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
- // 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
- alignment[0][i].cValue = 0; // and the score to zero
- }
+ 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
+ alignment[0][i].cValue = 0; // and the score to zero
+ }
+
+ for(int i=1;i<nRows;i++){
+ alignment[i][0].prevCell = 'u'; // initialize first column by pointing all poiters upwards
+ alignment[i][0].cValue = 0; // and the score to zero
+ }
- for(int i=1;i<nRows;i++){
- alignment[i][0].prevCell = 'u'; // initialize first column by pointing all poiters upwards
- alignment[i][0].cValue = 0; // and the score to zero
}
+ catch(exception& e) {
+ errorOut(e, "NeedlemanOverlap", "NeedlemanOverlap");
+ exit(1);
+ }
+
+
}
-
/**************************************************************************************************/
NeedlemanOverlap::~NeedlemanOverlap(){ /* do nothing */ }
/**************************************************************************************************/
void NeedlemanOverlap::align(string A, string B){
-
- 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
-
- 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;
-
- 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';
- }
- }
- else{
- if(up >= left){
- alignment[i][j].cValue = up;
- alignment[i][j].prevCell = 'u';
+ 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("Your one of your candidate sequences is longer than you longest template sequence."); 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;
+
+ 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';
+ }
}
else{
- alignment[i][j].cValue = left;
- alignment[i][j].prevCell = 'l';
+ if(up >= left){
+ alignment[i][j].cValue = up;
+ alignment[i][j].prevCell = 'u';
+ }
+ else{
+ alignment[i][j].cValue = left;
+ alignment[i][j].prevCell = 'l';
+ }
}
}
}
+ 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) {
+ errorOut(e, "NeedlemanOverlap", "align");
+ exit(1);
}
- 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
+
}
/**************************************************************************************************/
projects / mothur.git / blobdiff