string candAln = alignment->getSeqAAln();
string tempAln = alignment->getSeqBAln();
-
+
if(candAln == ""){
candidateSeq->setPairwise("");
candidateSeq->setPairwise(candAln); // set the pairwise sequences in the Sequence objects for
templateSeq->setPairwise(tempAln); // the candidate and template sequences
+
}
catch(exception& e) {
m->errorOut(e, "Nast", "pairwiseAlignSeqs");
// here we do steps C-F of Fig. 2 from DeSantis et al.
try {
-
- //cout << candAln << endl;
- //cout << tempAln << endl;
- //cout << newTemplateAlign << endl;
- //cout << endl;
int longAlignmentLength = newTemplateAlign.length();