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 javax.swing.JComponent;
37 import org.jmol.api.JmolAppConsoleInterface;
38 import org.jmol.java.BS;
39 import org.openscience.jmol.app.jmolpanel.console.AppConsole;
41 public class AppJmolBinding extends JalviewJmolBinding
43 public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
44 PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
45 DataSourceType protocol)
47 super(sSm, pdbentry, sequenceIs, protocol);
52 public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
54 return new SequenceRenderer(((AlignmentPanel) alignment).av);
58 public void sendConsoleEcho(String strEcho)
62 console.sendConsoleEcho(strEcho);
67 public void sendConsoleMessage(String strStatus)
69 if (console != null && strStatus != null)
70 // && !strStatus.equals("Script completed"))
71 // should we squash the script completed string ?
73 console.sendConsoleMessage(strStatus);
78 public void showUrl(String url, String target)
82 jalview.util.BrowserLauncher.openURL(url);
85 Cache.log.error("Failed to launch Jmol-associated url " + url, e);
86 // TODO: 2.6 : warn user if browser was not configured.
91 public void refreshGUI()
93 // appJmolWindow.repaint();
94 javax.swing.SwingUtilities.invokeLater(new Runnable()
99 JalviewStructureDisplayI theViewer = getViewer();
100 theViewer.updateTitleAndMenus();
101 ((JComponent) theViewer).revalidate();
107 public void updateColours(Object source)
109 AlignmentPanel ap = (AlignmentPanel) source;
110 // ignore events from panels not used to colour this view
111 if (!getViewer().isUsedForColourBy(ap))
115 if (!isLoadingFromArchive())
117 colourBySequence(ap);
122 public void notifyScriptTermination(String strStatus, int msWalltime)
124 // todo - script termination doesn't happen ?
125 // if (console != null)
126 // console.notifyScriptTermination(strStatus,
131 public void showUrl(String url)
133 showUrl(url, "jmol");
136 public void newJmolPopup(String menuName)
138 // jmolpopup = new JmolAwtPopup();
139 // jmolpopup.jpiInitialize((viewer), menuName);
143 public void selectionChanged(BS arg0)
145 // TODO Auto-generated method stub
150 public void refreshPdbEntries()
152 // TODO Auto-generated method stub
157 public void showConsole(boolean b)
159 getViewer().showConsole(b);
163 protected JmolAppConsoleInterface createJmolConsole(
164 Container consolePanel, String buttonsToShow)
166 jmolViewer.setJmolCallbackListener(this);
167 return new AppConsole(jmolViewer, consolePanel, buttonsToShow);
171 protected void releaseUIResources()
178 public void releaseReferences(Object svl)
180 if (svl instanceof SeqPanel)
182 getViewer().removeAlignmentPanel(((SeqPanel) svl).ap);
187 public Map<String, Object> getJSpecViewProperty(String arg0)
189 // TODO Auto-generated method stub