Sequence::rev_comp works on subsequences

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

diff --git a/alg/test/test_sequence.cpp b/alg/test/test_sequence.cpp
index 48492f79294fd9535a10210f3522a62f0a608d2f..6317144c026510016c8e7f1fe376f1105aab6d65 100644 (file)
--- a/alg/test/test_sequence.cpp
+++ b/alg/test/test_sequence.cpp
@@ -258,6 +258,32 @@ BOOST_AUTO_TEST_CASE( sequence_load_fasta_default )
                     sequence_invalid_load_error);
 }
 
+BOOST_AUTO_TEST_CASE( sequence_load_multiple_sequences_one_fasta ) 
+{
+  std::string fasta_file(
+    ">gi|10129974|gb|AF188002.1|AF188002\n"
+    "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC\n"
+    ">gi|180579|gb|M21487.1|HUMCKMM1\n"
+    "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC\n"
+    ">gi|1621|emb|X55146.1|OCMCK1\n"
+    "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC\n"
+  );
+  istringstream seq1_file(fasta_file);
+  Sequence seq1;
+  seq1.load_fasta(seq1_file, 1, 0, 0);
+  BOOST_CHECK_EQUAL(seq1.get_sequence(), "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC");
+  
+  istringstream seq2_file(fasta_file);
+  Sequence seq2;
+  seq2.load_fasta(seq2_file, 2, 0, 0);
+  BOOST_CHECK_EQUAL(seq2.get_sequence(), "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC");
+  
+  istringstream seq3_file(fasta_file);
+  Sequence seq3;
+  seq3.load_fasta(seq3_file, 3, 0, 0);  
+  BOOST_CHECK_EQUAL(seq3.get_sequence(), "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC"); 
+}
+
 BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
 {
   std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
@@ -287,6 +313,56 @@ BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
   BOOST_CHECK_EQUAL(rna_seq, rna_seq.rev_comp().rev_comp());
 }
 
+BOOST_AUTO_TEST_CASE( sequence_reverse_complement_subseq )
+{
+  std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
+  Sequence seq(dna_str, Sequence::reduced_dna_alphabet);
+  Sequence subseq = seq.subseq(8,4);
+  BOOST_CHECK_EQUAL( subseq, "AAGG");
+  Sequence rev_subseq = subseq.rev_comp();
+  BOOST_CHECK_EQUAL( rev_subseq.size(), subseq.size() );
+  BOOST_CHECK_EQUAL( rev_subseq.get_sequence(), "CCTT");
+}
+
+BOOST_AUTO_TEST_CASE( sequence_reverse_iterator )
+{
+  std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
+  std::string dna_str_reversed(dna_str.rbegin(), dna_str.rend());
+  Sequence seq(dna_str);
+  std::string seq_reversed(seq.rbegin(), seq.rend());
+  BOOST_CHECK_EQUAL(seq_reversed, dna_str_reversed);
+  
+  std::string substr = dna_str.substr(8,4);
+  Sequence subseq = seq.subseq(8,4);
+  BOOST_CHECK_EQUAL(substr, subseq);
+
+  std::string substr_reversed(substr.rbegin(), substr.rend());
+  std::string subseq_reversed(subseq.rbegin(), subseq.rend());
+  BOOST_CHECK_EQUAL(substr_reversed, subseq_reversed);  
+}
+
+BOOST_AUTO_TEST_CASE( sequence_empty_reverse_iterator)
+{
+  // so what happens with reverse interators when we have no sequence?
+  Sequence seq1;
+  Sequence seq2;
+  Sequence seq3("AGCT");
+  
+  // all the empty sequences should have equal iterators
+  BOOST_CHECK(seq1.rbegin() == seq1.rend());
+  BOOST_CHECK(seq1.rbegin() == seq2.rend());
+  
+  // none of the seq1 iterators should equal any of the seq3 iterators
+  BOOST_CHECK(seq1.rbegin() != seq3.rbegin());
+  BOOST_CHECK(seq1.rbegin() != seq3.rend());
+  BOOST_CHECK(seq1.rend() != seq3.rbegin());
+  BOOST_CHECK(seq1.rend() != seq3.rend());
+  
+  // seq3 iterators should work
+  BOOST_CHECK(seq3.rbegin() != seq3.rend());
+  
+}
+
 BOOST_AUTO_TEST_CASE( annotation_load )
 {
   string annot_data = "human\n"