/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/ |
H A D | blastdiag_unit_test.cpp | 49 BlastInitialWordOptions word_options; in BOOST_AUTO_TEST_CASE() local 53 word_options.window_size = kWindowSize; in BOOST_AUTO_TEST_CASE() 54 word_params.options = &word_options; in BOOST_AUTO_TEST_CASE() 86 BlastInitialWordOptions word_options; in BOOST_AUTO_TEST_CASE() local 90 word_options.window_size = kWindowSize; in BOOST_AUTO_TEST_CASE() 91 word_params.options = &word_options; in BOOST_AUTO_TEST_CASE() 124 BlastInitialWordOptions word_options; in BOOST_AUTO_TEST_CASE() local 128 word_options.window_size = kWindowSize; in BOOST_AUTO_TEST_CASE() 129 word_params.options = &word_options; in BOOST_AUTO_TEST_CASE()
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H A D | blastoptions_unit_test.cpp | 385 BlastInitialWordOptions* word_options; in BOOST_AUTO_TEST_CASE() local 410 word_options = BlastInitialWordOptionsFree(word_options); in BOOST_AUTO_TEST_CASE() 411 BOOST_REQUIRE(word_options == NULL); in BOOST_AUTO_TEST_CASE() 553 BlastInitialWordOptions* word_options; in BOOST_AUTO_TEST_CASE() local 579 word_options = BlastInitialWordOptionsFree(word_options); in BOOST_AUTO_TEST_CASE() 580 BOOST_REQUIRE(word_options == NULL); in BOOST_AUTO_TEST_CASE() 675 word_options = BlastInitialWordOptionsFree(word_options); in BOOST_AUTO_TEST_CASE() 676 BOOST_REQUIRE(word_options == NULL); in BOOST_AUTO_TEST_CASE() 1300 word_options->x_dropoff = 20; in BOOST_AUTO_TEST_CASE() 1316 word_options = BlastInitialWordOptionsFree(word_options); in BOOST_AUTO_TEST_CASE() [all …]
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H A D | ntscan_unit_test.cpp | 101 BlastInitialWordOptions* word_options; member 114 word_options = NULL; in TestFixture() 310 BlastInitialWordOptionsNew(program_number, &word_options); in SetUpLookupTable() 345 if (word_options) in TearDownLookupTable() 346 word_options = BlastInitialWordOptionsFree(word_options); in TearDownLookupTable() 750 retval = BlastInitialWordParametersNew(program_number, word_options, in SkipMaskedRangesCore()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/ |
H A D | blastdiag_unit_test.cpp | 49 BlastInitialWordOptions word_options; in BOOST_AUTO_TEST_CASE() local 53 word_options.window_size = kWindowSize; in BOOST_AUTO_TEST_CASE() 54 word_params.options = &word_options; in BOOST_AUTO_TEST_CASE() 86 BlastInitialWordOptions word_options; in BOOST_AUTO_TEST_CASE() local 90 word_options.window_size = kWindowSize; in BOOST_AUTO_TEST_CASE() 91 word_params.options = &word_options; in BOOST_AUTO_TEST_CASE() 124 BlastInitialWordOptions word_options; in BOOST_AUTO_TEST_CASE() local 128 word_options.window_size = kWindowSize; in BOOST_AUTO_TEST_CASE() 129 word_params.options = &word_options; in BOOST_AUTO_TEST_CASE()
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H A D | blastoptions_unit_test.cpp | 385 BlastInitialWordOptions* word_options; in BOOST_AUTO_TEST_CASE() local 410 word_options = BlastInitialWordOptionsFree(word_options); in BOOST_AUTO_TEST_CASE() 411 BOOST_REQUIRE(word_options == NULL); in BOOST_AUTO_TEST_CASE() 553 BlastInitialWordOptions* word_options; in BOOST_AUTO_TEST_CASE() local 579 word_options = BlastInitialWordOptionsFree(word_options); in BOOST_AUTO_TEST_CASE() 580 BOOST_REQUIRE(word_options == NULL); in BOOST_AUTO_TEST_CASE() 675 word_options = BlastInitialWordOptionsFree(word_options); in BOOST_AUTO_TEST_CASE() 676 BOOST_REQUIRE(word_options == NULL); in BOOST_AUTO_TEST_CASE() 1300 word_options->x_dropoff = 20; in BOOST_AUTO_TEST_CASE() 1316 word_options = BlastInitialWordOptionsFree(word_options); in BOOST_AUTO_TEST_CASE() [all …]
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H A D | ntscan_unit_test.cpp | 101 BlastInitialWordOptions* word_options; member 114 word_options = NULL; in TestFixture() 310 BlastInitialWordOptionsNew(program_number, &word_options); in SetUpLookupTable() 345 if (word_options) in TearDownLookupTable() 346 word_options = BlastInitialWordOptionsFree(word_options); in TearDownLookupTable() 750 retval = BlastInitialWordParametersNew(program_number, word_options, in SkipMaskedRangesCore()
