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.datamodel.PDBEntry;
25 import jalview.datamodel.SequenceI;
26 import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
27 import jalview.io.DataSourceType;
28 import jalview.structure.StructureSelectionManager;
30 public class JalviewChimeraBindingModel extends JalviewChimeraBinding
32 private ChimeraViewFrame cvf;
34 private FeatureRenderer fr = null;
36 public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
37 StructureSelectionManager ssm, PDBEntry[] pdbentry,
38 SequenceI[][] sequenceIs, String[][] chains,
39 DataSourceType protocol)
41 super(ssm, pdbentry, sequenceIs, chains, protocol);
42 cvf = chimeraViewFrame;
46 public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
48 AlignmentPanel ap = (alignment == null) ? cvf.getAlignmentPanel()
49 : (AlignmentPanel) alignment;
50 if (ap.av.isShowSequenceFeatures())
54 fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
58 ap.updateFeatureRenderer(fr);
66 public jalview.api.SequenceRenderer getSequenceRenderer(
67 AlignmentViewPanel alignment)
69 return new SequenceRenderer(((AlignmentPanel) alignment).av);
73 public void refreshGUI()
75 javax.swing.SwingUtilities.invokeLater(new Runnable()
80 cvf.updateTitleAndMenus();
87 public void updateColours(Object source)
89 AlignmentPanel ap = (AlignmentPanel) source;
90 // ignore events from panels not used to colour this view
91 if (!cvf.isUsedforcolourby(ap))
95 if (!isLoadingFromArchive())
97 colourBySequence(ap.av.isShowSequenceFeatures(), ap);
102 public void releaseReferences(Object svl)
107 protected void releaseUIResources()
112 public void refreshPdbEntries()
117 * Send an asynchronous command to Chimera, in a new thread, optionally with
118 * an 'in progress' message in a progress bar somewhere
121 protected void sendAsynchronousCommand(final String command,
122 final String progressMsg)
124 Thread thread = new Thread(new Runnable()
130 long stm = cvf.startProgressBar(progressMsg);
133 sendChimeraCommand(command, false);
136 cvf.stopProgressBar(null, stm);