NCBI C++ ToolKit
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blastoptions_unit_test.cpp File Reference

Unit tests for the BLAST options. More...

#include <ncbi_pch.hpp>
#include <corelib/test_boost.hpp>
#include <algo/blast/api/bl2seq.hpp>
#include "blast_setup.hpp"
#include "blast_objmgr_priv.hpp"
#include <algo/blast/core/blast_setup.h>
#include "test_objmgr.hpp"
#include <algo/blast/core/hspfilter_besthit.h>
#include <objects/blast/Blast4_parameter.hpp>
#include <objects/blast/Blast4_parameters.hpp>
+ Include dependency graph for blastoptions_unit_test.cpp:

Go to the source code of this file.

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Functions

 USING_SCOPE (blast)
 
 USING_SCOPE (objects)
 
 BOOST_AUTO_TEST_CASE (TestTasksDefinitionsAndDocumentation)
 
 BOOST_AUTO_TEST_CASE (RemoteOptionsTest)
 
 BOOST_AUTO_TEST_CASE (BogusProgramWithCreate)
 
 BOOST_AUTO_TEST_CASE (UnifiedPOptionsTest)
 
 BOOST_AUTO_TEST_CASE (GetSuggestedThresholdTest)
 
 BOOST_AUTO_TEST_CASE (GetSuggestedWindowSizeTest)
 
 BOOST_AUTO_TEST_CASE (GetProteinGapExistenceExtendParamsTest)
 
 BOOST_AUTO_TEST_CASE (GetNucleotideGapExistenceExtendParamsTest)
 
 BOOST_AUTO_TEST_CASE (FilterSetUpOptionsDustTest)
 
 BOOST_AUTO_TEST_CASE (FilterSetUpOptionsSegTest)
 
 BOOST_AUTO_TEST_CASE (FilterSetUpOptionsNULLInput)
 
 BOOST_AUTO_TEST_CASE (OptionsFreeNULLInput)
 
static void s_FillSearchSpace (BlastQueryInfo *query_info, Int8 searchsp)
 
static BlastInitialWordParameters * s_GetInitialWordParameters (EBlastProgramType program_number, BLAST_SequenceBlk *query_blk, BlastQueryInfo *query_info, BlastScoreBlk *sbp, const BlastInitialWordOptions *word_options, int subject_length, const BlastHitSavingParameters *hit_params)
 
 BOOST_AUTO_TEST_CASE (testCalcLinkHSPCutoffs)
 
static BlastScoreBlk * s_FillScoreBlkWithBadKbp (BlastQueryInfo *query_info)
 
 BOOST_AUTO_TEST_CASE (testBadKbpForLinkHSPCutoffs)
 
 BOOST_AUTO_TEST_CASE (testCalcLinkHSPCutoffsSmallDB)
 
 BOOST_AUTO_TEST_CASE (testCalcLinkHSPResetGapProb)
 
 BOOST_AUTO_TEST_CASE (testLargeWordSize)
 
static void MakeSomeInvalidKBP (Blast_KarlinBlk **kbp_array, Int4 num, Int4 good_one, BlastQueryInfo *query_info)
 
 BOOST_AUTO_TEST_CASE (testExtParamNewSomeInvalidKbp)
 
static void MakeSomeValidKBP (Blast_KarlinBlk **kbp_array, Int4 num, BlastQueryInfo *query_info)
 
 BOOST_AUTO_TEST_CASE (testExtensionParamsNew)
 
 BOOST_AUTO_TEST_CASE (testHitSavingParamNewSomeInvalidKbp)
 
 BOOST_AUTO_TEST_CASE (testHitSavingParamNewGappedTblastnLargeSubjectSequence)
 
 BOOST_AUTO_TEST_CASE (testHitSavingParamNewGappedTblastnMidsizeSubjectSequence)
 
 BOOST_AUTO_TEST_CASE (testHitSavingParamUpdateMultipleCalls)
 
 BOOST_AUTO_TEST_CASE (testHitSavingParamNewGappedTblastnSmallSubjectSequence)
 
 BOOST_AUTO_TEST_CASE (testInitialWordParamNewSomeInvalidKbp)
 
 BOOST_AUTO_TEST_CASE (testRemoteFilterString)
 
 BOOST_AUTO_TEST_CASE (testNewFilteringDefaults)
 
 BOOST_AUTO_TEST_CASE (testOptionsDeepCopy)
 

Variables

 USING_NCBI_SCOPE
 

Detailed Description

Unit tests for the BLAST options.

