X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=blobdiff_plain;f=alg%2Fsequence.hpp;h=fbd753fb46dc7d0142de209ece821626bd2e2577;hp=80aa49f75e17bcf9ca572de2d9b8c53658ea31af;hb=f3e6762bedaf3775619a36f4103c8cf35d2ca887;hpb=a5fdb434dd0e6d18fe98e9ee57cb5169ce4c5842

diff --git a/alg/sequence.hpp b/alg/sequence.hpp
index 80aa49f..fbd753f 100644
--- a/alg/sequence.hpp
+++ b/alg/sequence.hpp
@@ -72,7 +72,7 @@ struct motif : public annot
 {
   std::string sequence;
 
-  motif() :  annot(), sequence("") {};
+  motif() : annot(), sequence("") {};
   //! this constructor is for when we're adding motifs to our annotations
   motif(int begin, std::string motif);
   ~motif();
@@ -88,6 +88,8 @@ private:
 };
 BOOST_CLASS_EXPORT(motif);
 
+class Sequence;
+typedef boost::shared_ptr<Sequence> SequenceRef;
 
 //! sequence track for mussa.
 class Sequence 
@@ -111,9 +113,13 @@ public:
   Sequence(const std::string& seq,
            AlphabetRef a = reduced_dna_alphabet,
            SeqSpan::strand_type strand = SeqSpan::PlusStrand);
+  //! make a new sequence, with the same SeqSpan
   Sequence(const Sequence& seq);
+  //! make a new sequence, with the same SeqSpan
   Sequence(const Sequence *);
-  Sequence(const SeqSpanRef&); 
+  //! Make a new sequence using a copy of SeqSpan
+  Sequence(const SequenceRef); 
+  Sequence(const SeqSpanRef&);
   ~Sequence();
   //! assignment to constant sequences
   Sequence &operator=(const Sequence&);