X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=blobdiff_plain;f=alg%2Ftest%2Ftest_nway.cpp;h=9c7d34233ffae87ff562ecdf35d7bef3f817586b;hp=68ee988d4cb65187699d9b604c78cdd4eda2a817;hb=HEAD;hpb=8895e01b45d6df1973490d779c9051811f056cae

diff --git a/alg/test/test_nway.cpp b/alg/test/test_nway.cpp
index 68ee988..9c7d342 100644
--- a/alg/test/test_nway.cpp
+++ b/alg/test/test_nway.cpp
@@ -1,4 +1,7 @@
-#include <boost/test/auto_unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE test_nway
+#include <boost/test/unit_test.hpp>
+
 #include <boost/filesystem/path.hpp>
 namespace fs = boost::filesystem;
 
@@ -19,11 +22,18 @@ BOOST_AUTO_TEST_CASE( nway_null )
   string s2("TTTTNNNN");
 
   Mussa analysis;
-  analysis.add_a_seq(s0);
-  analysis.add_a_seq(s1);
-  analysis.add_a_seq(s2);
-  analysis.analyze(4,3);
+  analysis.append_sequence(s0);
+  analysis.append_sequence(s1);
+  analysis.append_sequence(s2);
+  analysis.set_window(4);
+  analysis.set_threshold(3);
+  analysis.analyze();
   NwayPaths npath = analysis.paths();
+  // we added 3 sequences, but none-matched
+  BOOST_CHECK_EQUAL( npath.sequence_count(), 0); 
+  BOOST_CHECK_EQUAL( npath.size(), 0 );
+  BOOST_CHECK_EQUAL( npath.path_size(), 0 );
+  BOOST_CHECK_EQUAL( npath.refined_path_size(), 0 );
   // there should be no paths for these sequences
   for (std::list<ConservedPath >::iterator pathz_i = npath.pathz.begin();
        pathz_i != npath.pathz.end();
@@ -40,10 +50,16 @@ BOOST_AUTO_TEST_CASE( nway_test )
   Sequence seq1(s1);
 
   Mussa analysis;
-  analysis.add_a_seq(s0);
-  analysis.add_a_seq(s1);
-  analysis.analyze(4,3);
+  analysis.append_sequence(s0);
+  analysis.append_sequence(s1);
+  analysis.set_window(4);
+  analysis.set_threshold(3);
+  analysis.analyze();
   NwayPaths npath = analysis.paths();
+  BOOST_CHECK_EQUAL( npath.sequence_count(), 2); 
+  BOOST_CHECK_EQUAL( npath.size(), 2 );
+  BOOST_CHECK_EQUAL( npath.path_size(), 2 );
+  BOOST_CHECK_EQUAL( npath.refined_path_size(), 2 );
   for (std::list<ConservedPath >::iterator pathz_i = npath.pathz.begin();
        pathz_i != npath.pathz.end();
        ++pathz_i)
@@ -59,23 +75,27 @@ BOOST_AUTO_TEST_CASE( nway_test )
 
 BOOST_AUTO_TEST_CASE( nway_refine )
 {
-  fs::path mupa_path( EXAMPLE_DIR );
+  fs::path mupa_path( EXAMPLE_DIR, fs::native );
   mupa_path /= "mck3test.mupa";
   Mussa m1;
   m1.load_mupa_file( mupa_path );
-  m1.analyze(0, 0);
+  m1.analyze();
   const NwayPaths& npath = m1.paths();
-  BOOST_CHECK_EQUAL (npath.path_size(), npath.refined_path_size());
+  //BOOST_CHECK_EQUAL (npath.path_size(), npath.refined_path_size());
+  // FIXME: shouldn't these be equal to start with?
+  BOOST_CHECK(npath.path_size() > npath.refined_path_size());
   size_t first_refined_size = npath.refined_path_size();
   BOOST_CHECK( first_refined_size > 0 );
 
   // we're using a window size 30 (threshold 20) example
-  m1.set_soft_thres(22);
+  m1.set_soft_threshold(22);
   m1.nway();
+  BOOST_CHECK_EQUAL( npath.path_size(), npath.size() );
+  BOOST_CHECK( npath.path_size() > 0 );
   BOOST_CHECK( npath.refined_path_size() > 0);
   BOOST_CHECK( npath.refined_path_size() < first_refined_size);
 
-  m1.set_soft_thres(20);
+  m1.set_soft_threshold(20);
   m1.nway();
   BOOST_CHECK_EQUAL(npath.refined_path_size(), first_refined_size);
 }
@@ -179,11 +199,13 @@ GTTTTAATAAATGCACAATGCTCTCTTCCTGTTCTTC";
 
   // now that we've got some data lets see if it crashes
   Mussa m1;
-  m1.add_a_seq(seq1);
-  m1.add_a_seq(seq2);
-  m1.add_a_seq(seq3);
+  m1.append_sequence(seq1);
+  m1.append_sequence(seq2);
+  m1.append_sequence(seq3);
 
-  m1.analyze(10, 8);
-  m1.set_soft_thres(10);
+  m1.set_window(10);
+  m1.set_threshold(8);
+  m1.analyze();
+  m1.set_soft_threshold(10);
   m1.nway();
 }