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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 "sequence.hpp"
#include "calculator.h"
class SequenceDB {
public:
SequenceDB();
SequenceDB(int); //makes data that size
SequenceDB(ifstream&); //reads file to fill data
SequenceDB(const SequenceDB& sdb) : data(sdb.data) {};
~SequenceDB(); //loops through data and delete each sequence
int getNumSeqs();
void set(int, string); //unaligned - should also set length
void set(int, Sequence); //unaligned - should also set length
Sequence get(int); //returns sequence name at that location
void push_back(Sequence); //adds unaligned sequence
void resize(int); //resizes data
void clear(); //clears data - remeber to loop through and delete the sequences inside or you will have a memory leak
int size(); //returns datas size
void print(ostream&); //loops through data using sequence class print
bool sameLength() { return samelength; }
private:
vector<Sequence> data;
string readName(ifstream&);
string readSequence(ifstream&);
MothurOut* m;
bool samelength;
int length;
};
#endif
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