removed readseqs, readfasta, readnexus, readclustal, readseqsphylip and updated seque...

[mothur.git] / sequencedb.h

diff --git a/sequencedb.h b/sequencedb.h
index 9ee88065be8976c7a38ed64fe44bc440db077799..88b31e2e5d7adc050c58e3d18cb7ffca7652370b 100644 (file)
--- a/sequencedb.h
+++ b/sequencedb.h
@@ -24,21 +24,24 @@ 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 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
                
 private:
-       vector<Sequence> data;
+       vector<Sequence*> data;
+       string readName(ifstream&);
+       string readSequence(ifstream&);
 
 };