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.util.Locale;
25 import java.awt.Color;
27 import java.io.IOException;
28 import java.util.ArrayList;
29 import java.util.Arrays;
30 import java.util.BitSet;
31 import java.util.HashMap;
32 import java.util.LinkedHashMap;
33 import java.util.List;
36 import javax.swing.SwingUtilities;
38 import jalview.api.AlignViewportI;
39 import jalview.api.AlignmentViewPanel;
40 import jalview.api.FeatureRenderer;
41 import jalview.api.SequenceRenderer;
42 import jalview.api.StructureSelectionManagerProvider;
43 import jalview.api.structures.JalviewStructureDisplayI;
44 import jalview.bin.Console;
45 import jalview.datamodel.AlignmentI;
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.StructureListener;
65 import jalview.structure.StructureMapping;
66 import jalview.structure.StructureSelectionManager;
67 import jalview.util.Comparison;
68 import jalview.util.MessageManager;
72 * A base class to hold common function for 3D structure model binding.
73 * Initial version created by refactoring JMol and Chimera binding models, but
74 * other structure viewers could in principle be accommodated in future.
79 public abstract class AAStructureBindingModel
80 extends SequenceStructureBindingModel
81 implements StructureListener, StructureSelectionManagerProvider
84 * Data bean class to simplify parameterisation in superposeStructures
86 public static class SuperposeData
88 public String filename;
92 public String chain = "";
95 * is the mapped sequence not protein ?
100 * The pdb residue number (if any) mapped to columns of the alignment
102 public int[] pdbResNo; // or use SparseIntArray?
104 public String modelId;
110 * width of alignment (number of columns that may potentially
111 * participate in superposition)
113 * structure viewer model number
115 public SuperposeData(int width, String model)
117 pdbResNo = new int[width];
122 private static final int MIN_POS_TO_SUPERPOSE = 4;
124 private static final String COLOURING_STRUCTURES = MessageManager
125 .getString("status.colouring_structures");
128 * the Jalview panel through which the user interacts
129 * with the structure viewer
131 private JalviewStructureDisplayI viewer;
134 * helper that generates command syntax
136 private StructureCommandsI commandGenerator;
138 private StructureSelectionManager ssm;
141 * modelled chains, formatted as "pdbid:chainCode"
143 private List<String> chainNames;
146 * lookup of pdb file name by key "pdbid:chainCode"
148 private Map<String, String> chainFile;
151 * distinct PDB entries (pdb files) associated
154 private PDBEntry[] pdbEntry;
157 * sequences mapped to each pdbentry
159 private SequenceI[][] sequence;
162 * array of target chains for sequences - tied to pdbentry and sequence[]
164 private String[][] chains;
167 * datasource protocol for access to PDBEntrylatest
169 DataSourceType protocol = null;
171 protected boolean colourBySequence = true;
174 * true if all sequences appear to be nucleotide
176 private boolean nucleotide;
178 private boolean finishedInit = false;
181 * current set of model filenames loaded in the viewer
183 protected String[] modelFileNames = null;
185 public String fileLoadingError;
187 protected Thread externalViewerMonitor;
195 public AAStructureBindingModel(StructureSelectionManager ssm,
199 this.sequence = seqs;
200 chainNames = new ArrayList<>();
201 chainFile = new HashMap<>();
212 public AAStructureBindingModel(StructureSelectionManager ssm,
213 PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
214 DataSourceType protocol)
216 this(ssm, sequenceIs);
217 this.nucleotide = Comparison.isNucleotide(sequenceIs);
218 this.pdbEntry = pdbentry;
219 this.protocol = protocol;
223 private boolean resolveChains()
226 * final count of chain mappings discovered
229 // JBPNote: JAL-2693 - this should be a list of chain mappings per
230 // [pdbentry][sequence]
231 String[][] newchains = new String[pdbEntry.length][];
233 for (PDBEntry pdb : pdbEntry)
235 SequenceI[] seqsForPdb = sequence[pe];
236 if (seqsForPdb != null)
238 newchains[pe] = new String[seqsForPdb.length];
240 for (SequenceI asq : seqsForPdb)
242 String chain = (chains != null && chains[pe] != null)
245 SequenceI sq = (asq.getDatasetSequence() == null) ? asq
246 : asq.getDatasetSequence();
247 if (sq.getAllPDBEntries() != null)
249 for (PDBEntry pdbentry : sq.getAllPDBEntries())
251 if (pdb.getFile() != null && pdbentry.getFile() != null
252 && pdb.getFile().equals(pdbentry.getFile()))
254 String chaincode = pdbentry.getChainCode();
255 if (chaincode != null && chaincode.length() > 0)
264 newchains[pe][se] = chain;
272 return chainmaps > 0;
275 public StructureSelectionManager getSsm()
281 * Returns the i'th PDBEntry (or null)
286 public PDBEntry getPdbEntry(int i)
288 return (pdbEntry != null && pdbEntry.length > i) ? pdbEntry[i] : null;
292 * Answers true if this binding includes the given PDB id, else false
297 public boolean hasPdbId(String pdbId)
299 if (pdbEntry != null)
301 for (PDBEntry pdb : pdbEntry)
303 if (pdb.getId().equals(pdbId))
313 * Returns the number of modelled PDB file entries.
