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.bin.Cache;
26 import jalview.datamodel.PDBEntry;
27 import jalview.datamodel.SequenceI;
28 import jalview.ext.jmol.JalviewJmolBinding;
29 import jalview.io.DataSourceType;
30 import jalview.structure.StructureSelectionManager;
31 import jalview.util.Platform;
33 import java.awt.Container;
35 import java.util.List;
38 import org.jmol.api.JmolAppConsoleInterface;
40 import javajs.util.BS;
42 public class AppJmolBinding extends JalviewJmolBinding
44 protected AppJmol appJmolWindow;
46 public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
47 PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
48 DataSourceType protocol)
50 super(sSm, pdbentry, sequenceIs, protocol);
51 appJmolWindow = appJmol;
55 protected IProgressIndicator getIProgressIndicator()
57 return appJmolWindow.progressBar;
61 public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
63 return new SequenceRenderer(((AlignmentPanel) alignment).av);
67 public void sendConsoleEcho(String strEcho)
71 console.sendConsoleEcho(strEcho);
76 public void sendConsoleMessage(String strStatus)
78 if (console != null && strStatus != null)
79 // && !strStatus.equals("Script completed"))
80 // should we squash the script completed string ?
82 console.sendConsoleMessage(strStatus);
87 public void showUrl(String url, String target)
91 jalview.util.BrowserLauncher.openURL(url);
94 Cache.log.error("Failed to launch Jmol-associated url " + url, e);
95 // TODO: 2.6 : warn user if browser was not configured.
100 public void refreshGUI()
102 // appJmolWindow.repaint();
103 javax.swing.SwingUtilities.invokeLater(new Runnable()
108 appJmolWindow.updateTitleAndMenus();
109 appJmolWindow.revalidate();
115 public void updateColours(Object source)
117 AlignmentPanel ap = (AlignmentPanel) source;
118 // ignore events from panels not used to colour this view
119 if (!appJmolWindow.isUsedforcolourby(ap))
123 if (!isLoadingFromArchive())
125 colourBySequence(ap);
130 public void notifyScriptTermination(String strStatus, int msWalltime)
132 // todo - script termination doesn't happen ?
133 // if (console != null)
134 // console.notifyScriptTermination(strStatus,
139 public void showUrl(String url)
141 showUrl(url, "jmol");
144 public void newJmolPopup(String menuName)
146 // jmolpopup = new JmolAwtPopup();
147 // jmolpopup.jpiInitialize((viewer), menuName);
151 public void selectionChanged(BS arg0)
153 // TODO Auto-generated method stub
158 public void refreshPdbEntries()
160 // TODO Auto-generated method stub
165 public void showConsole(boolean b)
167 appJmolWindow.showConsole(b);
171 protected JmolAppConsoleInterface createJmolConsole(
172 Container consolePanel, String buttonsToShow)
174 viewer.setJmolCallbackListener(this);
175 return null;//BH can't do this yet. new AppConsole(viewer, consolePanel, buttonsToShow);
179 protected void releaseUIResources()
181 appJmolWindow = null;
186 public void releaseReferences(Object svl)
188 if (svl instanceof SeqPanel)
190 appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
195 public Map<String, Object> getJSpecViewProperty(String arg0)
197 // TODO Auto-generated method stub
202 public JalviewStructureDisplayI getViewer()
204 return appJmolWindow;
208 public jalview.api.FeatureRenderer getFeatureRenderer(
209 AlignmentViewPanel alignment)
211 AlignmentPanel ap = (alignment == null)
212 ? appJmolWindow.getAlignmentPanel()
213 : (AlignmentPanel) alignment;
214 if (ap.av.isShowSequenceFeatures())
216 return ap.av.getAlignPanel().getSeqPanel().seqCanvas.fr;
222 @SuppressWarnings("unused")
223 public void cacheFiles(List<File> files)
231 String path = f.getAbsolutePath();
232 byte[] data = Platform.getFileBytes(f);
235 Platform.cacheFileData(path, data);