X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=399bad9d9c9d7cd0982644529885594e7bedea43;hb=b7cd96eaeb85474ee2ddec1de92181a3b88ceece;hp=b20f135c926adeb7da6c05dedd0e4670e0e12795;hpb=4994aa94fd62af0058f2db96f0ea6c4ca1abe80b;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index b20f135..399bad9 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; @@ -224,10 +222,11 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /* - * the following call should not be needed but is temporarily included, - * to avoid a stack trace error in Chimera after "stop really" is sent + * 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) + if (closeChimera && (getViewerType() == ViewerType.CHIMERA)) { chimeraManager.getChimeraProcess().destroy(); } @@ -312,7 +311,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel @Override public boolean isViewerRunning() { - return chimeraManager.isChimeraLaunched(); + return chimeraManager!=null && chimeraManager.isChimeraLaunched(); } /** @@ -338,8 +337,17 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel 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; @@ -417,19 +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; } /** @@ -441,40 +459,51 @@ 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(); } /** @@ -498,7 +527,7 @@ 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; @@ -534,34 +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. *

@@ -586,10 +587,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } else { - for (StructureCommandI command : commands) - { - sendAsynchronousCommand(command, null); - } + executeCommands(commands, false, null); } return commands.size(); } @@ -617,7 +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 " @@ -636,36 +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. * @@ -678,12 +646,12 @@ 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(); for (String residue : residues) @@ -711,7 +679,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel spec = parseAtomSpec(atomSpec); } catch (IllegalArgumentException e) { - System.err.println("Problem parsing atomspec " + atomSpec); + Console.error("Problem parsing atomspec " + atomSpec); continue; } @@ -751,10 +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; } /** @@ -788,19 +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; } /**