X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=399bad9d9c9d7cd0982644529885594e7bedea43;hb=b7cd96eaeb85474ee2ddec1de92181a3b88ceece;hp=cb2a9ca3b225f67189c446dfacc2b9388877bd84;hpb=c66902a9536b10a5477b58aaf7c2d75772890a5d;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index cb2a9ca..399bad9 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,29 +20,13 @@ */ package jalview.ext.rbvi.chimera; -import jalview.api.AlignmentViewPanel; -import jalview.api.FeatureRenderer; -import jalview.api.SequenceRenderer; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.io.AppletFormatAdapter; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.ResidueProperties; -import jalview.structure.StructureMapping; -import jalview.structure.StructureMappingcommandSet; -import jalview.structure.StructureSelectionManager; -import jalview.structures.models.AAStructureBindingModel; -import jalview.util.Comparison; -import jalview.util.MessageManager; - -import java.awt.Color; -import java.awt.event.ComponentEvent; 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.Enumeration; -import java.util.HashMap; +import java.util.Collections; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; @@ -51,137 +35,103 @@ 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.bin.Console; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SearchResultMatchI; +import jalview.datamodel.SearchResultsI; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.gui.StructureViewer.ViewerType; +import jalview.httpserver.AbstractRequestHandler; +import jalview.io.DataSourceType; +import jalview.structure.AtomSpec; +import jalview.structure.AtomSpecModel; +import jalview.structure.StructureCommand; +import jalview.structure.StructureCommandI; +import jalview.structure.StructureSelectionManager; +import jalview.structures.models.AAStructureBindingModel; 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"; - private ChimeraManager viewer; - - /** - * 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. + /* + * Object through which we talk to Chimera */ - private boolean loadingFromArchive = false; + private ChimeraManager chimeraManager; - /** - * second flag to indicate if the Chimera viewer should ignore sequence - * colouring events from the structure manager because the GUI is still - * setting up + /* + * Object which listens to Chimera notifications */ - private boolean loadingFinished = true; + private AbstractRequestHandler chimeraListener; - /** - * state flag used to check if the Chimera viewer's paint method can be called + /* + * Map of ChimeraModel objects keyed by PDB full local file name */ - private boolean finishedInit = false; + protected Map> chimeraMaps = new LinkedHashMap<>(); - public boolean isFinishedInit() - { - return finishedInit; - } - - public void setFinishedInit(boolean finishedInit) - { - this.finishedInit = finishedInit; - } - - boolean allChainsSelected = false; + String lastHighlightCommand; /** - * when true, try to search the associated datamodel for sequences that are - * associated with any unknown structures in the Chimera view. + * Returns a model of the structure positions described by the Chimera format atomspec + * @param atomSpec + * @return */ - private boolean associateNewStructs = false; - - List atomsPicked = new ArrayList(); - - public List chainNames; - - private Map chainFile; - - StringBuffer eval = new StringBuffer(); - - public String fileLoadingError; - - private Map> chimmaps = new LinkedHashMap>(); - - private List mdlToFile = new ArrayList(); + protected AtomSpec parseAtomSpec(String atomSpec) + { + return AtomSpec.fromChimeraAtomspec(atomSpec); + } /** - * the default or current model displayed if the model cannot be identified - * from the selection message + * 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. + * + * @param pe + * @return */ - int frameNo = 0; - - String lastCommand; - - String lastMessage; - - boolean loadedInline; - public boolean openFile(PDBEntry pe) { String file = pe.getFile(); try { - List oldList = viewer.getModelList(); - viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL); - List newList = viewer.getModelList(); - if (oldList.size() < newList.size()) + List modelsToMap = new ArrayList<>(); + List oldList = chimeraManager.getModelList(); + boolean alreadyOpen = false; + + /* + * If Chimera already has this model, don't reopen it, but do remap it. + */ + for (ChimeraModel open : oldList) { - while (oldList.size() > 0) + if (open.getModelName().equals(pe.getId())) { - oldList.remove(0); - newList.remove(0); - } - chimmaps.put(file, newList); - for (ChimeraModel cm : newList) - { - while (mdlToFile.size() < 1 + cm.getModelNumber()) - { - mdlToFile.add(new String("")); - } - mdlToFile.set(cm.getModelNumber(), file); + alreadyOpen = true; + modelsToMap.add(open); } + } - File fl = new File(file); - String protocol = AppletFormatAdapter.URL; - try - { - if (fl.exists()) - { - protocol = AppletFormatAdapter.FILE; - } - } catch (Exception e) - { - } catch (Error e) - { - } - // Explicitly map to the filename used by Chimera ; - // pdbentry[pe].getFile(), protocol); + /* + * If Chimera doesn't yet have this model, ask it to open it, and retrieve + * the model name(s) added by Chimera. + */ + if (!alreadyOpen) + { + chimeraManager.openModel(file, pe.getId(), ModelType.PDB_MODEL); + addChimeraModel(pe, modelsToMap); + } - if (getSsm() != null) - { - getSsm().addStructureViewerListener(this); - // ssm.addSelectionListener(this); - FeatureRenderer fr = getFeatureRenderer(null); - if (fr != null) - { - fr.featuresAdded(); - } - refreshGUI(); - } - return true; + chimeraMaps.put(file, modelsToMap); + + if (getSsm() != null) + { + getSsm().addStructureViewerListener(this); } + return true; } catch (Exception q) { log("Exception when trying to open model " + file + "\n" @@ -192,14 +142,29 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * current set of model filenames loaded + * Adds the ChimeraModel corresponding to the given PDBEntry, based on model + * name matching PDB id + * + * @param pe + * @param modelsToMap */ - String[] modelFileNames = null; - - - StringBuffer resetLastRes = new StringBuffer(); - - private List lastReply; + 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 @@ -207,1081 +172,631 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * @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()); } - /** - * Constructor - * - * @param ssm - * @param theViewer - */ - public JalviewChimeraBinding(StructureSelectionManager ssm, - ChimeraManager theViewer) + @Override + protected ViewerType getViewerType() { - super(ssm, null); - viewer = theViewer; - csm = viewer.getStructureManager(); + return ViewerType.CHIMERA; } /** - * Construct a title string for the viewer window based on the data Jalview - * knows about - * - * @param verbose - * @return + * Start a dedicated HttpServer to listen for Chimera notifications, and tell it + * to start listening */ - public String getViewerTitle(boolean verbose) + public void startChimeraListener() { - return getViewerTitle("Chimera", verbose); + try + { + chimeraListener = new ChimeraListener(this); + startListening(chimeraListener.getUri()); + } catch (BindException e) + { + System.err.println( + "Failed to start Chimera listener: " + e.getMessage()); + } } /** - * prepare the view for a given set of models/chains. chainList contains - * strings of the form 'pdbfilename:Chaincode' - * - * @param toshow - * list of chains to make visible + * Close down the Jalview viewer and listener, and (optionally) the associated + * Chimera window. */ - public void centerViewer(List toshow) + @Override + public void closeViewer(boolean closeChimera) { - StringBuilder cmd = new StringBuilder(64); - int mlength, p; - for (String lbl : toshow) + super.closeViewer(closeChimera); + if (this.chimeraListener != null) { - 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 "); + chimeraListener.shutdown(); + chimeraListener = null; } - if (cmd.length() > 0) + + /* + * 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)) { - cmd.setLength(cmd.length() - 4); + chimeraManager.getChimeraProcess().destroy(); } - String cmdstring = cmd.toString(); - evalStateCommand("~display #*; ~ribbon #*; ribbon " + cmdstring - + ";focus " + cmdstring, false); + + chimeraManager.clearOnChimeraExit(); + chimeraManager = null; } /** - * Close down the Jalview viewer, and (optionally) the associated Chimera - * window. + * 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 pdbfnum + * @return */ - public void closeViewer(boolean closeChimera) + protected String getModelSpec(int pdbfnum) { - getSsm().removeStructureViewerListener(this, this.getPdbFile()); - if (closeChimera) + if (pdbfnum < 0 || pdbfnum >= getPdbCount()) { - viewer.exitChimera(); + return "#" + pdbfnum; // temp hack for ChimeraX } - 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); + /* + * 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" : ""); } /** - * superpose the structures associated with sequences in the alignment - * according to their corresponding positions. + * Launch Chimera, unless an instance linked to this object is already + * running. Returns true if Chimera is successfully launched, or already + * running, else false. + * + * @return */ - public void superposeStructures(AlignmentI alignment) + public boolean launchChimera() { - superposeStructures(alignment, -1, null); + if (chimeraManager.isChimeraLaunched()) + { + return true; + } + + boolean launched = chimeraManager.launchChimera(getChimeraPaths()); + if (launched) + { + startExternalViewerMonitor(chimeraManager.getChimeraProcess()); + } + else + { + log("Failed to launch Chimera!"); + } + return launched; } /** - * superpose the structures associated with sequences in the alignment - * according to their corresponding positions. ded) + * Returns a list of candidate paths to the Chimera program executable * - * @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) + protected List getChimeraPaths() { - superposeStructures(alignment, refStructure, 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) - * @param hiddenCols - * TODO + * @return */ - public void superposeStructures(AlignmentI alignment, int refStructure, - ColumnSelection hiddenCols) + @Override + public boolean isViewerRunning() { - superposeStructures(new AlignmentI[] - { alignment }, new int[] - { refStructure }, new ColumnSelection[] - { hiddenCols }); + return chimeraManager!=null && chimeraManager.isChimeraLaunched(); } - public void superposeStructures(AlignmentI[] _alignment, - int[] _refStructure, ColumnSelection[] _hiddenCols) + /** + * Send a command to Chimera, and optionally log and return any responses. + * + * @param command + * @param getResponse + */ + @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; - } + // ? thread running after viewer shut down + return null; + } + 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) + { + reply = lastReply; + if (Console.isDebugEnabled()) { + Console.debug( + "Response from command ('" + cmd + "') was:\n" + lastReply); } - // 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; } - refreshPdbEntries(); - StringBuffer selectioncom = new StringBuffer(); - for (int a = 0; a < _alignment.length; a++) + else { - int refStructure = _refStructure[a]; - AlignmentI alignment = _alignment[a]; - ColumnSelection hiddenCols = _hiddenCols[a]; - if (a > 0 - && selectioncom.length() > 0 - && !selectioncom.substring(selectioncom.length() - 1).equals( - " ")) + if (Console.isDebugEnabled()) { - selectioncom.append(" "); + Console.debug("Command executed: " + cmd); } - // process this alignment - if (refStructure >= files.length) - { - System.err.println("Invalid reference structure value " - + refStructure); - refStructure = -1; - } - if (refStructure < -1) - { - refStructure = -1; - } - - 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(csm.