fixed memory leak in maligner minCoverageFilter function used by chimera slayer

[mothur.git] / sequence.hpp

diff --git a/sequence.hpp b/sequence.hpp
index f48bf13dc98d034cea520cf78b09124fff30cb33..48287af367092715ab999b9ffabf02229c68cacc 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);
@@ -31,6 +37,7 @@ public:
        void setAligned(string);
        void setLength();
        void reverseComplement();
+       void trim(int);
        
        string convert2ints();
        string getName();
@@ -42,6 +49,7 @@ public:
        int getEndPos();
        int getAlignLength();
        int getAmbigBases();
+       void removeAmbigBases();
        int getLongHomoPolymer();
        bool getIsAligned();
        void printSequence(ostream&);
@@ -51,6 +59,8 @@ private:
        void initialize();
        string getSequenceString(ifstream&);
        string getCommentString(ifstream&);
+       string getSequenceString(istringstream&);
+       string getCommentString(istringstream&);
        string name;
        string unaligned;
        string aligned;