X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=blobdiff_plain;f=alg%2Ftest%2Ftest_sequence.cpp;h=aefa6ac6c7aa6ec2b68285d674622d89d82ee127;hp=82ff14be6c1ff40c6d9ce1155def83c0c5e4dda7;hb=97498410e1fc5c39eac0282a6620b8fcb0f02ff3;hpb=67888dae3b16b9d69aa846e393f11e7ff3633f16

diff --git a/alg/test/test_sequence.cpp b/alg/test/test_sequence.cpp
index 82ff14b..aefa6ac 100644
--- a/alg/test/test_sequence.cpp
+++ b/alg/test/test_sequence.cpp
@@ -1,5 +1,7 @@
-#define BOOST_AUTO_TEST_MAIN
-#include <boost/test/auto_unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE
+#include <boost/test/unit_test.hpp>
+
 #include <boost/filesystem/path.hpp>
 #include <boost/filesystem/operations.hpp>
 namespace fs=boost::filesystem;
@@ -586,6 +588,22 @@ BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
   BOOST_CHECK_EQUAL( annots[0]->annotations()->get("type"), "type");
 }
 
+// when we do a subsequence (or something that calls copy_children)
+// the annotations need to be updated to have the right parent
+BOOST_AUTO_TEST_CASE( update_annotations_seqref )
+{
+  Sequence s1("AAAAGGGG");
+  s1.add_annotation("A", "A", 0, 4);
+  BOOST_CHECK_EQUAL(s1.annotations().size(), 1);
+  BOOST_CHECK_EQUAL(s1.seqspan(), s1.annotations().front()->parent() );
+  
+  Sequence subseq1(s1.subseq(2,4));
+  BOOST_CHECK_EQUAL(subseq1.annotations().size(), 1);
+  BOOST_CHECK_EQUAL(subseq1.annotations().front()->parentStart(), 0 );
+  BOOST_CHECK_EQUAL(subseq1.annotations().front()->parentStop(), 2 );
+  BOOST_CHECK_EQUAL(subseq1.seqspan(), subseq1.annotations().front()->parent() );
+}
+
 // ticket:83 when you try to load a sequence from a file that doesn't
 // have fasta headers it crashes. 
 BOOST_AUTO_TEST_CASE( sequence_past_end ) 
@@ -817,6 +835,48 @@ BOOST_AUTO_TEST_CASE( annotate_from_sequence )
   }
 }
 
+BOOST_AUTO_TEST_CASE( sequence_no_trailing_newline )
+{
+  // sorry about the long string...
+  string s = "AATTACACAAGGAATATAGGTAGTTTGAATAAAAATATCTTTAACAGCTTGGAGCTATTGAGACAGGAACACTTCCACGCACATGCACAGTTAAACAACTTGAGTGCAACACACAACATTGGCACTAAACGAGATTGAAGGGGGACTTTTTGTGTGTTTTTTTTTCTCTTTTCTTTTTTTGTTATAGTTACTTCAAGTAACACAGCTTGCTTCATATAAATAAGTTAAAACATCTATTTTTTTTCAAGACAAAGCCATTCAGGACAAAGAGATGAACAGAAAGCAGATCTACTTATACAGGCGCTATAATGGCAATAAACAGGCTCATGATTAAAAGATGAATTAGGGCAACGAGAACAGGGCTTCTTCACAGAAGGAACACAAGGGAGTTTCAGAAAGTCACCTTAGTACTGACACTACGCGGGATCCGCTAATACTGCTCAGTACTTTAAACGCTCAGATACTCAGGGACGGAAGGCCCCTCCTGCCGCGGCCATGCTCATGCTTTTCAGCTTATTATCTTTTTTCCACTTCATTCTCCGGTTTTGGAACCAGATTTTAATTTGTCTCTCGGAGAGGCAAAGAGCATGTGCTATTTCAATCCTCCTTCTGCGGGTCAGGTAACGGTTGAAGTGGAACTCCTTCTCCAGCTCCAGGGTCTGGTAGCGCGTGTAGGCCGTCCGGGCCCTTTTGCCTTCCGGGCCGCCTATGTTGTCTGCAATAGAAAAGTCAGCGGTTTAGCCACCAACTCCTGTCTTCCAAAGTCCGCCAGGGGGACAAGCTTGGGTCATGAGCAGGGAACCCAGGCGAAAAGCTCAACAAGTTCTGCCTACCAGCCCGCACACCCCTCCCGAATTTCCTTCTCTCTTCCTTTCTAGAAAGAAAACAATACGATTTGGACCCTGGGAACAATCTGCCCATCTGAGGCTGGGGCCGTGTCCCGGCGGACTCCGGCTTTCCCTGGCCCCTCTCCTGCCCCCTCCGCCCTGCCCCGGGCGCCCCGATCGGGAGGCACAGCCCTCCCAGGCTGCCCACCGCACAGAAACCCAGGAAGCAAGGCCCTTTCCTGAGCGCCCAAGTGGCCTTCGGGTCACCCTCCCTCAAAGTTCCAGCCCCGAGAGCCGCCTCCCGTTTCCAGCCTGCAGGGTTGGGGAGCCTGTTTTCTTTTTCTTCCCTTTCCTTCTCTCTCCCTCCTGCCCCCAAAATTCAGAATCCTGCAGGCTCTCGCCTCGATTCTTTCCCCCAAGCCCCTTTTCGGGGGCTGTAATTAGTAACGCTGTTTCCCCAGCGTAGCCCTCCTCATAAATTATCCGCCGTGACAAGCCCGATTCACGGCTGCTACAGCCATCCTCTACCTCTCTGCGCCTTGCTCGGCTGGCCTGACCCGGGAGCGCGTCCCAAGGCGTGGGGTTCCAGAGGGGTTTTTTGCTTCCTCCCCCTTCCAACGTCTAAACTGTCCCAGAGAACGCCCATTTCCCCCACTATTTGTGAGCGCAGGGTGCTCGCAAAGAAGAGGAGGAAGGAGGAAGGCAGGGGAGGGAGAACGGCAAGGAGAGCTCCGCAGGGCTGGGAGAAATGAGACCAAGAGAGACTGGGAGAGGGCGGCAGAGAAGAGAGGGGGGACCGAGAGCCGCGTCCCCGCGGTCGCGTGGATTTAGAAAAAGGCTGGCTTTACCATGACTTATGTGCAGCTTGCGCATCCAGGGGTAGATCTGGGGTTGGGCGGGCGGCGCCGGGCTCGGCTCGCTCTGCGCACTCGCCTGCTCGCTGCTGGCAGGGGCGTCCTCCTCGGCTCCGGACGCCGTGCCAACCCCCTCTCTGCTGCTGATGTGGGTGCTGCCGGCGTCGGCCGAGGCGCCGCTGGAGTTGCTTAGGGAGTTTTTCCCGCCGTGGTGGCTGTCGCTGCCGGGCGAGGGGGCCACGGCGGAGCAGGGCAGCGGATCGGGCTGAGGAGAGTGCGTGGACGTGGCCGGCTGGCTGTACCTGGGCTCGGCGGGCGCCGCGCTGGCGCTGGCAGCGTAGCTGCGGGCGCGCTCTCCGGAGCCAAAGTGGCCGGAGCCCGAGCGGCCGACGCTGAGATCCATGCCATTGTAGCCGTAGCCGTACCTGCCGGAGTGCATGCTCGCCGAGTCCCTGAATTGCTCGCTCACGGAACTATGATCTCCATAATTATGCAACTGGTAGTCCGGGCCATTTGGATAGCGACCGCAAAATGAGTTTACAAAATAAGAGCTCATTTGTTTTTTGATATGTGTGCTTGATTTGTGGCTCGCGGTCGTTTGTGCGTCTATAGCACCCTT";
+  std::string species = "HumanHXA5\n";
+  std::string header0 = ">hg18_knownGene_NM_019102_0\n";
+  std::string str0 = "GGGTGCTATAGACGCACAAACGACCGCGAGCCACAAATCAAGCACACATATCAAAAAACAAATGAGCTCTTATTTTGTAAACTCATTTTGCGGTCGCTATCCAAATGGCCCGGACTACCAGTTGCATAATTATGGAGATCATAGTTCCGTGAGCGAGCAATTCAGGGACTCGGCGAGCATGCACTCCGGCAGGTACGGCTACGGCTACAATGGCATGGATCTCAGCGTCGGCCGCTCGGGCTCCGGCCACTTTGGCTCCGGAGAGCGCGCCCGCAGCTACGCTGCCAGCGCCAGCGCGGCGCCCGCCGAGCCCAGGTACAGCCAGCCGGCCACGTCCACGCACTCTCCTCAGCCCGATCCGCTGCCCTGCTCCGCCGTGGCCCCCTCGCCCGGCAGCGACAGCCACCACGGCGGGAAAAACTCCCTAAGCAACTCCAGCGGCGCCTCGGCCGACGCCGGCAGCACCCACATCAGCAGCAGAGAGGGGGTTGGCACGGCGTCCGGAGCCGAGGAGGACGCCCCTGCCAGCAGCGAGCAGGCGAGTGCGCAGAGCGAGCCGAGCCCGGCGCCGCCCGCCCAACCCCAGATCTACCCCTGGATGCGCAAGCTGCACATAAGTCATG";
+  std::string header1 = ">hg18_knownGene_NM_019102_1\n";
+  std::string str1 = "ACAACATAGGCGGCCCGGAAGGCAAAAGGGCCCGGACGGCCTACACGCGCTACCAGACCCTGGAGCTGGAGAAGGAGTTCCACTTCAACCGTTACCTGACCCGCAGAAGGAGGATTGAAATAGCACATGCTCTTTGCCTCTCCGAGAGACAAATTAAAATCTGGTTCCAAAACCGGAGAATGAAGTGGAAAAAAGATAATAAGCTGAAAAGCATGAGCATGGCCGCGGCAGGAGGGGCCTTCCGTCCCTGAGTATCTGAGCGTTTAAAGTACTGAGCAGTATTAGCGGATCCCGCGTAGTGTCAGTACTAAGGTGACTTTCTGAAACTCCCTTGTGTTCCTTCTGTGAAGAAGCCCTGTTCTCGTTGCCCTAATTCATCTTTTAATCATGAGCCTGTTTATTGCCATTATAGCGCCTGTATAAGTAGATCTGCTTTCTGTTCATCTCTTTGTCCTGAATGGCTTTGTCTTGAAAAAAAATAGATGTTTTAACTTATTTATATGAAGCAAGCTGTGTTACTTGAAGTAACTATAACAAAAAAAGAAAAGAGAAAAAAAAACACACAAAAAGTCCCCCTTCAATCTCGTTTAGTGCCAATGTTGTGTGTTGCACTCAAGTTGTTTAACTGTGCATGTGCGTGGAAGTGTTCCTGTCTCAATAGCTCCAAGCTGTTAAAGATATTTTTATTCAAACTACCTATATTCCTTGT";
