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