X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=a82eecbcf52a91bb96b9f9bc07794308e262482f;hb=fc3c0910b7086411d72104c0a2cf4b8b45a95015;hp=3553d68777c715eb7057080529d9ad77f90607f7;hpb=42f4227ed213d422a87d3b22fc9e85d14ffaf53f;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 3553d68..a82eecb 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -20,24 +20,6 @@ */ package jalview.ext.rbvi.chimera; -import jalview.api.AlignmentViewPanel; -import jalview.api.structures.JalviewStructureDisplayI; -import jalview.bin.Cache; -import jalview.datamodel.AlignmentI; -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.StructureCommand; -import jalview.structure.StructureCommandI; -import jalview.structure.StructureSelectionManager; -import jalview.structures.models.AAStructureBindingModel; - import java.io.File; import java.io.FileOutputStream; import java.io.IOException; @@ -45,7 +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; @@ -54,19 +35,28 @@ 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_FEATURE_GROUP = "Chimera"; - - // Chimera clause to exclude alternate locations in atom selection - private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9"; - - private static final boolean debug = false; + public static final String CHIMERA_SESSION_EXTENSION = ".py"; - private static final String PHOSPHORUS = "P"; - - private static final String ALPHACARBON = "CA"; + public static final String CHIMERA_FEATURE_GROUP = "Chimera"; /* * Object through which we talk to Chimera @@ -85,13 +75,23 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel String lastHighlightCommand; - private Thread chimeraMonitor; + /** + * 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 @@ -181,9 +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 @@ -193,49 +196,18 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * Starts a thread that waits for the Chimera process to finish, so that we can - * then close the associated resources. This avoids leaving orphaned Chimera - * viewer panels in Jalview if the user closes Chimera. - */ - protected void startChimeraProcessMonitor() - { - final Process p = chimeraManager.getChimeraProcess(); - chimeraMonitor = new Thread(new Runnable() - { - - @Override - public void run() - { - try - { - p.waitFor(); - JalviewStructureDisplayI display = getViewer(); - if (display != null) - { - display.closeViewer(false); - } - } catch (InterruptedException e) - { - // exit thread if Chimera Viewer is closed in Jalview - } - } - }); - chimeraMonitor.start(); - } - - /** - * 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( + jalview.bin.Console.errPrintln( "Failed to start Chimera listener: " + e.getMessage()); } } @@ -244,25 +216,28 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * Close down the Jalview viewer and listener, and (optionally) the associated * Chimera window. */ + @Override public void closeViewer(boolean closeChimera) { - getSsm().removeStructureViewerListener(this, this.getStructureFiles()); - if (closeChimera) - { - chimeraManager.exitChimera(); - } + super.closeViewer(closeChimera); if (this.chimeraListener != null) { chimeraListener.shutdown(); chimeraListener = null; } - chimeraManager = null; - if (chimeraMonitor != 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)) { - chimeraMonitor.interrupt(); + chimeraManager.getChimeraProcess().destroy(); } - releaseUIResources(); + + chimeraManager.clearOnChimeraExit(); + chimeraManager = null; } /** @@ -313,7 +288,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel boolean launched = chimeraManager.launchChimera(getChimeraPaths()); if (launched) { - startChimeraProcessMonitor(); + startExternalViewerMonitor(chimeraManager.getChimeraProcess()); } else { @@ -338,9 +313,10 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * * @return */ - public boolean isChimeraRunning() + @Override + public boolean isViewerRunning() { - return chimeraManager.isChimeraLaunched(); + return chimeraManager != null && chimeraManager.isChimeraLaunched(); } /** @@ -361,14 +337,22 @@ 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; - if (debug) + if (Console.isDebugEnabled()) { - log("Response from command ('" + cmd + "') was:\n" + lastReply); + Console.debug( + "Response from command ('" + cmd + "') was:\n" + lastReply); + } + } + else + { + if (Console.isDebugEnabled()) + { + Console.debug("Command executed: " + cmd); } } @@ -388,8 +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) @@ -423,13 +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); @@ -447,19 +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; } /** @@ -470,25 +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 @@ -496,19 +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) { - System.err.println("Failed to parse atomspec: " + atomSpec); + Console.error("Failed to parse atomspec: " + atomSpec); } } return atomSpecs; @@ -540,90 +568,16 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel private void log(String message) { - System.err.println("## Chimera log: " + message); - } - - /** - * Ask Chimera to save its session to the given file. Returns true if - * successful, else false. - * - * @param filepath - * @return - */ - public boolean saveSession(String filepath) - { - if (isChimeraRunning()) - { - /* - * Chimera: https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/save.html - * ChimeraX: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html - */ - String command = getCommandGenerator().saveSession(filepath) - .getCommand(); - List reply = chimeraManager.sendChimeraCommand(command, true); - if (reply.contains("Session written")) - { - return true; - } - else - { - Cache.log - .error("Error saving Chimera session: " + reply.toString()); - } - } - return false; - } - - /** - * Ask Chimera to open a session file. Returns true if successful, else false. - * The filename must have a .py (Chimera) or .cxs (ChimeraX) extension for - * this command to work. - * - * @param filepath - * @return - */ - public boolean openSession(String filepath) - { - /* - * Chimera: https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/open.html - * ChimeraX: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html - */ - executeCommand(getCommandGenerator().loadFile(filepath), true); - // todo: test for failure - how? - return true; - } - - /** - * 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); - } + jalview.bin.Console.errPrintln("## Chimera log: " + message); } /** * Constructs and send commands to Chimera to set attributes on residues for - * features visible in Jalview + * 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 @@ -631,32 +585,26 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel public int sendFeaturesToViewer(AlignmentViewPanel avp) { // TODO refactor as required to pull up to an interface - String[] files = getStructureFiles(); - if (files == null) - { - return 0; - } + Map> featureValues = buildFeaturesMap( + avp); List commands = getCommandGenerator() - .setAttributesForFeatures(getSsm(), files, getSequence(), avp); + .setAttributes(featureValues); if (commands.size() > 10) { sendCommandsByFile(commands); } 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 */ @@ -676,17 +624,19 @@ 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 " - + e.getMessage()); + jalview.bin.Console.errPrintln( + "Sending commands to Chimera via file failed with " + + e.getMessage()); } } /** * Returns the file extension required for a file of commands to be read by * the structure viewer + * * @return */ protected String getCommandFileExtension() @@ -695,36 +645,6 @@ 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. * @@ -737,14 +657,13 @@ 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) { @@ -768,10 +687,10 @@ 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; } @@ -811,10 +730,13 @@ 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; } /** @@ -848,31 +770,43 @@ 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; } /** - * Returns the file extension to use for a saved viewer session file + * Returns the file extension to use for a saved viewer session file (.py) * * @return */ + @Override public String getSessionFileExtension() { - return ".py"; + return CHIMERA_SESSION_EXTENSION; } + @Override public String getHelpURL() { return "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide";