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 <blast_objmgr_priv.hpp>
#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/uniform_search.hpp>
#include <algo/blast/api/disc_nucl_options.hpp>
#include <algo/blast/core/blast_nalookup.h>
#include <algo/blast/core/lookup_util.h>
#include "test_objmgr.hpp"
#include "blast_test_util.hpp"
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Classes | |
struct | NtlookupTestFixture |
Macros | |
#define | NULL_NUCL_SENTINEL 0xf |
#define | SMALL_QUERY_GI 1945386 |
#define | LARGE_QUERY_GI 19572546 |
Functions | |
BOOST_AUTO_TEST_CASE (testStdLookupTable) | |
BOOST_AUTO_TEST_CASE (testMegablastLookupTable) | |
BOOST_AUTO_TEST_CASE (testDiscontiguousMBLookupTableCodingWordSize11) | |
BOOST_AUTO_TEST_CASE (testDiscontiguousMBLookupTableCodingWordSize12) | |
BOOST_AUTO_TEST_CASE (testDiscontiguousMBLookupTableOptimalWordSize11) | |
BOOST_AUTO_TEST_CASE (testDiscontiguousMBLookupTableOptimalWordSize12) | |
BOOST_AUTO_TEST_CASE (testDiscontiguousMBLookupTableTwoTemplatesWordSize11) | |
BOOST_AUTO_TEST_CASE (testHashLookupTableWordSize16) | |
BOOST_AUTO_TEST_CASE (testHashLookupTableWordSize16WithDbFilter) | |
BOOST_AUTO_TEST_CASE (testHashLookupTableMissingSeqSrc) | |
BOOST_AUTO_TEST_CASE (testStdLookupTableDebruijn) | |
BOOST_AUTO_TEST_CASE (testMegablastLookupTableDebruijn) | |
BOOST_AUTO_TEST_CASE (testStdTableSmallUnmaskedRegion) | |
BOOST_AUTO_TEST_CASE (testMegablastTableSmallUnmaskedRegion) | |
#define LARGE_QUERY_GI 19572546 |
Definition at line 74 of file ntlookup_unit_test.cpp.
#define NULL_NUCL_SENTINEL 0xf |
Definition at line 72 of file ntlookup_unit_test.cpp.
#define SMALL_QUERY_GI 1945386 |
Definition at line 73 of file ntlookup_unit_test.cpp.
BOOST_AUTO_TEST_CASE | ( | testDiscontiguousMBLookupTableCodingWordSize11 | ) |
Definition at line 255 of file ntlookup_unit_test.cpp.
References BLAST_FillLookupTableOptions(), BlastQuerySetUpOptionsFree(), BlastQuerySetUpOptionsNew(), eBlastTypeBlastn, eMBLookupTable, eMBWordCoding, TestUtil::EndianIndependentBufferHash(), lookup(), LookupTableOptionsFree(), LookupTableOptionsNew(), LookupTableWrapFree(), LookupTableWrapInit(), LookupTableWrap::lut, LookupTableWrap::lut_type, LookupTableOptions::mb_template_length, LookupTableOptions::mb_template_type, NULL, PV_ARRAY_TYPE, SMALL_QUERY_GI, and TRUE.
BOOST_AUTO_TEST_CASE | ( | testDiscontiguousMBLookupTableCodingWordSize12 | ) |
Definition at line 301 of file ntlookup_unit_test.cpp.
References BLAST_FillLookupTableOptions(), BlastQuerySetUpOptionsFree(), BlastQuerySetUpOptionsNew(), eBlastTypeBlastn, eMBLookupTable, eMBWordCoding, TestUtil::EndianIndependentBufferHash(), lookup(), LookupTableOptionsFree(), LookupTableOptionsNew(), LookupTableWrapFree(), LookupTableWrapInit(), LookupTableWrap::lut, LookupTableWrap::lut_type, LookupTableOptions::mb_template_length, LookupTableOptions::mb_template_type, NULL, PV_ARRAY_TYPE, SMALL_QUERY_GI, and TRUE.
BOOST_AUTO_TEST_CASE | ( | testDiscontiguousMBLookupTableOptimalWordSize11 | ) |
Definition at line 347 of file ntlookup_unit_test.cpp.
