X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=399bad9d9c9d7cd0982644529885594e7bedea43;hb=b7cd96eaeb85474ee2ddec1de92181a3b88ceece;hp=1434c7680afa9322d18d5ca974124f44d1359a00;hpb=f2f654875a6eb5f4e90b2c5c545bfed3a70f2b5f;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 1434c76..399bad9 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -20,10 +20,13 @@ */ package jalview.ext.rbvi.chimera; -import java.awt.Color; +import java.io.File; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.PrintWriter; import java.net.BindException; import java.util.ArrayList; -import java.util.HashMap; +import java.util.Collections; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; @@ -32,108 +35,61 @@ import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager; import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel; import ext.edu.ucsf.rbvi.strucviz2.StructureManager; import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType; - import jalview.api.AlignmentViewPanel; -import jalview.api.FeatureRenderer; -import jalview.api.SequenceRenderer; -import jalview.bin.Cache; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; +import jalview.bin.Console; import jalview.datamodel.PDBEntry; +import jalview.datamodel.SearchResultMatchI; +import jalview.datamodel.SearchResultsI; +import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.ResidueProperties; +import jalview.gui.StructureViewer.ViewerType; +import jalview.httpserver.AbstractRequestHandler; +import jalview.io.DataSourceType; import jalview.structure.AtomSpec; -import jalview.structure.StructureMapping; -import jalview.structure.StructureMappingcommandSet; +import jalview.structure.AtomSpecModel; +import jalview.structure.StructureCommand; +import jalview.structure.StructureCommandI; import jalview.structure.StructureSelectionManager; import jalview.structures.models.AAStructureBindingModel; -import jalview.util.Comparison; -import jalview.util.MessageManager; public abstract class JalviewChimeraBinding extends AAStructureBindingModel { + public static final String CHIMERA_SESSION_EXTENSION = ".py"; - private static final boolean debug = false; - - private static final String PHOSPHORUS = "P"; - - private static final String ALPHACARBON = "CA"; - - private StructureManager csm; + public static final String CHIMERA_FEATURE_GROUP = "Chimera"; /* * Object through which we talk to Chimera */ - private ChimeraManager viewer; + private ChimeraManager chimeraManager; /* * Object which listens to Chimera notifications */ - private ChimeraListener chimeraListener; - - /* - * set if chimera state is being restored from some source - instructs binding - * not to apply default display style when structure set is updated for first - * time. - */ - private boolean loadingFromArchive = false; - - /* - * flag to indicate if the Chimera viewer should ignore sequence colouring - * events from the structure manager because the GUI is still setting up - */ - private boolean loadingFinished = true; - - /* - * state flag used to check if the Chimera viewer's paint method can be called - */ - private boolean finishedInit = false; - - private List atomsPicked = new ArrayList(); - - private List chainNames; - - private Map chainFile; - - public String fileLoadingError; + private AbstractRequestHandler chimeraListener; /* * Map of ChimeraModel objects keyed by PDB full local file name */ - private Map> chimeraMaps = new LinkedHashMap>(); + protected Map> chimeraMaps = new LinkedHashMap<>(); - /* - * the default or current model displayed if the model cannot be identified - * from the selection message - */ - private int frameNo = 0; - - private String lastCommand; - - private boolean loadedInline; + String lastHighlightCommand; /** - * current set of model filenames loaded - */ - String[] modelFileNames = null; - - String lastMousedOverAtomSpec; - - private List lastReply; - - /* - * incremented every time a load notification is successfully handled - - * lightweight mechanism for other threads to detect when they can start - * referring to new structures. + * Returns a model of the structure positions described by the Chimera format atomspec + * @param atomSpec + * @return */ - private long loadNotifiesHandled = 0; + protected AtomSpec parseAtomSpec(String atomSpec) + { + return AtomSpec.fromChimeraAtomspec(atomSpec); + } /** * Open a PDB structure file in Chimera and set up mappings from Jalview. * - * We check if the PDB model id is already loaded in Chimera, if so don't - * reopen it. This is the case if Chimera has opened a saved session file. + * We check if the PDB model id is already loaded in Chimera, if so don't reopen + * it. This is the case if Chimera has opened a saved session file. * * @param pe * @return @@ -143,8 +99,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel String file = pe.getFile(); try { - List modelsToMap = new ArrayList(); - List oldList = viewer.getModelList(); + List modelsToMap = new ArrayList<>(); + List oldList = chimeraManager.getModelList(); boolean alreadyOpen = false; /* @@ -165,16 +121,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ if (!alreadyOpen) { - viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL); - List newList = viewer.getModelList(); - // JAL-1728 newList.removeAll(oldList) does not work - for (ChimeraModel cm : newList) - { - if (cm.getModelName().equals(pe.getId())) - { - modelsToMap.add(cm); - } - } + chimeraManager.openModel(file, pe.getId(), ModelType.PDB_MODEL); + addChimeraModel(pe, modelsToMap); } chimeraMaps.put(file, modelsToMap); @@ -182,13 +130,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel if (getSsm() != null) { getSsm().addStructureViewerListener(this); - // ssm.addSelectionListener(this); - FeatureRenderer fr = getFeatureRenderer(null); - if (fr != null) - { - fr.featuresAdded(); - } - refreshGUI(); } return true; } catch (Exception q) @@ -201,967 +142,661 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** + * Adds the ChimeraModel corresponding to the given PDBEntry, based on model + * name matching PDB id + * + * @param pe + * @param modelsToMap + */ + protected void addChimeraModel(PDBEntry pe, + List modelsToMap) + { + /* + * Chimera: query for actual models and find the one with + * matching model name - already set in viewer.openModel() + */ + List newList = chimeraManager.getModelList(); + // JAL-1728 newList.removeAll(oldList) does not work + for (ChimeraModel cm : newList) + { + if (cm.getModelName().equals(pe.getId())) + { + modelsToMap.add(cm); + } + } + } + + /** * Constructor * * @param ssm * @param pdbentry * @param sequenceIs - * @param chains * @param protocol */ public JalviewChimeraBinding(StructureSelectionManager ssm, - PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains, - String protocol) + PDBEntry[] pdbentry, SequenceI[][] sequenceIs, + DataSourceType protocol) { - super(ssm, pdbentry, sequenceIs, chains, protocol); - viewer = new ChimeraManager( - csm = new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true)); + super(ssm, pdbentry, sequenceIs, protocol); + boolean chimeraX = ViewerType.CHIMERAX.equals(getViewerType()); + chimeraManager = chimeraX ? new ChimeraXManager(new StructureManager(true)) : new ChimeraManager(new StructureManager(true)); + setStructureCommands(chimeraX ? new ChimeraXCommands() : new ChimeraCommands()); + } + + @Override + protected ViewerType getViewerType() + { + return ViewerType.CHIMERA; } /** - * Start a dedicated HttpServer to listen for Chimera notifications, and tell - * it to start listening + * Start a dedicated HttpServer to listen for Chimera notifications, and tell it + * to start listening */ public void startChimeraListener() { try { chimeraListener = new ChimeraListener(this); - viewer.startListening(chimeraListener.getUri()); + startListening(chimeraListener.getUri()); } catch (BindException e) { - System.err.println("Failed to start Chimera listener: " - + e.getMessage()); + System.err.println( + "Failed to start Chimera listener: " + e.getMessage()); } } /** - * Constructor - * - * @param ssm - * @param theViewer + * Close down the Jalview viewer and listener, and (optionally) the associated + * Chimera window. */ - public JalviewChimeraBinding(StructureSelectionManager ssm, - ChimeraManager theViewer) + @Override + public void closeViewer(boolean closeChimera) { - super(ssm, null); - viewer = theViewer; - csm = viewer.getStructureManager(); + super.closeViewer(closeChimera); + if (this.chimeraListener != null) + { + chimeraListener.shutdown(); + chimeraListener = null; + } + + /* + * the following call is added to avoid a stack trace error in Chimera + * after "stop really" is sent; Chimera > 1.14 will not need it; see also + * http://plato.cgl.ucsf.edu/trac/chimera/ticket/17597 + */ + if (closeChimera && (getViewerType() == ViewerType.CHIMERA)) + { + chimeraManager.getChimeraProcess().destroy(); + } + + chimeraManager.clearOnChimeraExit(); + chimeraManager = null; } /** - * Construct a title string for the viewer window based on the data Jalview - * knows about + * Helper method to construct model spec in Chimera format: + *
    + *
  • #0 (#1 etc) for a PDB file with no sub-models
    • + *
  • #0.1 (#1.1 etc) for a PDB file with sub-models
    • + *
      + * Note for now we only ever choose the first of multiple models. This + * corresponds to the hard-coded Jmol equivalent (compare {1.1}). Refactor in + * future if there is a need to select specific sub-models. * - * @param verbose + * @param pdbfnum * @return */ - public String getViewerTitle(boolean verbose) + protected String getModelSpec(int pdbfnum) { - return getViewerTitle("Chimera", verbose); + if (pdbfnum < 0 || pdbfnum >= getPdbCount()) + { + return "#" + pdbfnum; // temp hack for ChimeraX + } + + /* + * For now, the test for having sub-models is whether multiple Chimera + * models are mapped for the PDB file; the models are returned as a response + * to the Chimera command 'list models type molecule', see + * ChimeraManager.getModelList(). + */ + List maps = chimeraMaps.get(getStructureFiles()[pdbfnum]); + boolean hasSubModels = maps != null && maps.size() > 1; + return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : ""); } /** - * prepare the view for a given set of models/chains. chainList contains - * strings of the form 'pdbfilename:Chaincode' + * Launch Chimera, unless an instance linked to this object is already + * running. Returns true if Chimera is successfully launched, or already + * running, else false. * - * @param toshow - * list of chains to make visible + * @return */ - public void centerViewer(List toshow) + public boolean launchChimera() { - StringBuilder cmd = new StringBuilder(64); - int mlength, p; - for (String lbl : toshow) + if (chimeraManager.isChimeraLaunched()) { - mlength = 0; - do - { - p = mlength; - mlength = lbl.indexOf(":", p); - } while (p < mlength && mlength < (lbl.length() - 2)); - // TODO: lookup each pdb id and recover proper model number for it. - cmd.append("#" + getModelNum(chainFile.get(lbl)) + "." - + lbl.substring(mlength + 1) + " or "); - } - if (cmd.length() > 0) - { - cmd.setLength(cmd.length() - 4); + return true; } - String cmdstring = cmd.toString(); - evalStateCommand("~display #*; ~ribbon #*; ribbon " + cmdstring - + ";focus " + cmdstring, false); - } - /** - * Close down the Jalview viewer and listener, and (optionally) the associated - * Chimera window. - */ - public void closeViewer(boolean closeChimera) - { - getSsm().removeStructureViewerListener(this, this.getPdbFile()); - if (closeChimera) + boolean launched = chimeraManager.launchChimera(getChimeraPaths()); + if (launched) { - viewer.exitChimera(); + startExternalViewerMonitor(chimeraManager.getChimeraProcess()); } - if (this.chimeraListener != null) + else { - chimeraListener.shutdown(); - chimeraListener = null; + log("Failed to launch Chimera!"); } - lastCommand = null; - viewer = null; - - releaseUIResources(); - } - - public void colourByChain() - { - colourBySequence = false; - evalStateCommand("rainbow chain", false); - } - - public void colourByCharge() - { - colourBySequence = false; - evalStateCommand( - "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS", - false); + return launched; } /** - * superpose the structures associated with sequences in the alignment - * according to their corresponding positions. + * Returns a list of candidate paths to the Chimera program executable + * + * @return */ - public void superposeStructures(AlignmentI alignment) + protected List getChimeraPaths() { - superposeStructures(alignment, -1, null); + return StructureManager.getChimeraPaths(false); } /** - * superpose the structures associated with sequences in the alignment - * according to their corresponding positions. ded) + * Answers true if the Chimera process is still running, false if ended or not + * started. * - * @param refStructure - * - select which pdb file to use as reference (default is -1 - the - * first structure in the alignment) + * @return */ - public void superposeStructures(AlignmentI alignment, int refStructure) + @Override + public boolean isViewerRunning() { - superposeStructures(alignment, refStructure, null); + return chimeraManager!=null && chimeraManager.isChimeraLaunched(); } /** - * superpose the structures associated with sequences in the alignment - * according to their corresponding positions. ded) + * Send a command to Chimera, and optionally log and return any responses. * - * @param refStructure - * - select which pdb file to use as reference (default is -1 - the - * first structure in the alignment) - * @param hiddenCols - * TODO + * @param command + * @param getResponse */ - public void superposeStructures(AlignmentI alignment, int refStructure, - ColumnSelection hiddenCols) - { - superposeStructures(new AlignmentI[] - { alignment }, new int[] - { refStructure }, new ColumnSelection[] - { hiddenCols }); - } - - public void superposeStructures(AlignmentI[] _alignment, - int[] _refStructure, ColumnSelection[] _hiddenCols) + @Override + public List executeCommand(final StructureCommandI command, + boolean getResponse) { - assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length); - StringBuilder allComs = new StringBuilder(128); // Chimera superposition cmd - String[] files = getPdbFile(); - // check to see if we are still waiting for Chimera files - long starttime = System.currentTimeMillis(); - boolean waiting = true; - do + if (chimeraManager == null || command == null) { - waiting = false; - for (String file : files) - { - try - { - // HACK - in Jalview 2.8 this call may not be threadsafe so we catch - // every possible exception - StructureMapping[] sm = getSsm().getMapping(file); - if (sm == null || sm.length == 0) - { - waiting = true; - } - } catch (Exception x) - { - waiting = true; - } catch (Error q) - { - waiting = true; - } - } - // we wait around for a reasonable time before we give up - } while (waiting - && System.currentTimeMillis() < (10000 + 1000 * files.length + starttime)); - if (waiting) - { - System.err - .println("RUNTIME PROBLEM: Chimera seems to be taking a long time to process all the structures."); - return; + // ? thread running after viewer shut down + return null; } - refreshPdbEntries(); - StringBuffer selectioncom = new StringBuffer(); - for (int a = 0; a < _alignment.length; a++) + List reply = null; + // trim command or it may never find a match in the replyLog!! + String cmd = command.getCommand().trim(); + List lastReply = chimeraManager + .sendChimeraCommand(cmd, getResponse); + if (getResponse) { - int refStructure = _refStructure[a]; - AlignmentI alignment = _alignment[a]; - ColumnSelection hiddenCols = _hiddenCols[a]; - if (a > 0 - && selectioncom.length() > 0 - && !selectioncom.substring(selectioncom.length() - 1).equals( - " ")) - { - selectioncom.append(" "); + reply = lastReply; + if (Console.isDebugEnabled()) { + Console.debug( + "Response from command ('" + cmd + "') was:\n" + lastReply); } - // process this alignment - if (refStructure >= files.length) - { - System.err.println("Invalid reference structure value " - + refStructure); - refStructure = -1; - } - if (refStructure < -1) + } + else + { + if (Console.isDebugEnabled()) { - refStructure = -1; + Console.debug("Command executed: " + cmd); } + } - boolean matched[] = new boolean[alignment.getWidth()]; - for (int m = 0; m < matched.length; m++) - { - - matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true; - } + return reply; + } - int commonrpositions[][] = new