+  stringstream annot;
+  annot << species 
+        << header0 
+        << str0 << std::endl 
+        << std::endl 
+        << header1 
+        << str1;
+  // need to convert strings to sequences for reverse complementing
+  Sequence seq0(str0, reduced_dna_alphabet);
+  Sequence seq1(str1, reduced_dna_alphabet);
+
+  Sequence annotated_seq(s, reduced_dna_alphabet);
+  annotated_seq.load_annot(annot, 0, 0);
+
+  SeqSpanRefList annots_list = annotated_seq.annotations();
+  // both sequences were found
+  BOOST_REQUIRE_EQUAL( annots_list.size(),  2 );
+
+  std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
+  // are they the same sequence?
+  BOOST_CHECK_EQUAL( annots[0]->size(),  seq0.size());
+  BOOST_CHECK_EQUAL( annots[0]->sequence(), seq0.rev_comp() );
+  // this should hopefully catch the case when my hack in 
+  // sequence.cpp::push_back_seq::operator() is no longer needed.
+  // spirit (or my grammar was duplicating the last char, 
+  // the hack removes the duplicate. but if what ever's causing
+  // the dup gets fixed actual meaningful data will be being removed.
+  // see mussa ticket:265 for more information
+  BOOST_CHECK_EQUAL( annots[1]->size(),  seq1.size());
+  BOOST_CHECK_EQUAL( annots[1]->sequence(), seq1.rev_comp() );
+
+}
+
 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
 {
   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
@@ -840,22 +900,22 @@ BOOST_AUTO_TEST_CASE( subseq_annotation_test )
   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]->parentStart(),  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_CHECK_EQUAL( annots[1]->parentStart(), 5);
+  BOOST_CHECK_EQUAL( annots[1]->size(), 5);
   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]->parentStart(), 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]->parentStart(), 3);
   BOOST_CHECK_EQUAL( annots[3]->size(),  7);
   BOOST_REQUIRE( annots[3]->annotations() );
   BOOST_CHECK_EQUAL( annots[3]->annotations()->name(), "8-12");
@@ -909,7 +969,7 @@ BOOST_AUTO_TEST_CASE( get_name )
   seq.set_fasta_header("fasta human");
   BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
 }
-
+/*
 BOOST_AUTO_TEST_CASE( serialize_simple )
 {
   std::string seq_string = "AAGGCCTT";
@@ -1017,3 +1077,4 @@ BOOST_AUTO_TEST_CASE( serialize_xml_two )
   // test if our pointers are the same
   BOOST_CHECK_EQUAL(seq1_loaded.data(), seq2_loaded.data());
 }
+*/