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.
21 package jalview.structures.models;
23 import java.awt.Color;
25 import java.io.IOException;
26 import java.util.ArrayList;
27 import java.util.Arrays;
28 import java.util.BitSet;
29 import java.util.HashMap;
30 import java.util.LinkedHashMap;
31 import java.util.List;
32 import java.util.Locale;
35 import javax.swing.SwingUtilities;
37 import jalview.api.AlignViewportI;
38 import jalview.api.AlignmentViewPanel;
39 import jalview.api.FeatureRenderer;
40 import jalview.api.SequenceRenderer;
41 import jalview.api.StructureSelectionManagerProvider;
42 import jalview.api.structures.JalviewStructureDisplayI;
43 import jalview.bin.Console;
44 import jalview.datamodel.AlignmentI;
45 import jalview.datamodel.ColumnSelection;
46 import jalview.datamodel.HiddenColumns;
47 import jalview.datamodel.MappedFeatures;
48 import jalview.datamodel.PDBEntry;
49 import jalview.datamodel.SequenceFeature;
50 import jalview.datamodel.SequenceI;
51 import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
52 import jalview.gui.AlignmentPanel;
53 import jalview.gui.Desktop;
54 import jalview.gui.StructureViewer.ViewerType;
55 import jalview.io.DataSourceType;
56 import jalview.io.StructureFile;
57 import jalview.renderer.seqfeatures.FeatureColourFinder;
58 import jalview.schemes.ColourSchemeI;
59 import jalview.schemes.ResidueProperties;
60 import jalview.structure.AtomSpec;
61 import jalview.structure.AtomSpecModel;
62 import jalview.structure.StructureCommandI;
63 import jalview.structure.StructureCommandsI;
64 import jalview.structure.StructureCommandsI.AtomSpecType;
65 import jalview.structure.StructureListener;
66 import jalview.structure.StructureMapping;
67 import jalview.structure.StructureSelectionManager;
68 import jalview.util.Comparison;
69 import jalview.util.MessageManager;
73 * A base class to hold common function for 3D structure model binding. Initial
74 * version created by refactoring JMol and Chimera binding models, but other
75 * structure viewers could in principle be accommodated in future.
80 public abstract class AAStructureBindingModel
81 extends SequenceStructureBindingModel
82 implements StructureListener, StructureSelectionManagerProvider
85 * Data bean class to simplify parameterisation in superposeStructures
87 public static class SuperposeData
89 public String filename;
93 public String chain = "";
96 * is the mapped sequence not protein ?
101 * The pdb residue number (if any) mapped to columns of the alignment
103 public int[] pdbResNo; // or use SparseIntArray?
105 public String modelId;
111 * width of alignment (number of columns that may potentially
112 * participate in superposition)
114 * structure viewer model number
116 public SuperposeData(int width, String model)
118 pdbResNo = new int[width];
123 private static final int MIN_POS_TO_SUPERPOSE = 4;
125 private static final String COLOURING_STRUCTURES = MessageManager
126 .getString("status.colouring_structures");
129 * the Jalview panel through which the user interacts
130 * with the structure viewer
132 private JalviewStructureDisplayI viewer;
135 * helper that generates command syntax
137 private StructureCommandsI commandGenerator;
139 private StructureSelectionManager ssm;
142 * modelled chains, formatted as "pdbid:chainCode"
144 private List<String> chainNames;
147 * lookup of pdb file name by key "pdbid:chainCode"
149 private Map<String, String> chainFile;
152 * distinct PDB entries (pdb files) associated
155 private PDBEntry[] pdbEntry;
158 * sequences mapped to each pdbentry
160 private SequenceI[][] sequence;
163 * array of target chains for sequences - tied to pdbentry and sequence[]
165 private String[][] chains;
168 * datasource protocol for access to PDBEntrylatest
170 DataSourceType protocol = null;
172 protected boolean colourBySequence = true;
175 * true if all sequences appear to be nucleotide
177 private boolean nucleotide;
179 private boolean finishedInit = false;
182 * current set of model filenames loaded in the viewer
184 protected String[] modelFileNames = null;
186 public String fileLoadingError;
188 protected Thread externalViewerMonitor;
196 public AAStructureBindingModel(StructureSelectionManager ssm,
200 this.sequence = seqs;
201 chainNames = new ArrayList<>();
202 chainFile = new HashMap<>();
213 public AAStructureBindingModel(StructureSelectionManager ssm,
214 PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
215 DataSourceType protocol)
217 this(ssm, sequenceIs);
218 this.nucleotide = Comparison.isNucleotide(sequenceIs);
219 this.pdbEntry = pdbentry;
220 this.protocol = protocol;
224 private boolean resolveChains()
227 * final count of chain mappings discovered
230 // JBPNote: JAL-2693 - this should be a list of chain mappings per
231 // [pdbentry][sequence]
232 String[][] newchains = new String[pdbEntry.length][];
234 for (PDBEntry pdb : pdbEntry)
236 SequenceI[] seqsForPdb = sequence[pe];
237 if (seqsForPdb != null)
239 newchains[pe] = new String[seqsForPdb.length];
241 for (SequenceI asq : seqsForPdb)
243 String chain = (chains != null && chains[pe] != null)
246 SequenceI sq = (asq.getDatasetSequence() == null) ? asq
247 : asq.getDatasetSequence();
248 if (sq.getAllPDBEntries() != null)
250 for (PDBEntry pdbentry : sq.getAllPDBEntries())
252 if (pdb.getFile() != null && pdbentry.getFile() != null
253 && pdb.getFile().equals(pdbentry.getFile()))
255 String chaincode = pdbentry.getChainCode();
256 if (chaincode != null && chaincode.length() > 0)
265 newchains[pe][se] = chain;
273 return chainmaps > 0;
276 public StructureSelectionManager getSsm()
282 * Returns the i'th PDBEntry (or null)
287 public PDBEntry getPdbEntry(int i)
289 return (pdbEntry != null && pdbEntry.length > i) ? pdbEntry[i] : null;
293 * Answers true if this binding includes the given PDB id, else false
298 public boolean hasPdbId(String pdbId)
300 if (pdbEntry != null)
302 for (PDBEntry pdb : pdbEntry)
304 if (pdb.getId().equals(pdbId))
314 * Returns the number of modelled PDB file entries.
