working on nmds command

[mothur.git] / sequence.hpp

diff --git a/sequence.hpp b/sequence.hpp
index 21b4c3874c9ccb1f5ab9eab31fe78fbd7f0a40c6..48287af367092715ab999b9ffabf02229c68cacc 100644 (file)
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -26,12 +26,18 @@ public:
        Sequence(ifstream&);
        Sequence(istringstream&);
        
+       //these constructors just set the unaligned string to save space
+       Sequence(string, string, string);  
+       Sequence(ifstream&, string);
+       Sequence(istringstream&, string);
+       
        void setName(string);
        void setUnaligned(string);
        void setPairwise(string);
        void setAligned(string);
        void setLength();
        void reverseComplement();
+       void trim(int);
        
        string convert2ints();
        string getName();
@@ -43,13 +49,11 @@ public:
        int getEndPos();
        int getAlignLength();
        int getAmbigBases();
+       void removeAmbigBases();
        int getLongHomoPolymer();
        bool getIsAligned();
        void printSequence(ostream&);
        
-       int MPISend(int); //not working at the moment...
-       int MPIRecv(int); //not working at the moment...
-       
 private:
        MothurOut* m;
        void initialize();