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;
42 import java.io.FileOutputStream;
43 import java.io.IOException;
44 import java.io.PrintWriter;
45 import java.net.BindException;
46 import java.util.ArrayList;
47 import java.util.LinkedHashMap;
48 import java.util.List;
51 import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
52 import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
53 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
54 import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
56 public abstract class JalviewChimeraBinding extends AAStructureBindingModel
58 // Chimera clause to exclude alternate locations in atom selection
59 private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
61 private static final String COLOURING_CHIMERA = MessageManager
62 .getString("status.colouring_chimera");
64 private static final boolean debug = false;
66 private static final String PHOSPHORUS = "P";
68 private static final String ALPHACARBON = "CA";
71 * Object through which we talk to Chimera
73 private ChimeraManager viewer;
76 * Object which listens to Chimera notifications
78 private AbstractRequestHandler chimeraListener;
81 * set if chimera state is being restored from some source - instructs binding
82 * not to apply default display style when structure set is updated for first
85 private boolean loadingFromArchive = false;
88 * flag to indicate if the Chimera viewer should ignore sequence colouring
89 * events from the structure manager because the GUI is still setting up
91 private boolean loadingFinished = true;
93 public String fileLoadingError;
96 * Map of ChimeraModel objects keyed by PDB full local file name
98 private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<String, List<ChimeraModel>>();
101 * the default or current model displayed if the model cannot be identified
102 * from the selection message
104 private int frameNo = 0;
106 private String lastCommand;
108 String lastHighlightCommand;
111 * incremented every time a load notification is successfully handled -
112 * lightweight mechanism for other threads to detect when they can start
113 * referring to new structures.
115 private long loadNotifiesHandled = 0;
118 * Open a PDB structure file in Chimera and set up mappings from Jalview.
120 * We check if the PDB model id is already loaded in Chimera, if so don't
121 * reopen it. This is the case if Chimera has opened a saved session file.
126 public boolean openFile(PDBEntry pe)
128 String file = pe.getFile();
131 List<ChimeraModel> modelsToMap = new ArrayList<ChimeraModel>();
132 List<ChimeraModel> oldList = viewer.getModelList();
133 boolean alreadyOpen = false;
136 * If Chimera already has this model, don't reopen it, but do remap it.
138 for (ChimeraModel open : oldList)
140 if (open.getModelName().equals(pe.getId()))
143 modelsToMap.add(open);
148 * If Chimera doesn't yet have this model, ask it to open it, and retrieve
149 * the model name(s) added by Chimera.
153 viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
154 List<ChimeraModel> newList = viewer.getModelList();
155 // JAL-1728 newList.removeAll(oldList) does not work
156 for (ChimeraModel cm : newList)
158 if (cm.getModelName().equals(pe.getId()))
165 chimeraMaps.put(file, modelsToMap);
167 if (getSsm() != null)
169 getSsm().addStructureViewerListener(this);
170 // ssm.addSelectionListener(this);
171 FeatureRenderer fr = getFeatureRenderer(null);
179 } catch (Exception q)
181 log("Exception when trying to open model " + file + "\n"
197 public JalviewChimeraBinding(StructureSelectionManager ssm,
198 PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
201 super(ssm, pdbentry, sequenceIs, chains, protocol);
202 viewer = new ChimeraManager(
203 new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
207 * Start a dedicated HttpServer to listen for Chimera notifications, and tell
208 * it to start listening
210 public void startChimeraListener()