317 public int getPdbCount()
319 return pdbEntry == null ? 0 : pdbEntry.length;
322 public SequenceI[][] getSequence()
327 public String[][] getChains()
332 public DataSourceType getProtocol()
337 // TODO may remove this if calling methods can be pulled up here
338 protected void setPdbentry(PDBEntry[] pdbentry)
340 this.pdbEntry = pdbentry;
343 protected void setSequence(SequenceI[][] sequence)
345 this.sequence = sequence;
348 protected void setChains(String[][] chains)
350 this.chains = chains;
354 * Construct a title string for the viewer window based on the data Jalview
363 public String getViewerTitle(String viewerName, boolean verbose)
365 if (getSequence() == null || getSequence().length < 1
366 || getPdbCount() < 1 || getSequence()[0].length < 1)
368 return ("Jalview " + viewerName + " Window");
370 // TODO: give a more informative title when multiple structures are
372 StringBuilder title = new StringBuilder(64);
373 final PDBEntry pdbe = getPdbEntry(0);
374 title.append(viewerName + " view for " + getSequence()[0][0].getName()
375 + ":" + pdbe.getId());
379 String method = (String) pdbe.getProperty("method");
382 title.append(" Method: ").append(method);
384 String chain = (String) pdbe.getProperty("chains");
387 title.append(" Chain:").append(chain);
390 return title.toString();
394 * Called by after closeViewer is called, to release any resources and
395 * references so they can be garbage collected. Override if needed.
397 protected void releaseUIResources()
402 public void releaseReferences(Object svl)
406 public boolean isColourBySequence()
408 return colourBySequence;
412 * Called when the binding thinks the UI needs to be refreshed after a
413 * structure viewer state change. This could be because structures were
414 * loaded, or because an error has occurred. Default does nothing, override as
417 public void refreshGUI()
422 * Instruct the Jalview binding to update the pdbentries vector if necessary
423 * prior to matching the jmol view's contents to the list of structure files
424 * Jalview knows about. By default does nothing, override as required.
426 public void refreshPdbEntries()
430 public void setColourBySequence(boolean colourBySequence)
432 this.colourBySequence = colourBySequence;
435 protected void addSequenceAndChain(int pe, SequenceI[] seq,
438 if (pe < 0 || pe >= getPdbCount())
440 throw new Error(MessageManager.formatMessage(
441 "error.implementation_error_no_pdbentry_from_index",
443 { Integer.valueOf(pe).toString() }));
445 final String nullChain = "TheNullChain";
446 List<SequenceI> s = new ArrayList<>();
447 List<String> c = new ArrayList<>();
448 if (getChains() == null)
450 setChains(new String[getPdbCount()][]);
452 if (getSequence()[pe] != null)
454 for (int i = 0; i < getSequence()[pe].length; i++)
456 s.add(getSequence()[pe][i]);
457 if (getChains()[pe] != null)
459 if (i < getChains()[pe].length)
461 c.add(getChains()[pe][i]);
470 if (tchain != null && tchain.length > 0)
477 for (int i = 0; i < seq.length; i++)
479 if (!s.contains(seq[i]))
482 if (tchain != null && i < tchain.length)
484 c.add(tchain[i] == null ? nullChain : tchain[i]);
488 SequenceI[] tmp = s.toArray(new SequenceI[s.size()]);
489 getSequence()[pe] = tmp;
492 String[] tch = c.toArray(new String[c.size()]);
493 for (int i = 0; i < tch.length; i++)
495 if (tch[i] == nullChain)
500 getChains()[pe] = tch;
504 getChains()[pe] = null;
509 * add structures and any known sequence associations
511 * @returns the pdb entries added to the current set.
