-/**
+/*
+ * 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.
+ *
+ * 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.
+ *
+ * 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 <http://www.gnu.org/licenses/>.
*/
package jalview.gui;
+import java.awt.Container;
+import java.awt.event.ComponentEvent;
+import java.awt.event.ComponentListener;
+import java.awt.event.ContainerEvent;
+import java.awt.event.ContainerListener;
import java.util.BitSet;
+import javax.swing.JPanel;
+
+import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.structure.StructureSelectionManager;
+import org.jmol.api.JmolAppConsoleInterface;
+import org.jmol.api.JmolViewer;
import org.jmol.popup.JmolPopup;
+import org.openscience.jmol.app.jmolpanel.AppConsole;
public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
{
*/
private AppJmol appJmolWindow;
- public AppJmolBinding(AppJmol appJmol, PDBEntry[] pdbentry,
+ public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm, PDBEntry[] pdbentry,
SequenceI[][] sequenceIs, String[][] chains, String protocol)
{
- super(pdbentry, sequenceIs, chains, protocol);
+ super(sSm, pdbentry, sequenceIs, chains, protocol);
appJmolWindow = appJmol;
}
FeatureRenderer fr = null;
@Override
- public jalview.api.FeatureRenderer getFeatureRenderer()
+ public jalview.api.FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
- if (appJmolWindow.ap.av.showSequenceFeatures)
+ AlignmentPanel ap = (alignment==null) ? appJmolWindow.ap : (AlignmentPanel) alignment;
+ if (ap.av.showSequenceFeatures)
{
- if (fr == null)
+ if (fr==null)
{
- fr = new FeatureRenderer(appJmolWindow.ap);
+ fr=ap.cloneFeatureRenderer();
+ } else {
+ ap.updateFeatureRenderer(fr);
}
-
- fr.transferSettings(appJmolWindow.ap.seqPanel.seqCanvas
- .getFeatureRenderer());
}
return fr;
}
@Override
- public jalview.api.SequenceRenderer getSequenceRenderer()
+ public jalview.api.SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
- return new SequenceRenderer(appJmolWindow.ap.av);
+ return new SequenceRenderer(((AlignmentPanel)alignment).av);
}
public void sendConsoleEcho(String strEcho)
{
- if (appJmolWindow.scriptWindow != null)
+ if (console != null)
{
- appJmolWindow.scriptWindow.sendConsoleEcho(strEcho);
+ console.sendConsoleEcho(strEcho);
}
}
public void sendConsoleMessage(String strStatus)
{
- if (appJmolWindow.scriptWindow != null && strStatus != null)
+ if (console != null && strStatus != null)
// && !strStatus.equals("Script completed"))
// should we squash the script completed string ?
{
- appJmolWindow.scriptWindow.sendConsoleMessage(strStatus);
+ console.sendConsoleMessage(strStatus);
}
}
public void refreshGUI()
{
// appJmolWindow.repaint();
- appJmolWindow.updateTitleAndMenus();
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ appJmolWindow.updateTitleAndMenus();
+ appJmolWindow.revalidate();
+ }
+ });
}
public void updateColours(Object source)
{
- AlignmentPanel ap = (AlignmentPanel) source;
- if (appJmolWindow.ap.alignFrame.getCurrentView() != ap.av)
+ AlignmentPanel ap = (AlignmentPanel) source,topap;
+ // ignore events from panels not used to colour this view
+ if (!appJmolWindow.isUsedforcolourby(ap))
return;
-
- colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+ if (!isLoadingFromArchive()) {
+ colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+ }
}
public void notifyScriptTermination(String strStatus, int msWalltime)
{
- if (appJmolWindow.scriptWindow != null)
- appJmolWindow.scriptWindow.notifyScriptTermination(strStatus,
- msWalltime);
+ // todo - script termination doesn't happen ?
+ // if (console != null)
+ // console.notifyScriptTermination(strStatus,
+ // msWalltime);
}
public void showUrl(String url)
boolean asPopup)
{
- jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
+ jmolpopup = new JmolPopup();
+ jmolpopup.initialize(viewer, translateLocale, menuName,
asPopup);
}
}
+ public void showConsole(boolean b)
+ {
+ appJmolWindow.showConsole(b);
+ }
/**
* add the given sequences to the mapping scope for the given pdb file handle
}
}
-}
\ No newline at end of file
+ @Override
+ protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+ Container consolePanel, String buttonsToShow)
+ {
+ return new AppConsole(viewer, consolePanel, buttonsToShow);
+ }
+
+ @Override
+ protected void releaseUIResources()
+ {
+ appJmolWindow = null;
+ if (console != null)
+ {
+ try
+ {
+ console.setVisible(false);
+ } catch (Error e)
+ {
+ } catch (Exception x)
+ {
+ }
+ ;
+ console = null;
+ }
+
+ }
+
+ @Override
+ public void releaseReferences(Object svl)
+ {
+ if (svl instanceof SeqPanel) {
+ appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
+
+ };
+ }
+}