changing command name classify.shared to classifyrf.shared

[mothur.git] / database.hpp

diff --git a/database.hpp b/database.hpp
index 79050777acd7d695754d7a382741538d35409b94..49f39035e0aa95d6739616c0a6804858b53cdf9e 100644 (file)
--- 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 map<int, float> findClosest(Sequence*, int){ return results; }  // returns of n closest sequences to query and their search scores
+       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;
-       map<int, float> results;
+       vector<int> results;
+       vector<float> Scores;
 };
 /**************************************************************************************************/
 #endif