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 jalview.api.structures.JalviewStructureDisplayI;
24 import jalview.bin.Cache;
25 import jalview.datamodel.PDBEntry;
26 import jalview.datamodel.SequenceI;
27 import jalview.datamodel.StructureViewerModel;
28 import jalview.structure.StructureMapping;
29 import jalview.structure.StructureSelectionManager;
30 import jalview.util.MessageManager;
31 import jalview.util.Platform;
32 import jalview.ws.DBRefFetcher;
33 import jalview.ws.sifts.SiftsSettings;
35 import java.awt.Rectangle;
36 import java.util.ArrayList;
37 import java.util.HashMap;
38 import java.util.LinkedHashMap;
39 import java.util.List;
41 import java.util.Map.Entry;
44 * A proxy for handling structure viewers, that orchestrates adding selected
45 * structures, associated with sequences in Jalview, to an existing viewer, or
46 * opening a new one. Currently supports either Jmol or Chimera as the structure
51 public class StructureViewer
56 Platform.loadStaticResource("core/core_jvjmol.z.js",
57 "org.jmol.viewer.Viewer");
60 private static final String UNKNOWN_VIEWER_TYPE = "Unknown structure viewer type ";
62 StructureSelectionManager ssm;
65 * decide if new structures are aligned to existing ones
67 private boolean superposeAdded = true;
69 public enum ViewerType
77 * @param structureSelectionManager
79 public StructureViewer(StructureSelectionManager structureSelectionManager)
81 ssm = structureSelectionManager;
85 * Factory to create a proxy for modifying existing structure viewer
88 public static StructureViewer reconfigure(
89 JalviewStructureDisplayI display)
91 StructureViewer sv = new StructureViewer(display.getBinding().getSsm());
97 public String toString()
101 return sview.toString();
105 public ViewerType getViewerType()
107 String viewType = Cache.getDefault(Preferences.STRUCTURE_DISPLAY,
108 ViewerType.JMOL.name());
109 return ViewerType.valueOf(viewType);
112 public void setViewerType(ViewerType type)
114 Cache.setProperty(Preferences.STRUCTURE_DISPLAY, type.name());
118 * View multiple PDB entries, each with associated sequences
125 public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
126 SequenceI[] seqs, AlignmentPanel ap)
128 JalviewStructureDisplayI viewer = onlyOnePdb(pdbs, seqs, ap);
132 * user added structure to an existing viewer - all done
137 ViewerType viewerType = getViewerType();
139 Map<PDBEntry, SequenceI[]> seqsForPdbs = getSequencesForPdbs(pdbs,
141 PDBEntry[] pdbsForFile = seqsForPdbs.keySet().toArray(
142 new PDBEntry[seqsForPdbs.size()]);
143 SequenceI[][] theSeqs = seqsForPdbs.values().toArray(
144 new SequenceI[seqsForPdbs.size()][]);
147 sview.setAlignAddedStructures(superposeAdded);
148 new Thread(new Runnable()
154 for (int pdbep = 0; pdbep < pdbsForFile.length; pdbep++)
156 PDBEntry pdb = pdbsForFile[pdbep];
157 if (!sview.addAlreadyLoadedFile(theSeqs[pdbep], null, ap,
160 sview.addToExistingViewer(pdb, theSeqs[pdbep], null, ap,
165 sview.updateTitleAndMenus();
171 if (viewerType.equals(ViewerType.JMOL))
173 sview = new AppJmol(ap, superposeAdded, pdbsForFile, theSeqs);
175 else if (viewerType.equals(ViewerType.CHIMERA))
177 sview = new ChimeraViewFrame(pdbsForFile, superposeAdded, theSeqs,
182 Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
188 * Converts the list of selected PDB entries (possibly including duplicates
189 * for multiple chains), and corresponding sequences, into a map of sequences
190 * for each distinct PDB file. Returns null if either argument is null, or
191 * their lengths do not match.
197 Map<PDBEntry, SequenceI[]> getSequencesForPdbs(PDBEntry[] pdbs,
200 if (pdbs == null || seqs == null || pdbs.length != seqs.length)
206 * we want only one 'representative' PDBEntry per distinct file name
207 * (there may be entries for distinct chains)
209 Map<String, PDBEntry> pdbsSeen = new HashMap<>();
212 * LinkedHashMap preserves order of PDB entries (significant if they
213 * will get superimposed to the first structure)
215 Map<PDBEntry, List<SequenceI>> pdbSeqs = new LinkedHashMap<>();
216 for (int i = 0; i < pdbs.length; i++)
218 PDBEntry pdb = pdbs[i];
219 SequenceI seq = seqs[i];
220 String pdbFile = pdb.getFile();
221 if (pdbFile == null || pdbFile.length() == 0)
223 pdbFile = pdb.getId();
225 if (!pdbsSeen.containsKey(pdbFile))
227 pdbsSeen.put(pdbFile, pdb);
228 pdbSeqs.put(pdb, new ArrayList<SequenceI>());
232 pdb = pdbsSeen.get(pdbFile);
234 List<SequenceI> seqsForPdb = pdbSeqs.get(pdb);
235 if (!seqsForPdb.contains(seq))
242 * convert to Map<PDBEntry, SequenceI[]>
244 Map<PDBEntry, SequenceI[]> result = new LinkedHashMap<>();
245 for (Entry<PDBEntry, List<SequenceI>> entry : pdbSeqs.entrySet())
247 List<SequenceI> theSeqs = entry.getValue();
248 result.put(entry.getKey(),
249 theSeqs.toArray(new SequenceI[theSeqs.size()]));
256 * A strictly temporary method pending JAL-1761 refactoring. Determines if all
257 * the passed PDB entries are the same (this is the case if selected sequences
258 * to view structure for are chains of the same structure). If so, calls the
259 * single-pdb version of viewStructures and returns the viewer, else returns
267 private JalviewStructureDisplayI onlyOnePdb(PDBEntry[] pdbs,
268 SequenceI[] seqsForPdbs, AlignmentPanel ap)
270 List<SequenceI> seqs = new ArrayList<>();
271 if (pdbs == null || pdbs.length == 0)
276 String firstFile = pdbs[0].getFile();
277 for (PDBEntry pdb : pdbs)
279 String pdbFile = pdb.getFile();
280 if (pdbFile == null || !pdbFile.equals(firstFile))
284 SequenceI pdbseq = seqsForPdbs[i++];
290 return viewStructures(pdbs[0], seqs.toArray(new SequenceI[seqs.size()]),
294 JalviewStructureDisplayI sview = null;
296 public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
297 SequenceI[] seqsForPdb, AlignmentPanel ap)
301 sview.setAlignAddedStructures(superposeAdded);
302 String pdbId = pdb.getId();
303 if (!sview.addAlreadyLoadedFile(seqsForPdb, null, ap, pdbId))
305 sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdbId);
307 sview.updateTitleAndMenus();
311 ViewerType viewerType = getViewerType();
312 if (viewerType.equals(ViewerType.JMOL))
314 sview = new AppJmol(pdb, seqsForPdb, null, ap);
316 else if (viewerType.equals(ViewerType.CHIMERA))
318 sview = new ChimeraViewFrame(pdb, seqsForPdb, null, ap);
322 Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
328 * Create a new panel controlling a structure viewer.
