*/
#include "mothur.h"
-#include "globaldata.hpp"
class BlastDB : public Database {
+
public:
- BlastDB(string, float, float, float, float);
+ BlastDB(string, float, float, float, float, string, int);
+ BlastDB(string, int);
~BlastDB();
- Sequence* findClosestSequence(Sequence*);
-
+
+ void generateDB();
+ void addSequence(Sequence);
+ vector<int> findClosestSequences(Sequence*, int);
+ vector<int> findClosestMegaBlast(Sequence*, int, int);
+
private:
+
+ string scrubName(string);
+
string dbFileName;
string queryFileName;
string blastFileName;
string path;
+ int count, threadID;
float gapOpen;
float gapExtend;
float match;
float misMatch;
- Sequence* emptySequence;
- GlobalData* globaldata;
+
};
#endif