513 public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
514 SequenceI[][] seq, String[][] chns)
516 List<PDBEntry> v = new ArrayList<>();
517 List<int[]> rtn = new ArrayList<>();
518 for (int i = 0; i < getPdbCount(); i++)
520 v.add(getPdbEntry(i));
522 for (int i = 0; i < pdbe.length; i++)
524 int r = v.indexOf(pdbe[i]);
525 if (r == -1 || r >= getPdbCount())
527 rtn.add(new int[] { v.size(), i });
532 // just make sure the sequence/chain entries are all up to date
533 addSequenceAndChain(r, seq[i], chns[i]);
536 pdbe = v.toArray(new PDBEntry[v.size()]);
540 // expand the tied sequence[] and string[] arrays
541 SequenceI[][] sqs = new SequenceI[getPdbCount()][];
542 String[][] sch = new String[getPdbCount()][];
543 System.arraycopy(getSequence(), 0, sqs, 0, getSequence().length);
544 System.arraycopy(getChains(), 0, sch, 0, this.getChains().length);
547 pdbe = new PDBEntry[rtn.size()];
548 for (int r = 0; r < pdbe.length; r++)
550 int[] stri = (rtn.get(r));
551 // record the pdb file as a new addition
552 pdbe[r] = getPdbEntry(stri[0]);
553 // and add the new sequence/chain entries
554 addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]);
565 * Add sequences to the pe'th pdbentry's sequence set.
570 public void addSequence(int pe, SequenceI[] seq)
572 addSequenceAndChain(pe, seq, null);
576 * add the given sequences to the mapping scope for the given pdb file handle
579 * - pdbFile identifier
581 * - set of sequences it can be mapped to
583 public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
585 for (int pe = 0; pe < getPdbCount(); pe++)
587 if (getPdbEntry(pe).getFile().equals(pdbFile))
589 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();
876 * 'matched' bit i will be set for visible alignment columns i where
877 * all sequences have a residue with a mapping to their PDB structure
879 BitSet matched = new BitSet();
880 final int width = alignment.getWidth();
881 for (int m = 0; m < width; m++)
883 if (hiddenCols == null || hiddenCols.isVisible(m))
889 AAStructureBindingModel.SuperposeData[] structures = new AAStructureBindingModel.SuperposeData[files.length];
890 for (int f = 0; f < files.length; f++)
892 structures[f] = new AAStructureBindingModel.SuperposeData(width,
893 getModelIdForFile(files[f]));
897 * Calculate the superposable alignment columns ('matched'), and the
898 * corresponding structure residue positions (structures.pdbResNo)
900 int refStructure = findSuperposableResidues(alignment, matched,
904 * require at least 4 positions to be able to execute superposition
906 int nmatched = matched.cardinality();
907 if (nmatched < MIN_POS_TO_SUPERPOSE)
909 String msg = MessageManager
910 .formatMessage("label.insufficient_residues", nmatched);
911 error += view.getViewName() + ": " + msg + "; ";
916 * get a model of the superposable residues in the reference structure
918 AtomSpecModel refAtoms = getAtomSpec(structures[refStructure],
922 * Show all as backbone before doing superposition(s)
923 * (residues used for matching will be shown as ribbon)
925 // todo better way to ensure synchronous than setting getReply true!!