Definition in file blastoptions_unit_test.cpp.

Function Documentation

◆ BOOST_AUTO_TEST_CASE() [1/28]

BOOST_AUTO_TEST_CASE ( BogusProgramWithCreate  )

Definition at line 76 of file blastoptions_unit_test.cpp.

References CBlastOptionsFactory::Create(), and eBlastNotSet.

◆ BOOST_AUTO_TEST_CASE() [2/28]

BOOST_AUTO_TEST_CASE ( FilterSetUpOptionsDustTest  )

Definition at line 235 of file blastoptions_unit_test.cpp.

References SBlastFilterOptions::dustOptions, eDust, NULL, SBlastFilterOptionsFree(), SBlastFilterOptionsNew(), and SBlastFilterOptions::segOptions.

◆ BOOST_AUTO_TEST_CASE() [3/28]

BOOST_AUTO_TEST_CASE ( FilterSetUpOptionsNULLInput  )

Definition at line 261 of file blastoptions_unit_test.cpp.

References eSeg, NULL, and SBlastFilterOptionsNew().

◆ BOOST_AUTO_TEST_CASE() [4/28]

BOOST_AUTO_TEST_CASE ( FilterSetUpOptionsSegTest  )

Definition at line 248 of file blastoptions_unit_test.cpp.

References SBlastFilterOptions::dustOptions, eSeg, NULL, SBlastFilterOptionsFree(), SBlastFilterOptionsNew(), and SBlastFilterOptions::segOptions.

◆ BOOST_AUTO_TEST_CASE() [5/28]

BOOST_AUTO_TEST_CASE ( GetNucleotideGapExistenceExtendParamsTest  )

Definition at line 186 of file blastoptions_unit_test.cpp.

References BLAST_GetNucleotideGapExistenceExtendParams().

◆ BOOST_AUTO_TEST_CASE() [6/28]

BOOST_AUTO_TEST_CASE ( GetProteinGapExistenceExtendParamsTest  )

Definition at line 162 of file blastoptions_unit_test.cpp.

References BLAST_GetProteinGapExistenceExtendParams(), and NULL.

◆ BOOST_AUTO_TEST_CASE() [7/28]

BOOST_AUTO_TEST_CASE ( GetSuggestedThresholdTest  )

Definition at line 94 of file blastoptions_unit_test.cpp.

References BLAST_GetSuggestedThreshold(), BLASTERR_INVALIDPARAM, eBlastTypeBlastn, eBlastTypeBlastp, eBlastTypeBlastx, eBlastTypeTblastn, eBlastTypeTblastx, and NULL.

◆ BOOST_AUTO_TEST_CASE() [8/28]

BOOST_AUTO_TEST_CASE ( GetSuggestedWindowSizeTest  )

Definition at line 134 of file blastoptions_unit_test.cpp.

References BLAST_GetSuggestedWindowSize(), BLASTERR_INVALIDPARAM, eBlastTypeBlastn, eBlastTypeBlastp, eBlastTypeBlastx, NULL, and window_size.

◆ BOOST_AUTO_TEST_CASE() [9/28]

BOOST_AUTO_TEST_CASE ( OptionsFreeNULLInput  )

Definition at line 267 of file blastoptions_unit_test.cpp.

References BlastDatabaseOptionsFree(), BlastEffectiveLengthsOptionsFree(), BlastExtensionOptionsFree(), BlastHitSavingOptionsFree(), BlastInitialWordOptionsFree(), BlastQuerySetUpOptionsFree(), BlastScoringOptionsFree(), LookupTableOptionsFree(), NULL, PSIBlastOptionsFree(), and SBlastFilterOptionsFree().

