+/*
+ * 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 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;
+import javax.swing.SwingUtilities;
+
public class JalviewChimeraBindingModel extends JalviewChimeraBinding
{
private ChimeraViewFrame cvf;
- 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;
}
@Override
- public FeatureRenderer getFeatureRenderer(
- AlignmentViewPanel alignment)
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
AlignmentPanel ap = (alignment == null) ? cvf.getAlignmentPanel()
: (AlignmentPanel) alignment;
if (ap.av.isShowSequenceFeatures())
{
- if (fr == null)
- {
- fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
- }
- else
- {
- ap.updateFeatureRenderer(fr);
- }
+ return ap.getSeqPanel().seqCanvas.fr;
}
- return fr;
+ return null;
}
@Override
{
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 thread = new Thread(new Runnable()
+ final long handle = progressMsg == null ? 0
+ : cvf.startProgressBar(progressMsg);
+ SwingUtilities.invokeLater(new Runnable()
{
-
@Override
public void run()
{
- long stm = cvf.startProgressBar(progressMsg);
- try
- {
- sendChimeraCommand(command, false);
- } finally
- {
- cvf.stopProgressBar(null, stm);
- }
+ try
+ {
+ sendChimeraCommand(command, false);
+ } finally
+ {
+ if (progressMsg != null)
+ {
+ cvf.stopProgressBar(null, handle);
+ }
+ }
}
});
- thread.start();
+ }
+ @Override
+ public JalviewStructureDisplayI getViewer()
+ {
+ return cvf;
}
}