926 executeCommands(commandGenerator.showBackbone(), true, null);
928 boolean isNucleotide = structures[refStructure].isRna;
930 * superpose each (other) structure to the reference in turn
932 for (int i = 0; i < structures.length; i++)
934 if (i != refStructure)
936 AtomSpecModel atomSpec = getAtomSpec(structures[i], matched);
937 List<StructureCommandI> commands = commandGenerator
938 .superposeStructures(refAtoms, atomSpec,isNucleotide);
939 List<String> replies = executeCommands(commands, true, null);
940 for (String reply : replies)
942 // return this error (Chimera only) to the user
943 if (reply.toLowerCase(Locale.ROOT).contains("unequal numbers of atoms"))
945 error += "; " + reply;
955 private AtomSpecModel getAtomSpec(
956 AAStructureBindingModel.SuperposeData superposeData,
959 AtomSpecModel model = new AtomSpecModel();
960 int nextColumnMatch = matched.nextSetBit(0);
961 while (nextColumnMatch != -1)
963 int pdbResNum = superposeData.pdbResNo[nextColumnMatch];
964 model.addRange(superposeData.modelId, pdbResNum, pdbResNum,
965 superposeData.chain);
966 nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1);
973 * returns the current sequenceRenderer that should be used to colour the
980 public abstract SequenceRenderer getSequenceRenderer(
981 AlignmentViewPanel alignment);
984 * Sends a command to the structure viewer to colour each chain with a
985 * distinct colour (to the extent supported by the viewer)
987 public void colourByChain()
989 colourBySequence = false;
991 // TODO: JAL-628 colour chains distinctly across all visible models
993 executeCommand(false, COLOURING_STRUCTURES,
994 commandGenerator.colourByChain());
998 * Sends a command to the structure viewer to colour each chain with a
999 * distinct colour (to the extent supported by the viewer)
1001 public void colourByCharge()
1003 colourBySequence = false;
1005 executeCommands(commandGenerator.colourByCharge(), false,
1006 COLOURING_STRUCTURES);
1010 * Sends a command to the structure to apply a colour scheme (defined in
1011 * Jalview but not necessarily applied to the alignment), which defines a
1012 * colour per residue letter. More complex schemes (e.g. that depend on
1013 * consensus) cannot be used here and are ignored.
1017 public void colourByJalviewColourScheme(ColourSchemeI cs)
1019 colourBySequence = false;
1021 if (cs == null || !cs.isSimple())
1027 * build a map of {Residue3LetterCode, Color}
1029 Map<String, Color> colours = new HashMap<>();
1030 List<String> residues = ResidueProperties.getResidues(isNucleotide(),
1032 for (String resName : residues)
1034 char res = resName.length() == 3
1035 ? ResidueProperties.getSingleCharacterCode(resName)
1036 : resName.charAt(0);
1037 Color colour = cs.findColour(res, 0, null, null, 0f);
1038 colours.put(resName, colour);
1042 * pass to the command constructor, and send the command
1044 List<StructureCommandI> cmd = commandGenerator
1045 .colourByResidues(colours);
1046 executeCommands(cmd, false, COLOURING_STRUCTURES);
1049 public void setBackgroundColour(Color col)
1051 StructureCommandI cmd = commandGenerator.setBackgroundColour(col);
1052 executeCommand(false, null, cmd);
1056 * Execute one structure viewer command. If {@code getReply} is true, may
1057 * optionally return one or more reply messages, else returns null.
1062 protected abstract List<String> executeCommand(StructureCommandI cmd,
1066 * Executes one or more structure viewer commands
1072 protected List<String> executeCommands(List<StructureCommandI> commands,
1073 boolean getReply, String msg)
1075 return executeCommand(getReply, msg,
1076 commands.toArray(new StructureCommandI[commands.size()]));
1080 * Executes one or more structure viewer commands, optionally returning the
1081 * reply, and optionally showing a status message while the command is being
1084 * If a reply is wanted, the execution is done synchronously (waits),
1085 * otherwise it is done in a separate thread (doesn't wait). WARNING: if you
1086 * are sending commands that need to execute before later calls to
1087 * executeCommand (e.g. mouseovers, which clean up after previous ones) then
1088 * set getReply true to ensure that commands are not executed out of order.
