// ========================================================================== // SeqAn - The Library for Sequence Analysis // ========================================================================== // Copyright (c) 2006-2011, Knut Reinert, FU Berlin // All rights reserved. // // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are met: // // * Redistributions of source code must retain the above copyright // notice, this list of conditions and the following disclaimer. // * Redistributions in binary form must reproduce the above copyright // notice, this list of conditions and the following disclaimer in the // documentation and/or other materials provided with the distribution. // * Neither the name of Knut Reinert or the FU Berlin nor the names of // its contributors may be used to endorse or promote products derived // from this software without specific prior written permission. // // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE // ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE // FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL // DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR // SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER // CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT // LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY // OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH // DAMAGE. // // ========================================================================== // Author: Hannes Hauswedell // ========================================================================== // FASTA-Tests for seqan/stream/read_fasta_fastq.h // ========================================================================== #ifndef TEST_STREAM_TEST_STREAM_READ_EMBL_H_ #define TEST_STREAM_TEST_STREAM_READ_EMBL_H_ // Return an EMBL format string with two entries. char const * testHelperReturnEmblFile() { char const * result = "ID SC10H5 standard; DNA; PRO; 4870 BP.\n" "XX\n" "AC AL031232;\n" "XX\n" "DE Streptomyces coelicolor cosmid 10H5.\n" "XX\n" "KW integral membrane protein.\n" "XX\n" "OS Streptomyces coelicolor\n" "OC Eubacteria; Firmicutes; Actinomycetes; Streptomycetes;\n" "OC Streptomycetaceae; Streptomyces.\n" "XX\n" "RN [1]\n" "RP 1-4870\n" "RA Oliver K., Harris D.;\n" "RT ;\n" "RL Unpublished.\n" "XX\n" "RN [2]\n" "RP 1-4870\n" "RA Parkhill J., Barrell B.G., Rajandream M.A.;\n" "RT ;\n" "RL Submitted (10-AUG-1998) to the EMBL/GenBank/DDBJ databases.\n" "RL Streptomyces coelicolor sequencing project,\n" "RL Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA\n" "RL E-mail: barrell@sanger.ac.uk\n" "RL Cosmids supplied by Prof. David A. Hopwood, [3]\n" "RL John Innes Centre, Norwich Research Park, Colney,\n" "RL Norwich, Norfolk NR4 7UH, UK.\n" "XX\n" "RN [3]\n" "RP 1-4870\n" "RA Redenbach M., Kieser H.M., Denapaite D., Eichner A.,\n" "RA Cullum J., Kinashi H., Hopwood D.A.;\n" "RT \"A set of ordered cosmids and a detailed genetic and physical\n" "RT map for the 8 Mb Streptomyces coelicolor A3(2) chromosome.\";\n" "RL Mol. Microbiol. 21(1):77-96(1996).\n" "XX\n" "CC Notes:\n" "CC\n" "CC Streptomyces coelicolor sequencing at The Sanger Centre is funded \n" "CC by the BBSRC.