X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=database.hpp;h=49f39035e0aa95d6739616c0a6804858b53cdf9e;hp=9293f13d5f091251d77115d2f3dc5344868d2c5c;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=050220fe7822cc660615972a0054cf4a83eefbe4

diff --git a/database.hpp b/database.hpp
index 9293f13..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) {}
 };
 /**************************************************************************************************/
@@ -49,19 +50,22 @@ public:
 	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