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#ifndef KMERDB_HPP
#define KMERDB_HPP
/*
* kmerdb.h
*
*
* 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);
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:
int kmerSize;
int maxKmer, count;
string kmerDBName;
vector<vector<int> > kmerLocations;
};
#endif
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