1095 protected List<String> executeCommand(boolean getReply, String msg,
1096 StructureCommandI... cmds)
1098 JalviewStructureDisplayI theViewer = getViewer();
1099 final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
1104 * execute and wait for reply
1106 List<String> response = new ArrayList<>();
1109 for (StructureCommandI cmd : cmds)
1111 List<String> replies = executeCommand(cmd, true);
1112 if (replies != null)
1114 response.addAll(replies);
1122 theViewer.stopProgressBar(null, handle);
1130 String threadName = msg == null ? "StructureCommand" : msg;
1131 new Thread(new Runnable()
1138 for (StructureCommandI cmd : cmds)
1140 executeCommand(cmd, false);
1146 SwingUtilities.invokeLater(new Runnable()
1151 theViewer.stopProgressBar(null, handle);
1157 }, threadName).start();
1162 * Colours any structures associated with sequences in the given alignment as
1163 * coloured in the alignment view, provided colourBySequence is enabled
1165 public void colourBySequence(AlignmentViewPanel alignmentv)
1167 if (!colourBySequence || !isLoadingFinished() || getSsm() == null)
1171 Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, sequence,
1174 List<StructureCommandI> colourBySequenceCommands = commandGenerator
1175 .colourBySequence(colourMap);
1176 executeCommands(colourBySequenceCommands, false, COLOURING_STRUCTURES);
1180 * Centre the display in the structure viewer
1182 public void focusView()
1184 executeCommand(false, null, commandGenerator.focusView());
1188 * Generates and executes a command to show only specified chains in the
1189 * structure viewer. The list of chains to show should contain entries
1190 * formatted as "pdbid:chaincode".
1194 public void showChains(List<String> toShow)
1196 // todo or reformat toShow list entries as modelNo:pdbId:chainCode ?
1199 * Reformat the pdbid:chainCode values as modelNo:chainCode
1200 * since this is what is needed to construct the viewer command
1201 * todo: find a less messy way to do this
1203 List<String> showThese = new ArrayList<>();
1204 for (String chainId : toShow)
1206 String[] tokens = chainId.split("\\:");
1207 if (tokens.length == 2)
1209 String pdbFile = getFileForChain(chainId);
1210 String model = getModelIdForFile(pdbFile);
1211 showThese.add(model + ":" + tokens[1]);
1214 executeCommands(commandGenerator.showChains(showThese), false, null);
1218 * Answers the structure viewer's model id given a PDB file name. Returns an
1219 * empty string if model id is not found.
1224 protected abstract String getModelIdForFile(String chainId);
1226 public boolean hasFileLoadingError()
1228 return fileLoadingError != null && fileLoadingError.length() > 0;
1232 * Returns the FeatureRenderer for the given alignment view
1237 public FeatureRenderer getFeatureRenderer(AlignmentViewPanel avp)
1239 AlignmentViewPanel ap = (avp == null) ? getViewer().getAlignmentPanel()
1245 return ap.getFeatureRenderer();
1248 protected void setStructureCommands(StructureCommandsI cmd)
1250 commandGenerator = cmd;
1254 * Records association of one chain id (formatted as "pdbid:chainCode") with
1255 * the corresponding PDB file name
1260 public void addChainFile(String chainId, String fileName)
1262 chainFile.put(chainId, fileName);
1266 * Returns the PDB filename for the given chain id (formatted as
1267 * "pdbid:chainCode"), or null if not found
1272 protected String getFileForChain(String chainId)
1274 return chainFile.get(chainId);
1278 public void updateColours(Object source)
1280 AlignmentViewPanel ap = (AlignmentViewPanel) source;
1281 // ignore events from panels not used to colour this view
1282 if (!getViewer().isUsedForColourBy(ap))
1286 if (!isLoadingFromArchive())
1288 colourBySequence(ap);
1292 public StructureCommandsI getCommandGenerator()
1294 return commandGenerator;
1297 protected abstract ViewerType getViewerType();
1300 * Builds a data structure which records mapped structure residues for each
1301 * colour. From this we can easily generate the viewer commands for colour by
1302 * sequence. Constructs and returns a map of {@code Color} to
1303 * {@code AtomSpecModel}, where the atomspec model holds
1311 * Ordering is by order of addition (for colours), natural ordering (for
1312 * models and chains)
1319 protected Map<Object, AtomSpecModel> buildColoursMap(
1320 StructureSelectionManager ssm, SequenceI[][] sequence,
1321 AlignmentViewPanel viewPanel)
1323 String[] files = getStructureFiles();
1324 SequenceRenderer sr = getSequenceRenderer(viewPanel);
1325 FeatureRenderer fr = viewPanel.getFeatureRenderer();
