X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=blobdiff_plain;f=alg%2Ftest%2Ftest_sequence.cpp;h=9faa8d069c156376ce945202527664b9955d47e6;hp=82ff14be6c1ff40c6d9ce1155def83c0c5e4dda7;hb=15f9eb9d7ba5ffe32cbe7bc67a9d85b714c27871;hpb=9d76ff624ae315a1262d6ceba1faeb68484ebd85

diff --git a/alg/test/test_sequence.cpp b/alg/test/test_sequence.cpp
index 82ff14b..9faa8d0 100644
--- a/alg/test/test_sequence.cpp
+++ b/alg/test/test_sequence.cpp
@@ -586,6 +586,22 @@ BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
   BOOST_CHECK_EQUAL( annots[0]->annotations()->get("type"), "type");
 }
 
+// when we do a subsequence (or something that calls copy_children)
+// the annotations need to be updated to have the right parent
+BOOST_AUTO_TEST_CASE( update_annotations_seqref )
+{
+  Sequence s1("AAAAGGGG");
+  s1.add_annotation("A", "A", 0, 4);
+  BOOST_CHECK_EQUAL(s1.annotations().size(), 1);
+  BOOST_CHECK_EQUAL(s1.seqspan(), s1.annotations().front()->parent() );
+  
+  Sequence subseq1(s1.subseq(2,4));
+  BOOST_CHECK_EQUAL(subseq1.annotations().size(), 1);
+  BOOST_CHECK_EQUAL(subseq1.annotations().front()->parentStart(), 0 );
+  BOOST_CHECK_EQUAL(subseq1.annotations().front()->parentStop(), 2 );
+  BOOST_CHECK_EQUAL(subseq1.seqspan(), subseq1.annotations().front()->parent() );
+}
+
 // ticket:83 when you try to load a sequence from a file that doesn't
 // have fasta headers it crashes. 
 BOOST_AUTO_TEST_CASE( sequence_past_end ) 
@@ -840,22 +856,22 @@ BOOST_AUTO_TEST_CASE( subseq_annotation_test )
   BOOST_REQUIRE_EQUAL( annots_list.size(), 4 );
   
   std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
-  BOOST_CHECK_EQUAL( annots[0]->start(),  0);
+  BOOST_CHECK_EQUAL( annots[0]->parentStart(),  0);
   BOOST_CHECK_EQUAL( annots[0]->size(),  5);
   BOOST_REQUIRE( annots[0]->annotations() );
   BOOST_CHECK_EQUAL( annots[0]->annotations()->name(), "0-10");
 
-  BOOST_CHECK_EQUAL( annots[1]->start(), 5);
-  BOOST_CHECK_EQUAL( annots[1]->size(), 10);
+  BOOST_CHECK_EQUAL( annots[1]->parentStart(), 5);
+  BOOST_CHECK_EQUAL( annots[1]->size(), 5);
   BOOST_REQUIRE( annots[1]->annotations() );
   BOOST_CHECK_EQUAL( annots[1]->annotations()->name(), "10-20");
 
-  BOOST_CHECK_EQUAL( annots[2]->start(), 0);
+  BOOST_CHECK_EQUAL( annots[2]->parentStart(), 0);
   BOOST_CHECK_EQUAL( annots[2]->size(), 10);
   BOOST_REQUIRE( annots[2]->annotations() );
   BOOST_CHECK_EQUAL( annots[2]->annotations()->name(), "0-20");
 
-  BOOST_CHECK_EQUAL( annots[3]->start(), 3);
+  BOOST_CHECK_EQUAL( annots[3]->parentStart(), 3);
   BOOST_CHECK_EQUAL( annots[3]->size(),  7);
   BOOST_REQUIRE( annots[3]->annotations() );
   BOOST_CHECK_EQUAL( annots[3]->annotations()->name(), "8-12");