import jalview.ext.jmol.JalviewJmolBinding;
import jalview.io.DataSourceType;
import jalview.structure.StructureSelectionManager;
+import jalview.util.Platform;
import java.awt.Container;
+import java.io.File;
+import java.util.List;
import java.util.Map;
import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.java.BS;
-import org.openscience.jmol.app.jmolpanel.console.AppConsole;
+
+import javajs.util.BS;
public class AppJmolBinding extends JalviewJmolBinding
{
- private AppJmol appJmolWindow;
+ protected AppJmol appJmolWindow;
public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+ DataSourceType protocol)
{
super(sSm, pdbentry, sequenceIs, protocol);
appJmolWindow = appJmol;
}
@Override
+ protected IProgressIndicator getIProgressIndicator()
+ {
+ return appJmolWindow.progressBar;
+ }
+
+ @Override
public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
return new SequenceRenderer(((AlignmentPanel) alignment).av);
public void run()
{
appJmolWindow.updateTitleAndMenus();
+ // initiates a colourbySequence
+ // via seqColour_ActionPerformed.
appJmolWindow.revalidate();
}
});
Container consolePanel, String buttonsToShow)
{
viewer.setJmolCallbackListener(this);
- return new AppConsole(viewer, consolePanel, buttonsToShow);
+ return null;//BH can't do this yet. new AppConsole(viewer, consolePanel, buttonsToShow);
}
@Override
public jalview.api.FeatureRenderer getFeatureRenderer(
AlignmentViewPanel alignment)
{
- AlignmentPanel ap = (alignment == null) ? appJmolWindow
- .getAlignmentPanel() : (AlignmentPanel) alignment;
+ AlignmentPanel ap = (alignment == null)
+ ? appJmolWindow.getAlignmentPanel()
+ : (AlignmentPanel) alignment;
if (ap.av.isShowSequenceFeatures())
{
return ap.av.getAlignPanel().getSeqPanel().seqCanvas.fr;
return null;
}
+
+ @SuppressWarnings("unused")
+ public void cacheFiles(List<File> files)
+ {
+ if (files == null)
+ {
+ return;
+ }
+ for (File f : files)
+ {
+ Platform.cacheFileData(f);
+ }
+ }
}