alg/test/test_sequence.cpp

   1 #define BOOST_AUTO_TEST_MAIN
   2 #include <boost/test/auto_unit_test.hpp>
   3 #include <boost/filesystem/path.hpp>
   4 #include <boost/filesystem/operations.hpp>
   5 namespace fs=boost::filesystem;
   6
   7 #include <boost/algorithm/string/case_conv.hpp>
   8
   9 #include <list>
  10 #include <iostream>
  11 #include <sstream>
  12
  13 #include <boost/archive/text_oarchive.hpp>
  14 #include <boost/archive/text_iarchive.hpp>
  15 #include <boost/archive/xml_oarchive.hpp>
  16 #include <boost/archive/xml_iarchive.hpp>
  17
  18 #include "alg/sequence.hpp"
  19 #include "mussa_exceptions.hpp"
  20
  21 using namespace std;
  22
  23 BOOST_AUTO_TEST_CASE( sequence_copy_constructor )
  24 {
  25   SequenceRef s(new Sequence("AAAAGGGG"));
  26   s->set_species("foo");
  27   BOOST_CHECK_EQUAL(s->get_species(), "foo");
  28
  29   SequenceRef c(new Sequence(s));
  30   BOOST_CHECK_EQUAL(c->get_species(), "foo");
  31
  32   c->set_species("bar");
  33   BOOST_CHECK_EQUAL(s->get_species(), "foo");
  34   BOOST_CHECK_EQUAL(c->get_species(), "bar");
  35 }
  36
  37 BOOST_AUTO_TEST_CASE( sequence_copy_constructor_copy_motifs )
  38 {
  39   SequenceRef s(new Sequence("AAAAGGGGAAAA"));
  40   s->add_motif("AAGG");
  41   BOOST_CHECK_EQUAL(s->motifs().size(), 1);
  42
  43   SequenceRef c(new Sequence(s->subseq()));
  44   BOOST_CHECK_EQUAL(c->motifs().size(), 1);
  45
  46   s->clear_motifs();
  47   BOOST_CHECK_EQUAL(s->motifs().size(), 0);
  48   // FIXME: Technically c shouldn't lose its motifs.
  49   // FIXME: getting that to work is hard.
  50   // BOOST_CHECK_EQUAL(c->motifs().size(), 1);
  51   BOOST_CHECK_EQUAL(c->motifs().size(), 0);
  52 }
  53
  54 BOOST_AUTO_TEST_CASE( sequence_get_sequence )
  55 {
  56         Sequence s;
  57         // make sure that retrieving the sequence doesn't throw an error
  58         BOOST_CHECK_EQUAL(s.get_sequence(), std::string() );
  59 }
  60
  61 BOOST_AUTO_TEST_CASE( sequence_from_string )
  62 {
  63   std::string str1("AAAT");
  64   Sequence seq1(str1);
  65   BOOST_CHECK_EQUAL(seq1.get_sequence(), str1);
  66 }
  67
  68 BOOST_AUTO_TEST_CASE( sequence_find_first_not_of )
  69 {
  70   std::string str1("AAAAT");
  71   Sequence seq1(str1);
  72   BOOST_CHECK_EQUAL(seq1.find_first_not_of("A"), str1.find_first_not_of("A"));
  73
  74   std::string str2("AATTGGCC");
  75   Sequence seq2(str2);
  76   BOOST_CHECK_EQUAL(seq2.find_first_not_of("qwer"), str2.find_first_not_of("qwer"));
  77 }
  78
  79 //! when we try to load a missing file, do we get an error?
  80 BOOST_AUTO_TEST_CASE( sequence_load_exception )
  81 {
  82   Sequence s;
  83   // there should be errors when we try to load something that doesn't exist
  84   BOOST_CHECK_THROW( s.load_fasta("alkejralk", 1, 0, 0), mussa_load_error);
  85   BOOST_CHECK_THROW( s.load_annot("alkejralk", 0, 0), mussa_load_error);
  86 }
  87
  88 BOOST_AUTO_TEST_CASE( sequence_eol_conventions )
  89 {
  90   string header(">Header");
  91   string line1("AAAAGGGGCCCCTTTTT");
  92   string line2("AAAAGGGGCCCCTTTTT");
  93   int seq_len = line1.size() + line2.size();
  94
  95   stringstream cr;
  96   cr << header << "\015" << line1 << "\015" << line2 << "\015";
  97   Sequence seq_cr;
  98   seq_cr.load_fasta(cr);
  99
 100   stringstream crlf;
 101   crlf << header << "\015\012" << line1 << "\015\012" << line2 << "\015\012";
 102   Sequence seq_crlf;
 103   seq_crlf.load_fasta(crlf);
 104
 105   stringstream lf;
 106   lf << header << "\012" << line1 << "\012" << line2 << "\012";
 107   Sequence seq_lf;
 108   seq_lf.load_fasta(lf);
 109
 110   BOOST_CHECK_EQUAL(seq_cr.size(),   seq_len);
 111   BOOST_CHECK_EQUAL(seq_crlf.size(), seq_len);
 112   BOOST_CHECK_EQUAL(seq_cr.size(),   seq_len);
 113 }
 114
 115
 116 //! Do simple operations work correctly?
