// ========================================================================== // SeqAn - The Library for Sequence Analysis // ========================================================================== // Copyright (c) 2006-2010, 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: Manuel Holtgrewe // ========================================================================== // Tests for the stream module. // ========================================================================== #include #include #include #include "test_stream_char_array.h" #if SEQAN_HAS_ZLIB #include "test_stream_gz_file.h" #include "test_stream_bgzf.h" #endif // #if SEQAN_HAS_ZLIB #if SEQAN_HAS_BZIP2 #include "test_stream_bz2_file.h" #endif // #if SEQAN_HAS_BZIP2 #include "test_stream_adapt_cstdio.h" #include "test_stream_adapt_fstream.h" #include "test_stream_adapt_sstream.h" #include "test_stream_adapt_mmap.h" #include "test_stream_tokenize.h" #include "test_stream_lexical_cast.h" #include "test_stream_record_reader_fasta.h" #include "test_stream_record_reader_fastq.h" #include "test_stream_guess_stream_format.h" #include "test_stream_write_fasta.h" #include "test_stream_read_embl.h" #include "test_stream_read_genbank.h" #include "test_stream_read_auto_format.h" SEQAN_BEGIN_TESTSUITE(test_stream) { // Tests for Char Array Stream. SEQAN_CALL_TEST(test_stream_char_array_metafunctions); SEQAN_CALL_TEST(test_stream_char_array_read_simple_usage); SEQAN_CALL_TEST(test_stream_char_array_read_complex_usage); SEQAN_CALL_TEST(test_stream_char_array_write_simple_usage); SEQAN_CALL_TEST(test_stream_char_array_write_complex_usage); SEQAN_CALL_TEST(test_stream_char_array_eof); SEQAN_CALL_TEST(test_stream_char_array_peek); SEQAN_CALL_TEST(test_stream_char_array_read_char); SEQAN_CALL_TEST(test_stream_char_array_read_block); SEQAN_CALL_TEST(test_stream_char_array_write_block); SEQAN_CALL_TEST(test_stream_char_array_streamPut); SEQAN_CALL_TEST(test_stream_char_array_write_char); SEQAN_CALL_TEST(test_stream_char_array_flush); SEQAN_CALL_TEST(test_stream_char_array_seek); SEQAN_CALL_TEST(test_stream_char_array_tell); #if SEQAN_HAS_ZLIB // Enable tests for Stream, Stream if available. // Tests for BZ2 File Stream. SEQAN_CALL_TEST(test_stream_gz_file_metafunctions); SEQAN_CALL_TEST(test_stream_gz_file_read_simple_usage); SEQAN_CALL_TEST(test_stream_gz_file_read_complex_usage); SEQAN_CALL_TEST(test_stream_gz_file_write_simple_usage); SEQAN_CALL_TEST(test_stream_gz_file_write_complex_usage); SEQAN_CALL_TEST(test_stream_gz_file_eof); SEQAN_CALL_TEST(test_stream_gz_file_peek); SEQAN_CALL_TEST(test_stream_gz_file_read_char); SEQAN_CALL_TEST(test_stream_gz_file_read_block); SEQAN_CALL_TEST(test_stream_gz_file_write_block); SEQAN_CALL_TEST(test_stream_gz_file_streamPut); SEQAN_CALL_TEST(test_stream_gz_file_write_char); SEQAN_CALL_TEST(test_stream_gz_file_flush); SEQAN_CALL_TEST(test_stream_gz_file_seek); SEQAN_CALL_TEST(test_stream_gz_file_tell); // Test