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remove annot class in favor of SeqSpan
[mussa.git] / alg / test / test_sequence.cpp
diff --git a/alg/test/test_sequence.cpp b/alg/test/test_sequence.cpp
index 921c5ef7aa2437a177b6f8094279ccca50d71441..82ff14be6c1ff40c6d9ce1155def83c0c5e4dda7 100644 (file)
--- a/alg/test/test_sequence.cpp
+++ b/alg/test/test_sequence.cpp
@@ -463,16 +463,16 @@ BOOST_AUTO_TEST_CASE( sequence_empty_reverse_iterator)
 BOOST_AUTO_TEST_CASE( annotation_load )
 {
   string annot_data = "human\n"
-                      "0 10 name   type\n"
-                      "10 20 myf7\n"
-                      "20 30 myod\n"
-                      "50\t55 anothername\n"
-                      "60 50 backward\n"
-                      ">ident3 asdf\n"
+                      "0 10 name   type\n"     //0
+                      "10 20 myf7\n"           //1
+                      "20 30 myod\n"           //2
+                      "50\t55 anothername\n"   //3
+                      "60 50 backward\n"       //4
+                      ">ident3 asdf\n"         //7 (as these are added last)
                       "GCT\n"
                       "gCTn\n"
-                      "75\t90\tname2\ttype2\n"
-                      "100 120 name-asdf type!@#$%\n"
+                      "75\t90\tname2\ttype2\n" //5
+                      "100 120 name-asdf type!@#$%\n" //6
                       ;
   string s(100, 'A');
   s += "GCTGCTAATT";
@@ -480,27 +480,37 @@ BOOST_AUTO_TEST_CASE( annotation_load )
                      
   //istringstream annot_stream(annot_data);
   seq.parse_annot(annot_data, 0, 0);
-  std::list<annot> annots_list = seq.annotations();
-  std::vector<annot> annots(annots_list.begin(), annots_list.end());
+  SeqSpanRefList annots_list(seq.annotations());
+  std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
   BOOST_REQUIRE_EQUAL( annots.size(), 8);
-  BOOST_CHECK_EQUAL( annots[0].begin, 0 );
-  BOOST_CHECK_EQUAL( annots[0].end, 10 );
-  BOOST_CHECK_EQUAL( annots[0].type, "type");
-  BOOST_CHECK_EQUAL( annots[0].name, "name");
-  BOOST_CHECK_EQUAL( annots[1].name, "myf7");
-  BOOST_CHECK_EQUAL( annots[2].name, "myod");
-  BOOST_CHECK_EQUAL( annots[3].name, "anothername");
-  BOOST_CHECK_EQUAL( annots[4].name, "backward");
-  BOOST_CHECK_EQUAL( annots[5].name, "name2");
-  BOOST_CHECK_EQUAL( annots[5].end, 90);
-  BOOST_CHECK_EQUAL( annots[6].begin, 100);
-  BOOST_CHECK_EQUAL( annots[6].end, 120);
-  BOOST_CHECK_EQUAL( annots[6].name, "name-asdf");
-  BOOST_CHECK_EQUAL( annots[6].type, "type!@#$%");
+  BOOST_CHECK_EQUAL( annots[0]->start(), 0 );
+  BOOST_CHECK_EQUAL( annots[0]->stop(), 10 );
+  BOOST_REQUIRE( annots[0]->annotations() );
+  BOOST_CHECK_EQUAL( annots[0]->annotations()->get("type"), "type");
+  BOOST_CHECK_EQUAL( annots[0]->annotations()->name(), "name");
+  BOOST_REQUIRE( annots[1]->annotations() );
+  BOOST_CHECK_EQUAL( annots[1]->annotations()->name(), "myf7");
+  BOOST_REQUIRE( annots[2]->annotations() );
+  BOOST_CHECK_EQUAL( annots[2]->annotations()->name(), "myod");
+  BOOST_REQUIRE( annots[3]->annotations() );
+  BOOST_CHECK_EQUAL( annots[3]->annotations()->name(), "anothername");
+  BOOST_REQUIRE( annots[4]->annotations() );
+  BOOST_CHECK_EQUAL( annots[4]->annotations()->name(), "backward");
+  BOOST_REQUIRE( annots[5]->annotations() );
+  BOOST_CHECK_EQUAL( annots[5]->annotations()->name(), "name2");
+  BOOST_CHECK_EQUAL( annots[5]->start(), 75);
+  BOOST_CHECK_EQUAL( annots[5]->stop(), 90);
+  BOOST_CHECK_EQUAL( annots[6]->start(), 100);
+  BOOST_CHECK_EQUAL( annots[6]->stop(), 110);
+  BOOST_REQUIRE( annots[6]->annotations() );
+  BOOST_CHECK_EQUAL( annots[6]->annotations()->name(), "name-asdf");
+  BOOST_CHECK_EQUAL( annots[6]->annotations()->get("type"), "type!@#$%");
   // sequence defined annotations will always be after the
   // absolute positions
-  BOOST_CHECK_EQUAL( annots[7].name, "ident3 asdf");
-  BOOST_CHECK_EQUAL( annots[7].begin, 100);
+  BOOST_REQUIRE( annots[7]->annotations() );
+  BOOST_CHECK_EQUAL( annots[7]->annotations()->name(), "ident3 asdf");
+  BOOST_CHECK_EQUAL( annots[7]->start(), 100);
+  BOOST_CHECK_EQUAL( annots[7]->stop(), 107);
 