int[files.length][alignment.getWidth()]; - String isel[] = new String[files.length]; - String[] targetC = new String[files.length]; - String[] chainNames = new String[files.length]; - String[] atomSpec = new String[files.length]; - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) - { - StructureMapping[] mapping = getSsm().getMapping(files[pdbfnum]); - // RACE CONDITION - getMapping only returns Jmol loaded filenames once - // Jmol callback has completed. - if (mapping == null || mapping.length < 1) - { - throw new Error(MessageManager.getString("error.implementation_error_chimera_getting_data")); - } - int lastPos = -1; - final int seqCountForPdbFile = getSequence()[pdbfnum].length; - for (int s = 0; s < seqCountForPdbFile; s++) - { - for (int sp, m = 0; m < mapping.length; m++) - { - final SequenceI theSequence = getSequence()[pdbfnum][s]; - if (mapping[m].getSequence() == theSequence - && (sp = alignment.findIndex(theSequence)) > -1) - { - if (refStructure == -1) - { - refStructure = pdbfnum; - } - SequenceI asp = alignment.getSequenceAt(sp); - for (int r = 0; r < matched.length; r++) - { - if (!matched[r]) - { - continue; - } - matched[r] = false; // assume this is not a good site - if (r >= asp.getLength()) - { - continue; - } + @Override + public synchronized String[] getStructureFiles() + { + if (chimeraManager == null) + { + return new String[0]; + } - if (Comparison.isGap(asp.getCharAt(r))) - { - // no mapping to gaps in sequence - continue; - } - int t = asp.findPosition(r); // sequence position - int apos = mapping[m].getAtomNum(t); - int pos = mapping[m].getPDBResNum(t); + return chimeraMaps.keySet() + .toArray(modelFileNames = new String[chimeraMaps.size()]); + } - if (pos < 1 || pos == lastPos) - { - // can't align unmapped sequence - continue; - } - matched[r] = true; // this is a good ite - lastPos = pos; - // just record this residue position - commonrpositions[pdbfnum][r] = pos; - } - // create model selection suffix - isel[pdbfnum] = "#" + pdbfnum; - if (mapping[m].getChain() == null - || mapping[m].getChain().trim().length() == 0) - { - targetC[pdbfnum] = ""; - } - else - { - targetC[pdbfnum] = "." + mapping[m].getChain(); - } - chainNames[pdbfnum] = mapping[m].getPdbId() - + targetC[pdbfnum]; - atomSpec[pdbfnum] = asp.getRNA() != null ? PHOSPHORUS : ALPHACARBON; - // move on to next pdb file - s = seqCountForPdbFile; - break; - } - } - } - } + /** + * Construct and send a command to highlight zero, one or more atoms. We do this + * by sending an "rlabel" command to show the residue label at that position. + */ + @Override + public void highlightAtoms(List atoms) + { + if (atoms == null || atoms.size() == 0) + { + return; + } - // TODO: consider bailing if nmatched less than 4 because superposition - // not - // well defined. - // TODO: refactor superposable position search (above) from jmol selection - // construction (below) + boolean forChimeraX = chimeraManager.isChimeraX(); + StringBuilder cmd = new StringBuilder(128); + boolean first = true; + boolean found = false; - String[] selcom = new String[files.length]; - int nmatched = 0; - String sep = ""; - // generate select statements to select regions to superimpose structures + for (AtomSpec atom : atoms) + { + int pdbResNum = atom.getPdbResNum(); + String chain = atom.getChain(); + String pdbfile = atom.getPdbFile(); + List cms = chimeraMaps.get(pdbfile); + if (cms != null && !cms.isEmpty()) { - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + if (first) { - String chainCd = targetC[pdbfnum]; - int lpos = -1; - boolean run = false; - StringBuffer molsel = new StringBuffer(); - for (int r = 0; r < matched.length; r++) - { - if (matched[r]) - { - if (pdbfnum == 0) - { - nmatched++; - } - if (lpos != commonrpositions[pdbfnum][r] - 1) - { - // discontinuity - if (lpos != -1) - { - molsel.append((run ? "" : ":") + lpos); - molsel.append(chainCd); - molsel.append(","); - } - } - else - { - // continuous run - and lpos >-1 - if (!run) - { - // at the beginning, so add dash - molsel.append(":" + lpos); - molsel.append("-"); - } - run = true; - } - lpos = commonrpositions[pdbfnum][r]; - // molsel.append(lpos); - } - } - // add final selection phrase - if (lpos != -1) - { - molsel.append((run ? "" : ":") + lpos); - molsel.append(chainCd); - // molsel.append(""); - } - if (molsel.length() > 1) - { - selcom[pdbfnum] = molsel.toString(); - selectioncom.append("#" + pdbfnum); - selectioncom.append(selcom[pdbfnum]); - selectioncom.append(" "); - if (pdbfnum < files.length - 1) - { - selectioncom.append("| "); - } - } - else - { - selcom[pdbfnum] = null; - } + cmd.append(forChimeraX ? "label #" : "rlabel #"); } - } - StringBuilder command = new StringBuilder(256); - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) - { - if (pdbfnum == refStructure || selcom[pdbfnum] == null - || selcom[refStructure] == null) + else { - continue; + cmd.append(","); } - if (command.length() > 0) + first = false; + if (forChimeraX) { - command.append(";"); + cmd.append(cms.get(0).getModelNumber()) + .append("/").append(chain).append(":").append(pdbResNum); } - - /* - * Form Chimera match command, from the 'new' structure to the - * 'reference' structure e.g. (residues 1-91, chain B/A, alphacarbons): - * - * match #1:1-91.B@CA #0:1-91.A@CA - * - * @see - * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html - */ - command.append("match #" + pdbfnum /* +".1" */); - // TODO: handle sub-models - command.append(selcom[pdbfnum]); - command.append("@" + atomSpec[pdbfnum]); - command.append(" #" + refStructure /* +".1" */); - command.append(selcom[refStructure]); - command.append("@" + atomSpec[refStructure]); - } - if (selectioncom.length() > 0) - { - if (debug) + else { - System.out.println("Select regions:\n" + selectioncom.toString()); - System.out.println("Superimpose command(s):\n" - + command.toString()); + cmd.append(cms.get(0).getModelNumber()) + .append(":").append(pdbResNum); + if (!chain.equals(" ") && !forChimeraX) + { + cmd.append(".").append(chain); + } } - allComs.append("~display all; chain @CA|P; ribbon " - + selectioncom.toString() + ";"+command.toString()); - // selcom.append("; ribbons; "); + found = true; } } - if (selectioncom.length() > 0) - {// finally, mark all regions that were superposed. - if (selectioncom.substring(selectioncom.length() - 1).equals("|")) - { - selectioncom.setLength(selectioncom.length() - 1); - } - if (debug) - { - System.out.println("Select regions:\n" + selectioncom.toString()); - } - allComs.append("; ~display all; chain @CA|P; ribbon " - + selectioncom.toString() + "; focus"); - // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString()); - evalStateCommand(allComs.toString(), true /* false */); - } - - } + String command = cmd.toString(); - private void checkLaunched() - { - if (!viewer.isChimeraLaunched()) + /* + * avoid repeated commands for the same residue + */ + if (command.equals(lastHighlightCommand)) { - viewer.launchChimera(StructureManager.getChimeraPaths()); + return; } - if (!viewer.isChimeraLaunched()) + if (!found) { - log("Failed to launch Chimera!"); + // not a valid residue label command, so clear + cmd.setLength(0); + } + /* + * prepend with command + * to unshow the label for the previous residue + */ + if (lastHighlightCommand != null) + { + cmd.insert(0, ";"); + cmd.insert(0,lastHighlightCommand); + cmd.insert(0,"~"); + + } + if (cmd.length()>0) { + executeCommand(true, null, new StructureCommand(cmd.toString())); + } + + if (found) { + this.lastHighlightCommand = command; } } /** - * Answers true if the Chimera process is still running, false if ended or not - * started. - * - * @return + * Query Chimera for its current selection, and highlight it on the alignment */ - public boolean isChimeraRunning() + public void highlightChimeraSelection() { - return viewer.isChimeraLaunched(); + /* + * Ask Chimera for its current selection + */ + StructureCommandI command = getCommandGenerator().getSelectedResidues(); + + Runnable action = new Runnable() + { + @Override + public void run() + { + List chimeraReply = executeCommand(command, true); + + List selectedResidues = new ArrayList<>(); + if (chimeraReply != null) + { + /* + * expect 0, 1 or more lines of the format either + * Chimera: + * residue id #0:43.A type GLY + * ChimeraX: + * residue id /A:89 name THR index 88 + * We are only interested in the atomspec (third token of the reply) + */ + for (String inputLine : chimeraReply) + { + String[] inputLineParts = inputLine.split("\\s+"); + if (inputLineParts.length >= 5) + { + selectedResidues.add(inputLineParts[2]); + } + } + } + + /* + * Parse model number, residue and chain for each selected position, + * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain) + */ + List atomSpecs = convertStructureResiduesToAlignment( + selectedResidues); + + /* + * Broadcast the selection (which may be empty, if the user just cleared all + * selections) + */ + getSsm().mouseOverStructure(atomSpecs); + + } + }; + new Thread(action).start(); } /** - * Send a command to Chimera, launching it first if necessary, and optionally - * log any responses. + * Converts a list of Chimera(X) atomspecs to a list of AtomSpec representing the + * corresponding residues (if any) in Jalview * - * @param command - * @param logResponse + * @param structureSelection + * @return */ - public void evalStateCommand(final String command, boolean logResponse) + protected List convertStructureResiduesToAlignment( + List structureSelection) { - viewerCommandHistory(false); - checkLaunched(); - if (lastCommand == null || !lastCommand.equals(command)) + List atomSpecs = new ArrayList<>(); + for (String atomSpec : structureSelection) { - // trim command or it may never find a match in the replyLog!! - lastReply = viewer.sendChimeraCommand(command.trim(), logResponse); - if (debug && logResponse) + try { - log("Response from command ('" + command + "') was:\n" + lastReply); + AtomSpec spec = parseAtomSpec(atomSpec); + String pdbfilename = getPdbFileForModel(spec.getModelNumber()); + spec.setPdbFile(pdbfilename); + atomSpecs.add(spec); + } catch (IllegalArgumentException e) + { + Console.error("Failed to parse atomspec: " + atomSpec); } } - viewerCommandHistory(true); - lastCommand = command; + return atomSpecs; } /** - * colour any structures associated with sequences in the given alignment - * using the getFeatureRenderer() and getSequenceRenderer() renderers but only - * if colourBySequence is enabled. + * @param modelId + * @return */ - public void colourBySequence(boolean showFeatures, - jalview.api.AlignmentViewPanel alignmentv) + protected String getPdbFileForModel(int modelId) { - if (!colourBySequence || !loadingFinished) + /* + * Work out the pdbfilename from the model number + */ + String pdbfilename = modelFileNames[0]; + findfileloop: for (String pdbfile : this.chimeraMaps.keySet()) { - return; - } - if (getSsm() == null) - { - return; - } - String[] files = getPdbFile(); - - SequenceRenderer sr = getSequenceRenderer(alignmentv); - - FeatureRenderer fr = null; - if (showFeatures) - { - fr = getFeatureRenderer(alignmentv); - } - AlignmentI alignment = alignmentv.getAlignment(); - - for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands( - files, sr, fr, alignment)) - { - for (String command : cpdbbyseq.commands) + for (ChimeraModel cm : chimeraMaps.get(pdbfile)) { - executeWhenReady(command); + if (cm.getModelNumber() == modelId) + { + pdbfilename = pdbfile; + break findfileloop; + } } } + return pdbfilename; } - /** - * @param files - * @param sr - * @param fr - * @param alignment - * @return - */ - protected StructureMappingcommandSet[] getColourBySequenceCommands( - String[] files, SequenceRenderer sr, FeatureRenderer fr, - AlignmentI alignment) + private void log(String message) { - return ChimeraCommands.getColourBySequenceCommand(getSsm(), files, - getSequence(), sr, fr, alignment); + System.err.println("## Chimera log: " + message); } /** - * @param command + * Constructs and send commands to Chimera to set attributes on residues for + * features visible in Jalview. + *

      + * The syntax is: setattr r <attName> <attValue> <atomSpec> + *

      + * For example: setattr r jv_chain "Ferredoxin-1, Chloroplastic" #0:94.A + * + * @param avp + * @return */ - protected void executeWhenReady(String command) + public int sendFeaturesToViewer(AlignmentViewPanel avp) { - waitForChimera(); - evalStateCommand(command, false); - waitForChimera(); - } + // TODO refactor as required to pull up to an interface - private void waitForChimera() - { - while (viewer != null && viewer.isBusy()) + Map> featureValues = buildFeaturesMap( + avp); + List commands = getCommandGenerator() + .setAttributes(featureValues); + if (commands.size() > 10) { - try { - Thread.sleep(15); - } catch (InterruptedException q) - {} + sendCommandsByFile(commands); } - } - - - - // End StructureListener - // ////////////////////////// - - public Color getColour(int atomIndex, int pdbResNum, String chain, - String pdbfile) - { - if (getModelNum(pdbfile) < 0) + else { - return null; + executeCommands(commands, false, null); } - log("get model / residue colour attribute unimplemented"); - return null; + return commands.size(); } /** - * returns the current featureRenderer that should be used to colour the - * structures - * - * @param alignment + * Write commands to a temporary file, and send a command to Chimera to open the + * file as a commands script. For use when sending a large number of separate + * commands would overload the REST interface mechanism. * - * @return + * @param commands */ - public abstract FeatureRenderer getFeatureRenderer( - AlignmentViewPanel alignment); - - /** - * instruct the Jalview binding to update the pdbentries vector if necessary - * prior to matching the jmol view's contents to the list of structure files - * Jalview knows about. - */ - public abstract void refreshPdbEntries(); - - private int getModelNum(String modelFileName) + protected void sendCommandsByFile(List commands) { - String[] mfn = getPdbFile(); - if (mfn == null) - { - return -1; - } - for (int i = 0; i < mfn.length; i++) + try { - if (mfn[i].equalsIgnoreCase(modelFileName)) + File tmp = File.createTempFile("chim", getCommandFileExtension()); + tmp.deleteOnExit(); + PrintWriter out = new PrintWriter(new FileOutputStream(tmp)); + for (StructureCommandI command : commands) { - return i; + out.println(command.getCommand()); } - } - return -1; - } - - /** - * map between index of model filename returned from getPdbFile and the first - * index of models from this file in the viewer. Note - this is not trimmed - - * use getPdbFile to get number of unique models. - */ - private int _modelFileNameMap[]; - - // //////////////////////////////// - // /StructureListener - public synchronized String[] getPdbFile() - { - if (viewer == null) + out.flush(); + out.close(); + String path = tmp.getAbsolutePath(); + StructureCommandI command = getCommandGenerator() + .openCommandFile(path); + executeCommand(false, null, command); + } catch (IOException e) { - return new String[0]; + System.err.println("Sending commands to Chimera via file failed with " + + e.getMessage()); } - // if (modelFileNames == null) - // { - // Collection chimodels = viewer.getChimeraModels(); - // _modelFileNameMap = new int[chimodels.size()]; - // int j = 0; - // for (ChimeraModel chimodel : chimodels) - // { - // String mdlName = chimodel.getModelName(); - // } - // modelFileNames = new String[j]; - // // System.arraycopy(mset, 0, modelFileNames, 0, j); - // } - - return chimeraMaps.keySet().toArray( - modelFileNames = new String[chimeraMaps.size()]); } /** - * map from string to applet + * Returns the file extension required for a file of commands to be read by + * the structure viewer + * @return */ - public Map getRegistryInfo() + protected String getCommandFileExtension() { - // TODO Auto-generated method stub - return null; + return ".com"; } /** - * returns the current sequenceRenderer that should be used to colour the - * structures - * - * @param alignment - * - * @return - */ - public abstract SequenceRenderer getSequenceRenderer( - AlignmentViewPanel alignment); - - /** - * Construct and send a command to highlight an atom. + * Create features in Jalview for the given attribute name and structure + * residues. * * 

      -   * Done by generating a command like (to 'highlight' position 44)
-   *   ~show #0:43.C;show #0:44.C
-   * Note this removes the highlight from the previous position.
