+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.gui;
+import javax.swing.JComponent;
+import javax.swing.SwingUtilities;
+
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 ChimeraViewFrame cvf;
-
public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
StructureSelectionManager ssm, PDBEntry[] pdbentry,
- SequenceI[][] sequenceIs, String[][] chains, String protocol)
+ SequenceI[][] sequenceIs, DataSourceType protocol)
{
- super(ssm, pdbentry, sequenceIs, chains, protocol);
- cvf = chimeraViewFrame;
- }
-
- FeatureRenderer fr = null;
-
- @Override
- public jalview.api.FeatureRenderer getFeatureRenderer(
- AlignmentViewPanel alignment)
- {
- AlignmentPanel ap = (alignment == null) ? cvf.ap
- : (AlignmentPanel) alignment;
- if (ap.av.showSequenceFeatures)
- {
- if (fr == null)
- {
- fr = ap.cloneFeatureRenderer();
- }
- else
- {
- ap.updateFeatureRenderer(fr);
- }
- }
-
- return fr;
+ super(ssm, pdbentry, sequenceIs, protocol);
+ setViewer(chimeraViewFrame);
}
@Override
{
return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
+
@Override
public void refreshGUI()
{
- // appJmolWindow.repaint();
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
- cvf.updateTitleAndMenus();
- cvf.revalidate();
+ JalviewStructureDisplayI theViewer = getViewer();
+ theViewer.updateTitleAndMenus();
+ ((JComponent) theViewer).revalidate();
}
});
}
-
- public void updateColours(Object source)
- {
- AlignmentPanel ap = (AlignmentPanel) source, topap;
- // ignore events from panels not used to colour this view
- if (!cvf.isUsedforcolourby(ap))
- {
- return;
- }
- if (!isLoadingFromArchive())
- {
- colourBySequence(ap.av.getShowSequenceFeatures(), ap);
- }
- }
- @Override
- public void releaseReferences(Object svl)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- protected void releaseUIResources()
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void refreshPdbEntries()
- {
- // TODO Auto-generated method stub
-
- }
}