+ // ENFIN services are EOLed as of Jalview 2.8.1 release
+ if (false)
{
- if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
+ 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)
{
- // 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();
+ Cache.log
+ .info("Exception when trying to launch Envision2 workflow discovery.",
+ e);
+ Cache.log.info(e.getStackTrace());
}
- } 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())
@@ -2402,9 +2484,9 @@ 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
}
@@ -2441,28 +2523,58 @@ 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(
+ ""
+ + "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
@@ -2486,12 +2598,16 @@ 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()
{
@@ -2499,8 +2615,9 @@ 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)
@@ -2515,7 +2632,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
ex.printStackTrace();
}
- if (progress!=null) {
+ if (progress != null)
+ {
progress.setProgressBar(null, this.hashCode());
}
}
@@ -2533,5 +2651,96 @@ public class Desktop extends jalview.jbgui.GDesktop implements
return wsparamManager;
}
+ /**
+ * 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;
+ 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.");
+ }
+ }
+ // 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();
+ }
}