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: