WhatsThis update

[mussa.git] / alg / sequence.hpp

diff --git a/alg/sequence.hpp b/alg/sequence.hpp
index 20bf01872bfd44d2b8129091d30de882cb6bf457..5c8983cc2cc1cf2195071ff0ca85c064ceb268f4 100644 (file)
--- a/alg/sequence.hpp
+++ b/alg/sequence.hpp
@@ -156,10 +156,17 @@ public:
   const_iterator end() const;
   //! is our sequence empty?
   bool empty() const;
+  //! find first 
+  size_type find_first_not_of(const std::string&, size_type index=0); 
   //! how many base pairs are there in our sequence
   size_type size() const;
   //! alias for size (used by string)
   size_type length() const;
+  //! reverse iterator
+  const_reverse_iterator rbegin() const;
+  //! reverse end iterator
+  const_reverse_iterator rend() const;
+  //! is our sequence empty?
   //! start position relative to "base" sequence
   size_type start() const;
   //! one past the last position relative to "base" sequence
@@ -202,13 +209,13 @@ public:
                   alphabet_ref a, 
                   int seq_num=1, 
                              int start_index=0, int end_index=0);
-  void load_fasta(std::iostream& file, 
+  void load_fasta(std::istream& file, 
                   int seq_num=1, int start_index=0, int end_index=0);
   //! load sequence from stream
   //! \throw mussa_load_error
   //! \throw sequence_empty_error
   //! \throw sequence_empty_file_error
-  void load_fasta(std::iostream& file, 
+  void load_fasta(std::istream& file, 
                   alphabet_ref a,
                   int seq_num=1, 
                              int start_index=0, int end_index=0);