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[mothur.git] / sequencedb.h

diff --git a/sequencedb.h b/sequencedb.h
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+#ifndef SEQUENCEDB_H
+#define SEQUENCEDB_H
+
+/*
+ *  sequencedb.h
+ *  Mothur
+ *
+ *  Created by Thomas Ryabin on 4/13/09.
+ *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+
+using namespace std;
+
+#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
+
+       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 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
+               
+private:
+       vector<Sequence> data;
+
+};
+
+#endif