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 <serial/serial.hpp>
#include <serial/iterator.hpp>
#include <serial/objostr.hpp>
#include <algo/blast/api/bl2seq.hpp>
#include <algo/blast/api/seqsrc_multiseq.hpp>
#include <blast_objmgr_priv.hpp>
#include <algo/blast/core/blast_setup.h>
#include <algo/blast/core/blast_gapalign.h>
#include <algo/blast/core/blast_traceback.h>
#include <algo/blast/api/blast_options_handle.hpp>
#include <algo/blast/api/blast_prot_options.hpp>
#include <algo/blast/api/blastx_options.hpp>
#include <algo/blast/api/tblastn_options.hpp>
#include <algo/blast/api/blast_nucl_options.hpp>
#include <algo/blast/api/disc_nucl_options.hpp>
#include <algo/blast/core/blast_lookup.h>
#include <algo/blast/core/lookup_util.h>
#include <algo/blast/core/blast_hspstream.h>
#include <algo/blast/core/hspfilter_collector.h>
#include <algo/blast/api/seqsrc_seqdb.hpp>
#include <algo/blast/api/blast_types.hpp>
#include <algo/blast/api/query_data.hpp>
#include <algo/blast/api/objmgr_query_data.hpp>
#include <algo/blast/api/setup_factory.hpp>
#include <algo/blast/api/traceback_stage.hpp>
#include <algo/blast/api/blast_seqinfosrc.hpp>
#include <algo/blast/api/seqinfosrc_seqdb.hpp>
#include <common/test_data_path.h>
#include <corelib/ncbifile.hpp>
#include <algorithm>
#include "test_objmgr.hpp"
#include "blast_test_util.hpp"
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Classes | |
class | CTracebackTestFixture |
Functions | |
BOOST_AUTO_TEST_CASE (testHSPUpdateWithTraceback) | |
BOOST_AUTO_TEST_CASE (testBLASTNTraceBack) | |
BOOST_AUTO_TEST_CASE (testBLASTNTraceBackLargeXDrop) | |
BOOST_AUTO_TEST_CASE (testBLASTPTraceBack) | |
BOOST_AUTO_TEST_CASE (testTBLASTNTraceBack) | |
BOOST_AUTO_TEST_CASE (testNoHSPEvalueCutoffBeforeLink) | |
BOOST_AUTO_TEST_CASE (testFilterBlastResults_QueryCov) | |
BOOST_AUTO_TEST_CASE (testFilterBlastResults_MaxHsps) | |
BlastHSPList * | s_GetHSPList (int num_hsps, int oid, int len, int range_len) |
BOOST_AUTO_TEST_CASE (testUnit_TestsDataPath) | |
BOOST_AUTO_TEST_CASE (testSetupPartialFetching) | |
BOOST_AUTO_TEST_CASE (testPartialFetchingMT) | |
BOOST_AUTO_TEST_CASE | ( | testBLASTNTraceBack | ) |
Definition at line 210 of file traceback_unit_test.cpp.
References BlastHSPList::allocated, Blast_HSPListSortByScore(), Blast_HSPResultsFree(), BlastHSPStreamFree(), BlastHSPStreamWrite(), BlastSeqSrcFree(), BlastSeqSrcGetSeqLen(), calloc(), TestUtil::CheckForBlastSeqSrcErrors(), BlastHSP::context, context, BlastHSPList::do_not_reallocate, eBlastn, eNa_strand_both, BlastSeg::end, FALSE, BlastSeg::frame, BlastSeg::gapped_start, CBlastOptionsHandle::GetOptions(), CBl2Seq::GetOptionsHandle(), CBlastOptions::GetProgramType(), CBl2Seq::GetQueries(), CBlastOptions::GetStrandOption(), CBl2Seq::GetSubjects(), BlastHSPList::hsp_array, BlastHSPList::hsp_max, BlastHSPList::hspcnt, BlastHitList::hsplist_array, CTestObjMgr::Instance(), ITERATE, malloc(), MultiSeqBlastSeqSrcInit(), NULL, BlastHSP::num_ident, BlastSeg::offset, BlastHSPList::oid, prog, BlastHSP::query, results, BlastHSP::score, CBlastOptionsHandle::SetDbLength(), CBl2Seq::SetOptionsHandle(), SetupQueries(), SetupQueryInfo(), and BlastHSP::subject.
BOOST_AUTO_TEST_CASE | ( | testBLASTNTraceBackLargeXDrop | ) |
Definition at line 340 of file traceback_unit_test.cpp.
