alg/test/test_sequence.cpp

   1 #define BOOST_TEST_DYN_LINK
   2 #define BOOST_TEST_MODULE
   3 #include <boost/test/unit_test.hpp>
   4
   5 #include <boost/filesystem/path.hpp>
   6 #include <boost/filesystem/operations.hpp>
   7 namespace fs=boost::filesystem;
   8
   9 #include <boost/algorithm/string/case_conv.hpp>
  10
  11 #include <list>
  12 #include <iostream>
  13 #include <sstream>
  14
  15 #include <boost/archive/text_oarchive.hpp>
  16 #include <boost/archive/text_iarchive.hpp>
  17 #include <boost/archive/xml_oarchive.hpp>
  18 #include <boost/archive/xml_iarchive.hpp>
  19
  20 #include "alg/sequence.hpp"
  21 #include "mussa_exceptions.hpp"
  22
  23 using namespace std;
  24
  25 BOOST_AUTO_TEST_CASE( sequence_copy_constructor )
  26 {
  27   SequenceRef s(new Sequence("AAAAGGGG"));
  28   s->set_species("foo");
  29   BOOST_CHECK_EQUAL(s->get_species(), "foo");
  30
  31   SequenceRef c(new Sequence(s));
  32   BOOST_CHECK_EQUAL(c->get_species(), "foo");
  33
  34   c->set_species("bar");
  35   BOOST_CHECK_EQUAL(s->get_species(), "foo");
  36   BOOST_CHECK_EQUAL(c->get_species(), "bar");
  37 }
  38
  39 BOOST_AUTO_TEST_CASE( sequence_copy_constructor_copy_motifs )
  40 {
  41   SequenceRef s(new Sequence("AAAAGGGGAAAA"));
  42   s->add_motif("AAGG");
  43   BOOST_CHECK_EQUAL(s->motifs().size(), 1);
  44
  45   SequenceRef c(new Sequence(s->subseq()));
  46   BOOST_CHECK_EQUAL(c->motifs().size(), 1);
  47
  48   s->clear_motifs();
  49   BOOST_CHECK_EQUAL(s->motifs().size(), 0);
  50   // FIXME: Technically c shouldn't lose its motifs.
  51   // FIXME: getting that to work is hard.
  52   // BOOST_CHECK_EQUAL(c->motifs().size(), 1);
  53   BOOST_CHECK_EQUAL(c->motifs().size(), 0);
  54 }
  55
  56 BOOST_AUTO_TEST_CASE( sequence_get_sequence )
  57 {
  58         Sequence s;
  59         // make sure that retrieving the sequence doesn't throw an error
  60         BOOST_CHECK_EQUAL(s.get_sequence(), std::string() );
  61 }
  62
  63 BOOST_AUTO_TEST_CASE( sequence_from_string )
  64 {
  65   std::string str1("AAAT");
  66   Sequence seq1(str1);
  67   BOOST_CHECK_EQUAL(seq1.get_sequence(), str1);
  68 }
  69
  70 BOOST_AUTO_TEST_CASE( sequence_find_first_not_of )
  71 {
  72   std::string str1("AAAAT");
  73   Sequence seq1(str1);
  74   BOOST_CHECK_EQUAL(seq1.find_first_not_of("A"), str1.find_first_not_of("A"));
  75
  76   std::string str2("AATTGGCC");
  77   Sequence seq2(str2);
  78   BOOST_CHECK_EQUAL(seq2.find_first_not_of("qwer"), str2.find_first_not_of("qwer"));
  79 }
  80
  81 //! when we try to load a missing file, do we get an error?
  82 BOOST_AUTO_TEST_CASE( sequence_load_exception )
  83 {
  84   Sequence s;
  85   // there should be errors when we try to load something that doesn't exist
  86   BOOST_CHECK_THROW( s.load_fasta("alkejralk", 1, 0, 0), mussa_load_error);
  87   BOOST_CHECK_THROW( s.load_annot("alkejralk", 0, 0), mussa_load_error);
  88 }
  89
  90 BOOST_AUTO_TEST_CASE( sequence_eol_conventions )
  91 {
  92   string header(">Header");
  93   string line1("AAAAGGGGCCCCTTTTT");
  94   string line2("AAAAGGGGCCCCTTTTT");
  95   int seq_len = line1.size() + line2.size();
  96
  97   stringstream cr;
  98   cr << header << "\015" << line1 << "\015" << line2 << "\015";
  99   Sequence seq_cr;
 100   seq_cr.load_fasta(cr);
 101
 102   stringstream crlf;
 103   crlf << header << "\015\012" << line1 << "\015\012" << line2 << "\015\012";
 104   Sequence seq_crlf;
 105   seq_crlf.load_fasta(crlf);
 106
 107   stringstream lf;
 108   lf << header << "\012" << line1 << "\012" << line2 << "\012";
 109   Sequence seq_lf;
 110   seq_lf.load_fasta(lf);
 111
 112   BOOST_CHECK_EQUAL(seq_cr.size(),   seq_len);
 113   BOOST_CHECK_EQUAL(seq_crlf.size(), seq_len);
 114   BOOST_CHECK_EQUAL(seq_cr.size(),   seq_len);
 115 }
 116
 117
 118 //! Do simple operations work correctly?
