X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=blobdiff_plain;f=alg%2Ftest%2Ftest_sequence.cpp;h=9784621a01ab9da2273461e0056d365753240b97;hp=9faa8d069c156376ce945202527664b9955d47e6;hb=f3c0553a22b0e4ddc39ee45f51725352d92e97f1;hpb=5e4c30bbdd87540257a0414bdb09d61ba9690ba8

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"