2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 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 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/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 import java.awt.Container;
22 import java.util.BitSet;
24 import jalview.api.AlignmentViewPanel;
25 import jalview.bin.Cache;
26 import jalview.datamodel.PDBEntry;
27 import jalview.datamodel.SequenceI;
28 import jalview.structure.StructureSelectionManager;
30 import org.jmol.api.JmolAppConsoleInterface;
31 import org.jmol.api.JmolViewer;
32 import org.jmol.popup.JmolPopup;
33 import org.openscience.jmol.app.jmolpanel.AppConsole;
35 public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
41 private AppJmol appJmolWindow;
43 public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
44 PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
47 super(sSm, pdbentry, sequenceIs, chains, protocol);
48 appJmolWindow = appJmol;
51 FeatureRenderer fr = null;
54 public jalview.api.FeatureRenderer getFeatureRenderer(
55 AlignmentViewPanel alignment)
57 AlignmentPanel ap = (alignment == null) ? appJmolWindow.ap
58 : (AlignmentPanel) alignment;
59 if (ap.av.showSequenceFeatures)
63 fr = ap.cloneFeatureRenderer();
67 ap.updateFeatureRenderer(fr);
75 public jalview.api.SequenceRenderer getSequenceRenderer(
76 AlignmentViewPanel alignment)
78 return new SequenceRenderer(((AlignmentPanel) alignment).av);
81 public void sendConsoleEcho(String strEcho)
85 console.sendConsoleEcho(strEcho);
89 public void sendConsoleMessage(String strStatus)
91 if (console != null && strStatus != null)
92 // && !strStatus.equals("Script completed"))
93 // should we squash the script completed string ?
95 console.sendConsoleMessage(strStatus);
100 public void showUrl(String url, String target)
104 jalview.util.BrowserLauncher.openURL(url);
105 } catch (Exception e)
107 Cache.log.error("Failed to launch Jmol-associated url " + url, e);
108 // TODO: 2.6 : warn user if browser was not configured.
113 public void refreshGUI()
115 // appJmolWindow.repaint();
116 javax.swing.SwingUtilities.invokeLater(new Runnable()
120 appJmolWindow.updateTitleAndMenus();
121 appJmolWindow.revalidate();
126 public void updateColours(Object source)
128 AlignmentPanel ap = (AlignmentPanel) source, topap;
129 // ignore events from panels not used to colour this view
130 if (!appJmolWindow.isUsedforcolourby(ap))
132 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 = new JmolPopup();
156 jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
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)
227 appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);