/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.awt.Container;
-import java.util.BitSet;
-
+import jalview.api.AlignmentViewPanel;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.structure.StructureSelectionManager;
+
+import java.awt.Container;
+import java.util.BitSet;
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.api.JmolViewer;
-import org.jmol.applet.AppletConsole;
import org.jmol.popup.JmolPopup;
class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
*/
private AppletJmol appletJmolBinding;
- public AppletJmolBinding(AppletJmol appletJmol, PDBEntry[] pdbentry, SequenceI[][] seq,
- String[][] chains, String protocol)
+ public AppletJmolBinding(AppletJmol appletJmol,
+ StructureSelectionManager sSm, PDBEntry[] pdbentry,
+ SequenceI[][] seq, String[][] chains, String protocol)
{
- super(pdbentry, seq, chains, protocol);
+ super(sSm, pdbentry, seq, chains, protocol);
appletJmolBinding = appletJmol;
}
- public jalview.api.FeatureRenderer getFeatureRenderer()
+ public jalview.api.FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment)
{
- if (appletJmolBinding.ap.av.showSequenceFeatures)
+ AlignmentPanel ap = (AlignmentPanel) alignment;
+ if (appletJmolBinding.ap.av.isShowSequenceFeatures())
{
if (appletJmolBinding.fr == null)
{
- appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(appletJmolBinding.ap.av);
+ appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(
+ appletJmolBinding.ap.av);
}
- appletJmolBinding.fr.transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas.getFeatureRenderer());
+ appletJmolBinding.fr
+ .transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas
+ .getFeatureRenderer());
}
return appletJmolBinding.fr;
}
- public jalview.api.SequenceRenderer getSequenceRenderer()
+ public jalview.api.SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment)
{
- return new SequenceRenderer(appletJmolBinding.ap.av);
+ return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
public void sendConsoleEcho(String strEcho)
{
if (appletJmolBinding.scriptWindow == null)
+ {
appletJmolBinding.showConsole(true);
+ }
appletJmolBinding.history.append("\n" + strEcho);
}
{
appletJmolBinding.updateTitleAndMenus();
}
-
+
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
- colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+ colourBySequence(ap.av.isShowSequenceFeatures(), ap);
}
public void showUrl(String url)
{
try
{
- appletJmolBinding.ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
- "jmol");
+ appletJmolBinding.ap.av.applet.getAppletContext().showDocument(
+ new java.net.URL(url), "jmol");
} catch (java.net.MalformedURLException ex)
{
}
}
- public void newJmolPopup(boolean translateLocale, String menuName, boolean asPopup)
+ public void newJmolPopup(boolean translateLocale, String menuName,
+ boolean asPopup)
{
-
- jmolpopup = JmolPopup.newJmolPopup(viewer,translateLocale, menuName,asPopup);
+
+ jmolpopup = new JmolPopup();
+ jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
}
public void notifyScriptTermination(String strStatus, int msWalltime)
public void selectionChanged(BitSet arg0)
{
// TODO Auto-generated method stub
-
+
}
+ @Override
public void refreshPdbEntries()
{
- // TODO Auto-generated method stub
-
+ // noop
}
@Override
protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
Container consolePanel, String buttonsToShow)
{
- return new AppletConsole(viewer2, consolePanel);
+ // return new org.jmol.console.AppletConsole(viewer2, consolePanel);
+ JmolAppConsoleInterface appc = new org.jmol.console.AppletConsole()
+ .getAppConsole(viewer2);
+ return appc;
}
+
@Override
protected void releaseUIResources()
{
appletJmolBinding = null;
- if (console!=null) {
- try {
- console.setVisible(false);
- } catch (Error e) {} catch (Exception x) {};
- console=null;
- }
-
+ closeConsole();
+ }
+
+ @Override
+ public void releaseReferences(Object svl)
+ {
}
+ @Override
+ public void resizeInnerPanel(String data)
+ {
+ // TODO Auto-generated method stub
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff