working on chimera.perseus. made removeConfidences function smarter. Fixed bug in...

[mothur.git] / sequence.hpp

diff --git a/sequence.hpp b/sequence.hpp
index 48287af367092715ab999b9ffabf02229c68cacc..224ae5d7a7452172c3aa3be1e63906e0a876efe2 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);  
@@ -44,9 +49,12 @@ public:
        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();