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());
85 public String toString()
89 return sview.toString();
95 * @return ViewerType for currently configured structure viewer
97 public static ViewerType getViewerType()
99 String viewType = Cache.getDefault(Preferences.STRUCTURE_DISPLAY,
100 ViewerType.JMOL.name());
101 return ViewerType.valueOf(viewType);
104 public void setViewerType(ViewerType type)
106 Cache.setProperty(Preferences.STRUCTURE_DISPLAY, type.name());
110 * View multiple PDB entries, each with associated sequences
117 public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
118 SequenceI[] seqs, AlignmentPanel ap)
120 JalviewStructureDisplayI viewer = onlyOnePdb(pdbs, seqs, ap);
124 * user added structure to an existing viewer - all done
129 ViewerType viewerType = getViewerType();
131 Map<PDBEntry, SequenceI[]> seqsForPdbs = getSequencesForPdbs(pdbs,
133 PDBEntry[] pdbsForFile = seqsForPdbs.keySet().toArray(
134 new PDBEntry[seqsForPdbs.size()]);
135 SequenceI[][] theSeqs = seqsForPdbs.values().toArray(
136 new SequenceI[seqsForPdbs.size()][]);
139 sview.setAlignAddedStructures(superposeAdded);
140 new Thread(new Runnable()
146 for (int pdbep = 0; pdbep < pdbsForFile.length; pdbep++)
148 PDBEntry pdb = pdbsForFile[pdbep];
149 if (!sview.addAlreadyLoadedFile(theSeqs[pdbep], null, ap,
152 sview.addToExistingViewer(pdb, theSeqs[pdbep], null, ap,
157 sview.updateTitleAndMenus();
163 if (viewerType.equals(ViewerType.JMOL))
165 sview = new AppJmol(ap, superposeAdded, pdbsForFile, theSeqs);
167 else if (viewerType.equals(ViewerType.CHIMERA))
169 sview = new ChimeraViewFrame(pdbsForFile, superposeAdded, theSeqs,
172 else if (viewerType.equals(ViewerType.CHIMERAX))
174 sview = new ChimeraXViewFrame(pdbsForFile, superposeAdded, theSeqs,
177 else if (viewerType.equals(ViewerType.PYMOL))
179 sview = new PymolViewer(pdbsForFile, superposeAdded, theSeqs, ap);
183 Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
189 * Converts the list of selected PDB entries (possibly including duplicates
190 * for multiple chains), and corresponding sequences, into a map of sequences
191 * for each distinct PDB file. Returns null if either argument is null, or
192 * their lengths do not match.
198 Map<PDBEntry, SequenceI[]> getSequencesForPdbs(PDBEntry[] pdbs,
201 if (pdbs == null || seqs == null || pdbs.length != seqs.length)
207 * we want only one 'representative' PDBEntry per distinct file name
208 * (there may be entries for distinct chains)
210 Map<String, PDBEntry> pdbsSeen = new HashMap<>();
213 * LinkedHashMap preserves order of PDB entries (significant if they
214 * will get superimposed to the first structure)
216 Map<PDBEntry, List<SequenceI>> pdbSeqs = new LinkedHashMap<>();
217 for (int i = 0; i < pdbs.length; i++)
219 PDBEntry pdb = pdbs[i];
220 SequenceI seq = seqs[i];
221 String pdbFile = pdb.getFile();
222 if (pdbFile == null || pdbFile.length() == 0)
224 pdbFile = pdb.getId();
226 if (!pdbsSeen.containsKey(pdbFile))
228 pdbsSeen.put(pdbFile, pdb);
229 pdbSeqs.put(pdb, new ArrayList<SequenceI>());
233 pdb = pdbsSeen.get(pdbFile);
235 List<SequenceI> seqsForPdb = pdbSeqs.get(pdb);
236 if (!seqsForPdb.contains(seq))
243 * convert to Map<PDBEntry, SequenceI[]>
245 Map<PDBEntry, SequenceI[]> result = new LinkedHashMap<>();
246 for (Entry<PDBEntry, List<SequenceI>> entry : pdbSeqs.entrySet())
248 List<SequenceI> theSeqs = entry.getValue();
249 result.put(entry.getKey(),
250 theSeqs.toArray(new SequenceI[theSeqs.size()]));
257 * A strictly temporary method pending JAL-1761 refactoring. Determines if all
258 * the passed PDB entries are the same (this is the case if selected sequences
259 * to view structure for are chains of the same structure). If so, calls the
260 * single-pdb version of viewStructures and returns the viewer, else returns
268 private JalviewStructureDisplayI onlyOnePdb(PDBEntry[] pdbs,
269 SequenceI[] seqsForPdbs, AlignmentPanel ap)
271 List<SequenceI> seqs = new ArrayList<>();
272 if (pdbs == null || pdbs.length == 0)
277 String firstFile = pdbs[0].getFile();
278 for (PDBEntry pdb : pdbs)
280 String pdbFile = pdb.getFile();
281 if (pdbFile == null || !pdbFile.equals(firstFile))
285 SequenceI pdbseq = seqsForPdbs[i++];
291 return viewStructures(pdbs[0], seqs.toArray(new SequenceI[seqs.size()]),
295 JalviewStructureDisplayI sview = null;
297 public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
298 SequenceI[] seqsForPdb, AlignmentPanel ap)
302 sview.setAlignAddedStructures(superposeAdded);
303 String pdbId = pdb.getId();
304 if (!sview.addAlreadyLoadedFile(seqsForPdb, null, ap, pdbId))
306 sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdbId);
308 sview.updateTitleAndMenus();
312 ViewerType viewerType = getViewerType();
313 if (viewerType.equals(ViewerType.JMOL))
315 sview = new AppJmol(pdb, seqsForPdb, null, ap);
317 else if (viewerType.equals(ViewerType.CHIMERA))
319 sview = new ChimeraViewFrame(pdb, seqsForPdb, null, ap);
321 else if (viewerType.equals(ViewerType.CHIMERAX))
323 sview = new ChimeraXViewFrame(pdb, seqsForPdb, null, ap);
325 else if (viewerType.equals(ViewerType.PYMOL))
327 sview = new PymolViewer(pdb, seqsForPdb, null, ap);
331 Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
337 * Creates a new panel controlling a structure viewer
346 public static JalviewStructureDisplayI createView(ViewerType type,
347 AlignmentPanel alignPanel, StructureViewerModel viewerData,
348 String sessionFile, String vid)
350 JalviewStructureDisplayI viewer = null;
354 viewer = new AppJmol(viewerData, alignPanel, sessionFile, vid);
355 // todo or construct and then openSession(sessionFile)?
358 viewer = new ChimeraViewFrame(viewerData, alignPanel, sessionFile,
362 viewer = new ChimeraXViewFrame(viewerData, alignPanel, sessionFile,
366 viewer = new PymolViewer(viewerData, alignPanel, sessionFile, vid);
369 Cache.log.error(UNKNOWN_VIEWER_TYPE + type.toString());
375 public boolean isBusy()
379 if (!sview.hasMapping())
390 * @return true if view is already showing PDBid
392 public boolean hasPdbId(String pDBid)
399 return sview.getBinding().hasPdbId(pDBid);
402 public boolean isVisible()
404 return sview != null && sview.isVisible();
407 public void setSuperpose(boolean alignAddedStructures)
409 superposeAdded = alignAddedStructures;