NCBI C++ ToolKit
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#include <ncbi_pch.hpp>
#include <corelib/test_boost.hpp>
#include <corelib/ncbitime.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <objmgr/util/sequence.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Std_seg.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqalign/Score.hpp>
#include <serial/serial.hpp>
#include <serial/iterator.hpp>
#include <serial/objostr.hpp>
#include <algo/blast/api/blast_nucl_options.hpp>
#include <algo/blast/api/disc_nucl_options.hpp>
#include <algo/blast/api/seqsrc_multiseq.hpp>
#include <algo/blast/api/seqsrc_seqdb.hpp>
#include <algo/blast/api/local_blast.hpp>
#include <algo/blast/api/objmgr_query_data.hpp>
#include <algo/blast/api/prelim_stage.hpp>
#include <blast_objmgr_priv.hpp>
#include <algo/blast/core/blast_options.h>
#include <algo/blast/core/blast_engine.h>
#include <algo/blast/core/blast_gapalign.h>
#include <algo/blast/core/blast_traceback.h>
#include <algo/blast/core/blast_encoding.h>
#include <algo/blast/core/blast_setup.h>
#include <algo/blast/core/blast_hspstream.h>
#include <algo/blast/api/repeats_filter.hpp>
#include "test_objmgr.hpp"
#include "blast_test_util.hpp"
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Classes | |
struct | BlastEngineTestFixture |
Functions | |
void | testLongMatchDiagnostics (BlastDiagnostics *diagnostics) |
void | testShortMatchDiagnostics (BlastDiagnostics *diagnostics) |
BOOST_AUTO_TEST_CASE (testTBLASTNLongMatchBlastEngine) | |
BOOST_AUTO_TEST_CASE (testTBLASTNShortMatchBlastEngine) | |
BOOST_AUTO_TEST_CASE (testBlastnWithLargeWordSize) | |
BOOST_AUTO_TEST_CASE (testBlastnWithRepeatsFiltering) | |
BOOST_AUTO_TEST_CASE (testDiscMegaBlastPartialRun) | |
BOOST_AUTO_TEST_CASE (testBlastpPrelimSearch) | |
BOOST_AUTO_TEST_CASE (testGappedOffsets) | |
BOOST_AUTO_TEST_CASE | ( | testBlastnWithLargeWordSize | ) |
Definition at line 283 of file blastengine_unit_test.cpp.
References BlastSeqSrcFree(), CBlastPrelimSearch::ComputeBlastHSPResults(), eBlastTypeBlastn, GI_CONST, BlastHSPList::hspcnt, SInternalData::m_HspStream, MultiSeqBlastSeqSrcInit(), results, CBlastPrelimSearch::Run(), CBlastOptionsHandle::SetOptions(), and CBlastNucleotideOptionsHandle::SetWordSize().
BOOST_AUTO_TEST_CASE | ( | testBlastnWithRepeatsFiltering | ) |
Definition at line 317 of file blastengine_unit_test.cpp.
References Blast_FindRepeatFilterLoc(), BlastSeqSrcFree(), CBlastPrelimSearch::ComputeBlastHSPResults(), eBlastTypeBlastn, GI_CONST, BlastHSPList::hspcnt, SInternalData::m_HspStream, MultiSeqBlastSeqSrcInit(), results, CBlastPrelimSearch::Run(), CBlastOptionsHandle::SetEvalueThreshold(), CBlastOptionsHandle::SetOptions(), CBlastNucleotideOptionsHandle::SetRepeatFiltering(), and CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults().
BOOST_AUTO_TEST_CASE | ( | testBlastpPrelimSearch | ) |
Definition at line 423 of file blastengine_unit_test.cpp.
References CScope::AddDefaults(), BlastSeqSrcFree(), CBlastPrelimSearch::ComputeBlastHSPResults(), CBlastOptionsFactory::Create(), eBlastp, BlastSeg::end, GI_CONST, BlastHSPList::hsp_array, CTestObjMgr::Instance(), SInternalData::m_HspStream, BlastHSP::num_ident, BlastSeg::offset, BlastHSPList::oid, BlastHSP::query, results, CBlastPrelimSearch::Run(), BlastHSP::score, SeqDbBlastSeqSrcInit(), CBlastOptions::SetFilterString(), CBlastOptionsHandle::SetOptions(), CSeq_loc::SetWhole(), and BlastHSP::subject.
BOOST_AUTO_TEST_CASE | ( | testDiscMegaBlastPartialRun | ) |
Definition at line 356 of file blastengine_unit_test.cpp.