214 chimeraListener = new ChimeraListener(this);
215 viewer.startListening(chimeraListener.getUri());
216 } catch (BindException e)
218 System.err.println("Failed to start Chimera listener: "
224 * Construct a title string for the viewer window based on the data Jalview
230 public String getViewerTitle(boolean verbose)
232 return getViewerTitle("Chimera", verbose);
236 * Tells Chimera to display only the specified chains
240 public void showChains(List<String> toshow)
243 * Construct a chimera command like
245 * ~display #*;~ribbon #*;ribbon :.A,:.B
247 StringBuilder cmd = new StringBuilder(64);
248 boolean first = true;
249 for (String chain : toshow)
255 cmd.append(":.").append(chain);
260 * could append ";focus" to this command to resize the display to fill the
261 * window, but it looks more helpful not to (easier to relate chains to the
264 final String command = "~display #*; ~ribbon #*; ribbon "
266 sendChimeraCommand(command, false);
270 * Close down the Jalview viewer and listener, and (optionally) the associated
273 public void closeViewer(boolean closeChimera)
275 getSsm().removeStructureViewerListener(this, this.getPdbFile());
278 viewer.exitChimera();
280 if (this.chimeraListener != null)
282 chimeraListener.shutdown();
283 chimeraListener = null;
288 releaseUIResources();
291 public void colourByChain()
293 colourBySequence = false;
294 sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA);
298 * Constructs and sends a Chimera command to colour by charge
300 * <li>Aspartic acid and Glutamic acid (negative charge) red</li>
301 * <li>Lysine and Arginine (positive charge) blue</li>
302 * <li>Cysteine - yellow</li>
303 * <li>all others - white</li>
306 public void colourByCharge()
308 colourBySequence = false;
309 String command = "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS";
310 sendAsynchronousCommand(command, COLOURING_CHIMERA);
314 * Construct and send a command to align structures against a reference
315 * structure, based on one or more sequence alignments
318 * an array of alignments to process
319 * @param _refStructure
320 * an array of corresponding reference structures (index into pdb
321 * file array); if a negative value is passed, the first PDB file
322 * mapped to an alignment sequence is used as the reference for
325 * an array of corresponding hidden columns for each alignment
327 public void superposeStructures(AlignmentI[] _alignment,
328 int[] _refStructure, ColumnSelection[] _hiddenCols)
330 StringBuilder allComs = new StringBuilder(128);
331 String[] files = getPdbFile();
333 if (!waitForFileLoad(files))
339 StringBuilder selectioncom = new StringBuilder(256);
340 for (int a = 0; a < _alignment.length; a++)
342 int refStructure = _refStructure[a];
343 AlignmentI alignment = _alignment[a];
344 ColumnSelection hiddenCols = _hiddenCols[a];
346 if (refStructure >= files.length)
348 System.err.println("Ignoring invalid reference structure value "
354 * 'matched' array will hold 'true' for visible alignment columns where
355 * all sequences have a residue with a mapping to the PDB structure
357 boolean matched[] = new boolean[alignment.getWidth()];
358 for (int m = 0; m < matched.length; m++)
360 matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
363 SuperposeData[] structures = new SuperposeData[files.length];
364 for (int f = 0; f < files.length; f++)
366 structures[f] = new SuperposeData(alignment.getWidth());
370 * Calculate the superposable alignment columns ('matched'), and the
371 * corresponding structure residue positions (structures.pdbResNo)
373 int candidateRefStructure = findSuperposableResidues(alignment,
374 matched, structures);
375 if (refStructure < 0)
378 * If no reference structure was specified, pick the first one that has
379 * a mapping in the alignment
381 refStructure = candidateRefStructure;
385 for (boolean b : matched)
394 // TODO: bail out here because superposition illdefined?