 117 BOOST_AUTO_TEST_CASE( sequence_filter )
 118 {
 119   const char *core_seq = "AATTGGCC";
 120   Sequence s1(core_seq, reduced_dna_alphabet);
 121   BOOST_CHECK_EQUAL(s1, core_seq);
 122
 123   Sequence s2("aattggcc", reduced_dna_alphabet);
 124   BOOST_CHECK_EQUAL(s2, "AATTGGCC");
 125   BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
 126   BOOST_CHECK_EQUAL(s2.rev_comp(), "ggccaatt"); // we should be case insensitive now
 127   BOOST_CHECK_EQUAL(s2.size(), s2.size());
 128   //We're currently forcing sequences to uppercase
 129   BOOST_CHECK_EQUAL(s2.get_sequence(), "AATTGGCC");
 130
 131   Sequence s3("asdfg", reduced_dna_alphabet);
 132   BOOST_CHECK_EQUAL(s3, "ANNNG");
 133   BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
 134
 135   s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 0, 2);
 136   BOOST_CHECK_EQUAL(s3, "AA");
 137   s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 2, 2);
 138   BOOST_CHECK_EQUAL( s3, "GG");
 139   s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 4);
 140   BOOST_CHECK_EQUAL( s3, "CCTT");
 141
 142   s3 = "AAGGFF";
 143   BOOST_CHECK_EQUAL(s3, "AAGGNN");
 144 }
 145
 146 BOOST_AUTO_TEST_CASE( sequence_nucleic_alphabet )
 147 {
 148   std::string agct("AGCT");
 149   Sequence seq(agct, nucleic_alphabet);
 150   BOOST_CHECK_EQUAL(seq.size(), agct.size());
 151   BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
 152
 153   std::string bdv("BDv");
 154   Sequence seq_bdv(bdv, nucleic_alphabet);
 155   BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
 156   // forcing sequence to upper case
 157   BOOST_CHECK_EQUAL(seq_bdv.get_sequence(),
 158                     boost::algorithm::to_upper_copy(bdv));
 159
 160 }
 161
 162 BOOST_AUTO_TEST_CASE( sequence_default_alphabet )
 163 {
 164   std::string agct("AGCT");
 165   Sequence seq(agct);
 166   BOOST_CHECK_EQUAL(seq.size(), agct.size());
 167   BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
 168   BOOST_CHECK_EQUAL(seq[0], agct[0]);
 169   BOOST_CHECK_EQUAL(seq[1], agct[1]);
 170   BOOST_CHECK_EQUAL(seq[2], agct[2]);
 171   BOOST_CHECK_EQUAL(seq[3], agct[3]);
 172
 173   std::string bdv("BDv");
 174   Sequence seq_bdv(bdv);
 175   BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
 176   // default alphabet only allows AGCTUN
 177   BOOST_CHECK_EQUAL(seq_bdv.get_sequence(), "NNN");
 178 }
 179
 180 BOOST_AUTO_TEST_CASE( subseq_names )
 181 {
 182   Sequence s1("AAGGCCTT", reduced_dna_alphabet);
 183   s1.set_species("species");
 184   s1.set_fasta_header("a fasta header");
 185   Sequence s2 = s1.subseq(2,2);
 186   BOOST_CHECK_EQUAL(s2, "GG");
 187   BOOST_CHECK_EQUAL(s2.get_species(), s1.get_species());
 188   BOOST_CHECK_EQUAL(s2.get_fasta_header(), s1.get_fasta_header());
 189 }
 190
 191 BOOST_AUTO_TEST_CASE( sequence_start_stop )
 192 {
 193   Sequence s1;
 194   BOOST_CHECK_EQUAL( s1.start(), 0 );
 195   BOOST_CHECK_EQUAL( s1.stop(), 0 );
 196
 197   std::string seq_string("AAGGCCTT");
 198   Sequence s2(seq_string, reduced_dna_alphabet);
 199   BOOST_CHECK_EQUAL( s2.start(), 0 );
 200   BOOST_CHECK_EQUAL( s2.stop(), seq_string.size() );
 201
 202   std::string s3seq_string = seq_string.substr(2,3);
 203   Sequence s3 = s2.subseq(2,3);
 204   BOOST_CHECK_EQUAL( s3.start(), 2);
 205   BOOST_CHECK_EQUAL( s3.stop(), 2+3);
 206   BOOST_CHECK_EQUAL( s3.size(), 3);
 207   BOOST_CHECK_EQUAL( s3, s3seq_string);
 208
 209   std::string s4seq_string = s3seq_string.substr(1,1);
 210   Sequence s4 = s3.subseq(1,1);
 211   BOOST_CHECK_EQUAL( s4.start(), 1 );
 212   BOOST_CHECK_EQUAL( s4.stop(), 1+1);
 213   BOOST_CHECK_EQUAL( s4.size(), 1);
 214   BOOST_CHECK_EQUAL( s4, s4seq_string);
 215 }
 216
 217 //! Can we load data from a file
 218 BOOST_AUTO_TEST_CASE( sequence_load )
 219 {
 220   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq");
 221   seq_path /=  "human_mck_pro.fa";
 222   Sequence s;
 223   s.load_fasta(seq_path, reduced_dna_alphabet);
 224   BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
 225   BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
 226   BOOST_CHECK_EQUAL(s.get_fasta_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
 227                                     "muscle creatine kinase gene (CKMM), "
 228                                     "5' flank");
 229 }
 230
 231 BOOST_AUTO_TEST_CASE( sequence_load_fasta_error )
 232 {
 233   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
 234   seq_path /= "broken.fa";
 235   bool exception_thrown = false;
