+ }
+
+ Overlap over;
+ over.setOverlap(alignment, lA, lB, 0); // Fix gaps at the beginning and end of the sequences
+ traceBack(); // Traceback the alignment to populate seqAaln and seqBaln
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NeedlemanOverlap", "align");
+ exit(1);
+ }
+
+}
+/**************************************************************************************************/
+
+void NeedlemanOverlap::alignPrimer(string A, string B){
+ try {
+
+ seqA = ' ' + A; lA = seqA.length(); // algorithm requires a dummy space at the beginning of each string
+ seqB = ' ' + B; lB = seqB.length(); // algorithm requires a dummy space at the beginning of each string
+
+ if (lA > nRows) { m->mothurOut("One of your candidate sequences is longer than you longest template sequence. Your longest template sequence is " + toString(nRows) + ". Your candidate is " + toString(lA) + "."); m->mothurOutEndLine(); }
+
+ for(int i=1;i<lB;i++){ // This code was largely translated from Perl code provided in Ex 3.1
+
+ for(int j=1;j<lA;j++){ // of the O'Reilly BLAST book. I found that the example output had a
+
+ // number of errors
+ float diagonal;
+ if(isEquivalent(seqB[i],seqA[j])) { diagonal = alignment[i-1][j-1].cValue + match; }
+ else { diagonal = alignment[i-1][j-1].cValue + mismatch; }
+
+ float up = alignment[i-1][j].cValue + gap;
+ float left = alignment[i][j-1].cValue + gap;
+
+ if(diagonal >= up){
+ if(diagonal >= left){
+ alignment[i][j].cValue = diagonal;
+ alignment[i][j].prevCell = 'd';
+ }
+ else{
+ alignment[i][j].cValue = left;
+ alignment[i][j].prevCell = 'l';
+ }