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Move alphabet type into SeqString
[mussa.git] / alg / test / test_sequence.cpp
diff --git a/alg/test/test_sequence.cpp b/alg/test/test_sequence.cpp
index 3847252a80884fa06786afe18feb7cf7f387a1e4..6da21f166449c348c7b38c83f5dde803b7d01f54 100644 (file)
--- a/alg/test/test_sequence.cpp
+++ b/alg/test/test_sequence.cpp
@@ -86,10 +86,10 @@ BOOST_AUTO_TEST_CASE( sequence_eol_conventions )
 BOOST_AUTO_TEST_CASE( sequence_filter )
 {
   const char *core_seq = "AATTGGCC";
-  Sequence s1(core_seq, Sequence::reduced_dna_alphabet);
+  Sequence s1(core_seq, reduced_dna_alphabet);
   BOOST_CHECK_EQUAL(s1, core_seq);
 
-  Sequence s2("aattggcc", Sequence::reduced_dna_alphabet);
+  Sequence s2("aattggcc", reduced_dna_alphabet);
   BOOST_CHECK_EQUAL(s2, "AATTGGCC");
   BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
   BOOST_CHECK_EQUAL(s2.rev_comp(), "ggccaatt"); // we should be case insensitive now
@@ -97,15 +97,15 @@ BOOST_AUTO_TEST_CASE( sequence_filter )
   //We're currently forcing sequences to uppercase
   BOOST_CHECK_EQUAL(s2.get_sequence(), "AATTGGCC"); 
 
-  Sequence s3("asdfg", Sequence::reduced_dna_alphabet);
+  Sequence s3("asdfg", reduced_dna_alphabet);
   BOOST_CHECK_EQUAL(s3, "ANNNG");
   BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
 
-  s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 0, 2); 
+  s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 0, 2); 
   BOOST_CHECK_EQUAL(s3, "AA");
-  s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 2, 2);
+  s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 2, 2);
   BOOST_CHECK_EQUAL( s3, "GG");
-  s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 4);
+  s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 4);
   BOOST_CHECK_EQUAL( s3, "CCTT");
 
   s3 = "AAGGFF";
@@ -115,12 +115,12 @@ BOOST_AUTO_TEST_CASE( sequence_filter )
 BOOST_AUTO_TEST_CASE( sequence_nucleic_alphabet )
 {
   std::string agct("AGCT");
-  Sequence seq(agct, Sequence::nucleic_alphabet);
+  Sequence seq(agct, nucleic_alphabet);
   BOOST_CHECK_EQUAL(seq.size(), agct.size());
   BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
   
   std::string bdv("BDv");
-  Sequence seq_bdv(bdv, Sequence::nucleic_alphabet);
+  Sequence seq_bdv(bdv, nucleic_alphabet);
   BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
   // forcing sequence to upper case
   BOOST_CHECK_EQUAL(seq_bdv.get_sequence(), 
@@ -148,7 +148,7 @@ BOOST_AUTO_TEST_CASE( sequence_default_alphabet )
 
 BOOST_AUTO_TEST_CASE( subseq_names )
 {
-  Sequence s1("AAGGCCTT", Sequence::reduced_dna_alphabet);
+  Sequence s1("AAGGCCTT", reduced_dna_alphabet);
   s1.set_species("species");
   s1.set_fasta_header("a fasta header");
   Sequence s2 = s1.subseq(2,2);
@@ -164,7 +164,7 @@ BOOST_AUTO_TEST_CASE( sequence_start_stop )
   BOOST_CHECK_EQUAL( s1.stop(), 0 );
 
   std::string seq_string("AAGGCCTT");
-  Sequence s2(seq_string, Sequence::reduced_dna_alphabet);
+  Sequence s2(seq_string, reduced_dna_alphabet);
   BOOST_CHECK_EQUAL( s2.start(), 0 );
   BOOST_CHECK_EQUAL( s2.stop(), seq_string.size() );
 