\n" "CC\n" "CC Details of S. coelicolor sequencing at the Sanger Centre \n" "CC are available on the World Wide Web. \n" "CC (URL; http://www.sanger.ac.uk/Projects/S_coelicolor/)\n" "CC\n" "CC CDS are numbered using the following system eg SC7B7.01c. \n" "CC SC (S. coelicolor), 7B7 (cosmid name), .01 (first CDS), \n" "CC c (complementary strand).\n" "CC\n" "CC The more significant matches with motifs in the PROSITE\n" "CC database are also included but some of these may be fortuitous.\n" "CC\n" "CC The length in codons is given for each CDS.\n" "CC\n" "CC Usually the highest scoring match found by fasta -o is given for\n" "CC CDS which show significant similarity to other CDS in the database.\n" "CC The position of possible ribosome binding site sequences are\n" "CC given where these have been used to deduce the initiation codon.\n" "CC \n" "CC Gene prediction is based on positional base preference in codons \n" "CC using a specially developed Hidden Markov Model (Krogh et al., \n" "CC Nucleic Acids Research, 22(22):4768-4778(1994)) and the FramePlot \n" "CC program of Bibb et al., Gene 30:157-66(1984) as implemented at \n" "CC http://www.nih.go.jp/~jun/cgi-bin/frameplot.pl. CAUTION: We may \n" "CC not have predicted the correct initiation codon. Where possible \n" "CC we choose an initiation codon (atg, gtg, ttg or (att)) which is \n" "CC preceded by an upstream ribosome binding site sequence (optimally \n" "CC 5-13bp before the initiation codon). If this cannot be identified\n" "CC we choose the most upstream initiation codon.\n" "CC \n" "CC IMPORTANT: This sequence MAY NOT be the entire insert of\n" "CC the sequenced clone. It may be shorter because we only\n" "CC sequence overlapping sections once, or longer, because we\n" "CC arrange for a small overlap between neighbouring submissions.\n" "CC\n" "CC Cosmid 10H5 lies to the right of 3A7 on the AseI-B genomic restriction \n" "CC fragment.\n" "XX\n" "FH Key Location/Qualifiers\n" "FH\n" "FT source 1..4870\n" "FT /organism=\"Streptomyces coelicolor\"\n" "FT /strain=\"A3(2)\"\n" "FT /clone=\"cosmid 10H5\"\n" "FT CDS complement(<1..327)\n" "FT /note=\"SC10H5.01c, unknown, partial CDS, len >109 aa;\n" "FT possible integral membrane protein\"\n" "FT /gene=\"SC10H5.01c\"\n" "FT /product=\"hypothetical protein SC10H5.01c\"\n" "FT CDS complement(350..805)\n" "FT /note=\"SC10H5.02c, probable integral membrane protein, len:\n" "FT 151 aa; similar to S. coelicolor hypothetical protein\n" "FT TR:O54194 (EMBL:AL021411) SC7H1.35 (155 aa), fasta scores;\n" "FT opt: 431 z-score: 749.8 E(): 0, 53.5% identity in 114 aa\n" "FT overlap.\"\n" "FT /product=\"putative integral membrane protein\"\n" "FT /gene=\"SC10H5.02c\"\n" "FT RBS complement(812..815)\n" "FT /note=\"possible RBS upstream of SC10H5.02c\"\n" "FT CDS complement(837..1301)\n" "FT /note=\"SC10H5.03c, probable integral membrane protein, len:\n" "FT 154 aa\"\n" "FT /product=\"putative integral membrane protein\"\n" "FT /gene=\"SC10H5.03c\"\n" "FT RBS complement(1308..1312)\n" "FT /note=\"possible RBS upstream of SC10H5.03c\"\n" "FT CDS complement(1427..1735)\n" "FT /note=\"SC10H5.04c, unknown, len: 