 119 BOOST_AUTO_TEST_CASE( sequence_filter )
 120 {
 121   const char *core_seq = "AATTGGCC";
 122   Sequence s1(core_seq, reduced_dna_alphabet);
 123   BOOST_CHECK_EQUAL(s1, core_seq);
 124
 125   Sequence s2("aattggcc", reduced_dna_alphabet);
 126   BOOST_CHECK_EQUAL(s2, "AATTGGCC");
 127   BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
 128   BOOST_CHECK_EQUAL(s2.rev_comp(), "ggccaatt"); // we should be case insensitive now
 129   BOOST_CHECK_EQUAL(s2.size(), s2.size());
 130   //We're currently forcing sequences to uppercase
 131   BOOST_CHECK_EQUAL(s2.get_sequence(), "AATTGGCC");
 132
 133   Sequence s3("asdfg", reduced_dna_alphabet);
 134   BOOST_CHECK_EQUAL(s3, "ANNNG");
 135   BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
 136
 137   s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 0, 2);
 138   BOOST_CHECK_EQUAL(s3, "AA");
 139   s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 2, 2);
 140   BOOST_CHECK_EQUAL( s3, "GG");
 141   s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 4);
 142   BOOST_CHECK_EQUAL( s3, "CCTT");
 143
 144   s3 = "AAGGFF";
 145   BOOST_CHECK_EQUAL(s3, "AAGGNN");
 146 }
 147
 148 BOOST_AUTO_TEST_CASE( sequence_nucleic_alphabet )
 149 {
 150   std::string agct("AGCT");
 151   Sequence seq(agct, nucleic_alphabet);
 152   BOOST_CHECK_EQUAL(seq.size(), agct.size());
 153   BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
 154
 155   std::string bdv("BDv");
 156   Sequence seq_bdv(bdv, nucleic_alphabet);
 157   BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
 158   // forcing sequence to upper case
 159   BOOST_CHECK_EQUAL(seq_bdv.get_sequence(),
 160                     boost::algorithm::to_upper_copy(bdv));
 161
 162 }
 163
 164 BOOST_AUTO_TEST_CASE( sequence_default_alphabet )
 165 {
 166   std::string agct("AGCT");
 167   Sequence seq(agct);
 168   BOOST_CHECK_EQUAL(seq.size(), agct.size());
 169   BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
 170   BOOST_CHECK_EQUAL(seq[0], agct[0]);
 171   BOOST_CHECK_EQUAL(seq[1], agct[1]);
 172   BOOST_CHECK_EQUAL(seq[2], agct[2]);
 173   BOOST_CHECK_EQUAL(seq[3], agct[3]);
 174
 175   std::string bdv("BDv");
 176   Sequence seq_bdv(bdv);
 177   BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
 178   // default alphabet only allows AGCTUN
 179   BOOST_CHECK_EQUAL(seq_bdv.get_sequence(), "NNN");
 180 }
 181
 182 BOOST_AUTO_TEST_CASE( subseq_names )
 183 {
 184   Sequence s1("AAGGCCTT", reduced_dna_alphabet);
 185   s1.set_species("species");
 186   s1.set_fasta_header("a fasta header");
 187   Sequence s2 = s1.subseq(2,2);
 188   BOOST_CHECK_EQUAL(s2, "GG");
 189   BOOST_CHECK_EQUAL(s2.get_species(), s1.get_species());
 190   BOOST_CHECK_EQUAL(s2.get_fasta_header(), s1.get_fasta_header());
 191 }
 192
 193 BOOST_AUTO_TEST_CASE( sequence_start_stop )
 194 {
 195   Sequence s1;
 196   BOOST_CHECK_EQUAL( s1.start(), 0 );
 197   BOOST_CHECK_EQUAL( s1.stop(), 0 );
 198
 199   std::string seq_string("AAGGCCTT");
 200   Sequence s2(seq_string, reduced_dna_alphabet);
 201   BOOST_CHECK_EQUAL( s2.start(), 0 );
 202   BOOST_CHECK_EQUAL( s2.stop(), seq_string.size() );
 203
 204   std::string s3seq_string = seq_string.substr(2,3);
 205   Sequence s3 = s2.subseq(2,3);
 206   BOOST_CHECK_EQUAL( s3.start(), 2);
 207   BOOST_CHECK_EQUAL( s3.stop(), 2+3);
 208   BOOST_CHECK_EQUAL( s3.size(), 3);
 209   BOOST_CHECK_EQUAL( s3, s3seq_string);
 210
 211   std::string s4seq_string = s3seq_string.substr(1,1);
 212   Sequence s4 = s3.subseq(1,1);
 213   BOOST_CHECK_EQUAL( s4.start(), 1 );
 214   BOOST_CHECK_EQUAL( s4.stop(), 1+1);
 215   BOOST_CHECK_EQUAL( s4.size(), 1);
 216   BOOST_CHECK_EQUAL( s4, s4seq_string);
 217 }
 218
 219 //! Can we load data from a file
 220 BOOST_AUTO_TEST_CASE( sequence_load )
 221 {
 222   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq");
 223   seq_path /=  "human_mck_pro.fa";
 224   Sequence s;
 225   s.load_fasta(seq_path, reduced_dna_alphabet);
 226   BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
 227   BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
 228   BOOST_CHECK_EQUAL(s.get_fasta_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
 229                                     "muscle creatine kinase gene (CKMM), "
 230                                     "5' flank");
 231 }
 232
 233 BOOST_AUTO_TEST_CASE( sequence_load_fasta_error )
 234 {
 235   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
 236   seq_path /= "broken.fa";
 237   bool exception_thrown = false;
 238   std::string exception_filename;
 239   Sequence s;
 240   try {
 241     s.load_fasta(seq_path);
 242   } catch(sequence_invalid_load_error e) {
 243     exception_thrown = true;
 244     size_t native_string_size = seq_path.native_file_string().size();
 245     std:string estr(e.what());
 246     BOOST_REQUIRE(estr.size() > native_string_size);
 247     std::copy(estr.begin(), estr.begin()+native_string_size,
 248               std::back_inserter(exception_filename));
 249   }
 250   BOOST_CHECK_EQUAL(exception_thrown, true);
 251   BOOST_CHECK_EQUAL(seq_path.native_file_string(), exception_filename);
 252 }
 253
 254 BOOST_AUTO_TEST_CASE( sequence_load_annot_error )
 255 {
 256   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
 257   seq_path /= "mouse_mck_pro.fa";
 258   fs::path annot_path(fs::path(EXAMPLE_DIR, fs::native));
 259   annot_path /= "broken.annot";
 260   bool exception_thrown = false;
 261   Sequence s;
 262   s.load_fasta(seq_path);
 263
 264   std::string exception_filename;
 265   try {
 266     s.load_annot(annot_path, 0, 0);
 267   } catch(annotation_load_error e) {
 268     exception_thrown = true;
 269     std:string estr(e.what());
 270     size_t native_string_size = annot_path.native_file_string().size();
 271     BOOST_REQUIRE(estr.size() > native_string_size);
 272     std::copy(estr.begin(), estr.begin()+native_string_size,
 273               std::back_inserter(exception_filename));
 274   }
 275   BOOST_CHECK_EQUAL(exception_thrown, true);
 276   BOOST_CHECK_EQUAL(annot_path.native_file_string(), exception_filename);
 277 }
 278
 279 BOOST_AUTO_TEST_CASE( sequence_load_dna_reduced )
 280 {
 281   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 282   std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
 283   std::string invalid_dna_fasta_string(">wrong\nAUSSI\n");
 284   std::stringstream invalid_dna_fasta(invalid_dna_fasta_string);
 285   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN-\n");
 286   std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
 287   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 288   std::stringstream garbage_fasta(garbage_string);
 289
 290   Sequence s;
 291   s.load_fasta(reduced_dna_fasta, reduced_dna_alphabet);