@@ -189,7 +189,7 @@ BOOST_AUTO_TEST_CASE( sequence_load )
   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq");
   seq_path /=  "human_mck_pro.fa";
   Sequence s;
-  s.load_fasta(seq_path, Sequence::reduced_dna_alphabet);
+  s.load_fasta(seq_path, reduced_dna_alphabet);
   BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
   BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
   BOOST_CHECK_EQUAL(s.get_fasta_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
@@ -255,15 +255,15 @@ BOOST_AUTO_TEST_CASE( sequence_load_dna_reduced )
   std::stringstream garbage_fasta(garbage_string);
   
   Sequence s;
-  s.load_fasta(reduced_dna_fasta, Sequence::reduced_dna_alphabet);
+  s.load_fasta(reduced_dna_fasta, reduced_dna_alphabet);
   BOOST_CHECK_THROW(s.load_fasta(invalid_dna_fasta, 
-                                 Sequence::reduced_dna_alphabet),
+                                 reduced_dna_alphabet),
                     sequence_invalid_load_error);
   BOOST_CHECK_THROW(s.load_fasta(reduced_rna_fasta, 
-                                 Sequence::reduced_dna_alphabet),
+                                 reduced_dna_alphabet),
                     sequence_invalid_load_error);
   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta, 
-                                 Sequence::reduced_dna_alphabet),
+                                 reduced_dna_alphabet),
                     sequence_invalid_load_error);
 
 }
@@ -280,15 +280,15 @@ BOOST_AUTO_TEST_CASE( sequence_load_rna_reduced )
   std::stringstream garbage_fasta(garbage_string);
   
   Sequence s;
-  s.load_fasta(reduced_rna_fasta, Sequence::reduced_rna_alphabet);
+  s.load_fasta(reduced_rna_fasta, reduced_rna_alphabet);
   BOOST_CHECK_THROW(s.load_fasta(invalid_rna_fasta, 
-                                 Sequence::reduced_rna_alphabet),
+                                 reduced_rna_alphabet),
                     sequence_invalid_load_error);
   BOOST_CHECK_THROW(s.load_fasta(reduced_dna_fasta, 
-                                 Sequence::reduced_rna_alphabet),
+                                 reduced_rna_alphabet),
                     sequence_invalid_load_error);
   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta, 
-                                 Sequence::reduced_rna_alphabet),
+                                 reduced_rna_alphabet),
                     sequence_invalid_load_error);
 }
 
@@ -310,11 +310,11 @@ BOOST_AUTO_TEST_CASE( sequence_load_fasta_default )
   // there's two copies of reduced_rna_fasta because i didn't feel like
   // figuring out how to properly reset the read pointer in a stringstream
   s.load_fasta(reduced_rna_fasta1);
-  specific.load_fasta(reduced_rna_fasta2, Sequence::reduced_nucleic_alphabet);
+  specific.load_fasta(reduced_rna_fasta2, reduced_nucleic_alphabet);
   BOOST_CHECK_EQUAL(s, specific);
   
   s.load_fasta(reduced_dna_fasta1);
-  specific.load_fasta(reduced_dna_fasta2, Sequence::reduced_nucleic_alphabet);
+  specific.load_fasta(reduced_dna_fasta2, reduced_nucleic_alphabet);
   BOOST_CHECK_EQUAL(s, specific);
   
   BOOST_CHECK_THROW(s.load_fasta(invalid_nucleotide_fasta), 
@@ -352,7 +352,7 @@ BOOST_AUTO_TEST_CASE( sequence_load_multiple_sequences_one_fasta )
 BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
 {
   std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
-  Sequence seq(iupac_symbols, Sequence::nucleic_alphabet);
+  Sequence seq(iupac_symbols, nucleic_alphabet);
   Sequence seqr = seq.rev_comp();
   
