added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / sequence.hpp

diff --git a/sequence.hpp b/sequence.hpp
index 94d7d29b6117da80862e9fc8b3d0855c4adb8edd..6a50cb0b8aa31e4a3a3b6c9c97e77416f53eeeb1 100644 (file)
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -14,6 +14,9 @@
  *
  */
 
+
+//Data Structure for a fasta file.
+
 #include "mothur.h"
 #include "mothurout.h"
 
@@ -25,6 +28,8 @@ 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);  
@@ -60,9 +65,9 @@ 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;