 236   std::string exception_filename;
 237   Sequence s;
 238   try {
 239     s.load_fasta(seq_path);
 240   } catch(sequence_invalid_load_error e) {
 241     exception_thrown = true;
 242     size_t native_string_size = seq_path.native_file_string().size();
 243     std:string estr(e.what());
 244     BOOST_REQUIRE(estr.size() > native_string_size);
 245     std::copy(estr.begin(), estr.begin()+native_string_size,
 246               std::back_inserter(exception_filename));
 247   }
 248   BOOST_CHECK_EQUAL(exception_thrown, true);
 249   BOOST_CHECK_EQUAL(seq_path.native_file_string(), exception_filename);
 250 }
 251
 252 BOOST_AUTO_TEST_CASE( sequence_load_annot_error )
 253 {
 254   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
 255   seq_path /= "mouse_mck_pro.fa";
 256   fs::path annot_path(fs::path(EXAMPLE_DIR, fs::native));
 257   annot_path /= "broken.annot";
 258   bool exception_thrown = false;
 259   Sequence s;
 260   s.load_fasta(seq_path);
 261
 262   std::string exception_filename;
 263   try {
 264     s.load_annot(annot_path, 0, 0);
 265   } catch(annotation_load_error e) {
 266     exception_thrown = true;
 267     std:string estr(e.what());
 268     size_t native_string_size = annot_path.native_file_string().size();
 269     BOOST_REQUIRE(estr.size() > native_string_size);
 270     std::copy(estr.begin(), estr.begin()+native_string_size,
 271               std::back_inserter(exception_filename));
 272   }
 273   BOOST_CHECK_EQUAL(exception_thrown, true);
 274   BOOST_CHECK_EQUAL(annot_path.native_file_string(), exception_filename);
 275 }
 276
 277 BOOST_AUTO_TEST_CASE( sequence_load_dna_reduced )
 278 {
 279   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 280   std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
 281   std::string invalid_dna_fasta_string(">wrong\nAUSSI\n");
 282   std::stringstream invalid_dna_fasta(invalid_dna_fasta_string);
 283   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN-\n");
 284   std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
 285   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 286   std::stringstream garbage_fasta(garbage_string);
 287
 288   Sequence s;
 289   s.load_fasta(reduced_dna_fasta, reduced_dna_alphabet);
 290   BOOST_CHECK_THROW(s.load_fasta(invalid_dna_fasta,
 291                                  reduced_dna_alphabet),
 292                     sequence_invalid_load_error);
 293   BOOST_CHECK_THROW(s.load_fasta(reduced_rna_fasta,
 294                                  reduced_dna_alphabet),
 295                     sequence_invalid_load_error);
 296   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
 297                                  reduced_dna_alphabet),
 298                     sequence_invalid_load_error);
 299
 300 }
 301
 302 BOOST_AUTO_TEST_CASE( sequence_load_rna_reduced )
 303 {
 304   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
 305   std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
 306   std::string invalid_rna_fasta_string(">wrong\nATSSI\n");
 307   std::stringstream invalid_rna_fasta(invalid_rna_fasta_string);
 308   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 309   std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
 310   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 311   std::stringstream garbage_fasta(garbage_string);
 312
 313   Sequence s;
 314   s.load_fasta(reduced_rna_fasta, reduced_rna_alphabet);
 315   BOOST_CHECK_THROW(s.load_fasta(invalid_rna_fasta,
 316                                  reduced_rna_alphabet),
 317                     sequence_invalid_load_error);
 318   BOOST_CHECK_THROW(s.load_fasta(reduced_dna_fasta,
 319                                  reduced_rna_alphabet),
 320                     sequence_invalid_load_error);
 321   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
 322                                  reduced_rna_alphabet),
 323                     sequence_invalid_load_error);
 324 }
 325
 326 BOOST_AUTO_TEST_CASE( sequence_load_fasta_default )
 327 {
 328   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
 329   std::stringstream reduced_rna_fasta1(reduced_rna_fasta_string);
 330   std::stringstream reduced_rna_fasta2(reduced_rna_fasta_string);
 331   std::string invalid_nucleotide_fasta_string(">wrong\nATSSI\n");
 332   std::stringstream invalid_nucleotide_fasta(invalid_nucleotide_fasta_string);
 333   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 334   std::stringstream reduced_dna_fasta1(reduced_dna_fasta_string);
