2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.api.AlignmentViewPanel;
24 import jalview.api.structures.JalviewStructureDisplayI;
25 import jalview.datamodel.PDBEntry;
26 import jalview.datamodel.SequenceI;
27 import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
28 import jalview.io.DataSourceType;
29 import jalview.structure.StructureSelectionManager;
31 import javax.swing.JComponent;
32 import javax.swing.SwingUtilities;
34 public class JalviewChimeraBindingModel extends JalviewChimeraBinding
36 public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
37 StructureSelectionManager ssm, PDBEntry[] pdbentry,
38 SequenceI[][] sequenceIs, DataSourceType protocol)
40 super(ssm, pdbentry, sequenceIs, protocol);
41 setViewer(chimeraViewFrame);
45 public jalview.api.SequenceRenderer getSequenceRenderer(
46 AlignmentViewPanel alignment)
48 return new SequenceRenderer(((AlignmentPanel) alignment).av);
52 public void refreshGUI()
54 javax.swing.SwingUtilities.invokeLater(new Runnable()
59 JalviewStructureDisplayI theViewer = getViewer();
60 theViewer.updateTitleAndMenus();
61 ((JComponent) theViewer).revalidate();
67 public void updateColours(Object source)
69 AlignmentViewPanel ap = (AlignmentViewPanel) source;
70 // ignore events from panels not used to colour this view
71 if (!getViewer().isUsedForColourBy(ap))
75 if (!isLoadingFromArchive())
82 public void releaseReferences(Object svl)
87 protected void releaseUIResources()
92 public void refreshPdbEntries()
97 * Send an asynchronous command to Chimera, in a new thread, optionally with
98 * an 'in progress' message in a progress bar somewhere
101 protected void sendAsynchronousCommand(final String command,
102 final String progressMsg)
104 final JalviewStructureDisplayI theViewer = getViewer();
105 final long handle = progressMsg == null ? 0
106 : theViewer.startProgressBar(progressMsg);
107 SwingUtilities.invokeLater(new Runnable()
114 executeCommand(command, false);
117 if (progressMsg != null)
119 theViewer.stopProgressBar(null, handle);