Stream. SEQAN_CALL_TEST(test_stream_bgzf_metafunctions); SEQAN_CALL_TEST(test_stream_bgzf_read_simple_usage); SEQAN_CALL_TEST(test_stream_bgzf_read_complex_usage); SEQAN_CALL_TEST(test_stream_bgzf_write_simple_usage); SEQAN_CALL_TEST(test_stream_bgzf_write_complex_usage); SEQAN_CALL_TEST(test_stream_bgzf_eof); SEQAN_CALL_TEST(test_stream_bgzf_peek); SEQAN_CALL_TEST(test_stream_bgzf_read_char); SEQAN_CALL_TEST(test_stream_bgzf_read_block); SEQAN_CALL_TEST(test_stream_bgzf_write_block); SEQAN_CALL_TEST(test_stream_bgzf_streamPut); SEQAN_CALL_TEST(test_stream_bgzf_write_char); SEQAN_CALL_TEST(test_stream_bgzf_flush); SEQAN_CALL_TEST(test_stream_bgzf_seek); SEQAN_CALL_TEST(test_stream_bgzf_tell); SEQAN_CALL_TEST(test_stream_bgzf_write_large_and_compare_with_file); SEQAN_CALL_TEST(test_stream_bgzf_from_file_and_compare); #endif // #if SEQAN_HAS_ZLIB #if SEQAN_HAS_BZIP2 // Enable tests for Stream if available. // Tests for BZ2 File Stream. SEQAN_CALL_TEST(test_stream_bz2_file_metafunctions); SEQAN_CALL_TEST(test_stream_bz2_file_read_simple_usage); SEQAN_CALL_TEST(test_stream_bz2_file_read_complex_usage); SEQAN_CALL_TEST(test_stream_bz2_file_write_simple_usage); SEQAN_CALL_TEST(test_stream_bz2_file_write_complex_usage); SEQAN_CALL_TEST(test_stream_bz2_file_eof); SEQAN_CALL_TEST(test_stream_bz2_file_read_char); SEQAN_CALL_TEST(test_stream_bz2_file_read_block); SEQAN_CALL_TEST(test_stream_bz2_file_write_block); SEQAN_CALL_TEST(test_stream_bz2_file_write_char); SEQAN_CALL_TEST(test_stream_bz2_file_streamPut); SEQAN_CALL_TEST(test_stream_bz2_file_flush); #endif // #if SEQAN_HAS_BZIP2 // Tests for cstdio. SEQAN_CALL_TEST(test_stream_adapt_cstdio_metafunctions); SEQAN_CALL_TEST(test_stream_adapt_cstdio_read_simple_usage); SEQAN_CALL_TEST(test_stream_adapt_cstdio_read_complex_usage); SEQAN_CALL_TEST(test_stream_adapt_cstdio_write_simple_usage); SEQAN_CALL_TEST(test_stream_adapt_cstdio_write_complex_usage); SEQAN_CALL_TEST(test_stream_adapt_cstdio_eof); SEQAN_CALL_TEST(test_stream_adapt_cstdio_peek); SEQAN_CALL_TEST(test_stream_adapt_cstdio_read_char); SEQAN_CALL_TEST(test_stream_adapt_cstdio_read_block); SEQAN_CALL_TEST(test_stream_adapt_cstdio_write_block); SEQAN_CALL_TEST(test_stream_adapt_cstdio_write_char); SEQAN_CALL_TEST(test_stream_adapt_cstdio_streamPut); SEQAN_CALL_TEST(test_stream_adapt_cstdio_flush); SEQAN_CALL_TEST(test_stream_adapt_cstdio_seek); SEQAN_CALL_TEST(test_stream_adapt_cstdio_tell); // Tests for std::stringstream adaptions. SEQAN_CALL_TEST(test_stream_adapt_sstream_metafunctions); SEQAN_CALL_TEST(test_stream_adapt_sstream_read_simple_usage); SEQAN_CALL_TEST(test_stream_adapt_sstream_read_complex_usage); SEQAN_CALL_TEST(test_stream_adapt_sstream_write_simple_usage); SEQAN_CALL_TEST(test_stream_adapt_sstream_write_complex_usage); SEQAN_CALL_TEST(test_stream_adapt_sstream_eof); SEQAN_CALL_TEST(test_stream_adapt_sstream_peek); SEQAN_CALL_TEST(test_stream_adapt_sstream_read_char); SEQAN_CALL_TEST(test_stream_adapt_sstream_read_block); SEQAN_CALL_TEST(test_stream_adapt_sstream_write_char); SEQAN_CALL_TEST(test_stream_adapt_sstream_write_block); SEQAN_CALL_TEST(test_stream_adapt_sstream_streamPut); SEQAN_CALL_TEST(test_stream_adapt_sstream_flush); SEQAN_CALL_TEST(test_stream_adapt_sstream_seek); SEQAN_CALL_TEST(test_stream_adapt_sstream_tell); // Tests