X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=aebfede3de0d9ac0cc7379fde2b002b8f7912b5f;hb=51909770452369f94b4a0070482ab0acdd96fada;hp=bc4eef4914cf6a76223326be2b63c4097fbe964a;hpb=2fb924ec0d110eb3ca6c3fb06efa27acd34b2750;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index bc4eef4..aebfede 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -27,7 +27,6 @@ import java.io.PrintWriter; import java.net.BindException; import java.util.ArrayList; import java.util.Collections; -import java.util.Iterator; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; @@ -37,8 +36,7 @@ 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.Cache; -import jalview.datamodel.AlignmentI; +import jalview.bin.Console; import jalview.datamodel.PDBEntry; import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResultsI; @@ -78,10 +76,22 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel String lastHighlightCommand; /** + * Returns a model of the structure positions described by the Chimera format + * atomspec + * + * @param atomSpec + * @return + */ + 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 @@ -171,9 +181,12 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel DataSourceType protocol) { super(ssm, pdbentry, sequenceIs, protocol); - chimeraManager = new ChimeraManager(new StructureManager(true)); - chimeraManager.setChimeraX(ViewerType.CHIMERAX.equals(getViewerType())); - setStructureCommands(new ChimeraCommands()); + 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 @@ -183,15 +196,15 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * 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); - chimeraManager.startListening(chimeraListener.getUri()); + startListening(chimeraListener.getUri()); } catch (BindException e) { System.err.println( @@ -212,6 +225,17 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel 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; } @@ -292,7 +316,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel @Override public boolean isViewerRunning() { - return chimeraManager.isChimeraLaunched(); + return chimeraManager != null && chimeraManager.isChimeraLaunched(); } /** @@ -313,13 +337,23 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel 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); + List lastReply = chimeraManager.sendChimeraCommand(cmd, + getResponse); if (getResponse) { reply = lastReply; - Cache.log.debug( - "Response from command ('" + cmd + "') was:\n" + lastReply); + if (Console.isDebugEnabled()) + { + Console.debug( + "Response from command ('" + cmd + "') was:\n" + lastReply); + } + } + else + { + if (Console.isDebugEnabled()) + { + Console.debug("Command executed: " + cmd); + } } return reply; @@ -338,8 +372,9 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * 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. + * 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) @@ -373,13 +408,13 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel first = false; if (forChimeraX) { - cmd.append(cms.get(0).getModelNumber()) - .append("/").append(chain).append(":").append(pdbResNum); + cmd.append(cms.get(0).getModelNumber()).append("/").append(chain) + .append(":").append(pdbResNum); } else { - cmd.append(cms.get(0).getModelNumber()) - .append(":").append(pdbResNum); + cmd.append(cms.get(0).getModelNumber()).append(":") + .append(pdbResNum); if (!chain.equals(" ") && !forChimeraX) { cmd.append(".").append(chain); @@ -397,19 +432,31 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { return; } - + if (!found) + { + // not a valid residue label command, so clear + cmd.setLength(0); + } /* - * unshow the label for the previous residue + * prepend with command + * to unshow the label for the previous residue */ if (lastHighlightCommand != null) { - chimeraManager.sendChimeraCommand("~" + lastHighlightCommand, false); + cmd.insert(0, ";"); + cmd.insert(0, lastHighlightCommand); + cmd.insert(0, "~"); + + } + if (cmd.length() > 0) + { + executeCommand(true, null, new StructureCommand(cmd.toString())); } + if (found) { - chimeraManager.sendChimeraCommand(command, false); + this.lastHighlightCommand = command; } - this.lastHighlightCommand = command; } /** @@ -420,25 +467,57 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel /* * Ask Chimera for its current selection */ - List selection = chimeraManager.getSelectedResidueSpecs(); + StructureCommandI command = getCommandGenerator().getSelectedResidues(); - /* - * 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( - selection); + Runnable action = new Runnable() + { + @Override + public void run() + { + List chimeraReply = executeCommand(command, true); - /* - * Broadcast the selection (which may be empty, if the user just cleared all - * selections) - */ - getSsm().mouseOverStructure(atomSpecs); + 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(); } /** - * Converts a list of Chimera atomspecs to a list of AtomSpec representing the - * corresponding residues (if any) in Jalview + * Converts a list of Chimera(X) atomspecs to a list of AtomSpec representing + * the corresponding residues (if any) in Jalview * * @param structureSelection * @return @@ -446,19 +525,18 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel protected List convertStructureResiduesToAlignment( List structureSelection) { - boolean