fixed bug with shhh.flow from file path name in write functions, added "smart" featur...

[mothur.git] / database.hpp

diff --git a/database.hpp b/database.hpp
index a31075b4fddd46ec6d02d32186723a0608b7784d..b2817a779dc1b95070ef77fbe6e8bf5b11159a3c 100644 (file)
--- a/database.hpp
+++ b/database.hpp
@@ -45,26 +45,28 @@ class Database {
 
 public:
        Database();
+       Database(const Database& db) : numSeqs(db.numSeqs), longest(db.longest), searchScore(db.searchScore), results(db.results), Scores(db.Scores) { m = MothurOut::getInstance(); }
        virtual ~Database();
        virtual void generateDB() = 0; 
        virtual void addSequence(Sequence) = 0;  //add sequence to search engine
        virtual string getName(int) { return ""; }  
        virtual vector<int> findClosestSequences(Sequence*, int) = 0;  // returns indexes of n closest sequences to query
-       virtual vector<int> findClosestMegaBlast(Sequence*, int){return results;}
+       virtual vector<int> findClosestMegaBlast(Sequence*, int, int){return results;}
        virtual float getSearchScore();
-       virtual vector<float> getMegaBlastSearchScores() { return megaScores; } //assumes you already called findClosestMegaBlast
+       virtual vector<float> getSearchScores() { return Scores; } //assumes you already called findClosestMegaBlast
        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;       };
+       virtual int getReversed(int) { return 0; } 
+       virtual int getMaxKmer(){       return 1;       }
        
 protected:
        MothurOut* m;
        int numSeqs, longest;
        float searchScore;
        vector<int> results;
-       vector<float> megaScores;
+       vector<float> Scores;
 };
 /**************************************************************************************************/
 #endif