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 <objtools/simple/simple_om.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <serial/iterator.hpp>
#include <util/random_gen.hpp>
#include <objmgr/util/sequence.hpp>
#include <algo/blast/api/blast_aux.hpp>
#include "blast_objmgr_priv.hpp"
#include <algo/blast/api/bl2seq.hpp>
#include <algo/blast/api/blast_options_handle.hpp>
#include <algo/blast/api/blast_nucl_options.hpp>
#include <algo/blast/core/blast_setup.h>
#include <algo/blast/api/repeats_filter.hpp>
#include <algo/blast/api/windowmask_filter.hpp>
#include "winmask_filter.hpp"
#include "dust_filter.hpp"
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqloc/Packed_seqint.hpp>
#include "test_objmgr.hpp"
#include "blast_test_util.hpp"
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Classes | |
class | CBlastFilterTest |
Typedefs | |
typedef vector< TSeqRange > | TRangeVector |
Functions | |
static BlastSeqLoc * | s_RangeVector2BlastSeqLoc (const TRangeVector &rv) |
static void | x_TestGetSeqLocInfoVector (EBlastProgramType program, size_t num_seqs) |
static bool | x_AreAllBasesMasked (const Uint1 *sequence, int start, int stop) |
static void | x_TestGetFilteredQueryRegions (ENa_strand strand) |
BOOST_AUTO_TEST_CASE (TSeqLocVector2Packed_seqint_TestIntervals) | |
BOOST_AUTO_TEST_CASE (TSeqLocVector2Packed_seqint_TestNoIntervals) | |
BOOST_AUTO_TEST_CASE (TSeqLocVector2Packed_seqint_TestEmptyInput) | |
void | setupQueryStructures (TSeqLocVector &query_vector, const CBlastOptions &kOpts, BLAST_SequenceBlk **query_blk, BlastQueryInfo **qinfo) |
BOOST_AUTO_TEST_CASE (SegFilter) | |
BOOST_AUTO_TEST_CASE (RepeatsFilter) | |
BOOST_AUTO_TEST_CASE (WindowMasker) | |
BOOST_AUTO_TEST_CASE (RepeatsFilter_OnSeqInterval) | |
BOOST_AUTO_TEST_CASE (CSeqLocInfo_EqualityOperators) | |
BOOST_AUTO_TEST_CASE (CombineDustAndLowerCaseMasking_WithBlastQueryVector) | |
BOOST_AUTO_TEST_CASE (RepeatsAndDustFilter) | |
BOOST_AUTO_TEST_CASE (WindowMaskerAndDustFilter) | |
BOOST_AUTO_TEST_CASE (WindowMasker_OnSeqInterval) | |
BOOST_AUTO_TEST_CASE (RepeatsFilter_NoHitsFound) | |
BOOST_AUTO_TEST_CASE (WindowMasker_NoHitsFound) | |
BOOST_AUTO_TEST_CASE (RepeatsFilterWithMissingParameter) | |
BOOST_AUTO_TEST_CASE (WindowMaskerWithMissingParameter) | |
BOOST_AUTO_TEST_CASE (TestGetFilteredQueryRegions_BothStrandsOneQuery) | |
Test the conversion of a BlastMaskLoc internal structure to the TSeqLocInfoVector type, used in formatting. More... | |
BOOST_AUTO_TEST_CASE (TestGetFilteredQueryRegions_PlusStrandsOneQuery) | |
BOOST_AUTO_TEST_CASE (TestGetFilteredQueryRegions_MinusStrandsOneQuery) | |
BOOST_AUTO_TEST_CASE (RestrictLowerCaseMask) | |
BOOST_AUTO_TEST_CASE (BlastxLowerCaseMask) | |
