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[mothur.git] / sequence.hpp

diff --git a/sequence.hpp b/sequence.hpp
index e094fb520f7ad26c96cbcfa7226e194bd883f690..03cbab7ffddce5531e272cf6116069edfa0ebade 100644 (file)
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -19,21 +19,29 @@ using namespace std;
 class Sequence {
 public:
        Sequence();
-       Sequence(ifstream&);
+       Sequence(string, string);
+       
        void setName(string);
        void setUnaligned(string);
        void setPairwise(string);
        void setAligned(string);
+       void setLength();
+       
        string convert2ints();
-       string getSeqName();
+       string getName();
        string getAligned();
        string getPairwise();
        string getUnaligned();
+       int getLength();
+       void printSequence(ostream&);
+       
 private:
        string name;
        string unaligned;
-       string pairwise;
        string aligned;
+       string pairwise;
+       int length;
+       int lengthAligned;
 };
 
 /**************************************************************************************************/