| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/ |
| H A D | blast_options_local_priv.hpp | 431 return m_ExtnOpts; in GetExtnOpts()
1141 return m_ExtnOpts->gap_x_dropoff; in GetGapXDropoff()
1147 m_ExtnOpts->gap_x_dropoff = x; in SetGapXDropoff()
1165 return m_ExtnOpts->ePrelimGapExt; in GetGapExtnAlgorithm()
1171 m_ExtnOpts->ePrelimGapExt = a; in SetGapExtnAlgorithm()
1177 return m_ExtnOpts->eTbackExt; in GetGapTracebackAlgorithm()
1183 m_ExtnOpts->eTbackExt = a; in SetGapTracebackAlgorithm()
1219 return m_ExtnOpts->unifiedP; in GetUnifiedP()
1225 m_ExtnOpts->unifiedP = u; in SetUnifiedP()
1237 m_ExtnOpts->max_mismatches = m; in SetMaxMismatches()
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| H A D | setup_factory.cpp | 148 opts_memento->m_ExtnOpts->compositionBasedStats > 0) { in CreateScoreBlock()
150 opts_memento->m_ExtnOpts->compositionBasedStats = 0; in CreateScoreBlock()
292 opts_memento->m_ExtnOpts, TRUE, in CreateHspStream()
324 opts_memento->m_ExtnOpts->compositionBasedStats, in CreateHspWriter()
336 opts_memento->m_ExtnOpts->compositionBasedStats, in CreateHspWriter()
346 opts_memento->m_ExtnOpts->compositionBasedStats, in CreateHspWriter()
355 opts_memento->m_ExtnOpts->compositionBasedStats, in CreateHspWriter()
382 opts_memento->m_ExtnOpts->compositionBasedStats, in CreateHspPipe()
391 opts_memento->m_ExtnOpts->compositionBasedStats, in CreateHspPipe()
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| H A D | blast_memento_priv.hpp | 70 m_ExtnOpts = local_opts->m_ExtnOpts.Get(); in CBlastOptionsMemento()
94 BlastExtensionOptions* m_ExtnOpts; member in CBlastOptionsMemento
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| H A D | blast_options_local_priv.cpp | 56 m_ExtnOpts.Reset((BlastExtensionOptions*)calloc(1, sizeof(BlastExtensionOptions))); in BEGIN_SCOPE()
96 x_Copy_CBlastExtensionOptions(m_ExtnOpts, in x_DoDeepCopy()
97 optsLocal.m_ExtnOpts); in x_DoDeepCopy()
378 if (BLAST_ValidateOptions(GetProgramType(), m_ExtnOpts, in Validate()
406 m_ExtnOpts.DebugDump(ddc, depth); in DebugDump()
528 a = static_cast<void*>( (BlastExtensionOptions*) m_ExtnOpts); in operator ==()
529 b = static_cast<void*>( (BlastExtensionOptions*) rhs.m_ExtnOpts); in operator ==()
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| H A D | traceback_stage.cpp | 219 m_OptsMemento->m_ExtnOpts, in Run()
238 m_OptsMemento->m_ExtnOpts, in Run()
322 m_OptsMemento->m_ExtnOpts, in RunSimple()
341 m_OptsMemento->m_ExtnOpts, in RunSimple()
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| H A D | prelim_search_runner.hpp | 79 m_OptsMemento->m_ExtnOpts, in operator ()()
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| H A D | prelim_stage.cpp | 336 opts_memento->m_ExtnOpts, in ComputeBlastHSPResults()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/ |
| H A D | blast_options_local_priv.hpp | 431 return m_ExtnOpts; in GetExtnOpts()
1141 return m_ExtnOpts->gap_x_dropoff; in GetGapXDropoff()
1147 m_ExtnOpts->gap_x_dropoff = x; in SetGapXDropoff()
1165 return m_ExtnOpts->ePrelimGapExt; in GetGapExtnAlgorithm()
1171 m_ExtnOpts->ePrelimGapExt = a; in SetGapExtnAlgorithm()
1177 return m_ExtnOpts->eTbackExt; in GetGapTracebackAlgorithm()
1183 m_ExtnOpts->eTbackExt = a; in SetGapTracebackAlgorithm()
