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.ext.rbvi.chimera;
23 import jalview.api.AlignmentViewPanel;
24 import jalview.api.FeatureRenderer;
25 import jalview.api.SequenceRenderer;
26 import jalview.bin.Cache;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.ColumnSelection;
29 import jalview.datamodel.PDBEntry;
30 import jalview.datamodel.SequenceI;
31 import jalview.httpserver.AbstractRequestHandler;
32 import jalview.schemes.ColourSchemeI;
33 import jalview.schemes.ResidueProperties;
34 import jalview.structure.AtomSpec;
35 import jalview.structure.StructureMappingcommandSet;
36 import jalview.structure.StructureSelectionManager;
37 import jalview.structures.models.AAStructureBindingModel;
38 import jalview.util.MessageManager;
40 import java.awt.Color;
41 import java.net.BindException;
42 import java.util.ArrayList;
43 import java.util.LinkedHashMap;
44 import java.util.List;
47 import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
48 import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
49 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
50 import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
52 public abstract class JalviewChimeraBinding extends AAStructureBindingModel
54 // Chimera clause to exclude alternate locations in atom selection
55 private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
57 private static final String COLOURING_CHIMERA = MessageManager
58 .getString("status.colouring_chimera");
60 private static final boolean debug = false;
62 private static final String PHOSPHORUS = "P";
64 private static final String ALPHACARBON = "CA";
67 * Object through which we talk to Chimera
69 private ChimeraManager viewer;
72 * Object which listens to Chimera notifications
74 private AbstractRequestHandler chimeraListener;
77 * set if chimera state is being restored from some source - instructs binding
78 * not to apply default display style when structure set is updated for first
81 private boolean loadingFromArchive = false;
84 * flag to indicate if the Chimera viewer should ignore sequence colouring
85 * events from the structure manager because the GUI is still setting up
87 private boolean loadingFinished = true;
89 public String fileLoadingError;
92 * Map of ChimeraModel objects keyed by PDB full local file name
94 private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<String, List<ChimeraModel>>();
97 * the default or current model displayed if the model cannot be identified
98 * from the selection message
100 private int frameNo = 0;
102 private String lastCommand;
104 String lastHighlightCommand;
107 * incremented every time a load notification is successfully handled -
108 * lightweight mechanism for other threads to detect when they can start
109 * referring to new structures.
111 private long loadNotifiesHandled = 0;
114 * Open a PDB structure file in Chimera and set up mappings from Jalview.
116 * We check if the PDB model id is already loaded in Chimera, if so don't
117 * reopen it. This is the case if Chimera has opened a saved session file.
122 public boolean openFile(PDBEntry pe)
124 String file = pe.getFile();
127 List<ChimeraModel> modelsToMap = new ArrayList<ChimeraModel>();
128 List<ChimeraModel> oldList = viewer.getModelList();
129 boolean alreadyOpen = false;
132 * If Chimera already has this model, don't reopen it, but do remap it.
134 for (ChimeraModel open : oldList)
136 if (open.getModelName().equals(pe.getId()))
139 modelsToMap.add(open);
144 * If Chimera doesn't yet have this model, ask it to open it, and retrieve
145 * the model name(s) added by Chimera.