   //BOOST_CHECK_EQUAL( annots
 }
@@ -545,7 +555,7 @@ BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
     "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
   Sequence seq(s, reduced_dna_alphabet);
   seq.parse_annot(annot_data);
-  std::list<annot> annots = seq.annotations();
+  SeqSpanRefList annots(seq.annotations());
   BOOST_CHECK_EQUAL( annots.size(), 2);
 }
 
@@ -568,12 +578,12 @@ BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
                      
   //istringstream annot_stream(annot_data);
   seq.parse_annot(annot_data, 0, 0);
-  std::list<annot> annots_list = seq.annotations();
-  std::vector<annot> annots(annots_list.begin(), annots_list.end());
+  SeqSpanRefList annots_list(seq.annotations());
+  std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
   BOOST_REQUIRE_EQUAL( annots.size(), 8);
-  BOOST_CHECK_EQUAL( annots[0].begin, 0 );
-  BOOST_CHECK_EQUAL( annots[0].end, 10 );
-  BOOST_CHECK_EQUAL( annots[0].type, "type");
+  BOOST_CHECK_EQUAL( annots[0]->start(), 0 );
+  BOOST_CHECK_EQUAL( annots[0]->stop(), 10 );
+  BOOST_CHECK_EQUAL( annots[0]->annotations()->get("type"), "type");
 }
 
 // ticket:83 when you try to load a sequence from a file that doesn't
@@ -742,12 +752,14 @@ BOOST_AUTO_TEST_CASE( sequence_motif_subseq)
 
 BOOST_AUTO_TEST_CASE( annot_test )
 {
-  annot a(0, 10, "test", "thing");
-
-  BOOST_CHECK_EQUAL( a.begin, 0 );
-  BOOST_CHECK_EQUAL( a.end,   10 );
-  BOOST_CHECK_EQUAL( a.type,  "test" );
-  BOOST_CHECK_EQUAL( a.name,  "thing" );
+  Sequence s("AAAAAAAAAA");
+  s.add_annotation("test", "thing", 0, 10);
+  SeqSpanRef a(s.annotations().front());
+  
+  BOOST_CHECK_EQUAL( a->start(), 0 );
+  BOOST_CHECK_EQUAL( a->stop(),   10 );
+  BOOST_CHECK_EQUAL( a->annotations()->get("name"),  "test" );
+  BOOST_CHECK_EQUAL( a->annotations()->get("type"),  "thing" );
 
   motif m(10, "AAGGCC");
   BOOST_CHECK_EQUAL( m.begin, 10 );
@@ -795,12 +807,13 @@ BOOST_AUTO_TEST_CASE( annotate_from_sequence )
     }
   }
   BOOST_CHECK_EQUAL(seq.annotations().size(), count);
-  const std::list<annot> &a = seq.annotations();
-  for (std::list<annot>::const_iterator annot_i = a.begin();
+  const SeqSpanRefList& a = seq.annotations();
+  for (SeqSpanRefList::const_iterator annot_i = a.begin();
        annot_i != a.end();
        ++annot_i)
   {
-    int count = annot_i->end - annot_i->begin ;
+    //FIXME: was I doing something here?
+    int count = (*annot_i)->stop() - (*annot_i)->start();
   }
 }
 
@@ -816,29 +829,36 @@ BOOST_AUTO_TEST_CASE( subseq_annotation_test )
            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
   Sequence seq(s, reduced_dna_alphabet);
 
