added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff...

[mothur.git] / database.hpp

diff --git a/database.hpp b/database.hpp
index 79050777acd7d695754d7a382741538d35409b94..efc7ba7f111d956c31d20626d825c079cf7963c8 100644 (file)
--- a/database.hpp
+++ b/database.hpp
@@ -48,19 +48,24 @@ public:
        virtual void generateDB() = 0; 
        virtual void addSequence(Sequence) = 0;  //add sequence to search engine
        virtual vector<int> findClosestSequences(Sequence*, int) = 0;  // returns indexes of n closest sequences to query
-       virtual map<int, float> findClosest(Sequence*, int){ return results; }  // returns of n closest sequences to query and their search scores
+       virtual vector<int> findClosestMegaBlast(Sequence*, int){return results;}
        virtual float getSearchScore();
        virtual int getLongestBase(); 
        virtual void readKmerDB(ifstream&){};
        virtual void setNumSeqs(int i) {        numSeqs = i;    }
        virtual vector<int> getSequencesWithKmer(int){ vector<int> filler; return filler; };  
        virtual int getMaxKmer(){       return 1;       };
-
+       
+       #ifdef USE_MPI  
+       virtual int MPISend(int) = 0;
+       virtual int MPIRecv(int) = 0;
+       #endif
        
 protected:
+       MothurOut* m;
        int numSeqs, longest;
        float searchScore;
-       map<int, float> results;
+       vector<int> results;
 };
 /**************************************************************************************************/
 #endif