import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.structure.StructureSelectionManager;
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.api.JmolViewer;
*/
private AppJmol appJmolWindow;
- public AppJmolBinding(AppJmol appJmol, PDBEntry[] pdbentry,
+ public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm, PDBEntry[] pdbentry,
SequenceI[][] sequenceIs, String[][] chains, String protocol)
{
- super(pdbentry, sequenceIs, chains, protocol);
+ super(sSm, pdbentry, sequenceIs, chains, protocol);
appJmolWindow = appJmol;
}
{
if (fr == null)
{
- fr = new FeatureRenderer((AlignmentPanel)alignment);
+ fr = new FeatureRenderer(ap);
}
- fr.transferSettings(((AlignmentPanel)alignment).
+ fr.transferSettings(ap.
seqPanel.seqCanvas.getFeatureRenderer());
}
{
AlignmentPanel ap = (AlignmentPanel) source,topap;
// ignore events from unrelated or non-user interactive frames
- if ((topap=appJmolWindow.getAlignmentPanelFor(ap.av.getAlignment()))==null || topap.alignFrame.getCurrentView() != ap.av || appJmolWindow.isUsedforcolourby(ap))
+ if ((topap=appJmolWindow.getAlignmentPanelFor(ap.av.getAlignment()))==null || topap.alignFrame.getCurrentView() != ap.av || !appJmolWindow.isUsedforcolourby(ap))
return;
if (!isLoadingFromArchive()) {
colourBySequence(ap.av.getShowSequenceFeatures(), ap);