/**************************************************************************************************/
-NeedlemanOverlap::NeedlemanOverlap(float gO, float m, float mm, int r) :// note that we don't have a gap extend
-gap(gO), match(m), mismatch(mm), Alignment(r) { // the gap openning penalty is assessed for
+NeedlemanOverlap::NeedlemanOverlap(float gO, float f, float mm, int r) :// note that we don't have a gap extend
+gap(gO), match(f), mismatch(mm), Alignment(r) { // the gap openning penalty is assessed for
try { // every gapped position
for(int i=1;i<nCols;i++){
alignment[0][i].prevCell = 'l'; // initialize first row by pointing all poiters to the left
}
catch(exception& e) {
- errorOut(e, "NeedlemanOverlap", "NeedlemanOverlap");
+ m->errorOut(e, "NeedlemanOverlap", "NeedlemanOverlap");
exit(1);
}
}
void NeedlemanOverlap::align(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) { 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) + "."); mothurOutEndLine(); }
+ 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(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;
}
catch(exception& e) {
- errorOut(e, "NeedlemanOverlap", "align");
+ m->errorOut(e, "NeedlemanOverlap", "align");
exit(1);
}