BOOST_AUTO_TEST_CASE (BlastxLowerCaseMaskProteinLocations) | |
BOOST_AUTO_TEST_CASE (BlastnLowerCaseMask_SingleStrand) | |
BOOST_AUTO_TEST_CASE (BlastnLowerCaseMask_BothStrands) | |
BOOST_AUTO_TEST_CASE (LowerCaseMask_PlusStrand) | |
BOOST_AUTO_TEST_CASE (LowerCaseMask_MinusStrand) | |
BOOST_AUTO_TEST_CASE (LowerCaseMask_BothStrands) | |
BOOST_AUTO_TEST_CASE (LowerCaseMask_PlusStrand_Explicit) | |
BOOST_AUTO_TEST_CASE (LowerCaseMask_MinusStrand_Explicit) | |
BOOST_AUTO_TEST_CASE (LowerCaseMask_BothStrands_Explicit) | |
BOOST_AUTO_TEST_CASE (CombineRepeatAndLowerCaseMask) | |
BOOST_AUTO_TEST_CASE (CombineRepeatAndDustFilter) | |
BOOST_AUTO_TEST_CASE (FilterLocNuclBoth) | |
BOOST_AUTO_TEST_CASE (FilterLocNuclPlus) | |
BOOST_AUTO_TEST_CASE (FilterLocNuclMinus) | |
BOOST_AUTO_TEST_CASE (FilterLocProtein) | |
BOOST_AUTO_TEST_CASE (MaskProteinSequence) | |
BOOST_AUTO_TEST_CASE (MaskNucleotideBothStrands) | |
BOOST_AUTO_TEST_CASE (FilterMultipleQueriesLocNuclPlus) | |
BOOST_AUTO_TEST_CASE (MaskRestrictToInterval) | |
void | setupQueryInfoForOffsetTranslation (CBlastQueryInfo &query_info) |
BOOST_AUTO_TEST_CASE (ConvertTranslatedFilterOffsets) | |
BOOST_AUTO_TEST_CASE (FilterOptionsToStringFromNULL) | |
BOOST_AUTO_TEST_CASE (FilterOptionsToStringFromMaskAtHashOnly) | |
BOOST_AUTO_TEST_CASE (FilterOptionsToStringLargeData) | |
BOOST_AUTO_TEST_CASE (FilterOptionsFromNULLString) | |
BOOST_AUTO_TEST_CASE (FilterOptionsFromStringDustMaskAtHash) | |
BOOST_AUTO_TEST_CASE (FilterOptionsFromStringDust) | |
BOOST_AUTO_TEST_CASE (FilterOptionsFromStringSEGWithParams) | |
BOOST_AUTO_TEST_CASE (FilterOptionsFromBadStringSEGWithParams) | |
BOOST_AUTO_TEST_CASE (FilterOptionsFromStringBlastnL) | |
BOOST_AUTO_TEST_CASE (FilterOptionsFromStringBlastpL) | |
BOOST_AUTO_TEST_CASE (FilterOptionsFromStringBlastnW) | |
BOOST_AUTO_TEST_CASE (FilterMerge) | |
BOOST_AUTO_TEST_CASE (FilterStringFalse) | |
BOOST_AUTO_TEST_CASE (MergeOptionHandle) | |
BOOST_AUTO_TEST_CASE (OptionsHandleNotClear) | |
BOOST_AUTO_TEST_CASE (OptionsHandleClear) | |
BOOST_AUTO_TEST_CASE (GetSeqLocInfoVector_EmptyQueryIdVector) | |
BOOST_AUTO_TEST_CASE (GetSeqLocInfoVector_EmptyMasks) | |
BOOST_AUTO_TEST_CASE (BlastSeqLocCombineTest) | |
BOOST_AUTO_TEST_CASE (GetSeqLocInfoVector_AllPrograms) | |
BOOST_AUTO_TEST_CASE (TestBlastSeqLocCombine_MergeElems) | |
BOOST_AUTO_TEST_CASE (TestBlastSeqLocCombine_MergeIdenticals) | |
BOOST_AUTO_TEST_CASE (TestBlastSeqLocCombine_NoMerging) | |
void | BlastSeqLocListReverse (BlastSeqLoc **head) |
Reverse elements in the list. More... | |
BOOST_AUTO_TEST_CASE (TestBlastSeqLocListReverse) | |
BOOST_AUTO_TEST_CASE (TestGetTaxIdWithWindowMaskerSupport) | |
typedef vector<TSeqRange> TRangeVector |
Definition at line 70 of file blastfilter_unit_test.cpp.