 335   std::stringstream reduced_dna_fasta2(reduced_dna_fasta_string);
 336   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 337   std::stringstream garbage_fasta(garbage_string);
 338
 339   Sequence s;
 340   Sequence specific;
 341   // there's two copies of reduced_rna_fasta because i didn't feel like
 342   // figuring out how to properly reset the read pointer in a stringstream
 343   s.load_fasta(reduced_rna_fasta1);
 344   specific.load_fasta(reduced_rna_fasta2, reduced_nucleic_alphabet);
 345   BOOST_CHECK_EQUAL(s, specific);
 346
 347   s.load_fasta(reduced_dna_fasta1);
 348   specific.load_fasta(reduced_dna_fasta2, reduced_nucleic_alphabet);
 349   BOOST_CHECK_EQUAL(s, specific);
 350
 351   BOOST_CHECK_THROW(s.load_fasta(invalid_nucleotide_fasta),
 352                     sequence_invalid_load_error);
 353   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta),
 354                     sequence_invalid_load_error);
 355 }
 356
 357 BOOST_AUTO_TEST_CASE( sequence_load_multiple_sequences_one_fasta )
 358 {
 359   std::string fasta_file(
 360     ">gi|10129974|gb|AF188002.1|AF188002\n"
 361     "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC\n"
 362     ">gi|180579|gb|M21487.1|HUMCKMM1\n"
 363     "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC\n"
 364     ">gi|1621|emb|X55146.1|OCMCK1\n"
 365     "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC\n"
 366   );
 367   istringstream seq1_file(fasta_file);
 368   Sequence seq1;
 369   seq1.load_fasta(seq1_file, 1, 0, 0);
 370   BOOST_CHECK_EQUAL(seq1.get_sequence(), "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC");
 371
 372   istringstream seq2_file(fasta_file);
 373   Sequence seq2;
 374   seq2.load_fasta(seq2_file, 2, 0, 0);
 375   BOOST_CHECK_EQUAL(seq2.get_sequence(), "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC");
 376
 377   istringstream seq3_file(fasta_file);
 378   Sequence seq3;
 379   seq3.load_fasta(seq3_file, 3, 0, 0);
 380   BOOST_CHECK_EQUAL(seq3.get_sequence(), "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC");
 381 }
 382
 383 BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
 384 {
 385   std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
 386   Sequence seq(iupac_symbols, nucleic_alphabet);
 387   Sequence seqr = seq.rev_comp();
 388
 389   BOOST_CHECK( seq != seqr );
 390   BOOST_CHECK_EQUAL( seq, seqr.rev_comp() );
 391   // forcing sequence to upper case
 392   BOOST_CHECK_EQUAL( seq.get_sequence(),
 393                      boost::algorithm::to_upper_copy(iupac_symbols) );
 394 }
 395
 396 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
 397 {
 398   std::string dna_str("AGCTN");
 399   Sequence dna_seq(dna_str, reduced_dna_alphabet);
 400   BOOST_CHECK_EQUAL(dna_seq.rev_comp(), "NAGCT");
 401   BOOST_CHECK_EQUAL(dna_seq, dna_seq.rev_comp().rev_comp());
 402 }
 403
 404 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
 405 {
 406   std::string rna_str("AGCUN");
 407   Sequence rna_seq(rna_str, reduced_rna_alphabet);
 408   BOOST_CHECK_EQUAL(rna_seq.rev_comp().get_sequence(), "NAGCU");
 409   BOOST_CHECK_EQUAL(rna_seq.get_sequence(),
 410                     rna_seq.rev_comp().rev_comp().get_sequence());
 411 }
 412
 413 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_subseq )
 414 {
 415   std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
 416   Sequence seq(dna_str, reduced_dna_alphabet);
 417   Sequence subseq = seq.subseq(8,4);
 418   BOOST_CHECK_EQUAL( subseq, "AAGG");
 419   Sequence rev_subseq = subseq.rev_comp();
 420   BOOST_CHECK_EQUAL( rev_subseq.size(), subseq.size() );
 421   BOOST_CHECK_EQUAL( rev_subseq.get_sequence(), "CCTT");
 422 }
 423
 424 BOOST_AUTO_TEST_CASE( sequence_reverse_iterator )
 425 {
 426   std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
 427   std::string dna_str_reversed(dna_str.rbegin(), dna_str.rend());
 428   Sequence seq(dna_str);
 429   std::string seq_reversed(seq.rbegin(), seq.rend());
 430   BOOST_CHECK_EQUAL(seq_reversed, dna_str_reversed);
 431
 432   std::string substr = dna_str.substr(8,4);
 433   Sequence subseq = seq.subseq(8,4);
 434   BOOST_CHECK_EQUAL(substr, subseq);
 435
 436   std::string substr_reversed(substr.rbegin(), substr.rend());
 437   std::string subseq_reversed(subseq.rbegin(), subseq.rend());
 438   BOOST_CHECK_EQUAL(substr_reversed, subseq_reversed);
 439 }
 440
 441 BOOST_AUTO_TEST_CASE( sequence_empty_reverse_iterator)
 442 {
 443   // so what happens with reverse interators when we have no sequence?