103 aa; possible membrane\"\n" "FT /gene=\"SC10H5.04c\"\n" "FT /product=\"hypothetical protein SC10H5.04c\"\n" "FT RBS complement(1738..1741)\n" "FT /note=\"possible RBS upstream of SC10H5.05c\"\n" "FT misc_feature 1800^1801\n" "FT /note=\"Zero-length feature added to test Bioperl parsing\"\n" "FT CDS 1933..2022\n" "FT /note=\"SC10H5.05, questionable ORF, len: 29 aa\"\n" "FT /gene=\"SC10H5.05\"\n" "FT /product=\"hypothetical protein SC10H5.05\"\n" "FT CDS 2019..2642\n" "FT /note=\"SC10H5.06, probable membrane protein, len: 207 aa;\n" "FT similar to S. coelicolor TR:O54192 SC7H1.33c (191 aa),\n" "FT fasta scores; opt: 312 z-score: 355.2 E(): 1.6e-12, 36.8%\n" "FT identity in 182 aa overlap\"\n" "FT /product=\"putative membrane protein\"\n" "FT /gene=\"SC10H5.06\"\n" "FT RBS 2627..2631\n" "FT /note=\"possible RBS upstream of SC10H5.07\"\n" "FT CDS 2639..4048\n" "FT /note=\"SC10H5.07, unknown, len: 469 aa\"\n" "FT /gene=\"SC10H5.07\"\n" "FT /product=\"hypothetical protein SC10H5.07\"\n" "FT CDS complement(4100..4297)\n" "FT /note=\"SC10H5.08c, unknown, len: 65 aa\"\n" "FT /gene=\"SC10H5.08c\"\n" "FT /product=\"hypothetical protein SC10H5.08c\"\n" "FT RBS complement(4314..4319)\n" "FT /note=\"possible RBS upstream of SC10H5.08c\"\n" "FT CDS complement(4439..>4870)\n" "FT /note=\"SC10H5.09c, probable integral membrane protein,\n" "FT partial CDS len: >143 aa; some similarity in C-terminus to\n" "FT S. coelicolor hypothetical protein TR:O54106\n" "FT (EMBL:AL021529) SC10A5.15 (114 aa), fasta scores; opt: 145\n" "FT z-score: 233.8 E(): 9.2e-06, 33.3% identity in 81 aa\n" "FT overlap. Overlaps and extends SC3A7.01c\"\n" "FT /product=\"putative integral membrane protein\"\n" "FT /gene=\"SC10H5.09c\"\n" "FT misc_feature 4769..4870\n" "FT /note=\"overlap with cosmid 3A7 from 1 to 102\"\n" "XX\n" "SQ Sequence 4870 BP; 769 A; 1717 C; 1693 G; 691 T; 0 other;\n" " gatcagtaga cccagcgaca gcagggcggg gcccagcagg ccggccgtgg cgtagagcgc 60\n" " gaggacggcg accggcgtgg ccaccgacag gatggctgcg gcgacgcgga cgacaccgga 120\n" " gtgtgccagg gcccaccaca cgccgatggc cgcgagcgcg agtcccgcgc tgccgaacag 180\n" " ggcccacagc acactgcgca gaccggcggc cacgagtggc gccaggacgg tgcccagcag 240\n" " gagcagcagg gtgacgtggg cgcgcgctgc actgtggccg ccccgtccgc ccgacgcgcg 300\n" " cggctcgtca tctcgcggtc ccaccaccgg tcggccccat tactcgtcct caaccctgtg 360\n" " gcgactgacg ttccccggac aggtcgtacc gattgccgcc acgccccacc acgcacaggg 420\n" " cccagacgac gaagcctgac atggtgatca tgacgacgga ccacaccggg tagtacggca 480\n" " gcgagaggaa gttggcgatg atcaccagcc cggcgatggc gaccccggtg acacgtgccc 540\n" " acatcgccgt tttgagcagc ccggcgctga cgaccatggc gagcgcgccg agcgcgagat 600\n" " ggatccaccc ccacccggtg agatcgaact ggaaaacgta gttgggcgtg gtgacgaaga 660\n" " cgtcgtcctc ggcgatggcc atgatgcccc ggaagaggct gagcagcccg gcgaggaaga 720\n" " gcatcaccgc cgcgaaggcg gtaaggcccg tcgcccattc ctgcctcgcg gtgtgtgccg 780\n" " ggtggtgggt atgtgacgtg gtcatctcgg acctcgtttc gtggaatgcg gatgcttcag 840\n" " cgagcggagg cgccggtgcc cgccgcgccc gtgtgccctg ccgggccgtg accggacagg 900\n" " accaattcct tcgccttgcg gaactcctcg tccgtgatgg caccccggtc tcggatctcg 960\n" " gagagccggg ccagctcgtc gacgctgctg gacccgccgc ccacggtctt cctgatgtag 