void BlastSeqLocListReverse | ( | BlastSeqLoc ** | head | ) |
Reverse elements in the list.
head | pointer to pointer to the head of the list. [in|out] (this is not declared static so that it can be tested in the unit tests |
Definition at line 705 of file blast_filter.c.
References ASSERT, head, i, BlastSeqLoc::next, NULL, s_BlastSeqLocListToArrayOfPointers(), and sfree.
Referenced by BLAST_ComplementMaskLocations(), and BOOST_AUTO_TEST_CASE().
BOOST_AUTO_TEST_CASE | ( | BlastnLowerCaseMask_BothStrands | ) |
Definition at line 1059 of file blastfilter_unit_test.cpp.
References CSeq_id_Base::e_Gi, eBlastTypeBlastn, CSeqLocInfo::eFrameMinus1, CSeqLocInfo::eFramePlus1, CBlastQueryFilteredFrames::Empty(), CBlastQueryFilteredFrames::GetNumFrames(), ITERATE, CBlastQueryFilteredFrames::ListFrames(), mask, NULL, CBlastQueryFilteredFrames::QueryHasMultipleFrames(), and CRef< C, Locker >::Reset().
BOOST_AUTO_TEST_CASE | ( | BlastnLowerCaseMask_SingleStrand | ) |
Definition at line 1031 of file blastfilter_unit_test.cpp.
References CSeq_id_Base::e_Gi, eBlastTypeBlastn, CSeqLocInfo::eFramePlus1, CBlastQueryFilteredFrames::Empty(), CBlastQueryFilteredFrames::GetNumFrames(), ITERATE, CBlastQueryFilteredFrames::ListFrames(), mask, NULL, and CBlastQueryFilteredFrames::QueryHasMultipleFrames().
BOOST_AUTO_TEST_CASE | ( | BlastSeqLocCombineTest | ) |
Definition at line 1946 of file blastfilter_unit_test.cpp.
References BlastSeqLocCombine(), BlastSeqLocFree(), BlastSeqLocNew(), count, head, SSeqRange::left, BlastSeqLoc::next, NULL, result, SSeqRange::right, and BlastSeqLoc::ssr.
BOOST_AUTO_TEST_CASE | ( | BlastxLowerCaseMask | ) |
Definition at line 949 of file blastfilter_unit_test.cpp.
References CSeq_id_Base::e_Gi, eBlastTypeBlastx, CSeqLocInfo::eFramePlus1, CBlastQueryFilteredFrames::Empty(), CBlastQueryFilteredFrames::GetNumFrames(), ITERATE, CBlastQueryFilteredFrames::ListFrames(), NULL, NUM_FRAMES, CBlastQueryFilteredFrames::QueryHasMultipleFrames(), and compile_time_bits::range().
BOOST_AUTO_TEST_CASE | ( | BlastxLowerCaseMaskProteinLocations | ) |
Definition at line 984 of file blastfilter_unit_test.cpp.
References CSeq_id_Base::e_Gi, eBlastTypeBlastx, CSeqLocInfo::eFrameMinus1, CSeqLocInfo::eFrameMinus2, CSeqLocInfo::eFrameMinus3, CSeqLocInfo::eFramePlus1, CSeqLocInfo::eFramePlus2, CSeqLocInfo::eFramePlus3, ITERATE, SSeqRange::left, compile_time_bits::range(), SSeqRange::right, BlastSeqLoc::ssr, and CBlastQueryFilteredFrames::UseProteinCoords().
