/*
- * 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, 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;
*
*
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.155 $
*/
public class Desktop extends jalview.jbgui.GDesktop implements
- DropTargetListener, ClipboardOwner, IProgressIndicator
+ DropTargetListener, ClipboardOwner, IProgressIndicator, jalview.api.StructureSelectionManagerProvider
{
- private class JalviewChangeSupport implements PropertyChangeListener
- {
- public void propertyChange(PropertyChangeEvent evt)
- {
- // Handle change events - most are simply routed to other sources
- changeSupport.firePropertyChange(evt);
- }
-
- /**
- * change listeners are notified of changes to resources so they can update
- * their state. E.g. - the 'services' property notifies when the available
- * set of web service endpoints have changed.
- */
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
- this);
-
- /**
- * @param propertyName
- * @param listener
- * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.lang.String,
- * java.beans.PropertyChangeListener)
- */
- public void addJalviewPropertyChangeListener(String propertyName,
- PropertyChangeListener listener)
- {
- changeSupport.addPropertyChangeListener(propertyName, listener);
- }
-
- /**
- * @param listener
- * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
- */
- public void addJalviewPropertyChangeListener(
- PropertyChangeListener listener)
- {
- changeSupport.addPropertyChangeListener(listener);
- }
-
- /*
- * @param propertyName
- *
- * @param oldValue
- *
- * @param newValue
- *
- * @see
- * java.beans.PropertyChangeSupport#firePropertyChange(java.lang.String,
- * java.lang.Object, java.lang.Object) public void firePropertyChange(String
- * propertyName, Object oldValue, Object newValue) {
- * changeSupport.firePropertyChange(propertyName, oldValue, newValue); }
- */
-
- /**
- * @param propertyName
- * @param listener
- * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.lang.String,
- * java.beans.PropertyChangeListener)
- */
- public void removeJalviewPropertyChangeListener(String propertyName,
- PropertyChangeListener listener)
- {
- changeSupport.removePropertyChangeListener(propertyName, listener);
- }
-
- }
-
private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
/**
+ * news reader - null if it was never started.
+ */
+ private BlogReader jvnews=null;
+
+ /**
* @param listener
- * @see jalview.gui.Desktop.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
+ * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
*/
public void addJalviewPropertyChangeListener(
PropertyChangeListener listener)
/**
* @param propertyName
* @param listener
- * @see jalview.gui.Desktop.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String,
+ * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String,
* java.beans.PropertyChangeListener)
*/
public void addJalviewPropertyChangeListener(String propertyName,
/**
* @param propertyName
* @param listener
- * @see jalview.gui.Desktop.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String,
+ * @see jalview.gui.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String,
* java.beans.PropertyChangeListener)
*/
public void removeJalviewPropertyChangeListener(String propertyName,
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);
}
showMemusage.setSelected(selmemusage);
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);
getContentPane().add(desktop, BorderLayout.CENTER);
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)
{
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.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()
Cache.log.debug("Filechooser init thread finished.");
}
}).start();
+ // Add the service change listener
+ changeSupport.addJalviewPropertyChangeListener("services",
+ new PropertyChangeListener()
+ {
+
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ Cache.log.debug("Firing service changed event for "
+ + evt.getNewValue());
+ JalviewServicesChanged(evt);
+ }
+
+ });
+ }
+
+ 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();
+ }
+ }
}
/**
}
}
});
+ menuItem.addMouseListener(new MouseListener()
+ {
+
+ @Override
+ public void mouseReleased(MouseEvent e)
+ {
+ }
+
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ }
+
+ @Override
+ public void mouseExited(MouseEvent e)
+ {
+ try
+ {
+ frame.setSelected(false);
+ } catch (PropertyVetoException e1)
+ {
+ }
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ try
+ {
+ frame.setSelected(true);
+ } catch (PropertyVetoException e1)
+ {
+ }
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+
+ }
+ });
windowMenu.add(menuItem);
} catch (java.beans.PropertyVetoException ve)
{
}
+ 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);
+ }
}
public void lostOwnership(Clipboard clipboard, Transferable contents)
storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds());
jconsole.stopConsole();
}
+ if (jvnews!=null)