341 public JalviewStructureDisplayI createView(ViewerType type, String[] pdbf,
342 String[] id, SequenceI[][] sq, AlignmentPanel alignPanel,
343 StructureViewerModel viewerData, String fileloc, Rectangle rect,
346 final boolean useinViewerSuperpos = viewerData.isAlignWithPanel();
347 final boolean usetoColourbyseq = viewerData.isColourWithAlignPanel();
348 final boolean viewerColouring = viewerData.isColourByViewer();
353 sview = new AppJmol(pdbf, id, sq, alignPanel, usetoColourbyseq,
354 useinViewerSuperpos, viewerColouring, fileloc, rect, vid);
358 "Unsupported structure viewer type " + type.toString());
361 Cache.log.error(UNKNOWN_VIEWER_TYPE + type.toString());
366 public boolean isBusy()
370 if (!sview.hasMapping())
381 * @return true if view is already showing PDBid
383 public boolean hasPdbId(String pDBid)
390 return sview.getBinding().hasPdbId(pDBid);
393 public boolean isVisible()
395 return sview != null && sview.isVisible();
398 public void setSuperpose(boolean alignAddedStructures)
400 superposeAdded = alignAddedStructures;
404 * Launch a minimal implementation of a StructureViewer.
411 public static StructureViewer launchStructureViewer(
412 AlignmentPanel alignPanel, PDBEntry pdb, SequenceI[] seqs)
414 return launchStructureViewer(alignPanel, new PDBEntry[] { pdb }, seqs,
419 * Launch a structure viewer with or without an open StructureChooser.
421 * Moved from StructureChooser to enable JalviewJS startup with structure
425 * @param pdbEntriesToView
432 protected static StructureViewer launchStructureViewer(
433 final AlignmentPanel ap,
434 final PDBEntry[] pdbEntriesToView, SequenceI[] sequences,
435 boolean superimpose, StructureViewer theViewer,
436 IProgressIndicator pb)
438 final StructureSelectionManager ssm = ap.getStructureSelectionManager();
439 long progressId = sequences.hashCode();
442 pb.setProgressBar(MessageManager
443 .getString("status.launching_3d_structure_viewer"), progressId);
445 if (theViewer == null)
447 theViewer = new StructureViewer(ssm);
449 theViewer.setSuperpose(superimpose);
453 pb.setProgressBar(null, progressId);
455 if (SiftsSettings.isMapWithSifts())
457 List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
459 // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
460 // real PDB ID. For moment, we can also safely do this if there is already
461 // a known mapping between the PDBEntry and the sequence.
462 for (SequenceI seq : sequences)
464 PDBEntry pdbe = pdbEntriesToView[p++];
465 if (pdbe != null && pdbe.getFile() != null)
467 StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
468 if (smm != null && smm.length > 0)
470 for (StructureMapping sm : smm)
472 if (sm.getSequence() == seq)
479 if (seq.getPrimaryDBRefs().isEmpty())
481 seqsWithoutSourceDBRef.add(seq);
485 if (!seqsWithoutSourceDBRef.isEmpty())
487 int y = seqsWithoutSourceDBRef.size();
490 pb.setProgressBar(MessageManager.formatMessage(
491 "status.fetching_dbrefs_for_sequences_without_valid_refs",
494 SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
495 .toArray(new SequenceI[y]);
496 DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
497 dbRefFetcher.fetchDBRefs(true);
501 pb.setProgressBar("Fetch complete.", progressId); // todo i18n
505 if (pdbEntriesToView.length > 1)
509 pb.setProgressBar(MessageManager.getString(
510 "status.fetching_3d_structures_for_selected_entries"),
513 theViewer.viewStructures(pdbEntriesToView, sequences, ap);
519 pb.setProgressBar(MessageManager.formatMessage(
520 "status.fetching_3d_structures_for",
521 pdbEntriesToView[0].getId()),progressId);
523 theViewer.viewStructures(pdbEntriesToView[0], sequences, ap);
527 pb.setProgressBar(null, progressId);
529 // remember the last viewer we used...
530 Desktop.getInstance().lastTargetedView = theViewer;