149 viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
150 List<ChimeraModel> newList = viewer.getModelList();
151 // JAL-1728 newList.removeAll(oldList) does not work
152 for (ChimeraModel cm : newList)
154 if (cm.getModelName().equals(pe.getId()))
161 chimeraMaps.put(file, modelsToMap);
163 if (getSsm() != null)
165 getSsm().addStructureViewerListener(this);
166 // ssm.addSelectionListener(this);
167 FeatureRenderer fr = getFeatureRenderer(null);
175 } catch (Exception q)
177 log("Exception when trying to open model " + file + "\n"
193 public JalviewChimeraBinding(StructureSelectionManager ssm,
194 PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
197 super(ssm, pdbentry, sequenceIs, chains, protocol);
198 viewer = new ChimeraManager(
199 new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
203 * Start a dedicated HttpServer to listen for Chimera notifications, and tell
204 * it to start listening
206 public void startChimeraListener()
210 chimeraListener = new ChimeraListener(this);
211 viewer.startListening(chimeraListener.getUri());
212 } catch (BindException e)
214 System.err.println("Failed to start Chimera listener: "
220 * Construct a title string for the viewer window based on the data Jalview
226 public String getViewerTitle(boolean verbose)
228 return getViewerTitle("Chimera", verbose);
232 * Tells Chimera to display only the specified chains
236 public void showChains(List<String> toshow)
239 * Construct a chimera command like
241 * ~display #*;~ribbon #*;ribbon :.A,:.B
243 StringBuilder cmd = new StringBuilder(64);
244 boolean first = true;
245 for (String chain : toshow)
251 cmd.append(":.").append(chain);
256 * could append ";focus" to this command to resize the display to fill the
257 * window, but it looks more helpful not to (easier to relate chains to the
260 final String command = "~display #*; ~ribbon #*; ribbon "
262 sendChimeraCommand(command, false);
266 * Close down the Jalview viewer and listener, and (optionally) the associated
269 public void closeViewer(boolean closeChimera)
271 getSsm().removeStructureViewerListener(this, this.getPdbFile());
274 viewer.exitChimera();
276 if (this.chimeraListener != null)
278 chimeraListener.shutdown();
279 chimeraListener = null;
284 releaseUIResources();
287 public void colourByChain()
289 colourBySequence = false;
290 sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA);
294 * Constructs and sends a Chimera command to colour by charge
296 * <li>Aspartic acid and Glutamic acid (negative charge) red</li>
297 * <li>Lysine and Arginine (positive charge) blue</li>
298 * <li>Cysteine - yellow</li>
299 * <li>all others - white</li>
302 public void colourByCharge()
304 colourBySequence = false;
305 String command = "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS";
306 sendAsynchronousCommand(command, COLOURING_CHIMERA);
310 * Construct and send a command to align structures against a reference
311 * structure, based on one or more sequence alignments
314 * an array of alignments to process
315 * @param _refStructure
316 * an array of corresponding reference structures (index into pdb
317 * file array); if a negative value is passed, the first PDB file
318 * mapped to an alignment sequence is used as the reference for
321 * an array of corresponding hidden columns for each alignment
323 public void superposeStructures(AlignmentI[] _alignment,
324 int[] _refStructure, ColumnSelection[] _hiddenCols)
326 StringBuilder allComs = new StringBuilder(128);
327 String[] files = getPdbFile();
329 if (!waitForFileLoad(files))
335 StringBuilder selectioncom = new StringBuilder(256);
336 for (int a = 0; a < _alignment.length; a++)
338 int refStructure = _refStructure[a];
339 AlignmentI alignment = _alignment[a];
340 ColumnSelection hiddenCols = _hiddenCols[a];
342 if (refStructure >= files.length)
344 System.err.println("Ignoring invalid reference structure value "
350 * 'matched' array will hold 'true' for visible alignment columns where
351 * all sequences have a residue with a mapping to the PDB structure
353 boolean matched[] = new boolean[alignment.getWidth()];
354 for (int m = 0; m < matched.length; m++)
356 matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
359 SuperposeData[] structures = new SuperposeData[files.length];
360 for (int f = 0; f < files.length; f++)
362 structures[f] = new SuperposeData(alignment.getWidth());
366 * Calculate the superposable alignment columns ('matched'), and the
367 * corresponding structure residue positions (structures.pdbResNo)
369 int candidateRefStructure = findSuperposableResidues(alignment,
370 matched, structures);
371 if (refStructure < 0)
374 * If no reference structure was specified, pick the first one that has
375 * a mapping in the alignment
377 refStructure = candidateRefStructure;
381 for (boolean b : matched)
390 // TODO: bail out here because superposition illdefined?