References BLAST_FillLookupTableOptions(), BlastQuerySetUpOptionsFree(), BlastQuerySetUpOptionsNew(), eBlastTypeBlastn, eMBLookupTable, eMBWordOptimal, TestUtil::EndianIndependentBufferHash(), lookup(), LookupTableOptionsFree(), LookupTableOptionsNew(), LookupTableWrapFree(), LookupTableWrapInit(), LookupTableWrap::lut, LookupTableWrap::lut_type, LookupTableOptions::mb_template_length, LookupTableOptions::mb_template_type, NULL, PV_ARRAY_TYPE, SMALL_QUERY_GI, and TRUE.
BOOST_AUTO_TEST_CASE | ( | testDiscontiguousMBLookupTableOptimalWordSize12 | ) |
Definition at line 393 of file ntlookup_unit_test.cpp.
References BLAST_FillLookupTableOptions(), BlastQuerySetUpOptionsFree(), BlastQuerySetUpOptionsNew(), eBlastTypeBlastn, eMBLookupTable, eMBWordOptimal, TestUtil::EndianIndependentBufferHash(), lookup(), LookupTableOptionsFree(), LookupTableOptionsNew(), LookupTableWrapFree(), LookupTableWrapInit(), LookupTableWrap::lut, LookupTableWrap::lut_type, LookupTableOptions::mb_template_length, LookupTableOptions::mb_template_type, NULL, PV_ARRAY_TYPE, SMALL_QUERY_GI, and TRUE.
BOOST_AUTO_TEST_CASE | ( | testDiscontiguousMBLookupTableTwoTemplatesWordSize11 | ) |
Definition at line 439 of file ntlookup_unit_test.cpp.
References BLAST_FillLookupTableOptions(), BlastQuerySetUpOptionsFree(), BlastQuerySetUpOptionsNew(), eBlastTypeBlastn, eMBLookupTable, eMBWordTwoTemplates, TestUtil::EndianIndependentBufferHash(), lookup(), LookupTableOptionsFree(), LookupTableOptionsNew(), LookupTableWrapFree(), LookupTableWrapInit(), LookupTableWrap::lut, LookupTableWrap::lut_type, LookupTableOptions::mb_template_length, LookupTableOptions::mb_template_type, NULL, PV_ARRAY_TYPE, SMALL_QUERY_GI, and TRUE.
BOOST_AUTO_TEST_CASE | ( | testHashLookupTableMissingSeqSrc | ) |
Definition at line 618 of file ntlookup_unit_test.cpp.
References BLAST_FillLookupTableOptions(), BlastQuerySetUpOptionsNew(), LookupTableOptions::db_filter, eBlastTypeMapping, FALSE, LARGE_QUERY_GI, LookupTableOptionsFree(), LookupTableOptionsNew(), LookupTableWrapInit(), NULL, and TRUE.
BOOST_AUTO_TEST_CASE | ( | testHashLookupTableWordSize16 | ) |
Definition at line 490 of file ntlookup_unit_test.cpp.
References BLAST_FillLookupTableOptions(), BlastNaHashLookupTableDestruct(), BlastNaHashLookupTableNew(), BlastQuerySetUpOptionsFree(), BlastQuerySetUpOptionsNew(), eBlastTypeMapping, TestUtil::EndianIndependentBufferHash(), FALSE, for(), hash_func, i, LARGE_QUERY_GI, lookup(), LookupTableOptionsFree(), LookupTableOptionsNew(), NA_OFFSETS_PER_HASH, NULL, PV_ARRAY_TYPE, and LookupTableOptions::word_size.
BOOST_AUTO_TEST_CASE | ( | testHashLookupTableWordSize16WithDbFilter | ) |
Definition at line 552 of file ntlookup_unit_test.cpp.
References BLAST_FillLookupTableOptions(), BlastQuerySetUpOptionsFree(), BlastQuerySetUpOptionsNew(), LookupTableOptions::db_filter, CSearchDatabase::eBlastDbIsNucleotide, eBlastTypeMapping, eNaHashLookupTable, TestUtil::EndianIndependentBufferHash(), FALSE, for(), hash_func, i, LARGE_QUERY_GI, lookup(), LookupTableOptionsFree(), LookupTableOptionsNew(), LookupTableWrapFree(), LookupTableWrapInit(), LookupTableWrap::lut, LookupTableWrap::lut_type, CLocalDbAdapter::MakeSeqSrc(), NULL, PV_ARRAY_TYPE, and TRUE.
