added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / database.hpp

diff --git a/database.hpp b/database.hpp
index f52cdd58be86d31be87951df68d13983dc9bc921..b2817a779dc1b95070ef77fbe6e8bf5b11159a3c 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) {}
 };
 /**************************************************************************************************/
@@ -44,21 +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 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