318 public int getPdbCount()
320 return pdbEntry == null ? 0 : pdbEntry.length;
323 public SequenceI[][] getSequence()
328 public String[][] getChains()
333 public DataSourceType getProtocol()
338 // TODO may remove this if calling methods can be pulled up here
339 protected void setPdbentry(PDBEntry[] pdbentry)
341 this.pdbEntry = pdbentry;
344 protected void setSequence(SequenceI[][] sequence)
346 this.sequence = sequence;
349 protected void setChains(String[][] chains)
351 this.chains = chains;
355 * Construct a title string for the viewer window based on the data Jalview
364 public String getViewerTitle(String viewerName, boolean verbose)
366 if (getSequence() == null || getSequence().length < 1
367 || getPdbCount() < 1 || getSequence()[0].length < 1)
369 return ("Jalview " + viewerName + " Window");
371 // TODO: give a more informative title when multiple structures are
373 StringBuilder title = new StringBuilder(64);
374 final PDBEntry pdbe = getPdbEntry(0);
375 title.append(viewerName + " view for " + getSequence()[0][0].getName()
376 + ":" + pdbe.getId());
380 String method = (String) pdbe.getProperty("method");
383 title.append(" Method: ").append(method);
385 String chain = (String) pdbe.getProperty("chains");
388 title.append(" Chain:").append(chain);
391 return title.toString();
395 * Called by after closeViewer is called, to release any resources and
396 * references so they can be garbage collected. Override if needed.
398 protected void releaseUIResources()
403 public void releaseReferences(Object svl)
407 public boolean isColourBySequence()
409 return colourBySequence;
413 * Called when the binding thinks the UI needs to be refreshed after a
414 * structure viewer state change. This could be because structures were
415 * loaded, or because an error has occurred. Default does nothing, override as
418 public void refreshGUI()
423 * Instruct the Jalview binding to update the pdbentries vector if necessary
424 * prior to matching the jmol view's contents to the list of structure files
425 * Jalview knows about. By default does nothing, override as required.
427 public void refreshPdbEntries()
431 public void setColourBySequence(boolean colourBySequence)
433 this.colourBySequence = colourBySequence;
436 protected void addSequenceAndChain(int pe, SequenceI[] seq,
439 if (pe < 0 || pe >= getPdbCount())
441 throw new Error(MessageManager.formatMessage(
442 "error.implementation_error_no_pdbentry_from_index",
444 { Integer.valueOf(pe).toString() }));
446 final String nullChain = "TheNullChain";
447 List<SequenceI> s = new ArrayList<>();
448 List<String> c = new ArrayList<>();
449 if (getChains() == null)
451 setChains(new String[getPdbCount()][]);
453 if (getSequence()[pe] != null)
455 for (int i = 0; i < getSequence()[pe].length; i++)
457 s.add(getSequence()[pe][i]);
458 if (getChains()[pe] != null)
460 if (i < getChains()[pe].length)
462 c.add(getChains()[pe][i]);
471 if (tchain != null && tchain.length > 0)
478 for (int i = 0; i < seq.length; i++)
480 if (!s.contains(seq[i]))
483 if (tchain != null && i < tchain.length)
485 c.add(tchain[i] == null ? nullChain : tchain[i]);
489 SequenceI[] tmp = s.toArray(new SequenceI[s.size()]);
490 getSequence()[pe] = tmp;
493 String[] tch = c.toArray(new String[c.size()]);
494 for (int i = 0; i < tch.length; i++)
496 if (tch[i] == nullChain)
501 getChains()[pe] = tch;
505 getChains()[pe] = null;
510 * add structures and any known sequence associations
512 * @returns the pdb entries added to the current set.
