X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=blobdiff_plain;f=alg%2Ftest%2Ftest_sequence.cpp;h=aefa6ac6c7aa6ec2b68285d674622d89d82ee127;hp=9faa8d069c156376ce945202527664b9955d47e6;hb=97498410e1fc5c39eac0282a6620b8fcb0f02ff3;hpb=15f9eb9d7ba5ffe32cbe7bc67a9d85b714c27871

diff --git a/alg/test/test_sequence.cpp b/alg/test/test_sequence.cpp
index 9faa8d0..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;
@@ -833,6 +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"
@@ -925,7 +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";
@@ -1033,3 +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());
 }
+*/