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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/
H A Dblastdiag_unit_test.cpp49 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()
H A Dblastoptions_unit_test.cpp385 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 …]
H A Dntscan_unit_test.cpp101 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/
H A Dblastdiag_unit_test.cpp49 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()
H A Dblastoptions_unit_test.cpp385 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 …]
H A Dntscan_unit_test.cpp101 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()
/dports/biology/ncbi-toolkit/ncbi/algo/blast/api/
H A Dblast_prelim.c53 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()
H A Dblast_options_api.c50 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()
H A Dtwoseq_api.c104 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()
H A Dblast_prelim.h66 const BlastInitialWordOptions* word_options; /**< Options for ungapped member
105 const BlastInitialWordOptions* word_options,
H A Dblast_returns.h101 const BlastInitialWordOptions* word_options,
163 const BlastInitialWordOptions* word_options,
H A Dblast_api.c329 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()
H A Dblast_returns.c473 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()
H A Drepeats_filter.c61 if (!options || !options->score_options || !options->word_options || in s_SetRepeatsSearchOptions()
77 options->word_options->x_dropoff = REPEATS_SEARCH_XDROP_UNGAPPED; in s_SetRepeatsSearchOptions()
/dports/security/gcr/gcr-3.40.0/gcr/
H A Dgcr-openssh.c166 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/core/
H A Dblast_engine.h97 const BlastInitialWordOptions* word_options,
138 const BlastInitialWordOptions* word_options,
171 const BlastInitialWordOptions* word_options,
204 const BlastInitialWordOptions* word_options,
/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/
H A Dblast_engine.h97 const BlastInitialWordOptions* word_options,
138 const BlastInitialWordOptions* word_options,
171 const BlastInitialWordOptions* word_options,
204 const BlastInitialWordOptions* word_options,
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/core/
H A Dblast_engine.h97 const BlastInitialWordOptions* word_options,
138 const BlastInitialWordOptions* word_options,
171 const BlastInitialWordOptions* word_options,
204 const BlastInitialWordOptions* word_options,
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/
H A Dblast_dbindex.cpp185 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
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H A Dprelim_stage.cpp220 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/
H A Dblast_dbindex.cpp185 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 …]
H A Dprelim_stage.cpp220 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()
/dports/biology/ncbi-toolkit/ncbi/demo/
H A Drpsblast.c466 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()
H A Dblast_driver.c254 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/api/
H A Dblast_dbindex.hpp129 BlastInitialWordOptions * word_options );

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