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.util.ArrayList;
24 import java.util.HashMap;
25 import java.util.LinkedHashMap;
26 import java.util.List;
28 import java.util.Map.Entry;
30 import jalview.api.structures.JalviewStructureDisplayI;
31 import jalview.bin.Cache;
32 import jalview.datamodel.PDBEntry;
33 import jalview.datamodel.SequenceI;
34 import jalview.datamodel.StructureViewerModel;
35 import jalview.structure.StructureSelectionManager;
38 * A proxy for handling structure viewers, that orchestrates adding selected
39 * structures, associated with sequences in Jalview, to an existing viewer, or
40 * opening a new one. Currently supports either Jmol or Chimera as the structure
45 public class StructureViewer
47 private static final String UNKNOWN_VIEWER_TYPE = "Unknown structure viewer type ";
49 StructureSelectionManager ssm;
52 * decide if new structures are aligned to existing ones
54 private boolean superposeAdded = true;
56 public enum ViewerType
58 JMOL, CHIMERA, CHIMERAX, PYMOL
64 * @param structureSelectionManager
66 public StructureViewer(StructureSelectionManager structureSelectionManager)
68 ssm = structureSelectionManager;
72 * Factory to create a proxy for modifying existing structure viewer
75 public static StructureViewer reconfigure(
76 JalviewStructureDisplayI display)
78 StructureViewer sv = new StructureViewer(display.getBinding().getSsm());
84 public String toString()
88 return sview.toString();
92 public ViewerType getViewerType()
94 String viewType = Cache.getDefault(Preferences.STRUCTURE_DISPLAY,
95 ViewerType.JMOL.name());
96 return ViewerType.valueOf(viewType);
99 public void setViewerType(ViewerType type)
101 Cache.setProperty(Preferences.STRUCTURE_DISPLAY, type.name());
105 * View multiple PDB entries, each with associated sequences
112 public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
113 SequenceI[] seqs, AlignmentPanel ap)
115 JalviewStructureDisplayI viewer = onlyOnePdb(pdbs, seqs, ap);
119 * user added structure to an existing viewer - all done
124 ViewerType viewerType = getViewerType();
126 Map<PDBEntry, SequenceI[]> seqsForPdbs = getSequencesForPdbs(pdbs,
128 PDBEntry[] pdbsForFile = seqsForPdbs.keySet().toArray(
129 new PDBEntry[seqsForPdbs.size()]);
130 SequenceI[][] theSeqs = seqsForPdbs.values().toArray(
131 new SequenceI[seqsForPdbs.size()][]);
134 sview.setAlignAddedStructures(superposeAdded);
135 new Thread(new Runnable()
141 for (int pdbep = 0; pdbep < pdbsForFile.length; pdbep++)
143 PDBEntry pdb = pdbsForFile[pdbep];
144 if (!sview.addAlreadyLoadedFile(theSeqs[pdbep], null, ap,
147 sview.addToExistingViewer(pdb, theSeqs[pdbep], null, ap,
152 sview.updateTitleAndMenus();
158 if (viewerType.equals(ViewerType.JMOL))
160 sview = new AppJmol(ap, superposeAdded, pdbsForFile, theSeqs);
162 else if (viewerType.equals(ViewerType.CHIMERA))
164 sview = new ChimeraViewFrame(pdbsForFile, superposeAdded, theSeqs,
167 else if (viewerType.equals(ViewerType.CHIMERAX))
169 sview = new ChimeraXViewFrame(pdbsForFile, superposeAdded, theSeqs,
172 else if (viewerType.equals(ViewerType.PYMOL))
174 sview = new PymolViewer(pdbsForFile, superposeAdded, theSeqs, ap);
178 Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
184 * Converts the list of selected PDB entries (possibly including duplicates
185 * for multiple chains), and corresponding sequences, into a map of sequences
186 * for each distinct PDB file. Returns null if either argument is null, or
187 * their lengths do not match.