398 * Generate select statements to select regions to superimpose structures
400 String[] selcom = new String[files.length];
401 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
403 String chainCd = "." + structures[pdbfnum].chain;
406 StringBuilder molsel = new StringBuilder();
407 for (int r = 0; r < matched.length; r++)
411 int pdbResNum = structures[pdbfnum].pdbResNo[r];
412 if (lpos != pdbResNum - 1)
415 * discontiguous - append last residue now
419 molsel.append(String.valueOf(lpos));
420 molsel.append(chainCd);
428 * extending a contiguous run
433 * start the range selection
435 molsel.append(String.valueOf(lpos));
445 * and terminate final selection
449 molsel.append(String.valueOf(lpos));
450 molsel.append(chainCd);
452 if (molsel.length() > 1)
454 selcom[pdbfnum] = molsel.toString();
455 selectioncom.append("#").append(String.valueOf(pdbfnum))
457 selectioncom.append(selcom[pdbfnum]);
458 selectioncom.append(" ");
459 if (pdbfnum < files.length - 1)
461 selectioncom.append("| ");
466 selcom[pdbfnum] = null;
470 StringBuilder command = new StringBuilder(256);
471 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
473 if (pdbfnum == refStructure || selcom[pdbfnum] == null
474 || selcom[refStructure] == null)
478 if (command.length() > 0)
484 * Form Chimera match command, from the 'new' structure to the
485 * 'reference' structure e.g. (50 residues, chain B/A, alphacarbons):
487 * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA
490 * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
492 command.append("match ").append(getModelSpec(pdbfnum)).append(":");
493 command.append(selcom[pdbfnum]);
494 command.append("@").append(
495 structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON);
496 // JAL-1757 exclude alternate CA locations
497 command.append(NO_ALTLOCS);
498 command.append(" ").append(getModelSpec(refStructure)).append(":");
499 command.append(selcom[refStructure]);
500 command.append("@").append(
501 structures[refStructure].isRna ? PHOSPHORUS : ALPHACARBON);
502 command.append(NO_ALTLOCS);
504 if (selectioncom.length() > 0)
508 System.out.println("Select regions:\n" + selectioncom.toString());
509 System.out.println("Superimpose command(s):\n"
510 + command.toString());
512 allComs.append("~display all; chain @CA|P; ribbon ")
513 .append(selectioncom.toString())
514 .append(";" + command.toString());
517 if (selectioncom.length() > 0)
519 // TODO: visually distinguish regions that were superposed
520 if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
522 selectioncom.setLength(selectioncom.length() - 1);
526 System.out.println("Select regions:\n" + selectioncom.toString());
528 allComs.append("; ~display all; chain @CA|P; ribbon ")
529 .append(selectioncom.toString()).append("; focus");
530 sendChimeraCommand(allComs.toString(), false);
536 * Helper method to construct model spec in Chimera format:
538 * <li>#0 (#1 etc) for a PDB file with no sub-models</li>
539 * <li>#0.1 (#1.1 etc) for a PDB file with sub-models</li>
541 * Note for now we only ever choose the first of multiple models. This
542 * corresponds to the hard-coded Jmol equivalent (compare {1.1}). Refactor in
543 * future if there is a need to select specific sub-models.
548 protected String getModelSpec(int pdbfnum)
550 if (pdbfnum < 0 || pdbfnum >= getPdbCount())
556 * For now, the test for having sub-models is whether multiple Chimera
557 * models are mapped for the PDB file; the models are returned as a response
558 * to the Chimera command 'list models type molecule', see
559 * ChimeraManager.getModelList().
561 List<ChimeraModel> maps = chimeraMaps.get(getPdbFile()[pdbfnum]);
562 boolean hasSubModels = maps != null && maps.size() > 1;
563 return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
567 * Launch Chimera, unless an instance linked to this object is already
568 * running. Returns true if chimera is successfully launched, or already
569 * running, else false.
573 public boolean launchChimera()
575 if (!viewer.isChimeraLaunched())
577 return viewer.launchChimera(StructureManager.getChimeraPaths());
579 if (viewer.isChimeraLaunched())
583 log("Failed to launch Chimera!");
588 * Answers true if the Chimera process is still running, false if ended or not
593 public boolean isChimeraRunning()
595 return viewer.isChimeraLaunched();
599 * Send a command to Chimera, and optionally log any responses.
604 public void sendChimeraCommand(final String command, boolean logResponse)
608 // ? thread running after viewer shut down
611 viewerCommandHistory(false);
612 if (lastCommand == null || !lastCommand.equals(command))
614 // trim command or it may never find a match in the replyLog!!
615 List<String> lastReply = viewer.sendChimeraCommand(command.trim(),
617 if (logResponse && debug)
619 log("Response from command ('" + command + "') was:\n" + lastReply);
622 viewerCommandHistory(true);
623 lastCommand = command;
627 * Send a Chimera command asynchronously in a new thread. If the progress
628 * message is not null, display this message while the command is executing.
633 protected abstract void sendAsynchronousCommand(String command,
637 * colour any structures associated with sequences in the given alignment
638 * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
639 * if colourBySequence is enabled.
641 public void colourBySequence(boolean showFeatures,
642 jalview.api.AlignmentViewPanel alignmentv)
644 if (!colourBySequence || !loadingFinished)
648 if (getSsm() == null)
652 String[] files = getPdbFile();
654 SequenceRenderer sr = getSequenceRenderer(alignmentv);
656 FeatureRenderer fr = null;
659 fr = getFeatureRenderer(alignmentv);
661 AlignmentI alignment = alignmentv.getAlignment();
663 StructureMappingcommandSet colourBySequenceCommands = ChimeraCommands
664 .getColourBySequenceCommand(getSsm(), files, getSequence(), sr,
666 for (String command : colourBySequenceCommands.commands)
668 sendAsynchronousCommand(command, COLOURING_CHIMERA);
675 protected void executeWhenReady(String command)
678 sendChimeraCommand(command, false);
682 private void waitForChimera()
684 while (viewer != null && viewer.isBusy())
689 } catch (InterruptedException q)
695 // End StructureListener
696 // //////////////////////////
699 * returns the current featureRenderer that should be used to colour the
706 public abstract FeatureRenderer getFeatureRenderer(
707 AlignmentViewPanel alignment);
710 * instruct the Jalview binding to update the pdbentries vector if necessary
711 * prior to matching the viewer's contents to the list of structure files
712 * Jalview knows about.
714 public abstract void refreshPdbEntries();
716 private int getModelNum(String modelFileName)
718 String[] mfn = getPdbFile();
723 for (int i = 0; i < mfn.length; i++)
725 if (mfn[i].equalsIgnoreCase(modelFileName))
734 * map between index of model filename returned from getPdbFile and the first
735 * index of models from this file in the viewer. Note - this is not trimmed -
736 * use getPdbFile to get number of unique models.
738 private int _modelFileNameMap[];
740 // ////////////////////////////////
741 // /StructureListener
743 public synchronized String[] getPdbFile()
747 return new String[0];
749 // if (modelFileNames == null)
751 // Collection<ChimeraModel> chimodels = viewer.getChimeraModels();
752 // _modelFileNameMap = new int[chimodels.size()];
754 // for (ChimeraModel chimodel : chimodels)
756 // String mdlName = chimodel.getModelName();
758 // modelFileNames = new String[j];
759 // // System.arraycopy(mset, 0, modelFileNames, 0, j);
762 return chimeraMaps.keySet().toArray(
763 modelFileNames = new String[chimeraMaps.size()]);
767 * returns the current sequenceRenderer that should be used to colour the
774 public abstract SequenceRenderer getSequenceRenderer(
775 AlignmentViewPanel alignment);
778 * Construct and send a command to highlight zero, one or more atoms. We do
779 * this by sending an "rlabel" command to show the residue label at that
783 public void highlightAtoms(List<AtomSpec> atoms)
785 if (atoms == null || atoms.size() == 0)
790 StringBuilder cmd = new StringBuilder(128);
791 boolean first = true;
792 boolean found = false;
794 for (AtomSpec atom : atoms)
796 int pdbResNum = atom.getPdbResNum();
797 String chain = atom.getChain();
798 String pdbfile = atom.getPdbFile();
799 List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
800 if (cms != null && !cms.isEmpty())