 444   Sequence seq1;
 445   Sequence seq2;
 446   Sequence seq3("AGCT");
 447
 448   // all the empty sequences should have equal iterators
 449   BOOST_CHECK(seq1.rbegin() == seq1.rend());
 450   BOOST_CHECK(seq1.rbegin() == seq2.rend());
 451
 452   // none of the seq1 iterators should equal any of the seq3 iterators
 453   BOOST_CHECK(seq1.rbegin() != seq3.rbegin());
 454   BOOST_CHECK(seq1.rbegin() != seq3.rend());
 455   BOOST_CHECK(seq1.rend() != seq3.rbegin());
 456   BOOST_CHECK(seq1.rend() != seq3.rend());
 457
 458   // seq3 iterators should work
 459   BOOST_CHECK(seq3.rbegin() != seq3.rend());
 460
 461 }
 462
 463 BOOST_AUTO_TEST_CASE( annotation_load )
 464 {
 465   string annot_data = "human\n"
 466                       "0 10 name   type\n"
 467                       "10 20 myf7\n"
 468                       "20 30 myod\n"
 469                       "50\t55 anothername\n"
 470                       "60 50 backward\n"
 471                       ">ident3 asdf\n"
 472                       "GCT\n"
 473                       "gCTn\n"
 474                       "75\t90\tname2\ttype2\n"
 475                       "100 120 name-asdf type!@#$%\n"
 476                       ;
 477   string s(100, 'A');
 478   s += "GCTGCTAATT";
 479   Sequence seq(s, reduced_dna_alphabet);
 480
 481   //istringstream annot_stream(annot_data);
 482   seq.parse_annot(annot_data, 0, 0);
 483   std::list<annot> annots_list = seq.annotations();
 484   std::vector<annot> annots(annots_list.begin(), annots_list.end());
 485   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 486   BOOST_CHECK_EQUAL( annots[0].begin, 0 );
 487   BOOST_CHECK_EQUAL( annots[0].end, 10 );
 488   BOOST_CHECK_EQUAL( annots[0].type, "type");
 489   BOOST_CHECK_EQUAL( annots[0].name, "name");
 490   BOOST_CHECK_EQUAL( annots[1].name, "myf7");
 491   BOOST_CHECK_EQUAL( annots[2].name, "myod");
 492   BOOST_CHECK_EQUAL( annots[3].name, "anothername");
 493   BOOST_CHECK_EQUAL( annots[4].name, "backward");
 494   BOOST_CHECK_EQUAL( annots[5].name, "name2");
 495   BOOST_CHECK_EQUAL( annots[5].end, 90);
 496   BOOST_CHECK_EQUAL( annots[6].begin, 100);
 497   BOOST_CHECK_EQUAL( annots[6].end, 120);
 498   BOOST_CHECK_EQUAL( annots[6].name, "name-asdf");
 499   BOOST_CHECK_EQUAL( annots[6].type, "type!@#$%");
 500   // sequence defined annotations will always be after the
 501   // absolute positions
 502   BOOST_CHECK_EQUAL( annots[7].name, "ident3 asdf");
 503   BOOST_CHECK_EQUAL( annots[7].begin, 100);
 504
 505   //BOOST_CHECK_EQUAL( annots
 506 }
 507
 508 BOOST_AUTO_TEST_CASE( annotation_broken_load )
 509 {
 510   string annot_data = "human\n"
 511                       "0 10 name   type\n"
 512                       "blah60 50 backward\n"
 513                       ">ident3 asdf\n"
 514                       "GCT\n"
 515                       "gCTn\n"
 516                       ;
 517   string s(100, 'A');
 518   s += "GCTGCTAATT";
 519   Sequence seq(s, reduced_dna_alphabet);
 520
 521   BOOST_CHECK_THROW(seq.parse_annot(annot_data, 0, 0), annotation_load_error);
 522   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 523   }
 524
 525 BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
 526 {
 527   // this actually is basically what's returned by UCSC
 528   // (well actually with some of the sequence and copies of fasta blocks
 529   // removed to make the example shorter
 530   string annot_data = "\n"
 531     "<PRE>\n"
 532     ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 533     "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
 534     "&gt;hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 535     "GGTGGAGACGACCTGGACCCTAACTACGT\n"
 536     "</PRE>\n"
 537     "\n"
 538     "</BODY>\n"
 539     "</HTML>\n"
 540     ;
 541
 542   string s =
 543     "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
 544     "AAAAA"
 545     "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
 546   Sequence seq(s, reduced_dna_alphabet);
 547   seq.parse_annot(annot_data);
 548   std::list<annot> annots = seq.annotations();
 549   BOOST_CHECK_EQUAL( annots.size(), 2);
 550 }
 551
 552 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
 553 {
 554   string annot_data = "0 10 name   type\n"
 555                       "10 20 myf7\n"
 556                       "20 30 myod\n"
 557                       "50\t55 anothername\n"
 558                       "60 50 backward\n"
 559                       ">ident3 asdf\n"
 560                       "GCT\n"
 561                       "gCTn\n"
 562                       "75\t90\tname2\ttype2\n"
 563                       "100 120 name-asdf type!@#$%\n"
 564                       ;
 565   string s(100, 'A');
 566   s += "GCTGCTAATT";
 567   Sequence seq(s, reduced_dna_alphabet);
 568
 569   //istringstream annot_stream(annot_data);
 570   seq.parse_annot(annot_data, 0, 0);
 571   std::list<annot> annots_list = seq.annotations();
 572   std::vector<annot> annots(annots_list.begin(), annots_list.end());
 573   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 574   BOOST_CHECK_EQUAL( annots[0].begin, 0 );
 575   BOOST_CHECK_EQUAL( annots[0].end, 10 );
 576   BOOST_CHECK_EQUAL( annots[0].type, "type");
 577 }
 578
 579 // ticket:83 when you try to load a sequence from a file that doesn't
 580 // have fasta headers it crashes.
