X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=b7057d17e11216a8b99c9bfe1f556f561a4e18dc;hb=d8ddf2968124b3518e567a91411357b1d291ff77;hp=f8d2bf034db89a0c101b125e2a4d1b12d13c74f2;hpb=367c039ca47ca16fbf722c53acde68a3842784c3;p=jalview.git
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index f8d2bf0..b7057d1 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,47 +1,97 @@
/*
- * 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 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* 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.
- *
+ * 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
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.bin.Cache;
-import jalview.io.*;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
import jalview.ws.params.ParamManager;
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.dnd.*;
-import java.awt.event.*;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.GridLayout;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.ClipboardOwner;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.beans.PropertyVetoException;
import java.io.BufferedInputStream;
-import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileOutputStream;
-import java.io.InputStream;
import java.lang.reflect.Constructor;
import java.net.URL;
-import java.net.URLConnection;
-import java.nio.channels.ReadableByteChannel;
-import java.util.*;
-
-import javax.swing.*;
+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;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JComponent;
+import javax.swing.JDesktopPane;
+import javax.swing.JFrame;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+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
@@ -51,7 +101,8 @@ 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();
@@ -59,7 +110,7 @@ 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
@@ -164,6 +215,10 @@ 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);
}
@@ -200,6 +255,11 @@ 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);
}
@@ -238,16 +298,17 @@ 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)
{
@@ -273,17 +334,7 @@ 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()
- {
- jvnews = new BlogReader(me);
- showNews.setVisible(true);
- }
- }).start();
-
+
this.addWindowListener(new WindowAdapter()
{
public void windowClosing(WindowEvent evt)
@@ -292,7 +343,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
});
- this.addMouseListener(new MouseAdapter()
+ MouseAdapter ma;
+ this.addMouseListener(ma = new MouseAdapter()
{
public void mousePressed(MouseEvent evt)
{
@@ -302,7 +354,26 @@ 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)
+ {
+ Cache.log.debug("Relaying windows after focus gain");
+ // make sure that we sort windows properly after we gain focus
+ instance.relayerWindows();
+ }
+ });
this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
// Spawn a thread that shows the splashscreen
SwingUtilities.invokeLater(new Runnable()
@@ -345,29 +416,46 @@ 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)
{
{
- 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() {
+ 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();
}
@@ -474,7 +562,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
void showPasteMenu(int x, int y)
{
JPopupMenu popup = new JPopupMenu();
- JMenuItem item = new JMenuItem("Paste To New Window");
+ JMenuItem item = new JMenuItem(
+ MessageManager.getString("label.paste_new_window"));
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
@@ -564,8 +653,9 @@ 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;
}
@@ -630,17 +720,17 @@ 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)
{
@@ -651,7 +741,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
}
}
-
+
@Override
public void mouseEntered(MouseEvent e)
{
@@ -662,11 +752,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
}
}
-
+
@Override
public void mouseClicked(MouseEvent e)
{
-
+
}
});
@@ -680,10 +770,11 @@ 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);
}
}
@@ -721,6 +812,7 @@ 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;
@@ -769,6 +861,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
}
} catch (Exception e)
{
+ success = false;
}
if (files != null)
@@ -797,8 +890,11 @@ 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
}
/**
@@ -816,8 +912,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Open local file");
- chooser.setToolTipText("Open");
+ chooser.setDialogTitle(MessageManager
+ .getString("label.open_local_file"));
+ chooser.setToolTipText(MessageManager.getString("action.open"));
int value = chooser.showOpenDialog(this);
@@ -828,7 +925,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
.getSelectedFile().getParent());
String format = null;
- if (chooser.getSelectedFormat().equals("Jalview"))
+ if (chooser.getSelectedFormat() != null
+ && chooser.getSelectedFormat().equals("Jalview"))
{
format = "Jalview";
}
@@ -859,7 +957,8 @@ 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));
@@ -884,7 +983,8 @@ 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)
{
@@ -960,12 +1060,16 @@ 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);
}
@@ -989,30 +1093,84 @@ 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(
+ "AUTHORFNAMES",
+ "The Jalview Authors (See AUTHORS file for current list)")
+ + "
Development managed by The Barton Group, University of Dundee, Scotland, UK.