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/dports/biology/ncbi-toolkit/ncbi/algo/blast/api/ |
H A D | blast_prelim.c | 53 const BlastInitialWordOptions* word_options, in BlastPrelimSearchThreadDataInit() argument 71 data->word_options = word_options; in BlastPrelimSearchThreadDataInit() 107 search_data->word_options, search_data->ext_options, in Blast_PrelimSearchThreadRun()
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H A D | blast_options_api.c | 50 BlastInitialWordOptions* word_options=NULL; in SBlastOptionsNew() local 78 &word_options, &ext_options, &hit_options, &score_options, in SBlastOptionsNew() 98 options->word_options = word_options; in SBlastOptionsNew() 121 BlastInitialWordOptionsFree(options->word_options); in SBlastOptionsFree() 176 if (!options || !options->score_options || !options->word_options) in SBlastOptionsSetWindowSize() 192 options->word_options->window_size = window_size; in SBlastOptionsSetWindowSize()
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H A D | twoseq_api.c | 104 BlastInitialWordOptions* word_options = options->word_options; in s_TwoSeqBasicFillOptions() local 185 BLAST_FillInitialWordOptions(word_options, in s_TwoSeqBasicFillOptions() 194 word_options->window_size = 0; in s_TwoSeqBasicFillOptions() 196 word_options->window_size = BLAST_WINDOW_SIZE_PROT; in s_TwoSeqBasicFillOptions()
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H A D | blast_prelim.h | 66 const BlastInitialWordOptions* word_options; /**< Options for ungapped member 105 const BlastInitialWordOptions* word_options,
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H A D | blast_returns.h | 101 const BlastInitialWordOptions* word_options, 163 const BlastInitialWordOptions* word_options,
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H A D | blast_api.c | 329 const BlastInitialWordOptions* word_options = options->word_options; in s_BlastThreadManager() local 372 word_options, ext_options, hit_options, eff_len_options, in s_BlastThreadManager() 407 seq_src, score_options, sbp, lookup_wrap, word_options, in s_BlastThreadManager() 416 word_options, ext_options, hit_options, in s_BlastThreadManager() 436 word_options, ext_options, hit_options, in s_BlastThreadManager() 619 lookup_options, options->word_options, hit_options, in Blast_RunSearch()
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H A D | blast_returns.c | 473 const BlastInitialWordOptions* word_options, in Blast_SearchParamsFill() argument 518 search_params_lcl->window_size = word_options->window_size; in Blast_SearchParamsFill() 559 const BlastInitialWordOptions* word_options, in Blast_SummaryReturnFill() argument 573 word_options == NULL || ext_options == NULL || hit_options == NULL || in Blast_SummaryReturnFill() 582 lookup_options, hit_options, query_setup, word_options, in Blast_SummaryReturnFill()
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H A D | repeats_filter.c | 61 if (!options || !options->score_options || !options->word_options || in s_SetRepeatsSearchOptions() 77 options->word_options->x_dropoff = REPEATS_SEARCH_XDROP_UNGAPPED; in s_SetRepeatsSearchOptions()
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/dports/security/gcr/gcr-3.40.0/gcr/ |
H A D | gcr-openssh.c | 166 const gchar *word_bits, *word_exponent, *word_modulus, *word_options, *outer; in parse_v1_public_line() local 198 word_options = NULL; in parse_v1_public_line() 201 if (!next_word (&line, &length, &word_options, &len_options)) in parse_v1_public_line() 230 if (word_options) in parse_v1_public_line() 231 options = g_strndup (word_options, len_options); in parse_v1_public_line() 477 const gchar *word_options, *word_algo, *word_key; in parse_v2_public_line() local 511 word_options = word_algo; in parse_v2_public_line() 519 word_options = NULL; in parse_v2_public_line() 532 if (word_options) in parse_v2_public_line() 533 options = g_strndup (word_options, len_options); in parse_v2_public_line()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/core/ |