1326 FeatureColourFinder finder = new FeatureColourFinder(fr);
1327 AlignViewportI viewport = viewPanel.getAlignViewport();
1328 HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
1329 AlignmentI al = viewport.getAlignment();
1330 Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<>();
1331 Color lastColour = null;
1333 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
1335 final String modelId = getModelIdForFile(files[pdbfnum]);
1336 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
1338 if (mapping == null || mapping.length < 1)
1343 int startPos = -1, lastPos = -1;
1344 String lastChain = "";
1345 for (int s = 0; s < sequence[pdbfnum].length; s++)
1347 for (int sp, m = 0; m < mapping.length; m++)
1349 final SequenceI seq = sequence[pdbfnum][s];
1350 if (mapping[m].getSequence() == seq
1351 && (sp = al.findIndex(seq)) > -1)
1353 SequenceI asp = al.getSequenceAt(sp);
1354 for (int r = 0; r < asp.getLength(); r++)
1356 // no mapping to gaps in sequence
1357 if (Comparison.isGap(asp.getCharAt(r)))
1361 int pos = mapping[m].getPDBResNum(asp.findPosition(r));
1363 if (pos < 1 || pos == lastPos)
1368 Color colour = sr.getResidueColour(seq, r, finder);
1371 * darker colour for hidden regions
1373 if (!cs.isVisible(r))
1375 colour = Color.GRAY;
1378 final String chain = mapping[m].getChain();
1381 * Just keep incrementing the end position for this colour range
1382 * _unless_ colour, PDB model or chain has changed, or there is a
1383 * gap in the mapped residue sequence
1385 final boolean newColour = !colour.equals(lastColour);
1386 final boolean nonContig = lastPos + 1 != pos;
1387 final boolean newChain = !chain.equals(lastChain);
1388 if (newColour || nonContig || newChain)
1392 addAtomSpecRange(colourMap, lastColour, modelId, startPos,
1393 lastPos, lastChain);
1397 lastColour = colour;
1401 // final colour range
1402 if (lastColour != null)
1404 addAtomSpecRange(colourMap, lastColour, modelId, startPos,
1405 lastPos, lastChain);
1416 * todo better refactoring (map lookup or similar to get viewer structure id)
1422 protected String getModelId(int pdbfnum, String file)
1424 return String.valueOf(pdbfnum);
1428 * Saves chains, formatted as "pdbId:chainCode", and lookups from this to the
1429 * full PDB file path
1434 public void stashFoundChains(StructureFile pdb, String file)
1436 for (int i = 0; i < pdb.getChains().size(); i++)
1438 String chid = pdb.getId() + ":" + pdb.getChains().elementAt(i).id;
1439 addChainFile(chid, file);
1440 getChainNames().add(chid);
1445 * Helper method to add one contiguous range to the AtomSpec model for the
1446 * given value (creating the model if necessary). As used by Jalview,
1449 * <li>a colour, when building a 'colour structure by sequence' command</li>
1450 * <li>a feature value, when building a 'set Chimera attributes from features'
1461 public static final void addAtomSpecRange(Map<Object, AtomSpecModel> map,
1462 Object value, String model, int startPos, int endPos,
1466 * Get/initialize map of data for the colour
1468 AtomSpecModel atomSpec = map.get(value);
1469 if (atomSpec == null)
1471 atomSpec = new AtomSpecModel();
1472 map.put(value, atomSpec);
1475 atomSpec.addRange(model, startPos, endPos, chain);
1479 * Returns the file extension (including '.' separator) to use for a saved
1480 * viewer session file. Default is to return null (not supported), override as
1485 public String getSessionFileExtension()
1491 * If supported, saves the state of the structure viewer to a temporary file
1492 * and returns the file. Returns null and logs an error on any failure.
1496 public File saveSession()
1498 String prefix = getViewerType().toString();
1499 String suffix = getSessionFileExtension();
1503 f = File.createTempFile(prefix, suffix);
1505 } catch (IOException e)
1507 Console.error(String.format("Error saving %s session: %s", prefix,
1515 * Saves the structure viewer session to the given file
1519 protected void saveSession(File f)
1521 StructureCommandI cmd = commandGenerator.saveSession(f.getPath());
1524 executeCommand(cmd, false);
1529 * Returns true if the viewer is an external structure viewer for which the
1530 * process is still alive, else false (for Jmol, or an external viewer which
1531 * the user has independently closed)
1535 public boolean isViewerRunning()
1541 * Closes Jalview's structure viewer panel and releases associated resources.
1542 * If it is managing an external viewer program, and {@code forceClose} is
1543 * true, also asks that program to close.
