add seq_forward

its one more step toward getting a sequence to have all of its necessary
sequence location information.

I also changed the test in set_filtered_sequence for the count from 0 to
npos.

diff --git a/alg/sequence.hpp b/alg/sequence.hpp
index b335dcd1dfac1401ce473ef22258334b705d0cd5..aa1460fcb1152201ab527b2c032a6b53b497a77a 100644 (file)
--- a/alg/sequence.hpp
+++ b/alg/sequence.hpp
@@ -223,7 +223,13 @@ public:
   void load_museq(boost::filesystem::path load_file_path, int seq_num); 
   
 private:
+  //! hold a shared pointer to our sequence string
   boost::shared_ptr<seq_string> seq;
+  //! start offset into the sequence
+  size_type seq_start;
+  //! number of basepairs of the shared sequence we represent
+  size_type seq_count;
+  //! fasta header
   std::string header;
   //! species name
   std::string species;
@@ -243,6 +249,8 @@ private:
   template<class Archive>
   void serialize(Archive& ar, const unsigned int /*version*/) {
     ar & BOOST_SERIALIZATION_NVP(seq);
+    ar & BOOST_SERIALIZATION_NVP(seq_start);
+    ar & BOOST_SERIALIZATION_NVP(seq_count);
     ar & BOOST_SERIALIZATION_NVP(header);
     ar & BOOST_SERIALIZATION_NVP(species);
     ar & BOOST_SERIALIZATION_NVP(annots);