   BOOST_CHECK( seq != seqr );
@@ -365,7 +365,7 @@ BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
 {
   std::string dna_str("AGCTN");
-  Sequence dna_seq(dna_str, Sequence::reduced_dna_alphabet);
+  Sequence dna_seq(dna_str, reduced_dna_alphabet);
   BOOST_CHECK_EQUAL(dna_seq.rev_comp(), "NAGCT");  
   BOOST_CHECK_EQUAL(dna_seq, dna_seq.rev_comp().rev_comp());
 }
@@ -373,7 +373,7 @@ BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
 {
   std::string rna_str("AGCUN");
-  Sequence rna_seq(rna_str, Sequence::reduced_rna_alphabet);
+  Sequence rna_seq(rna_str, reduced_rna_alphabet);
   BOOST_CHECK_EQUAL(rna_seq.rev_comp(), "NAGCU");  
   BOOST_CHECK_EQUAL(rna_seq, rna_seq.rev_comp().rev_comp());
 }
@@ -381,7 +381,7 @@ BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_subseq )
 {
   std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
-  Sequence seq(dna_str, Sequence::reduced_dna_alphabet);
+  Sequence seq(dna_str, reduced_dna_alphabet);
   Sequence subseq = seq.subseq(8,4);
   BOOST_CHECK_EQUAL( subseq, "AAGG");
   Sequence rev_subseq = subseq.rev_comp();
@@ -444,7 +444,7 @@ BOOST_AUTO_TEST_CASE( annotation_load )
                       ;
   string s(100, 'A');
   s += "GCTGCTAATT";
-  Sequence seq(s, Sequence::reduced_dna_alphabet);
+  Sequence seq(s, reduced_dna_alphabet);
                      
   //istringstream annot_stream(annot_data);
   seq.parse_annot(annot_data, 0, 0);
@@ -484,7 +484,7 @@ BOOST_AUTO_TEST_CASE( annotation_broken_load )
                       ;
   string s(100, 'A');
   s += "GCTGCTAATT";
-  Sequence seq(s, Sequence::reduced_dna_alphabet);
+  Sequence seq(s, reduced_dna_alphabet);
                      
   BOOST_CHECK_THROW(seq.parse_annot(annot_data, 0, 0), annotation_load_error);
   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
@@ -511,7 +511,7 @@ BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
     "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
     "AAAAA"
     "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
-  Sequence seq(s, Sequence::reduced_dna_alphabet);
+  Sequence seq(s, reduced_dna_alphabet);
   seq.parse_annot(annot_data);
   std::list<annot> annots = seq.annotations();
   BOOST_CHECK_EQUAL( annots.size(), 2);
@@ -532,7 +532,7 @@ BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
                       ;
   string s(100, 'A');
   s += "GCTGCTAATT";
-  Sequence seq(s, Sequence::reduced_dna_alphabet);
+  Sequence seq(s, reduced_dna_alphabet);
                      
   //istringstream annot_stream(annot_data);
   seq.parse_annot(annot_data, 0, 0);
@@ -583,12 +583,12 @@ BOOST_AUTO_TEST_CASE ( sequence_size )
 
 BOOST_AUTO_TEST_CASE( sequence_empty_equality )
 {
-  Sequence szero("", Sequence::reduced_dna_alphabet);
+  Sequence szero("", reduced_dna_alphabet);
   BOOST_CHECK_EQUAL(szero.empty(), true);
   BOOST_CHECK_EQUAL(szero, szero);
   BOOST_CHECK_EQUAL(szero, "");
 
-  Sequence sclear("AGCT", Sequence::reduced_dna_alphabet);
+  Sequence sclear("AGCT", reduced_dna_alphabet);
   sclear.clear();
   BOOST_CHECK_EQUAL(sclear.empty(), true);
   BOOST_CHECK_EQUAL(sclear, sclear);
@@ -599,7 +599,7 @@ BOOST_AUTO_TEST_CASE( sequence_empty_equality )
 BOOST_AUTO_TEST_CASE ( sequence_iterators )
 {
   std::string seq_string = "AAGGCCTTNNTATA";
-  Sequence s(seq_string, Sequence::reduced_dna_alphabet);
+  Sequence s(seq_string, reduced_dna_alphabet);
   const Sequence cs(s);
   std::string::size_type count = 0;
 
