/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
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;
}
AlignmentPanel ap = (alignment==null) ? appJmolWindow.ap : (AlignmentPanel) alignment;
if (ap.av.showSequenceFeatures)
{
- if (fr == null)
+ if (fr==null)
{
- fr = new FeatureRenderer((AlignmentPanel)alignment);
+ fr=ap.cloneFeatureRenderer();
+ } else {
+ ap.updateFeatureRenderer(fr);
}
-
- fr.transferSettings(((AlignmentPanel)alignment).
- seqPanel.seqCanvas.getFeatureRenderer());
}
return fr;
public void updateColours(Object source)
{
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))
+ // ignore events from panels not used to colour this view
+ if (!appJmolWindow.isUsedforcolourby(ap))
return;
if (!isLoadingFromArchive()) {
colourBySequence(ap.av.getShowSequenceFeatures(), ap);
boolean asPopup)
{
- jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
+ jmolpopup = new JmolPopup();
+ jmolpopup.initialize(viewer, translateLocale, menuName,
asPopup);
}