BOOST_AUTO_TEST_CASE | ( | testMegablastLookupTable | ) |
Definition at line 212 of file ntlookup_unit_test.cpp.
References BLAST_FillLookupTableOptions(), BlastQuerySetUpOptionsFree(), BlastQuerySetUpOptionsNew(), eBlastTypeBlastn, eMBLookupTable, TestUtil::EndianIndependentBufferHash(), LARGE_QUERY_GI, lookup(), LookupTableOptionsFree(), LookupTableOptionsNew(), LookupTableWrapFree(), LookupTableWrapInit(), LookupTableWrap::lut, LookupTableWrap::lut_type, NULL, PV_ARRAY_TYPE, and TRUE.
BOOST_AUTO_TEST_CASE | ( | testMegablastLookupTableDebruijn | ) |
Definition at line 687 of file ntlookup_unit_test.cpp.
References BLAST_FillLookupTableOptions(), BlastQuerySetUpOptionsFree(), BlastQuerySetUpOptionsNew(), eBlastTypeBlastn, eMBLookupTable, lookup(), LookupTableOptionsFree(), LookupTableOptionsNew(), LookupTableWrapFree(), LookupTableWrapInit(), LookupTableWrap::lut, LookupTableWrap::lut_type, NULL, PV_ARRAY_TYPE, and TRUE.
BOOST_AUTO_TEST_CASE | ( | testMegablastTableSmallUnmaskedRegion | ) |
Definition at line 783 of file ntlookup_unit_test.cpp.
References BLAST_FillLookupTableOptions(), BlastQuerySetUpOptionsFree(), BlastQuerySetUpOptionsNew(), BlastSeqLocFree(), BlastSeqLocNew(), eBlastTypeBlastn, eMBLookupTable, LARGE_QUERY_GI, lookup(), LookupTableOptionsFree(), LookupTableOptionsNew(), LookupTableWrapFree(), LookupTableWrapInit(), LookupTableWrap::lut, LookupTableWrap::lut_type, NULL, offset, PV_ARRAY_TYPE, and TRUE.
BOOST_AUTO_TEST_CASE | ( | testStdLookupTable | ) |
Definition at line 176 of file ntlookup_unit_test.cpp.
References BLAST_FillLookupTableOptions(), BlastQuerySetUpOptionsFree(), BlastQuerySetUpOptionsNew(), eBlastTypeBlastn, eSmallNaLookupTable, FALSE, lookup(), LookupTableOptionsFree(), LookupTableOptionsNew(), LookupTableWrapFree(), LookupTableWrapInit(), LookupTableWrap::lut, LookupTableWrap::lut_type, NULL, and SMALL_QUERY_GI.
BOOST_AUTO_TEST_CASE | ( | testStdLookupTableDebruijn | ) |
Definition at line 641 of file ntlookup_unit_test.cpp.
References BLAST_FillLookupTableOptions(), BlastQuerySetUpOptionsFree(), BlastQuerySetUpOptionsNew(), eBlastTypeBlastn, eNaLookupTable, FALSE, lookup(), LookupTableOptionsFree(), LookupTableOptionsNew(), LookupTableWrapFree(), LookupTableWrapInit(), LookupTableWrap::lut, LookupTableWrap::lut_type, NULL, PV_ARRAY_BTS, and PV_ARRAY_TYPE.
BOOST_AUTO_TEST_CASE | ( | testStdTableSmallUnmaskedRegion | ) |
Definition at line 737 of file ntlookup_unit_test.cpp.
References BLAST_FillLookupTableOptions(), BlastQuerySetUpOptionsFree(), BlastQuerySetUpOptionsNew(), BlastSeqLocFree(), BlastSeqLocNew(), eBlastTypeBlastn, eSmallNaLookupTable, FALSE, lookup(), LookupTableOptionsFree(), LookupTableOptionsNew(), LookupTableWrapFree(), LookupTableWrapInit(), LookupTableWrap::lut, LookupTableWrap::lut_type, NULL, and SMALL_QUERY_GI.