finished added bygroup processing of chimeras in chimera.slayer and chimera.uchime...

[mothur.git] / kmerdb.hpp

diff --git a/kmerdb.hpp b/kmerdb.hpp
index d50c8b2607347aa337b8cc57fc0566b40ccbb01b..62d4836a066f9bc10cf1a041e21cb07e1e0a1f84 100644 (file)
--- a/kmerdb.hpp
+++ b/kmerdb.hpp
@@ -26,14 +26,23 @@ class KmerDB : public Database {
        
 public:
        KmerDB(string, int);
+       KmerDB(const KmerDB& kdb) : kmerSize(kdb.kmerSize), maxKmer(kdb.maxKmer), count(kdb.count), kmerDBName(kdb.kmerDBName), kmerLocations(kdb.kmerLocations), Database(kdb) {}
+       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;
 };