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 - */ - public boolean isChimeraRunning() - { - return viewer.isChimeraLaunched(); - } - - /** - * Send a command to Chimera, and optionally log any responses. - * - * @param command - * @param logResponse + * Query Chimera for its current selection, and highlight it on the alignment */ - public void evalStateCommand(final String command, boolean logResponse) + public void highlightChimeraSelection() { - viewerCommandHistory(false); - checkLaunched(); - if (lastCommand == null || !lastCommand.equals(command)) + /* + * Ask Chimera for its current selection + */ + StructureCommandI command = getCommandGenerator().getSelectedResidues(); + + Runnable action = new Runnable() { -// Thread t = new Thread(new Runnable() -// { -// @Override -// public void run() -// { - // trim command or it may never find a match in the replyLog!! - lastReply = viewer.sendChimeraCommand(command.trim(), logResponse); - if (debug && logResponse) + @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) { - log("Response from command ('" + command + "') was:\n" - + lastReply); + String[] inputLineParts = inputLine.split("\\s+"); + if (inputLineParts.length >= 5) + { + selectedResidues.add(inputLineParts[2]); + } } -// } -// }); - // TODO - use j7/8 thread management -// try -// { -// t.join(); -// } catch (InterruptedException foo) -// { -// } -// ; - } - viewerCommandHistory(true); - lastCommand = command; + } + + /* + * 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(); } /** - * colour any structures associated with sequences in the given alignment - * using the getFeatureRenderer() and getSequenceRenderer() renderers but only - * if colourBySequence is enabled. + * Converts a list of Chimera(X) atomspecs to a list of AtomSpec representing the + * corresponding residues (if any) in Jalview + * + * @param structureSelection + * @return */ - public void colourBySequence(boolean showFeatures, - jalview.api.AlignmentViewPanel alignmentv) + protected List convertStructureResiduesToAlignment( + List structureSelection) { - if (!colourBySequence || !loadingFinished) - { - 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)) + List atomSpecs = new ArrayList<>(); + for (String atomSpec : structureSelection) { - for (String command : cpdbbyseq.commands) + try + { + AtomSpec spec = parseAtomSpec(atomSpec); + String pdbfilename = getPdbFileForModel(spec.getModelNumber()); + spec.setPdbFile(pdbfilename); + atomSpecs.add(spec); + } catch (IllegalArgumentException e) { - executeWhenReady(command); + Console.error("Failed to parse atomspec: " + atomSpec); } } + return atomSpecs; } /** - * @param files - * @param sr - * @param fr - * @param alignment + * @param modelId * @return */ - protected StructureMappingcommandSet[] getColourBySequenceCommands( - String[] files, SequenceRenderer sr, FeatureRenderer fr, - AlignmentI alignment) + protected String getPdbFileForModel(int modelId) { - return ChimeraCommands - .getColourBySequenceCommand(getSsm(), files, getSequence(), sr, - fr, - alignment); - } - - /** - * @param command - */ - protected void executeWhenReady(String command) - { - waitForChimera(); - evalStateCommand(command, false); - waitForChimera(); - } - - private void waitForChimera() - { - while (viewer != null && viewer.isBusy()) + /* + * Work out the pdbfilename from the model number + */ + String pdbfilename = modelFileNames[0]; + findfileloop: for (String pdbfile : this.chimeraMaps.keySet()) { - try { - Thread.sleep(15); - } catch (InterruptedException q) - {} + for (ChimeraModel cm : chimeraMaps.get(pdbfile)) + { + if (cm.getModelNumber() == modelId) + { + pdbfilename = pdbfile; + break findfileloop; + } + } } + return pdbfilename; } - - - // End StructureListener - // ////////////////////////// - - public Color getColour(int atomIndex, int pdbResNum, String chain, - String pdbfile) + private void log(String message) { - if (getModelNum(pdbfile) < 0) - { - return null; - } - log("get model / residue colour attribute unimplemented"); - return null; + System.err.println("## Chimera log: " + message); } /** - * returns the current featureRenderer that should be used to colour the - * structures - * - * @param alignment + * 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 */ - 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) + public int sendFeaturesToViewer(AlignmentViewPanel avp) { - String[] mfn = getPdbFile(); - if (mfn == null) + // TODO refactor as required to pull up to an interface + + Map> featureValues = buildFeaturesMap( + avp); + List commands = getCommandGenerator() + .setAttributes(featureValues); + if (commands.size() > 10) { - return -1; + sendCommandsByFile(commands); } - for (int i = 0; i < mfn.length; i++) + else { - if (mfn[i].equalsIgnoreCase(modelFileName)) - { - return i; - } + executeCommands(commands, false, null); } - return -1; + return commands.size(); } /** - * 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. + * 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. + * + * @param commands */ - private int _modelFileNameMap[]; - - // //////////////////////////////// - // /StructureListener - public synchronized String[] getPdbFile() + protected void sendCommandsByFile(List commands) { - if (viewer == null) + try { - return new String[0]; + File tmp = File.createTempFile("chim", getCommandFileExtension()); + tmp.deleteOnExit(); + PrintWriter out = new PrintWriter(new FileOutputStream(tmp)); + for (StructureCommandI command : commands) + { + out.println(command.getCommand()); + } + out.flush(); + out.close(); + String path = tmp.getAbsolutePath(); + StructureCommandI command = getCommandGenerator() + .openCommandFile(path); + executeCommand(false, null, command); + } catch (IOException e) + { + 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 chimmaps.keySet().toArray( - modelFileNames = new String[chimmaps.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 + * Create features in Jalview for the given attribute name and structure + * residues. * - * @param alignment + * 

      +   * 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
+   *
      * - * @return + * @param attName + * @param residues + * @return the number of features added */ - public abstract SequenceRenderer getSequenceRenderer( - AlignmentViewPanel alignment); - - // jmol/ssm only - public void highlightAtom(int atomIndex, int pdbResNum, String chain, - String pdbfile) + protected int createFeaturesForAttributes(String attName, + List residues) { - List cms = chimmaps.get(pdbfile); - if (cms != null) - { - int mdlNum = cms.get(0).getModelNumber(); + int featuresAdded = 0; + String featureGroup = getViewerFeatureGroup(); - viewerCommandHistory(false); - // viewer.stopListening(); - if (resetLastRes.length() > 0) + for (String residue : residues) + { + AtomSpec spec = null; + String[] tokens = residue.split(" "); + if (tokens.length < 5) { - eval.setLength(0); - eval.append(resetLastRes.toString() + ";"); + continue; } - - eval.append("display "); // +modelNum - - resetLastRes.setLength(0); - resetLastRes.append("~display "); + String atomSpec = tokens[2]; + String attValue = tokens[4]; + + /* + * ignore 'None' (e.g. for phi) or 'False' (e.g. for isHelix) + */ + if ("None".equalsIgnoreCase(attValue) + || "False".equalsIgnoreCase(attValue)) { - eval.append(" #" + (mdlNum)); - resetLastRes.append(" #" + (mdlNum)); + continue; } - // complete select string - eval.append(":" + pdbResNum); - resetLastRes.append(":" + pdbResNum); - if (!chain.equals(" ")) + try { - eval.append("." + chain); - resetLastRes.append("." + chain); - } - - viewer.sendChimeraCommand(eval.toString(), false); - viewerCommandHistory(true); - // viewer.startListening(); - } - } - - 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")); - } - - public void loadInline(String string) - { - loadedInline = true; - // TODO: re JAL-623 - // viewer.loadInline(strModel, isAppend); - // could do this: - // construct fake fullPathName and fileName so we can identify the file - // later. - // Then, construct pass a reader for the string to Jmol. - // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName, - // fileName, null, reader, false, null, null, 0); - // viewer.openStringInline(string); - log("cannot load inline in Chimera, yet"); - } - - public void mouseOverStructure(int atomIndex, String strInfo) - { - // function to parse a mouseOver event from Chimera - // - int pdbResNum; - int alocsep = strInfo.indexOf("^"); - int mdlSep = strInfo.indexOf("/"); - int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1; - - if (chainSeparator == -1) - { - chainSeparator = strInfo.indexOf("."); - if (mdlSep > -1 && mdlSep < chainSeparator) + spec = parseAtomSpec(atomSpec); + } catch (IllegalArgumentException e) { - chainSeparator1 = chainSeparator; - chainSeparator = mdlSep; + Console.error("Problem parsing atomspec " + atomSpec); + continue; } - } - // handle insertion codes - if (alocsep != -1) - { - pdbResNum = Integer.parseInt(strInfo.substring( - strInfo.indexOf("]") + 1, alocsep)); - - } - else - { - pdbResNum = Integer.parseInt(strInfo.substring( - strInfo.indexOf("]") + 1, chainSeparator)); - } - String chainId; - - if (strInfo.indexOf(":") > -1) - { - chainId = strInfo.substring(strInfo.indexOf(":") + 1, - strInfo.indexOf(".")); - } - else - { - chainId = " "; - } - String pdbfilename = modelFileNames[frameNo]; // default is first or current - // model - if (mdlSep > -1) - { - if (chainSeparator1 == -1) - { - chainSeparator1 = strInfo.indexOf(".", mdlSep); - } - String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1, - chainSeparator1) : strInfo.substring(mdlSep + 1); + String chainId = spec.getChain(); + String description = attValue; + float score = Float.NaN; try { - // recover PDB filename for the model hovered over. - int _mp = _modelFileNameMap.length - 1, mnumber = new Integer(mdlId) - .intValue() - 1; - while (mnumber < _modelFileNameMap[_mp]) - { - _mp--; - } - pdbfilename = modelFileNames[_mp]; - if (pdbfilename == null) - { - // pdbfilename = new File(viewer.getModelFileName(mnumber)) - // .getAbsolutePath(); - } - - } catch (Exception e) + score = Float.valueOf(attValue); + description = chainId; + } catch (NumberFormatException e) { + // was not a float value } - ; - } - if (lastMessage == null || !lastMessage.equals(strInfo)) - { - getSsm().mouseOverStructure(pdbResNum, chainId, pdbfilename); - } - lastMessage = strInfo; - } + String pdbFile = getPdbFileForModel(spec.getModelNumber()); + spec.setPdbFile(pdbFile); - public void notifyAtomPicked(int atomIndex, String strInfo, String strData) - { - /** - * this implements the toggle label behaviour copied from the original - * structure viewer, MCView - */ - if (strData != null) - { - System.err.println("Ignoring additional pick data string " + strData); - } - // rewrite these selections for chimera (DNA, RNA and protein) - int chainSeparator = strInfo.indexOf(":"); - int p = 0; - if (chainSeparator == -1) - { - chainSeparator = strInfo.indexOf("."); - } - - String picked = strInfo.substring(strInfo.indexOf("]") + 1, - chainSeparator); - String mdlString = ""; - if ((p = strInfo.indexOf(":")) > -1) - { - picked += strInfo.substring(p + 1, strInfo.indexOf(".")); - } + List atoms = Collections.singletonList(spec); - if ((p = strInfo.indexOf("/")) > -1) - { - mdlString += strInfo.substring(p, strInfo.indexOf(" #")); - } - picked = "((" + picked + ".CA" + mdlString + ")|(" + picked + ".P" - + mdlString + "))"; - viewerCommandHistory(false); + /* + * locate the mapped position in the alignment (if any) + */ + SearchResultsI sr = getSsm() + .findAlignmentPositionsForStructurePositions(atoms); - if (!atomsPicked.contains(picked)) - { - viewer.select(picked); - atomsPicked.add(picked); - } - else - { - viewer.select("not " + picked); - atomsPicked.remove(picked); - } - viewerCommandHistory(true); - // TODO: in application this happens - // - // if (scriptWindow != null) - // { - // scriptWindow.sendConsoleMessage(strInfo); - // scriptWindow.sendConsoleMessage("\n"); - // } - - } - - // incremented every time a load notification is successfully handled - - // lightweight mechanism for other threads to detect when they can start - // referring to new structures. - private long loadNotifiesHandled = 0; - - public long getLoadNotifiesHandled() - { - return loadNotifiesHandled; - } - - public void notifyFileLoaded(String fullPathName, String fileName2, - String modelName, String errorMsg, int modelParts) - { - if (errorMsg != null) - { - fileLoadingError = errorMsg; - refreshGUI(); - return; - } - // TODO: deal sensibly with models loaded inLine: - // modelName will be null, as will fullPathName. - - // the rest of this routine ignores the arguments, and simply interrogates - // the Jmol view to find out what structures it contains, and adds them to - // the structure selection manager. - fileLoadingError = null; - String[] oldmodels = modelFileNames; - modelFileNames = null; - chainNames = new ArrayList(); - chainFile = new HashMap(); - boolean notifyLoaded = false; - String[] modelfilenames = getPdbFile(); - // first check if we've lost any structures - if (oldmodels != null && oldmodels.length > 0) - { - int oldm = 0; - for (int i = 0; i < oldmodels.length; i++) - { - for (int n = 0; n < modelfilenames.length; n++) - { - if (modelfilenames[n] == oldmodels[i]) - { - oldmodels[i] = null; - break; - } - } - if (oldmodels[i] != null) - { - oldm++; - } - } - if (oldm > 0) + /* + * expect one matched alignment position, or none + * (if the structure position is not mapped) + */ + for (SearchResultMatchI m : sr.getResults()) { - String[] oldmfn = new String[oldm]; - oldm = 0; - for (int i = 0; i < oldmodels.length; i++) + 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 (oldmodels[i] != null) - { - oldmfn[oldm++] = oldmodels[i]; - } + featuresAdded++; } - // deregister the Jmol instance for these structures - we'll add - // ourselves again at the end for the current structure set. - getSsm().removeStructureViewerListener(this, oldmfn); - } - } - - // register ourselves as a listener and notify the gui that it needs to - // update itself. - getSsm().addStructureViewerListener(this); - - if (notifyLoaded) - { - FeatureRenderer fr = getFeatureRenderer(null); - if (fr != null) - { - fr.featuresAdded(); } - refreshGUI(); - loadNotifiesHandled++; } - setLoadingFromArchive(false); - } - - public void setJalviewColourScheme(ColourSchemeI cs) - { - colourBySequence = false; - - if (cs == null) - { - return; - } - - String res; - 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 - Enumeration en = ResidueProperties.aa3Hash.keys(); - StringBuilder command = new StringBuilder(128); - command.append("color white;"); - while (en.hasMoreElements()) - { - res = en.nextElement().toString(); - index = ((Integer) 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) + * @return */ - public boolean isLoadingFromArchive() + protected String getViewerFeatureGroup() { - return loadingFromArchive && !loadingFinished; + // todo pull up to interface + return CHIMERA_FEATURE_GROUP; } - /** - * 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) + @Override + public String getModelIdForFile(String pdbFile) { - loadingFinished = finishedLoading; + List foundModels = chimeraMaps.get(pdbFile); + if (foundModels != null && !foundModels.isEmpty()) + { + return String.valueOf(foundModels.get(0).getModelNumber()); + } + return ""; } /** - * Send the Chimera 'background solid " command. + * Answers a (possibly empty) list of attribute names in Chimera[X], excluding + * any which were added from Jalview * - * @see https - * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background - * .html - * @param col + * @return */ - public void setBackgroundColour(Color col) + public List getChimeraAttributes() { - 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); + List attributes = new ArrayList<>(); + StructureCommandI command = getCommandGenerator().listResidueAttributes(); + final List reply = executeCommand(command, true); + if (reply != null) + { + for (String inputLine : reply) + { + 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 attributes; } /** + * Returns the file extension to use for a saved viewer session file (.py) * - * @param pdbfile - * @return text report of alignment between pdbfile and any associated - * alignment sequences + * @return */ - public String printMapping(String pdbfile) + @Override + public String getSessionFileExtension() { - return getSsm().printMapping(pdbfile); + return CHIMERA_SESSION_EXTENSION; } - /** - * Ask Chimera to save its session to the given file. Returns true if - * successful, else false. - * - * @param filepath - * @return - */ - public boolean saveSession(String filepath) + @Override + public String getHelpURL() { - if (isChimeraRunning()) - { - List reply = viewer.sendChimeraCommand("save " + filepath, - true); - System.out.println(reply); - } - return false; + return "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide"; } - }