/*
- * 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;
private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
/**
+ * news reader - null if it was never started.
+ */
+ private BlogReader jvnews=null;
+
+ /**
* @param listener
* @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
*/
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)
}
}
});
-
+ 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()
});
}
+ protected void showNews_actionPerformed(ActionEvent e)
+ {
+ showNews(showNews.isSelected());
+ }
+ void showNews(boolean visible)
+ {
+ {
+ Cache.log.debug((visible?"Showing":"Hiding")+" news.");
+ showNews.setSelected(visible);
+ if (visible && !jvnews.isVisible())
+ {
+ 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();
+ }
+ }
+ }
+
/**
* recover the last known dimensions for a jalview window
*
storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds());
jconsole.stopConsole();
}
+ if (jvnews!=null)
+ {
+ storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds());
+
+ }
+
System.exit(0);
}
*/
public void aboutMenuItem_actionPerformed(ActionEvent e)
{
- StringBuffer message = new StringBuffer("Jalview version "
+ StringBuffer message = getAboutMessage(false);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+
+ message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
+ }
+ public StringBuffer getAboutMessage(boolean shortv)
+ {
+ StringBuffer message=new StringBuffer();
+ message.append("<html>");
+ if (shortv)
+ {
+ 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>");
+
+ } else {
+
+ message.append("<strong>Jalview version "
+ jalview.bin.Cache.getProperty("VERSION") + "; last updated: "
+ jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
-
- if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
- jalview.bin.Cache.getProperty("VERSION")))
+ }
+
+ if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking").equals(
+ "Checking"))
{
- message.append("\n\n!! Jalview version "
- + jalview.bin.Cache.getProperty("LATEST_VERSION")
- + " is available for download from http://www.jalview.org !!\n");
-
+ message.append("<br>...Checking latest version...</br>");
}
- // TODO: update this text for each release or centrally store it for lite
- // and application
- message.append("\nAuthors: Jim Procter, Jan Engelhardt, Lauren Lui, 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);
+ 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;
}
/**
}
JPanel progressPanel;
-
+ ArrayList<JPanel> fileLoadingPanels=new ArrayList<JPanel>();
public void startLoading(final String fileName)
{
if (fileLoadingCount == 0)
{
- addProgressPanel("Loading File: " + fileName + " ");
-
+ fileLoadingPanels.add(addProgressPanel("Loading File: " + fileName + " "));
}
fileLoadingCount++;
}
- private JProgressBar addProgressPanel(String string)
+ private JPanel addProgressPanel(String string)
{
if (progressPanel == null)
{
- progressPanel = new JPanel(new BorderLayout());
+ progressPanel = new JPanel(new GridLayout(1,1));
totalProgressCount = 0;
+ instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
}
+ JPanel thisprogress=new JPanel(new BorderLayout(10,5));
JProgressBar progressBar = new JProgressBar();
progressBar.setIndeterminate(true);
- progressPanel.add(new JLabel(string), BorderLayout.WEST);
-
- progressPanel.add(progressBar, BorderLayout.CENTER);
+ thisprogress.add(new JLabel(string), BorderLayout.WEST);
- instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
- totalProgressCount++;
- validate();
- return progressBar;
+ thisprogress.add(progressBar, BorderLayout.CENTER);
+ progressPanel.add(thisprogress);
+ ((GridLayout)progressPanel.getLayout()).setRows(((GridLayout)progressPanel.getLayout()).getRows()+1);
+ ++totalProgressCount;
+ instance.validate();
+ return thisprogress;
}
int totalProgressCount = 0;
- private void removeProgressPanel(JProgressBar progbar)
+ private void removeProgressPanel(JPanel progbar)
{
if (progressPanel != null)
{
progressPanel.remove(progbar);
+ GridLayout gl = (GridLayout) progressPanel.getLayout();
+ gl.setRows(gl.getRows()-1);
if (--totalProgressCount < 1)
{
this.getContentPane().remove(progressPanel);
fileLoadingCount--;
if (fileLoadingCount < 1)
{
- if (progressPanel != null)
+ for (JPanel flp : fileLoadingPanels)
{
- this.getContentPane().remove(progressPanel);
- progressPanel = null;
+ removeProgressPanel(flp);
}
+ fileLoadingPanels.clear();
fileLoadingCount = 0;
}
validate();
if (value == JalviewFileChooser.APPROVE_OPTION)
{
java.io.File choice = chooser.getSelectedFile();
- JProgressBar progpanel = addProgressPanel("Saving VAMSAS Document to "
+ JPanel progpanel = addProgressPanel("Saving VAMSAS Document to "
+ choice.getName());
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
String warnmsg = null;
}
}
- JProgressBar vamUpdate = null;
+ JPanel vamUpdate = null;
/**
* hide vamsas user gui bits when a vamsas document event is being handled.
}
+ /**
+ * fixes stacking order after a modal dialog to ensure windows that should be on top actually are
+ */
+ public void relayerWindows()
+ {
+
+ }
+
protected JMenuItem groovyShell;
public void doGroovyCheck()
/**
* Progress bars managed by the IProgressIndicator method.
*/
- private Hashtable progressBars, progressBarHandlers;
+ private Hashtable<Long,JPanel> progressBars;
+ private Hashtable<Long,IProgressIndicatorHandler> progressBarHandlers;
/*
* (non-Javadoc)
{
if (progressBars == null)
{
- progressBars = new Hashtable();
- progressBarHandlers = new Hashtable();
+ progressBars = new Hashtable<Long,JPanel>();
+ progressBarHandlers = new Hashtable<Long,IProgressIndicatorHandler>();
}
if (progressBars.get(new Long(id)) != null)
{
- JProgressBar progressPanel = (JProgressBar) progressBars
+ JPanel progressPanel = progressBars
.remove(new Long(id));
if (progressBarHandlers.contains(new Long(id)))
{
// register PCS handler for desktop.
discoverer.addPropertyChangeListener(changeSupport);
}
- if (Cache.getDefault("SHOW_JWS1_SERVICES", true))
+ // JAL-940 - disabled JWS1 service configuration - always start discoverer until we phase out completely
+ if (true)
{
(t0 = new Thread(discoverer)).start();
}
git://source.jalview.org / jalview.git / blobdiff