for std::istringstream adaptions. SEQAN_CALL_TEST(test_stream_adapt_istringstream_metafunctions); SEQAN_CALL_TEST(test_stream_adapt_istringstream_read_simple_usage); SEQAN_CALL_TEST(test_stream_adapt_istringstream_read_complex_usage); SEQAN_CALL_TEST(test_stream_adapt_istringstream_eof); SEQAN_CALL_TEST(test_stream_adapt_istringstream_peek); SEQAN_CALL_TEST(test_stream_adapt_istringstream_read_char); SEQAN_CALL_TEST(test_stream_adapt_istringstream_read_block); SEQAN_CALL_TEST(test_stream_adapt_istringstream_seek); SEQAN_CALL_TEST(test_stream_adapt_istringstream_tell); // Tests for std::ostringstream adaptions. SEQAN_CALL_TEST(test_stream_adapt_ostringstream_metafunctions); SEQAN_CALL_TEST(test_stream_adapt_ostringstream_write_simple_usage); SEQAN_CALL_TEST(test_stream_adapt_ostringstream_write_complex_usage); SEQAN_CALL_TEST(test_stream_adapt_ostringstream_write_char); SEQAN_CALL_TEST(test_stream_adapt_ostringstream_write_block); SEQAN_CALL_TEST(test_stream_adapt_ostringstream_streamPut); SEQAN_CALL_TEST(test_stream_adapt_ostringstream_flush); SEQAN_CALL_TEST(test_stream_adapt_ostringstream_seek); SEQAN_CALL_TEST(test_stream_adapt_ostringstream_tell); // Tests for std::fstream adaptions. SEQAN_CALL_TEST(test_stream_adapt_fstream_metafunctions); SEQAN_CALL_TEST(test_stream_adapt_fstream_read_simple_usage); SEQAN_CALL_TEST(test_stream_adapt_fstream_read_complex_usage); SEQAN_CALL_TEST(test_stream_adapt_fstream_write_simple_usage); SEQAN_CALL_TEST(test_stream_adapt_fstream_write_complex_usage); SEQAN_CALL_TEST(test_stream_adapt_fstream_eof); SEQAN_CALL_TEST(test_stream_adapt_fstream_peek); SEQAN_CALL_TEST(test_stream_adapt_fstream_read_char); SEQAN_CALL_TEST(test_stream_adapt_fstream_read_block); SEQAN_CALL_TEST(test_stream_adapt_fstream_write_block); SEQAN_CALL_TEST(test_stream_adapt_fstream_write_char); SEQAN_CALL_TEST(test_stream_adapt_fstream_streamPut); SEQAN_CALL_TEST(test_stream_adapt_fstream_flush); SEQAN_CALL_TEST(test_stream_adapt_fstream_seek); SEQAN_CALL_TEST(test_stream_adapt_fstream_tell); // Tests for std::ifstream adaptions. SEQAN_CALL_TEST(test_stream_adapt_ifstream_metafunctions); SEQAN_CALL_TEST(test_stream_adapt_ifstream_read_simple_usage); SEQAN_CALL_TEST(test_stream_adapt_ifstream_read_complex_usage); SEQAN_CALL_TEST(test_stream_adapt_ifstream_eof); SEQAN_CALL_TEST(test_stream_adapt_ifstream_peek); SEQAN_CALL_TEST(test_stream_adapt_ifstream_read_char); SEQAN_CALL_TEST(test_stream_adapt_ifstream_read_block); SEQAN_CALL_TEST(test_stream_adapt_ifstream_seek); SEQAN_CALL_TEST(test_stream_adapt_ifstream_tell); // Tests for std::ofstream adaptions. SEQAN_CALL_TEST(test_stream_adapt_ofstream_metafunctions); SEQAN_CALL_TEST(test_stream_adapt_ofstream_write_simple_usage); SEQAN_CALL_TEST(test_stream_adapt_ofstream_write_complex_usage); SEQAN_CALL_TEST(test_stream_adapt_ofstream_write_block); SEQAN_CALL_TEST(test_stream_adapt_ofstream_write_char); SEQAN_CALL_TEST(test_stream_adapt_ofstream_streamPut); SEQAN_CALL_TEST(test_stream_adapt_ofstream_flush); // Tests for mmap-stream adaptation SEQAN_CALL_TEST(test_stream_adapt_mmap_streamPut); // Tests for tokenize.h SEQAN_CALL_TEST(test_stream_tokenizing_readUntil); SEQAN_CALL_TEST(test_stream_tokenizing_readNChars); SEQAN_CALL_TEST(test_stream_tokenizing_readIgnoring); SEQAN_CALL_TEST(test_stream_tokenizing_readLine); SEQAN_CALL_TEST(test_stream_tokenizing_skipUntil); SEQAN_CALL_TEST(test_stream_tokenizing_skipWhile); SEQAN_CALL_TEST(test_stream_tokenizing_skipLine); SEQAN_CALL_TEST(test_stream_tokenizing_skipUntilString); SEQAN_CALL_TEST(test_stream_tokenizing_skipUntilLineBeginsWithChar); SEQAN_CALL_TEST(test_stream_tokenizing_skipUntilLineBeginsWithStr); SEQAN_CALL_TEST(test_stream_tokenizing_skipUntilLineBeginsWithOneCharOfStr); SEQAN_CALL_TEST(test_stream_tokenizing_read_until_tab_or_line_break); SEQAN_CALL_TEST(test_stream_tokenizing_read_until_one_of); // Tests for lexical_cast SEQAN_CALL_TEST(test_stream_lexical_cast_1_stdstring); SEQAN_CALL_TEST(test_stream_lexical_cast_1_chararray); SEQAN_CALL_TEST(test_stream_lexical_cast_1_seqanstring); SEQAN_CALL_TEST(test_stream_lexical_cast_2_stdstring); SEQAN_CALL_TEST(test_stream_lexical_cast_2_chararray); SEQAN_CALL_TEST(test_stream_lexical_cast_2_seqanstring); // -------------- File format specific code ------------------ /* RecordReader is tested for each Format with fstream and mmap-backend. * Every backend is tested with single-pass record-reading, those that have * double-pass implementations are also tested for double-pass * record-reading and batch reading (double-pass whole document). For the * last case an additional test for concat-direct-strings is performed. */ // Tests for FASTA SEQAN_CALL_TEST(test_stream_record_reader_fasta_single_fstream); SEQAN_CALL_TEST(test_stream_record_reader_fasta_double_fstream); SEQAN_CALL_TEST(test_stream_record_reader_fasta_batch_single_fstream); SEQAN_CALL_TEST(test_stream_record_reader_fasta_batch_double_fstream); SEQAN_CALL_TEST(test_stream_record_reader_fasta_single_mmap); SEQAN_CALL_TEST(test_stream_record_reader_fasta_double_mmap); SEQAN_CALL_TEST(test_stream_record_reader_fasta_batch_single_mmap); SEQAN_CALL_TEST(test_stream_record_reader_fasta_batch_single_concat_mmap); SEQAN_CALL_TEST(test_stream_record_reader_fasta_batch_double_mmap); SEQAN_CALL_TEST(test_stream_record_reader_fasta_batch_double_concat_mmap); // Tests for FASTQ SEQAN_CALL_TEST(test_stream_record_reader_fastq_single_fstream); SEQAN_CALL_TEST(test_stream_record_reader_fastq_double_fstream); SEQAN_CALL_TEST(test_stream_record_reader_fastq_batch_single_fstream); SEQAN_CALL_TEST(test_stream_record_reader_fastq_batch_double_fstream); SEQAN_CALL_TEST(test_stream_record_reader_fastq_single_mmap); SEQAN_CALL_TEST(test_stream_record_reader_fastq_double_mmap); SEQAN_CALL_TEST(test_stream_record_reader_fastq_batch_single_mmap); SEQAN_CALL_TEST(test_stream_record_reader_fastq_batch_single_concat_mmap); SEQAN_CALL_TEST(test_stream_record_reader_fastq_batch_double_mmap); SEQAN_CALL_TEST(test_stream_record_reader_fastq_batch_double_concat_mmap); SEQAN_CALL_TEST(test_stream_record_reader_fastq_check_stream_format); // Tests for EMBL SEQAN_CALL_TEST(test_stream_read_embl_single_char_array_stream); SEQAN_CALL_TEST(test_stream_read_embl_record_char_array_stream); SEQAN_CALL_TEST(test_stream_read_embl_batch_char_array_stream); SEQAN_CALL_TEST(test_stream_read_embl_single_mmap); SEQAN_CALL_TEST(test_stream_read_embl_single_batch_mmap); SEQAN_CALL_TEST(test_stream_read_embl_single_batch_concat_mmap); // Tests for GenBank SEQAN_CALL_TEST(test_stream_read_genbank_single_char_array_stream); SEQAN_CALL_TEST(test_stream_read_genbank_record_char_array_stream); SEQAN_CALL_TEST(test_stream_read_genbank_batch_char_array_stream); SEQAN_CALL_TEST(test_stream_read_genbank_single_mmap); SEQAN_CALL_TEST(test_stream_read_genbank_single_batch_mmap); SEQAN_CALL_TEST(test_stream_read_genbank_single_batch_concat_mmap); // TODO Tests for other formats once they are supported // Tests for file format auto-detection SEQAN_CALL_TEST(test_stream_guess_stream_format_auto_fasta); SEQAN_CALL_TEST(test_stream_guess_stream_format_auto_fastq); SEQAN_CALL_TEST(test_stream_guess_stream_format_auto_bogus); // Tests for reading with automatic file format detection. SEQAN_CALL_TEST(test_stream_read_record_auto_format_quals_fasta); SEQAN_CALL_TEST(test_stream_read_record_auto_format_quals_fastq); SEQAN_CALL_TEST(test_stream_read_record_auto_format_no_quals_fasta); SEQAN_CALL_TEST(test_stream_read_record_auto_format_no_quals_fastq); SEQAN_CALL_TEST(test_stream_read_auto_format_quals_fasta); SEQAN_CALL_TEST(test_stream_read_auto_format_quals_fastq); SEQAN_CALL_TEST(test_stream_read_auto_format_no_quals_fasta); SEQAN_CALL_TEST(test_stream_read_auto_format_no_quals_fastq); // Tests for FASTA with Amino Acid alphabet. SEQAN_CALL_TEST(test_stream_record_reader_fasta_protein_single_fstream); /* Tests for writing file formats. * Only fstream used as a representative */ // Tests for FASTA SEQAN_CALL_TEST(test_stream_write_record_fasta_default); SEQAN_CALL_TEST(test_stream_write_record_fasta_nolinebreaks); SEQAN_CALL_TEST(test_stream_write_record_fastq_default_separate_qual); SEQAN_CALL_TEST(test_stream_write_record_fastq_default_qual_in_seq); SEQAN_CALL_TEST(test_stream_write_record_fastq_linebreaks_qualmeta); SEQAN_CALL_TEST(test_stream_write2_fasta_default); SEQAN_CALL_TEST(test_stream_write2_fastq_default_separate_qual); SEQAN_CALL_TEST(test_stream_write2_fastq_default_qual_in_seq); } SEQAN_END_TESTSUITE