From f3c0553a22b0e4ddc39ee45f51725352d92e97f1 Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@caltech.edu>
Date: Thu, 21 Jun 2007 00:52:58 +0000
Subject: [PATCH] test annotating a sequence with fasta records in a stream I
 split the load_annot function int one that opens the file and one that reads
 the stream. (which is called by the file handling one)

This was so I could test some random sequence that Steven was having
trouble with. (which seems to be working correctly.)
---
 alg/sequence.cpp              | 26 ++++++++++++++++----------
 alg/sequence.hpp              |  2 +-
 alg/test/test_annotations.cpp |  3 ++-
 alg/test/test_sequence.cpp    | 18 ++++++++++++++++++
 4 files changed, 37 insertions(+), 12 deletions(-)

diff --git a/alg/sequence.cpp b/alg/sequence.cpp
index 1f21bd5..521496d 100644
--- a/alg/sequence.cpp
+++ b/alg/sequence.cpp
@@ -324,6 +324,21 @@ Sequence::load_annot(fs::path file_path, int start_index, int end_index)
     throw mussa_load_error("Error loading annotation file " + file_path.string());
   }
 
+  try {  
+    load_annot(data_stream, start_index, end_index);
+  }  catch(annotation_load_error e) {
+    std::ostringstream msg;
+    msg << file_path.native_file_string()
+        << " "
+        << e.what();
+    throw annotation_load_error(msg.str());
+  }
+  data_stream.close();
+}
+
+void
+Sequence::load_annot(std::istream& data_stream, int start_index, int end_index)
+{
   // so i should probably be passing the parse function some iterators
   // but the annotations files are (currently) small, so i think i can 
   // get away with loading the whole file into memory
@@ -333,17 +348,8 @@ Sequence::load_annot(fs::path file_path, int start_index, int end_index)
     data_stream.get(c);
     data.push_back(c);
   }
-  data_stream.close();
 
-  try {  
-    parse_annot(data, start_index, end_index);
-  } catch(annotation_load_error e) {
-    std::ostringstream msg;
-    msg << file_path.native_file_string()
-        << " "
-        << e.what();
-    throw annotation_load_error(msg.str());
-  }
+  parse_annot(data, start_index, end_index);
 }
 
 /* If this works, yikes, this is some brain hurting code.
diff --git a/alg/sequence.hpp b/alg/sequence.hpp
index 1a4c9eb..fc8a0cf 100644
--- a/alg/sequence.hpp
+++ b/alg/sequence.hpp
@@ -203,7 +203,7 @@ public:
   void load_annot(const boost::filesystem::path file_path, int start_index, int end_index);
   //! load sequence annotations
   //! \throws mussa_load_error 
-  void load_annot(std::fstream& data_stream, int start_index, int end_index);
+  void load_annot(std::istream& data_stream, int start_index, int end_index);
   //! parse annotation file
   /*! \throws annotation_load_error 
    */
diff --git a/alg/test/test_annotations.cpp b/alg/test/test_annotations.cpp
index 970d516..2e4cb50 100644
--- a/alg/test/test_annotations.cpp
+++ b/alg/test/test_annotations.cpp
@@ -71,4 +71,5 @@ BOOST_AUTO_TEST_CASE( annotations_has_key )
   BOOST_CHECK_EQUAL(asp->has_key("header"), true);
   BOOST_CHECK_EQUAL(asp->has_key("name"), true);
   BOOST_CHECK_EQUAL(asp->has_key("secret"), false);
-}
\ No newline at end of file
+}
+
diff --git a/alg/test/test_sequence.cpp b/alg/test/test_sequence.cpp
index 9faa8d0..9784621 100644
--- a/alg/test/test_sequence.cpp
+++ b/alg/test/test_sequence.cpp
@@ -833,6 +833,24 @@ BOOST_AUTO_TEST_CASE( annotate_from_sequence )
   }
 }
 
+BOOST_AUTO_TEST_CASE( sequence_annoted_with_reversed_sequence )
+{
+  // sorry about the long string...
