changes for chimera slayer

[mothur.git] / blastdb.hpp

diff --git a/blastdb.hpp b/blastdb.hpp
index f0f17f9ce58bc8ee2b466cc9be6b95ddf53e207a..9b8965d017b69a8f8cf27884261ea1095f77e176 100644 (file)
--- a/blastdb.hpp
+++ b/blastdb.hpp
@@ -12,26 +12,31 @@
  */
 
 #include "mothur.h"
-#include "globaldata.hpp"
 
 class BlastDB : public Database {
+
 public:
-       BlastDB(string, float, float, float, float);
+       BlastDB(float, float, float, float);
+       BlastDB();
        ~BlastDB();
-       Sequence findClosestSequence(Sequence*);
-
+       
+       void generateDB();
+       void addSequence(Sequence);
+       vector<int> findClosestSequences(Sequence*, int);
+       vector<int> findClosestMegaBlast(Sequence*, int, int);
+       
 private:
        string dbFileName;
        string queryFileName;
        string blastFileName;
        string path;
        
+       int count;
        float gapOpen;
        float gapExtend;
        float match;
        float misMatch;
-       Sequence emptySequence;
-       GlobalData* globaldata;
+       
 };
 
 #endif