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;
32 import java.awt.Container;
35 import org.jmol.api.JmolAppConsoleInterface;
36 import org.jmol.java.BS;
37 import org.openscience.jmol.app.jmolpanel.console.AppConsole;
39 public class AppJmolBinding extends JalviewJmolBinding
41 private AppJmol appJmolWindow;
43 public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
44 PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
46 super(sSm, pdbentry, sequenceIs, protocol);
47 appJmolWindow = appJmol;
51 protected IProgressIndicator getIProgressIndicator()
53 return appJmolWindow.progressBar;
57 public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
59 return new SequenceRenderer(((AlignmentPanel) alignment).av);
63 public void sendConsoleEcho(String strEcho)
67 console.sendConsoleEcho(strEcho);
72 public void sendConsoleMessage(String strStatus)
74 if (console != null && strStatus != null)
75 // && !strStatus.equals("Script completed"))
76 // should we squash the script completed string ?
78 console.sendConsoleMessage(strStatus);
83 public void showUrl(String url, String target)
87 jalview.util.BrowserLauncher.openURL(url);
90 Cache.log.error("Failed to launch Jmol-associated url " + url, e);
91 // TODO: 2.6 : warn user if browser was not configured.
96 public void refreshGUI()
98 // appJmolWindow.repaint();
99 javax.swing.SwingUtilities.invokeLater(new Runnable()
104 appJmolWindow.updateTitleAndMenus();
105 appJmolWindow.revalidate();
111 public void updateColours(Object source)
113 AlignmentPanel ap = (AlignmentPanel) source;
114 // ignore events from panels not used to colour this view
115 if (!appJmolWindow.isUsedforcolourby(ap))
119 if (!isLoadingFromArchive())
121 colourBySequence(ap);
126 public void notifyScriptTermination(String strStatus, int msWalltime)
128 // todo - script termination doesn't happen ?
129 // if (console != null)
130 // console.notifyScriptTermination(strStatus,
135 public void showUrl(String url)
137 showUrl(url, "jmol");
140 public void newJmolPopup(String menuName)
142 // jmolpopup = new JmolAwtPopup();
143 // jmolpopup.jpiInitialize((viewer), menuName);
147 public void selectionChanged(BS arg0)
149 // TODO Auto-generated method stub
154 public void refreshPdbEntries()
156 // TODO Auto-generated method stub
161 public void showConsole(boolean b)
163 appJmolWindow.showConsole(b);
167 protected JmolAppConsoleInterface createJmolConsole(
168 Container consolePanel, String buttonsToShow)
170 viewer.setJmolCallbackListener(this);
171 return new AppConsole(viewer, consolePanel, buttonsToShow);
175 protected void releaseUIResources()
177 appJmolWindow = null;
182 public void releaseReferences(Object svl)
184 if (svl instanceof SeqPanel)
186 appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
191 public Map<String, Object> getJSpecViewProperty(String arg0)
193 // TODO Auto-generated method stub
198 public JalviewStructureDisplayI getViewer()
200 return appJmolWindow;
204 public jalview.api.FeatureRenderer getFeatureRenderer(
205 AlignmentViewPanel alignment)
207 AlignmentPanel ap = (alignment == null) ? appJmolWindow
208 .getAlignmentPanel() : (AlignmentPanel) alignment;
209 if (ap.av.isShowSequenceFeatures())
211 return ap.av.getAlignPanel().getSeqPanel().seqCanvas.fr;