+   * The residue list should be 0, 1 or more reply lines of the format: 
+   *     residue id #0:5.A isHelix -155.000836316 index 5 
+   * or 
+   *     residue id #0:6.A isHelix None
    *
      + * + * @param attName + * @param residues + * @return the number of features added */ - public void highlightAtom(int atomIndex, int pdbResNum, String chain, - String pdbfile) + protected int createFeaturesForAttributes(String attName, + List residues) { - List cms = chimeraMaps.get(pdbfile); - if (cms != null) + int featuresAdded = 0; + String featureGroup = getViewerFeatureGroup(); + + for (String residue : residues) { - StringBuilder sb = new StringBuilder(); - sb.append(" #" + cms.get(0).getModelNumber()); - sb.append(":" + pdbResNum); - if (!chain.equals(" ")) + AtomSpec spec = null; + String[] tokens = residue.split(" "); + if (tokens.length < 5) { - sb.append("." + chain); + continue; } - String atomSpec = sb.toString(); + String atomSpec = tokens[2]; + String attValue = tokens[4]; - StringBuilder command = new StringBuilder(32); - if (lastMousedOverAtomSpec != null) + /* + * ignore 'None' (e.g. for phi) or 'False' (e.g. for isHelix) + */ + if ("None".equalsIgnoreCase(attValue) + || "False".equalsIgnoreCase(attValue)) { - command.append("~show " + lastMousedOverAtomSpec + ";"); + continue; } - viewerCommandHistory(false); - command.append("show ").append(atomSpec); - String cmd = command.toString(); - if (cmd.length() > 0) + + try + { + spec = parseAtomSpec(atomSpec); + } catch (IllegalArgumentException e) { - viewer.stopListening(chimeraListener.getUri()); - viewer.sendChimeraCommand(cmd, false); - viewer.startListening(chimeraListener.getUri()); + Console.error("Problem parsing atomspec " + atomSpec); + continue; } - viewerCommandHistory(true); - this.lastMousedOverAtomSpec = atomSpec; - } - } - /** - * Query Chimera for its current selection, and highlight it on the alignment - */ - public void highlightChimeraSelection() - { - List selection = viewer.getSelectedResidueSpecs(); - // System.out.println("Chimera selection: " + selection.toString()); - - // TODO handle more than one!! - if (selection.size() > 0) - { - highlightChimeraSelection(selection); - } - } - - private void log(String message) - { - System.err.println("## Chimera log: " + message); - } - - private void viewerCommandHistory(boolean enable) - { - // log("(Not yet implemented) History " - // + ((debug || enable) ? "on" : "off")); - } - - /** - * Propagate atom selections from Chimera - * - * @param atoms - * for example "#0:70.A" (model/residue/chain) - */ - public void highlightChimeraSelection(List atoms) - { - List atomSpecs = new ArrayList(); - for (String atomSpec : atoms) - { - int hashPos = atomSpec.indexOf("#"); - int colonPos = atomSpec.indexOf(":"); - int dotPos = atomSpec.indexOf("."); - - if (colonPos == -1) + String chainId = spec.getChain(); + String description = attValue; + float score = Float.NaN; + try + { + score = Float.valueOf(attValue); + description = chainId; + } catch (NumberFormatException e) { - continue; // malformed + // was not a float value } - int pdbResNum = Integer.parseInt(dotPos == -1 ? atomSpec - .substring(colonPos) : atomSpec.substring(colonPos + 1, - dotPos)); - String chainId = dotPos == -1 ? "" : atomSpec.substring(dotPos + 1); - int modelId = 0; - try { - modelId = Integer.valueOf(atomSpec.substring(hashPos + 1, colonPos)); - } catch (NumberFormatException e) { - // ignore, default to model 0 - } + String pdbFile = getPdbFileForModel(spec.getModelNumber()); + spec.setPdbFile(pdbFile); + + List atoms = Collections.singletonList(spec); /* - * Work out the pdbfilename from the model number + * locate the mapped position in the alignment (if any) */ - String pdbfilename = modelFileNames[frameNo]; - findfileloop: for (String pdbfile : this.chimeraMaps.keySet()) + SearchResultsI sr = getSsm() + .findAlignmentPositionsForStructurePositions(atoms); + + /* + * expect one matched alignment position, or none + * (if the structure position is not mapped) + */ + for (SearchResultMatchI m : sr.getResults()) { - for (ChimeraModel cm : chimeraMaps.get(pdbfile)) + SequenceI seq = m.getSequence(); + int start = m.getStart(); + int end = m.getEnd(); + SequenceFeature sf = new SequenceFeature(attName, description, + start, end, score, featureGroup); + // todo: should SequenceFeature have an explicit property for chain? + // note: repeating the action shouldn't duplicate features + if (seq.addSequenceFeature(sf)) { - if (cm.getModelNumber() == modelId) - { - pdbfilename = pdbfile; - break findfileloop; - } + featuresAdded++; } } - atomSpecs.add(new AtomSpec(pdbfilename, chainId, pdbResNum, 0)); - } - if (!atomSpecs.isEmpty()) - { - getSsm().mouseOverStructure(atomSpecs); - } - } - - public long getLoadNotifiesHandled() - { - return loadNotifiesHandled; - } - - public void setJalviewColourScheme(ColourSchemeI