test annotating a sequence with fasta records in a stream

[mussa.git] / alg / test / test_sequence.cpp

diff --git a/alg/test/test_sequence.cpp b/alg/test/test_sequence.cpp
index 9faa8d069c156376ce945202527664b9955d47e6..9784621a01ab9da2273461e0056d365753240b97 100644 (file)
--- 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"