@@ -628,7 +628,7 @@ BOOST_AUTO_TEST_CASE( sequence_motifs )
 {
   string m("AAAA");
   string bogus("AATTGGAA");
-  Sequence s1("AAAAGGGGCCCCTTTT", Sequence::reduced_dna_alphabet);
+  Sequence s1("AAAAGGGGCCCCTTTT", reduced_dna_alphabet);
 
   list<motif>::const_iterator motif_i = s1.motifs().begin();
   list<motif>::const_iterator motif_end = s1.motifs().end();
@@ -683,7 +683,7 @@ BOOST_AUTO_TEST_CASE( sequence_motif_subseq)
   // only search the subsequence ticket:199
   string aaaa("AAAA");
   string cccc("CCCC");
-  Sequence s1("AAAANCCCC", Sequence::reduced_dna_alphabet);
+  Sequence s1("AAAANCCCC", reduced_dna_alphabet);
 
   // this shouldn't show up
   s1.add_motif(cccc);
@@ -736,7 +736,7 @@ BOOST_AUTO_TEST_CASE( annotate_from_sequence )
            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
   string gc("GCCCCC");
   string gga("GGACACCTC");
-  Sequence seq(s, Sequence::reduced_dna_alphabet);
+  Sequence seq(s, reduced_dna_alphabet);
 
   std::list<Sequence> query_list;
   std::list<string> string_list;
@@ -782,7 +782,7 @@ BOOST_AUTO_TEST_CASE( subseq_annotation_test )
            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
-  Sequence seq(s, Sequence::reduced_dna_alphabet);
+  Sequence seq(s, reduced_dna_alphabet);
 
 
   seq.add_annotation(annot(0, 10, "0-10", "0-10"));
@@ -819,7 +819,7 @@ BOOST_AUTO_TEST_CASE( motif_annotation_update )
            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
-  Sequence seq(s, Sequence::reduced_dna_alphabet);
+  Sequence seq(s, reduced_dna_alphabet);
 
   // starting conditions
   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
@@ -840,7 +840,7 @@ BOOST_AUTO_TEST_CASE( motif_annotation_update )
 BOOST_AUTO_TEST_CASE( out_operator )
 {
   string s("AAGGCCTT");
-  Sequence seq(s, Sequence::reduced_dna_alphabet);
+  Sequence seq(s, reduced_dna_alphabet);
 
   ostringstream buf;
   buf << s;
@@ -849,7 +849,7 @@ BOOST_AUTO_TEST_CASE( out_operator )
 
 BOOST_AUTO_TEST_CASE( get_name )
 {
-  Sequence seq("AAGGCCTT", Sequence::reduced_dna_alphabet);
+  Sequence seq("AAGGCCTT", reduced_dna_alphabet);
 
   BOOST_CHECK_EQUAL( seq.get_name(), "" );
   seq.set_species("hooman"); // anyone remember tradewars?
@@ -861,7 +861,7 @@ BOOST_AUTO_TEST_CASE( get_name )
 BOOST_AUTO_TEST_CASE( serialize_simple )
 {
   std::string seq_string = "AAGGCCTT";
-  Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
+  Sequence seq(seq_string, reduced_dna_alphabet);
   seq.set_species("ribbet");
   std::ostringstream oss;
   // allocate/deallocate serialization components
@@ -884,7 +884,7 @@ BOOST_AUTO_TEST_CASE( serialize_simple )
 BOOST_AUTO_TEST_CASE( serialize_tree )
 {
   std::string seq_string = "AAGGCCTT";
-  Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
+  Sequence seq(seq_string, reduced_dna_alphabet);
   seq.set_species("ribbet");
   seq.add_motif("AA");
   seq.add_motif("GC");
@@ -914,7 +914,7 @@ BOOST_AUTO_TEST_CASE( serialize_tree )
 BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
 {
   std::string seq_string = "AAGGCCTT";
-  Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
+  Sequence seq(seq_string, reduced_dna_alphabet);
   seq.set_species("ribbet");
   seq.add_motif("AA");
   seq.add_motif("GC");
@@ -941,7 +941,7 @@ BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
 BOOST_AUTO_TEST_CASE( serialize_xml_two )
 {
   std::string seq_string = "AAGGCCTT";
-  Sequence seq1(seq_string, Sequence::reduced_dna_alphabet);
+  Sequence seq1(seq_string, reduced_dna_alphabet);
   Sequence seq2(seq1);
 
   std::ostringstream oss;
MUSSA multi-species alignment tool