193 Map<PDBEntry, SequenceI[]> getSequencesForPdbs(PDBEntry[] pdbs,
196 if (pdbs == null || seqs == null || pdbs.length != seqs.length)
202 * we want only one 'representative' PDBEntry per distinct file name
203 * (there may be entries for distinct chains)
205 Map<String, PDBEntry> pdbsSeen = new HashMap<>();
208 * LinkedHashMap preserves order of PDB entries (significant if they
209 * will get superimposed to the first structure)
211 Map<PDBEntry, List<SequenceI>> pdbSeqs = new LinkedHashMap<>();
212 for (int i = 0; i < pdbs.length; i++)
214 PDBEntry pdb = pdbs[i];
215 SequenceI seq = seqs[i];
216 String pdbFile = pdb.getFile();
217 if (pdbFile == null || pdbFile.length() == 0)
219 pdbFile = pdb.getId();
221 if (!pdbsSeen.containsKey(pdbFile))
223 pdbsSeen.put(pdbFile, pdb);
224 pdbSeqs.put(pdb, new ArrayList<SequenceI>());
228 pdb = pdbsSeen.get(pdbFile);
230 List<SequenceI> seqsForPdb = pdbSeqs.get(pdb);
231 if (!seqsForPdb.contains(seq))
238 * convert to Map<PDBEntry, SequenceI[]>
240 Map<PDBEntry, SequenceI[]> result = new LinkedHashMap<>();
241 for (Entry<PDBEntry, List<SequenceI>> entry : pdbSeqs.entrySet())
243 List<SequenceI> theSeqs = entry.getValue();
244 result.put(entry.getKey(),
245 theSeqs.toArray(new SequenceI[theSeqs.size()]));
252 * A strictly temporary method pending JAL-1761 refactoring. Determines if all
253 * the passed PDB entries are the same (this is the case if selected sequences
254 * to view structure for are chains of the same structure). If so, calls the
255 * single-pdb version of viewStructures and returns the viewer, else returns
263 private JalviewStructureDisplayI onlyOnePdb(PDBEntry[] pdbs,
264 SequenceI[] seqsForPdbs, AlignmentPanel ap)
266 List<SequenceI> seqs = new ArrayList<>();
267 if (pdbs == null || pdbs.length == 0)
272 String firstFile = pdbs[0].getFile();
273 for (PDBEntry pdb : pdbs)
275 String pdbFile = pdb.getFile();
276 if (pdbFile == null || !pdbFile.equals(firstFile))
280 SequenceI pdbseq = seqsForPdbs[i++];
286 return viewStructures(pdbs[0], seqs.toArray(new SequenceI[seqs.size()]),
290 JalviewStructureDisplayI sview = null;
292 public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
293 SequenceI[] seqsForPdb, AlignmentPanel ap)
297 sview.setAlignAddedStructures(superposeAdded);
298 String pdbId = pdb.getId();
299 if (!sview.addAlreadyLoadedFile(seqsForPdb, null, ap, pdbId))
301 sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdbId);
303 sview.updateTitleAndMenus();
307 ViewerType viewerType = getViewerType();
308 if (viewerType.equals(ViewerType.JMOL))
310 sview = new AppJmol(pdb, seqsForPdb, null, ap);
312 else if (viewerType.equals(ViewerType.CHIMERA))
314 sview = new ChimeraViewFrame(pdb, seqsForPdb, null, ap);
316 else if (viewerType.equals(ViewerType.CHIMERAX))
318 sview = new ChimeraXViewFrame(pdb, seqsForPdb, null, ap);
320 else if (viewerType.equals(ViewerType.PYMOL))
322 sview = new PymolViewer(pdb, seqsForPdb, null, ap);
326 Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
332 * Creates a new panel controlling a structure viewer
341 public static JalviewStructureDisplayI createView(ViewerType type,
342 AlignmentPanel alignPanel, StructureViewerModel viewerData,
343 String sessionFile, String vid)
345 JalviewStructureDisplayI viewer = null;
349 viewer = new AppJmol(viewerData, alignPanel, sessionFile, vid);
350 // todo or construct and then openSession(sessionFile)?
353 viewer = new ChimeraViewFrame(viewerData, alignPanel, sessionFile,
357 viewer = new ChimeraXViewFrame(viewerData, alignPanel, sessionFile,
361 viewer = new PymolViewer(viewerData, alignPanel, sessionFile, vid);
364 Cache.log.error(UNKNOWN_VIEWER_TYPE + type.toString());
369 public boolean isBusy()
373 if (!sview.hasMapping())
384 * @return true if view is already showing PDBid
386 public boolean hasPdbId(String pDBid)
393 return sview.getBinding().hasPdbId(pDBid);
396 public boolean isVisible()
398 return sview != null && sview.isVisible();
401 public void setSuperpose(boolean alignAddedStructures)
403 superposeAdded = alignAddedStructures;