X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=kmerdb.hpp;h=ead3d7e0b20d7b0ee070caebaad74aedeaae7dd3;hb=bd27c2b0612942815b7417c79f7ee41f669a2a34;hp=5019858dcf477c2e27bcc9ad3007617e26d3ce96;hpb=02909d6cae9963ba00dc746969a370fa8ca934fc;p=mothur.git

diff --git a/kmerdb.hpp b/kmerdb.hpp
index 5019858..ead3d7e 100644
--- 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;
 };