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;
57 public enum ViewerType
59 JMOL, CHIMERA, CHIMERAX, PYMOL
65 * @param structureSelectionManager
67 public StructureViewer(
68 StructureSelectionManager structureSelectionManager)
70 ssm = structureSelectionManager;
74 * Factory to create a proxy for modifying existing structure viewer
77 public static StructureViewer reconfigure(
78 JalviewStructureDisplayI display)
80 StructureViewer sv = new StructureViewer(display.getBinding().getSsm());
86 public String toString()
90 return sview.toString();
97 * @return ViewerType for currently configured structure viewer
99 public static ViewerType getViewerType()
101 String viewType = Cache.getDefault(Preferences.STRUCTURE_DISPLAY,
102 ViewerType.JMOL.name());
103 return ViewerType.valueOf(viewType);
106 public void setViewerType(ViewerType type)
108 Cache.setProperty(Preferences.STRUCTURE_DISPLAY, type.name());
112 * View multiple PDB entries, each with associated sequences
119 public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
120 SequenceI[] seqs, AlignmentPanel ap)
122 JalviewStructureDisplayI viewer = onlyOnePdb(pdbs, seqs, ap);
126 * user added structure to an existing viewer - all done
131 ViewerType viewerType = getViewerType();
133 Map<PDBEntry, SequenceI[]> seqsForPdbs = getSequencesForPdbs(pdbs,
135 PDBEntry[] pdbsForFile = seqsForPdbs.keySet()
136 .toArray(new PDBEntry[seqsForPdbs.size()]);
137 SequenceI[][] theSeqs = seqsForPdbs.values()
138 .toArray(new SequenceI[seqsForPdbs.size()][]);
141 sview.setAlignAddedStructures(superposeAdded);
142 new Thread(new Runnable()
148 for (int pdbep = 0; pdbep < pdbsForFile.length; pdbep++)
150 PDBEntry pdb = pdbsForFile[pdbep];
151 if (!sview.addAlreadyLoadedFile(theSeqs[pdbep], null, ap,
154 sview.addToExistingViewer(pdb, theSeqs[pdbep], null, ap,
159 sview.updateTitleAndMenus();
165 if (viewerType.equals(ViewerType.JMOL))
167 sview = new AppJmol(ap, superposeAdded, pdbsForFile, theSeqs);
169 else if (viewerType.equals(ViewerType.CHIMERA))
171 sview = new ChimeraViewFrame(pdbsForFile, superposeAdded, theSeqs,
174 else if (viewerType.equals(ViewerType.CHIMERAX))
176 sview = new ChimeraXViewFrame(pdbsForFile, superposeAdded, theSeqs,
179 else if (viewerType.equals(ViewerType.PYMOL))
181 sview = new PymolViewer(pdbsForFile, superposeAdded, theSeqs, ap);
185 Console.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
191 * Converts the list of selected PDB entries (possibly including duplicates
192 * for multiple chains), and corresponding sequences, into a map of sequences
193 * for each distinct PDB file. Returns null if either argument is null, or
194 * their lengths do not match.
