modified trim.seqs to account for primers of different lengths

[mothur.git] / blastdb.hpp

diff --git a/blastdb.hpp b/blastdb.hpp
index fea55c8256e561af5477356b3c5bc545b30d6960..d61aaecb5e0712b47458e000416b881719cc7e65 100644 (file)
--- a/blastdb.hpp
+++ b/blastdb.hpp
@@ -18,13 +18,19 @@ class BlastDB : public Database {
 
 public:
        BlastDB(float, float, float, float);
+       BlastDB();
        ~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);
+       
+       #ifdef USE_MPI  
+       int MPISend(int); //just sends gapOpen, gapExtend, match and mismatch
+       int MPIRecv(int);
+       #endif
+       
 private:
        string dbFileName;
        string queryFileName;