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> 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 getMaxKmer(){ return 1; }
protected:
MothurOut* m;
int numSeqs, longest;
float searchScore;
vector<int> results;
+ vector<float> Scores;
};
/**************************************************************************************************/
#endif