ticket:62 fix local alignment

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

diff --git a/alg/test/test_mussa.cpp b/alg/test/test_mussa.cpp
index da17b226bc510bca0f96799222eec4dc36518dfa..f215816efd396bc8925ebc9e242b375ff8da0873 100644 (file)
--- a/alg/test/test_mussa.cpp
+++ b/alg/test/test_mussa.cpp
@@ -1,6 +1,10 @@
 #include <boost/test/auto_unit_test.hpp>
 #include <boost/filesystem/operations.hpp>
 namespace fs = boost::filesystem;
+#include <boost/assign/list_of.hpp>
+#include <boost/assign/list_inserter.hpp>
+#include <boost/assign.hpp>
+namespace assign = boost::assign;
 
 #include <string>
 #include <sstream>
@@ -160,3 +164,76 @@ BOOST_AUTO_TEST_CASE( mussa_add_motif )
   m1.add_motifs(motifs, colors);
   BOOST_CHECK_EQUAL( first_size, m1.motifs().size() );
 }
+
+static void 
+local_align_test(const vector<Sequence> &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') )
+                   ('T', assign::list_of('T')('A') )
+                   ('G', assign::list_of('G')('C') )
+                   ('C', assign::list_of('C')('G') );
+  list<vector<bool> >::const_iterator rc_i = reversed.begin();
+
+  for(list<ConservedPath::path_type>::const_iterator base_i = result.begin();
+      base_i != result.end();
+      ++base_i, ++rc_i)
+  {
+    // since the reverse compliment flag is relative to the first sequence
+    // the first one should always be false
+    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];
+    // 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
+    const char complimented_second = m[second_basepair][second_compliment_index];
+   
+    BOOST_CHECK_EQUAL( first_basepair, complimented_second) ;
+  }
+}
+
+                 
+BOOST_AUTO_TEST_CASE( local_alignment )
+{
+  string s0("GCGCATAT");
+  string s1("AAAAAAAT");
+  Sequence seq1(s1);
+
+  Mussa analysis;
+  analysis.add_a_seq(s0);
+  analysis.add_a_seq(s1);
+  analysis.analyze(4,3);
+  NwayPaths npath = analysis.paths();
+  list<ConservedPath::path_type> result;
+  list<vector<bool> > reversed;
+  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);
+
+  local_align_test(analysis.sequences(), result, reversed);
+
+  ++pathz_i;
+  result.clear();
+  reversed.clear();
+  selected_paths.clear();
+  selected_paths.push_back(*pathz_i);
+  analysis.createLocalAlignment(selected_paths.begin(), 
+                                selected_paths.end(),
+                                result,
+                                reversed);
+  local_align_test(analysis.sequences(), result, reversed);
+
+
+}
+
+