+ {
+ storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds());
+
+ }
+
System.exit(0);
}
{
message.append("\n\n!! Jalview version "
+ jalview.bin.Cache.getProperty("LATEST_VERSION")
- + " is available for download from http://www.jalview.org !!\n");
+ + " is available for download from "+jalview.bin.Cache.getDefault("www.jalview.org","http://www.jalview.org")+" !!\n");
}
// TODO: update this text for each release or centrally store it for lite
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- java.io.File choice = chooser.getSelectedFile();
+ final Desktop me = this;
+ final java.io.File choice = chooser.getSelectedFile();
+ new Thread(new Runnable()
+ {
+ 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);
Cache.log
.error("Problems whilst trying to save to "
+ choice.getName(), ex);
- JOptionPane.showMessageDialog(this,
+ JOptionPane.showMessageDialog(me,
"Error whilst saving current state to " + choice.getName(),
"Couldn't save project", JOptionPane.WARNING_MESSAGE);
}
setProgressBar(null, choice.hashCode());
-
+ }
+ }).start();
}
}
}
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();
}
- public static int getViewCount(String viewId)
+ public static int getViewCount(String alignmentId)
{
- AlignViewport[] aps = getViewports(viewId);
+ AlignViewport[] aps = getViewports(alignmentId);
return (aps == null) ? 0 : aps.length;
}
/**
*
- * @param viewId
- * @return all AlignmentPanels concerning the viewId sequence set
+ * @param alignmentId
+ * @return all AlignmentPanels concerning the alignmentId sequence set
*/
- public static AlignmentPanel[] getAlignmentPanels(String viewId)
+ public static AlignmentPanel[] getAlignmentPanels(String alignmentId)
{
int count = 0;
if (Desktop.desktop == null)
AlignFrame af = (AlignFrame) frames[t];
for (int a = 0; a < af.alignPanels.size(); a++)
{
- if (viewId
+ if (alignmentId
.equals(((AlignmentPanel) af.alignPanels.elementAt(a)).av
.getSequenceSetId()))
{
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;
avp.clear();
return afs;
}
+ public AppJmol[] getJmols()
+ {
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+
+ if (frames == null)
+ {
+ return null;
+ }
+ Vector avp = new Vector();
+ try
+ {
+ // REVERSE ORDER
+ for (int i = frames.length - 1; i > -1; i--)
+ {
+ if (frames[i] instanceof AppJmol)
+ {
+ AppJmol af = (AppJmol) frames[i];
+ avp.addElement(af);
+ }
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ if (avp.size() == 0)
+ {
+ return null;
+ }
+ AppJmol afs[] = new AppJmol[avp.size()];
+ for (int i = 0, j = avp.size(); i < j; i++)
+ {
+ afs[i] = (AppJmol) avp.elementAt(i);
+ }
+ avp.clear();
+ return afs;
+ }
/**
* Add Groovy Support to Jalview
/**
* 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();
}
}
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
- jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
- .addPropertyChangeListener(changeSupport);
- (t2 = new Thread(jalview.ws.jws2.Jws2Discoverer.getDiscoverer()))
- .start();
+ if (jalview.ws.jws2.Jws2Discoverer.getDiscoverer().isRunning())
+ {
+ jalview.ws.jws2.Jws2Discoverer.getDiscoverer().setAborted(true);
+ }
+ t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer(
+ changeSupport);
+
+ }
+ Thread t3=null;
+ {
+ // TODO: do rest service discovery
}
if (blocking)
{
}
alive = (t1 != null && t1.isAlive())
|| (t2 != null && t2.isAlive())
+ || (t3 != null && t3.isAlive())
|| (t0 != null && t0.isAlive());
}
}
}
/**
+ * called to check if the service discovery process completed successfully.
+ *
+ * @param evt
+ */
+ protected void JalviewServicesChanged(PropertyChangeEvent evt)
+ {
+ if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
+ {
+ final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+ .getErrorMessages();
+ if (ermsg != null)
+ {
+ 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;
+
+ }
+ });
+ }
+ }
+ else
+ {
+ Cache.log
+ .error("Errors reported by JABA discovery service. Check web services preferences.\n"
+ + ermsg);
+ }
+ }
+ }
+ }
+
+ private Runnable serviceChangedDialog = null;
+
+ /**
* start a thread to open a URL in the configured browser. Pops up a warning
* dialog to the user if there is an exception when calling out to the browser
* to open the URL.
*/
public static void showUrl(final String url)
{
+ showUrl(url, Desktop.instance);
+ }
+ /**
+ * Like showUrl but allows progress handler to be specified
+ * @param url
+ * @param progress (null) or object implementing IProgressIndicator
+ */
+ public static void showUrl(final String url, final IProgressIndicator progress)
+ {
new Thread(new Runnable()
{
public void run()
{
try
{
+ if (progress!=null) {
+ progress.setProgressBar("Opening "+url, this.hashCode());
+ }
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
ex.printStackTrace();
}
+ if (progress!=null) {
+ progress.setProgressBar(null, this.hashCode());
+ }
}
}).start();
}
return wsparamManager;
}
+
}
git://source.jalview.org / jalview.git / blobdiff