-/**
+/*
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.util.BitSet;
-
+import jalview.api.AlignmentViewPanel;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.io.DataSourceType;
+import jalview.structure.StructureSelectionManager;
+
+import java.awt.Container;
+import java.util.Map;
-import org.jmol.popup.JmolPopup;
+import org.jmol.api.JmolAppConsoleInterface;
+import org.jmol.console.AppletConsole;
+import org.jmol.java.BS;
-class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
+class AppletJmolBinding extends 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, DataSourceType protocol)
{
- super(pdbentry, seq, chains, protocol);
+ super(sSm, pdbentry, seq, protocol);
appletJmolBinding = appletJmol;
}
- public jalview.api.FeatureRenderer getFeatureRenderer()
+ @Override
+ public jalview.api.FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment)
{
- if (appletJmolBinding.ap.av.showSequenceFeatures)
- {
- if (appletJmolBinding.fr == null)
- {
- appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(appletJmolBinding.ap.av);
- }
-
- appletJmolBinding.fr.transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas.getFeatureRenderer());
- }
-
- return appletJmolBinding.fr;
+ return appletJmolBinding.ap.getFeatureRenderer();
}
- public jalview.api.SequenceRenderer getSequenceRenderer()
+ @Override
+ public jalview.api.SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment)
{
- return new SequenceRenderer(appletJmolBinding.ap.av);
+ return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
+ @Override
public void sendConsoleEcho(String strEcho)
{
if (appletJmolBinding.scriptWindow == null)
+ {
appletJmolBinding.showConsole(true);
+ }
- appletJmolBinding.history.append("\n" + strEcho);
+ appletJmolBinding.addToHistory(strEcho);
}
+ @Override
public void sendConsoleMessage(String strStatus)
{
if (appletJmolBinding.history != null && strStatus != null
&& !strStatus.equals("Script completed"))
{
- appletJmolBinding.history.append("\n" + strStatus);
+ appletJmolBinding.addToHistory(strStatus);
}
}
+ @Override
public void showUrl(String url, String target)
{
appletJmolBinding.ap.alignFrame.showURL(url, target);
}
- public void updateUI()
+ @Override
+ public void refreshGUI()
{
appletJmolBinding.updateTitleAndMenus();
}
-
+
+ @Override
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
- colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+ colourBySequence(ap);
}
+ @Override
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 JmolAwtPopup(); // is this used?
+ // jmolpopup.jpiInitialize((viewer), menuName);
}
+ @Override
public void notifyScriptTermination(String strStatus, int msWalltime)
{
// do nothing.
}
- public void selectionChanged(BitSet arg0)
+ @Override
+ public void selectionChanged(BS arg0)
{
// TODO Auto-generated method stub
-
+
}
+ @Override
public void refreshPdbEntries()
{
- // TODO Auto-generated method stub
-
+ // noop
+ }
+
+ @Override
+ public void showConsole(boolean show)
+ {
+ appletJmolBinding.showConsole(show);
+ }
+
+ @Override
+ protected JmolAppConsoleInterface createJmolConsole(
+ Container consolePanel, String buttonsToShow)
+ {
+ JmolAppConsoleInterface appc = new AppletConsole();
+ appc.start(viewer);
+ return appc;
}
-}
\ No newline at end of file
+ @Override
+ protected void releaseUIResources()
+ {
+ appletJmolBinding = null;
+ closeConsole();
+ }
+
+ @Override
+ public void releaseReferences(Object svl)
+ {
+ }
+
+ @Override
+ public int[] resizeInnerPanel(String data)
+ {
+ return null;
+ }
+
+ @Override
+ public Map<String, Object> getJSpecViewProperty(String arg0)
+ {
+ return null;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff