ticket:62 fix local alignment

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

diff --git a/alg/test/test_conserved_path.cpp b/alg/test/test_conserved_path.cpp
index 7050a73a11bfc5b4e625d4cc76c22fcda51ac5a5..f8d670c31fd62a81faf084bc997709e110c2701c 100644 (file)
--- a/alg/test/test_conserved_path.cpp
+++ b/alg/test/test_conserved_path.cpp
@@ -22,7 +22,7 @@ BOOST_AUTO_TEST_CASE ( conserved_path_simple )
   cp1.track_indexes = path;
   BOOST_CHECK_EQUAL( cp1.size(), path.size() );
 
-  ConservedPath cp2(18, path);
+  ConservedPath cp2(20, 18, path);
   BOOST_CHECK_EQUAL (cp1, cp2);
   BOOST_CHECK_EQUAL( cp2.size(), path.size() );
 
@@ -69,7 +69,7 @@ BOOST_AUTO_TEST_CASE ( conserved_path_reverse_compliment )
   vector<int> path;
   path += 3,4,-5,1; // magic from boost assign
 
-  ConservedPath cp1(10, path);
+  ConservedPath cp1(20, 10, path);
   vector<bool> reversed = cp1.reverseComplimented();
 
   BOOST_CHECK_EQUAL( path.size(), reversed.size());
@@ -88,24 +88,24 @@ BOOST_AUTO_TEST_CASE ( extended_conserved_path_simple )
   vector<int> path;
   path += 3,4,5,1; // magic from boost assign
 
-  ExtendedConservedPath ecp1;
+  ConservedPath ecp1;
   ecp1.window_size = 30;
   ecp1.score = 18;
   ecp1.track_indexes = path;
   BOOST_CHECK_EQUAL ( ecp1.size(), path.size() );
 
-  ExtendedConservedPath ecp2(30, 18.0, path);
+  ConservedPath ecp2(30, 18.0, path);
   BOOST_CHECK_EQUAL ( ecp1, ecp2 );
   BOOST_CHECK_EQUAL ( ecp2.size(), path.size() );
 
-  ExtendedConservedPath ecp_ne(35, 20.0, path);
+  ConservedPath ecp_ne(35, 20.0, path);
   BOOST_CHECK(ecp2 != ecp_ne);
 
   ConservedPath cp1;
   cp1.score = 18;
   cp1.track_indexes = path;
 
-  ExtendedConservedPath ecp3(30, cp1);
+  ConservedPath ecp3(cp1);
   BOOST_CHECK_EQUAL( ecp2, ecp3 );
   BOOST_CHECK_EQUAL( ecp3.size(), path.size() );
 }
@@ -123,10 +123,10 @@ BOOST_AUTO_TEST_CASE ( extended_conserved_path_growth )
   path_not_next += 4,5,6,5; 
   const int window_size = 4;
 
-  ExtendedConservedPath ecp_base(window_size, 20, path_base);
-  ConservedPath cp_next(25, path_next);
-  ConservedPath cp_next_reversed(25, path_next_reversed);
-  ConservedPath cp_not_next(22, path_not_next);
+  ConservedPath ecp_base(window_size, 20, path_base);
+  ConservedPath cp_next(window_size, 25, path_next);
+  ConservedPath cp_next_reversed(window_size, 25, path_next_reversed);
+  ConservedPath cp_not_next(window_size, 22, path_not_next);
 
   BOOST_CHECK(ecp_base.nextTo(cp_next));
   BOOST_CHECK(!ecp_base.nextTo(cp_not_next));
@@ -145,7 +145,7 @@ BOOST_AUTO_TEST_CASE ( extended_conserved_normalized )
   vector<int> normalized_path;
   normalized_path += 3,4, 5,9;
 
-  ExtendedConservedPath ecp1;
+  ConservedPath ecp1;
   ecp1.window_size = 10;
   ecp1.score = 18;
   ecp1.track_indexes = path;