 292   BOOST_CHECK_THROW(s.load_fasta(invalid_dna_fasta,
 293                                  reduced_dna_alphabet),
 294                     sequence_invalid_load_error);
 295   BOOST_CHECK_THROW(s.load_fasta(reduced_rna_fasta,
 296                                  reduced_dna_alphabet),
 297                     sequence_invalid_load_error);
 298   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
 299                                  reduced_dna_alphabet),
 300                     sequence_invalid_load_error);
 301
 302 }
 303
 304 BOOST_AUTO_TEST_CASE( sequence_load_rna_reduced )
 305 {
 306   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
 307   std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
 308   std::string invalid_rna_fasta_string(">wrong\nATSSI\n");
 309   std::stringstream invalid_rna_fasta(invalid_rna_fasta_string);
 310   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 311   std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
 312   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 313   std::stringstream garbage_fasta(garbage_string);
 314
 315   Sequence s;
 316   s.load_fasta(reduced_rna_fasta, reduced_rna_alphabet);
 317   BOOST_CHECK_THROW(s.load_fasta(invalid_rna_fasta,
 318                                  reduced_rna_alphabet),
 319                     sequence_invalid_load_error);
 320   BOOST_CHECK_THROW(s.load_fasta(reduced_dna_fasta,
 321                                  reduced_rna_alphabet),
 322                     sequence_invalid_load_error);
 323   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
 324                                  reduced_rna_alphabet),
 325                     sequence_invalid_load_error);
 326 }
 327
 328 BOOST_AUTO_TEST_CASE( sequence_load_fasta_default )
 329 {
 330   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
 331   std::stringstream reduced_rna_fasta1(reduced_rna_fasta_string);
 332   std::stringstream reduced_rna_fasta2(reduced_rna_fasta_string);
 333   std::string invalid_nucleotide_fasta_string(">wrong\nATSSI\n");
 334   std::stringstream invalid_nucleotide_fasta(invalid_nucleotide_fasta_string);
 335   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 336   std::stringstream reduced_dna_fasta1(reduced_dna_fasta_string);
 337   std::stringstream reduced_dna_fasta2(reduced_dna_fasta_string);
 338   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 339   std::stringstream garbage_fasta(garbage_string);
 340
 341   Sequence s;
 342   Sequence specific;
 343   // there's two copies of reduced_rna_fasta because i didn't feel like
 344   // figuring out how to properly reset the read pointer in a stringstream
 345   s.load_fasta(reduced_rna_fasta1);
 346   specific.load_fasta(reduced_rna_fasta2, reduced_nucleic_alphabet);
 347   BOOST_CHECK_EQUAL(s, specific);
 348
 349   s.load_fasta(reduced_dna_fasta1);
 350   specific.load_fasta(reduced_dna_fasta2, reduced_nucleic_alphabet);
 351   BOOST_CHECK_EQUAL(s, specific);
 352
 353   BOOST_CHECK_THROW(s.load_fasta(invalid_nucleotide_fasta),
 354                     sequence_invalid_load_error);
 355   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta),
 356                     sequence_invalid_load_error);
 357 }
 358
 359 BOOST_AUTO_TEST_CASE( sequence_load_multiple_sequences_one_fasta )
 360 {
 361   std::string fasta_file(
 362     ">gi|10129974|gb|AF188002.1|AF188002\n"
 363     "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC\n"
 364     ">gi|180579|gb|M21487.1|HUMCKMM1\n"
 365     "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC\n"
 366     ">gi|1621|emb|X55146.1|OCMCK1\n"
 367     "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC\n"
 368   );
 369   istringstream seq1_file(fasta_file);
 370   Sequence seq1;
 371   seq1.load_fasta(seq1_file, 1, 0, 0);
 372   BOOST_CHECK_EQUAL(seq1.get_sequence(), "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC");
 373
 374   istringstream seq2_file(fasta_file);
 375   Sequence seq2;
 376   seq2.load_fasta(seq2_file, 2, 0, 0);
 377   BOOST_CHECK_EQUAL(seq2.get_sequence(), "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC");
 378
 379   istringstream seq3_file(fasta_file);
 380   Sequence seq3;
 381   seq3.load_fasta(seq3_file, 3, 0, 0);
 382   BOOST_CHECK_EQUAL(seq3.get_sequence(), "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC");
 383 }
 384
 385 BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
 386 {
 387   std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
 388   Sequence seq(iupac_symbols, nucleic_alphabet);
 389   Sequence seqr = seq.rev_comp();
 390
 391   BOOST_CHECK( seq != seqr );
 392   BOOST_CHECK_EQUAL( seq, seqr.rev_comp() );
 393   // forcing sequence to upper case
 394   BOOST_CHECK_EQUAL( seq.get_sequence(),
 395                      boost::algorithm::to_upper_copy(iupac_symbols) );
 396 }
 397
 398 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
 399 {
 400   std::string dna_str("AGCTN");
 401   Sequence dna_seq(dna_str, reduced_dna_alphabet);
 402   BOOST_CHECK_EQUAL(dna_seq.rev_comp(), "NAGCT");
 403   BOOST_CHECK_EQUAL(dna_seq, dna_seq.rev_comp().rev_comp());
 404 }
 405
 406 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
 407 {
 408   std::string rna_str("AGCUN");
 409   Sequence rna_seq(rna_str, reduced_rna_alphabet);
 410   BOOST_CHECK_EQUAL(rna_seq.rev_comp().get_sequence(), "NAGCU");
 411   BOOST_CHECK_EQUAL(rna_seq.get_sequence(),
 412                     rna_seq.rev_comp().rev_comp().get_sequence());
 413 }
 414
 415 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_subseq )
 416 {
 417   std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
 418   Sequence seq(dna_str, reduced_dna_alphabet);
 419   Sequence subseq = seq.subseq(8,4);
 420   BOOST_CHECK_EQUAL( subseq, "AAGG");
 421   Sequence rev_subseq = subseq.rev_comp();
 422   BOOST_CHECK_EQUAL( rev_subseq.size(), subseq.size() );
 423   BOOST_CHECK_EQUAL( rev_subseq.get_sequence(), "CCTT");
 424 }
 425
 426 BOOST_AUTO_TEST_CASE( sequence_reverse_iterator )
 427 {
 428   std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
 429   std::string dna_str_reversed(dna_str.rbegin(), dna_str.rend());
 430   Sequence seq(dna_str);
 431   std::string seq_reversed(seq.rbegin(), seq.rend());
 432   BOOST_CHECK_EQUAL(seq_reversed, dna_str_reversed);
 433
 434   std::string substr = dna_str.substr(8,4);
 435   Sequence subseq = seq.subseq(8,4);
 436   BOOST_CHECK_EQUAL(substr, subseq);
 437
 438   std::string substr_reversed(substr.rbegin(), substr.rend());
 439   std::string subseq_reversed(subseq.rbegin(), subseq.rend());
 440   BOOST_CHECK_EQUAL(substr_reversed, subseq_reversed);
 441 }
 442
 443 BOOST_AUTO_TEST_CASE( sequence_empty_reverse_iterator)
 444 {
 445   // so what happens with reverse interators when we have no sequence?
