*/
package jalview.gui;
-import java.awt.Container;
-import java.util.BitSet;
-
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JalviewJmolBinding;
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.popup.JmolPopup;
import org.openscience.jmol.app.jmolpanel.AppConsole;
-public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
+public class AppJmolBinding extends JalviewJmolBinding
{
-
- /**
- *
- */
private AppJmol appJmolWindow;
+ private FeatureRenderer fr = null;
+
public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
String protocol)
appJmolWindow = appJmol;
}
- FeatureRenderer fr = null;
-
@Override
- public jalview.api.FeatureRenderer getFeatureRenderer(
+ public FeatureRenderer getFeatureRenderer(
AlignmentViewPanel alignment)
{
AlignmentPanel ap = (alignment == null) ? appJmolWindow.ap
}
@Override
- public jalview.api.SequenceRenderer getSequenceRenderer(
+ public SequenceRenderer getSequenceRenderer(
AlignmentViewPanel alignment)
{
return new SequenceRenderer(((AlignmentPanel) alignment).av);
AlignmentPanel ap = (AlignmentPanel) source, topap;
// ignore events from panels not used to colour this view
if (!appJmolWindow.isUsedforcolourby(ap))
+ {
return;
+ }
if (!isLoadingFromArchive())
{
colourBySequence(ap.av.getShowSequenceFeatures(), ap);
public void newJmolPopup(boolean translateLocale, String menuName,
boolean asPopup)
{
-
jmolpopup = new JmolPopup();
jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
}
*/
public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
{
- for (int pe = 0; pe < pdbentry.length; pe++)
+ for (int pe = 0; pe < getPdbCount(); pe++)
{
- if (pdbentry[pe].getFile().equals(pdbFile))
+ if (getPdbEntry(pe).getFile().equals(pdbFile))
{
addSequence(pe, seq);
}
protected void releaseUIResources()
{
appJmolWindow = null;
- if (console != null)
- {
- try
- {
- console.setVisible(false);
- } catch (Error e)
- {
- } catch (Exception x)
- {
- }
- ;
- console = null;
- }
-
+ closeConsole();
}
@Override
if (svl instanceof SeqPanel)
{
appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
-
}
- ;
}
}