BOOST_AUTO_TEST_CASE | ( | CombineDustAndLowerCaseMasking_WithBlastQueryVector | ) |
Definition at line 669 of file blastfilter_unit_test.cpp.
References CBlastQueryVector::AddQuery(), Blast_FindDustFilterLoc(), CTestObjMgr::CreateBlastSearchQuery(), CSeqLocInfo::eFramePlus1, eNa_strand_both, CBlastException::eNotSupported, CBlastNucleotideOptionsHandle::GetDustFilteringLevel(), CBlastNucleotideOptionsHandle::GetDustFilteringLinker(), CBlastNucleotideOptionsHandle::GetDustFilteringWindow(), CException::GetErrCode(), CBlastQueryVector::GetMaskedRegions(), CBlastQueryVector::GetMasks(), CException::GetMsg(), CTestObjMgr::Instance(), CRef< C, Locker >::NotEmpty(), NPOS, query, r(), and CBlastNucleotideOptionsHandle::SetDustFiltering().
BOOST_AUTO_TEST_CASE | ( | CombineRepeatAndDustFilter | ) |
Definition at line 1169 of file blastfilter_unit_test.cpp.
References Blast_FindDustFilterLoc(), Blast_FindRepeatFilterLoc(), eNa_strand_both, CTestObjMgr::Instance(), ITERATE, mask, CBlastNucleotideOptionsHandle::SetDustFiltering(), and CBlastNucleotideOptionsHandle::SetRepeatFiltering().
BOOST_AUTO_TEST_CASE | ( | CombineRepeatAndLowerCaseMask | ) |
Definition at line 1124 of file blastfilter_unit_test.cpp.
References Blast_FindRepeatFilterLoc(), eNa_strand_both, CTestObjMgr::Instance(), ITERATE, mask, and CBlastNucleotideOptionsHandle::SetRepeatFiltering().
BOOST_AUTO_TEST_CASE | ( | ConvertTranslatedFilterOffsets | ) |
Definition at line 1591 of file blastfilter_unit_test.cpp.
References BlastMaskLocDNAToProtein(), BlastMaskLocNew(), BlastMaskLocProteinToDNA(), calloc(), BlastQueryInfo::last_context, SSeqRange::left, malloc(), NUM_FRAMES, compile_time_bits::range(), SSeqRange::right, BlastMaskLoc::seqloc_array, setupQueryInfoForOffsetTranslation(), BlastSeqLoc::ssr, and BlastMaskLoc::total_size.
BOOST_AUTO_TEST_CASE | ( | CSeqLocInfo_EqualityOperators | ) |
Definition at line 657 of file blastfilter_unit_test.cpp.
References a, b, CSeqLocInfo::eFramePlus1, and r().
BOOST_AUTO_TEST_CASE | ( | FilterLocNuclBoth | ) |
Definition at line 1202 of file blastfilter_unit_test.cpp.
References Blast_FindDustFilterLoc(), eNa_strand_both, CTestObjMgr::Instance(), ITERATE, mask, and CBlastNucleotideOptionsHandle::SetDustFiltering().
BOOST_AUTO_TEST_CASE | ( | FilterLocNuclMinus | ) |
Definition at line 1262 of file blastfilter_unit_test.cpp.
References Blast_FindDustFilterLoc(), eNa_strand_minus, CTestObjMgr::Instance(), IsReverse(), ITERATE, mask, and CBlastNucleotideOptionsHandle::SetDustFiltering().
BOOST_AUTO_TEST_CASE | ( | FilterLocNuclPlus | ) |
Definition at line 1232 of file blastfilter_unit_test.cpp.
References Blast_FindDustFilterLoc(), eNa_strand_plus, CTestObjMgr::Instance(), ITERATE, mask, and CBlastNucleotideOptionsHandle::SetDustFiltering().
BOOST_AUTO_TEST_CASE | ( | FilterLocProtein | ) |
Definition at line 1300 of file blastfilter_unit_test.cpp.
