X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=blobdiff_plain;f=alg%2Fsequence.hpp;h=9c7ddd4a1e9fb8a397e1332f95dd346ac19ca462;hp=fbd753fb46dc7d0142de209ece821626bd2e2577;hb=8b38b5bc63e5c62983d0814aa75d3f88b9116e49;hpb=4b9dd885cdfef6d73c82bae5f112a063588766a9

diff --git a/alg/sequence.hpp b/alg/sequence.hpp
index fbd753f..9c7ddd4 100644
--- a/alg/sequence.hpp
+++ b/alg/sequence.hpp
@@ -105,6 +105,9 @@ public:
   typedef SeqString::const_reference const_reference;
   typedef SeqString::size_type size_type;
   static const size_type npos = SeqString::npos;
+  
+  typedef std::list<motif> MotifList;
+  typedef boost::shared_ptr<MotifList> MotifListRef;
                       
   Sequence(AlphabetRef a = reduced_dna_alphabet);
   Sequence(const char* seq, 
@@ -225,7 +228,7 @@ public:
   //! add an annotation to our list of annotations
   void add_annotation(const annot& a);
   const std::list<annot>& annotations() const;
-  const std::list<motif>& motifs() const;
+  const MotifList& motifs() const;
 
   //! add a motif to our list of motifs
   void add_motif(const Sequence& a_motif);
@@ -251,7 +254,7 @@ protected:
   //! store our oldstyle annotations
   std::list<annot> annots;
   //! a seperate list for motifs since we're currently not saving them
-  std::list<motif> motif_list;
+  MotifListRef motif_list;
 
   //! copy over all our annotation children
   void copy_children(Sequence &, size_type start, size_type count) const;