Move alphabet type into SeqString

[mussa.git] / alg / seq_span.hpp

diff --git a/alg/seq_span.hpp b/alg/seq_span.hpp
index ec94c2717cf8d074933261f7d61863497b663b4d..8d1991360df0bdcebee6e83cab7b926686630a9a 100644 (file)
--- a/alg/seq_span.hpp
+++ b/alg/seq_span.hpp
@@ -39,7 +39,9 @@ public:
 public:
   SeqSpan(const SeqSpan &);
   SeqSpan(const SeqSpan *);
-  explicit SeqSpan(const std::string &);
+  explicit SeqSpan(const std::string &, 
+               AlphabetRef = reduced_nucleic_alphabet
+           );
   SeqSpan(const SeqSpanRef, size_type start=0, size_type count=npos);
 
   //! assignment
@@ -50,6 +52,7 @@ public:
   friend bool operator==(const SeqSpan&, const SeqSpan&);
   friend bool operator!=(const SeqSpan&, const SeqSpan&);
     
+  const Alphabet& get_alphabet() const { return seq->get_alphabet(); }
   //! \defgroup string_operators
   //! @{
   //! retrive element at specific position