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.
21 package jalview.appletgui;
23 import jalview.api.AlignmentViewPanel;
24 import jalview.api.FeatureRenderer;
25 import jalview.api.SequenceRenderer;
26 import jalview.datamodel.PDBEntry;
27 import jalview.datamodel.SequenceI;
28 import jalview.ext.jmol.JalviewJmolBinding;
29 import jalview.io.DataSourceType;
31 import java.awt.Container;
32 import java.util.ArrayList;
33 import java.util.List;
35 import java.util.Vector;
37 import org.jmol.api.JmolAppConsoleInterface;
38 import javajs.util.BS;
39 import org.jmol.viewer.Viewer;
42 * bind an alignment view to an external Jmol instance.
47 public class ExtJmol extends JalviewJmolBinding
50 private AlignmentPanel ap;
52 protected ExtJmol(AlignFrame alframe, PDBEntry[] pdbentry,
53 SequenceI[][] seq, DataSourceType protocol)
55 super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
59 public ExtJmol(Viewer viewer, AlignmentPanel alignPanel,
62 super(alignPanel.getStructureSelectionManager(), seqs, viewer);
64 notifyFileLoaded(null, null, null, null, 0);
68 public void updateColours(Object source)
73 public void showUrl(String arg0)
75 showUrl(arg0, "jmol");
79 public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
81 AlignmentPanel alignPanel = (AlignmentPanel) alignment;
82 if (alignPanel.av.isShowSequenceFeatures())
84 return alignPanel.getFeatureRenderer();
94 public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
96 return ((AlignmentPanel) alignment).getSequenceRenderer();
100 public void notifyScriptTermination(String strStatus, int msWalltime)
106 public void sendConsoleEcho(String strEcho)
112 public void sendConsoleMessage(String strStatus)
118 public void showUrl(String url, String target)
120 ap.alignFrame.showURL(url, target);
124 public void refreshGUI()
130 public void selectionChanged(BS arg0)
132 System.out.println(arg0);
136 public void refreshPdbEntries()
138 List<PDBEntry> pdbe = new ArrayList<>();
139 List<String> fileids = new ArrayList<>();
140 SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
141 for (int s = 0; s < sq.length; s++)
143 Vector<PDBEntry> pdbids = sq[s].getAllPDBEntries();
146 for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)
148 PDBEntry pentry = pdbids.elementAt(pe);
149 if (!fileids.contains(pentry.getId()))
155 fileids.add(pentry.getId());
160 PDBEntry[] newEntries = new PDBEntry[pdbe.size()];
161 for (int pe = 0; pe < pdbe.size(); pe++)
163 newEntries[pe] = pdbe.get(pe);
165 setPdbentry(newEntries);
169 public void showConsole(boolean show)
171 // This never gets called because we haven't overriden the associated Jmol's
174 "WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="
179 protected JmolAppConsoleInterface createJmolConsole(
180 Container consolePanel, String buttonsToShow)
186 protected void releaseUIResources()
194 public void releaseReferences(Object svl)
199 public Map<String, Object> getJSpecViewProperty(String arg0)