cs) - { - colourBySequence = false; - - if (cs == null) - { - return; - } - - int index; - Color col; - // Chimera expects RBG values in the range 0-1 - final double normalise = 255D; - viewerCommandHistory(false); - // TODO: Switch between nucleotide or aa selection expressions - StringBuilder command = new StringBuilder(128); - command.append("color white;"); - for (String res : ResidueProperties.aa3Hash.keySet()) - { - index = ResidueProperties.aa3Hash.get(res).intValue(); - if (index > 20) - { - continue; - } - - col = cs.findColour(ResidueProperties.aa[index].charAt(0)); - command.append("color " + col.getRed() / normalise + "," - + col.getGreen() / normalise + "," + col.getBlue() - / normalise + " ::" + res + ";"); } - - evalStateCommand(command.toString(),false); - viewerCommandHistory(true); - } - - /** - * called when the binding thinks the UI needs to be refreshed after a Chimera - * state change. this could be because structures were loaded, or because an - * error has occurred. - */ - public abstract void refreshGUI(); - - public void setLoadingFromArchive(boolean loadingFromArchive) - { - this.loadingFromArchive = loadingFromArchive; + return featuresAdded; } /** + * Answers the feature group name to apply to features created in Jalview from + * Chimera attributes * - * @return true if Chimeral is still restoring state or loading is still going - * on (see setFinsihedLoadingFromArchive) - */ - public boolean isLoadingFromArchive() - { - return loadingFromArchive && !loadingFinished; - } - - /** - * modify flag which controls if sequence colouring events are honoured by the - * binding. Should be true for normal operation - * - * @param finishedLoading - */ - public void setFinishedLoadingFromArchive(boolean finishedLoading) - { - loadingFinished = finishedLoading; - } - - /** - * Send the Chimera 'background solid " command. - * - * @see https - * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background - * .html - * @param col + * @return */ - public void setBackgroundColour(Color col) + protected String getViewerFeatureGroup() { - viewerCommandHistory(false); - double normalise = 255D; - final String command = "background solid " + col.getRed() / normalise + "," - + col.getGreen() / normalise + "," + col.getBlue() - / normalise + ";"; - viewer.sendChimeraCommand(command, false); - viewerCommandHistory(true); + // todo pull up to interface + return CHIMERA_FEATURE_GROUP; } - /** - * - * @param pdbfile - * @return text report of alignment between pdbfile and any associated - * alignment sequences - */ - public String printMapping(String pdbfile) + @Override + public String getModelIdForFile(String pdbFile) { - return getSsm().printMapping(pdbfile); + List foundModels = chimeraMaps.get(pdbFile); + if (foundModels != null && !foundModels.isEmpty()) + { + return String.valueOf(foundModels.get(0).getModelNumber()); + } + return ""; } /** - * Ask Chimera to save its session to the given file. Returns true if - * successful, else false. + * Answers a (possibly empty) list of attribute names in Chimera[X], excluding + * any which were added from Jalview * - * @param filepath * @return */ - public boolean saveSession(String filepath) + public List getChimeraAttributes() { - if (isChimeraRunning()) + List attributes = new ArrayList<>(); + StructureCommandI command = getCommandGenerator().listResidueAttributes(); + final List reply = executeCommand(command, true); + if (reply != null) { - List reply = viewer.sendChimeraCommand("save " + filepath, - true); - if (reply.contains("Session written")) + for (String inputLine : reply) { - return true; - } - else - { - Cache.log - .error("Error saving Chimera session: " + reply.toString()); + String[] lineParts = inputLine.split("\\s"); + if (lineParts.length == 2 && lineParts[0].equals("resattr")) + { + String attName = lineParts[1]; + /* + * exclude attributes added from Jalview + */ + if (!attName.startsWith(ChimeraCommands.NAMESPACE_PREFIX)) + { + attributes.add(attName); + } + } } } - return false; + return attributes; } /** - * Ask Chimera to open a session file. Returns true if successful, else false. - * The filename must have a .py extension for this command to work. + * Returns the file extension to use for a saved viewer session file (.py) * - * @param filepath * @return */ - public boolean openSession(String filepath) + @Override + public String getSessionFileExtension() { - evalStateCommand("open " + filepath, true); - // todo: test for failure - how? - return true; + return CHIMERA_SESSION_EXTENSION; } - public boolean isFinishedInit() + @Override + public String getHelpURL() { - return finishedInit; + return "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide"; } - - public void setFinishedInit(boolean finishedInit) - { - this.finishedInit = finishedInit; - } - - public List getChainNames() - { - return chainNames; - } - }