514 public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
515 SequenceI[][] seq, String[][] chns)
517 List<PDBEntry> v = new ArrayList<>();
518 List<int[]> rtn = new ArrayList<>();
519 for (int i = 0; i < getPdbCount(); i++)
521 v.add(getPdbEntry(i));
523 for (int i = 0; i < pdbe.length; i++)
525 int r = v.indexOf(pdbe[i]);
526 if (r == -1 || r >= getPdbCount())
528 rtn.add(new int[] { v.size(), i });
533 // just make sure the sequence/chain entries are all up to date
534 addSequenceAndChain(r, seq[i], chns[i]);
537 pdbe = v.toArray(new PDBEntry[v.size()]);
541 // expand the tied sequence[] and string[] arrays
542 SequenceI[][] sqs = new SequenceI[getPdbCount()][];
543 String[][] sch = new String[getPdbCount()][];
544 System.arraycopy(getSequence(), 0, sqs, 0, getSequence().length);
545 System.arraycopy(getChains(), 0, sch, 0, this.getChains().length);
548 pdbe = new PDBEntry[rtn.size()];
549 for (int r = 0; r < pdbe.length; r++)
551 int[] stri = (rtn.get(r));
552 // record the pdb file as a new addition
553 pdbe[r] = getPdbEntry(stri[0]);
554 // and add the new sequence/chain entries
555 addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]);
566 * Add sequences to the pe'th pdbentry's sequence set.
571 public void addSequence(int pe, SequenceI[] seq)
573 addSequenceAndChain(pe, seq, null);
577 * add the given sequences to the mapping scope for the given pdb file handle
580 * - pdbFile identifier
582 * - set of sequences it can be mapped to
584 public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
586 for (int pe = 0; pe < getPdbCount(); pe++)
588 if (getPdbEntry(pe).getFile().equals(pdbFile))
590 addSequence(pe, seq);
596 public abstract void highlightAtoms(List<AtomSpec> atoms);
598 protected boolean isNucleotide()
600 return this.nucleotide;
604 * Returns a readable description of all mappings for the wrapped pdbfile to
605 * any mapped sequences
611 public String printMappings()
613 if (pdbEntry == null)
617 StringBuilder sb = new StringBuilder(128);
618 for (int pdbe = 0; pdbe < getPdbCount(); pdbe++)
620 String pdbfile = getPdbEntry(pdbe).getFile();
621 List<SequenceI> seqs = Arrays.asList(getSequence()[pdbe]);
622 sb.append(getSsm().printMappings(pdbfile, seqs));
624 return sb.toString();
628 * Returns the mapped structure position for a given aligned column of a given
629 * sequence, or -1 if the column is gapped, beyond the end of the sequence, or
630 * not mapped to structure.
637 protected int getMappedPosition(SequenceI seq, int alignedPos,
638 StructureMapping mapping)
640 if (alignedPos >= seq.getLength())
645 if (Comparison.isGap(seq.getCharAt(alignedPos)))
649 int seqPos = seq.findPosition(alignedPos);
650 int pos = mapping.getPDBResNum(seqPos);
655 * Helper method to identify residues that can participate in a structure
656 * superposition command. For each structure, identify a sequence in the
657 * alignment which is mapped to the structure. Identify non-gapped columns in
658 * the sequence which have a mapping to a residue in the structure. Returns
659 * the index of the first structure that has a mapping to the alignment.
662 * the sequence alignment which is the basis of structure
665 * a BitSet, where bit j is set to indicate that every structure has
666 * a mapped residue present in column j (so the column can
667 * participate in structure alignment)
669 * an array of data beans corresponding to pdb file index
672 protected int findSuperposableResidues(AlignmentI alignment,
674 AAStructureBindingModel.SuperposeData[] structures)
676 int refStructure = -1;
677 String[] files = getStructureFiles();
682 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
684 StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]);
688 * Find the first mapped sequence (if any) for this PDB entry which is in
691 final int seqCountForPdbFile = getSequence()[pdbfnum].length;
692 for (int s = 0; s < seqCountForPdbFile; s++)
694 for (StructureMapping mapping : mappings)
696 final SequenceI theSequence = getSequence()[pdbfnum][s];
697 if (mapping.getSequence() == theSequence
698 && alignment.findIndex(theSequence) > -1)
700 if (refStructure < 0)
702 refStructure = pdbfnum;
704 for (int r = 0; r < alignment.getWidth(); r++)
710 int pos = getMappedPosition(theSequence, r, mapping);
711 if (pos < 1 || pos == lastPos)
717 structures[pdbfnum].pdbResNo[r] = pos;
719 String chain = mapping.getChain();
720 if (chain != null && chain.trim().length() > 0)
722 structures[pdbfnum].chain = chain;
724 structures[pdbfnum].pdbId = mapping.getPdbId();
725 structures[pdbfnum].isRna = !theSequence.isProtein();
728 * move on to next pdb file (ignore sequences for other chains
729 * for the same structure)
731 s = seqCountForPdbFile;
732 break; // fixme break out of two loops here!
741 * Returns true if the structure viewer has loaded all of the files of
742 * interest (identified by the file mapping having been set up), or false if
743 * any are still not loaded after a timeout interval.