◆ BOOST_AUTO_TEST_CASE() [10/28]

BOOST_AUTO_TEST_CASE ( RemoteOptionsTest  )

Definition at line 65 of file blastoptions_unit_test.cpp.

References CBlastOptions::eRemote, CBlastOptions::SetDustFiltering(), CBlastOptions::SetFilterString(), CBlastOptions::SetMaskAtHash(), CBlastOptions::SetRepeatFiltering(), CBlastOptions::SetRepeatFilteringDB(), and CBlastOptions::SetSegFiltering().

◆ BOOST_AUTO_TEST_CASE() [11/28]

BOOST_AUTO_TEST_CASE ( testBadKbpForLinkHSPCutoffs  )

Definition at line 442 of file blastoptions_unit_test.cpp.

References BlastExtensionOptionsFree(), BlastExtensionOptionsNew(), BlastHitSavingOptionsFree(), BlastHitSavingOptionsNew(), BlastHitSavingParametersFree(), BlastHitSavingParametersNew(), BlastQueryInfoNew(), BlastScoreBlkFree(), CalculateLinkHSPCutoffs(), calloc(), BlastQueryInfo::contexts, BlastLinkHSPParameters::cutoff_big_gap, BlastInitialWordParameters::cutoff_score_min, BlastLinkHSPParameters::cutoff_small_gap, BlastHitSavingOptions::do_sum_stats, eBlastTypeTblastx, BlastQueryInfo::first_context, BlastQueryInfo::last_context, BlastHitSavingParameters::link_hsp_params, NULL, BlastContextInfo::query_length, BlastContextInfo::query_offset, s_FillScoreBlkWithBadKbp(), s_FillSearchSpace(), and sfree.

◆ BOOST_AUTO_TEST_CASE() [12/28]

BOOST_AUTO_TEST_CASE ( testCalcLinkHSPCutoffs  )

Definition at line 327 of file blastoptions_unit_test.cpp.

References BLAST_FillScoringOptions(), BlastExtensionOptionsFree(), BlastExtensionOptionsNew(), BlastFindMatrixPath(), BlastHitSavingOptionsFree(), BlastHitSavingOptionsNew(), BlastHitSavingParametersFree(), BlastHitSavingParametersNew(), BlastInitialWordOptionsFree(), BlastInitialWordOptionsNew(), BlastInitialWordParametersFree(), BlastScoreBlkFree(), BlastScoringOptionsFree(), BlastScoringOptionsNew(), BlastSetup_ScoreBlkInit(), CalculateLinkHSPCutoffs(), BlastLinkHSPParameters::cutoff_big_gap, BlastLinkHSPParameters::cutoff_small_gap, BlastHitSavingOptions::do_sum_stats, eBlastp, eBlastTypeBlastp, eNa_strand_both, FALSE, BlastScoringOptions::gapped_calculation, CBlastOptionsHandle::GetOptions(), CBl2Seq::GetOptionsHandle(), CBlastOptions::GetProgramType(), CBl2Seq::GetQueries(), CBlastOptions::GetStrandOption(), CTestObjMgr::Instance(), ITERATE, BlastHitSavingParameters::link_hsp_params, NULL, prog, s_FillSearchSpace(), s_GetInitialWordParameters(), SetupQueries(), and SetupQueryInfo().

◆ BOOST_AUTO_TEST_CASE() [13/28]

BOOST_AUTO_TEST_CASE ( testCalcLinkHSPCutoffsSmallDB  )

Definition at line 496 of file blastoptions_unit_test.cpp.