References BlastHSPList::allocated, Blast_HSPListSortByScore(), Blast_HSPResultsFree(), BlastHSPStreamFree(), BlastHSPStreamWrite(), BlastSeqSrcFree(), BlastSeqSrcGetSeqLen(), calloc(), TestUtil::CheckForBlastSeqSrcErrors(), BlastHSP::context, context, BlastHSPList::do_not_reallocate, eNa_strand_both, BlastSeg::end, FALSE, BlastSeg::frame, BlastSeg::gapped_start, CBlastOptionsHandle::GetOptions(), CBl2Seq::GetOptionsHandle(), CBlastOptions::GetProgramType(), CBl2Seq::GetQueries(), CBlastOptions::GetStrandOption(), CBl2Seq::GetSubjects(), BlastHSPList::hsp_array, BlastHSPList::hsp_max, BlastHSPList::hspcnt, BlastHitList::hsplist_array, CTestObjMgr::Instance(), ITERATE, malloc(), MultiSeqBlastSeqSrcInit(), NULL, BlastHSP::num_ident, BlastSeg::offset, BlastHSPList::oid, prog, BlastHSP::query, results, BlastHSP::score, CBlastOptionsHandle::SetDbLength(), CBlastOptionsHandle::SetGapXDropoffFinal(), CBlastNucleotideOptionsHandle::SetMatchReward(), CBl2Seq::SetOptionsHandle(), CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults(), SetupQueries(), SetupQueryInfo(), and BlastHSP::subject.
BOOST_AUTO_TEST_CASE | ( | testBLASTPTraceBack | ) |
Definition at line 476 of file traceback_unit_test.cpp.
References BlastHSPList::allocated, Blast_HSPListSortByScore(), Blast_HSPResultsFree(), BlastHSPStreamFree(), BlastHSPStreamWrite(), BlastSeqSrcFree(), BlastSeqSrcGetSeqLen(), calloc(), TestUtil::CheckForBlastSeqSrcErrors(), BlastHSPList::do_not_reallocate, eNa_strand_unknown, BlastSeg::end, FALSE, BlastSeg::gapped_start, CBlastOptionsHandle::GetOptions(), CBl2Seq::GetOptionsHandle(), CBlastOptions::GetProgramType(), CBl2Seq::GetQueries(), CBlastOptions::GetStrandOption(), CBl2Seq::GetSubjects(), BlastHSPList::hsp_array, BlastHSPList::hsp_max, BlastHSPList::hspcnt, BlastHitList::hsplist_array, CTestObjMgr::Instance(), ITERATE, malloc(), MultiSeqBlastSeqSrcInit(), NULL, BlastHSP::num_ident, BlastSeg::offset, BlastHSPList::oid, prog, BlastHSP::query, results, BlastHSP::score, CBlastOptionsHandle::SetDbLength(), CBl2Seq::SetOptionsHandle(), SetupQueries(), SetupQueryInfo(), and BlastHSP::subject.
BOOST_AUTO_TEST_CASE | ( | testFilterBlastResults_MaxHsps | ) |
Definition at line 951 of file traceback_unit_test.cpp.
References BlastHSPList::allocated, Blast_HSPListSortByScore(), Blast_HSPResultsFree(), BlastHSPStreamFree(), BlastHSPStreamWrite(), BlastSeqSrcFree(), BlastSeqSrcGetSeqLen(), calloc(), TestUtil::CheckForBlastSeqSrcErrors(), BlastHSP::context, context, BlastHSPList::do_not_reallocate, eBlastn, eNa_strand_both, BlastSeg::end, FALSE, BlastSeg::frame, BlastSeg::gapped_start, CBlastOptionsHandle::GetOptions(), CBl2Seq::GetOptionsHandle(), CBlastOptions::GetProgramType(), CBl2Seq::GetQueries(), CBlastOptions::GetStrandOption(), CBl2Seq::GetSubjects(), BlastHSPList::hsp_array, BlastHSPList::hsp_max, BlastHSPList::hspcnt, BlastHitList::hsplist_array, CTestObjMgr::Instance(), ITERATE, malloc(), MultiSeqBlastSeqSrcInit(), NULL, BlastSeg::offset, BlastHSPList::oid, prog, BlastHSP::query, results, BlastHSP::score, CBlastOptionsHandle::SetDbLength(), CBlastOptionsHandle::SetMaxHspsPerSubject(), CBl2Seq::SetOptionsHandle(), SetupQueries(), SetupQueryInfo(), and BlastHSP::subject.
