package jalview.gui;
import jalview.api.AlignmentViewPanel;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
+import jalview.io.DataSourceType;
import jalview.structure.StructureSelectionManager;
public class JalviewChimeraBindingModel extends JalviewChimeraBinding
private FeatureRenderer fr = null;
+
public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
StructureSelectionManager ssm, PDBEntry[] pdbentry,
- SequenceI[][] sequenceIs, String[][] chains, String protocol)
+ SequenceI[][] sequenceIs, DataSourceType protocol)
{
- super(ssm, pdbentry, sequenceIs, chains, protocol);
+ super(ssm, pdbentry, sequenceIs, protocol);
cvf = chimeraViewFrame;
}
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
cvf.updateTitleAndMenus();
});
}
+ @Override
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
}
if (!isLoadingFromArchive())
{
- colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+ colourBySequence(ap);
}
}
* Send an asynchronous command to Chimera, in a new thread, optionally with
* an 'in progress' message in a progress bar somewhere
*/
+ @Override
protected void sendAsynchronousCommand(final String command,
final String progressMsg)
{
thread.start();
}
+
+ @Override
+ public JalviewStructureDisplayI getViewer()
+ {
+ return cvf;
+ }
}