References CScope::AddDefaults(), CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Gi, CSearchDatabase::eBlastDbIsNucleotide, CSeq_align_set_Base::Get(), CTextseq_id_Base::GetAccession(), CSeq_id_Base::GetDdbj(), CSeq_id_Base::GetGi(), CSeq_align::GetNamedScore(), CSeq_align::GetSeq_id(), CTextseq_id_Base::GetVersion(), GI_CONST, CTestObjMgr::Instance(), CSeq_id::PreferAccessionOverGi(), results, CLocalBlast::Run(), CBlastNucleotideOptionsHandle::SetGapExtensionCost(), CBlastNucleotideOptionsHandle::SetGapOpeningCost(), CBlastOptionsHandle::SetMaskAtHash(), CBlastNucleotideOptionsHandle::SetMatchReward(), CBlastNucleotideOptionsHandle::SetMismatchPenalty(), CBlastOptionsHandle::SetPercentIdentity(), CSeq_loc::SetWhole(), CBlastOptionsHandle::SetWindowSize(), and CSeq_id_Base::Which().
BOOST_AUTO_TEST_CASE | ( | testGappedOffsets | ) |
Definition at line 487 of file blastengine_unit_test.cpp.
References BLAST_FillScoringOptions(), BLAST_GAP_EXTN_PROT, BLAST_GAP_OPEN_PROT, Blast_HSPNew(), Blast_ScoreBlkMatrixInit(), BLASTAA_SEQ_CODE, BlastGetOffsetsForGappedAlignment(), BlastScoreBlkNew(), BlastScoringOptionsFree(), BlastScoringOptionsNew(), eBlastTypeBlastp, BlastSeg::end, FALSE, NULL, BlastSeg::offset, BlastHSP::query, query, BlastHSP::score, BlastHSP::subject, and subject.
BOOST_AUTO_TEST_CASE | ( | testTBLASTNLongMatchBlastEngine | ) |
Definition at line 148 of file blastengine_unit_test.cpp.
References Blast_HSPListIsSortedByScore(), Blast_HSPListSortByEvalue(), BlastSeqSrcFree(), CBlastPrelimSearch::ComputeBlastHSPResults(), CBlastOptionsFactory::Create(), eBlastTypeTblastn, BlastSeg::end, eTblastn, BlastHSP::evalue, fabs, GI_CONST, BlastHSPList::hsp_array, BlastHSPList::hspcnt, kEffectiveSearchSpace, SInternalData::m_Diagnostics, SInternalData::m_HspStream, MultiSeqBlastSeqSrcInit(), BlastSeg::offset, BlastHSP::query, results, CBlastPrelimSearch::Run(), BlastHSP::score, CBlastOptionsHandle::SetEffectiveSearchSpace(), CBlastOptionsHandle::SetFilterString(), CBlastOptionsHandle::SetOptions(), and testLongMatchDiagnostics().
BOOST_AUTO_TEST_CASE | ( | testTBLASTNShortMatchBlastEngine | ) |
Definition at line 220 of file blastengine_unit_test.cpp.
References Blast_HSPListIsSortedByScore(), Blast_HSPListSortByEvalue(), BlastSeqSrcFree(), CBlastPrelimSearch::ComputeBlastHSPResults(), CBlastOptionsFactory::Create(), eBlastTypeTblastn, BlastSeg::end, eTblastn, BlastHSP::evalue, fabs, GI_CONST, BlastHSPList::hsp_array, BlastHSPList::hspcnt, kEffectiveSearchSpace, SInternalData::m_Diagnostics, SInternalData::m_HspStream, MultiSeqBlastSeqSrcInit(), BlastSeg::offset, BlastHSP::query, results, CBlastPrelimSearch::Run(), BlastHSP::score, CBlastOptionsHandle::SetEffectiveSearchSpace(), CBlastOptionsHandle::SetFilterString(), CBlastOptionsHandle::SetOptions(), and testShortMatchDiagnostics().
void testLongMatchDiagnostics | ( | BlastDiagnostics * | diagnostics | ) |
Definition at line 110 of file blastengine_unit_test.cpp.
References BlastGappedStats::extensions, BlastGappedStats::good_extensions, BlastUngappedStats::good_init_extends, BlastUngappedStats::init_extends, and BlastUngappedStats::lookup_hits.
Referenced by BOOST_AUTO_TEST_CASE().
void testShortMatchDiagnostics | ( | BlastDiagnostics * | diagnostics | ) |
Definition at line 124 of file blastengine_unit_test.cpp.
References BlastGappedStats::extensions, BlastDiagnostics::gapped_stat, BlastGappedStats::good_extensions, BlastUngappedStats::good_init_extends, BlastUngappedStats::init_extends, BlastUngappedStats::lookup_hits, and BlastDiagnostics::ungapped_stat.
Referenced by BOOST_AUTO_TEST_CASE().