put basepair alphabets into the Sequence class

[mussa.git] / alg / sequence.hpp

diff --git a/alg/sequence.hpp b/alg/sequence.hpp
index 67f6c9f84dad1ae36212c79ff444f529d810c972..0e0e2e6b2c8e42d2c91bdbbbb3f46af762f9329b 100644 (file)
--- a/alg/sequence.hpp
+++ b/alg/sequence.hpp
@@ -93,6 +93,17 @@ public:
   typedef std::string::size_type size_type;
   static const size_type npos = std::string::npos;
 
+  // some standard dna alphabets 
+  // Include nl (\012), and cr (\015) to make sequence parsing eol 
+  // convention independent.
+
+  static const std::string dna_alphabet;
+  static const std::string rna_alphabet;
+  //! this is the general iupac alphabet for nucleotides
+  static const std::string nucleic_iupac_alphabet;
+  //! the protein alphabet
+  static const std::string protein_alphabet;
+
   Sequence();
   ~Sequence();
   Sequence(const char* seq);