747 protected boolean waitForFileLoad(String[] files)
750 * give up after 10 secs plus 1 sec per file
752 long starttime = System.currentTimeMillis();
753 long endTime = 10000 + 1000 * files.length + starttime;
754 String notLoaded = null;
756 boolean waiting = true;
757 while (waiting && System.currentTimeMillis() < endTime)
760 for (String file : files)
769 StructureMapping[] sm = getSsm().getMapping(file);
770 if (sm == null || sm.length == 0)
774 } catch (Throwable x)
784 "Timed out waiting for structure viewer to load file "
792 public boolean isListeningFor(SequenceI seq)
794 if (sequence != null)
796 for (SequenceI[] seqs : sequence)
800 for (SequenceI s : seqs)
802 if (s == seq || (s.getDatasetSequence() != null
803 && s.getDatasetSequence() == seq.getDatasetSequence()))
814 public boolean isFinishedInit()
819 public void setFinishedInit(boolean fi)
821 this.finishedInit = fi;
825 * Returns a list of chains mapped in this viewer, formatted as
830 public List<String> getChainNames()
836 * Returns the Jalview panel hosting the structure viewer (if any)
840 public JalviewStructureDisplayI getViewer()
845 public void setViewer(JalviewStructureDisplayI v)
851 * Constructs and sends a command to align structures against a reference
852 * structure, based on one or more sequence alignments. May optionally return
853 * an error or warning message for the alignment command(s).
856 * an array of one or more alignment views to process
859 public String superposeStructures(List<AlignmentViewPanel> alignWith)
862 String[] files = getStructureFiles();
864 if (!waitForFileLoad(files))
870 for (AlignmentViewPanel view : alignWith)
872 AlignmentI alignment = view.getAlignment();
873 HiddenColumns hiddenCols = alignment.getHiddenColumns();
875 * 'matched' bit i will be set for visible alignment columns i where
876 * all sequences have a residue with a mapping to their PDB structure
878 final int width = alignment.getWidth();
879 BitSet matched = new BitSet();
880 ColumnSelection cs = view.getAlignViewport().getColumnSelection();
881 // restrict to active column selection, if there is one
882 if (cs != null && cs.hasSelectedColumns()
883 && cs.getSelected().size() >= 4)
885 for (int s : cs.getSelected())
887 if (hiddenCols == null)
893 matched.set(hiddenCols.visibleToAbsoluteColumn(s));
899 for (int m = 0; m < width; m++)
901 if (hiddenCols == null || hiddenCols.isVisible(m))
907 AAStructureBindingModel.SuperposeData[] structures = new AAStructureBindingModel.SuperposeData[files.length];
908 for (int f = 0; f < files.length; f++)
910 structures[f] = new AAStructureBindingModel.SuperposeData(width,
911 getModelIdForFile(files[f]));
915 * Calculate the superposable alignment columns ('matched'), and the
916 * corresponding structure residue positions (structures.pdbResNo)
918 int refStructure = findSuperposableResidues(alignment, matched,
922 * require at least 4 positions to be able to execute superposition
924 int nmatched = matched.cardinality();
925 if (nmatched < MIN_POS_TO_SUPERPOSE)
927 String msg = MessageManager
928 .formatMessage("label.insufficient_residues", nmatched);
929 error += view.getViewName() + ": " + msg + "; ";
934 * get a model of the superposable residues in the reference structure
936 AtomSpecModel refAtoms = getAtomSpec(structures[refStructure],
940 * Show all as backbone before doing superposition(s)
941 * (residues used for matching will be shown as ribbon)
943 // todo better way to ensure synchronous than setting getReply true!!
944 executeCommands(commandGenerator.showBackbone(), true, null);
946 AtomSpecType backbone = structures[refStructure].isRna
947 ? AtomSpecType.PHOSPHATE
948 : AtomSpecType.ALPHA;
949 List<AtomSpecModel> models = new ArrayList<AtomSpecModel>();
950 models.add(refAtoms);
952 * superpose each (other) structure to the reference in turn
954 for (int i = 0; i < structures.length; i++)
956 if (i != refStructure)
958 AtomSpecModel atomSpec = getAtomSpec(structures[i], matched);
959 List<StructureCommandI> commands = commandGenerator
960 .superposeStructures(refAtoms, atomSpec, backbone);
961 List<String> replies = executeCommands(commands, true, null);
962 for (String reply : replies)
964 // return this error (Chimera only) to the user
965 if (reply.toLowerCase(Locale.ROOT)
966 .contains("unequal numbers of atoms"))
968 error += "; " + reply;
971 models.add(atomSpec);
974 List<StructureCommandI> finalView = commandGenerator
975 .centerViewOn(models);
976 executeCommands(finalView, false, "Centered on Superposition");
981 private AtomSpecModel getAtomSpec(
982 AAStructureBindingModel.SuperposeData superposeData,
985 AtomSpecModel model = new AtomSpecModel();
986 int nextColumnMatch = matched.nextSetBit(0);
987 while (nextColumnMatch != -1)
989 int pdbResNum = superposeData.pdbResNo[nextColumnMatch];
990 model.addRange(superposeData.modelId, pdbResNum, pdbResNum,
991 superposeData.chain);
992 nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1);
999 * returns the current sequenceRenderer that should be used to colour the
1006 public abstract SequenceRenderer getSequenceRenderer(
1007 AlignmentViewPanel alignment);
1010 * Sends a command to the structure viewer to colour each chain with a
1011 * distinct colour (to the extent supported by the viewer)
1013 public void colourByChain()
1015 colourBySequence = false;
1017 // TODO: JAL-628 colour chains distinctly across all visible models
1019 executeCommand(false, COLOURING_STRUCTURES,
1020 commandGenerator.colourByChain());
1024 * Sends a command to the structure viewer to colour each chain with a
1025 * distinct colour (to the extent supported by the viewer)
1027 public void colourByCharge()
1029 colourBySequence = false;
1031 executeCommands(commandGenerator.colourByCharge(), false,
1032 COLOURING_STRUCTURES);
1036 * Sends a command to the structure to apply a colour scheme (defined in
1037 * Jalview but not necessarily applied to the alignment), which defines a
1038 * colour per residue letter. More complex schemes (e.g. that depend on
1039 * consensus) cannot be used here and are ignored.