+  string s = "CTGGGTCGGGGGCGCTGGGGGCTGCTGGTAnnnnnnnnnnnnnnnnnnnnnnnnnTCTGCGCCGCCCGAGCCGCTGTGCTGCGCGTACTCCTCGAAGGGAGGGAACTTGGGCTCGATGTAGTTGGAGTTTATCAAAAACGAGCTCATGGTCATTAATTTGTGAAGTGCAAAAATACTAATTTTTCTCGCGTTGTCGTTTTTTCTGGGCTTGCCGAGGnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnGCAGACGCCGCCACCAAAGTTCGAGCCGCTCCTCCCCAGCCCAGCGCGCGCCCCGCCCCGTGCCCCACGTGCAGCGCCCCCACCAATGGGCGCACCGCGCGCGCGGACCCGGATCAGGAAACGCGCGGGTGCGTGATGGATGCTGCTGTCCGGCCCCTGGGCTGGGGGAGGGAGCAGGAGCTTTGGACCCCAGCCCCCCAGCTTTGGTTCCCGCTGGGAATTCAGGCCCTGTCAGGCTGTAGGTCCTCTCGGGAGCCCTCTGCCTGCCCTACTGCTGGCCTAGGCCTCGGGCTGTCTGGCGGCCGCGACTCAGCGCTGACCTCGGGCGCAACCCAGTCAGGCTTCGTGTCCTTCAGGGGTTCTAGGCTAACAGGCGAAAGGAAGGGCGTTGGGACCGAGGGGCATCCTGGTTTTTATGTACGCCACTGAGAGGCCACCAGACACATTTTCTCAACCGCAGATCCCCCTTCCCCACACCCTGCTCCTTGCGTGTCAGCCTGAGAGCCCTTGCTTTGAGAAGCTTGGCAGAAGCTGCAAAGGGTGGGCGGGCAGCTAAGAGAAATCGACCCAAGGATGTAAATCGAGGCCATTCCATTATAACTGGATGGACACTTTTCATTTTTTCCTTCTTTCAGAGACAATCTGTTTCGTGTTTTCCTAAGAAAAATTGGAACCTTCGTAATAGCATCTAATTTGACGGGGGTTGTCGATGTGAGAGCTAAATATGCCCGCATTTACTAGGTGCGATTGTGAGAGAGAAGGTGGCCCAAGGATGGGAATGGATAGAAGCAACACCTCCACAGAACCGAGCTTTGAAAACAATAACTTCCTATTTCAGAACTATCCCCAAACAAAAACAAGCTAAGGGTAGAATAAACACCTTGCCGGGTCTGATCGCTGATGGGTCTTTTCCAGCTAAGAATTTCATGTTTTCTCTTTTAGATCCTGCTTTCTCAGGCAGTATCTGAGGCTAGAGTTATATTTGCAGGACAGTCTATAATTTCTGAATTGCTGAAAATTAGCGTATTAACGATATCAGAAGCTCCGGAAAGGAGGGAGAGGAGACTGTTGCCTGCTATTTGGTAATTGAAATTTGATGGGTACACTAATTACGCCATTATTAACAAATAAATTACTTATTAATTCCACCTAATGTTGATCTTTGAAGTAAATACTGATGCCTTATTTGTGCTGTGTGCTTTCTCCCTTTCTTTTCTGAGTAGTAGACATATCTAGATCCTCTACTTTTCAGCCTAAATTAAAGCAGTGTAAACTAGCATAGTCACCATTCTAAAAATATTTTCATATTGGCATGCAAAAGCAAGGATTTTTCAGCTGGTGCACCTTAGTTGATTTTTCAAAGAGCAGTATAAACAGCCTTCTCACAACTGAGTCTGGAACGCAGACAAGGAAAATTATTTCCTAAGCCTGGAGACACTTGAAAAGGAATGTCAATTCTATCTTCATTCATACTGGTTACTCATATGAGTTACTAAATGCTGGAATATATCCATTTGATGGATAGTCACTTAATGCTTAGCCACATAAAGCCTATTATATGGGACTAATCTTTAAACTAATTTAGGAAAAGAGGTTAAAAAGGGGATCATATTAGCTTTCTAACTGGAATCACCCTGAAGAGGTACAAAGAGATTTTCCACGTTAGGTGTATATGAGTGTGAAGAGTGCTGTCCATTCACATGAGGCACCCTGAAAATTTGTTTTTAAAGAAATTTGAGCCACAGACAGAAATCAACACTGAGTGTAATCTTTAGCCATCCTCTCTAGACTGGAGGAAAAATTTAGAATGTGATACATCTACCTGAACCAATATCTCTCCCTAGCAAGAAAAAATAATATACACATAGGnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnGACATACGTATTACAAATCTGAACCCTATAAGTTTCAGGGGGACAAAAAGCATGACAAGGAAATCTTCCCTCCTTCTCATGTCATCAGCCTTGAGTACTAGGGTCTTAACCATATCTGTTTAATATTTACAGACACTAAAACACAAAATTCTGTTGTTTAGCCTCAGAACCTTGTACCAAGTTTCTATTTTTAAGTATTAACGAGACATAAACACTGTTTTGTATACGGTTAACCCAAACGAGTTAGCTGTGCCTGTGTTTTGTGTGATTCTATTACTTTAGGAAGATGGCCTTACACAGAATCCCCCAAGGCCTGTAACTTGTCTTTGTGGTTCGTATCATAAACACAAACGGAGCCAGGACCACCAAGTGTTATCTCAACACCGACATTTTGACATTTTACTGCAAGATTTATGGCTGTAATAAACAATCTCAGTACCTTTTCTGAACCTTCCTCAATCTCCCTTTGCAAACCATAGCATCATTCCATTGAATCAAATAATCTTTTGAAAAACATTTAAAAAAAATACCTCTTGCCTTTACACAATATCCAAGACACCAAAGTAAAGCCAGGAAGAAACTAACTCAATTAATAAACAAACTGAAGTTTACCAGCAGCATCTCGCCTGAGAAAAGATGGGATGCCCTGAAATGTAGCAGAGAGGGAGCATGCTAATCCTCACACACCAACTGGCTCCAGTCCCAAGCGGGGTGAAAGCGTTATCCTTTCCTTAGGAAACTGGTGAGCACGTTTGCTCATTTCCACGTGCAGGGATAACATATATTCCCAACAAAAGCTTTCTTAAAATCCCATTAGGTGAAATAACTTTTCATCATGTCCTCGAATCCCAGATGGAGAAGAGTGAAGGGAGTCGGAGGGAGAGGGAGGGTGCAAGGGAGGCAATGTTTTGCAGCTTGGTTTGAATCTGATTTGAATCATTTTGAATATATTTGTAACAGCATTCCCTCTTGAATGCAACCCTGTCCCAAGTTTCAAAGTGACCGAACAGTGACACCGTGTGCATTTTGTTTCTTATTAATCTTACACATTGACAGTCTTTGTTAAATCACAAGGCGCGCCCTTCACTAGCCGACATTTTCATATTTGTTAGACGCACTGACCTGAAGTTCACCTCGGCCTTGGACTTTGCGCTTCTAAAAGGTCTATACAGTGTCTTTTAGAGAGCAGGGTGCTTTGCCCAGGTCACTCCTTCTCAGGAAAAACCAAGGGGAAAAGCCAAAGGAAATGTAAACGTTATGGAATGTATTGACTGTATTTGTCCTTTGTTCTTTAGAGCGAGAGTCCCCCAGACTGTTCTCTATCTGATGCATGTCTCTAGAGCTGAACAGTGGAATGGCAGAATTTCAAAACGCCTGATGGTGGCATTTGAAGGCTTCCCCACCACCTACACTAGACACAAGATTTGAGAGGAACAACACTTTACCAGCCATTTGACCAATTAATTCTTTGGGGATAATTTTCTTGTAGTAGTTTAAAATAATGCACACAACGCAGGGATGAGGACTGATATTCATATTGGGATTACACATGAATTTTAACTGGGATTGTTTGAGAGGCCTGAGGTTCAAAATCCTCCAGATAAAGCAAGCACACTAAAAGCAATAAATTCTGCAAGTACTCTTTTCTTTTACTTTGAAGACTAGCTAAGAGGTATCTATGGTTTTTGAAGCTGACATGTCTATAAGGTGTGTCACATGTTTTTAACCAAAAAGCACAATAAAAAGGTTTTTCCCAAAGAGACACGTAATTGTCTTGTTGACTCATCGAGGGGTTTCAGTTTTCCTCATTTCACTAGCCCAAATGTGGTGAAATGTTCACTGCTGCAACAGCAATCACCACAGTTGTTTCCTTTCTTCTGTTTCATCTGGCAAACCCCCATTTGGCTTCAAGCTCTTGGCCAGAGTGAAAACTTTACACATTGCACAGAAGCACCCTGATTACTTCCATGAAGGCAGTGTTTGGAAAATATTTACTTTACCACTGAACATACCTGGCACCATTAAATCCAATCAACCAAAATATTGGGATGATCTTAAACATTCCTGCAAGAGTCCACATTCTGAGTAGATGAATTATTTCCAAAGTTAAAAAAGAAAAACCTAGGGAAAATATTTCACTTTTCTCTTCTCTGTTTTCCTATACTGATCCCTTGAAGGTCAATTCATAGAAAAGGGAAATATGTCCTCTGGAAAATAGATTCTTACAGCACCAACACTTAAAGCCATTCTAGATGCATGAAAAATAAAATATTGTTTAGCTCTTCAGTTGCAACTCACACATGAGGCATGGTTCTAGTCGGCTTCCTTAATACACTATTCTCTTTCTTTTCTGCTCTCCCACCCTTCTTCTTAGGTTGCTTTATCTTCTCCTTGGCTTTTTTTTTTAATTCCACGTGTATCATTAAAAAGTACATTCTGAAGAATAGAAAATATTCTATTCTGTCCTGGTGGTCTTACAGAGTAGCCTGTTATTTGTGGATTTCACCTTTCTGCATTCCCTACAGTCTAGTTATTCACTTATAGCTTGTAGCATTTCTCTTACATTCAATTGTGGTTTAATAATAAACATTAAAAAAATTTCCAAACAGGAACATTTTCATGGCACCAGTAAGCATTTTGTCACTGGCAGTGGTGGTGGAAGGGGTGAAGGGAGAATTCTGTGTCTTTCAGGAGGGTTTCCACTTCCTTCCTTCCCCTTCTCAGATCTCAGAACGCTTTGCATTCAGCGGACTGTAGTTTCAGAAAAAGCATATTCTGTGTTTGAAAACTGCAAAGATTATATTTTGCAAGAAGTGTCTGTGTTTGCATTTATTCTTACACACTTTAGGGGTCATCATGTGTACTAAAAAGACAAAAAACCGGCCAATCAGAATCCCTCTTTTCAAATAAAGGAGGTTTCCTGCACCATTCTGTTGCCTTTGAAGGCATAATGAAATATTGGAAACTTGTGACATTAGTTTTTAAAGCTCCACAGATGAGTTTTTAGCATTTTTATTTTGTGACAAACCCACAGACTCCTGGTTCTCCAACACCTAAGGTGTTGATGTTTCAGTAATCTATGCCTATTTACCTGCTGCTATTCCCTCAGAATGGGAGCGATAATTCAAGATGAGATACAGCATGTATTACTCTTGAAAAGAGGAATTTTCTATCCTTTCCTCCGTAATTGAGGTCATTCAACCACTAGGGTTCACCTGGAGTCCATACCGTGATACACGCGTCACTCTGAGCCATTTTATCTTTTGTGCTGATAGTCAAGATCACAGCTCTAACATTGACATCAAACTCTGTCTGGGCAGATGACTAAGAGCACTGCACAATGTAAACTTTTGACCCTCAACTTTTTGACCTGCAGTTGTAACGCACTAACCGCAAAGATACACAAAGCCGAGCCTCTTCTTTCAGGGGGAAGGGGCCCCCCAGCATCTCAGGATGCCCTGCTTCTGCCACTGCCATTTGAAATTAGAGGGTGAAATGGATATTTTTGTGTGTTTGTGACTGTACTTTTTGTTAAATCAGCCTATGACCTCTTCGTTAGCACCTAGGAACTAGATTAACTTGAAATCACTCGTGATTCTATTTTACAAGGAAAATTTGGAGCAGAATGGGAGAACCTTGCAAAAAGTGAAAGAAAAGAGAAGATGGGGGAAAGCAGGCAATGGGAGGTGGAGACACTTTTTCCCTTTATTTAAAACTAAAGACGCAGCCCTAATTGTTGGGAGAGCTGGCCCAAGCGGGTGAATTGACTGTGAACTTGTACTAAAGCGTGCTCTGCTGGCGATTCCTAGGGTGTGCAGATTTATCTTCTCTGCATTTACTTAACCCGGCAGTGAACTGCGCGGGCGTCATTTGTTAGGCGATGACAGACTTCACCTCCAGCAAGGGCTGCTTCACAAAATCGCAATAATTATCTAATAACCTTCATAACAAATATTATTATTGAAAAGACTGGTTTGTGGGGAGGGGACCTGGTGGGAGAACAAATTTATTTGTGAACAACAACAAACAAAACAAACCTGGGCAGACCTTCAAGTTCTGGGGCTTAGAATGGCTGGGGCTGTGGATCCCCTCCCCTACTTGGGTGGGAGCTTAGGCTGACCCCCTCAGCCCTGCCTGGGAGCCCCGTTTATAGTTTTGCCATTGACTAGAAGGAAACTCCTCCTCAGAAACCAAAGGGAGGGAGCCCACAATGCTCTGCACTCTCCATGGTGGGCAAGCCATGGACAGACCCCCAGCCAAGGCAGGGGGGAGGCTGAGAAGGGCATCTTTTAAGCTAAAAGGATTGTTTTCCTCTTTAATTGCCTATCTTTTAAGATGTGATTTGCTTTCCACTCACTAATTATTTCGATATAATACTCTCAGAATCTCAACAAATGAACAGGACTCTGTTTTTTGGTGGGAAATTCTGTCTTGCTCTCTCAGAGCCGCCAACAATGAAGCAGGGGAAAGAGCAGGAGAAAGGGAATCTTGGCATAATGTTGTGAAATTAGACCATGGAAACCCTAACAAACCACTAAGTAAGTGTGACCAGAAGCTTCCTGTTGTATTTATAGTTCAGAAATATTGTCTCTTCAGCTTGTGGGAACAAACGAGCCCCCGCACATTGCCGCTGAGGAGGAGCACAGACACGCACTTCTGCCACCGGCTGAGGCTGGATGTCTTCATAAAGCCCTCAGTGACAGACATATTTTTTCTTAGTAAGTTCCTCTGCAAGAACAACCCAAAAGAATCCACAAAAGAAATAACTTATCTACAGAATGAGCAGAAAACCAGCCATCCTCTTTATTATGCTTCCTATGAAAATAGGAAGAAAGAAAAAAATCTTCCAGTAACACATAGGTCTGACTGCATGATGTATTTTTAAAGTCATTTTAATTCCATGTGGCCATGTGGGTTTGCCTGCTCTCTTAAATTCTACTTAAGTTTTGTGAAGATTAAAACAGACAGAAATAAGCAAGCTGACAATATTTACAGCCTGTAATTTTTCTCATTCCTTGGAAAGATTCTCTATGTTCTGTGGTACTGGATATGACTTCAACAGGCTTTCTGCTCATTCCCACACCCCAGGGTGGAATATGGCCATGAAGTAGTGTGGATATTTTCTGTGTAAGTAACTCAAATTAAACTGGCAGAATCCCCGTCACTCTTTTTTTTTTCTAATTTCAATCACCAAGAAATCACTCAAGCAAGATCACCAAATCAGTAACTAAAATGGAACCATAACGCAATATTTTCCAATAAGGAGCCCAAAATTCAGAGCAGCAAAACAAGGAATCCAGTATTCTCACAGACACATAACATTATAAAAGAGAACCCATACCCATGTAGAGTTTATATCCTTGTTCCCACTAAGATGTGGACACATCTTCTTGAATGCTGAAATACCAATGTTTACTTTAATAGGTTACACACAATGACTTCAGGATTCTTCACCTTGCCACTATTCATGAGAAGTAGCACTTGTGGGAGGGTTTTGATTTTTCAAAAAAACTTTCTAGGTTTTGCTTTCTGGACCTCTGACTTTAGGGACATCTGTTGGACTTATGTTGAGTGTAGGTGGCCTCTGCACAATAAGTTTATTGAAATTCCAAATCTATACTTTCAATTTTTTCACTTTAAGCACTTAATAGGTATCTTTACCAATTAATACTTGCTGAAAACTGCCCAGCTCCTAAGGAGAAAAGCAGATCCTATTTTTTGTTTCATTTCTGAATGCAGTAGGAGAATTTGGCTTAATTCCTAAAATAGGATTGGAGGAAATCTACTGGGTCCCTTGTGGGTACCCATCCAGAAAAAGATCCCAGGACAGGCCACAGTCCCCAGTCACTGGGCTTGGGTTTTGCCATTGAAGAATATGGGGGGTTGGGGCCAGAAGGGGTGACTGGGGCCAATATGGAATTGTGCCCAGGATAAACTTATTTCACCTTACTTCACCCATTGGTGCAATTTTGGAGACTGTTCTGGAAATCATAGATTATGTAAATTTCCTGGGATCAAACAGAAAGAGCAACTAACAAAAGAAAGGCGGAAATCTCCTACTGACAAAGGACCAATTTCTTCCCTAAACTACCGTTTATGATGTGTCAGGAAAAACAACCTAATGGCTCTGGGGACTTTTAAGTTGGGCACTGAAGACACCTCAATTTCCCCCAAAACTTTAGAGCACAGTTTGGAACAGAGAATTCGCCTGTATGTTGAGGGGGAGTGAATTTCTCCAATCTTAATGTTATCCAGGGGGCCGCCTAAGTTGCCTTCTGAGGGTCCTGTGCGTAGATGTTTTTAATTCTACnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnGCGCTTTAACCCCTTTCAATTAGCCTGGGGATTCAAAGACTAAAGTTAAATCCGGCCATAAAGTTTATTGCTTCAGACTCACAAGCGGCTGAGAACAGTCCCGCCGAAATAAAAAGAACATGCAGGCAAACAGGGTTCAGGGCCTGGTCCCGGGTGCGGGGGAGGGGGTCCTGAACACCCCCCCACACCAGGGTGGGGATCCTTGGTCCTCAGGGTCCAGTGGGCGCTAGCAGCCCAGGATCCACCTTGCAACCCGGGGGCCCAGCCTGGAGGTGCAGCCCCAGCCTCGCCGGCCTCTGCCACCCTCCCGCTCTCGCGAGCTAGCCTGAAACCCGGCCCCGAAGGCCGCCGCCTCAATTCAGCCCTGCCAAATGACCCCGGCCCGCGAAGACATATTGCCACAGCCCCGTAAGGAATCCCGCCAGAGTCCGCCTCGGCCCTGCCCCGGCCTTTCTTTCAAACTCCTGAGCGCAnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnACTGTCTCCCAGCCCCGACCCCAGGGCTCCGCGACCCCCAGGAGCTGGCCCCGGCCGGCCCAGCAATTGCGCGGGGGACTGGGGGTGCGGCCCTGCCAGGTCCCCACACACAGGCCCATTCGCACACAAAAATCATCTTTTTGCACGCCGGCGGGAGCAGCGGAAGTCATTAACATCCGCGGTTGTGCTGCAATTAAAGTTAGGCCTGGGGATGCGGCGCGGCCACAGGCGCTGCTCACTCTGCTGCCTCCGCAGAGTTGGCTCCTGGCGCTGCTCTTTTGGGCAGAGGGAAAGTTTGCTCTGCCTTTTCGAATTCAGAGGCAGCCTGAGTTATTGAACCnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnTTTCCAAAGTACAAATAAACTTGAAAGCGCTCAGGAGGCGAGCTTACCTTAACTCGGAGGGAGCCATTTTTCAGAGAGTTTTGAGAACTTGTGGTTTGGACACTTCTGGACCTAAAATTGACAGTTTGAATGGCCAGGCGGCACACGTAGCCTGCAAAAGAGTCAAATGGAGTCCAGCGTTAGTGAGATTATATGTTATGTGGTATATAATGTTGGATGTCAACTCCCCAAAACCATAAAACTTACTTTAATGGCCCCACGTGACGTTTTATAGCCAGTGAGCCGATCTGTCTGTGCTATGGATGATTTTACGATCTAATTCATAGACAAAACCCTATTCATTTGGCACCCAAATGTCATATAGCCGGAACTGGGGCTTATAAAGTTTACTGTTTTATAACTTTTAAAAGGAAAGACGGCATCAGTGTAAGCAGTCGGTAAATGTGCAAATCTCTAGTTGCGCTTTAGCTGCTCTGAGGAGTTTCCCAATCGAGCTAGGATGGGGTAAGTACCTTCAATTTGTAGCAAATTAATTGTAGCAAAAGAAGCCAACTGGGTCCCGGGTGAAGAGTGGGGAAGGGGTGCTGGGATGGGTTAAGGGCAGAGGGTTTGGGGTCCACAGACAGACATAGCAGCGTCTTCAGCAAGTGGAGGCCTAGGACAGCCTTAGGAAAGAGGCAGGATCTGTGTGGCCTGAGGGCGGCTAACAAAGCCCTGGGTTTTTTCTCCTTTTTTCTTGCTCTTTCTCTCTTTTTTGTACCCAGCAAGTTAACTTGGTTTCCTCAGAGATGGACAGGGTGTTCTGGGGCTTTGGAACAGCCTACAGCTTTTTCCACCTTCTGCCCTGAACTTTGCAATGGGTCAGAGGTAGGGAAGCGATGGGACAGTGTTGGTATGAGGTCTCCCTGCACAGGTCATCTGCTCAGGTAGCCTCAGACCCAACAGCTTCCAAGACTGCACAGACAGACAGAAAAGCAGACAGAGCCGCTCACTATTTGGCACAAACCAGACCAAGAGAACTTACAATAGAAAGTTTATTTTTTGTTCCAGTCAGTATTTTTTCCTTnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnGCTGATCACAGTTTGCTTAAAACAGCCAGACTTGGACAATATTTGTAACTTTGTTCACAAAAACATACATCACTGAAGCTGCGCTTATAAGAGCCACTTCCAGAGTTCGTGCAAAGGGTCCTATAAAGGCACGCAGGGACACACCGCTTGGAGTCACAGTTTTCATCACAGAGTCACTAGTCACTACACGTCGAACAAGTTGTGTCTCATCAAGTCACCTCTACAACAGCATTAATTACACAAGGAATATAGGTAGTTTGAATAAAAATATCTTTAACAGCTTGGAGCTATTGAGACAGGAACACTTCCACGCACATGCACAGTTAAACAACTTGAGTGCAACACACAACATTGGCACTAAACGAGATTGAAGGGGGACTTTTTGTGTGTTTTTTTTTCTCTTTTCTTTTTTTGTTATAGTTACTTCAAGTAACACAGCTTGCTTCATATAAATAAGTTAAAACATCTATTTTTTTTCAAGACAAAGCCATTCAGGACAAAGAGATGAACAGAAAGCAGATCTACTTATACAGGCGCTATAATGGCAATAAACAGGCTCATGATTAAAAGATGAATTAGGGCAACGAGAACAGGGCTTCTTCACAGAAGGAACACAAGGGAGTTTCAGAAAGTCACCTTAGTACTGACACTACGCGGGATCCGCTAATACTGCTCAGTACTTTAAACGCTCAGATACTCAGGGACGGAAGGCCCCTCCTGCCGCGGCCATGCTCATGCTTTTCAGCTTATTATCTTTTTTCCACTTCATTCTCCGGTTTTGGAACCAGATTTTAATTTGTCTCTCGGAGAGGCAAAGAGCATGTGCTATTTCAATCCTCCTTCTGCGGGTCAGGTAACGGTTGAAGTGGAACTCCTTCTCCAGCTCCAGGGTCTGGTAGCGCGTGTAGGCCGTCCGGGCCCTTTTGCCTTCCGGGCCGCCTATGTTGTCTGCAATAGAAAAGTCAGCGGTTTAGCCACCAACTCCTGTCTTCCAAAGTCCGCCAGGGGGACAAGCTTGGGTCATGAGCAGGGAACCCAGGCGAAAAGCTCAACAAGTTCTGCCTACCAGCCCGCACACCCCTCCCGAATTTCCTTCTCTCTTCCTTTCTAGAAAGAAAACAATACGATTTGGACCCTGGGAACAATCTGCCCATCTGAGGCTGGGGCCGTGTCCCGGCGGACTCCGGCTTTCCCTGGCCCCTCTCCTGCCCCCTCCGCCCTGCCCCGGGCGCCCCGATCGGGAGGCACAGCCCTCCCAGGCTGCCCACCGCACAGAAACCCAGGAAGCAAGGCCCTTTCCTGAGCGCCCAAGTGGCCTTCGGGTCACCCTCCCTCAAAGTTCCAGCCCCGAGAGCCGCCTCCCGTTTCCAGCCTGCAGGGTTGGGGAGCCTGTTTTCTTTTTCTTCCCTTTCCTTCTCTCTCCCTCCTGCCCCCAAAATTCAGAATCCTGCAGGCTCTCGCCTCGATTCTTTCCCCCAAGCCCCTTTTCGGGGGCTGTAATTAGTAACGCTGTTTCCCCAGCGTAGCCCTCCTCATAAATTATCCGCCGTGACAAGCCCGATTCACGGCTGCTACAGCCATCCTCTACCTCTCTGCGCCTTGCTCGGCTGGCCTGACCCGGGAGCGCGTCCCAAGGCGTGGGGTTCCAGAGGGGTTTTTTGCTTCCTCCCCCTTCCAACGTCTAAACTGTCCCAGAGAACGCCCATTTCCCCCACTATTTGTGAGCGCAGGGTGCTCGCAAAGAAGAGGAGGAAGGAGGAAGGCAGGGGAGGGAGAACGGCAAGGAGAGCTCCGCAGGGCTGGGAGAAATGAGACCAAGAGAGACTGGGAGAGGGCGGCAGAGAAGAGAGGGGGGACCGAGAGCCGCGTCCCCGCGGTCGCGTGGATTTAGAAAAAGGCTGGCTTTACCATGACTTATGTGCAGCTTGCGCATCCAGGGGTAGATCTGGGGTTGGGCGGGCGGCGCCGGGCTCGGCTCGCTCTGCGCACTCGCCTGCTCGCTGCTGGCAGGGGCGTCCTCCTCGGCTCCGGACGCCGTGCCAACCCCCTCTCTGCTGCTGATGTGGGTGCTGCCGGCGTCGGCCGAGGCGCCGCTGGAGTTGCTTAGGGAGTTTTTCCCGCCGTGGTGGCTGTCGCTGCCGGGCGAGGGGGCCACGGCGGAGCAGGGCAGCGGATCGGGCTGAGGAGAGTGCGTGGACGTGGCCGGCTGGCTGTACCTGGGCTCGGCGGGCGCCGCGCTGGCGCTGGCAGCGTAGCTGCGGGCGCGCTCTCCGGAGCCAAAGTGGCCGGAGCCCGAGCGGCCGACGCTGAGATCCATGCCATTGTAGCCGTAGCCGTACCTGCCGGAGTGCATGCTCGCCGAGTCCCTGAATTGCTCGCTCACGGAACTATGATCTCCATAATTATGCAACTGGTAGTCCGGGCCATTTGGATAGCGACCGCAAAATGAGTTTACAAAATAAGAGCTCATTTGTTTTTTGATATGTGTGCTTGATTTGTGGCTCGCGGTCGTTTGTGCGTCTATAGCACCCTTGCACAATTTATGATGAATTATGGAAATGACTGGGACATGTACTTGGTTCCCTCCTACGTAGGCACCCAAATATGGGGTACGACTTCGAATCACGTGCTTTTGTTGTCCAGTCGTAAATCCTGCCTGATGACCTCTAGAGGTAAACTCGTGCACTAATAGGGGAGTTGGGTGGAGGCGAGGGGGGTnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnAGTTGCCGCCGTTCAGCCGGACTCGAGCGCCACCCGCTGGAGGCAGGGCTCATCGCCCAGCTTCCGACCGGGGGCTGCAAGGGCCGGGGTCGAATTGAGGTTACAGCCCATTATGGCAAAATTATTGCATTTCCCTCGCAGTTCCATTAGGATGTACCAATTGTTAGGCCGTCAGCTGCCGATCGCGCGCCCGGCGAGGATGCAGAGGATTGGGGGGAGGTGGTGACTTGCATTTTATTTACAACAACTTTATTTCCCCCGTTTTGCAGCCCCTCTTATTTTTGTGTCGAGGTTGGGGTCGGTACTGACCGTCCTGCCAGCAGCTCTGAATTTTGAAAATACAGATATCACCTTCGGGGAAGGGGGAAAGCCATTTAGCCAATTGGAGAAATAAATCCTGCCCGCAGCAGCAGCAGCTACAATTACGGCTCTGTTTTTGCGAGCGCATGAGGGACAGTGTCCCTGCCGCTCTTAAATGACAGGCGTCTATTAAAGATAGCTTTTGTGTAGTGTTTCTCCAAGGCGAGGTCAAATTCCATACACTTTTATAACCGTAGTCGATTTTTCTTTCGTGTGAATATGGTTTTCGTGTCATTAGTTTGCGATTTGATTTGCTTACGTATCCAGCCTGGAAAATCTTCATCACAGGGTCCGGTTCCTCGAGCCAGCCGGGCCCCAAGTCGGAGGGTTCTCCTTGAACCCAGCGAGTGGGCCCAGGCTCCCTGCAGCCACAGAGGCTGCCTGGGGTCTGGGGATCCGTGGGGCGGGTTACTGGGGTCTTGCTTAGACCTCCAGGAGTAAAATGAGGGCGATAATGGAAGCATTCCTTGGCAGTGCCTAGTATCTCTGTAGTTATTTTCCACGGCTCCGAAAGACTCAAGTAAATCACAAATATAGCTGAGAGGCAAGTGGAGTCTCCCCGCTGGAGGCCCGGCGTTGCAGGCGCCCCTGGCACGTCTGGAAGCCAGGACTCTGGCGGCTCCCATGGCCCTGGGCCCCTCGTTGGGTCCTGAACGCTGCTGTGGCGGCGACGCGGGCGCTATCGGAGGCTGGGAGCGGGAATCCGGAGCCGGGAGCCTACCCCGGGCTGTAATGTTCCACCCGCGCCCAGGTTAACTCGCCTCGGCTGAGGCTGCTTCTCTTCCACTGACGGTTGCACACGCGGGACCGAGAGACTGGGCTCTGTTGGGGCCCCCTTTGTTCCTCGAGCTTCCTTCCTGTTCTGGGAGGCGGCTTGGGAGGCCGCGACAAGGCCGGGCTCCAGCTCTTAGACCCCCTCTTTCCACTGGCCAGAGATGATTTGATGATGCCCTTCGGGACTTACTGGCGAGGGACTTAGGCAGAGACGCCCAGACACGAAACGGGGCTCGGCCCAGGGCTCTTTCCTCCCCAGCAGCCCCGCGTCCCGAGGTCGGGGAGCTCAGAGACACTAGCACAGGAGCCCCAGACGCATTCAGGGCGCACCCCAGAACTCCGGAGCCGGTTTGGGCATCCTTGTGGAGCGGGACTGGGTGTGTGCAGTGCGCCCCGCTCCACCGCTGGTATTGGCTGTGTGTGAGnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnAAGAAATAAATGCACAGACGCTTGCAAAGCTCCGGGCTCCCCTGAAGCTGCGGAAGCCCCCAGATGGGAGCAGGCGGGGAGAAAAGTTGGGGAACAGGCGAGGGCAAGGGGGCAAAGCCGAAGGAGGTTGCAGCGCTGGCCTGGTCCCTGCCCAGGCATCTACTCGCCCGCCTTTGCCTCTGAGTCCTCCCCGCTGGGCTGCGTGGAATTGATGAGCTTGTTTTCCTTTTTCCACTTCATGCGGCGGTTCTGGAACCAGATCTTGATCTGGCGCTCGGTGAGGCAGAGCGCGTTGGCGATCTCGATGCGGCGGCGCCGTGTCAGGTAGCGGTTGAAGTGGAACTCCTTCTCCAGCTCCAGTGTCTG";
+  Sequence seq(s, reduced_dna_alphabet);
+  string a = "HumanHXA5\n"
+">hg18_knownGene_NM_019102_0\n"
+"GGGTGCTATAGACGCACAAACGACCGCGAGCCACAAATCAAGCACACATATCAAAAAACAAATGAGCTCTTATTTTGTAAACTCATTTTGCGGTCGCTATCCAAATGGCCCGGACTACCAGTTGCATAATTATGGAGATCATAGTTCCGTGAGCGAGCAATTCAGGGACTCGGCGAGCATGCACTCCGGCAGGTACGGCTACGGCTACAATGGCATGGATCTCAGCGTCGGCCGCTCGGGCTCCGGCCACTTTGGCTCCGGAGAGCGCGCCCGCAGCTACGCTGCCAGCGCCAGCGCGGCGCCCGCCGAGCCCAGGTACAGCCAGCCGGCCACGTCCACGCACTCTCCTCAGCCCGATCCGCTGCCCTGCTCCGCCGTGGCCCCCTCGCCCGGCAGCGACAGCCACCACGGCGGGAAAAACTCCCTAAGCAACTCCAGCGGCGCCTCGGCCGACGCCGGCAGCACCCACATCAGCAGCAGAGAGGGGGTTGGCACGGCGTCCGGAGCCGAGGAGGACGCCCCTGCCAGCAGCGAGCAGGCGAGTGCGCAGAGCGAGCCGAGCCCGGCGCCGCCCGCCCAACCCCAGATCTACCCCTGGATGCGCAAGCTGCACATAAGTCATG\n"
+"\n"
+">hg18_knownGene_NM_019102_1\n"
+"ACAACATAGGCGGCCCGGAAGGCAAAAGGGCCCGGACGGCCTACACGCGCTACCAGACCCTGGAGCTGGAGAAGGAGTTCCACTTCAACCGTTACCTGACCCGCAGAAGGAGGATTGAAATAGCACATGCTCTTTGCCTCTCCGAGAGACAAATTAAAATCTGGTTCCAAAACCGGAGAATGAAGTGGAAAAAAGATAATAAGCTGAAAAGCATGAGCATGGCCGCGGCAGGAGGGGCCTTCCGTCCCTGAGTATCTGAGCGTTTAAAGTACTGAGCAGTATTAGCGGATCCCGCGTAGTGTCAGTACTAAGGTGACTTTCTGAAACTCCCTTGTGTTCCTTCTGTGAAGAAGCCCTGTTCTCGTTGCCCTAATTCATCTTTTAATCATGAGCCTGTTTATTGCCATTATAGCGCCTGTATAAGTAGATCTGCTTTCTGTTCATCTCTTTGTCCTGAATGGCTTTGTCTTGAAAAAAAATAGATGTTTTAACTTATTTATATGAAGCAAGCTGTGTTACTTGAAGTAACTATAACAAAAAAAGAAAAGAGAAAAAAAAACACACAAAAAGTCCCCCTTCAATCTCGTTTAGTGCCAATGTTGTGTGTTGCACTCAAGTTGTTTAACTGTGCATGTGCGTGGAAGTGTTCCTGTCTCAATAGCTCCAAGCTGTTAAAGATATTTTTATTCAAACTACCTATATTCCTTGT\n";
+  stringstream annot(a);
+
+  seq.load_annot(annot, 0, 0);
+
+  BOOST_CHECK_EQUAL( seq.annotations().size(),  2 );
+}
+
 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
 {
   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
-- 
2.30.2