* As of 12/18/08 these included alignments based on blastn, needleman-wunsch, and the Gotoh algorithms
*
*/
-using namespace std;
#include "mothur.h"
#include "alignmentcell.hpp"
public:
Alignment(int);
Alignment();
+ virtual ~Alignment();
virtual void align(string, string) = 0;
- float getAlignmentScore();
+
+// float getAlignmentScore();
string getSeqAAln();
string getSeqBAln();
int getCandidateStartPos();
int getCandidateEndPos();
int getTemplateStartPos();
int getTemplateEndPos();
-
+
int getPairwiseLength();
+ void resize(int);
+ int getnRows() { return nRows; }
// int getLongestTemplateGap();
protected:
int pairwiseLength;
int nRows, nCols, lA, lB;
vector<vector<AlignmentCell> > alignment;
+ MothurOut* m;
};
/**************************************************************************************************/