a few modifications for 1.9

[mothur.git] / blastdb.hpp

diff --git a/blastdb.hpp b/blastdb.hpp
index a952897f05e496e09a6faaacf7c4de97d49bd132..d61aaecb5e0712b47458e000416b881719cc7e65 100644 (file)
--- a/blastdb.hpp
+++ b/blastdb.hpp
@@ -12,23 +12,37 @@
  */
 
 #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);
+       
+       #ifdef USE_MPI  
+       int MPISend(int); //just sends gapOpen, gapExtend, match and mismatch
+       int MPIRecv(int);
+       #endif
+       
 private:
        string dbFileName;
        string queryFileName;
        string blastFileName;
+       string path;
        
+       int count;
        float gapOpen;
        float gapExtend;
        float match;
        float misMatch;
-       Sequence* emptySequence;
+       GlobalData* globaldata;
 };
 
 #endif