*/
#include "mothur.h"
+#include "globaldata.hpp"
class BlastAlignment : public Alignment {
BlastAlignment(float, float, float, float);
~BlastAlignment();
void align(string, string);
+ void setMatrix(int){};
+
private:
string candidateFileName;
string templateFileName;
string blastFileName;
+ string path;
void setPairwiseSeqs();
float match;
float mismatch;
float gapOpen;
float gapExtend;
+ GlobalData* globaldata;
};