more error messages for loading an annotation.

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

diff --git a/alg/test/test_mussa.cpp b/alg/test/test_mussa.cpp
index cfa873515c7234d3ffbd8646c7d8be9db9ceb6c4..16068473c01500185aedec71871fd90cd1818374 100644 (file)
--- a/alg/test/test_mussa.cpp
+++ b/alg/test/test_mussa.cpp
@@ -1,3 +1,4 @@
+#define BOOST_AUTO_TEST_MAIN
 #include <boost/test/auto_unit_test.hpp>
 #include <boost/filesystem/path.hpp>
 #include <boost/filesystem/operations.hpp>
@@ -160,6 +161,14 @@ BOOST_AUTO_TEST_CASE( mussa_mupa_is_file_not_directory )
   BOOST_CHECK_THROW(m1.load_mupa_file( curdir ), mussa_load_error );
 }
 
+// catch error if annotation isn't a file
+BOOST_AUTO_TEST_CASE( mussa_annotation_is_not_file )
+{
+  Mussa m1;
+  fs::path full_path(fs::path(EXAMPLE_DIR, fs::native) / "directory.mupa");
+  BOOST_CHECK_THROW( m1.load_mupa_file( full_path ), mussa_load_error );
+}
+
 BOOST_AUTO_TEST_CASE( mussa_load_analysis )
 {
   fs::path example_dir(EXAMPLE_DIR, fs::native);
@@ -360,9 +369,9 @@ BOOST_AUTO_TEST_CASE( mussa_add_motif )
 }
 
 static void 
-local_align_test(const Mussa::vector_sequence_type &seqs, 
-                 const list<ConservedPath::path_type>& result,
-                 const list<vector<bool> >& reversed)
+two_way_local_align_test(const Mussa::vector_sequence_type &seqs, 
+                         const list<ConservedPath::path_type>& result,
+                         const list<vector<bool> >& reversed)
 {
   map<char, vector <char> >  m;
   assign::insert(m)('A', assign::list_of('A')('T') )
@@ -390,9 +399,8 @@ local_align_test(const Mussa::vector_sequence_type &seqs,
     BOOST_CHECK_EQUAL( first_basepair, complimented_second) ;
   }
 }
-
                  
-BOOST_AUTO_TEST_CASE( local_alignment )
+BOOST_AUTO_TEST_CASE( two_way_local_alignment )
 {
   string s0("GCGCATAT");
   string s1("AAAAAAAT");
@@ -405,6 +413,8 @@ BOOST_AUTO_TEST_CASE( local_alignment )
   analysis.set_window(4);
   analysis.analyze();
   NwayPaths npath = analysis.paths();
+  BOOST_REQUIRE_EQUAL( npath.pathz.size(), 2 );
+  
   list<ConservedPath::path_type> result;
   list<vector<bool> > reversed;
   list<ConservedPath>::iterator pathz_i = npath.pathz.begin();
@@ -416,7 +426,7 @@ BOOST_AUTO_TEST_CASE( local_alignment )
                                 result,
                                 reversed);
 
-  local_align_test(analysis.sequences(), result, reversed);
+  two_way_local_align_test(analysis.sequences(), result, reversed);
 
   ++pathz_i;
   result.clear();
@@ -427,9 +437,64 @@ BOOST_AUTO_TEST_CASE( local_alignment )
                                 selected_paths.end(),
                                 result,
                                 reversed);
-  local_align_test(analysis.sequences(), result, reversed);
+  two_way_local_align_test(analysis.sequences(), result, reversed);
+}
 
+BOOST_AUTO_TEST_CASE( three_way_local_alignment )
+{
+  string s0("AGCAGGGAGGGTTTAAATGGCACCCAGCAGTTGGTGTGAGG");
+  string s1("AGCGGGAAGGGTTTAAATGGCACCGGGCAGTTGGCGTGAGG");
+  string s2("CAGCGCCGGGGTTTAAATGGCACCGAGCAGTTGGCGCAGGG");
+  
+  Mussa analysis;
+  analysis.append_sequence(s0);
+  analysis.append_sequence(s1);
+  analysis.append_sequence(s2);
+  analysis.set_threshold(23);
+  analysis.set_window(30);
+  analysis.analyze();
+  NwayPaths npath = analysis.paths();
+  BOOST_CHECK_EQUAL( npath.refined_pathz.size(), 1 );
+  
+  list<ConservedPath::path_type> result;
+  list<vector<bool> > reversed;
+  // grab 1 path (since there's only one)
+  list<ConservedPath>::iterator pathz_i = npath.pathz.begin();
+  list<ConservedPath> selected_paths;
+  selected_paths.push_back(*pathz_i);
+  analysis.createLocalAlignment(selected_paths.begin(), 
+                                selected_paths.end(),
+                                result,
+                                reversed);
+                                
+  for(std::list<ConservedPath::path_type>::iterator result_i = result.begin();
+      result_i != result.end();
+      ++result_i)
+  {
+    ConservedPath::path_element first_element = *(result_i->begin());
+    for (ConservedPath::path_type::iterator element_i = result_i->begin();
+         element_i != result_i->end();
+         ++element_i)
+    {
+      BOOST_CHECK_EQUAL( *element_i, first_element );
+      BOOST_CHECK_EQUAL( s0[*element_i], s1[*element_i] );
+      BOOST_CHECK_EQUAL( s1[*element_i], s2[*element_i] );
+      BOOST_CHECK_EQUAL( s0[*element_i], s2[*element_i] );
+    }
+  }   
+}
 
+BOOST_AUTO_TEST_CASE( mussa_window_larger_than_sequence )
+{
+  string s0("AGCAGGG");
+  string s1("CAGCGGG");
+  
+  Mussa analysis;
+  analysis.append_sequence(s0);
+  analysis.append_sequence(s1);
+  analysis.set_threshold(23);
+  analysis.set_window(30);
+  BOOST_CHECK_THROW(analysis.analyze(), seqcomp_error);
 }
 
 BOOST_AUTO_TEST_CASE( subanalysis )