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 java.awt.Container;
25 import java.io.FileWriter;
26 import java.io.IOException;
29 import javax.swing.JComponent;
31 import org.jmol.api.JmolAppConsoleInterface;
32 import org.jmol.java.BS;
33 import org.openscience.jmol.app.jmolpanel.console.AppConsole;
35 import jalview.api.AlignmentViewPanel;
36 import jalview.api.structures.JalviewStructureDisplayI;
37 import jalview.bin.Cache;
38 import jalview.datamodel.PDBEntry;
39 import jalview.datamodel.SequenceI;
40 import jalview.ext.jmol.JalviewJmolBinding;
41 import jalview.io.DataSourceType;
42 import jalview.structure.StructureSelectionManager;
44 public class AppJmolBinding extends JalviewJmolBinding
46 public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
47 PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
48 DataSourceType protocol)
50 super(sSm, pdbentry, sequenceIs, protocol);
55 public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
57 return new SequenceRenderer(((AlignmentPanel) alignment).av);
61 public void sendConsoleEcho(String strEcho)
65 console.sendConsoleEcho(strEcho);
70 public void sendConsoleMessage(String strStatus)
72 if (console != null && strStatus != null)
73 // && !strStatus.equals("Script completed"))
74 // should we squash the script completed string ?
76 console.sendConsoleMessage(strStatus);
81 public void showUrl(String url, String target)
85 jalview.util.BrowserLauncher.openURL(url);
88 Cache.log.error("Failed to launch Jmol-associated url " + url, e);
89 // TODO: 2.6 : warn user if browser was not configured.
94 public void refreshGUI()
96 // appJmolWindow.repaint();
97 javax.swing.SwingUtilities.invokeLater(new Runnable()
102 JalviewStructureDisplayI theViewer = getViewer();
103 theViewer.updateTitleAndMenus();
104 ((JComponent) theViewer).revalidate();
110 public void notifyScriptTermination(String strStatus, int msWalltime)
112 // todo - script termination doesn't happen ?
113 // if (console != null)
114 // console.notifyScriptTermination(strStatus,
119 public void showUrl(String url)
121 showUrl(url, "jmol");
124 public void newJmolPopup(String menuName)
126 // jmolpopup = new JmolAwtPopup();
127 // jmolpopup.jpiInitialize((viewer), menuName);
131 public void selectionChanged(BS arg0)
136 public void showConsole(boolean b)
138 getViewer().showConsole(b);
142 protected JmolAppConsoleInterface createJmolConsole(
143 Container consolePanel, String buttonsToShow)
145 jmolViewer.setJmolCallbackListener(this);
146 return new AppConsole(jmolViewer, consolePanel, buttonsToShow);
150 protected void releaseUIResources()
157 public void releaseReferences(Object svl)
159 if (svl instanceof SeqPanel)
161 getViewer().removeAlignmentPanel(((SeqPanel) svl).ap);
166 public Map<String, Object> getJSpecViewProperty(String arg0)
168 // TODO Auto-generated method stub
173 * Overrides the default method to save a session to file, in order to
174 * guarantee it is done synchronously. Jmol command 'write STATE path' would
175 * execute asynchronously, so instead we get the state and write it directly
179 protected void saveSession(File f)
181 String state = jmolViewer.getStateInfo();
186 FileWriter fw = new FileWriter(f);
189 } catch (IOException e)
191 Cache.log.error("Error writing Jmol state: " + e.toString());
196 Cache.log.error("Error requesting Jmol state to save");