 446   Sequence seq1;
 447   Sequence seq2;
 448   Sequence seq3("AGCT");
 449
 450   // all the empty sequences should have equal iterators
 451   BOOST_CHECK(seq1.rbegin() == seq1.rend());
 452   BOOST_CHECK(seq1.rbegin() == seq2.rend());
 453
 454   // none of the seq1 iterators should equal any of the seq3 iterators
 455   BOOST_CHECK(seq1.rbegin() != seq3.rbegin());
 456   BOOST_CHECK(seq1.rbegin() != seq3.rend());
 457   BOOST_CHECK(seq1.rend() != seq3.rbegin());
 458   BOOST_CHECK(seq1.rend() != seq3.rend());
 459
 460   // seq3 iterators should work
 461   BOOST_CHECK(seq3.rbegin() != seq3.rend());
 462
 463 }
 464
 465 BOOST_AUTO_TEST_CASE( annotation_load )
 466 {
 467   string annot_data = "human\n"
 468                       "0 10 name   type\n"     //0
 469                       "10 20 myf7\n"           //1
 470                       "20 30 myod\n"           //2
 471                       "50\t55 anothername\n"   //3
 472                       "60 50 backward\n"       //4
 473                       ">ident3 asdf\n"         //7 (as these are added last)
 474                       "GCT\n"
 475                       "gCTn\n"
 476                       "75\t90\tname2\ttype2\n" //5
 477                       "100 120 name-asdf type!@#$%\n" //6
 478                       ;
 479   string s(100, 'A');
 480   s += "GCTGCTAATT";
 481   Sequence seq(s, reduced_dna_alphabet);
 482
 483   //istringstream annot_stream(annot_data);
 484   seq.parse_annot(annot_data, 0, 0);
 485   SeqSpanRefList annots_list(seq.annotations());
 486   std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
 487   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 488   BOOST_CHECK_EQUAL( annots[0]->start(), 0 );
 489   BOOST_CHECK_EQUAL( annots[0]->stop(), 10 );
 490   BOOST_REQUIRE( annots[0]->annotations() );
 491   BOOST_CHECK_EQUAL( annots[0]->annotations()->get("type"), "type");
 492   BOOST_CHECK_EQUAL( annots[0]->annotations()->name(), "name");
 493   BOOST_REQUIRE( annots[1]->annotations() );
 494   BOOST_CHECK_EQUAL( annots[1]->annotations()->name(), "myf7");
 495   BOOST_REQUIRE( annots[2]->annotations() );
 496   BOOST_CHECK_EQUAL( annots[2]->annotations()->name(), "myod");
 497   BOOST_REQUIRE( annots[3]->annotations() );
 498   BOOST_CHECK_EQUAL( annots[3]->annotations()->name(), "anothername");
 499   BOOST_REQUIRE( annots[4]->annotations() );
 500   BOOST_CHECK_EQUAL( annots[4]->annotations()->name(), "backward");
 501   BOOST_REQUIRE( annots[5]->annotations() );
 502   BOOST_CHECK_EQUAL( annots[5]->annotations()->name(), "name2");
 503   BOOST_CHECK_EQUAL( annots[5]->start(), 75);
 504   BOOST_CHECK_EQUAL( annots[5]->stop(), 90);
 505   BOOST_CHECK_EQUAL( annots[6]->start(), 100);
 506   BOOST_CHECK_EQUAL( annots[6]->stop(), 110);
 507   BOOST_REQUIRE( annots[6]->annotations() );
 508   BOOST_CHECK_EQUAL( annots[6]->annotations()->name(), "name-asdf");
 509   BOOST_CHECK_EQUAL( annots[6]->annotations()->get("type"), "type!@#$%");
 510   // sequence defined annotations will always be after the
 511   // absolute positions
 512   BOOST_REQUIRE( annots[7]->annotations() );
 513   BOOST_CHECK_EQUAL( annots[7]->annotations()->name(), "ident3 asdf");
 514   BOOST_CHECK_EQUAL( annots[7]->start(), 100);
 515   BOOST_CHECK_EQUAL( annots[7]->stop(), 107);
 516
 517   //BOOST_CHECK_EQUAL( annots
 518 }
 519
 520 BOOST_AUTO_TEST_CASE( annotation_broken_load )
 521 {
 522   string annot_data = "human\n"
 523                       "0 10 name   type\n"
 524                       "blah60 50 backward\n"
 525                       ">ident3 asdf\n"
 526                       "GCT\n"
 527                       "gCTn\n"
 528                       ;
 529   string s(100, 'A');
 530   s += "GCTGCTAATT";
 531   Sequence seq(s, reduced_dna_alphabet);
 532
 533   BOOST_CHECK_THROW(seq.parse_annot(annot_data, 0, 0), annotation_load_error);
 534   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 535   }
 536
 537 BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
 538 {
 539   // this actually is basically what's returned by UCSC
 540   // (well actually with some of the sequence and copies of fasta blocks
 541   // removed to make the example shorter
 542   string annot_data = "\n"
 543     "<PRE>\n"
 544     ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 545     "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
 546     "&gt;hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 547     "GGTGGAGACGACCTGGACCCTAACTACGT\n"
 548     "</PRE>\n"
 549     "\n"
 550     "</BODY>\n"
 551     "</HTML>\n"
 552     ;
 553
 554   string s =
 555     "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
 556     "AAAAA"
 557     "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
 558   Sequence seq(s, reduced_dna_alphabet);
 559   seq.parse_annot(annot_data);
 560   SeqSpanRefList annots(seq.annotations());
 561   BOOST_CHECK_EQUAL( annots.size(), 2);
 562 }
 563
 564 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
 565 {
 566   string annot_data = "0 10 name   type\n"
 567                       "10 20 myf7\n"
 568                       "20 30 myod\n"
 569                       "50\t55 anothername\n"
 570                       "60 50 backward\n"
 571                       ">ident3 asdf\n"
 572                       "GCT\n"
 573                       "gCTn\n"
 574                       "75\t90\tname2\ttype2\n"
 575                       "100 120 name-asdf type!@#$%\n"
 576                       ;
 577   string s(100, 'A');
 578   s += "GCTGCTAATT";
 579   Sequence seq(s, reduced_dna_alphabet);
 580
 581   //istringstream annot_stream(annot_data);
 582   seq.parse_annot(annot_data, 0, 0);
 583   SeqSpanRefList annots_list(seq.annotations());
 584   std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
 585   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 586   BOOST_CHECK_EQUAL( annots[0]->start(), 0 );
 587   BOOST_CHECK_EQUAL( annots[0]->stop(), 10 );
 588   BOOST_CHECK_EQUAL( annots[0]->annotations()->get("type"), "type");
 589 }
 590
 591 // when we do a subsequence (or something that calls copy_children)
 592 // the annotations need to be updated to have the right parent
 593 BOOST_AUTO_TEST_CASE( update_annotations_seqref )
 594 {
 595   Sequence s1("AAAAGGGG");
 596   s1.add_annotation("A", "A", 0, 4);
 597   BOOST_CHECK_EQUAL(s1.annotations().size(), 1);
 598   BOOST_CHECK_EQUAL(s1.seqspan(), s1.annotations().front()->parent() );
 599
 600   Sequence subseq1(s1.subseq(2,4));
 601   BOOST_CHECK_EQUAL(subseq1.annotations().size(), 1);
 602   BOOST_CHECK_EQUAL(subseq1.annotations().front()->parentStart(), 0 );
 603   BOOST_CHECK_EQUAL(subseq1.annotations().front()->parentStop(), 2 );
 604   BOOST_CHECK_EQUAL(subseq1.seqspan(), subseq1.annotations().front()->parent() );
 605 }
 606
 607 // ticket:83 when you try to load a sequence from a file that doesn't
 608 // have fasta headers it crashes.
 609 BOOST_AUTO_TEST_CASE( sequence_past_end )
 610 {
 611   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq" );
 612   seq_path /=  "misformated_seq.fa";
 613   Sequence s;
 614   BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
 615 }
 616
 617 BOOST_AUTO_TEST_CASE ( sequence_empty )
 618 {
 619
 620   Sequence s;
 621   BOOST_CHECK_EQUAL( s.empty(), true );
 622   s = "AAAGGG";
 623   BOOST_CHECK_EQUAL( s.empty(), false );
 624   s.clear();
 625   BOOST_CHECK_EQUAL( s.empty(), true);
 626   s = "";
 627   BOOST_CHECK_EQUAL( s.empty(), true);
 628 }
 629
 630 BOOST_AUTO_TEST_CASE ( sequence_size )
 631 {
 632
 633   Sequence s;
 634   BOOST_CHECK_EQUAL( s.size(), 0);
 635   std::string seq_string("AAAGGG");
 636   s = seq_string;
 637   BOOST_CHECK_EQUAL( s.size(), seq_string.size() );
 638   s.clear();
 639   BOOST_CHECK_EQUAL( s.size(), 0);
 640   s = "";
 641   BOOST_CHECK_EQUAL( s.size(), 0);
 642 }
 643
 644 BOOST_AUTO_TEST_CASE( sequence_empty_equality )
 645 {
 646   Sequence szero("", reduced_dna_alphabet);
 647   BOOST_CHECK_EQUAL(szero.empty(), true);
 648   BOOST_CHECK_EQUAL(szero, szero);
 649   BOOST_CHECK_EQUAL(szero, "");
 650
 651   Sequence sclear("AGCT", reduced_dna_alphabet);
 652   sclear.clear();
 653   BOOST_CHECK_EQUAL(sclear.empty(), true);
 654   BOOST_CHECK_EQUAL(sclear, sclear);
 655   BOOST_CHECK_EQUAL(sclear, szero);
 656   BOOST_CHECK_EQUAL(sclear, "");
 657
 658 }
 659 BOOST_AUTO_TEST_CASE ( sequence_iterators )
 660 {
 661   std::string seq_string = "AAGGCCTTNNTATA";
 662   Sequence s(seq_string, reduced_dna_alphabet);
 663   const Sequence cs(s);
 664   std::string::size_type count = 0;
 665
 666   std::string::iterator str_itor;
 667   Sequence::const_iterator s_itor;
 668   Sequence::const_iterator cs_itor;
 669
 670   for( str_itor = seq_string.begin(),
 671        s_itor   = s.begin(),
 672        cs_itor  = cs.begin();
 673        str_itor != seq_string.end() and
 674        s_itor   != s.end() and
 675        cs_itor  != cs.end();
 676        ++str_itor, ++s_itor, ++cs_itor, ++count)
 677   {
 678     BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
 679     BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
 680     BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
 681   }
 682   BOOST_CHECK_EQUAL( seq_string.size(), count );
 683   BOOST_CHECK_EQUAL( s.size(), count );
 684   BOOST_CHECK_EQUAL( cs.size(), count );
 685 }
 686
 687 BOOST_AUTO_TEST_CASE( sequence_motifs )
 688 {
 689   string m("AAAA");
 690   string bogus("AATTGGAA");
 691   Sequence s1("AAAAGGGGCCCCTTTT", reduced_dna_alphabet);
 692
 693   list<motif>::const_iterator motif_i = s1.motifs().begin();
 694   list<motif>::const_iterator motif_end = s1.motifs().end();
 695
 696   // do our iterators work?
 697   BOOST_CHECK( motif_i == s1.motifs().begin() );
 698   BOOST_CHECK( motif_end == s1.motifs().end() );
 699   BOOST_CHECK( motif_i == motif_end );
 700
 701   // this shouldn't show up
 702   s1.add_motif(bogus);
 703   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 704   BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
 705
 706   s1.add_motif(m);
 707   BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
 708   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 709
 710   for(motif_i = s1.motifs().begin();
 711       motif_i != s1.motifs().end();
 712       ++motif_i)
 713   {
 714     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 715     BOOST_CHECK_EQUAL( motif_i->name, m);
 716     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 717   }
 718
 719   s1.clear_motifs();
 720   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 721
 722   /* FIXME: enable this when i find a way of passing storing the motif name
 723   // does our annotation travel?
