if (getResponse)
{
reply = lastReply;
- Cache.log.debug(
- "Response from command ('" + cmd + "') was:\n" + lastReply);
+ if (Cache.log.isDebugEnabled()) {
+ Cache.log.debug(
+ "Response from command ('" + cmd + "') was:\n" + lastReply);
+ }
}
return reply;
* Ask Chimera for its current selection
*/
StructureCommandI command = getCommandGenerator().getSelectedResidues();
- List<String> chimeraReply = executeCommand(command, true);
- List<String> 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<String> chimeraReply = executeCommand(command, true);
+
+ List<String> 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<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(
- selectedResidues);
-
- /*
- * Broadcast the selection (which may be empty, if the user just cleared all
- * selections)
- */
- getSsm().mouseOverStructure(atomSpecs);
+ /*
+ * 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<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(
+ selectedResidues);
+
+ /*
+ * Broadcast the selection (which may be empty, if the user just cleared all
+ * selections)
+ */
+ getSsm().mouseOverStructure(atomSpecs);
+
+ }
+ };
+ new Thread(action).start();
}
/**
}
/**
- * 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.
* <p>