1043 public void colourByJalviewColourScheme(ColourSchemeI cs)
1045 colourBySequence = false;
1047 if (cs == null || !cs.isSimple())
1053 * build a map of {Residue3LetterCode, Color}
1055 Map<String, Color> colours = new HashMap<>();
1056 List<String> residues = ResidueProperties.getResidues(isNucleotide(),
1058 for (String resName : residues)
1060 char res = resName.length() == 3
1061 ? ResidueProperties.getSingleCharacterCode(resName)
1062 : resName.charAt(0);
1063 Color colour = cs.findColour(res, 0, null, null, 0f);
1064 colours.put(resName, colour);
1068 * pass to the command constructor, and send the command
1070 List<StructureCommandI> cmd = commandGenerator
1071 .colourByResidues(colours);
1072 executeCommands(cmd, false, COLOURING_STRUCTURES);
1075 public void setBackgroundColour(Color col)
1077 StructureCommandI cmd = commandGenerator.setBackgroundColour(col);
1078 executeCommand(false, null, cmd);
1082 * Execute one structure viewer command. If {@code getReply} is true, may
1083 * optionally return one or more reply messages, else returns null.
1088 protected abstract List<String> executeCommand(StructureCommandI cmd,
1092 * Executes one or more structure viewer commands
1098 protected List<String> executeCommands(List<StructureCommandI> commands,
1099 boolean getReply, String msg)
1101 return executeCommand(getReply, msg,
1102 commands.toArray(new StructureCommandI[commands.size()]));
1106 * Executes one or more structure viewer commands, optionally returning the
1107 * reply, and optionally showing a status message while the command is being
1110 * If a reply is wanted, the execution is done synchronously (waits),
1111 * otherwise it is done in a separate thread (doesn't wait). WARNING: if you
1112 * are sending commands that need to execute before later calls to
1113 * executeCommand (e.g. mouseovers, which clean up after previous ones) then
1114 * set getReply true to ensure that commands are not executed out of order.
1121 protected List<String> executeCommand(boolean getReply, String msg,
1122 StructureCommandI... cmds)
1124 JalviewStructureDisplayI theViewer = getViewer();
1125 final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
1130 * execute and wait for reply
1132 List<String> response = new ArrayList<>();
1135 for (StructureCommandI cmd : cmds)
1137 List<String> replies = executeCommand(cmd, true);
1138 if (replies != null)
1140 response.addAll(replies);
1148 theViewer.stopProgressBar(null, handle);
1156 String threadName = msg == null ? "StructureCommand" : msg;
1157 new Thread(new Runnable()
1164 for (StructureCommandI cmd : cmds)
1166 executeCommand(cmd, false);
1172 SwingUtilities.invokeLater(new Runnable()
1177 theViewer.stopProgressBar(null, handle);
1183 }, threadName).start();
1188 * Colours any structures associated with sequences in the given alignment as
1189 * coloured in the alignment view, provided colourBySequence is enabled
1191 public void colourBySequence(AlignmentViewPanel alignmentv)
1193 if (!colourBySequence || !isLoadingFinished() || getSsm() == null)
1197 Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, sequence,
1200 List<StructureCommandI> colourBySequenceCommands = commandGenerator
1201 .colourBySequence(colourMap);
1202 executeCommands(colourBySequenceCommands, false, COLOURING_STRUCTURES);
1206 * Centre the display in the structure viewer
1208 public void focusView()
1210 executeCommand(false, null, commandGenerator.focusView());
1214 * Generates and executes a command to show only specified chains in the
1215 * structure viewer. The list of chains to show should contain entries
1216 * formatted as "pdbid:chaincode".
1220 public void showChains(List<String> toShow)
1222 // todo or reformat toShow list entries as modelNo:pdbId:chainCode ?
1225 * Reformat the pdbid:chainCode values as modelNo:chainCode
1226 * since this is what is needed to construct the viewer command
1227 * todo: find a less messy way to do this
1229 List<String> showThese = new ArrayList<>();
1230 for (String chainId : toShow)
1232 String[] tokens = chainId.split("\\:");
1233 if (tokens.length == 2)
1235 String pdbFile = getFileForChain(chainId);
1236 String model = getModelIdForFile(pdbFile);
1237 showThese.add(model + ":" + tokens[1]);
1240 executeCommands(commandGenerator.showChains(showThese), false, null);
1244 * Answers the structure viewer's model id given a PDB file name. Returns an
1245 * empty string if model id is not found.