394 * Generate select statements to select regions to superimpose structures
396 String[] selcom = new String[files.length];
397 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
399 String chainCd = "." + structures[pdbfnum].chain;
402 StringBuilder molsel = new StringBuilder();
403 for (int r = 0; r < matched.length; r++)
407 int pdbResNum = structures[pdbfnum].pdbResNo[r];
408 if (lpos != pdbResNum - 1)
411 * discontiguous - append last residue now
415 molsel.append(String.valueOf(lpos));
416 molsel.append(chainCd);
424 * extending a contiguous run
429 * start the range selection
431 molsel.append(String.valueOf(lpos));
441 * and terminate final selection
445 molsel.append(String.valueOf(lpos));
446 molsel.append(chainCd);
448 if (molsel.length() > 1)
450 selcom[pdbfnum] = molsel.toString();
451 selectioncom.append("#").append(String.valueOf(pdbfnum))
453 selectioncom.append(selcom[pdbfnum]);
454 selectioncom.append(" ");
455 if (pdbfnum < files.length - 1)
457 selectioncom.append("| ");
462 selcom[pdbfnum] = null;
466 StringBuilder command = new StringBuilder(256);
467 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
469 if (pdbfnum == refStructure || selcom[pdbfnum] == null
470 || selcom[refStructure] == null)
474 if (command.length() > 0)
480 * Form Chimera match command, from the 'new' structure to the
481 * 'reference' structure e.g. (50 residues, chain B/A, alphacarbons):
483 * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA
486 * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
488 command.append("match ").append(getModelSpec(pdbfnum)).append(":");
489 command.append(selcom[pdbfnum]);
490 command.append("@").append(
491 structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON);
492 // JAL-1757 exclude alternate CA locations
493 command.append(NO_ALTLOCS);
494 command.append(" ").append(getModelSpec(refStructure)).append(":");
495 command.append(selcom[refStructure]);
496 command.append("@").append(
497 structures[refStructure].isRna ? PHOSPHORUS : ALPHACARBON);
498 command.append(NO_ALTLOCS);
500 if (selectioncom.length() > 0)
504 System.out.println("Select regions:\n" + selectioncom.toString());
505 System.out.println("Superimpose command(s):\n"
506 + command.toString());
508 allComs.append("~display all; chain @CA|P; ribbon ")
509 .append(selectioncom.toString())
510 .append(";" + command.toString());
513 if (selectioncom.length() > 0)
515 // TODO: visually distinguish regions that were superposed
516 if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
518 selectioncom.setLength(selectioncom.length() - 1);
522 System.out.println("Select regions:\n" + selectioncom.toString());
524 allComs.append("; ~display all; chain @CA|P; ribbon ")
525 .append(selectioncom.toString()).append("; focus");
526 sendChimeraCommand(allComs.toString(), false);
532 * Helper method to construct model spec in Chimera format:
534 * <li>#0 (#1 etc) for a PDB file with no sub-models</li>
535 * <li>#0.1 (#1.1 etc) for a PDB file with sub-models</li>
537 * Note for now we only ever choose the first of multiple models. This
538 * corresponds to the hard-coded Jmol equivalent (compare {1.1}). Refactor in
539 * future if there is a need to select specific sub-models.
544 protected String getModelSpec(int pdbfnum)
546 if (pdbfnum < 0 || pdbfnum >= getPdbCount())
552 * For now, the test for having sub-models is whether multiple Chimera
553 * models are mapped for the PDB file; the models are returned as a response
554 * to the Chimera command 'list models type molecule', see
555 * ChimeraManager.getModelList().
557 List<ChimeraModel> maps = chimeraMaps.get(getPdbFile()[pdbfnum]);
558 boolean hasSubModels = maps != null && maps.size() > 1;
559 return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
563 * Launch Chimera, unless an instance linked to this object is already
564 * running. Returns true if chimera is successfully launched, or already
565 * running, else false.
569 public boolean launchChimera()
571 if (!viewer.isChimeraLaunched())
573 return viewer.launchChimera(StructureManager.getChimeraPaths());
575 if (viewer.isChimeraLaunched())
579 log("Failed to launch Chimera!");
584 * Answers true if the Chimera process is still running, false if ended or not
589 public boolean isChimeraRunning()
591 return viewer.isChimeraLaunched();
595 * Send a command to Chimera, and optionally log any responses.
600 public void sendChimeraCommand(final String command, boolean logResponse)
604 // ? thread running after viewer shut down
607 viewerCommandHistory(false);
608 if (lastCommand == null || !lastCommand.equals(command))
610 // trim command or it may never find a match in the replyLog!!
611 List<String> lastReply = viewer.sendChimeraCommand(command.trim(),
613 if (logResponse && debug)
615 log("Response from command ('" + command + "') was:\n" + lastReply);
618 viewerCommandHistory(true);
619 lastCommand = command;
623 * Send a Chimera command asynchronously in a new thread. If the progress
624 * message is not null, display this message while the command is executing.
629 protected abstract void sendAsynchronousCommand(String command,
633 * colour any structures associated with sequences in the given alignment
634 * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
635 * if colourBySequence is enabled.
