* Mothur
*
* Created by Thomas Ryabin on 4/13/09.
- * Copyright 2009 __MyCompanyName__. All rights reserved.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
-using namespace std;
+/* 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(); //loops through data and delete each sequence
+ 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 add(Sequence); //adds unaligned sequence
- void changeSize(int); //resizes data
+ 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(ofstream&); //loops through data using sequence class print
+ void print(ostream&); //loops through data using sequence class print
private:
vector<Sequence> data;
+ string readName(ifstream&);
+ string readSequence(ifstream&);
};