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, PDBEntry[] pdbentry,
50 SequenceI[][] sequenceIs, String[][] chains, String protocol)
52 super(sSm, pdbentry, sequenceIs, chains, protocol);
53 appJmolWindow = appJmol;
56 FeatureRenderer fr = null;
59 public jalview.api.FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
61 AlignmentPanel ap = (alignment==null) ? appJmolWindow.ap : (AlignmentPanel) alignment;
62 if (ap.av.showSequenceFeatures)
66 fr = new FeatureRenderer(ap);
69 fr.transferSettings(ap.
70 seqPanel.seqCanvas.getFeatureRenderer());
77 public jalview.api.SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
79 return new SequenceRenderer(((AlignmentPanel)alignment).av);
82 public void sendConsoleEcho(String strEcho)
86 console.sendConsoleEcho(strEcho);
90 public void sendConsoleMessage(String strStatus)
92 if (console != null && strStatus != null)
93 // && !strStatus.equals("Script completed"))
94 // should we squash the script completed string ?
96 console.sendConsoleMessage(strStatus);
101 public void showUrl(String url, String target)
105 jalview.util.BrowserLauncher.openURL(url);
106 } catch (Exception e)
108 Cache.log.error("Failed to launch Jmol-associated url " + url, e);
109 // TODO: 2.6 : warn user if browser was not configured.
114 public void refreshGUI()
116 // appJmolWindow.repaint();
117 javax.swing.SwingUtilities.invokeLater(new Runnable()
121 appJmolWindow.updateTitleAndMenus();
122 appJmolWindow.revalidate();
127 public void updateColours(Object source)
129 AlignmentPanel ap = (AlignmentPanel) source,topap;
130 // ignore events from panels not used to colour this view
131 if (!appJmolWindow.isUsedforcolourby(ap))
133 if (!isLoadingFromArchive()) {
134 colourBySequence(ap.av.getShowSequenceFeatures(), ap);
138 public void notifyScriptTermination(String strStatus, int msWalltime)
140 // todo - script termination doesn't happen ?
141 // if (console != null)
142 // console.notifyScriptTermination(strStatus,
146 public void showUrl(String url)
148 showUrl(url, "jmol");
151 public void newJmolPopup(boolean translateLocale, String menuName,
155 jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
159 public void selectionChanged(BitSet arg0)
161 // TODO Auto-generated method stub
165 public void refreshPdbEntries()
167 // TODO Auto-generated method stub
171 public void showConsole(boolean b)
173 appJmolWindow.showConsole(b);
177 * add the given sequences to the mapping scope for the given pdb file handle
180 * - pdbFile identifier
182 * - set of sequences it can be mapped to
184 public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
186 for (int pe = 0; pe < pdbentry.length; pe++)
188 if (pdbentry[pe].getFile().equals(pdbFile))
190 addSequence(pe, seq);
196 protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
197 Container consolePanel, String buttonsToShow)
199 return new AppConsole(viewer, consolePanel, buttonsToShow);
203 protected void releaseUIResources()
205 appJmolWindow = null;
210 console.setVisible(false);
213 } catch (Exception x)
223 public void releaseReferences(Object svl)
225 if (svl instanceof SeqPanel) {
226 appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);