637 public void colourBySequence(boolean showFeatures,
638 jalview.api.AlignmentViewPanel alignmentv)
640 if (!colourBySequence || !loadingFinished)
644 if (getSsm() == null)
648 String[] files = getPdbFile();
650 SequenceRenderer sr = getSequenceRenderer(alignmentv);
652 FeatureRenderer fr = null;
655 fr = getFeatureRenderer(alignmentv);
657 AlignmentI alignment = alignmentv.getAlignment();
659 for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
660 files, sr, fr, alignment))
662 for (String command : cpdbbyseq.commands)
664 sendAsynchronousCommand(command, COLOURING_CHIMERA);
676 protected StructureMappingcommandSet[] getColourBySequenceCommands(
677 String[] files, SequenceRenderer sr, FeatureRenderer fr,
678 AlignmentI alignment)
680 return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
681 getSequence(), sr, fr, alignment);
687 protected void executeWhenReady(String command)
690 sendChimeraCommand(command, false);
694 private void waitForChimera()
696 while (viewer != null && viewer.isBusy())
701 } catch (InterruptedException q)
707 // End StructureListener
708 // //////////////////////////
711 * returns the current featureRenderer that should be used to colour the
718 public abstract FeatureRenderer getFeatureRenderer(
719 AlignmentViewPanel alignment);
722 * instruct the Jalview binding to update the pdbentries vector if necessary
723 * prior to matching the viewer's contents to the list of structure files
724 * Jalview knows about.
726 public abstract void refreshPdbEntries();
728 private int getModelNum(String modelFileName)
730 String[] mfn = getPdbFile();
735 for (int i = 0; i < mfn.length; i++)
737 if (mfn[i].equalsIgnoreCase(modelFileName))
746 * map between index of model filename returned from getPdbFile and the first
747 * index of models from this file in the viewer. Note - this is not trimmed -
748 * use getPdbFile to get number of unique models.
750 private int _modelFileNameMap[];
752 // ////////////////////////////////
753 // /StructureListener
755 public synchronized String[] getPdbFile()
759 return new String[0];
761 // if (modelFileNames == null)
763 // Collection<ChimeraModel> chimodels = viewer.getChimeraModels();
764 // _modelFileNameMap = new int[chimodels.size()];
766 // for (ChimeraModel chimodel : chimodels)
768 // String mdlName = chimodel.getModelName();
770 // modelFileNames = new String[j];
771 // // System.arraycopy(mset, 0, modelFileNames, 0, j);
774 return chimeraMaps.keySet().toArray(
775 modelFileNames = new String[chimeraMaps.size()]);
779 * returns the current sequenceRenderer that should be used to colour the
786 public abstract SequenceRenderer getSequenceRenderer(
787 AlignmentViewPanel alignment);
790 * Construct and send a command to highlight zero, one or more atoms. We do
791 * this by sending an "rlabel" command to show the residue label at that
795 public void highlightAtoms(List<AtomSpec> atoms)
797 if (atoms == null || atoms.size() == 0)
802 StringBuilder cmd = new StringBuilder(128);
803 boolean first = true;
804 boolean found = false;
806 for (AtomSpec atom : atoms)
808 int pdbResNum = atom.getPdbResNum();
809 String chain = atom.getChain();
810 String pdbfile = atom.getPdbFile();
811 List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
812 if (cms != null && !cms.isEmpty())
816 cmd.append("rlabel #").append(cms.get(0).getModelNumber())
824 cmd.append(pdbResNum);
825 if (!chain.equals(" "))
827 cmd.append(".").append(chain);
832 String command = cmd.toString();
835 * avoid repeated commands for the same residue
837 if (command.equals(lastHighlightCommand))
843 * unshow the label for the previous residue
845 if (lastHighlightCommand != null)
847 viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
851 viewer.sendChimeraCommand(command, false);
853 this.lastHighlightCommand = command;
857 * Query Chimera for its current selection, and highlight it on the alignment
859 public void highlightChimeraSelection()
862 * Ask Chimera for its current selection
864 List<String> selection = viewer.getSelectedResidueSpecs();
867 * Parse model number, residue and chain for each selected position,
868 * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
870 List<AtomSpec> atomSpecs = new ArrayList<AtomSpec>();
871 for (String atomSpec : selection)
873 int colonPos = atomSpec.indexOf(":");
876 continue; // malformed
879 int hashPos = atomSpec.indexOf("#");
880 String modelSubmodel = atomSpec.substring(hashPos + 1, colonPos);
881 int dotPos = modelSubmodel.indexOf(".");
885 modelId = Integer.valueOf(dotPos == -1 ? modelSubmodel
886 : modelSubmodel.substring(0, dotPos));
887 } catch (NumberFormatException e)
889 // ignore, default to model 0
892 String residueChain = atomSpec.substring(colonPos + 1);
893 dotPos = residueChain.indexOf(".");