-
-  seq.add_annotation(annot(0, 10, "0-10", "0-10"));
-  seq.add_annotation(annot(10, 20, "10-20", "10-20"));
-  seq.add_annotation(annot(0, 20, "0-20", "0-20"));
-  seq.add_annotation(annot(8, 12, "8-12", "8-12"));
-  seq.add_annotation(annot(100, 5000, "100-5000", "100-5000"));
+  seq.add_annotation("0-10", "0-10", 0, 10);
+  seq.add_annotation("10-20", "10-20", 10, 20);
+  seq.add_annotation("0-20", "0-20", 0, 20);
+  seq.add_annotation("8-12", "8-12", 8, 12);
+  seq.add_annotation("100-5000", "100-5000", 100, 5000);
 
   Sequence subseq = seq.subseq(5, 10);
-  const list<annot> annots = subseq.annotations();
-  // generate some ground truth
-  list<annot> correct;
-  correct.push_back(annot(0, 5, "0-10",  "0-10"));
-  correct.push_back(annot(5,10, "10-20", "10-20"));
-  correct.push_back(annot(0,10, "0-20",  "0-20"));
-  correct.push_back(annot(3, 7, "8-12",  "8-12"));
-  BOOST_REQUIRE_EQUAL( annots.size(), correct.size() );
-
-  list<annot>::iterator correct_i = correct.begin();
-  list<annot>::const_iterator annot_i = annots.begin();
-  for(; annot_i != annots.end(); ++annot_i, ++correct_i)
-  {
-    BOOST_CHECK( *annot_i == *correct_i );
-  }
+  SeqSpanRefList annots_list = subseq.annotations();
+  BOOST_REQUIRE_EQUAL( annots_list.size(), 4 );
+  
+  std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
+  BOOST_CHECK_EQUAL( annots[0]->start(),  0);
+  BOOST_CHECK_EQUAL( annots[0]->size(),  5);
+  BOOST_REQUIRE( annots[0]->annotations() );
+  BOOST_CHECK_EQUAL( annots[0]->annotations()->name(), "0-10");
+
+  BOOST_CHECK_EQUAL( annots[1]->start(), 5);
+  BOOST_CHECK_EQUAL( annots[1]->size(), 10);
+  BOOST_REQUIRE( annots[1]->annotations() );
+  BOOST_CHECK_EQUAL( annots[1]->annotations()->name(), "10-20");
+
+  BOOST_CHECK_EQUAL( annots[2]->start(), 0);
+  BOOST_CHECK_EQUAL( annots[2]->size(), 10);
+  BOOST_REQUIRE( annots[2]->annotations() );
+  BOOST_CHECK_EQUAL( annots[2]->annotations()->name(), "0-20");
+
+  BOOST_CHECK_EQUAL( annots[3]->start(), 3);
+  BOOST_CHECK_EQUAL( annots[3]->size(),  7);
+  BOOST_REQUIRE( annots[3]->annotations() );
+  BOOST_CHECK_EQUAL( annots[3]->annotations()->name(), "8-12");
 }
 
 BOOST_AUTO_TEST_CASE( motif_annotation_update )
@@ -856,9 +876,9 @@ BOOST_AUTO_TEST_CASE( motif_annotation_update )
   // starting conditions
   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
-  seq.add_annotation(annot(0, 10, "0-10", "0-10"));
-  seq.add_annotation(annot(10, 20, "10-20", "10-20"));
-  seq.add_annotation(annot(0, 20, "0-20", "0-20"));
+  seq.add_annotation("0-10", "0-10", 0, 10);
+  seq.add_annotation("10-20", "10-20", 10, 20);
+  seq.add_annotation("0-20", "0-20", 0, 20);
   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
   seq.add_motif("CCGTCCC");
@@ -920,8 +940,7 @@ BOOST_AUTO_TEST_CASE( serialize_tree )
   seq.set_species("ribbet");
   seq.add_motif("AA");
   seq.add_motif("GC");
-  annot a1(6,7,"t","t");
-  seq.add_annotation(a1);
+  seq.add_annotation("t", "t", 6, 7);
 
   std::ostringstream oss;
   // allocate/deallocate serialization components
@@ -950,8 +969,7 @@ BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
   seq.set_species("ribbet");
   seq.add_motif("AA");
   seq.add_motif("GC");
-  annot a1(6,7,"t","t");
-  seq.add_annotation(a1);
+  seq.add_annotation("t", "t", 6, 7);
 
   std::ostringstream oss;
   // allocate/deallocate serialization components
MUSSA multi-species alignment tool