1020\n" " gcgtcgaact cctcctgctg agcccgtgcc cgcgttgtct cccggctgcc catgttcttg 1080\n" " ccgcgagcga tcacgtagac gaaaacgccc aggaagggca ggaggatgca gaacaccaac 1140\n" " cagccggcct tcgcccagcc actcagtccg tcgtcccgga agatgtcggt gacgacgcgg 1200\n" " aagagcagga cgaaccacat gatccacagg aagatcatca gcatcgtcca gaaggcaccc 1260\n" " agcagtgggt agtcgtacgc caggtaggtc tgtgcactca tgtccgtcct ccgtcctccg 1320\n" " gggcgcggcc cggcggccct cgttccgtac tgacatcagg gtggtcacgg gtcccaccgg 1380\n" " tcggcatcac ccggcacggg tgagtggggc gccgaggccg tcgtggtcag gcccgggaca 1440\n" " ccggtgtgac cctggtggaa ggacgcgtcc cgtggggcac gcaccgccgg ccgagggcga 1500\n" " ccaccgcctc ggtcagtccg agcaggccca gccacaggcc gagaagtcgg gtcagggcac 1560\n" " gggccgactc ggcgggcagc gcgaggacga cgattccggc gacgtcgacg gccagcgggt 1620\n" " tgcgcaggcc cagcactccg gccggggcgc ccggcaccag cgtggcgagg gccgatgcca 1680\n" " tgagccaggt ccaggaaccc ccaagcctgg cgaggacgtg cgccggatcg ctcaatgctc 1740\n" " cggtgaccgc cccgcccgac ccgtctccct tgtcggcagg ttccgccgca tcacgcggaa 1800\n" " cggagatggc tcccctgtgg atcgggcggc cgctgcgggg ccgcccggtt ggtcggtcgg 1860\n" " tgagcgccgg actccccctt cagctcttcc agggtcgggg tcgacaccga ggtcctggat 1920\n" " cacccgtcag gggtgatccg ggcatgccgt cgtggcggtg aggtgggata cgggaacgat 1980\n" " cggcccacgg gggaccggac gagacgaaga gacgtgagat gagcgatacg aactcgggcg 2040\n" " gcgggcgcca ggccgcttcc ggaccggccc cacgtggccg actccctttc cgccggcgcg 2100\n" " tggccctggt cgctgtcgca cgtcccctga tcgtcacggt cggtctcgtc accgcctact 2160\n" " acctgcttcc cctggacgag agactcagcg ccggcaccct ggtgtcgctg gtgtgcggac 2220\n" " tgctcgcagt ccttctggtg ttctgctggg aggtgcgggc catcacgcgc tccccgcatc 2280\n" " cgcgtctgag agcgatcgag ggcctggccg ccacgctggt gctgttcctg gtcctcttcg 2340\n" " ccggctccta ctacctgctg ggtcgctccg cgcccggctc cttcagcgag ccgctgaaca 2400\n" " ggacggacgc gctgtacttc actctgacca cgttcgccac cgtcggcttc ggggacatca 2460\n" " ccgcacgctc cgagaccggg cggatcctca cgatggcgca gatgacggga gggctactgc 2520\n" " tcgtcggagt cgccgcccgg gtgctggcga gcgcagtgca ggcggggctg caccgacagg 2580\n" " gccggggacc ggcggcatcg ccacgctccg gtgctgcgga ggagccggag gccggaccat 2640\n" " gaccgtaccc ggtggcttca ccgcctccct gccgccggcc gagcgagccg cgtacggcag 2700\n" " gaaggcccgt aaaagggcct cacgttcgtg ccacggctgg tacgagccgg ggcagcggcg 2760\n" " gcctgacccc gtcgacctgc tggagcgcca gtccggcgag cgtgtcccgg cactcgtgcc 2820\n" " catccgctac ggtcgcatgc tggagtcgcc gttccgcttc taccgcggtg cggcagcgat 2880\n" " catggcggcg gacctggcac ccctgcccag cagcggactc caggtgcaat tgtgcgggga 2940\n" " cgcgcacccg ttgaacttcc ggctcctggc ctcaccggag cgccggctgg tcttcgacat 3000\n" " caacgacttc gacgagacgc tgcccggccc cttcgagtgg gacgtcaaac ggctggcggc 3060\n" " cggattcgtg atcgcggccc ggtcgaacgg cttctcgtcc aaggaacaga accgcaccgt 3120\n" " tcgggcctgt gtgcgggcct accgggagcg catgagggag ttcgccgtca tgccgaccct 3180\n" " ggacatctgg tacgcccagg acgacgccga ccacgtacgg caactgctgg ctacggaggc 3240\n" " cagaggagaa gctgagcagc ggctcaggga cgcggctgcg aaggcccgca cacgcaccca 3300\n" " catgagggcg ttcgcgaagc tcacccgcgt cacggccgag ggccggcgca tcacccccga 3360\n" " cccgccgctg atcaccccac tcggcgatct gctcaccgac ccggccgaag ccggccggga 3420\n" " ggaggaactg cggtccgtcg tgaacggcta cgcacggtcc ctgccgcccg agcgccggca 3480\n" " cctgctgcgt cactaccggc ttgtggacat ggcgcgcaag