 724   Sequence motif_seq(m);
 725   motif_seq.set_fasta_header("hi");
 726   s1.add_motif(motif_seq);
 727
 728   BOOST_CHECK_EQUAL(s1.motifs().size(), 2);
 729   for(motif_i = s1.motifs().begin();
 730       motif_i != s1.motifs().end();
 731       ++motif_i)
 732   {
 733     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 734     BOOST_CHECK_EQUAL( motif_i->name, "hi");
 735     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 736   }
 737   */
 738 }
 739
 740 BOOST_AUTO_TEST_CASE( sequence_motif_subseq)
 741 {
 742   // when searching for a motif on a subsequence we should
 743   // only search the subsequence ticket:199
 744   string aaaa("AAAA");
 745   string cccc("CCCC");
 746   Sequence s1("AAAANCCCC", reduced_dna_alphabet);
 747
 748   // this shouldn't show up
 749   s1.add_motif(cccc);
 750   BOOST_CHECK_EQUAL( s1.motifs().size(), 1 );
 751
 752   s1.add_motif(aaaa);
 753   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 754
 755   Sequence subseq1 = s1.subseq(4,5);
 756   BOOST_CHECK_EQUAL(subseq1.motifs().size(), 2);
 757   subseq1.clear_motifs();
 758   BOOST_CHECK_EQUAL(subseq1.motifs().size(), 0);
 759   // this is outside of our subsequence, and so shouldn't be found
 760   subseq1.add_motif(aaaa);
 761   BOOST_CHECK_EQUAL( subseq1.motifs().size(), 0 );
 762
 763   subseq1.add_motif(cccc);
 764   BOOST_CHECK_EQUAL( subseq1.motifs().size(), 1);
 765   std::list<motif>::const_iterator motif_i = subseq1.motifs().begin();
 766   BOOST_REQUIRE(motif_i != subseq1.motifs().end());
 767   BOOST_CHECK_EQUAL(motif_i->begin, 1);
 768   BOOST_CHECK_EQUAL(motif_i->end, 5);
 769 }
 770
 771 BOOST_AUTO_TEST_CASE( annot_test )
 772 {
 773   Sequence s("AAAAAAAAAA");
 774   s.add_annotation("test", "thing", 0, 10);
 775   SeqSpanRef a(s.annotations().front());
 776
 777   BOOST_CHECK_EQUAL( a->start(), 0 );
 778   BOOST_CHECK_EQUAL( a->stop(),   10 );
 779   BOOST_CHECK_EQUAL( a->annotations()->get("name"),  "test" );
 780   BOOST_CHECK_EQUAL( a->annotations()->get("type"),  "thing" );
 781
 782   motif m(10, "AAGGCC");
 783   BOOST_CHECK_EQUAL( m.begin, 10 );
 784   BOOST_CHECK_EQUAL( m.type, "motif" );
 785   BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
 786   BOOST_CHECK_EQUAL( m.end,  10+6 );
 787 }
 788
 789 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
 790 {
 791   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 792            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 793            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 794            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 795            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 796            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 797            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 798            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 799   string gc("GCCCCC");
 800   string gga("GGACACCTC");
 801   Sequence seq(s, reduced_dna_alphabet);
 802
 803   std::list<Sequence> query_list;
 804   std::list<string> string_list;
 805   query_list.push_back(Sequence(gc));
 806   string_list.push_back(gc);
 807   query_list.push_back(Sequence(gga));
 808   string_list.push_back(gga);
 809
 810   BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
 811   seq.find_sequences(query_list.begin(), query_list.end());
 812
 813   int count = 0;
 814   for(list<string>::iterator string_i = string_list.begin();
 815       string_i != string_list.end();
 816       ++string_i)
 817   {
 818     string::size_type pos=0;
 819     while(pos != string::npos) {
 820       pos = s.find(*string_i, pos);
 821       if (pos != string::npos) {
 822         ++count;
 823         ++pos;
 824       }
 825     }
 826   }
 827   BOOST_CHECK_EQUAL(seq.annotations().size(), count);
 828   const SeqSpanRefList& a = seq.annotations();
 829   for (SeqSpanRefList::const_iterator annot_i = a.begin();
 830        annot_i != a.end();
 831        ++annot_i)
 832   {
 833     //FIXME: was I doing something here?
 834     int count = (*annot_i)->stop() - (*annot_i)->start();
 835   }
 836 }
 837
 838 BOOST_AUTO_TEST_CASE( sequence_no_trailing_newline )
 839 {
 840   // sorry about the long string...
