X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=a292e881efa3d124f970ebdc8cb0ed712638eb30;hb=8a2a0cda7067530f8481c2aec203e18d555f2dfd;hp=487e93b26a5b2f01590f73414a910761f68a4ee9;hpb=663e58dcf0754621ce271a657da649fae653ba35;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 487e93b..a292e88 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; @@ -78,11 +76,13 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel String lastHighlightCommand; /** - * Returns a model of the structure positions described by the Chimera format atomspec + * Returns a model of the structure positions described by the Chimera format + * atomspec + * * @param atomSpec * @return */ - protected AtomSpec parseAtomSpec(String atomSpec) + protected AtomSpec parseAtomSpec(String atomSpec) { return AtomSpec.fromChimeraAtomspec(atomSpec); } @@ -90,8 +90,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel /** * 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 @@ -182,8 +182,11 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { 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()); + chimeraManager = chimeraX + ? new ChimeraXManager(new StructureManager(true)) + : new ChimeraManager(new StructureManager(true)); + setStructureCommands( + chimeraX ? new ChimeraXCommands() : new ChimeraCommands()); } @Override @@ -193,8 +196,8 @@ 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() { @@ -204,7 +207,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel startListening(chimeraListener.getUri()); } catch (BindException e) { - System.err.println( + jalview.bin.Console.errPrintln( "Failed to start Chimera listener: " + e.getMessage()); } } @@ -222,7 +225,7 @@ 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 @@ -313,7 +316,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel @Override public boolean isViewerRunning() { - return chimeraManager.isChimeraLaunched(); + return chimeraManager != null && chimeraManager.isChimeraLaunched(); } /** @@ -334,13 +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; @@ -359,8 +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) @@ -394,13 +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); @@ -418,19 +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; } /** @@ -442,45 +468,56 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * Ask Chimera for its current selection */ StructureCommandI command = getCommandGenerator().getSelectedResidues(); - List chimeraReply = executeCommand(command, true); - List selectedResidues = new ArrayList<>(); - if (chimeraReply != null) + + Runnable action = new Runnable() { - /* - * 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) + @Override + public void run() { - String[] inputLineParts = inputLine.split("\\s+"); - if (inputLineParts.length >= 5) + List chimeraReply = executeCommand(command, true); + + List selectedResidues = new ArrayList<>(); + if (chimeraReply != null) { - selectedResidues.add(inputLineParts[2]); + /* + * 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); + /* + * 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(X) 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 @@ -499,7 +536,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel atomSpecs.add(spec); } catch (IllegalArgumentException e) { - Cache.log.error("Failed to parse atomspec: " + atomSpec); + Console.error("Failed to parse atomspec: " + atomSpec); } } return atomSpecs; @@ -531,7 +568,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel private void log(String message) { - System.err.println("## Chimera log: " + message); + jalview.bin.Console.errPrintln("## Chimera log: " + message); } /** @@ -559,18 +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 */ @@ -590,10 +624,10 @@ 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 " + jalview.bin.Console.errPrintln("Sending commands to Chimera via file failed with " + e.getMessage()); } } @@ -601,6 +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() @@ -654,7 +689,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel spec = parseAtomSpec(atomSpec); } catch (IllegalArgumentException e) { - Cache.log.error("Problem parsing atomspec " + atomSpec); + Console.error("Problem parsing atomspec " + atomSpec); continue; } @@ -735,7 +770,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel public List getChimeraAttributes() { List attributes = new ArrayList<>(); - StructureCommandI command = getCommandGenerator().listResidueAttributes(); + StructureCommandI command = getCommandGenerator() + .listResidueAttributes(); final List reply = executeCommand(command, true); if (reply != null) {