chimeraX = chimeraManager.isChimeraX(); List atomSpecs = new ArrayList<>(); for (String atomSpec : structureSelection) { try { - AtomSpec spec = AtomSpec.fromChimeraAtomspec(atomSpec, chimeraX); + AtomSpec spec = parseAtomSpec(atomSpec); String pdbfilename = getPdbFileForModel(spec.getModelNumber()); spec.setPdbFile(pdbfilename); atomSpecs.add(spec); } catch (IllegalArgumentException e) { - Cache.log.error("Failed to parse atomspec: " + atomSpec); + Console.error("Failed to parse atomspec: " + atomSpec); } } return atomSpecs; @@ -494,34 +572,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * Send a 'show' command for all atoms in the currently selected columns - * - * TODO: pull up to abstract structure viewer interface - * - * @param vp - */ - public void highlightSelection(AlignmentViewPanel vp) - { - List cols = vp.getAlignViewport().getColumnSelection() - .getSelected(); - AlignmentI alignment = vp.getAlignment(); - StructureSelectionManager sm = getSsm(); - for (SequenceI seq : alignment.getSequences()) - { - /* - * convert selected columns into sequence positions - */ - int[] positions = new int[cols.size()]; - int i = 0; - for (Integer col : cols) - { - positions[i++] = seq.findPosition(col); - } - sm.highlightStructure(this, seq, positions); - } - } - - /** * Constructs and send commands to Chimera to set attributes on residues for * features visible in Jalview. *

@@ -546,18 +596,15 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } else { - for (StructureCommandI command : commands) - { - sendAsynchronousCommand(command, null); - } + executeCommands(commands, false, null); } return commands.size(); } /** - * 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. + * 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 */ @@ -577,7 +624,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel String path = tmp.getAbsolutePath(); StructureCommandI command = getCommandGenerator() .openCommandFile(path); - sendAsynchronousCommand(command, null); + executeCommand(false, null, command); } catch (IOException e) { System.err.println("Sending commands to Chimera via file failed with " @@ -588,6 +635,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel /** * Returns the file extension required for a file of commands to be read by * the structure viewer + * * @return */ protected String getCommandFileExtension() @@ -596,36 +644,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * Get Chimera residues which have the named attribute, find the mapped - * positions in the Jalview sequence(s), and set as sequence features - * - * @param attName - * @param alignmentPanel - */ - public void copyStructureAttributesToFeatures(String attName, - AlignmentViewPanel alignmentPanel) - { - // todo pull up to AAStructureBindingModel (and interface?) - - /* - * ask Chimera to list residues with the attribute, reporting its value - */ - // this alternative command - // list residues spec ':*/attName' attr attName - // doesn't report 'None' values (which is good), but - // fails for 'average.bfactor' (which is bad): - - String cmd = "list residues attr '" + attName + "'"; - List residues = executeCommand(new StructureCommand(cmd), true); - - boolean featureAdded = createFeaturesForAttributes(attName, residues); - if (featureAdded) - { - alignmentPanel.getFeatureRenderer().featuresAdded(); - } - } - - /** * Create features in Jalview for the given attribute name and structure * residues. * @@ -638,14 +656,13 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * * @param attName * @param residues - * @return + * @return the number of features added */ - protected boolean createFeaturesForAttributes(String attName, + protected int createFeaturesForAttributes(String attName, List residues) { - boolean featureAdded = false; + int featuresAdded = 0; String featureGroup = getViewerFeatureGroup(); - boolean chimeraX = chimeraManager.isChimeraX(); for (String residue : residues) { @@ -669,10 +686,10 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel try { - spec = AtomSpec.fromChimeraAtomspec(atomSpec, chimeraX); + spec = parseAtomSpec(atomSpec); } catch (IllegalArgumentException e) { - System.err.println("Problem parsing atomspec " + atomSpec); + Console.error("Problem parsing atomspec " + atomSpec); continue; } @@ -712,10 +729,13 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel start, end, score, featureGroup); // todo: should SequenceFeature have an explicit property for chain? // note: repeating the action shouldn't duplicate features - featureAdded |= seq.addSequenceFeature(sf); + if (seq.addSequenceFeature(sf)) + { + featuresAdded++; + } } } - return featureAdded; + return featuresAdded; } /** @@ -749,19 +769,29 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ public List getChimeraAttributes() { - List atts = chimeraManager.getAttrList(); - Iterator it = atts.iterator(); - while (it.hasNext()) + List attributes = new ArrayList<>(); + StructureCommandI command = getCommandGenerator() + .listResidueAttributes(); + final List reply = executeCommand(command, true); + if (reply != null) { - if (it.next().startsWith(ChimeraCommands.NAMESPACE_PREFIX)) + for (String inputLine : reply) { - /* - * attribute added from Jalview - exclude it - */ - it.remove(); + 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 atts; + return attributes; } /**