 581 BOOST_AUTO_TEST_CASE( sequence_past_end )
 582 {
 583   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq" );
 584   seq_path /=  "misformated_seq.fa";
 585   Sequence s;
 586   BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
 587 }
 588
 589 BOOST_AUTO_TEST_CASE ( sequence_empty )
 590 {
 591
 592   Sequence s;
 593   BOOST_CHECK_EQUAL( s.empty(), true );
 594   s = "AAAGGG";
 595   BOOST_CHECK_EQUAL( s.empty(), false );
 596   s.clear();
 597   BOOST_CHECK_EQUAL( s.empty(), true);
 598   s = "";
 599   BOOST_CHECK_EQUAL( s.empty(), true);
 600 }
 601
 602 BOOST_AUTO_TEST_CASE ( sequence_size )
 603 {
 604
 605   Sequence s;
 606   BOOST_CHECK_EQUAL( s.size(), 0);
 607   std::string seq_string("AAAGGG");
 608   s = seq_string;
 609   BOOST_CHECK_EQUAL( s.size(), seq_string.size() );
 610   s.clear();
 611   BOOST_CHECK_EQUAL( s.size(), 0);
 612   s = "";
 613   BOOST_CHECK_EQUAL( s.size(), 0);
 614 }
 615
 616 BOOST_AUTO_TEST_CASE( sequence_empty_equality )
 617 {
 618   Sequence szero("", reduced_dna_alphabet);
 619   BOOST_CHECK_EQUAL(szero.empty(), true);
 620   BOOST_CHECK_EQUAL(szero, szero);
 621   BOOST_CHECK_EQUAL(szero, "");
 622
 623   Sequence sclear("AGCT", reduced_dna_alphabet);
 624   sclear.clear();
 625   BOOST_CHECK_EQUAL(sclear.empty(), true);
 626   BOOST_CHECK_EQUAL(sclear, sclear);
 627   BOOST_CHECK_EQUAL(sclear, szero);
 628   BOOST_CHECK_EQUAL(sclear, "");
 629
 630 }
 631 BOOST_AUTO_TEST_CASE ( sequence_iterators )
 632 {
 633   std::string seq_string = "AAGGCCTTNNTATA";
 634   Sequence s(seq_string, reduced_dna_alphabet);
 635   const Sequence cs(s);
 636   std::string::size_type count = 0;
 637
 638   std::string::iterator str_itor;
 639   Sequence::const_iterator s_itor;
 640   Sequence::const_iterator cs_itor;
 641
 642   for( str_itor = seq_string.begin(),
 643        s_itor   = s.begin(),
 644        cs_itor  = cs.begin();
 645        str_itor != seq_string.end() and
 646        s_itor   != s.end() and
 647        cs_itor  != cs.end();
 648        ++str_itor, ++s_itor, ++cs_itor, ++count)
 649   {
 650     BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
 651     BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
 652     BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
 653   }
 654   BOOST_CHECK_EQUAL( seq_string.size(), count );
 655   BOOST_CHECK_EQUAL( s.size(), count );
 656   BOOST_CHECK_EQUAL( cs.size(), count );
 657 }
 658
 659 BOOST_AUTO_TEST_CASE( sequence_motifs )
 660 {
 661   string m("AAAA");
 662   string bogus("AATTGGAA");
 663   Sequence s1("AAAAGGGGCCCCTTTT", reduced_dna_alphabet);
 664
 665   list<motif>::const_iterator motif_i = s1.motifs().begin();
 666   list<motif>::const_iterator motif_end = s1.motifs().end();
 667
 668   // do our iterators work?
 669   BOOST_CHECK( motif_i == s1.motifs().begin() );
 670   BOOST_CHECK( motif_end == s1.motifs().end() );
 671   BOOST_CHECK( motif_i == motif_end );
 672
 673   // this shouldn't show up
 674   s1.add_motif(bogus);
 675   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 676   BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
 677
 678   s1.add_motif(m);
 679   BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
 680   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 681
 682   for(motif_i = s1.motifs().begin();
 683       motif_i != s1.motifs().end();
 684       ++motif_i)
 685   {
 686     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 687     BOOST_CHECK_EQUAL( motif_i->name, m);
 688     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 689   }
 690
 691   s1.clear_motifs();
 692   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 693
 694   /* FIXME: enable this when i find a way of passing storing the motif name
 695   // does our annotation travel?
