added modify names parameter to set.dir

[mothur.git] / kmerdb.hpp

diff --git a/kmerdb.hpp b/kmerdb.hpp
index 5019858dcf477c2e27bcc9ad3007617e26d3ce96..ead3d7e0b20d7b0ee070caebaad74aedeaae7dd3 100644 (file)
--- a/kmerdb.hpp
+++ b/kmerdb.hpp
@@ -20,19 +20,29 @@
  */
 
 #include "mothur.h"
+#include "database.hpp"
 
 class KmerDB : public Database {
        
 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 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;
 };