*
*/
+
+/* 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 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){return results;}
+ 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;
+ MothurOut* m;
+ int numSeqs, longest;
+ float searchScore;
+ vector<int> results;
};
-
+/**************************************************************************************************/
#endif