// float getAlignmentScore();
string getSeqAAln();
string getSeqBAln();
+ map<int, int> getSeqAAlnBaseMap();
+ map<int, int> getSeqBAlnBaseMap();
int getCandidateStartPos();
int getCandidateEndPos();
int getTemplateStartPos();
int pairwiseLength;
int nRows, nCols, lA, lB;
vector<vector<AlignmentCell> > alignment;
+ map<int, int> ABaseMap;
+ map<int, int> BBaseMap;
+ MothurOut* m;
};
/**************************************************************************************************/