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.structure.StructureSelectionManager;
29 public class JalviewChimeraBindingModel extends JalviewChimeraBinding
31 private ChimeraViewFrame cvf;
33 private FeatureRenderer fr = null;
36 public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
37 StructureSelectionManager ssm, PDBEntry[] pdbentry,
38 SequenceI[][] sequenceIs, String protocol)
40 super(ssm, pdbentry, sequenceIs, protocol);
41 cvf = chimeraViewFrame;
45 public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
47 AlignmentPanel ap = (alignment == null) ? cvf.getAlignmentPanel()
48 : (AlignmentPanel) alignment;
49 if (ap.av.isShowSequenceFeatures())
53 fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
57 ap.updateFeatureRenderer(fr);
65 public jalview.api.SequenceRenderer getSequenceRenderer(
66 AlignmentViewPanel alignment)
68 return new SequenceRenderer(((AlignmentPanel) alignment).av);
72 public void refreshGUI()
74 javax.swing.SwingUtilities.invokeLater(new Runnable()
79 cvf.updateTitleAndMenus();
86 public void updateColours(Object source)
88 AlignmentPanel ap = (AlignmentPanel) source;
89 // ignore events from panels not used to colour this view
90 if (!cvf.isUsedforcolourby(ap))
94 if (!isLoadingFromArchive())
96 colourBySequence(ap.av.isShowSequenceFeatures(), ap);
101 public void releaseReferences(Object svl)
106 protected void releaseUIResources()
111 public void refreshPdbEntries()
116 * Send an asynchronous command to Chimera, in a new thread, optionally with
117 * an 'in progress' message in a progress bar somewhere
120 protected void sendAsynchronousCommand(final String command,
121 final String progressMsg)
123 Thread thread = new Thread(new Runnable()
129 long stm = cvf.startProgressBar(progressMsg);
132 sendChimeraCommand(command, false);
135 cvf.stopProgressBar(null, stm);