References BLAST_FillScoringOptions(), BlastExtensionOptionsFree(), BlastExtensionOptionsNew(), BlastFindMatrixPath(), BlastHitSavingOptionsFree(), BlastHitSavingOptionsNew(), BlastHitSavingParametersFree(), BlastHitSavingParametersNew(), BlastInitialWordOptionsFree(), BlastInitialWordOptionsNew(), BlastInitialWordParametersFree(), BlastScoreBlkFree(), BlastScoringOptionsFree(), BlastScoringOptionsNew(), BlastSetup_ScoreBlkInit(), CalculateLinkHSPCutoffs(), BlastLinkHSPParameters::cutoff_big_gap, BlastLinkHSPParameters::cutoff_small_gap, eBlastp, eBlastTypeBlastp, eNa_strand_both, FALSE, BlastScoringOptions::gapped_calculation, CBlastOptionsHandle::GetOptions(), CBl2Seq::GetOptionsHandle(), CBlastOptions::GetProgramType(), CBl2Seq::GetQueries(), CBlastOptions::GetStrandOption(), CTestObjMgr::Instance(), ITERATE, BlastHitSavingParameters::link_hsp_params, NULL, prog, s_FillSearchSpace(), s_GetInitialWordParameters(), SetupQueries(), and SetupQueryInfo().

◆ BOOST_AUTO_TEST_CASE() [14/28]

BOOST_AUTO_TEST_CASE ( testCalcLinkHSPResetGapProb  )

Definition at line 584 of file blastoptions_unit_test.cpp.

References BLAST_FillScoringOptions(), BlastExtensionOptionsFree(), BlastExtensionOptionsNew(), BlastFindMatrixPath(), BlastHitSavingOptionsFree(), BlastHitSavingOptionsNew(), BlastHitSavingParametersFree(), BlastHitSavingParametersNew(), BlastInitialWordOptionsFree(), BlastInitialWordOptionsNew(), BlastInitialWordParametersFree(), BlastScoreBlkFree(), BlastScoringOptionsFree(), BlastScoringOptionsNew(), BlastSequenceBlkFree(), BlastSetup_ScoreBlkInit(), CalculateLinkHSPCutoffs(), BlastLinkHSPParameters::cutoff_big_gap, BlastLinkHSPParameters::cutoff_small_gap, BlastHitSavingOptions::do_sum_stats, eBlastp, eBlastTypeBlastp, eNa_strand_both, FALSE, BlastLinkHSPParameters::gap_decay_rate, BlastLinkHSPParameters::gap_prob, BlastScoringOptions::gapped_calculation, CBlastOptionsHandle::GetOptions(), CBl2Seq::GetOptionsHandle(), CBlastOptions::GetProgramType(), CBl2Seq::GetQueries(), CBlastOptions::GetStrandOption(), CTestObjMgr::Instance(), ITERATE, BlastHitSavingParameters::link_hsp_params, NULL, prog, s_FillSearchSpace(), s_GetInitialWordParameters(), SetupQueries(), and SetupQueryInfo().

◆ BOOST_AUTO_TEST_CASE() [15/28]

BOOST_AUTO_TEST_CASE ( testExtensionParamsNew  )

Definition at line 797 of file blastoptions_unit_test.cpp.

References Blast_KarlinBlkFree(), BlastExtensionOptionsFree(), BlastExtensionOptionsNew(), BlastExtensionParametersFree(), BlastExtensionParametersNew(), BlastQueryInfoNew(), calloc(), eBlastTypeBlastn, eBlastTypeBlastx, FALSE, BlastQueryInfo::first_context, BlastExtensionOptions::gap_x_dropoff, BlastExtensionParameters::gap_x_dropoff, BlastExtensionOptions::gap_x_dropoff_final, BlastExtensionParameters::gap_x_dropoff_final, CBlastQueryInfo::Get(), BlastScoreBlk::kbp, BlastScoreBlk::kbp_gap, MakeSomeValidKBP(), BlastScoreBlk::matrix_only_scoring, NULL, BlastScoreBlk::scale_factor, and sfree.

◆ BOOST_AUTO_TEST_CASE() [16/28]

BOOST_AUTO_TEST_CASE ( testExtParamNewSomeInvalidKbp  )

Definition at line 733 of file blastoptions_unit_test.cpp.

