changing command name classify.shared to classifyrf.shared

[mothur.git] / database.hpp

diff --git a/database.hpp b/database.hpp
index 02cad03d0e34e33fac8324541266758d91f8693d..49f39035e0aa95d6739616c0a6804858b53cdf9e 100644 (file)
--- a/database.hpp
+++ b/database.hpp
@@ -11,22 +11,61 @@
  */
 
 
-/* This class is a parent to blastdb, distancedb, kmerdb, suffixdb.  Which are used to convert a squencedb object into that form. */
+/* This class is a parent to blastdb, kmerdb, suffixdb.  */
 
 #include "mothur.h"
+#include "sequence.hpp"
 
-class Sequence;
+/**************************************************************************************************/
+struct seqMatch {  //used to select top n matches
+               int seq;
+               int match;
+               seqMatch() {}
+               seqMatch(int s, int m) : seq(s), match(m) {}
+};
+/**************************************************************************************************/
+inline bool compareSeqMatches (seqMatch member, seqMatch member2){ //sorts largest to smallest
+       if(member.match > member2.match){
+               return true;   }   
+       else{
+               return false; 
+       }
+}
+/**************************************************************************************************/
+inline bool compareSeqMatchesReverse (seqMatch member, seqMatch member2){ //sorts largest to smallest
+       if(member.match < member2.match){
+               return true;   }   
+       else{
+               return false; 
+       }
+}
 
+/**************************************************************************************************/
 class Database {
+
 public:
-       Database(string);
+       Database();
        virtual ~Database();
-       virtual Sequence findClosestSequence(Sequence*) = 0;
+       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:
-       int numSeqs;
+       MothurOut* m;
+       int numSeqs, longest;
        float searchScore;
-       vector<Sequence> templateSequences;
+       vector<int> results;
+       vector<float> Scores;
 };
-
+/**************************************************************************************************/
 #endif