mods to seq.errror

[mothur.git] / sequence.hpp

diff --git a/sequence.hpp b/sequence.hpp
index f48bf13dc98d034cea520cf78b09124fff30cb33..94d7d29b6117da80862e9fc8b3d0855c4adb8edd 100644 (file)
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -24,6 +24,12 @@ public:
        Sequence();
        Sequence(string, string);
        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);
@@ -31,17 +37,22 @@ public:
        void setAligned(string);
        void setLength();
        void reverseComplement();
+       void trim(int);
        
        string convert2ints();
        string getName();
        string getAligned();
        string getPairwise();
        string getUnaligned();
+       string getInlineSeq();
        int getNumBases();
        int getStartPos();
        int getEndPos();
+       void padToPos(int);
+       void padFromPos(int);
        int getAlignLength();
        int getAmbigBases();
+       void removeAmbigBases();
        int getLongHomoPolymer();
        bool getIsAligned();
        void printSequence(ostream&);
@@ -51,6 +62,8 @@ private:
        void initialize();
        string getSequenceString(ifstream&);
        string getCommentString(ifstream&);
+       string getSequenceString(istringstream&);
+       string getCommentString(istringstream&);
        string name;
        string unaligned;
        string aligned;