X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=294beaccaaec81e8b5c02f68c1b36b1d3617913e;hb=e43ffeb12a7e4bbadebe734cab824a14175b34a2;hp=3205cab493019bd9958c4ee490f45c85b598bada;hpb=f215c30c91a7532eb97655349b70b9eb73a283d5;p=jalview.git
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 3205cab..294beac 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 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
*
* This file is part of Jalview.
*
@@ -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;
@@ -79,9 +83,12 @@ 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;
import javax.swing.event.MenuListener;
+import javax.swing.event.HyperlinkEvent.EventType;
/**
* Jalview Desktop
@@ -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);
}
@@ -282,12 +298,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
//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)
{
@@ -313,16 +331,6 @@ 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()
- {
- jvnews = new BlogReader(me);
- showNews.setVisible(true);
- }
- }).start();
this.addWindowListener(new WindowAdapter()
{
@@ -332,7 +340,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
});
- this.addMouseListener(new MouseAdapter()
+ MouseAdapter ma;
+ this.addMouseListener(ma=new MouseAdapter()
{
public void mousePressed(MouseEvent evt)
{
@@ -342,6 +351,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
}
});
+ desktop.addMouseListener(ma);
+
this.addFocusListener(new FocusListener()
{
@@ -402,6 +413,22 @@ 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());
@@ -409,22 +436,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements
void showNews(boolean visible)
{
{
- jvnews.setVisible(visible);
+ Cache.log.debug((visible?"Showing":"Hiding")+" news.");
showNews.setSelected(visible);
- if (visible)
+ if (visible && !jvnews.isVisible())
{
- jvnews.refreshNews();
- jvnews.toFront();
- // try real hard to get focus when the news is first opened
new Thread(new Runnable() {
@Override
public void run()
{
- while (jvnews.isVisible() && !jvnews.requestFocusInWindow())
- {
- try { Thread.sleep(50); } catch (InterruptedException x) {};
- }
-
+ long instance=System.currentTimeMillis();
+ Desktop.instance.setProgressBar("Refreshing news", instance);
+ jvnews.refreshNews();
+ Desktop.instance.setProgressBar(null, instance);
+ jvnews.showNews();
}
}).start();
}
@@ -1022,6 +1046,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds());
}
+ if (dialogExecutor!=null)
+ {
+ dialogExecutor.shutdownNow();
+ }
System.exit(0);
}
@@ -1046,30 +1074,78 @@ public class Desktop extends jalview.jbgui.GDesktop implements
*/
public void aboutMenuItem_actionPerformed(ActionEvent e)
{
- StringBuffer message = new StringBuffer("Jalview version "
- + jalview.bin.Cache.getProperty("VERSION") + "; last updated: "
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+// 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();
+ message.append("");
+ if (shortv)
+ {
+ message.append("
Version: "
+ + jalview.bin.Cache.getProperty("VERSION")
+ + "
");
+ message.append("Last Updated: "
+ + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
+ + "");
- if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
- jalview.bin.Cache.getProperty("VERSION")))
+ }
+ else
{
- message.append("\n\n!! Jalview version "
- + jalview.bin.Cache.getProperty("LATEST_VERSION")
- + " is available for download from "+jalview.bin.Cache.getDefault("www.jalview.org","http://www.jalview.org")+" !!\n");
+ message.append("Version "
+ + jalview.bin.Cache.getProperty("VERSION")
+ + "; last updated: "
+ + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
}
- // TODO: update this text for each release or centrally store it for lite
- // and application
- message.append("\nAuthors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,\n David Martin & Geoff Barton."
- + "\nDevelopment managed by The Barton Group, University of Dundee, Scotland, UK.\n"
- + "\nFor help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list\n"
- + "\nIf you use Jalview, please cite:"
- + "\nWaterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
- + "\nJalview Version 2 - a multiple sequence alignment editor and analysis workbench"
- + "\nBioinformatics doi: 10.1093/bioinformatics/btp033");
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
+ if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking").equals(
+ "Checking"))
+ {
+ message.append("
...Checking latest version...");
+ }
+ else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
+ .equals(jalview.bin.Cache.getProperty("VERSION")))
+ {
+ boolean red = false;
+ if (jalview.bin.Cache.getProperty("VERSION").toLowerCase()
+ .indexOf("automated build") == -1)
+ {
+ red = true;
+ // Displayed when code version and jnlp version do not match and code
+ // version is not a development build
+ message.append("");
+ }
+
+ 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")
+ + "
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"
+ + "
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"
+ + "
Bioinformatics doi: 10.1093/bioinformatics/btp033"
+ + "");
+ return message;
}
/**
@@ -1578,7 +1654,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
source.viewport.gatherViewsHere = true;
source.viewport.explodedPosition = source.getBounds();
JInternalFrame[] frames = desktop.getAllFrames();
- String viewId = source.viewport.sequenceSetID;
+ String viewId = source.viewport.getSequenceSetId();
for (int t = 0; t < frames.length; t++)
{
@@ -2052,7 +2128,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
}
}
-
}
/**
@@ -2060,10 +2135,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
*/
public void relayerWindows()
{
- if (jvnews!=null && jvnews.isVisible())
- {
- jvnews.toFront();
- }
+
}
protected JMenuItem groovyShell;
@@ -2271,6 +2343,20 @@ 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
*
@@ -2411,28 +2497,58 @@ 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()
+ 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()
{
- 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;
-
- }
- });
+ // 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
@@ -2503,5 +2619,78 @@ 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();
+ }
}