From: Diane Trout <diane@caltech.edu>
Date: Tue, 12 Sep 2006 01:03:26 +0000 (+0000)
Subject: add seq_forward
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=commitdiff_plain;h=31bade8ed7660565a8088229849580758157dfa8

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 b335dcd..aa1460f 100644
--- 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);