1250 protected abstract String getModelIdForFile(String chainId);
1252 public boolean hasFileLoadingError()
1254 return fileLoadingError != null && fileLoadingError.length() > 0;
1258 * Returns the FeatureRenderer for the given alignment view
1263 public FeatureRenderer getFeatureRenderer(AlignmentViewPanel avp)
1265 AlignmentViewPanel ap = (avp == null) ? getViewer().getAlignmentPanel()
1271 return ap.getFeatureRenderer();
1274 protected void setStructureCommands(StructureCommandsI cmd)
1276 commandGenerator = cmd;
1280 * Records association of one chain id (formatted as "pdbid:chainCode") with
1281 * the corresponding PDB file name
1286 public void addChainFile(String chainId, String fileName)
1288 chainFile.put(chainId, fileName);
1292 * Returns the PDB filename for the given chain id (formatted as
1293 * "pdbid:chainCode"), or null if not found
1298 protected String getFileForChain(String chainId)
1300 return chainFile.get(chainId);
1304 public void updateColours(Object source)
1306 if (getViewer() == null)
1308 // can happen if a viewer was not instantiated or cleaned up and is still
1309 // registered - mostly during tests
1312 AlignmentViewPanel ap = (AlignmentViewPanel) source;
1313 // ignore events from panels not used to colour this view
1314 if (!getViewer().isUsedForColourBy(ap))
1318 if (!isLoadingFromArchive())
1320 colourBySequence(ap);
1324 public StructureCommandsI getCommandGenerator()
1326 return commandGenerator;
1329 protected abstract ViewerType getViewerType();
1332 * Builds a data structure which records mapped structure residues for each
1333 * colour. From this we can easily generate the viewer commands for colour by
1334 * sequence. Constructs and returns a map of {@code Color} to
1335 * {@code AtomSpecModel}, where the atomspec model holds
1343 * Ordering is by order of addition (for colours), natural ordering (for
1344 * models and chains)
1351 protected Map<Object, AtomSpecModel> buildColoursMap(
1352 StructureSelectionManager ssm, SequenceI[][] sequence,
1353 AlignmentViewPanel viewPanel)
1355 String[] files = getStructureFiles();
1356 SequenceRenderer sr = getSequenceRenderer(viewPanel);
1357 FeatureRenderer fr = viewPanel.getFeatureRenderer();
1358 FeatureColourFinder finder = new FeatureColourFinder(fr);
1359 AlignViewportI viewport = viewPanel.getAlignViewport();
1360 HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
1361 AlignmentI al = viewport.getAlignment();
1362 Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<>();
1363 Color lastColour = null;
1365 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
1367 final String modelId = getModelIdForFile(files[pdbfnum]);
1368 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
1370 if (mapping == null || mapping.length < 1)
1375 int startPos = -1, lastPos = -1;
1376 String lastChain = "";
1377 for (int s = 0; s < sequence[pdbfnum].length; s++)
1379 for (int sp, m = 0; m < mapping.length; m++)
1381 final SequenceI seq = sequence[pdbfnum][s];
1382 if (mapping[m].getSequence() == seq
1383 && (sp = al.findIndex(seq)) > -1)
1385 SequenceI asp = al.getSequenceAt(sp);
1386 for (int r = 0; r < asp.getLength(); r++)
1388 // no mapping to gaps in sequence
1389 if (Comparison.isGap(asp.getCharAt(r)))
1393 int pos = mapping[m].getPDBResNum(asp.findPosition(r));
1395 if (pos < 1 || pos == lastPos)
1400 Color colour = sr.getResidueColour(seq, r, finder);
1403 * darker colour for hidden regions
1405 if (!cs.isVisible(r))
1407 colour = Color.GRAY;
1410 final String chain = mapping[m].getChain();
1413 * Just keep incrementing the end position for this colour range
1414 * _unless_ colour, PDB model or chain has changed, or there is a
1415 * gap in the mapped residue sequence
1417 final boolean newColour = !colour.equals(lastColour);
1418 final boolean nonContig = lastPos + 1 != pos;
1419 final boolean newChain = !chain.equals(lastChain);
1420 if (newColour || nonContig || newChain)
1424 addAtomSpecRange(colourMap, lastColour, modelId, startPos,
1425 lastPos, lastChain);
1429 lastColour = colour;
1433 // final colour range
1434 if (lastColour != null)
1436 addAtomSpecRange(colourMap, lastColour, modelId, startPos,
1437 lastPos, lastChain);
1448 * todo better refactoring (map lookup or similar to get viewer structure id)
1454 protected String getModelId(int pdbfnum, String file)
1456 return String.valueOf(pdbfnum);
1460 * Saves chains, formatted as "pdbId:chainCode", and lookups from this to the
1461 * full PDB file path
1466 public void stashFoundChains(StructureFile pdb, String file)
1468 for (int i = 0; i < pdb.getChains().size(); i++)
1470 String chid = pdb.getId() + ":" + pdb.getChains().elementAt(i).id;
1471 addChainFile(chid, file);
1472 getChainNames().add(chid);
1477 * Helper method to add one contiguous range to the AtomSpec model for the
1478 * given value (creating the model if necessary). As used by Jalview,
1481 * <li>a colour, when building a 'colour structure by sequence' command</li>
1482 * <li>a feature value, when building a 'set Chimera attributes from features'
1493 public static final void addAtomSpecRange(Map<Object, AtomSpecModel> map,
1494 Object value, String model, int startPos, int endPos,
1498 * Get/initialize map of data for the colour
1500 AtomSpecModel atomSpec = map.get(value);
1501 if (atomSpec == null)
1503 atomSpec = new AtomSpecModel();
1504 map.put(value, atomSpec);
1507 atomSpec.addRange(model, startPos, endPos, chain);
1511 * Returns the file extension (including '.' separator) to use for a saved
1512 * viewer session file. Default is to return null (not supported), override as
1517 public String getSessionFileExtension()
1523 * If supported, saves the state of the structure viewer to a temporary file
1524 * and returns the file. Returns null and logs an error on any failure.
