+ return chainNames;
+ }
+
+ /**
+ * Send a 'focus' command to Chimera to recentre the visible display
+ */
+ public void focusView()
+ {
+ sendChimeraCommand("focus", false);
+ }
+
+ /**
+ * 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<Integer> 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
+ *
+ * @param avp
+ * @return
+ */
+ public int sendFeaturesToViewer(AlignmentViewPanel avp)
+ {
+ // TODO refactor as required to pull up to an interface
+ AlignmentI alignment = avp.getAlignment();
+
+ String[] files = getStructureFiles();
+ if (files == null)
+ {
+ return 0;
+ }
+
+ StructureMappingcommandSet commandSet = ChimeraCommands
+ .getSetAttributeCommandsForFeatures(getSsm(), files,
+ getSequence(), avp);
+ String[] commands = commandSet.commands;
+ if (commands.length > 10)
+ {
+ sendCommandsByFile(commands);
+ }
+ else
+ {
+ for (String command : commands)
+ {
+ sendAsynchronousCommand(command, null);
+ }
+ }
+ return commands.length;
+ }
+
+ /**
+ * 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
+ */
+ protected void sendCommandsByFile(String[] commands)
+ {
+ try
+ {
+ File tmp = File.createTempFile("chim", ".com");
+ tmp.deleteOnExit();
+ PrintWriter out = new PrintWriter(new FileOutputStream(tmp));
+ for (String command : commands)
+ {
+ out.println(command);
+ }
+ out.flush();
+ out.close();
+ String path = tmp.getAbsolutePath();
+ sendAsynchronousCommand("open cmd:" + path, null);
+ } catch (IOException e)
+ {
+ System.err.println("Sending commands to Chimera via file failed with "
+ + e.getMessage());
+ }
+ }
+
+ /**
+ * 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<String> residues = sendChimeraCommand(cmd, true);
+
+ boolean featureAdded = createFeaturesForAttributes(attName, residues);
+ if (featureAdded)
+ {
+ alignmentPanel.getFeatureRenderer().featuresAdded();
+ }
+ }
+
+ /**
+ * Create features in Jalview for the given attribute name and structure
+ * residues.
+ *
+ * <pre>
+ * The residue list should be 0, 1 or more reply lines of the format:
+ * residue id #0:5.A isHelix -155.000836316 index 5
+ * or
+ * residue id #0:6.A isHelix None
+ * </pre>
+ *
+ * @param attName
+ * @param residues
+ * @return
+ */
+ protected boolean createFeaturesForAttributes(String attName,
+ List<String> residues)
+ {
+ boolean featureAdded = false;
+ String featureGroup = getViewerFeatureGroup();
+
+ for (String residue : residues)