X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=database.hpp;h=b2817a779dc1b95070ef77fbe6e8bf5b11159a3c;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=01916d1924bb86466798dc2667f83aaeda174c3d;hpb=63e089e0b3aad1741bab60119ed7ccc784dce347;p=mothur.git

diff --git a/database.hpp b/database.hpp
index 01916d1..b2817a7 100644
--- a/database.hpp
+++ b/database.hpp
@@ -20,6 +20,7 @@
 struct seqMatch {  //used to select top n matches
 		int seq;
 		int match;
+		seqMatch() {}
 		seqMatch(int s, int m) : seq(s), match(m) {}
 };
 /**************************************************************************************************/
@@ -44,18 +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, 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 getReversed(int) { return 0; } 
+	virtual int getMaxKmer(){	return 1;	}
 	
 protected:
+	MothurOut* m;
 	int numSeqs, longest;
 	float searchScore;
+	vector<int> results;
+	vector<float> Scores;
 };
 /**************************************************************************************************/
 #endif