Getting closer to a subanalysis mode

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

diff --git a/alg/test/test_mussa.cpp b/alg/test/test_mussa.cpp
index 79356abcbe85ee46baddc0d406cefd1f74b0d4d0..2ab594a10107eb0bcd2c3bc82193ccad966722b7 100644 (file)
--- a/alg/test/test_mussa.cpp
+++ b/alg/test/test_mussa.cpp
@@ -70,9 +70,9 @@ BOOST_AUTO_TEST_CASE( mussa_sequences )
   analysis.append_sequence(s2);
 
   BOOST_CHECK_EQUAL( analysis.sequences().size(), 3 );
-  BOOST_CHECK_EQUAL( analysis.sequences()[0], s0);
-  BOOST_CHECK_EQUAL( analysis.sequences()[1], s1);
-  BOOST_CHECK_EQUAL( analysis.sequences()[2], s2);
+  BOOST_CHECK_EQUAL( *(analysis.sequences()[0]), s0);
+  BOOST_CHECK_EQUAL( *(analysis.sequences()[1]), s1);
+  BOOST_CHECK_EQUAL( *(analysis.sequences()[2]), s2);
 }
 
 // for some reason we can call nway once safely but it
@@ -147,11 +147,11 @@ BOOST_AUTO_TEST_CASE( mussa_load_motif )
   m1.append_sequence("GGGCCCCTTGGTT");
   m1.load_motifs(test_istream);
 
-  for (vector<Sequence>::const_iterator seq_i = m1.sequences().begin();
+  for (Mussa::vector_sequence_type::const_iterator seq_i = m1.sequences().begin();
        seq_i != m1.sequences().end();
        ++seq_i)
   {
-    BOOST_CHECK( seq_i->motifs().size() > 0 );
+    BOOST_CHECK( (*seq_i)->motifs().size() > 0 );
   }
 }
 
@@ -173,7 +173,7 @@ BOOST_AUTO_TEST_CASE( mussa_add_motif )
 }
 
 static void 
-local_align_test(const vector<Sequence> &seqs, 
+local_align_test(const Mussa::vector_sequence_type &seqs, 
                  const list<ConservedPath::path_type>& result,
                  const list<vector<bool> >& reversed)
 {
@@ -193,8 +193,8 @@ local_align_test(const vector<Sequence> &seqs,
     BOOST_CHECK_EQUAL( (*rc_i)[0], false );
     const int first_path_basepair_index = (*base_i)[0];
     const int second_path_basepair_index = (*base_i)[1];
-    const char first_basepair = seqs[0][first_path_basepair_index];
-    const char second_basepair = seqs[1][second_path_basepair_index];
+    const char first_basepair = (*seqs[0])[first_path_basepair_index];
+    const char second_basepair = (*seqs[1])[second_path_basepair_index];
     // get our index into our reverse compliment map m
     const int second_compliment_index = (*rc_i)[1];
     // lookup the forward or reverse compliment depending on our rc flag