References Blast_KarlinBlkFree(), BlastExtensionOptionsFree(), BlastExtensionOptionsNew(), BlastExtensionParametersFree(), BlastExtensionParametersNew(), BlastQueryInfoNew(), calloc(), eBlastTypeBlastn, eBlastTypeBlastx, BlastQueryInfo::first_context, BlastExtensionOptions::gap_x_dropoff, BlastExtensionParameters::gap_x_dropoff, BlastExtensionOptions::gap_x_dropoff_final, BlastExtensionParameters::gap_x_dropoff_final, BlastScoreBlk::kbp, BlastScoreBlk::kbp_gap, MakeSomeInvalidKBP(), BlastScoreBlk::matrix_only_scoring, NULL, BlastScoreBlk::scale_factor, and sfree.

◆ BOOST_AUTO_TEST_CASE() [17/28]

BOOST_AUTO_TEST_CASE ( testHitSavingParamNewGappedTblastnLargeSubjectSequence  )

Definition at line 937 of file blastoptions_unit_test.cpp.

References BLAST_FillScoringOptions(), BlastExtensionOptionsFree(), BlastExtensionOptionsNew(), BlastFindMatrixPath(), BlastHitSavingOptionsFree(), BlastHitSavingOptionsNew(), BlastHitSavingParametersFree(), BlastHitSavingParametersNew(), BlastScoreBlkFree(), BlastScoringOptionsFree(), BlastScoringOptionsNew(), BlastSetup_ScoreBlkInit(), CBlastOptionsFactory::Create(), BlastHitSavingParameters::cutoff_score_min, eBlastTypeTblastn, eNa_strand_both, eTblastn, FALSE, BlastScoringOptions::gapped_calculation, CBlastOptionsHandle::GetOptions(), CBlastOptions::GetProgramType(), CBlastOptions::GetStrandOption(), CTestObjMgr::Instance(), ITERATE, NULL, BlastHitSavingParameters::prelim_evalue, prog, s_FillSearchSpace(), SetupQueries(), and SetupQueryInfo().

◆ BOOST_AUTO_TEST_CASE() [18/28]

BOOST_AUTO_TEST_CASE ( testHitSavingParamNewGappedTblastnMidsizeSubjectSequence  )

Definition at line 1008 of file blastoptions_unit_test.cpp.

References BLAST_FillScoringOptions(), BlastExtensionOptionsFree(), BlastExtensionOptionsNew(), BlastFindMatrixPath(), BlastHitSavingOptionsFree(), BlastHitSavingOptionsNew(), BlastHitSavingParametersFree(), BlastHitSavingParametersNew(), BlastScoreBlkFree(), BlastScoringOptionsFree(), BlastScoringOptionsNew(), BlastSetup_ScoreBlkInit(), CBlastOptionsFactory::Create(), BlastHitSavingParameters::cutoff_score_min, eBlastTypeTblastn, eNa_strand_both, eTblastn, FALSE, BlastScoringOptions::gapped_calculation, CBlastOptionsHandle::GetOptions(), CBlastOptions::GetProgramType(), CBlastOptions::GetStrandOption(), CTestObjMgr::Instance(), ITERATE, NULL, BlastHitSavingParameters::prelim_evalue, prog, s_FillSearchSpace(), SetupQueries(), and SetupQueryInfo().

◆ BOOST_AUTO_TEST_CASE() [19/28]

BOOST_AUTO_TEST_CASE ( testHitSavingParamNewGappedTblastnSmallSubjectSequence  )

Definition at line 1164 of file blastoptions_unit_test.cpp.

