X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=database.hpp;h=b2817a779dc1b95070ef77fbe6e8bf5b11159a3c;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=f9c0c4878c31a67e2df415387f5ee5cf3bbda939;hpb=0571957d68cbbc0e425af1db8e808f826010b9e2;p=mothur.git

diff --git a/database.hpp b/database.hpp
index f9c0c48..b2817a7 100644
--- a/database.hpp
+++ b/database.hpp
@@ -45,19 +45,21 @@ 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> 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;