1528 public File saveSession()
1530 String prefix = getViewerType().toString();
1531 String suffix = getSessionFileExtension();
1535 f = File.createTempFile(prefix, suffix);
1537 } catch (IOException e)
1539 Console.error(String.format("Error saving %s session: %s", prefix,
1547 * Saves the structure viewer session to the given file
1551 protected void saveSession(File f)
1553 StructureCommandI cmd = commandGenerator.saveSession(f.getPath());
1556 executeCommand(cmd, false);
1561 * Returns true if the viewer is an external structure viewer for which the
1562 * process is still alive, else false (for Jmol, or an external viewer which
1563 * the user has independently closed)
1567 public boolean isViewerRunning()
1573 * Closes Jalview's structure viewer panel and releases associated resources.
1574 * If it is managing an external viewer program, and {@code forceClose} is
1575 * true, also asks that program to close.
1579 public void closeViewer(boolean forceClose)
1581 getSsm().removeStructureViewerListener(this, this.getStructureFiles());
1582 releaseUIResources();
1585 * end the thread that closes this panel if the external viewer closes
1587 if (externalViewerMonitor != null)
1589 externalViewerMonitor.interrupt();
1590 externalViewerMonitor = null;
1597 StructureCommandI cmd = getCommandGenerator().closeViewer();
1600 executeCommand(cmd, false);
1606 * Returns the URL of a help page for the structure viewer, or null if none is
1611 public String getHelpURL()
1618 * Helper method to build a map of
1619 * { featureType, { feature value, AtomSpecModel } }
1625 protected Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
1626 AlignmentViewPanel viewPanel)
1628 Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<>();
1629 String[] files = getStructureFiles();
1635 FeatureRenderer fr = viewPanel.getFeatureRenderer();
1641 AlignViewportI viewport = viewPanel.getAlignViewport();
1642 List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
1645 * if alignment is showing features from complement, we also transfer
1646 * these features to the corresponding mapped structure residues
1648 boolean showLinkedFeatures = viewport.isShowComplementFeatures();
1649 List<String> complementFeatures = new ArrayList<>();
1650 FeatureRenderer complementRenderer = null;
1651 if (showLinkedFeatures)
1653 AlignViewportI comp = fr.getViewport().getCodingComplement();
1656 complementRenderer = Desktop.getAlignFrameFor(comp)
1657 .getFeatureRenderer();
1658 complementFeatures = complementRenderer.getDisplayedFeatureTypes();
1661 if (visibleFeatures.isEmpty() && complementFeatures.isEmpty())
1666 AlignmentI alignment = viewPanel.getAlignment();
1667 SequenceI[][] seqs = getSequence();
1669 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
1671 String modelId = getModelIdForFile(files[pdbfnum]);
1672 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
1674 if (mapping == null || mapping.length < 1)
1679 for (int seqNo = 0; seqNo < seqs[pdbfnum].length; seqNo++)
1681 for (int m = 0; m < mapping.length; m++)
1683 final SequenceI seq = seqs[pdbfnum][seqNo];
1684 int sp = alignment.findIndex(seq);
1685 StructureMapping structureMapping = mapping[m];
1686 if (structureMapping.getSequence() == seq && sp > -1)
1689 * found a sequence with a mapping to a structure;
1690 * now scan its features
1692 if (!visibleFeatures.isEmpty())
1694 scanSequenceFeatures(visibleFeatures, structureMapping, seq,
1697 if (showLinkedFeatures)
1699 scanComplementFeatures(complementRenderer, structureMapping,
1700 seq, theMap, modelId);
1710 * Ask the structure viewer to open a session file. Returns true if
1711 * successful, else false (or not supported).
1716 public boolean openSession(String filepath)
1718 StructureCommandI cmd = getCommandGenerator().openSession(filepath);
1723 executeCommand(cmd, true);
1724 // todo: test for failure - how?
1729 * Scans visible features in mapped positions of the CDS/peptide complement,
1730 * and adds any found to the map of attribute values/structure positions
1732 * @param complementRenderer
1733 * @param structureMapping
1736 * @param modelNumber
1738 protected static void scanComplementFeatures(
1739 FeatureRenderer complementRenderer,
1740 StructureMapping structureMapping, SequenceI seq,
1741 Map<String, Map<Object, AtomSpecModel>> theMap,
1745 * for each sequence residue mapped to a structure position...
