2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 import java.awt.Container;
21 import java.awt.event.ComponentEvent;
22 import java.awt.event.ComponentListener;
23 import java.awt.event.ContainerEvent;
24 import java.awt.event.ContainerListener;
25 import java.util.BitSet;
27 import javax.swing.JPanel;
29 import jalview.api.AlignmentViewPanel;
30 import jalview.bin.Cache;
31 import jalview.datamodel.AlignmentI;
32 import jalview.datamodel.PDBEntry;
33 import jalview.datamodel.SequenceI;
34 import jalview.structure.StructureSelectionManager;
36 import org.jmol.api.JmolAppConsoleInterface;
37 import org.jmol.api.JmolViewer;
38 import org.jmol.popup.JmolPopup;
39 import org.openscience.jmol.app.jmolpanel.AppConsole;
41 public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
47 private AppJmol appJmolWindow;
49 public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
50 PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
53 super(sSm, pdbentry, sequenceIs, chains, protocol);
54 appJmolWindow = appJmol;
57 FeatureRenderer fr = null;
60 public jalview.api.FeatureRenderer getFeatureRenderer(
61 AlignmentViewPanel alignment)
63 AlignmentPanel ap = (alignment == null) ? appJmolWindow.ap
64 : (AlignmentPanel) alignment;
65 if (ap.av.showSequenceFeatures)
69 fr = ap.cloneFeatureRenderer();
73 ap.updateFeatureRenderer(fr);
81 public jalview.api.SequenceRenderer getSequenceRenderer(
82 AlignmentViewPanel alignment)
84 return new SequenceRenderer(((AlignmentPanel) alignment).av);
87 public void sendConsoleEcho(String strEcho)
91 console.sendConsoleEcho(strEcho);
95 public void sendConsoleMessage(String strStatus)
97 if (console != null && strStatus != null)
98 // && !strStatus.equals("Script completed"))
99 // should we squash the script completed string ?
101 console.sendConsoleMessage(strStatus);
106 public void showUrl(String url, String target)
110 jalview.util.BrowserLauncher.openURL(url);
111 } catch (Exception e)
113 Cache.log.error("Failed to launch Jmol-associated url " + url, e);
114 // TODO: 2.6 : warn user if browser was not configured.
119 public void refreshGUI()
121 // appJmolWindow.repaint();
122 javax.swing.SwingUtilities.invokeLater(new Runnable()
126 appJmolWindow.updateTitleAndMenus();
127 appJmolWindow.revalidate();
132 public void updateColours(Object source)
134 AlignmentPanel ap = (AlignmentPanel) source, topap;
135 // ignore events from panels not used to colour this view
136 if (!appJmolWindow.isUsedforcolourby(ap))
138 if (!isLoadingFromArchive())
140 colourBySequence(ap.av.getShowSequenceFeatures(), ap);
144 public void notifyScriptTermination(String strStatus, int msWalltime)
146 // todo - script termination doesn't happen ?
147 // if (console != null)
148 // console.notifyScriptTermination(strStatus,
152 public void showUrl(String url)
154 showUrl(url, "jmol");
157 public void newJmolPopup(boolean translateLocale, String menuName,
161 jmolpopup = new JmolPopup();
162 jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
165 public void selectionChanged(BitSet arg0)
167 // TODO Auto-generated method stub
171 public void refreshPdbEntries()
173 // TODO Auto-generated method stub
177 public void showConsole(boolean b)
179 appJmolWindow.showConsole(b);
183 * add the given sequences to the mapping scope for the given pdb file handle
186 * - pdbFile identifier
188 * - set of sequences it can be mapped to
190 public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
192 for (int pe = 0; pe < pdbentry.length; pe++)
194 if (pdbentry[pe].getFile().equals(pdbFile))
196 addSequence(pe, seq);
202 protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
203 Container consolePanel, String buttonsToShow)
205 return new AppConsole(viewer, consolePanel, buttonsToShow);
209 protected void releaseUIResources()
211 appJmolWindow = null;
216 console.setVisible(false);
219 } catch (Exception x)
229 public void releaseReferences(Object svl)
231 if (svl instanceof SeqPanel)
233 appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);