200 Map<PDBEntry, SequenceI[]> getSequencesForPdbs(PDBEntry[] pdbs,
203 if (pdbs == null || seqs == null || pdbs.length != seqs.length)
209 * we want only one 'representative' PDBEntry per distinct file name
210 * (there may be entries for distinct chains)
212 Map<String, PDBEntry> pdbsSeen = new HashMap<>();
215 * LinkedHashMap preserves order of PDB entries (significant if they
216 * will get superimposed to the first structure)
218 Map<PDBEntry, List<SequenceI>> pdbSeqs = new LinkedHashMap<>();
219 for (int i = 0; i < pdbs.length; i++)
221 PDBEntry pdb = pdbs[i];
222 SequenceI seq = seqs[i];
223 String pdbFile = pdb.getFile();
224 if (pdbFile == null || pdbFile.length() == 0)
226 pdbFile = pdb.getId();
228 if (!pdbsSeen.containsKey(pdbFile))
230 pdbsSeen.put(pdbFile, pdb);
231 pdbSeqs.put(pdb, new ArrayList<SequenceI>());
235 pdb = pdbsSeen.get(pdbFile);
237 List<SequenceI> seqsForPdb = pdbSeqs.get(pdb);
238 if (!seqsForPdb.contains(seq))
245 * convert to Map<PDBEntry, SequenceI[]>
247 Map<PDBEntry, SequenceI[]> result = new LinkedHashMap<>();
248 for (Entry<PDBEntry, List<SequenceI>> entry : pdbSeqs.entrySet())
250 List<SequenceI> theSeqs = entry.getValue();
251 result.put(entry.getKey(),
252 theSeqs.toArray(new SequenceI[theSeqs.size()]));
259 * A strictly temporary method pending JAL-1761 refactoring. Determines if all
260 * the passed PDB entries are the same (this is the case if selected sequences
261 * to view structure for are chains of the same structure). If so, calls the
262 * single-pdb version of viewStructures and returns the viewer, else returns
270 private JalviewStructureDisplayI onlyOnePdb(PDBEntry[] pdbs,
271 SequenceI[] seqsForPdbs, AlignmentPanel ap)
273 List<SequenceI> seqs = new ArrayList<>();
274 if (pdbs == null || pdbs.length == 0)
279 String firstFile = pdbs[0].getFile();
280 for (PDBEntry pdb : pdbs)
282 String pdbFile = pdb.getFile();
283 if (pdbFile == null || !pdbFile.equals(firstFile))
287 SequenceI pdbseq = seqsForPdbs[i++];
293 return viewStructures(pdbs[0], seqs.toArray(new SequenceI[seqs.size()]),
297 JalviewStructureDisplayI sview = null;
299 public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
300 SequenceI[] seqsForPdb, AlignmentPanel ap)
304 sview.setAlignAddedStructures(superposeAdded);
305 String pdbId = pdb.getId();
306 if (!sview.addAlreadyLoadedFile(seqsForPdb, null, ap, pdbId))
308 sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdbId);
310 sview.updateTitleAndMenus();
314 ViewerType viewerType = getViewerType();
315 if (viewerType.equals(ViewerType.JMOL))
317 sview = new AppJmol(pdb, seqsForPdb, null, ap);
319 else if (viewerType.equals(ViewerType.CHIMERA))
321 sview = new ChimeraViewFrame(pdb, seqsForPdb, null, ap);
323 else if (viewerType.equals(ViewerType.CHIMERAX))
325 sview = new ChimeraXViewFrame(pdb, seqsForPdb, null, ap);
327 else if (viewerType.equals(ViewerType.PYMOL))
329 sview = new PymolViewer(pdb, seqsForPdb, null, ap);
333 Console.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
339 * Creates a new panel controlling a structure viewer
348 public static JalviewStructureDisplayI createView(ViewerType type,
349 AlignmentPanel alignPanel, StructureViewerModel viewerData,
350 String sessionFile, String vid)
352 JalviewStructureDisplayI viewer = null;
356 viewer = new AppJmol(viewerData, alignPanel, sessionFile, vid);
357 // todo or construct and then openSession(sessionFile)?
360 viewer = new ChimeraViewFrame(viewerData, alignPanel, sessionFile,
364 viewer = new ChimeraXViewFrame(viewerData, alignPanel, sessionFile,
368 viewer = new PymolViewer(viewerData, alignPanel, sessionFile, vid);
371 Console.error(UNKNOWN_VIEWER_TYPE + type.toString());
376 public boolean isBusy()
380 if (!sview.hasMapping())
391 * @return true if view is already showing PDBid
393 public boolean hasPdbId(String pDBid)
400 return sview.getBinding().hasPdbId(pDBid);
403 public boolean isVisible()
405 return sview != null && sview.isVisible();
408 public void setSuperpose(boolean alignAddedStructures)
410 superposeAdded = alignAddedStructures;