a few changes to chimera classes

[mothur.git] / database.hpp

diff --git a/database.hpp b/database.hpp
index e497fa42fea869d84502387638279a8a9896bbab..f52cdd58be86d31be87951df68d13983dc9bc921 100644 (file)
--- a/database.hpp
+++ b/database.hpp
@@ -10,14 +10,55 @@
  *
  */
 
+
+/* This class is a parent to blastdb, kmerdb, suffixdb.  */
+
+#include "mothur.h"
+#include "sequence.hpp"
+
+/**************************************************************************************************/
+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);
-       virtual Sequence* findClosestSequence(Sequence*) = 0;
+       Database();
+       virtual ~Database();
+       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;    }
+       virtual vector<int> getSequencesWithKmer(int){ vector<int> filler; return filler; };  
+       virtual int getMaxKmer(){       return 1;       };
+
        
 protected:
-       int numSeqs;
-       vector<Sequence*> templateSequences;    
+       int numSeqs, longest;
+       float searchScore;
 };
-
+/**************************************************************************************************/
 #endif