X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;fp=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=aebfede3de0d9ac0cc7379fde2b002b8f7912b5f;hb=afbff636fa2dfa01daa1f4ec4e8a936e61e3cf16;hp=7169fa2974379fd8460efc25495235d1b295a523;hpb=c6df3928336440918d23b4e7cb579f134e2f48dd;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 7169fa2..aebfede 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -36,7 +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.bin.Console; import jalview.datamodel.PDBEntry; import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResultsI; @@ -76,11 +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); } @@ -88,8 +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 @@ -180,8 +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 @@ -191,8 +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() { @@ -220,7 +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 @@ -311,7 +316,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel @Override public boolean isViewerRunning() { - return chimeraManager.isChimeraLaunched(); + return chimeraManager != null && chimeraManager.isChimeraLaunched(); } /** @@ -332,21 +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 (Cache.log.isDebugEnabled()) { - Cache.log.debug( - "Response from command ('" + cmd + "') was:\n" + lastReply); + if (Console.isDebugEnabled()) + { + Console.debug( + "Response from command ('" + cmd + "') was:\n" + lastReply); } } else { - if (Cache.log.isDebugEnabled()) + if (Console.isDebugEnabled()) { - Cache.log.debug("Command executed: " + cmd); + Console.debug("Command executed: " + cmd); } } @@ -366,8 +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) @@ -401,13 +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); @@ -437,15 +444,17 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel if (lastHighlightCommand != null) { cmd.insert(0, ";"); - cmd.insert(0,lastHighlightCommand); - cmd.insert(0,"~"); - + cmd.insert(0, lastHighlightCommand); + cmd.insert(0, "~"); + } - if (cmd.length()>0) { - executeCommand(true, null, new StructureCommand(cmd.toString())); + if (cmd.length() > 0) + { + executeCommand(true, null, new StructureCommand(cmd.toString())); } - - if (found) { + + if (found) + { this.lastHighlightCommand = command; } } @@ -459,14 +468,14 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * Ask Chimera for its current selection */ StructureCommandI command = getCommandGenerator().getSelectedResidues(); - + Runnable action = new Runnable() { @Override public void run() { List chimeraReply = executeCommand(command, true); - + List selectedResidues = new ArrayList<>(); if (chimeraReply != null) { @@ -500,15 +509,15 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * 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 @@ -527,7 +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; @@ -593,9 +602,9 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * 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 */ @@ -626,6 +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() @@ -679,7 +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; } @@ -760,7 +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) {