1547 public void closeViewer(boolean forceClose)
1549 getSsm().removeStructureViewerListener(this, this.getStructureFiles());
1550 releaseUIResources();
1553 * end the thread that closes this panel if the external viewer closes
1555 if (externalViewerMonitor != null)
1557 externalViewerMonitor.interrupt();
1558 externalViewerMonitor = null;
1565 StructureCommandI cmd = getCommandGenerator().closeViewer();
1568 executeCommand(cmd, false);
1574 * Returns the URL of a help page for the structure viewer, or null if none is
1579 public String getHelpURL()
1586 * Helper method to build a map of
1587 * { featureType, { feature value, AtomSpecModel } }
1593 protected Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
1594 AlignmentViewPanel viewPanel)
1596 Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<>();
1597 String[] files = getStructureFiles();
1603 FeatureRenderer fr = viewPanel.getFeatureRenderer();
1609 AlignViewportI viewport = viewPanel.getAlignViewport();
1610 List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
1613 * if alignment is showing features from complement, we also transfer
1614 * these features to the corresponding mapped structure residues
1616 boolean showLinkedFeatures = viewport.isShowComplementFeatures();
1617 List<String> complementFeatures = new ArrayList<>();
1618 FeatureRenderer complementRenderer = null;
1619 if (showLinkedFeatures)
1621 AlignViewportI comp = fr.getViewport().getCodingComplement();
1624 complementRenderer = Desktop.getAlignFrameFor(comp)
1625 .getFeatureRenderer();
1626 complementFeatures = complementRenderer.getDisplayedFeatureTypes();
1629 if (visibleFeatures.isEmpty() && complementFeatures.isEmpty())
1634 AlignmentI alignment = viewPanel.getAlignment();
1635 SequenceI[][] seqs = getSequence();
1637 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
1639 String modelId = getModelIdForFile(files[pdbfnum]);
1640 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
1642 if (mapping == null || mapping.length < 1)
1647 for (int seqNo = 0; seqNo < seqs[pdbfnum].length; seqNo++)
1649 for (int m = 0; m < mapping.length; m++)
1651 final SequenceI seq = seqs[pdbfnum][seqNo];
1652 int sp = alignment.findIndex(seq);
1653 StructureMapping structureMapping = mapping[m];
1654 if (structureMapping.getSequence() == seq && sp > -1)
1657 * found a sequence with a mapping to a structure;
1658 * now scan its features
1660 if (!visibleFeatures.isEmpty())
1662 scanSequenceFeatures(visibleFeatures, structureMapping, seq,
1665 if (showLinkedFeatures)
1667 scanComplementFeatures(complementRenderer, structureMapping,
1668 seq, theMap, modelId);
1678 * Ask the structure viewer to open a session file. Returns true if
1679 * successful, else false (or not supported).
1684 public boolean openSession(String filepath)
1686 StructureCommandI cmd = getCommandGenerator().openSession(filepath);
1691 executeCommand(cmd, true);
1692 // todo: test for failure - how?
1697 * Scans visible features in mapped positions of the CDS/peptide complement,
1698 * and adds any found to the map of attribute values/structure positions
1700 * @param complementRenderer
1701 * @param structureMapping
1704 * @param modelNumber
1706 protected static void scanComplementFeatures(
1707 FeatureRenderer complementRenderer,
1708 StructureMapping structureMapping, SequenceI seq,
1709 Map<String, Map<Object, AtomSpecModel>> theMap,
1713 * for each sequence residue mapped to a structure position...
1715 for (int seqPos : structureMapping.getMapping().keySet())
1718 * find visible complementary features at mapped position(s)
1720 MappedFeatures mf = complementRenderer
1721 .findComplementFeaturesAtResidue(seq, seqPos);
1724 for (SequenceFeature sf : mf.features)
1726 String type = sf.getType();
1729 * Don't copy features which originated from Chimera
1731 if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
1732 .equals(sf.getFeatureGroup()))
1738 * record feature 'value' (score/description/type) as at the
1739 * corresponding structure position
1741 List<int[]> mappedRanges = structureMapping
1742 .getPDBResNumRanges(seqPos, seqPos);
1744 if (!mappedRanges.isEmpty())
1746 String value = sf.getDescription();
1747 if (value == null || value.length() == 0)
1751 float score = sf.getScore();
1752 if (score != 0f && !Float.isNaN(score))
1754 value = Float.toString(score);
1756 Map<Object, AtomSpecModel> featureValues = theMap.get(type);
1757 if (featureValues == null)
1759 featureValues = new HashMap<>();
1760 theMap.put(type, featureValues);
1762 for (int[] range : mappedRanges)
1764 addAtomSpecRange(featureValues, value, modelNumber, range[0],
1765 range[1], structureMapping.getChain());
1774 * Inspect features on the sequence; for each feature that is visible,
1775 * determine its mapped ranges in the structure (if any) according to the
1776 * given mapping, and add them to the map.
1778 * @param visibleFeatures
1784 protected static void scanSequenceFeatures(List<String> visibleFeatures,
1785 StructureMapping mapping, SequenceI seq,
1786 Map<String, Map<Object, AtomSpecModel>> theMap, String modelId)
1788 List<SequenceFeature> sfs = seq.getFeatures().getPositionalFeatures(
1789 visibleFeatures.toArray(new String[visibleFeatures.size()]));
1790 for (SequenceFeature sf : sfs)
1792 String type = sf.getType();
1795 * Don't copy features which originated from Chimera
1797 if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
1798 .equals(sf.getFeatureGroup()))
1803 List<int[]> mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(),
1806 if (!mappedRanges.isEmpty())
1808 String value = sf.getDescription();
1809 if (value == null || value.length() == 0)
1813 float score = sf.getScore();
1814 if (score != 0f && !Float.isNaN(score))
1816 value = Float.toString(score);
1818 Map<Object, AtomSpecModel> featureValues = theMap.get(type);
1819 if (featureValues == null)
1821 featureValues = new HashMap<>();
1822 theMap.put(type, featureValues);
1824 for (int[] range : mappedRanges)
1826 addAtomSpecRange(featureValues, value, modelId, range[0],
1827 range[1], mapping.getChain());
1834 * Returns the number of structure files in the structure viewer and mapped to
1835 * Jalview. This may be zero if the files are still in the process of loading
1840 public int getMappedStructureCount()
1842 String[] files = getStructureFiles();
1843 return files == null ? 0 : files.length;
1847 * Starts a thread that waits for the external viewer program process to
1848 * finish, so that we can then close the associated resources. This avoids
1849 * leaving orphaned viewer panels in Jalview if the user closes the external
1854 protected void startExternalViewerMonitor(Process p)
1856 externalViewerMonitor = new Thread(new Runnable()
1865 JalviewStructureDisplayI display = getViewer();
1866 if (display != null)
1868 display.closeViewer(false);
1870 } catch (InterruptedException e)
1872 // exit thread if Chimera Viewer is closed in Jalview
1876 externalViewerMonitor.start();
1880 * If supported by the external structure viewer, sends it commands to notify
1881 * model or selection changes to the specified URL (where Jalview has started
1886 protected void startListening(String uri)
1888 List<StructureCommandI> commands = getCommandGenerator()
1889 .startNotifications(uri);
1890 if (commands != null)
1892 executeCommands(commands, false, null);
1897 * If supported by the external structure viewer, sends it commands to stop
1898 * notifying model or selection changes
1900 protected void stopListening()
1902 List<StructureCommandI> commands = getCommandGenerator()
1903 .stopNotifications();
1904 if (commands != null)
1906 executeCommands(commands, false, null);
1911 * If supported by the structure viewer, queries it for all residue attributes
1912 * with the given attribute name, and creates features on corresponding
1913 * residues of the alignment. Returns the number of features added.
1916 * @param alignmentPanel
1919 public int copyStructureAttributesToFeatures(String attName,
1920 AlignmentPanel alignmentPanel)
1922 StructureCommandI cmd = getCommandGenerator()
1923 .getResidueAttributes(attName);
1928 List<String> residueAttributes = executeCommand(cmd, true);
1930 int featuresAdded = createFeaturesForAttributes(attName,
1932 if (featuresAdded > 0)
1934 alignmentPanel.getFeatureRenderer().featuresAdded();
1936 return featuresAdded;
1940 * Parses {@code residueAttributes} and creates sequence features on any
1941 * mapped alignment residues. Returns the number of features created.
1943 * {@code residueAttributes} is the reply from the structure viewer to a
1944 * command to list any residue attributes for the given attribute name. Syntax
1945 * and parsing of this is viewer-specific.
1948 * @param residueAttributes
1951 protected int createFeaturesForAttributes(String attName,
1952 List<String> residueAttributes)