started work on classify.seqs command. changed the database class so that it does...

[mothur.git] / database.hpp

diff --git a/database.hpp b/database.hpp
index 01393c130adb3250ffaf5c9ed97fd8a2d4043c1e..01916d1924bb86466798dc2667f83aaeda174c3d 100644 (file)
--- a/database.hpp
+++ b/database.hpp
@@ -11,24 +11,51 @@
  */
 
 
-/* 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(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 vector<int> findClosestSequences(Sequence*, int) = 0;  // returns indexes of n closest sequences to query
        virtual float getSearchScore();
        virtual int getLongestBase(); 
+       virtual void readKmerDB(ifstream&){};
+       virtual void setNumSeqs(int i) {        numSeqs = i;    }
        
 protected:
        int numSeqs, longest;
        float searchScore;
-       vector<Sequence> templateSequences;
 };
-
+/**************************************************************************************************/
 #endif