X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=kmerdb.hpp;h=ead3d7e0b20d7b0ee070caebaad74aedeaae7dd3;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=d50c8b2607347aa337b8cc57fc0566b40ccbb01b;hpb=1244c4907c07baea86b0f0676d098a29d2e95a39;p=mothur.git

diff --git a/kmerdb.hpp b/kmerdb.hpp
index d50c8b2..ead3d7e 100644
--- a/kmerdb.hpp
+++ b/kmerdb.hpp
@@ -26,14 +26,23 @@ 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;
 };