X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=kmerdb.hpp;h=ead3d7e0b20d7b0ee070caebaad74aedeaae7dd3;hb=bd27c2b0612942815b7417c79f7ee41f669a2a34;hp=af52789dedc231eb5495f4a2f10cbc0efe73a37c;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d;p=mothur.git

diff --git a/kmerdb.hpp b/kmerdb.hpp
index af52789..ead3d7e 100644
--- a/kmerdb.hpp
+++ b/kmerdb.hpp
@@ -8,21 +8,41 @@
  *  Created by Pat Schloss on 12/16/08.
  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
  *
+ *	This class is a child class of the Database class, which stores the template sequences as a kmer table and provides
+ *	a method of searching the kmer table for the sequence with the most kmers in common with a query sequence.
+ *	kmerLocations is the primary storage variable that is a two-dimensional vector where each row represents the
+ *	different number of kmers and each column contains the index to sequences that use that kmer.
+ *
+ *	Construction of an object of this type will first look for an appropriately named database file and if it is found
+ *	then will read in the database file (readKmerDB), otherwise it will generate one and store the data in memory
+ *	(generateKmerDB)
+
  */
 
 #include "mothur.h"
+#include "database.hpp"
 
 class KmerDB : public Database {
 	
 public:
 	KmerDB(string, int);
-	Sequence* findClosestSequence(Sequence*);
-
+	KmerDB();
+	~KmerDB();
+	
+	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;
 };