*/
#include "mothur.h"
+#include "database.hpp"
class KmerDB : public Database {
public:
KmerDB(string, int);
- Sequence* findClosestSequence(Sequence*);
-
+ KmerDB();
+ ~KmerDB();
+
+ void generateDB();
+ void addSequence(Sequence);
+ vector<int> findClosestSequences(Sequence*, int);
+ void readKmerDB(ifstream&);
+ int getCount(int); //returns number of sequences with that kmer number
+ vector<int> getSequencesWithKmer(int); //returns vector of sequences that contain kmer passed in
+ int getReversed(int); //returns reverse compliment kmerNumber
+ int getMaxKmer() { return maxKmer; }
+
private:
- void generateKmerDB(string);
- void readKmerDB(string, ifstream&);
+
int kmerSize;
- int maxKmer;
+ int maxKmer, count;
+ string kmerDBName;
vector<vector<int> > kmerLocations;
};