 841   string s = "AATTACACAAGGAATATAGGTAGTTTGAATAAAAATATCTTTAACAGCTTGGAGCTATTGAGACAGGAACACTTCCACGCACATGCACAGTTAAACAACTTGAGTGCAACACACAACATTGGCACTAAACGAGATTGAAGGGGGACTTTTTGTGTGTTTTTTTTTCTCTTTTCTTTTTTTGTTATAGTTACTTCAAGTAACACAGCTTGCTTCATATAAATAAGTTAAAACATCTATTTTTTTTCAAGACAAAGCCATTCAGGACAAAGAGATGAACAGAAAGCAGATCTACTTATACAGGCGCTATAATGGCAATAAACAGGCTCATGATTAAAAGATGAATTAGGGCAACGAGAACAGGGCTTCTTCACAGAAGGAACACAAGGGAGTTTCAGAAAGTCACCTTAGTACTGACACTACGCGGGATCCGCTAATACTGCTCAGTACTTTAAACGCTCAGATACTCAGGGACGGAAGGCCCCTCCTGCCGCGGCCATGCTCATGCTTTTCAGCTTATTATCTTTTTTCCACTTCATTCTCCGGTTTTGGAACCAGATTTTAATTTGTCTCTCGGAGAGGCAAAGAGCATGTGCTATTTCAATCCTCCTTCTGCGGGTCAGGTAACGGTTGAAGTGGAACTCCTTCTCCAGCTCCAGGGTCTGGTAGCGCGTGTAGGCCGTCCGGGCCCTTTTGCCTTCCGGGCCGCCTATGTTGTCTGCAATAGAAAAGTCAGCGGTTTAGCCACCAACTCCTGTCTTCCAAAGTCCGCCAGGGGGACAAGCTTGGGTCATGAGCAGGGAACCCAGGCGAAAAGCTCAACAAGTTCTGCCTACCAGCCCGCACACCCCTCCCGAATTTCCTTCTCTCTTCCTTTCTAGAAAGAAAACAATACGATTTGGACCCTGGGAACAATCTGCCCATCTGAGGCTGGGGCCGTGTCCCGGCGGACTCCGGCTTTCCCTGGCCCCTCTCCTGCCCCCTCCGCCCTGCCCCGGGCGCCCCGATCGGGAGGCACAGCCCTCCCAGGCTGCCCACCGCACAGAAACCCAGGAAGCAAGGCCCTTTCCTGAGCGCCCAAGTGGCCTTCGGGTCACCCTCCCTCAAAGTTCCAGCCCCGAGAGCCGCCTCCCGTTTCCAGCCTGCAGGGTTGGGGAGCCTGTTTTCTTTTTCTTCCCTTTCCTTCTCTCTCCCTCCTGCCCCCAAAATTCAGAATCCTGCAGGCTCTCGCCTCGATTCTTTCCCCCAAGCCCCTTTTCGGGGGCTGTAATTAGTAACGCTGTTTCCCCAGCGTAGCCCTCCTCATAAATTATCCGCCGTGACAAGCCCGATTCACGGCTGCTACAGCCATCCTCTACCTCTCTGCGCCTTGCTCGGCTGGCCTGACCCGGGAGCGCGTCCCAAGGCGTGGGGTTCCAGAGGGGTTTTTTGCTTCCTCCCCCTTCCAACGTCTAAACTGTCCCAGAGAACGCCCATTTCCCCCACTATTTGTGAGCGCAGGGTGCTCGCAAAGAAGAGGAGGAAGGAGGAAGGCAGGGGAGGGAGAACGGCAAGGAGAGCTCCGCAGGGCTGGGAGAAATGAGACCAAGAGAGACTGGGAGAGGGCGGCAGAGAAGAGAGGGGGGACCGAGAGCCGCGTCCCCGCGGTCGCGTGGATTTAGAAAAAGGCTGGCTTTACCATGACTTATGTGCAGCTTGCGCATCCAGGGGTAGATCTGGGGTTGGGCGGGCGGCGCCGGGCTCGGCTCGCTCTGCGCACTCGCCTGCTCGCTGCTGGCAGGGGCGTCCTCCTCGGCTCCGGACGCCGTGCCAACCCCCTCTCTGCTGCTGATGTGGGTGCTGCCGGCGTCGGCCGAGGCGCCGCTGGAGTTGCTTAGGGAGTTTTTCCCGCCGTGGTGGCTGTCGCTGCCGGGCGAGGGGGCCACGGCGGAGCAGGGCAGCGGATCGGGCTGAGGAGAGTGCGTGGACGTGGCCGGCTGGCTGTACCTGGGCTCGGCGGGCGCCGCGCTGGCGCTGGCAGCGTAGCTGCGGGCGCGCTCTCCGGAGCCAAAGTGGCCGGAGCCCGAGCGGCCGACGCTGAGATCCATGCCATTGTAGCCGTAGCCGTACCTGCCGGAGTGCATGCTCGCCGAGTCCCTGAATTGCTCGCTCACGGAACTATGATCTCCATAATTATGCAACTGGTAGTCCGGGCCATTTGGATAGCGACCGCAAAATGAGTTTACAAAATAAGAGCTCATTTGTTTTTTGATATGTGTGCTTGATTTGTGGCTCGCGGTCGTTTGTGCGTCTATAGCACCCTT";
 842   std::string species = "HumanHXA5\n";
 843   std::string header0 = ">hg18_knownGene_NM_019102_0\n";
 844   std::string str0 = "GGGTGCTATAGACGCACAAACGACCGCGAGCCACAAATCAAGCACACATATCAAAAAACAAATGAGCTCTTATTTTGTAAACTCATTTTGCGGTCGCTATCCAAATGGCCCGGACTACCAGTTGCATAATTATGGAGATCATAGTTCCGTGAGCGAGCAATTCAGGGACTCGGCGAGCATGCACTCCGGCAGGTACGGCTACGGCTACAATGGCATGGATCTCAGCGTCGGCCGCTCGGGCTCCGGCCACTTTGGCTCCGGAGAGCGCGCCCGCAGCTACGCTGCCAGCGCCAGCGCGGCGCCCGCCGAGCCCAGGTACAGCCAGCCGGCCACGTCCACGCACTCTCCTCAGCCCGATCCGCTGCCCTGCTCCGCCGTGGCCCCCTCGCCCGGCAGCGACAGCCACCACGGCGGGAAAAACTCCCTAAGCAACTCCAGCGGCGCCTCGGCCGACGCCGGCAGCACCCACATCAGCAGCAGAGAGGGGGTTGGCACGGCGTCCGGAGCCGAGGAGGACGCCCCTGCCAGCAGCGAGCAGGCGAGTGCGCAGAGCGAGCCGAGCCCGGCGCCGCCCGCCCAACCCCAGATCTACCCCTGGATGCGCAAGCTGCACATAAGTCATG";
 845   std::string header1 = ">hg18_knownGene_NM_019102_1\n";
 846   std::string str1 = "ACAACATAGGCGGCCCGGAAGGCAAAAGGGCCCGGACGGCCTACACGCGCTACCAGACCCTGGAGCTGGAGAAGGAGTTCCACTTCAACCGTTACCTGACCCGCAGAAGGAGGATTGAAATAGCACATGCTCTTTGCCTCTCCGAGAGACAAATTAAAATCTGGTTCCAAAACCGGAGAATGAAGTGGAAAAAAGATAATAAGCTGAAAAGCATGAGCATGGCCGCGGCAGGAGGGGCCTTCCGTCCCTGAGTATCTGAGCGTTTAAAGTACTGAGCAGTATTAGCGGATCCCGCGTAGTGTCAGTACTAAGGTGACTTTCTGAAACTCCCTTGTGTTCCTTCTGTGAAGAAGCCCTGTTCTCGTTGCCCTAATTCATCTTTTAATCATGAGCCTGTTTATTGCCATTATAGCGCCTGTATAAGTAGATCTGCTTTCTGTTCATCTCTTTGTCCTGAATGGCTTTGTCTTGAAAAAAAATAGATGTTTTAACTTATTTATATGAAGCAAGCTGTGTTACTTGAAGTAACTATAACAAAAAAAGAAAAGAGAAAAAAAAACACACAAAAAGTCCCCCTTCAATCTCGTTTAGTGCCAATGTTGTGTGTTGCACTCAAGTTGTTTAACTGTGCATGTGCGTGGAAGTGTTCCTGTCTCAATAGCTCCAAGCTGTTAAAGATATTTTTATTCAAACTACCTATATTCCTTGT";
 847   stringstream annot;
 848   annot << species
 849         << header0
 850         << str0 << std::endl
 851         << std::endl
 852         << header1
 853         << str1;
 854   // need to convert strings to sequences for reverse complementing
 855   Sequence seq0(str0, reduced_dna_alphabet);
 856   Sequence seq1(str1, reduced_dna_alphabet);
 857
 858   Sequence annotated_seq(s, reduced_dna_alphabet);
 859   annotated_seq.load_annot(annot, 0, 0);
 860
 861   SeqSpanRefList annots_list = annotated_seq.annotations();
 862   // both sequences were found
 863   BOOST_REQUIRE_EQUAL( annots_list.size(),  2 );
 864
 865   std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
 866   // are they the same sequence?
 867   BOOST_CHECK_EQUAL( annots[0]->size(),  seq0.size());
 868   BOOST_CHECK_EQUAL( annots[0]->sequence(), seq0.rev_comp() );
 869   // this should hopefully catch the case when my hack in
 870   // sequence.cpp::push_back_seq::operator() is no longer needed.
 871   // spirit (or my grammar was duplicating the last char,
 872   // the hack removes the duplicate. but if what ever's causing
 873   // the dup gets fixed actual meaningful data will be being removed.