References BLAST_FillScoringOptions(), BlastExtensionOptionsFree(), BlastExtensionOptionsNew(), BlastFindMatrixPath(), BlastHitSavingOptionsFree(), BlastHitSavingOptionsNew(), BlastHitSavingParametersFree(), BlastHitSavingParametersNew(), BlastScoreBlkFree(), BlastScoringOptionsFree(), BlastScoringOptionsNew(), BlastSetup_ScoreBlkInit(), CBlastOptionsFactory::Create(), BlastGappedCutoffs::cutoff_score, BlastGappedCutoffs::cutoff_score_max, BlastHitSavingParameters::cutoff_score_min, BlastHitSavingParameters::cutoffs, eBlastTypeTblastn, eNa_strand_both, eTblastn, FALSE, BlastScoringOptions::gapped_calculation, CBlastOptionsHandle::GetOptions(), CBlastOptions::GetProgramType(), CBlastOptions::GetStrandOption(), CTestObjMgr::Instance(), ITERATE, NULL, prog, s_FillSearchSpace(), SetupQueries(), and SetupQueryInfo().

◆ BOOST_AUTO_TEST_CASE() [20/28]

BOOST_AUTO_TEST_CASE ( testHitSavingParamNewSomeInvalidKbp  )

Definition at line 851 of file blastoptions_unit_test.cpp.

References BLAST_FillScoringOptions(), BlastExtensionOptionsFree(), BlastExtensionOptionsNew(), BlastFindMatrixPath(), BlastHitSavingOptionsFree(), BlastHitSavingOptionsNew(), BlastHitSavingParametersFree(), BlastHitSavingParametersNew(), BlastScoreBlkFree(), BlastScoringOptionsFree(), BlastScoringOptionsNew(), BlastSetup_ScoreBlkInit(), CBlastOptionsFactory::Create(), BlastHitSavingParameters::cutoff_score_min, eBlastn, eBlastTypeBlastn, eNa_strand_both, FALSE, BlastScoringOptions::gapped_calculation, CBlastQueryInfo::Get(), CBlastOptionsHandle::GetOptions(), CBlastOptions::GetProgramType(), CBlastOptions::GetStrandOption(), CTestObjMgr::Instance(), ITERATE, BlastScoreBlk::kbp, BlastScoreBlk::kbp_gap, BlastQueryInfo::last_context, MakeSomeInvalidKBP(), NULL, prog, s_FillSearchSpace(), SetupQueries(), and SetupQueryInfo().

◆ BOOST_AUTO_TEST_CASE() [21/28]

BOOST_AUTO_TEST_CASE ( testHitSavingParamUpdateMultipleCalls  )

Definition at line 1076 of file blastoptions_unit_test.cpp.

References BLAST_FillScoringOptions(), BlastExtensionOptionsFree(), BlastExtensionOptionsNew(), BlastFindMatrixPath(), BlastHitSavingOptionsFree(), BlastHitSavingOptionsNew(), BlastHitSavingParametersFree(), BlastHitSavingParametersNew(), BlastHitSavingParametersUpdate(), BlastScoreBlkFree(), BlastScoringOptionsFree(), BlastScoringOptionsNew(), BlastSetup_ScoreBlkInit(), CBlastOptionsFactory::Create(), BlastGappedCutoffs::cutoff_score, BlastGappedCutoffs::cutoff_score_max, BlastHitSavingParameters::cutoff_score_min, BlastHitSavingParameters::cutoffs, eBlastTypeTblastn, eNa_strand_both, eTblastn, FALSE, BlastScoringOptions::gapped_calculation, CBlastOptionsHandle::GetMaxHspsPerSubject(), CBlastOptionsHandle::GetOptions(), CBlastOptions::GetProgramType(), CBlastOptionsHandle::GetQueryCovHspPerc(), CBlastOptions::GetStrandOption(), CTestObjMgr::Instance(), ITERATE, BlastHitSavingOptions::max_hsps_per_subject, NULL, BlastHitSavingParameters::prelim_evalue, prog, BlastHitSavingOptions::query_cov_hsp_perc, s_FillSearchSpace(), CBlastOptionsHandle::SetMaxHspsPerSubject(), CBlastOptionsHandle::SetQueryCovHspPerc(), SetupQueries(), and SetupQueryInfo().

◆ BOOST_AUTO_TEST_CASE() [22/28]

BOOST_AUTO_TEST_CASE ( testInitialWordParamNewSomeInvalidKbp  )

Definition at line 1232 of file blastoptions_unit_test.cpp.