804 cmd.append("rlabel #").append(cms.get(0).getModelNumber())
812 cmd.append(pdbResNum);
813 if (!chain.equals(" "))
815 cmd.append(".").append(chain);
820 String command = cmd.toString();
823 * avoid repeated commands for the same residue
825 if (command.equals(lastHighlightCommand))
831 * unshow the label for the previous residue
833 if (lastHighlightCommand != null)
835 viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
839 viewer.sendChimeraCommand(command, false);
841 this.lastHighlightCommand = command;
845 * Query Chimera for its current selection, and highlight it on the alignment
847 public void highlightChimeraSelection()
850 * Ask Chimera for its current selection
852 List<String> selection = viewer.getSelectedResidueSpecs();
855 * Parse model number, residue and chain for each selected position,
856 * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
858 List<AtomSpec> atomSpecs = new ArrayList<AtomSpec>();
859 for (String atomSpec : selection)
861 int colonPos = atomSpec.indexOf(":");
864 continue; // malformed
867 int hashPos = atomSpec.indexOf("#");
868 String modelSubmodel = atomSpec.substring(hashPos + 1, colonPos);
869 int dotPos = modelSubmodel.indexOf(".");
873 modelId = Integer.valueOf(dotPos == -1 ? modelSubmodel
874 : modelSubmodel.substring(0, dotPos));
875 } catch (NumberFormatException e)
877 // ignore, default to model 0
880 String residueChain = atomSpec.substring(colonPos + 1);
881 dotPos = residueChain.indexOf(".");
882 int pdbResNum = Integer.parseInt(dotPos == -1 ? residueChain
883 : residueChain.substring(0, dotPos));
885 String chainId = dotPos == -1 ? "" : residueChain
886 .substring(dotPos + 1);
889 * Work out the pdbfilename from the model number
891 String pdbfilename = modelFileNames[frameNo];
892 findfileloop: for (String pdbfile : this.chimeraMaps.keySet())
894 for (ChimeraModel cm : chimeraMaps.get(pdbfile))
896 if (cm.getModelNumber() == modelId)
898 pdbfilename = pdbfile;
903 atomSpecs.add(new AtomSpec(pdbfilename, chainId, pdbResNum, 0));
907 * Broadcast the selection (which may be empty, if the user just cleared all
910 getSsm().mouseOverStructure(atomSpecs);
913 private void log(String message)
915 System.err.println("## Chimera log: " + message);
918 private void viewerCommandHistory(boolean enable)
920 // log("(Not yet implemented) History "
921 // + ((debug || enable) ? "on" : "off"));
924 public long getLoadNotifiesHandled()
926 return loadNotifiesHandled;
929 public void setJalviewColourScheme(ColourSchemeI cs)
931 colourBySequence = false;
938 // Chimera expects RBG values in the range 0-1
939 final double normalise = 255D;
940 viewerCommandHistory(false);
941 StringBuilder command = new StringBuilder(128);
943 List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
945 for (String res : residueSet)
947 Color col = cs.findColour(res.charAt(0));
948 command.append("color " + col.getRed() / normalise + ","
949 + col.getGreen() / normalise + "," + col.getBlue()
950 / normalise + " ::" + res + ";");
953 sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
954 viewerCommandHistory(true);
958 * called when the binding thinks the UI needs to be refreshed after a Chimera
959 * state change. this could be because structures were loaded, or because an
960 * error has occurred.
962 public abstract void refreshGUI();
965 public void setLoadingFromArchive(boolean loadingFromArchive)
967 this.loadingFromArchive = loadingFromArchive;
972 * @return true if Chimeral is still restoring state or loading is still going
973 * on (see setFinsihedLoadingFromArchive)
976 public boolean isLoadingFromArchive()
978 return loadingFromArchive && !loadingFinished;
982 * modify flag which controls if sequence colouring events are honoured by the
983 * binding. Should be true for normal operation
985 * @param finishedLoading
988 public void setFinishedLoadingFromArchive(boolean finishedLoading)
990 loadingFinished = finishedLoading;
994 * Send the Chimera 'background solid <color>" command.