BOOST_AUTO_TEST_CASE | ( | testFilterBlastResults_QueryCov | ) |
Definition at line 846 of file traceback_unit_test.cpp.
References BlastHSPList::allocated, Blast_HSPListSortByScore(), Blast_HSPResultsFree(), BlastHSPStreamFree(), BlastHSPStreamWrite(), BlastSeqSrcFree(), BlastSeqSrcGetSeqLen(), calloc(), TestUtil::CheckForBlastSeqSrcErrors(), BlastHSPList::do_not_reallocate, eNa_strand_unknown, BlastSeg::end, FALSE, BlastSeg::gapped_start, CBlastOptionsHandle::GetOptions(), CBl2Seq::GetOptionsHandle(), CBlastOptions::GetProgramType(), CBl2Seq::GetQueries(), CBlastOptions::GetStrandOption(), CBl2Seq::GetSubjects(), BlastHSPList::hsp_array, BlastHSPList::hsp_max, BlastHSPList::hspcnt, BlastHitList::hsplist_array, CTestObjMgr::Instance(), ITERATE, malloc(), MultiSeqBlastSeqSrcInit(), NULL, BlastSeg::offset, BlastHSPList::oid, prog, BlastHSP::query, results, BlastHSP::score, CBlastOptionsHandle::SetDbLength(), CBl2Seq::SetOptionsHandle(), CBlastOptionsHandle::SetQueryCovHspPerc(), SetupQueries(), SetupQueryInfo(), and BlastHSP::subject.
BOOST_AUTO_TEST_CASE | ( | testHSPUpdateWithTraceback | ) |
Definition at line 182 of file traceback_unit_test.cpp.
References BLAST_GapAlignStructFree(), Blast_HSPFree(), Blast_HSPNew(), Blast_HSPUpdateWithTraceback(), calloc(), BlastGapAlignStruct::edit_script, BlastSeg::end, BlastHSP::gap_info, kOffset, NULL, BlastSeg::offset, BlastHSP::query, BlastGapAlignStruct::query_start, BlastGapAlignStruct::query_stop, BlastGapAlignStruct::score, BlastHSP::score, BlastHSP::subject, BlastGapAlignStruct::subject_start, and BlastGapAlignStruct::subject_stop.
BOOST_AUTO_TEST_CASE | ( | testNoHSPEvalueCutoffBeforeLink | ) |
Definition at line 750 of file traceback_unit_test.cpp.
References Blast_HSPListNew(), Blast_HSPListSortByScore(), Blast_HSPNew(), BlastExtensionOptionsFree(), BlastExtensionOptionsNew(), BlastHitSavingOptionsFree(), BlastHitSavingOptionsNew(), BlastHSPCollectorInfoNew(), BlastHSPCollectorParamsNew(), BlastHSPStreamFree(), BlastHSPStreamNew(), BlastHSPStreamWrite(), BlastHSPWriterNew(), BlastScoringOptionsFree(), BlastScoringOptionsNew(), BlastExtensionOptions::compositionBasedStats, CBlastOptionsFactory::Create(), CTestObjMgr::CreateBlastSearchQuery(), eBlastTypeTblastn, eNa_strand_unknown, BlastSeg::end, CSeqDB::eNucleotide, eTblastn, FALSE, BlastSeg::frame, BlastScoringOptions::gapped_calculation, BlastSeg::gapped_start, CBlastSeqSrc::Get(), CSearchResultSet::GetNumResults(), CBlastOptionsHandle::GetOptions(), BlastHSPList::hsp_array, BlastHSPList::hspcnt, CTestObjMgr::Instance(), NULL, BlastSeg::offset, BlastHSP::query, query, CBlastTracebackSearch::Run(), BlastHSP::score, SeqDbBlastSeqSrcInit(), CBlastOptionsHandle::SetEffectiveSearchSpace(), BlastHSP::subject, and WrapStruct().
BOOST_AUTO_TEST_CASE | ( | testPartialFetchingMT | ) |
Definition at line 1147 of file traceback_unit_test.cpp.