H A D | blast_engine.h | 97 const BlastInitialWordOptions* word_options, 138 const BlastInitialWordOptions* word_options, 171 const BlastInitialWordOptions* word_options, 204 const BlastInitialWordOptions* word_options,
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/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/ |
H A D | blast_engine.h | 97 const BlastInitialWordOptions* word_options, 138 const BlastInitialWordOptions* word_options, 171 const BlastInitialWordOptions* word_options, 204 const BlastInitialWordOptions* word_options,
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/core/ |
H A D | blast_engine.h | 97 const BlastInitialWordOptions* word_options, 138 const BlastInitialWordOptions* word_options, 171 const BlastInitialWordOptions* word_options, 204 const BlastInitialWordOptions* word_options,
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/ |
H A D | blast_dbindex.cpp | 185 BlastInitialWordOptions * word_options ) = 0; 288 BlastInitialWordOptions * word_options ); 301 BlastInitialWordOptions * word_options ) in DoPreSearch() argument 305 lut_options, word_options ); in DoPreSearch() 524 BlastInitialWordOptions * word_options ); 577 BlastInitialWordOptions * word_options ) in IndexedDbRunSearch() argument 581 idb->DoPreSearch( queries, lut_options, word_options ); in IndexedDbRunSearch() 890 BlastInitialWordOptions * word_options ) in DoPreSearch() argument 894 sopt_.two_hits = word_options->window_size; in DoPreSearch() 1019 BlastInitialWordOptions * word_options ) in PreSearch() argument [all …]
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H A D | prelim_stage.cpp | 220 BlastInitialWordOptions * word_options = opts_memento->m_InitWordOpts; in Run() local 246 chunk_queries, lut_options, word_options ); in Run() 297 GetDbIndexRunSearchFn()( queries, lut_options, word_options ); in Run()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/ |
H A D | blast_dbindex.cpp | 185 BlastInitialWordOptions * word_options ) = 0; 288 BlastInitialWordOptions * word_options ); 301 BlastInitialWordOptions * word_options ) in DoPreSearch() argument 305 lut_options, word_options ); in DoPreSearch() 524 BlastInitialWordOptions * word_options ); 577 BlastInitialWordOptions * word_options ) in IndexedDbRunSearch() argument 581 idb->DoPreSearch( queries, lut_options, word_options ); in IndexedDbRunSearch() 890 BlastInitialWordOptions * word_options ) in DoPreSearch() argument 894 sopt_.two_hits = word_options->window_size; in DoPreSearch() 1019 BlastInitialWordOptions * word_options ) in PreSearch() argument [all …]
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H A D | prelim_stage.cpp | 220 BlastInitialWordOptions * word_options = opts_memento->m_InitWordOpts; in Run() local 246 chunk_queries, lut_options, word_options ); in Run() 297 GetDbIndexRunSearchFn()( queries, lut_options, word_options ); in Run()
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/dports/biology/ncbi-toolkit/ncbi/demo/ |
H A D | rpsblast.c | 466 BlastInitialWordOptions* word_options = options->word_options; in s_FillOptions() local 482 BLAST_FillInitialWordOptions(word_options, kProgram, in s_FillOptions() 487 word_options->window_size = 0; in s_FillOptions() 526 lookup_options, word_options, hit_options, in s_FillOptions()
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H A D | blast_driver.c | 254 BlastInitialWordOptions* word_options = options->word_options; in s_FillOptions() local 306 BLAST_FillInitialWordOptions(word_options, program_number, in s_FillOptions() 311 word_options->window_size = 0; in s_FillOptions() 313 else if (word_options->window_size == 0 && in s_FillOptions() 315 word_options->window_size = 40; in s_FillOptions() 413 if (word_options->window_size > 0) { in s_FillOptions()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/api/ |
H A D | blast_dbindex.hpp | 129 BlastInitialWordOptions * word_options );
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