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;
30 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
32 import javax.swing.SwingUtilities;
34 public class JalviewChimeraBindingModel extends JalviewChimeraBinding
36 private ChimeraViewFrame cvf;
38 public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
39 StructureSelectionManager ssm, PDBEntry[] pdbentry,
40 SequenceI[][] sequenceIs, DataSourceType protocol)
42 super(ssm, pdbentry, sequenceIs, protocol);
43 cvf = chimeraViewFrame;
47 public FeatureRendererModel getFeatureRenderer(AlignmentViewPanel alignment)
49 AlignmentPanel ap = (alignment == null) ? cvf.getAlignmentPanel()
50 : (AlignmentPanel) alignment;
51 if (ap.av.isShowSequenceFeatures())
53 return ap.getSeqPanel().seqCanvas.fr;
60 public jalview.api.SequenceRenderer getSequenceRenderer(
61 AlignmentViewPanel alignment)
63 return new SequenceRenderer(((AlignmentPanel) alignment).av);
67 public void refreshGUI()
69 javax.swing.SwingUtilities.invokeLater(new Runnable()
74 cvf.updateTitleAndMenus();
81 public void updateColours(Object source)
83 AlignmentPanel ap = (AlignmentPanel) source;
84 // ignore events from panels not used to colour this view
85 if (!cvf.isUsedforcolourby(ap))
89 if (!isLoadingFromArchive())
96 public void releaseReferences(Object svl)
101 protected void releaseUIResources()
106 public void refreshPdbEntries()
111 * Send an asynchronous command to Chimera, in a new thread, optionally with
112 * an 'in progress' message in a progress bar somewhere
115 protected void sendAsynchronousCommand(final String command,
116 final String progressMsg)
118 final long handle = progressMsg == null ? 0
119 : cvf.startProgressBar(progressMsg);
120 SwingUtilities.invokeLater(new Runnable()
127 sendChimeraCommand(command, false);
130 if (progressMsg != null)
132 cvf.stopProgressBar(null, handle);
140 public JalviewStructureDisplayI getViewer()