+/*
+ * 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;
{
private ChimeraViewFrame cvf;
+ private FeatureRenderer fr = null;
+
public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
StructureSelectionManager ssm, PDBEntry[] pdbentry,
SequenceI[][] sequenceIs, String[][] chains, String protocol)
cvf = chimeraViewFrame;
}
- FeatureRenderer fr = null;
-
@Override
- public jalview.api.FeatureRenderer getFeatureRenderer(
- AlignmentViewPanel alignment)
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
- AlignmentPanel ap = (alignment == null) ? cvf.ap
+ AlignmentPanel ap = (alignment == null) ? cvf.getAlignmentPanel()
: (AlignmentPanel) alignment;
if (ap.av.isShowSequenceFeatures())
{
{
return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
+
@Override
public void refreshGUI()
{
- // appJmolWindow.repaint();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
public void run()
public void updateColours(Object source)
{
- AlignmentPanel ap = (AlignmentPanel) source, topap;
+ AlignmentPanel ap = (AlignmentPanel) source;
// ignore events from panels not used to colour this view
if (!cvf.isUsedforcolourby(ap))
{
colourBySequence(ap.av.isShowSequenceFeatures(), 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
-
}
- @Override
- public void showUrl(String url, String target)
+ /**
+ * Send an asynchronous command to Chimera, in a new thread, optionally with
+ * an 'in progress' message in a progress bar somewhere
+ */
+ protected void sendAsynchronousCommand(final String command,
+ final String progressMsg)
{
- // TODO Auto-generated method stub
+ Thread thread = new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ long stm = cvf.startProgressBar(progressMsg);
+ try
+ {
+ sendChimeraCommand(command, false);
+ } finally
+ {
+ cvf.stopProgressBar(null, stm);
+ }
+ }
+ });
+ thread.start();
}
}