References BLAST_FillScoringOptions(), BlastExtensionOptionsFree(), BlastExtensionOptionsNew(), BlastFindMatrixPath(), BlastHitSavingOptionsFree(), BlastHitSavingOptionsNew(), BlastHitSavingParametersFree(), BlastHitSavingParametersNew(), BlastInitialWordOptionsFree(), BlastInitialWordOptionsNew(), BlastInitialWordParametersFree(), BlastScoreBlkFree(), BlastScoringOptionsFree(), BlastScoringOptionsNew(), BlastSetup_ScoreBlkInit(), CBlastOptionsFactory::Create(), BlastInitialWordParameters::cutoff_score_min, BlastHitSavingParameters::cutoff_score_min, eBlastn, eBlastTypeBlastn, eNa_strand_both, FALSE, BlastScoringOptions::gapped_calculation, CBlastQueryInfo::Get(), CBlastOptionsHandle::GetOptions(), CBlastOptions::GetProgramType(), CBlastOptions::GetStrandOption(), CTestObjMgr::Instance(), ITERATE, BlastScoreBlk::kbp, BlastScoreBlk::kbp_gap, BlastQueryInfo::last_context, MakeSomeInvalidKBP(), NULL, prog, s_FillSearchSpace(), s_GetInitialWordParameters(), SetupQueries(), SetupQueryInfo(), BlastInitialWordOptions::x_dropoff, and BlastInitialWordParameters::x_dropoff_max.

◆ BOOST_AUTO_TEST_CASE() [23/28]

BOOST_AUTO_TEST_CASE ( testLargeWordSize  )

Definition at line 680 of file blastoptions_unit_test.cpp.

References BLAST_FillLookupTableOptions(), BlastInitialWordOptionsNew(), eBlastTypeBlastn, FALSE, LookupTableOptionsNew(), and LookupTableOptions::word_size.

◆ BOOST_AUTO_TEST_CASE() [24/28]

BOOST_AUTO_TEST_CASE ( testNewFilteringDefaults  )

Definition at line 1362 of file blastoptions_unit_test.cpp.

References CBlastOptionsFactory::Create(), eBlastp, eTblastn, CBlastOptionsHandle::GetFilterString(), CRef< C, Locker >::NotEmpty(), and sfree.

◆ BOOST_AUTO_TEST_CASE() [25/28]

BOOST_AUTO_TEST_CASE ( testOptionsDeepCopy  )

Definition at line 1379 of file blastoptions_unit_test.cpp.

References CBlastOptions::Clone(), CBlastOptionsFactory::Create(), eBlastp, CBlastOptions::GetBestHitOverhang(), CBlastOptions::GetBestHitScoreEdge(), CBlastOptions::GetDbLength(), CBlastOptions::GetFilterString(), CBlastOptionsHandle::GetOptions(), CBlastOptions::GetPHIPattern(), CBlastOptions::GetQueryCovHspPerc(), kBestHit_OverhangDflt, kBestHit_ScoreEdgeDflt, CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), CBlastOptions::SetBestHitOverhang(), CBlastOptions::SetBestHitScoreEdge(), CBlastOptionsHandle::SetDbLength(), CBlastOptionsHandle::SetFilterString(), CBlastOptionsHandle::SetOptions(), CBlastOptions::SetPHIPattern(), and CBlastOptions::SetQueryCovHspPerc().

◆ BOOST_AUTO_TEST_CASE() [26/28]

BOOST_AUTO_TEST_CASE ( testRemoteFilterString  )

Definition at line 1324 of file blastoptions_unit_test.cpp.

References eBlastn, eBlastp, eBlastx, CBlastOptions::eRemote, eTblastn, eTblastx, CBlastOptions::GetBlast4AlgoOpts(), CBlastOptions::SetFilterString(), and CBlastOptions::SetProgram().

◆ BOOST_AUTO_TEST_CASE() [27/28]

BOOST_AUTO_TEST_CASE ( TestTasksDefinitionsAndDocumentation  )

Definition at line 53 of file blastoptions_unit_test.cpp.