 696   Sequence motif_seq(m);
 697   motif_seq.set_fasta_header("hi");
 698   s1.add_motif(motif_seq);
 699
 700   BOOST_CHECK_EQUAL(s1.motifs().size(), 2);
 701   for(motif_i = s1.motifs().begin();
 702       motif_i != s1.motifs().end();
 703       ++motif_i)
 704   {
 705     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 706     BOOST_CHECK_EQUAL( motif_i->name, "hi");
 707     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 708   }
 709   */
 710 }
 711
 712 BOOST_AUTO_TEST_CASE( sequence_motif_subseq)
 713 {
 714   // when searching for a motif on a subsequence we should
 715   // only search the subsequence ticket:199
 716   string aaaa("AAAA");
 717   string cccc("CCCC");
 718   Sequence s1("AAAANCCCC", reduced_dna_alphabet);
 719
 720   // this shouldn't show up
 721   s1.add_motif(cccc);
 722   BOOST_CHECK_EQUAL( s1.motifs().size(), 1 );
 723
 724   s1.add_motif(aaaa);
 725   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 726
 727   Sequence subseq1 = s1.subseq(4,5);
 728   BOOST_CHECK_EQUAL(subseq1.motifs().size(), 2);
 729   subseq1.clear_motifs();
 730   BOOST_CHECK_EQUAL(subseq1.motifs().size(), 0);
 731   // this is outside of our subsequence, and so shouldn't be found
 732   subseq1.add_motif(aaaa);
 733   BOOST_CHECK_EQUAL( subseq1.motifs().size(), 0 );
 734
 735   subseq1.add_motif(cccc);
 736   BOOST_CHECK_EQUAL( subseq1.motifs().size(), 1);
 737   std::list<motif>::const_iterator motif_i = subseq1.motifs().begin();
 738   BOOST_REQUIRE(motif_i != subseq1.motifs().end());
 739   BOOST_CHECK_EQUAL(motif_i->begin, 1);
 740   BOOST_CHECK_EQUAL(motif_i->end, 5);
 741 }
 742
 743 BOOST_AUTO_TEST_CASE( annot_test )
 744 {
 745   annot a(0, 10, "test", "thing");
 746
 747   BOOST_CHECK_EQUAL( a.begin, 0 );
 748   BOOST_CHECK_EQUAL( a.end,   10 );
 749   BOOST_CHECK_EQUAL( a.type,  "test" );
 750   BOOST_CHECK_EQUAL( a.name,  "thing" );
 751
 752   motif m(10, "AAGGCC");
 753   BOOST_CHECK_EQUAL( m.begin, 10 );
 754   BOOST_CHECK_EQUAL( m.type, "motif" );
 755   BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
 756   BOOST_CHECK_EQUAL( m.end,  10+6 );
 757 }
 758
 759 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
 760 {
 761   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 762            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 763            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 764            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 765            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 766            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 767            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 768            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 769   string gc("GCCCCC");
 770   string gga("GGACACCTC");
 771   Sequence seq(s, reduced_dna_alphabet);
 772
 773   std::list<Sequence> query_list;
 774   std::list<string> string_list;
 775   query_list.push_back(Sequence(gc));
 776   string_list.push_back(gc);
 777   query_list.push_back(Sequence(gga));
 778   string_list.push_back(gga);
 779
 780   BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
 781   seq.find_sequences(query_list.begin(), query_list.end());
 782
 783   int count = 0;
 784   for(list<string>::iterator string_i = string_list.begin();
 785       string_i != string_list.end();
 786       ++string_i)
 787   {
 788     string::size_type pos=0;
 789     while(pos != string::npos) {
 790       pos = s.find(*string_i, pos);
 791       if (pos != string::npos) {
 792         ++count;
 793         ++pos;
 794       }
 795     }
 796   }
 797   BOOST_CHECK_EQUAL(seq.annotations().size(), count);
 798   const std::list<annot> &a = seq.annotations();
 799   for (std::list<annot>::const_iterator annot_i = a.begin();
 800        annot_i != a.end();
 801        ++annot_i)
 802   {
 803     int count = annot_i->end - annot_i->begin ;
 804   }
 805 }
 806
 807 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
 808 {
 809   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 810            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 811            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 812            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 813            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 814            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 815            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 816            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 817   Sequence seq(s, reduced_dna_alphabet);
 818
 819
 820   seq.add_annotation(annot(0, 10, "0-10", "0-10"));
 821   seq.add_annotation(annot(10, 20, "10-20", "10-20"));
 822   seq.add_annotation(annot(0, 20, "0-20", "0-20"));
 823   seq.add_annotation(annot(8, 12, "8-12", "8-12"));
 824   seq.add_annotation(annot(100, 5000, "100-5000", "100-5000"));
 825
 826   Sequence subseq = seq.subseq(5, 10);
 827   const list<annot> annots = subseq.annotations();
 828   // generate some ground truth
 829   list<annot> correct;
 830   correct.push_back(annot(0, 5, "0-10",  "0-10"));
 831   correct.push_back(annot(5,10, "10-20", "10-20"));
 832   correct.push_back(annot(0,10, "0-20",  "0-20"));
 833   correct.push_back(annot(3, 7, "8-12",  "8-12"));
 834   BOOST_REQUIRE_EQUAL( annots.size(), correct.size() );
 835
 836   list<annot>::iterator correct_i = correct.begin();
 837   list<annot>::const_iterator annot_i = annots.begin();
 838   for(; annot_i != annots.end(); ++annot_i, ++correct_i)
 839   {
 840     BOOST_CHECK( *annot_i == *correct_i );
 841   }
 842 }
 843
 844 BOOST_AUTO_TEST_CASE( motif_annotation_update )
 845 {
 846   string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 847            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 848            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 849            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 850            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 851            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 852            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 853            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 854   Sequence seq(s, reduced_dna_alphabet);
 855
 856   // starting conditions
 857   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 858   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 859   seq.add_annotation(annot(0, 10, "0-10", "0-10"));
 860   seq.add_annotation(annot(10, 20, "10-20", "10-20"));
 861   seq.add_annotation(annot(0, 20, "0-20", "0-20"));
 862   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 863   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 864   seq.add_motif("CCGTCCC");
 865   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 866   BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
 867   seq.clear_motifs();
 868   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 869   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 870 }
 871
 872 BOOST_AUTO_TEST_CASE( out_operator )
 873 {
 874   string s("AAGGCCTT");
 875   Sequence seq(s, reduced_dna_alphabet);
 876
 877   ostringstream buf;
 878   buf << s;
 879   BOOST_CHECK_EQUAL( s, buf.str() );
 880 }
 881
 882 BOOST_AUTO_TEST_CASE( get_name )
 883 {
 884   Sequence seq("AAGGCCTT", reduced_dna_alphabet);
 885
 886   BOOST_CHECK_EQUAL( seq.get_name(), "" );
 887   seq.set_species("hooman"); // anyone remember tradewars?
