/**
* Annotate the residues with their corresponding positions in s1 using the
* alignment in as
- *
+ * NOTE: This clears all atom.alignmentMapping values on the structure.
* @param as
* @param s1
*/
{
int pdbpos = as.getSeq2Start() - 2;
int alignpos = s1.getStart() + as.getSeq1Start() - 3;
-
+ // first clear out any old alignmentMapping values:
+ for (Atom atom: (Vector<Atom>) atoms) {
+ atom.alignmentMapping=-1;
+ }
+ // and now trace the alignment onto the atom set.
for (int i = 0; i < as.astr1.length(); i++)
{
if (as.astr1.charAt(i) != '-')