Store Sequence sequence location in a shared_ptr class

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

diff --git a/alg/test/test_glseqbrowser.cpp b/alg/test/test_glseqbrowser.cpp
index 9e23d28436b32e03dcaf93d3f6f82b6471170620..bbed0623312d5252e4a80f8eab1403408ac376aa 100644 (file)
--- a/alg/test/test_glseqbrowser.cpp
+++ b/alg/test/test_glseqbrowser.cpp
@@ -1,3 +1,4 @@
+#define BOOST_AUTO_TEST_MAIN
 #include <boost/test/auto_unit_test.hpp>
 #include <boost/assign/std/vector.hpp>
 using namespace boost::assign;
@@ -34,27 +35,88 @@ BOOST_AUTO_TEST_CASE ( gltracks_connect )
   vector<int> path;
                 path += 1,1,1; gt.link(path, rc, 1);
   path.clear(); path += 1,1,3; gt.link(path, rc, 1); 
+  path.clear(); path += 1,2,1; gt.link(path, rc, 1);                 
   path.clear(); path += 2,3,3; gt.link(path, rc, 1); 
   path.clear(); path += 3,3,3; gt.link(path, rc, 1);
 
+  // this represents the "depth" of the path_segment AKA sequences -1
   BOOST_CHECK_EQUAL( gt.path_segments.size(), 2 );
-  GlSeqBrowser::segment_key p(1, 1);
-  GlSeqBrowser::pair_segment_map::iterator psm_i = gt.path_segments[0].find(p);
+  BOOST_CHECK_EQUAL( gt.path_segments[0].size(), 4);
+  BOOST_CHECK_EQUAL( gt.path_segments[1].size(), 4);
+  GlSeqBrowser::segment_key p11(1, 1);
+  GlSeqBrowser::segment_key p23(2, 3);
+  GlSeqBrowser::segment_key p33(3, 3);
+  GlSeqBrowser::segment_key p13(1, 3);
+  GlSeqBrowser::pair_segment_map::iterator psm_i = gt.path_segments[0].find(p11);
   BOOST_CHECK( psm_i != gt.path_segments[0].end() );
   BOOST_CHECK_EQUAL( psm_i->second.path_ids.size(), 2 );
-
+  // exaustively test the other keys in the first row
+  psm_i = gt.path_segments[0].find(p23);
+  BOOST_CHECK( psm_i != gt.path_segments[0].end());
+  psm_i = gt.path_segments[0].find(p33);
+  BOOST_CHECK( psm_i != gt.path_segments[0].end());
+  // should be missing
+  psm_i = gt.path_segments[0].find(p13); 
+  BOOST_CHECK( psm_i == gt.path_segments[0].end());
+  
   gt.clear();
   BOOST_CHECK_EQUAL( gt.path_segments.size(), 0 );
 }
 
+BOOST_AUTO_TEST_CASE ( gltracks_connect_different_lengths )
+{
+  string s0("AAGGCCTT");
+  string s1("TTGGCCAA");
+  string s2("GATTACAA");
+  Sequence seq0(s0);
+  Sequence seq1(s1);
+  Sequence seq2(s2);
+
+  GlSeqBrowser gt;
+  gt.push_sequence(seq0);
+  gt.push_sequence(seq1);
+  gt.push_sequence(seq2);
+
+  // make up some sample data
+  vector<bool> rc;
+  rc += false, false, false;
+  vector<int> path;
+                path += 1,1,1; gt.link(path, rc, 5);
+  path.clear(); path += 1,1,3; gt.link(path, rc, 1); 
+  path.clear(); path += 2,3,3; gt.link(path, rc, 1); 
+  path.clear(); path += 3,3,3; gt.link(path, rc, 3);
+  path.clear(); path += 4,3,3; gt.link(path, rc, 2);
+
+  // this represents the "depth" of the path_segment AKA sequences -1
+  BOOST_CHECK_EQUAL( gt.path_segments.size(), 2 );
+  BOOST_CHECK_EQUAL( gt.path_segments[0].size(), 4);
+  BOOST_CHECK_EQUAL( gt.path_segments[1].size(), 3);
+  GlSeqBrowser::segment_key p1(1, 1);
+  GlSeqBrowser::pair_segment_map::iterator psm1_i = gt.path_segments[0].find(p1);
+  BOOST_CHECK( psm1_i != gt.path_segments[0].end() );
+  BOOST_CHECK_EQUAL( psm1_i->second.start.x, 1); //start segment x coordinate
+  BOOST_CHECK_EQUAL( psm1_i->second.end.x, 1); //end segment x coordinate
+  BOOST_CHECK_EQUAL( psm1_i->second.length, 5); 
+  // there should be two paths, the sizes don't match
+  BOOST_CHECK_EQUAL( psm1_i->second.path_ids.size(), 2 );
+  
+  // look at the second row
+  GlSeqBrowser::segment_key p2(3,3);
+  GlSeqBrowser::pair_segment_map::iterator psm2_i = gt.path_segments[1].find(p2);
+  BOOST_CHECK( psm2_i != gt.path_segments[1].end() );
+  BOOST_CHECK_EQUAL( psm2_i->second.start.x, 3); //start segment x coordinate
+  BOOST_CHECK_EQUAL( psm2_i->second.end.x, 3); //end segment x coordinate
+  BOOST_CHECK_EQUAL( psm2_i->second.length, 3); 
+}
+
 BOOST_AUTO_TEST_CASE( glseqbrowser_center )
 {
   string s0("AAGGCCTT");
   string s1("TTGGCCAA");
   string s2("GATTACAA");
-  boost::shared_ptr<Sequence> seq0(new Sequence(s0));
-  boost::shared_ptr<Sequence> seq1(new Sequence(s1));
-  boost::shared_ptr<Sequence> seq2(new Sequence(s2));
+  Sequence seq0(s0);
+  Sequence seq1(s1);
+  Sequence seq2(s2);
   boost::shared_ptr<AnnotationColors> cm(new AnnotationColors);
   GlSequence glseq0(seq0, cm);
   GlSequence glseq1(seq1, cm);