working on pam

[mothur.git] / sequencedb.h

diff --git a/sequencedb.h b/sequencedb.h
index 88b31e2e5d7adc050c58e3d18cb7ffca7652370b..8f7640ed3f90f1feb827448120759911d2da8e21 100644 (file)
--- a/sequencedb.h
+++ b/sequencedb.h
@@ -30,18 +30,22 @@ public:
        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 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;
+       vector<Sequence> data;
        string readName(ifstream&);
        string readSequence(ifstream&);
+       MothurOut* m;
+       bool samelength;
+       int length;
 
 };