X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=database.hpp;h=49f39035e0aa95d6739616c0a6804858b53cdf9e;hp=7fd29b3ae4d09ede0d5227f639e1ea6308f778a0;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=9ada98592a54c82d08f3d46c9b1d8c3e472a922d

diff --git a/database.hpp b/database.hpp
index 7fd29b3..49f3903 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) {}
 };
 /**************************************************************************************************/
@@ -47,20 +48,24 @@ public:
 	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;
 	int numSeqs, longest;
 	float searchScore;
 	vector<int> results;
+	vector<float> Scores;
 };
 /**************************************************************************************************/
 #endif