removed unused copy constructors and comments within comments that where causing...

[mothur.git] / sequence.hpp

diff --git a/sequence.hpp b/sequence.hpp
index b4337405a811545d4c3b2f64dc8771d42898d1fc..af0cba814baece3ae9ce4abae02b3fa7370769cf 100644 (file)
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -14,6 +14,9 @@
  *
  */
 
+
+//Data Structure for a fasta file.
+
 #include "mothur.h"
 #include "mothurout.h"
 
@@ -25,9 +28,6 @@ public:
        Sequence(string, string);
        Sequence(ifstream&);
        Sequence(istringstream&);
-       Sequence(const Sequence& se) : name(se.name), unaligned(se.unaligned), aligned(se.aligned), pairwise(se.pairwise), numBases(se.numBases), startPos(se.startPos), endPos(se.endPos),
-                                                                       alignmentLength(se.alignmentLength), isAligned(se.isAligned), longHomoPolymer(se.longHomoPolymer), ambigBases(se.ambigBases) { m = MothurOut::getInstance(); }
-       
        //these constructors just set the unaligned string to save space
        Sequence(string, string, string);  
        Sequence(ifstream&, string);
@@ -62,9 +62,9 @@ public:
 private:
        MothurOut* m;
        void initialize();
-       string getSequenceString(ifstream&);
+       string getSequenceString(ifstream&, int&);
        string getCommentString(ifstream&);
-       string getSequenceString(istringstream&);
+       string getSequenceString(istringstream&, int&);
        string getCommentString(istringstream&);
        string name;
        string unaligned;