gtggtcggcg tcggcagtgt 3540\n" " cggcacccgc tgctgggtac tgcttctgct cggcagggac gacgacgatc ctctgctgct 3600\n" " ccaggccaag gaagcctcgg aatcggtgct ggcggcccac acgggcggcg aacgctacga 3660\n" " ccatcagggc cgcagggtcg tggccggcca gcgtctgatc cagaccaccg gtgacatctt 3720\n" " tctcggctgg gcgcgcgtca ccggcttcga cggaaaggcc cgggacttct acgtgcgtca 3780\n" " actgtgggac tggaagggcg tcgcgcggcc ggaaaccatg gggcccgacc tgctctccct 3840\n" " cttcgcccgg ctgtgcggtg cctgcctggc gagggcccac gcccgttccg gtgaccccgt 3900\n" " cgcgctcgcc gcgtacctgg gcggcagcga ccgcttcgac ggcgcgctca ccgagttcgc 3960\n" " ccagtcctac gccgatcaga atgaacgcga ccacgaagct ctgctggcgg cctgccgctc 4020\n" " cggcagggtc acggccgccc gtttgtgagg ccgacccggg aacggccggc gggctggcac 4080\n" " acaccgccgc cggtcggcgt cattccggaa gctgccgcat ctccaggacg cgcaggccca 4140\n" " gcgactggca gcgggtgagc aacccgtaca gatgggcctc gtcgatcacc gtgccgaaca 4200\n" " gcacggtctg gccggacatg acgacgtgct ccagctccgg gaacgcgttg gccagcgtcc 4260\n" " gtgacaggtg tccctcgacg cggatctcgt agcgcacgag cggtcctttc accgtaggag 4320\n" " ctcgggacac cgcccggggc tccgggtcgg acggtgctct tggtgacgag cctgcgcctc 4380\n" " gtcgccctcc ggtgccctca cccagcacag gtgactccaa ccgcagtgtc agtgcctttc 4440\n" " agtgcgtcac tgtgatcttg acgacgacga tcaccaggcc gagcagtacg ttgaccgtcg 4500\n" " cggtgacggc caccagtcgt cgcgaggcgc ccgcgcggtg cgccgcggcg acggaccagc 4560\n" " ccacctgacc ggcgacggcg acggacagcg ccagccacag ggtgcccggg acgtccagcc 4620\n" " ccagtacggg gctgacggcg atggccgcgg ccggaggcac ggcggccttg acgatcggcc 4680\n" " actcctcgcg gcacacacgc agaatcaccc gccggtccgg agtgtgccgc gcgagacgcg 4740\n" " ctccgaacag ttcggcgtgg acgtgagcga tccagaacac caagctggtg agcaacagca 4800\n" " gaagaaccag ttcggcgcgg gggaacgagc ccagggtgcc ggcgccgatc acgacggagg 4860\n" " ctgcgagcat 4870\n" "//\n" "ID AB000263 standard; RNA; PRI; 368 BP.\n" "XX\n" "AC AB000263;\n" "XX\n" "DE Homo sapiens mRNA for prepro cortistatin like peptide, complete cds.\n" "XX\n" "SQ Sequence 368 BP;\n" " acaagatgcc attgtccccc ggcctcctgc tgctgctgct ctccggggcc acggccaccg 60\n" " ctgccctgcc cctggagggt ggccccaccg gccgagacag cgagcatatg caggaagcgg 120\n" " caggaataag gaaaagcagc ctcctgactt tcctcgcttg gtggtttgag tggacctccc 180\n" " aggccagtgc cgggcccctc ataggagagg aagctcggga ggtggccagg cggcaggaag 240\n" " gcgcaccccc ccagcaatcc gcgcgccggg acagaatgcc ctgcaggaac ttcttctgga 300\n" " agaccttctc ctcctgcaaa taaaacctca cccatgaatg ctcacgcaag tttaattaca 360\n" " gacctgaa 368\n" "//\n"; return result; } template void testHelperReadEmblSingle(TRecordReader & reader) { using namespace seqan; CharString buffer, k, v; // First record. // Read EMBL headers, split ID header, skip rest. SEQAN_ASSERT_EQ(readRecord(buffer, reader, EmblHeader()), 0); SEQAN_ASSERT_EQ(buffer, CharString("ID SC10H5 standard; DNA; PRO; 4870 BP.")); splitEmblHeader(k, v, buffer); SEQAN_ASSERT_EQ(k, CharString("ID")); SEQAN_ASSERT_EQ(v, CharString("SC10H5 standard; DNA; PRO; 4870 BP.")); while (nextIs(reader, EmblHeader())) SEQAN_ASSERT_EQ(readRecord(buffer, reader, EmblHeader()), 0); // Read EMBL sequence. SEQAN_ASSERT(nextIs(reader, EmblSequence())); DnaString seq; SEQAN_ASSERT_EQ(readRecord(seq, reader, EmblSequence()), 0); SEQAN_ASSERT_EQ(length(seq), 4870u); // Second