1747 for (int seqPos : structureMapping.getMapping().keySet())
1750 * find visible complementary features at mapped position(s)
1752 MappedFeatures mf = complementRenderer
1753 .findComplementFeaturesAtResidue(seq, seqPos);
1756 for (SequenceFeature sf : mf.features)
1758 String type = sf.getType();
1761 * Don't copy features which originated from Chimera
1763 if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
1764 .equals(sf.getFeatureGroup()))
1770 * record feature 'value' (score/description/type) as at the
1771 * corresponding structure position
1773 List<int[]> mappedRanges = structureMapping
1774 .getPDBResNumRanges(seqPos, seqPos);
1776 if (!mappedRanges.isEmpty())
1778 String value = sf.getDescription();
1779 if (value == null || value.length() == 0)
1783 float score = sf.getScore();
1784 if (score != 0f && !Float.isNaN(score))
1786 value = Float.toString(score);
1788 Map<Object, AtomSpecModel> featureValues = theMap.get(type);
1789 if (featureValues == null)
1791 featureValues = new HashMap<>();
1792 theMap.put(type, featureValues);
1794 for (int[] range : mappedRanges)
1796 addAtomSpecRange(featureValues, value, modelNumber, range[0],
1797 range[1], structureMapping.getChain());
1806 * Inspect features on the sequence; for each feature that is visible,
1807 * determine its mapped ranges in the structure (if any) according to the
1808 * given mapping, and add them to the map.
1810 * @param visibleFeatures
1816 protected static void scanSequenceFeatures(List<String> visibleFeatures,
1817 StructureMapping mapping, SequenceI seq,
1818 Map<String, Map<Object, AtomSpecModel>> theMap, String modelId)
1820 List<SequenceFeature> sfs = seq.getFeatures().getPositionalFeatures(
1821 visibleFeatures.toArray(new String[visibleFeatures.size()]));
1822 for (SequenceFeature sf : sfs)
1824 String type = sf.getType();
1827 * Don't copy features which originated from Chimera
1829 if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
1830 .equals(sf.getFeatureGroup()))
1835 List<int[]> mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(),
1838 if (!mappedRanges.isEmpty())
1840 String value = sf.getDescription();
1841 if (value == null || value.length() == 0)
1845 float score = sf.getScore();
1846 if (score != 0f && !Float.isNaN(score))
1848 value = Float.toString(score);
1850 Map<Object, AtomSpecModel> featureValues = theMap.get(type);
1851 if (featureValues == null)
1853 featureValues = new HashMap<>();
1854 theMap.put(type, featureValues);
1856 for (int[] range : mappedRanges)
1858 addAtomSpecRange(featureValues, value, modelId, range[0],
1859 range[1], mapping.getChain());
1866 * Returns the number of structure files in the structure viewer and mapped to
1867 * Jalview. This may be zero if the files are still in the process of loading
1872 public int getMappedStructureCount()
1874 String[] files = getStructureFiles();
1875 return files == null ? 0 : files.length;
1879 * Starts a thread that waits for the external viewer program process to
1880 * finish, so that we can then close the associated resources. This avoids
1881 * leaving orphaned viewer panels in Jalview if the user closes the external
1886 protected void startExternalViewerMonitor(Process p)
1888 externalViewerMonitor = new Thread(new Runnable()
1897 JalviewStructureDisplayI display = getViewer();
1898 if (display != null)
1900 display.closeViewer(false);
1902 } catch (InterruptedException e)
1904 // exit thread if Chimera Viewer is closed in Jalview
1908 externalViewerMonitor.start();
1912 * If supported by the external structure viewer, sends it commands to notify
1913 * model or selection changes to the specified URL (where Jalview has started
1918 protected void startListening(String uri)
1920 List<StructureCommandI> commands = getCommandGenerator()
1921 .startNotifications(uri);
1922 if (commands != null)
1924 executeCommands(commands, false, null);
1929 * If supported by the external structure viewer, sends it commands to stop
1930 * notifying model or selection changes
1932 protected void stopListening()
1934 List<StructureCommandI> commands = getCommandGenerator()
1935 .stopNotifications();
1936 if (commands != null)
1938 executeCommands(commands, false, null);
1943 * If supported by the structure viewer, queries it for all residue attributes
1944 * with the given attribute name, and creates features on corresponding
1945 * residues of the alignment. Returns the number of features added.
1948 * @param alignmentPanel
1951 public int copyStructureAttributesToFeatures(String attName,
1952 AlignmentPanel alignmentPanel)
1954 StructureCommandI cmd = getCommandGenerator()
1955 .getResidueAttributes(attName);
1960 List<String> residueAttributes = executeCommand(cmd, true);
1962 int featuresAdded = createFeaturesForAttributes(attName,
1964 if (featuresAdded > 0)
1966 alignmentPanel.getFeatureRenderer().featuresAdded();
1968 return featuresAdded;
1972 * Parses {@code residueAttributes} and creates sequence features on any
1973 * mapped alignment residues. Returns the number of features created.
1975 * {@code residueAttributes} is the reply from the structure viewer to a
1976 * command to list any residue attributes for the given attribute name. Syntax
1977 * and parsing of this is viewer-specific.
1980 * @param residueAttributes
1983 protected int createFeaturesForAttributes(String attName,
1984 List<String> residueAttributes)