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.bin.Console;
33 import jalview.datamodel.PDBEntry;
34 import jalview.datamodel.SequenceI;
35 import jalview.datamodel.StructureViewerModel;
36 import jalview.structure.StructureSelectionManager;
39 * A proxy for handling structure viewers, that orchestrates adding selected
40 * structures, associated with sequences in Jalview, to an existing viewer, or
41 * opening a new one. Currently supports either Jmol or Chimera as the structure
46 public class StructureViewer
48 private static final String UNKNOWN_VIEWER_TYPE = "Unknown structure viewer type ";
50 StructureSelectionManager ssm;
53 * decide if new structures are aligned to existing ones
55 private boolean superposeAdded = true;
58 * whether to open structures in their own thread or not
60 private boolean async = true;
62 public void setAsync(boolean b)
67 public enum ViewerType
69 JMOL, CHIMERA, CHIMERAX, PYMOL
75 * @param structureSelectionManager
77 public StructureViewer(
78 StructureSelectionManager structureSelectionManager)
80 ssm = structureSelectionManager;
84 * Factory to create a proxy for modifying existing structure viewer
87 public static StructureViewer reconfigure(
88 JalviewStructureDisplayI display)
90 StructureViewer sv = new StructureViewer(display.getBinding().getSsm());
96 public String toString()
100 return sview.toString();
107 * @return ViewerType for currently configured structure viewer
109 public static ViewerType getViewerType()
111 String viewType = Cache.getDefault(Preferences.STRUCTURE_DISPLAY,
112 ViewerType.JMOL.name());
113 return ViewerType.valueOf(viewType);
116 public void setViewerType(ViewerType type)
118 Cache.setProperty(Preferences.STRUCTURE_DISPLAY, type.name());
122 * View multiple PDB entries, each with associated sequences
129 public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
130 SequenceI[] seqs, AlignmentPanel ap)
132 return viewStructures(pdbs, seqs, ap, null);
135 public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
136 SequenceI[] seqs, AlignmentPanel ap, ViewerType viewerType)
138 JalviewStructureDisplayI viewer = onlyOnePdb(pdbs, seqs, ap);
142 * user added structure to an existing viewer - all done
147 if (viewerType == null)
148 viewerType = getViewerType();
150 Map<PDBEntry, SequenceI[]> seqsForPdbs = getSequencesForPdbs(pdbs,
152 PDBEntry[] pdbsForFile = seqsForPdbs.keySet()
153 .toArray(new PDBEntry[seqsForPdbs.size()]);
154 SequenceI[][] theSeqs = seqsForPdbs.values()
155 .toArray(new SequenceI[seqsForPdbs.size()][]);
158 sview.setAlignAddedStructures(superposeAdded);
160 Runnable viewRunnable = new Runnable()
166 for (int pdbep = 0; pdbep < pdbsForFile.length; pdbep++)
168 PDBEntry pdb = pdbsForFile[pdbep];
169 if (!sview.addAlreadyLoadedFile(theSeqs[pdbep], null, ap,
172 sview.addToExistingViewer(pdb, theSeqs[pdbep], null, ap,
177 sview.updateTitleAndMenus();
182 new Thread(viewRunnable).start();
191 if (viewerType.equals(ViewerType.JMOL))
193 sview = new AppJmol(ap, superposeAdded, pdbsForFile, theSeqs);
195 else if (viewerType.equals(ViewerType.CHIMERA))
197 sview = new ChimeraViewFrame(pdbsForFile, superposeAdded, theSeqs,
200 else if (viewerType.equals(ViewerType.CHIMERAX))
202 sview = new ChimeraXViewFrame(pdbsForFile, superposeAdded, theSeqs,
205 else if (viewerType.equals(ViewerType.PYMOL))
207 sview = new PymolViewer(pdbsForFile, superposeAdded, theSeqs, ap);
211 Console.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
217 * Converts the list of selected PDB entries (possibly including duplicates
218 * for multiple chains), and corresponding sequences, into a map of sequences
219 * for each distinct PDB file. Returns null if either argument is null, or
220 * their lengths do not match.