 888   BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
 889   seq.set_fasta_header("fasta human");
 890   BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
 891 }
 892
 893 BOOST_AUTO_TEST_CASE( serialize_simple )
 894 {
 895   std::string seq_string = "AAGGCCTT";
 896   Sequence seq(seq_string, reduced_dna_alphabet);
 897   seq.set_species("ribbet");
 898   std::ostringstream oss;
 899   // allocate/deallocate serialization components
 900   {
 901     boost::archive::text_oarchive oarchive(oss);
 902     const Sequence& const_seq(seq);
 903     BOOST_CHECK_EQUAL(seq, const_seq);
 904     oarchive << const_seq;
 905   }
 906   Sequence seq_loaded;
 907   {
 908     std::istringstream iss(oss.str());
 909     boost::archive::text_iarchive iarchive(iss);
 910     iarchive >> seq_loaded;
 911   }
 912   BOOST_CHECK_EQUAL(seq_loaded, seq);
 913   BOOST_CHECK_EQUAL(seq.get_species(), "ribbet");
 914 }
 915
 916 BOOST_AUTO_TEST_CASE( serialize_tree )
 917 {
 918   std::string seq_string = "AAGGCCTT";
 919   Sequence seq(seq_string, reduced_dna_alphabet);
 920   seq.set_species("ribbet");
 921   seq.add_motif("AA");
 922   seq.add_motif("GC");
 923   annot a1(6,7,"t","t");
 924   seq.add_annotation(a1);
 925
 926   std::ostringstream oss;
 927   // allocate/deallocate serialization components
 928   {
 929     boost::archive::text_oarchive oarchive(oss);
 930     const Sequence& const_seq(seq);
 931     BOOST_CHECK_EQUAL(seq, const_seq);
 932     oarchive << const_seq;
 933   }
 934
 935   Sequence seq_loaded;
 936   {
 937     std::istringstream iss(oss.str());
 938     boost::archive::text_iarchive iarchive(iss);
 939     iarchive >> seq_loaded;
 940   }
 941   BOOST_CHECK_EQUAL(seq_loaded, seq);
 942 }
 943
 944 // this writes out an "old" style annotated sequence
 945 // with annotations attached as "motifs" and "annots"
 946 BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
 947 {
 948   std::string seq_string = "AAGGCCTT";
 949   Sequence seq(seq_string, reduced_dna_alphabet);
 950   seq.set_species("ribbet");
 951   seq.add_motif("AA");
 952   seq.add_motif("GC");
 953   annot a1(6,7,"t","t");
 954   seq.add_annotation(a1);
 955
 956   std::ostringstream oss;
 957   // allocate/deallocate serialization components
 958   {
 959     boost::archive::xml_oarchive oarchive(oss);
 960     const Sequence& const_seq(seq);
 961     BOOST_CHECK_EQUAL(seq, const_seq);
 962     oarchive << boost::serialization::make_nvp("root", const_seq);
 963   }
 964   Sequence seq_loaded;
 965   {
 966     std::istringstream iss(oss.str());
 967     boost::archive::xml_iarchive iarchive(iss);
 968     iarchive >> boost::serialization::make_nvp("root", seq_loaded);
 969   }
 970   BOOST_CHECK_EQUAL(seq_loaded, seq);
 971 }
 972
 973 BOOST_AUTO_TEST_CASE( serialize_xml_two )
 974 {
 975   std::string seq_string = "AAGGCCTT";
 976   Sequence seq1(seq_string, reduced_dna_alphabet);
 977   Sequence seq2(seq1);
 978
 979   std::ostringstream oss;
 980   // allocate/deallocate serialization components
 981   {
 982     boost::archive::xml_oarchive oarchive(oss);
 983     const Sequence& const_seq1(seq1);
 984     const Sequence& const_seq2(seq2);
 985     oarchive << boost::serialization::make_nvp("seq1", const_seq1);
 986     oarchive << boost::serialization::make_nvp("seq2", const_seq2);
 987   }
 988   //std::cout << "xml: " << oss.str() << std::endl;
 989   Sequence seq1_loaded;
 990   Sequence seq2_loaded;
 991   {
 992     std::istringstream iss(oss.str());
 993     boost::archive::xml_iarchive iarchive(iss);
 994     iarchive >> boost::serialization::make_nvp("seq1", seq1_loaded);
 995     iarchive >> boost::serialization::make_nvp("seq2", seq2_loaded);
 996   }
 997   BOOST_CHECK_EQUAL(seq1_loaded, seq1);
 998   BOOST_CHECK_EQUAL(seq2_loaded, seq2);
 999   // test if our pointers are the same
1000   BOOST_CHECK_EQUAL(seq1_loaded.data(), seq2_loaded.data());
1001 }