/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
package jalview.gui;
import jalview.api.AlignmentViewPanel;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
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.api.JmolAppConsoleInterface;
-import org.jmol.java.BS;
+import javajs.util.BS;
import org.openscience.jmol.app.jmolpanel.console.AppConsole;
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)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+ DataSourceType protocol)
{
- super(sSm, pdbentry, sequenceIs, chains, protocol);
+ super(sSm, pdbentry, sequenceIs, protocol);
appJmolWindow = appJmol;
}
@Override
- public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+ protected IProgressIndicator getIProgressIndicator()
{
- AlignmentPanel ap = (alignment == null) ? appJmolWindow
- .getAlignmentPanel() : (AlignmentPanel) alignment;
- if (ap.av.isShowSequenceFeatures())
- {
- if (fr == null)
- {
- fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
- }
- else
- {
- ap.updateFeatureRenderer(fr);
- }
- }
-
- return fr;
+ return appJmolWindow.progressBar;
}
@Override
// appJmolWindow.repaint();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
appJmolWindow.updateTitleAndMenus();
});
}
+ @Override
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
// msWalltime);
}
+ @Override
public void showUrl(String url)
{
showUrl(url, "jmol");
// TODO Auto-generated method stub
return null;
}
+
+ @Override
+ public JalviewStructureDisplayI getViewer()
+ {
+ return appJmolWindow;
+ }
+
+ @Override
+ public jalview.api.FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment)
+ {
+ AlignmentPanel ap = (alignment == null)
+ ? appJmolWindow.getAlignmentPanel()
+ : (AlignmentPanel) alignment;
+ if (ap.av.isShowSequenceFeatures())
+ {
+ return ap.av.getAlignPanel().getSeqPanel().seqCanvas.fr;
+ }
+
+ return null;
+ }
}