226 Map<PDBEntry, SequenceI[]> getSequencesForPdbs(PDBEntry[] pdbs,
229 if (pdbs == null || seqs == null || pdbs.length != seqs.length)
235 * we want only one 'representative' PDBEntry per distinct file name
236 * (there may be entries for distinct chains)
238 Map<String, PDBEntry> pdbsSeen = new HashMap<>();
241 * LinkedHashMap preserves order of PDB entries (significant if they
242 * will get superimposed to the first structure)
244 Map<PDBEntry, List<SequenceI>> pdbSeqs = new LinkedHashMap<>();
245 for (int i = 0; i < pdbs.length; i++)
247 PDBEntry pdb = pdbs[i];
248 SequenceI seq = seqs[i];
249 String pdbFile = pdb.getFile();
250 if (pdbFile == null || pdbFile.length() == 0)
252 pdbFile = pdb.getId();
254 if (!pdbsSeen.containsKey(pdbFile))
256 pdbsSeen.put(pdbFile, pdb);
257 pdbSeqs.put(pdb, new ArrayList<SequenceI>());
261 pdb = pdbsSeen.get(pdbFile);
263 List<SequenceI> seqsForPdb = pdbSeqs.get(pdb);
264 if (!seqsForPdb.contains(seq))
271 * convert to Map<PDBEntry, SequenceI[]>
273 Map<PDBEntry, SequenceI[]> result = new LinkedHashMap<>();
274 for (Entry<PDBEntry, List<SequenceI>> entry : pdbSeqs.entrySet())
276 List<SequenceI> theSeqs = entry.getValue();
277 result.put(entry.getKey(),
278 theSeqs.toArray(new SequenceI[theSeqs.size()]));
285 * A strictly temporary method pending JAL-1761 refactoring. Determines if all
286 * the passed PDB entries are the same (this is the case if selected sequences
287 * to view structure for are chains of the same structure). If so, calls the
288 * single-pdb version of viewStructures and returns the viewer, else returns
296 private JalviewStructureDisplayI onlyOnePdb(PDBEntry[] pdbs,
297 SequenceI[] seqsForPdbs, AlignmentPanel ap)
299 List<SequenceI> seqs = new ArrayList<>();
300 if (pdbs == null || pdbs.length == 0)
305 String firstFile = pdbs[0].getFile();
306 for (PDBEntry pdb : pdbs)
308 String pdbFile = pdb.getFile();
309 if (pdbFile == null || !pdbFile.equals(firstFile))
313 SequenceI pdbseq = seqsForPdbs[i++];
319 return viewStructures(pdbs[0], seqs.toArray(new SequenceI[seqs.size()]),
323 JalviewStructureDisplayI sview = null;
325 public JalviewStructureDisplayI getJalviewStructureDisplay()
330 public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
331 SequenceI[] seqsForPdb, AlignmentPanel ap)
333 return viewStructures(pdb, seqsForPdb, ap, null);
336 public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
337 SequenceI[] seqsForPdb, AlignmentPanel ap, ViewerType viewerType)
341 sview.setAlignAddedStructures(superposeAdded);
342 String pdbId = pdb.getId();
343 if (!sview.addAlreadyLoadedFile(seqsForPdb, null, ap, pdbId))
345 sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdbId);
347 sview.updateTitleAndMenus();
351 if (viewerType == null)
352 viewerType = getViewerType();
353 if (viewerType.equals(ViewerType.JMOL))
355 sview = new AppJmol(pdb, seqsForPdb, null, ap);
357 else if (viewerType.equals(ViewerType.CHIMERA))
359 sview = new ChimeraViewFrame(pdb, seqsForPdb, null, ap);
361 else if (viewerType.equals(ViewerType.CHIMERAX))
363 sview = new ChimeraXViewFrame(pdb, seqsForPdb, null, ap);
365 else if (viewerType.equals(ViewerType.PYMOL))
367 sview = new PymolViewer(pdb, seqsForPdb, null, ap);
371 Console.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
377 * Creates a new panel controlling a structure viewer
386 public static JalviewStructureDisplayI createView(ViewerType type,
387 AlignmentPanel alignPanel, StructureViewerModel viewerData,
388 String sessionFile, String vid)
390 JalviewStructureDisplayI viewer = null;
394 viewer = new AppJmol(viewerData, alignPanel, sessionFile, vid);
395 // todo or construct and then openSession(sessionFile)?
398 viewer = new ChimeraViewFrame(viewerData, alignPanel, sessionFile,
402 viewer = new ChimeraXViewFrame(viewerData, alignPanel, sessionFile,
406 viewer = new PymolViewer(viewerData, alignPanel, sessionFile, vid);
409 Console.error(UNKNOWN_VIEWER_TYPE + type.toString());
414 public boolean isBusy()
418 if (!sview.hasMapping())
429 * @return true if view is already showing PDBid
431 public boolean hasPdbId(String pDBid)
438 return sview.getBinding().hasPdbId(pDBid);
441 public boolean isVisible()
443 return sview != null && sview.isVisible();
446 public void setSuperpose(boolean alignAddedStructures)
448 superposeAdded = alignAddedStructures;