X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=d2c991f6ec51796b64b48a968c0ace50a30a93b4;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;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..d2c991f 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; @@ -38,7 +37,6 @@ 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.datamodel.PDBEntry; import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResultsI; @@ -78,6 +76,16 @@ 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 @@ -171,9 +179,9 @@ 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 @@ -191,7 +199,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel try { chimeraListener = new ChimeraListener(this); - chimeraManager.startListening(chimeraListener.getUri()); + startListening(chimeraListener.getUri()); } catch (BindException e) { System.err.println( @@ -212,6 +220,17 @@ 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; } @@ -318,8 +337,17 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel if (getResponse) { reply = lastReply; - Cache.log.debug( - "Response from command ('" + cmd + "') was:\n" + lastReply); + if (Cache.isDebugEnabled()) { + Cache.debug( + "Response from command ('" + cmd + "') was:\n" + lastReply); + } + } + else + { + if (Cache.isDebugEnabled()) + { + Cache.debug("Command executed: " + cmd); + } } return reply; @@ -397,19 +425,29 @@ 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 (found) - { - chimeraManager.sendChimeraCommand(command, false); + if (cmd.length()>0) { + executeCommand(true, null, new StructureCommand(cmd.toString())); + } + + if (found) { + this.lastHighlightCommand = command; } - this.lastHighlightCommand = command; } /** @@ -420,24 +458,56 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel /* * Ask Chimera for its current selection */ - List selection = chimeraManager.getSelectedResidueSpecs(); + 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( - selection); + /* + * 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); + /* + * 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 + * Converts a list of Chimera(X) atomspecs to a list of AtomSpec representing the * corresponding residues (if any) in Jalview * * @param structureSelection @@ -446,19 +516,18 @@ 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); + Cache.error("Failed to parse atomspec: " + atomSpec); } } return atomSpecs; @@ -494,34 +563,6 @@ 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. *

@@ -546,10 +587,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } else { - for (StructureCommandI command : commands) - { - sendAsynchronousCommand(command, null); - } + executeCommands(commands, false, null); } return commands.size(); } @@ -577,7 +615,7 @@ 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 " @@ -596,36 +634,6 @@ 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 +646,13 @@ 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 +676,10 @@ 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); + Cache.error("Problem parsing atomspec " + atomSpec); continue; } @@ -712,10 +719,13 @@ 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 +759,28 @@ 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; } /**