References CBlastOptionsFactory::CreateTask(), CBlastOptionsFactory::GetDocumentation(), CBlastOptionsFactory::GetTasks(), ITERATE, and CRef< C, Locker >::Reset().

◆ BOOST_AUTO_TEST_CASE() [28/28]

BOOST_AUTO_TEST_CASE ( UnifiedPOptionsTest  )

Definition at line 83 of file blastoptions_unit_test.cpp.

References CBlastOptions::GetUnifiedP(), and CBlastOptions::SetUnifiedP().

◆ MakeSomeInvalidKBP()

static void MakeSomeInvalidKBP ( Blast_KarlinBlk **  kbp_array,
Int4  num,
Int4  good_one,
BlastQueryInfo *  query_info 
)
static

Definition at line 697 of file blastoptions_unit_test.cpp.

References Blast_KarlinBlkFree(), Blast_KarlinBlkNew(), BlastQueryInfo::contexts, FALSE, Blast_KarlinBlk::H, BlastContextInfo::is_valid, Blast_KarlinBlk::K, Blast_KarlinBlk::Lambda, Blast_KarlinBlk::logK, NULL, and TRUE.

Referenced by BOOST_AUTO_TEST_CASE().

◆ MakeSomeValidKBP()

static void MakeSomeValidKBP ( Blast_KarlinBlk **  kbp_array,
Int4  num,
BlastQueryInfo *  query_info 
)
static

Definition at line 779 of file blastoptions_unit_test.cpp.

References Blast_KarlinBlkFree(), Blast_KarlinBlkNew(), BlastQueryInfo::contexts, Blast_KarlinBlk::H, BlastContextInfo::is_valid, Blast_KarlinBlk::K, Blast_KarlinBlk::Lambda, Blast_KarlinBlk::logK, NULL, and TRUE.

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_FillScoreBlkWithBadKbp()

static BlastScoreBlk* s_FillScoreBlkWithBadKbp ( BlastQueryInfo *  query_info)
static

Definition at line 416 of file blastoptions_unit_test.cpp.

References Blast_KarlinBlkNew(), BLASTAA_SEQ_CODE, BlastScoreBlkNew(), BlastQueryInfo::contexts, FALSE, Blast_KarlinBlk::H, BlastContextInfo::is_valid, Blast_KarlinBlk::K, BlastScoreBlk::kbp, BlastScoreBlk::kbp_std, Blast_KarlinBlk::Lambda, Blast_KarlinBlk::logK, and TRUE.

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_FillSearchSpace()

static void s_FillSearchSpace ( BlastQueryInfo *  query_info,
Int8  searchsp 
)
static

Definition at line 283 of file blastoptions_unit_test.cpp.

References BlastQueryInfo::contexts, BlastContextInfo::eff_searchsp, BlastQueryInfo::first_context, i, and BlastContextInfo::query_length.

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_GetInitialWordParameters()

static BlastInitialWordParameters* s_GetInitialWordParameters ( EBlastProgramType  program_number,
BLAST_SequenceBlk *  query_blk,
BlastQueryInfo *  query_info,
BlastScoreBlk *  sbp,
const BlastInitialWordOptions *  word_options,
int  subject_length,
const BlastHitSavingParameters *  hit_params 
)
static

Definition at line 294 of file blastoptions_unit_test.cpp.

References BlastInitialWordParametersNew(), BlastQuerySetUpOptionsFree(), BlastQuerySetUpOptionsNew(), BlastSeqLocFree(), BlastSeqLocNew(), BlastQueryInfo::contexts, LookupTableOptionsFree(), LookupTableOptionsNew(), LookupTableWrapFree(), LookupTableWrapInit(), NULL, and BlastContextInfo::query_length.

Referenced by BOOST_AUTO_TEST_CASE().

◆ USING_SCOPE() [1/2]

USING_SCOPE ( blast  )

◆ USING_SCOPE() [2/2]

USING_SCOPE ( objects  )

Variable Documentation

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 47 of file blastoptions_unit_test.cpp.

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