/*
- * 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.
*
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.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 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.MenuEvent;
import javax.swing.event.MenuListener;
public void dragFrame(JComponent f, int newX, int newY)
{
+ if (newY<0)
+ {
+ newY=0;
+ }
delegate.dragFrame(f, newX, newY);
}
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);
}
//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)
{
@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.addMouseListener(new MouseAdapter()
+ MouseAdapter ma;
+ this.addMouseListener(ma=new MouseAdapter()
{
public void mousePressed(MouseEvent evt)
{
}
}
});
-
+ 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()
{
showNews(showNews.isSelected());
}
- void showNews(boolean default1)
+ void showNews(boolean visible)
{
{
- jvnews.setVisible(default1);
- if (default1)
+ Cache.log.debug((visible?"Showing":"Hiding")+" news.");
+ showNews.setSelected(visible);
+ if (visible && !jvnews.isVisible())
{
- jvnews.refreshNews();
- jvnews.toFront();
+ new Thread(new Runnable() {
+ @Override
+ public void run()
+ {
+ long instance=System.currentTimeMillis();
+ Desktop.instance.setProgressBar("Refreshing news", instance);
+ jvnews.refreshNews();
+ Desktop.instance.setProgressBar(null, instance);
+ jvnews.showNews();
+ }
+ }).start();
}
}
}
*/
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,
- if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
- jalview.bin.Cache.getProperty("VERSION")))
+ message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
+ }
+
+ public StringBuffer getAboutMessage(boolean shortv)
+ {
+ StringBuffer message = new StringBuffer();
+ message.append("<html>");
+ if (shortv)
{
- 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("<h1><strong>Jalview "
+ + jalview.bin.Cache.getProperty("VERSION")
+ + "</strong></h1><br>");
+ message.append("<strong>Last Updated: <em>"
+ + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
+ + "</em></strong>");
}
- // 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,
+ else
+ {
- message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
+ message.append("<strong>Jalview 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"))
+ {
+ message.append("<br>...Checking latest version...</br>");
+ }
+ 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("<div style=\"color: #FF0000;font-style: bold;\">");
+ }
+
+ message.append("<br>!! 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("</div>");
+ }
+ }
+ message.append("<br>Authors: "
+ + jalview.bin.Cache
+ .getDefault(
+ "AUTHORNAMES",
+ "Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton")
+ + "<br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
+ + "<br>For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list"
+ + "<br>If you use Jalview, please cite:"
+ + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+ + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+ + "<br>Bioinformatics doi: 10.1093/bioinformatics/btp033"
+ + "</html>");
+ return message;
}
/**
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++)
{
}
}
}
+ }
+ /**
+ * fixes stacking order after a modal dialog to ensure windows that should be on top actually are
+ */
+ public void relayerWindows()
+ {
+
}
protected JMenuItem groovyShell;
git://source.jalview.org / jalview.git / blobdiff