1219 return m_ExtnOpts->unifiedP; in GetUnifiedP()
1225 m_ExtnOpts->unifiedP = u; in SetUnifiedP()
1237 m_ExtnOpts->max_mismatches = m; in SetMaxMismatches()
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| H A D | setup_factory.cpp | 148 opts_memento->m_ExtnOpts->compositionBasedStats > 0) { in CreateScoreBlock()
150 opts_memento->m_ExtnOpts->compositionBasedStats = 0; in CreateScoreBlock()
292 opts_memento->m_ExtnOpts, TRUE, in CreateHspStream()
324 opts_memento->m_ExtnOpts->compositionBasedStats, in CreateHspWriter()
336 opts_memento->m_ExtnOpts->compositionBasedStats, in CreateHspWriter()
346 opts_memento->m_ExtnOpts->compositionBasedStats, in CreateHspWriter()
355 opts_memento->m_ExtnOpts->compositionBasedStats, in CreateHspWriter()
382 opts_memento->m_ExtnOpts->compositionBasedStats, in CreateHspPipe()
391 opts_memento->m_ExtnOpts->compositionBasedStats, in CreateHspPipe()
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| H A D | blast_memento_priv.hpp | 70 m_ExtnOpts = local_opts->m_ExtnOpts.Get(); in CBlastOptionsMemento()
94 BlastExtensionOptions* m_ExtnOpts; member in CBlastOptionsMemento
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| H A D | blast_options_local_priv.cpp | 56 m_ExtnOpts.Reset((BlastExtensionOptions*)calloc(1, sizeof(BlastExtensionOptions))); in BEGIN_SCOPE()
96 x_Copy_CBlastExtensionOptions(m_ExtnOpts, in x_DoDeepCopy()
97 optsLocal.m_ExtnOpts); in x_DoDeepCopy()
378 if (BLAST_ValidateOptions(GetProgramType(), m_ExtnOpts, in Validate()
406 m_ExtnOpts.DebugDump(ddc, depth); in DebugDump()
528 a = static_cast<void*>( (BlastExtensionOptions*) m_ExtnOpts); in operator ==()
529 b = static_cast<void*>( (BlastExtensionOptions*) rhs.m_ExtnOpts); in operator ==()
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| H A D | traceback_stage.cpp | 219 m_OptsMemento->m_ExtnOpts, in Run()
238 m_OptsMemento->m_ExtnOpts, in Run()
322 m_OptsMemento->m_ExtnOpts, in RunSimple()
341 m_OptsMemento->m_ExtnOpts, in RunSimple()
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| H A D | prelim_search_runner.hpp | 79 m_OptsMemento->m_ExtnOpts, in operator ()()
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| H A D | prelim_stage.cpp | 336 opts_memento->m_ExtnOpts, in ComputeBlastHSPResults()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/ |
| H A D | blastextend_unit_test.cpp | 87 BlastExtensionOptions* m_ExtnOpts; member
92 m_ExtnOpts = NULL; in CBlastExtendTestFixture()
113 BlastExtensionOptionsFree(m_ExtnOpts); in ~CBlastExtendTestFixture()
222 status = BlastExtensionOptionsNew(kCoreProgramType, &m_ExtnOpts, true); in setupStructures()
224 m_ExtnOpts->ePrelimGapExt = eGreedyScoreOnly; in setupStructures()
229 m_ExtnOpts, m_ipScoreBlk, in setupStructures()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/ |
| H A D | blastextend_unit_test.cpp | 87 BlastExtensionOptions* m_ExtnOpts; member
92 m_ExtnOpts = NULL; in CBlastExtendTestFixture()
113 BlastExtensionOptionsFree(m_ExtnOpts); in ~CBlastExtendTestFixture()
222 status = BlastExtensionOptionsNew(kCoreProgramType, &m_ExtnOpts, true); in setupStructures()
224 m_ExtnOpts->ePrelimGapExt = eGreedyScoreOnly; in setupStructures()
229 m_ExtnOpts, m_ipScoreBlk, in setupStructures()
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