 874   // see mussa ticket:265 for more information
 875   BOOST_CHECK_EQUAL( annots[1]->size(),  seq1.size());
 876   BOOST_CHECK_EQUAL( annots[1]->sequence(), seq1.rev_comp() );
 877
 878 }
 879
 880 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
 881 {
 882   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 883            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 884            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 885            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 886            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 887            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 888            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 889            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 890   Sequence seq(s, reduced_dna_alphabet);
 891
 892   seq.add_annotation("0-10", "0-10", 0, 10);
 893   seq.add_annotation("10-20", "10-20", 10, 20);
 894   seq.add_annotation("0-20", "0-20", 0, 20);
 895   seq.add_annotation("8-12", "8-12", 8, 12);
 896   seq.add_annotation("100-5000", "100-5000", 100, 5000);
 897
 898   Sequence subseq = seq.subseq(5, 10);
 899   SeqSpanRefList annots_list = subseq.annotations();
 900   BOOST_REQUIRE_EQUAL( annots_list.size(), 4 );
 901
 902   std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
 903   BOOST_CHECK_EQUAL( annots[0]->parentStart(),  0);
 904   BOOST_CHECK_EQUAL( annots[0]->size(),  5);
 905   BOOST_REQUIRE( annots[0]->annotations() );
 906   BOOST_CHECK_EQUAL( annots[0]->annotations()->name(), "0-10");
 907
 908   BOOST_CHECK_EQUAL( annots[1]->parentStart(), 5);
 909   BOOST_CHECK_EQUAL( annots[1]->size(), 5);
 910   BOOST_REQUIRE( annots[1]->annotations() );
 911   BOOST_CHECK_EQUAL( annots[1]->annotations()->name(), "10-20");
 912
 913   BOOST_CHECK_EQUAL( annots[2]->parentStart(), 0);
 914   BOOST_CHECK_EQUAL( annots[2]->size(), 10);
 915   BOOST_REQUIRE( annots[2]->annotations() );
 916   BOOST_CHECK_EQUAL( annots[2]->annotations()->name(), "0-20");
 917
 918   BOOST_CHECK_EQUAL( annots[3]->parentStart(), 3);
 919   BOOST_CHECK_EQUAL( annots[3]->size(),  7);
 920   BOOST_REQUIRE( annots[3]->annotations() );
 921   BOOST_CHECK_EQUAL( annots[3]->annotations()->name(), "8-12");
 922 }
 923
 924 BOOST_AUTO_TEST_CASE( motif_annotation_update )
 925 {
 926   string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 927            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 928            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 929            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 930            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 931            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 932            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 933            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 934   Sequence seq(s, reduced_dna_alphabet);
 935
 936   // starting conditions
 937   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 938   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 939   seq.add_annotation("0-10", "0-10", 0, 10);
 940   seq.add_annotation("10-20", "10-20", 10, 20);
 941   seq.add_annotation("0-20", "0-20", 0, 20);
 942   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 943   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 944   seq.add_motif("CCGTCCC");
 945   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 946   BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
 947   seq.clear_motifs();
 948   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 949   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 950 }
 951
 952 BOOST_AUTO_TEST_CASE( out_operator )
 953 {
 954   string s("AAGGCCTT");
 955   Sequence seq(s, reduced_dna_alphabet);
 956
 957   ostringstream buf;
 958   buf << s;
 959   BOOST_CHECK_EQUAL( s, buf.str() );
 960 }
 961
 962 BOOST_AUTO_TEST_CASE( get_name )
 963 {
 964   Sequence seq("AAGGCCTT", reduced_dna_alphabet);
 965
 966   BOOST_CHECK_EQUAL( seq.get_name(), "" );
 967   seq.set_species("hooman"); // anyone remember tradewars?
 968   BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
 969   seq.set_fasta_header("fasta human");
 970   BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
 971 }
 972 /*
 973 BOOST_AUTO_TEST_CASE( serialize_simple )
 974 {
 975   std::string seq_string = "AAGGCCTT";
 976   Sequence seq(seq_string, reduced_dna_alphabet);
 977   seq.set_species("ribbet");
 978   std::ostringstream oss;
 979   // allocate/deallocate serialization components
 980   {
 981     boost::archive::text_oarchive oarchive(oss);
 982     const Sequence& const_seq(seq);
 983     BOOST_CHECK_EQUAL(seq, const_seq);
 984     oarchive << const_seq;
 985   }
 986   Sequence seq_loaded;
 987   {
 988     std::istringstream iss(oss.str());
 989     boost::archive::text_iarchive iarchive(iss);
 990     iarchive >> seq_loaded;
 991   }
 992   BOOST_CHECK_EQUAL(seq_loaded, seq);
 993   BOOST_CHECK_EQUAL(seq.get_species(), "ribbet");
 994 }
 995
 996 BOOST_AUTO_TEST_CASE( serialize_tree )
 997 {
 998   std::string seq_string = "AAGGCCTT";
 999   Sequence seq(seq_string, reduced_dna_alphabet);
1000   seq.set_species("ribbet");
1001   seq.add_motif("AA");
1002   seq.add_motif("GC");
1003   seq.add_annotation("t", "t", 6, 7);
1004
1005   std::ostringstream oss;
1006   // allocate/deallocate serialization components
1007   {
1008     boost::archive::text_oarchive oarchive(oss);
1009     const Sequence& const_seq(seq);
1010     BOOST_CHECK_EQUAL(seq, const_seq);
1011     oarchive << const_seq;
1012   }
1013
1014   Sequence seq_loaded;
1015   {
1016     std::istringstream iss(oss.str());
1017     boost::archive::text_iarchive iarchive(iss);
1018     iarchive >> seq_loaded;
1019   }
1020   BOOST_CHECK_EQUAL(seq_loaded, seq);
1021 }
1022
1023 // this writes out an "old" style annotated sequence
1024 // with annotations attached as "motifs" and "annots"
1025 BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
1026 {
1027   std::string seq_string = "AAGGCCTT";
1028   Sequence seq(seq_string, reduced_dna_alphabet);
1029   seq.set_species("ribbet");
1030   seq.add_motif("AA");
1031   seq.add_motif("GC");
1032   seq.add_annotation("t", "t", 6, 7);
1033
1034   std::ostringstream oss;
1035   // allocate/deallocate serialization components
1036   {
1037     boost::archive::xml_oarchive oarchive(oss);
1038     const Sequence& const_seq(seq);
1039     BOOST_CHECK_EQUAL(seq, const_seq);
1040     oarchive << boost::serialization::make_nvp("root", const_seq);
1041   }
1042   Sequence seq_loaded;
1043   {
1044     std::istringstream iss(oss.str());
1045     boost::archive::xml_iarchive iarchive(iss);
1046     iarchive >> boost::serialization::make_nvp("root", seq_loaded);
1047   }
1048   BOOST_CHECK_EQUAL(seq_loaded, seq);
1049 }
1050
1051 BOOST_AUTO_TEST_CASE( serialize_xml_two )
1052 {
1053   std::string seq_string = "AAGGCCTT";
1054   Sequence seq1(seq_string, reduced_dna_alphabet);
1055   Sequence seq2(seq1);
1056
1057   std::ostringstream oss;
1058   // allocate/deallocate serialization components
1059   {
1060     boost::archive::xml_oarchive oarchive(oss);
1061     const Sequence& const_seq1(seq1);
1062     const Sequence& const_seq2(seq2);
1063     oarchive << boost::serialization::make_nvp("seq1", const_seq1);
1064     oarchive << boost::serialization::make_nvp("seq2", const_seq2);
1065   }
1066   //std::cout << "xml: " << oss.str() << std::endl;
1067   Sequence seq1_loaded;
1068   Sequence seq2_loaded;
1069   {
1070     std::istringstream iss(oss.str());
1071     boost::archive::xml_iarchive iarchive(iss);
1072     iarchive >> boost::serialization::make_nvp("seq1", seq1_loaded);
1073     iarchive >> boost::serialization::make_nvp("seq2", seq2_loaded);
1074   }
1075   BOOST_CHECK_EQUAL(seq1_loaded, seq1);
1076   BOOST_CHECK_EQUAL(seq2_loaded, seq2);
1077   // test if our pointers are the same
1078   BOOST_CHECK_EQUAL(seq1_loaded.data(), seq2_loaded.data());
1079 }
1080 */