record. // Read EMBL headers, split ID header, skip rest. SEQAN_ASSERT_EQ(readRecord(buffer, reader, EmblHeader()), 0); SEQAN_ASSERT_EQ(buffer, CharString("ID AB000263 standard; RNA; PRI; 368 BP.")); splitEmblHeader(k, v, buffer); SEQAN_ASSERT_EQ(k, CharString("ID")); SEQAN_ASSERT_EQ(v, CharString("AB000263 standard; RNA; PRI; 368 BP.")); while (nextIs(reader, EmblHeader())) SEQAN_ASSERT_EQ(readRecord(buffer, reader, EmblHeader()), 0); // Read EMBL sequence. SEQAN_ASSERT(nextIs(reader, EmblSequence())); SEQAN_ASSERT_EQ(readRecord(seq, reader, EmblSequence()), 0); SEQAN_ASSERT_EQ(length(seq), 368u); SEQAN_ASSERT(atEnd(reader)); } template void testHelperReadEmblRecord(TRecordReader & reader) { using namespace seqan; CharString id; Dna5String seq; SEQAN_ASSERT_EQ(readRecord(id, seq, reader, Embl()), 0); SEQAN_ASSERT_EQ(id, CharString("SC10H5 standard; DNA; PRO; 4870 BP.")); SEQAN_ASSERT_EQ(length(seq), 4870u); SEQAN_ASSERT_EQ(readRecord(id, seq, reader, Embl()), 0); SEQAN_ASSERT_EQ(id, CharString("AB000263 standard; RNA; PRI; 368 BP.")); SEQAN_ASSERT_EQ(length(seq), 368u); } template void testHelperReadEmblBatch(TRecordReader & reader) { using namespace seqan; StringSet ids; StringSet seqs; SEQAN_ASSERT_EQ(read2(ids, seqs, reader, Embl()), 0); SEQAN_ASSERT_EQ(ids[0], CharString("SC10H5 standard; DNA; PRO; 4870 BP.")); SEQAN_ASSERT_EQ(length(seqs[0]), 4870u); SEQAN_ASSERT_EQ(ids[1], CharString("AB000263 standard; RNA; PRI; 368 BP.")); SEQAN_ASSERT_EQ(length(seqs[1]), 368u); } SEQAN_DEFINE_TEST(test_stream_read_embl_single_char_array_stream) { using namespace seqan; typedef Stream > TStream; char const * emblString = testHelperReturnEmblFile(); TStream stream(emblString, emblString + strlen(emblString)); RecordReader > reader(stream); testHelperReadEmblSingle(reader); } SEQAN_DEFINE_TEST(test_stream_read_embl_record_char_array_stream) { using namespace seqan; typedef Stream > TStream; char const * emblString = testHelperReturnEmblFile(); TStream stream(emblString, emblString + strlen(emblString)); RecordReader > reader(stream); testHelperReadEmblRecord(reader); } SEQAN_DEFINE_TEST(test_stream_read_embl_batch_char_array_stream) { using namespace seqan; typedef Stream > TStream; char const * emblString = testHelperReturnEmblFile(); TStream stream(emblString, emblString + strlen(emblString)); RecordReader > reader(stream); testHelperReadEmblBatch(reader); } SEQAN_DEFINE_TEST(test_stream_read_embl_single_mmap) { using namespace seqan; typedef String > TString; TString mmapString; mmapString = testHelperReturnEmblFile(); RecordReader > reader(mmapString); testHelperReadEmblSingle(reader); } SEQAN_DEFINE_TEST(test_stream_read_embl_single_batch_mmap) { using namespace seqan; typedef String > TString; TString mmapString; mmapString = testHelperReturnEmblFile(); RecordReader > reader(mmapString); testHelperReadEmblRecord(reader); } SEQAN_DEFINE_TEST(test_stream_read_embl_single_batch_concat_mmap) { using namespace seqan; typedef String > TString; TString mmapString; mmapString = testHelperReturnEmblFile(); RecordReader > reader(mmapString); testHelperReadEmblBatch(reader); } #endif // TEST_STREAM_TEST_STREAM_READ_EMBL_H_