997 * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
1001 public void setBackgroundColour(Color col)
1003 viewerCommandHistory(false);
1004 double normalise = 255D;
1005 final String command = "background solid " + col.getRed() / normalise
1006 + "," + col.getGreen() / normalise + "," + col.getBlue()
1008 viewer.sendChimeraCommand(command, false);
1009 viewerCommandHistory(true);
1013 * Ask Chimera to save its session to the given file. Returns true if
1014 * successful, else false.
1019 public boolean saveSession(String filepath)
1021 if (isChimeraRunning())
1023 List<String> reply = viewer.sendChimeraCommand("save " + filepath,
1025 if (reply.contains("Session written"))
1032 .error("Error saving Chimera session: " + reply.toString());
1039 * Ask Chimera to open a session file. Returns true if successful, else false.
1040 * The filename must have a .py extension for this command to work.
1045 public boolean openSession(String filepath)
1047 sendChimeraCommand("open " + filepath, true);
1048 // todo: test for failure - how?
1053 * Returns a list of chains mapped in this viewer. Note this list is not
1054 * currently scoped per structure.
1058 public List<String> getChainNames()
1060 List<String> names = new ArrayList<String>();
1061 String[][] allNames = getChains();
1062 if (allNames != null)
1064 for (String[] chainsForPdb : allNames)
1066 if (chainsForPdb != null)
1068 for (String chain : chainsForPdb)
1070 if (chain != null && !names.contains(chain))
1082 * Send a 'focus' command to Chimera to recentre the visible display
1084 public void focusView()
1086 sendChimeraCommand("focus", false);
1090 * Send a 'show' command for all atoms in the currently selected columns
1092 * TODO: pull up to abstract structure viewer interface
1096 public void highlightSelection(AlignmentViewPanel vp)
1098 List<Integer> cols = vp.getAlignViewport().getColumnSelection()
1100 AlignmentI alignment = vp.getAlignment();
1101 StructureSelectionManager sm = getSsm();
1102 for (SequenceI seq : alignment.getSequences())
1105 * convert selected columns into sequence positions
1107 int[] positions = new int[cols.size()];
1109 for (Integer col : cols)
1111 positions[i++] = seq.findPosition(col);
1113 sm.highlightStructure(this, seq, positions);
1118 * Constructs and send commands to Chimera to set attributes on residues for
1119 * features visible in Jalview
1123 public void sendFeaturesToChimera(AlignmentViewPanel avp)
1125 AlignmentI alignment = avp.getAlignment();
1126 FeatureRenderer fr = getFeatureRenderer(avp);
1129 * fr is null if feature display is turned off
1136 String[] files = getPdbFile();
1142 StructureMappingcommandSet commandSet = ChimeraCommands
1143 .getSetAttributeCommandsForFeatures(getSsm(), files,
1144 getSequence(), fr, alignment);
1145 // for (String command : commandSet.commands)
1147 // sendAsynchronousCommand(command, null);
1149 sendCommandsByFile(commandSet.commands);
1153 * Write commands to a temporary file, and send a command to Chimera to open
1154 * the file as a commands script. For use when sending a large number of
1155 * separate commands would overload the REST interface mechanism.
1159 protected void sendCommandsByFile(String[] commands)
1163 File tmp = File.createTempFile("chim", ".com");
1165 PrintWriter out = new PrintWriter(new FileOutputStream(tmp));
1166 for (String command : commands)
1168 out.println(command);
1172 String path = tmp.getAbsolutePath();
1173 sendAsynchronousCommand("open cmd:" + path, null);
1174 } catch (IOException e)
1177 .println("Sending commands to Chimera via file failed with "