working on pam

[mothur.git] / sequencedb.h

diff --git a/sequencedb.h b/sequencedb.h
index 5dcf9bd9ffb721378a2523cc447702d887dd22a8..8f7640ed3f90f1feb827448120759911d2da8e21 100644 (file)
--- a/sequencedb.h
+++ b/sequencedb.h
@@ -11,35 +11,41 @@
  */
 
 
-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
+       bool sameLength() { return samelength; }
                
 private:
        vector<Sequence> data;
+       string readName(ifstream&);
+       string readSequence(ifstream&);
+       MothurOut* m;
+       bool samelength;
+       int length;
 
 };