894 int pdbResNum = Integer.parseInt(dotPos == -1 ? residueChain
895 : residueChain.substring(0, dotPos));
897 String chainId = dotPos == -1 ? "" : residueChain
898 .substring(dotPos + 1);
901 * Work out the pdbfilename from the model number
903 String pdbfilename = modelFileNames[frameNo];
904 findfileloop: for (String pdbfile : this.chimeraMaps.keySet())
906 for (ChimeraModel cm : chimeraMaps.get(pdbfile))
908 if (cm.getModelNumber() == modelId)
910 pdbfilename = pdbfile;
915 atomSpecs.add(new AtomSpec(pdbfilename, chainId, pdbResNum, 0));
919 * Broadcast the selection (which may be empty, if the user just cleared all
922 getSsm().mouseOverStructure(atomSpecs);
925 private void log(String message)
927 System.err.println("## Chimera log: " + message);
930 private void viewerCommandHistory(boolean enable)
932 // log("(Not yet implemented) History "
933 // + ((debug || enable) ? "on" : "off"));
936 public long getLoadNotifiesHandled()
938 return loadNotifiesHandled;
941 public void setJalviewColourScheme(ColourSchemeI cs)
943 colourBySequence = false;
950 // Chimera expects RBG values in the range 0-1
951 final double normalise = 255D;
952 viewerCommandHistory(false);
953 StringBuilder command = new StringBuilder(128);
955 List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
957 for (String res : residueSet)
959 Color col = cs.findColour(res.charAt(0));
960 command.append("color " + col.getRed() / normalise + ","
961 + col.getGreen() / normalise + "," + col.getBlue()
962 / normalise + " ::" + res + ";");
965 sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
966 viewerCommandHistory(true);
970 * called when the binding thinks the UI needs to be refreshed after a Chimera
971 * state change. this could be because structures were loaded, or because an
972 * error has occurred.
974 public abstract void refreshGUI();
977 public void setLoadingFromArchive(boolean loadingFromArchive)
979 this.loadingFromArchive = loadingFromArchive;
984 * @return true if Chimeral is still restoring state or loading is still going
985 * on (see setFinsihedLoadingFromArchive)
988 public boolean isLoadingFromArchive()
990 return loadingFromArchive && !loadingFinished;
994 * modify flag which controls if sequence colouring events are honoured by the
995 * binding. Should be true for normal operation
997 * @param finishedLoading
1000 public void setFinishedLoadingFromArchive(boolean finishedLoading)
1002 loadingFinished = finishedLoading;
1006 * Send the Chimera 'background solid <color>" command.
1009 * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
1013 public void setBackgroundColour(Color col)
1015 viewerCommandHistory(false);
1016 double normalise = 255D;
1017 final String command = "background solid " + col.getRed() / normalise
1018 + "," + col.getGreen() / normalise + "," + col.getBlue()
1020 viewer.sendChimeraCommand(command, false);
1021 viewerCommandHistory(true);
1025 * Ask Chimera to save its session to the given file. Returns true if
1026 * successful, else false.
1031 public boolean saveSession(String filepath)
1033 if (isChimeraRunning())
1035 List<String> reply = viewer.sendChimeraCommand("save " + filepath,
1037 if (reply.contains("Session written"))
1044 .error("Error saving Chimera session: " + reply.toString());
1051 * Ask Chimera to open a session file. Returns true if successful, else false.
1052 * The filename must have a .py extension for this command to work.
1057 public boolean openSession(String filepath)
1059 sendChimeraCommand("open " + filepath, true);
1060 // todo: test for failure - how?
1065 * Returns a list of chains mapped in this viewer. Note this list is not
1066 * currently scoped per structure.
1070 public List<String> getChainNames()
1072 List<String> names = new ArrayList<String>();
1073 String[][] allNames = getChains();
1074 if (allNames != null)
1076 for (String[] chainsForPdb : allNames)
1078 if (chainsForPdb != null)
1080 for (String chain : chainsForPdb)
1082 if (chain != null && !names.contains(chain))
1094 * Send a 'focus' command to Chimera to recentre the visible display
1096 public void focusView()
1098 sendChimeraCommand("focus", false);
1102 * Send a 'show' command for all atoms in the currently selected columns
1104 * TODO: pull up to abstract structure viewer interface
1108 public void highlightSelection(AlignmentViewPanel vp)
1110 List<Integer> cols = vp.getAlignViewport().getColumnSelection()
1112 AlignmentI alignment = vp.getAlignment();
1113 StructureSelectionManager sm = getSsm();
1114 for (SequenceI seq : alignment.getSequences())
1117 * convert selected columns into sequence positions
1119 int[] positions = new int[cols.size()];
1121 for (Integer col : cols)
1123 positions[i++] = seq.findPosition(col);
1125 sm.highlightStructure(this, seq, positions);