/**************************************************************************************************/
-GotohOverlap::GotohOverlap(float gO, float gE, float m, float mm, int r) :
- gapOpen(gO), gapExtend(gE), match(m), mismatch(mm), Alignment(r) {
+GotohOverlap::GotohOverlap(float gO, float gE, float f, float mm, int r) :
+ gapOpen(gO), gapExtend(gE), match(f), mismatch(mm), Alignment(r) {
- for(int i=1;i<nCols;i++){ // we initialize the dynamic programming matrix by setting the pointers in
- alignment[0][i].prevCell = 'l'; // the first row to the left
- alignment[0][i].cValue = 0;
- alignment[0][i].dValue = 0;
+ try {
+ for(int i=1;i<nCols;i++){ // we initialize the dynamic programming matrix by setting the pointers in
+ alignment[0][i].prevCell = 'l'; // the first row to the left
+ alignment[0][i].cValue = 0;
+ alignment[0][i].dValue = 0;
+ }
+
+ for(int i=1;i<nRows;i++){ // we initialize the dynamic programming matrix by setting the pointers in
+ alignment[i][0].prevCell = 'u'; // the first column upward
+ alignment[i][0].cValue = 0;
+ alignment[i][0].iValue = 0;
+ }
+
}
-
- for(int i=1;i<nRows;i++){ // we initialize the dynamic programming matrix by setting the pointers in
- alignment[i][0].prevCell = 'u'; // the first column upward
- alignment[i][0].cValue = 0;
- alignment[i][0].iValue = 0;
+ catch(exception& e) {
+ m->errorOut(e, "GotohOverlap", "GotohOverlap");
+ exit(1);
}
}
/**************************************************************************************************/
void GotohOverlap::align(string A, string B){
-
- seqA = ' ' + A; lA = seqA.length(); // the algorithm requires that the first character be a dummy value
- seqB = ' ' + B; lB = seqB.length(); // the algorithm requires that the first character be a dummy value
-
- for(int i=1;i<lB;i++){ // the recursion here is shown in Webb and Miller, Fig. 1A. Note that
- for(int j=1;j<lA;j++){ // if we need to conserve on space we should see Fig. 1B, which is linear
- // in space, which I think is unnecessary
- float diagonal;
- if(seqB[i] == seqA[j]) { diagonal = alignment[i-1][j-1].cValue + match; }
- else { diagonal = alignment[i-1][j-1].cValue + mismatch; }
-
- alignment[i][j].iValue = max(alignment[i][j-1].iValue, alignment[i][j-1].cValue + gapOpen) + gapExtend;
- alignment[i][j].dValue = max(alignment[i-1][j].dValue, alignment[i-1][j].cValue + gapOpen) + gapExtend;
-
- if(alignment[i][j].iValue > alignment[i][j].dValue){
- if(alignment[i][j].iValue > diagonal){
- alignment[i][j].cValue = alignment[i][j].iValue;
- alignment[i][j].prevCell = 'l';
+ try {
+ seqA = ' ' + A; lA = seqA.length(); // the algorithm requires that the first character be a dummy value
+ seqB = ' ' + B; lB = seqB.length(); // the algorithm requires that the first character be a dummy value
+
+ for(int i=1;i<lB;i++){ // the recursion here is shown in Webb and Miller, Fig. 1A. Note that
+ for(int j=1;j<lA;j++){ // if we need to conserve on space we should see Fig. 1B, which is linear
+ // in space, which I think is unnecessary
+ float diagonal;
+ if(seqB[i] == seqA[j]) { diagonal = alignment[i-1][j-1].cValue + match; }
+ else { diagonal = alignment[i-1][j-1].cValue + mismatch; }
+
+ alignment[i][j].iValue = max(alignment[i][j-1].iValue, alignment[i][j-1].cValue + gapOpen) + gapExtend;
+ alignment[i][j].dValue = max(alignment[i-1][j].dValue, alignment[i-1][j].cValue + gapOpen) + gapExtend;
+
+ if(alignment[i][j].iValue > alignment[i][j].dValue){
+ if(alignment[i][j].iValue > diagonal){
+ alignment[i][j].cValue = alignment[i][j].iValue;
+ alignment[i][j].prevCell = 'l';
+ }
+ else{
+ alignment[i][j].cValue = diagonal;
+ alignment[i][j].prevCell = 'd';
+ }
}
else{
- alignment[i][j].cValue = diagonal;
- alignment[i][j].prevCell = 'd';
+ if(alignment[i][j].dValue > diagonal){
+ alignment[i][j].cValue = alignment[i][j].dValue;
+ alignment[i][j].prevCell = 'u';
+ }
+ else{
+ alignment[i][j].cValue = diagonal;
+ alignment[i][j].prevCell = 'd';
+ }
}
+
}
- else{
- if(alignment[i][j].dValue > diagonal){
- alignment[i][j].cValue = alignment[i][j].dValue;
- alignment[i][j].prevCell = 'u';
- }
- else{
- alignment[i][j].cValue = diagonal;
- alignment[i][j].prevCell = 'd';
- }
- }
-
}
+ Overlap over;
+ over.setOverlap(alignment, lA, lB, 0); // Fix the gaps at the ends of the sequences
+ traceBack(); // Construct the alignment and set seqAaln and seqBaln
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GotohOverlap", "align");
+ exit(1);
}
- Overlap over;
- over.setOverlap(alignment, lA, lB, 0); // Fix the gaps at the ends of the sequences
- traceBack(); // Construct the alignment and set seqAaln and seqBaln
}
/**************************************************************************************************/
projects / mothur.git / blobdiff