public:
KmerDB(string, int);
+ KmerDB();
~KmerDB();
- Sequence findClosestSequence(Sequence*);
-
+
+ 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 getMaxKmer() { return maxKmer; }
+
private:
- void generateKmerDB(string);
- void readKmerDB(string, ifstream&);
+
int kmerSize;
- int maxKmer;
+ int maxKmer, count;
+ string kmerDBName;
vector<vector<int> > kmerLocations;
};