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#ifndef SEQUENCEDB_H
#define SEQUENCEDB_H
/*
* sequencedb.h
* Mothur
*
* Created by Thomas Ryabin on 4/13/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
/* This class is a container to store the sequences. */
#include "storagedatabase.hpp"
#include "sequence.hpp"
class SequenceDB : public StorageDatabase {
public:
SequenceDB();
SequenceDB(int); //makes data that size
SequenceDB(ifstream&); //reads file to fill data
SequenceDB(ifstream&, int, vector< vector< int > >&, vector< int >&); //filehandle, kmersize, kmerdb, lengths
SequenceDB(const SequenceDB& sdb) : data(sdb.data) {};
SequenceDB(const SequenceDB& sdb, unordered_set<string> names); //creates a new sequenceDB containing only the reads in names
SequenceDB(const SequenceDB& sdb, unordered_set<string> names, int kmerSize, vector< vector< int > >& kmerDB, vector< int >& lengths);
~SequenceDB(); //loops through data and delete each sequence
int getNumSeqs();
Sequence getSeq(int); //returns sequence at that location
void push_back(Sequence); //adds unaligned sequence
bool sameLength() { return samelength; }
void print(string); //prints fasta file containing sequences in this db
private:
vector<Sequence> data;
};
#endif
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