References b, BLAST_SetupPartialFetching(), Blast_TracebackGetEncoding(), BlastSeqSrcCopy(), BlastSeqSrcFree(), BlastSeqSrcGetInitError(), BlastSeqSrcGetSeqLen(), BlastSeqSrcGetSequence(), BlastSeqSrcSetRangesArgFree(), BlastSequenceBlkFree(), calloc(), BlastSeqSrcGetSeqArg::check_oid_exclusion, CDirEntry::ConcatPath(), eBlastTypeBlastn, BlastSeqSrcGetSeqArg::encoding, BlastSeg::end, free(), CDirEntry::GetPathSeparator(), BlastHSPList::hsp_array, BlastHSPList::hspcnt, i, len, NCBI_GetTestDataPath(), NULL, BlastSeg::offset, BlastHSPList::oid, BlastSeqSrcGetSeqArg::oid, r(), BlastSeqSrcGetSeqArg::ranges, BlastSeqSrcGetSeqArg::reset_ranges, s_GetHSPList(), BlastSeqSrcGetSeqArg::seq, SeqDbBlastSeqSrcInit(), BLAST_SequenceBlk::sequence_start, and BlastHSP::subject.
BOOST_AUTO_TEST_CASE | ( | testSetupPartialFetching | ) |
Definition at line 1103 of file traceback_unit_test.cpp.
References BlastHSPList::allocated, BLAST_SetupPartialFetching(), BlastSeqSrcGetInitError(), BlastSeqSrcGetSeqLen(), calloc(), CDirEntry::ConcatPath(), BlastHSP::context, BlastHSPList::do_not_reallocate, eBlastTypeBlastn, BlastSeg::end, FALSE, BlastSeg::frame, free(), BlastSeg::gapped_start, CDirEntry::GetPathSeparator(), BlastHSPList::hsp_array, BlastHSPList::hsp_max, BlastHSPList::hspcnt, len, malloc(), NCBI_GetTestDataPath(), NULL, BlastSeqSrcSetRangesArg::num_ranges, BlastSeg::offset, BlastHSPList::oid, BlastHSP::query, BlastSeqSrcSetRangesArg::ranges, BlastHSP::score, SeqDbBlastSeqSrcInit(), and BlastHSP::subject.
BOOST_AUTO_TEST_CASE | ( | testTBLASTNTraceBack | ) |
Definition at line 600 of file traceback_unit_test.cpp.
References BlastHSPList::allocated, Blast_HSPListSortByScore(), Blast_HSPResultsFree(), BlastHSPStreamFree(), BlastHSPStreamWrite(), BlastSeqSrcFree(), BlastSeqSrcGetSeqLen(), calloc(), TestUtil::CheckForBlastSeqSrcErrors(), BlastHSPList::do_not_reallocate, eNa_strand_both, eNa_strand_unknown, BlastSeg::end, eNoCompositionBasedStats, FALSE, BlastSeg::frame, BlastSeg::gapped_start, CBlastOptionsHandle::GetOptions(), CBl2Seq::GetOptionsHandle(), CBlastOptions::GetProgramType(), CBl2Seq::GetQueries(), CBlastOptions::GetStrandOption(), CBl2Seq::GetSubjects(), BlastHSPList::hsp_array, BlastHSPList::hsp_max, BlastHSPList::hspcnt, BlastHitList::hsplist_array, CTestObjMgr::Instance(), ITERATE, malloc(), MultiSeqBlastSeqSrcInit(), NULL, BlastHSP::num, BlastHSP::num_ident, BlastSeg::offset, BlastHSPList::oid, prog, BlastHSP::query, results, BlastHSP::score, CBlastOptions::SetCompositionBasedStats(), CBlastOptionsHandle::SetDbLength(), CBlastOptionsHandle::SetOptions(), CBl2Seq::SetOptionsHandle(), CBlastOptions::SetSegFiltering(), SetupQueries(), SetupQueryInfo(), and BlastHSP::subject.
BOOST_AUTO_TEST_CASE | ( | testUnit_TestsDataPath | ) |
Definition at line 1088 of file traceback_unit_test.cpp.
References BlastSeqSrcGetInitError(), CDirEntry::ConcatPath(), CDirEntry::GetPathSeparator(), NCBI_GetTestDataPath(), NULL, and SeqDbBlastSeqSrcInit().
BlastHSPList* s_GetHSPList | ( | int | num_hsps, |
int | oid, | ||
int | len, | ||
int | range_len | ||
) |
Definition at line 1057 of file traceback_unit_test.cpp.
References BlastHSPList::allocated, calloc(), BlastHSP::context, BlastHSPList::do_not_reallocate, BlastSeg::end, FALSE, BlastSeg::frame, BlastSeg::gapped_start, BlastHSPList::hsp_array, BlastHSPList::hsp_max, BlastHSPList::hspcnt, i, len, malloc(), BlastSeg::offset, BlastHSPList::oid, BlastHSP::query, BlastHSP::score, and BlastHSP::subject.
Referenced by BOOST_AUTO_TEST_CASE().