"
+ + "
For help, see the FAQ at www.jalview.org/faq 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;
}
/**
@@ -1224,7 +1382,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "jar" }, new String[]
+ { "jvp" }, new String[]
{ "Jalview Project" }, "Jalview Project");
chooser.setFileView(new JalviewFileView());
@@ -1241,28 +1399,31 @@ 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();
}
@@ -1278,8 +1439,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "jar" }, new String[]
- { "Jalview Project" }, "Jalview Project");
+ { "jvp", "jar" }, new String[]
+ { "Jalview Project", "Jalview Project (old)" },
+ "Jalview Project");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Restore state");
@@ -1322,12 +1484,15 @@ 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++;
}
@@ -1336,11 +1501,11 @@ 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);
@@ -1348,7 +1513,8 @@ 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;
@@ -1360,13 +1526,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
if (progressPanel != null)
{
- progressPanel.remove(progbar);
- GridLayout gl = (GridLayout) progressPanel.getLayout();
- gl.setRows(gl.getRows()-1);
- if (--totalProgressCount < 1)
+ synchronized (progressPanel)
{
- this.getContentPane().remove(progressPanel);
- progressPanel = null;
+ progressPanel.remove(progbar);
+ GridLayout gl = (GridLayout) progressPanel.getLayout();
+ gl.setRows(gl.getRows() - 1);
+ if (--totalProgressCount < 1)
+ {
+ this.getContentPane().remove(progressPanel);
+ progressPanel = null;
+ }
}
}
validate();
@@ -1377,9 +1546,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
fileLoadingCount--;
if (fileLoadingCount < 1)
{
- for (JPanel flp : fileLoadingPanels)
+ while (fileLoadingPanels.size() > 0)
{
- removeProgressPanel(flp);
+ removeProgressPanel(fileLoadingPanels.remove(0));
}
fileLoadingPanels.clear();
fileLoadingCount = 0;
@@ -1416,9 +1585,8 @@ 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));
}
@@ -1521,7 +1689,7 @@ 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++)
{
@@ -1563,7 +1731,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Open a saved VAMSAS session");
- chooser.setToolTipText("select a vamsas session to be opened as a new vamsas session.");
+ chooser.setToolTipText(MessageManager
+ .getString("label.select_vamsas_session_opened_as_new_vamsas_session"));
int value = chooser.showOpenDialog(this);
@@ -1572,10 +1741,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
String fle = chooser.getSelectedFile().toString();
if (!vamsasImport(chooser.getSelectedFile()))
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Couldn't import '" + fle + "' as a new vamsas session.",
- "Vamsas Document Import Failed",
- JOptionPane.ERROR_MESSAGE);
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.couldnt_import_as_vamsas_session",
+ new String[]
+ { fle }),
+ MessageManager
+ .getString("label.vamsas_document_import_failed"),
+ JOptionPane.ERROR_MESSAGE);
}
}
}
@@ -1717,7 +1892,7 @@ 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
@@ -1729,7 +1904,8 @@ 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)
@@ -1765,7 +1941,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
JMenuItem sessit = new JMenuItem();
sessit.setText(sess[i]);
- sessit.setToolTipText("Connect to session " + sess[i]);
+ sessit.setToolTipText(MessageManager.formatMessage(
+ "label.connect_to_session", new String[]
+ { sess[i] }));
final Desktop dsktp = this;
final String mysesid = sess[i];
sessit.addActionListener(new ActionListener()
@@ -1987,26 +2165,24 @@ public class Desktop extends jalview.jbgui.GDesktop implements
FontMetrics fm = g.getFontMetrics();
if (fm != null)
{
- g.drawString(
- "Total Free Memory: " + df.format(totalFreeMemory)
- + "MB; Max Memory: " + df.format(maxMemory)
- + "MB; " + df.format(percentUsage) + "%", 10,
+ g.drawString(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()
{
- if (jvnews!=null && jvnews.isVisible())
- {
- jvnews.toFront();
- }
+
}
protected JMenuItem groovyShell;
@@ -2016,7 +2192,7 @@ 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)
@@ -2068,6 +2244,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
avp.clear();
return afs;
}
+
public AppJmol[] getJmols()
{
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
@@ -2145,8 +2322,9 @@ 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)
@@ -2157,14 +2335,13 @@ 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));
@@ -2195,7 +2372,8 @@ 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()
{
@@ -2214,6 +2392,20 @@ 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
*
@@ -2276,37 +2468,43 @@ public class Desktop extends jalview.jbgui.GDesktop implements
{
boolean alive = true;
Thread t0 = null, t1 = null, t2 = null;
-
- // todo: changesupport handlers need to be transferred
- if (discoverer == null)
- {
- discoverer = new jalview.ws.jws1.Discoverer();
- // register PCS handler for desktop.
- discoverer.addPropertyChangeListener(changeSupport);
- }
- // JAL-940 - disabled JWS1 service configuration - always start discoverer until we phase out completely
+ // 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)
+ {
+ discoverer = new jalview.ws.jws1.Discoverer();
+ // register PCS handler for desktop.
+ discoverer.addPropertyChangeListener(changeSupport);
+ }
+ // 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
{
- // 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();
+ 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());
}
- } 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())
@@ -2315,9 +2513,9 @@ 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
}
@@ -2354,28 +2552,58 @@ 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
@@ -2399,12 +2627,16 @@ 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()
{
@@ -2412,8 +2644,9 @@ 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)
@@ -2428,7 +2661,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
ex.printStackTrace();
}
- if (progress!=null) {
+ if (progress != null)
+ {
progress.setProgressBar(null, this.hashCode());
}
}
@@ -2446,5 +2680,112 @@ 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();
+ }
+ @Override
+ protected void snapShotWindow_actionPerformed(ActionEvent e)
+ {
+ invalidate();
+ File of;
+ ImageMaker im = new jalview.util.ImageMaker(this, ImageMaker.EPS, "View of Desktop", getWidth(), getHeight(), of=new File("Jalview_snapshot"+System.currentTimeMillis()+".eps"), "View of desktop");
+ try {
+ paintAll(im.getGraphics());
+ im.writeImage();
+ } catch (Exception q)
+ {
+ Cache.log.error("Couldn't write snapshot to "+of.getAbsolutePath(),q);
+ return;
+ }
+ Cache.log.info("Successfully written snapshot to file "+of.getAbsolutePath());
+ }
}