*/
String[] modelFileNames = null;
- String lastMousedOverAtomSpec;
+ String lastHighlightCommand;
private List<String> lastReply;
* Construct and send a command to highlight zero, one or more atoms.
*
* <pre>
- * Done by generating a command like (to 'highlight' position 44)
- * show #0:44.C
+ * Done by generating a command like (to 'highlight' positions 44 and 46)
+ * show #0:44,46.C
* </pre>
*/
@Override
{
return;
}
- StringBuilder atomSpecs = new StringBuilder();
+ StringBuilder cmd = new StringBuilder(128);
boolean first = true;
+ boolean found = false;
for (AtomSpec atom : atoms)
{
List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
if (cms != null && !cms.isEmpty())
{
- atomSpecs.append(first ? "" : ",");
+ if (first)
+ {
+ cmd.append("show #").append(cms.get(0).getModelNumber())
+ .append(":");
+ }
+ else
+ {
+ cmd.append(",");
+ }
first = false;
- atomSpecs.append(cms.get(0).getModelNumber());
- atomSpecs.append(":" + pdbResNum);
+ cmd.append(cms.get(0).getModelNumber()).append(":");
+ cmd.append(pdbResNum);
if (!chain.equals(" "))
{
- atomSpecs.append("." + chain);
+ cmd.append(".").append(chain);
}
+ found = true;
}
}
- String atomSpec = atomSpecs.toString();
+ String command = cmd.toString();
/*
* Avoid repeated commands for the same residue
*/
- if (atomSpec.equals(lastMousedOverAtomSpec))
+ if (command.equals(lastHighlightCommand))
{
return;
}
- StringBuilder command = new StringBuilder(32);
viewerCommandHistory(false);
- if (atomSpec.length() > 0)
+ if (found)
{
- command.append("show #").append(atomSpec);
viewer.sendChimeraCommand(command.toString(), false);
}
viewerCommandHistory(true);
- this.lastMousedOverAtomSpec = atomSpec;
+ this.lastHighlightCommand = command;
}
/**
{
sendChimeraCommand("focus", false);
}
+
+ /**
+ * Send a 'show' command for all atoms in the currently selected columns
+ *
+ * @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);
+ }
+ }
}