References BlastMaskLocFree(), BlastSetUp_GetFilteringLocations(), CBlastOptionsFactory::Create(), eBlastp, eBlastTypeBlastp, eSeg, CBlastOptionsHandle::GetOptions(), CTestObjMgr::Instance(), SSeqRange::left, BlastSeqLoc::next, NULL, SSeqRange::right, SBlastFilterOptionsFree(), SBlastFilterOptionsNew(), BlastMaskLoc::seqloc_array, setupQueryStructures(), and BlastSeqLoc::ssr.
BOOST_AUTO_TEST_CASE | ( | FilterMerge | ) |
Definition at line 1831 of file blastfilter_unit_test.cpp.
References SBlastFilterOptions::dustOptions, eDust, eRepeats, SDustOptions::level, SBlastFilterOptions::mask_at_hash, NULL, result, SBlastFilterOptionsFree(), SBlastFilterOptionsMerge(), SBlastFilterOptionsNew(), and SDustOptions::window.
BOOST_AUTO_TEST_CASE | ( | FilterMultipleQueriesLocNuclPlus | ) |
Definition at line 1441 of file blastfilter_unit_test.cpp.
References Blast_FindDustFilterLoc(), CBlastOptionsFactory::Create(), eBlastn, eNa_strand_both, CTestObjMgr::Instance(), ITERATE, mask, and CBlastNucleotideOptionsHandle::SetDustFiltering().
BOOST_AUTO_TEST_CASE | ( | FilterOptionsFromBadStringSEGWithParams | ) |
Definition at line 1770 of file blastfilter_unit_test.cpp.
References BlastFilteringOptionsFromString(), eBlastTypeBlastp, and NULL.
BOOST_AUTO_TEST_CASE | ( | FilterOptionsFromNULLString | ) |
Definition at line 1699 of file blastfilter_unit_test.cpp.
References BlastFilteringOptionsFromString(), SBlastFilterOptions::dustOptions, eBlastTypeBlastn, SBlastFilterOptions::mask_at_hash, NULL, SBlastFilterOptionsFree(), and SBlastFilterOptions::segOptions.
BOOST_AUTO_TEST_CASE | ( | FilterOptionsFromStringBlastnL | ) |
Definition at line 1780 of file blastfilter_unit_test.cpp.
References BlastFilteringOptionsFromString(), BlastFilteringOptionsToString(), SBlastFilterOptions::dustOptions, eBlastTypeBlastn, AutoPtr< X, Del >::get(), SBlastFilterOptions::mask_at_hash, NULL, SBlastFilterOptionsFree(), SBlastFilterOptions::segOptions, and util::strcmp().
BOOST_AUTO_TEST_CASE | ( | FilterOptionsFromStringBlastnW | ) |
Definition at line 1812 of file blastfilter_unit_test.cpp.
References BlastFilteringOptionsFromString(), BlastFilteringOptionsToString(), SBlastFilterOptions::dustOptions, eBlastTypeBlastn, AutoPtr< X, Del >::get(), SBlastFilterOptions::mask_at_hash, NULL, SBlastFilterOptions::repeatFilterOptions, SBlastFilterOptionsFree(), SBlastFilterOptions::segOptions, util::strcmp(), and SBlastFilterOptions::windowMaskerOptions.
BOOST_AUTO_TEST_CASE | ( | FilterOptionsFromStringBlastpL | ) |
Definition at line 1796 of file blastfilter_unit_test.cpp.
References BlastFilteringOptionsFromString(), BlastFilteringOptionsToString(), SBlastFilterOptions::dustOptions, eBlastTypeBlastp, AutoPtr< X, Del >::get(), SBlastFilterOptions::mask_at_hash, NULL, SBlastFilterOptionsFree(), SBlastFilterOptions::segOptions, and util::strcmp().
BOOST_AUTO_TEST_CASE | ( | FilterOptionsFromStringDust | ) |
Definition at line 1732 of file blastfilter_unit_test.cpp.
References BlastFilteringOptionsFromString(), BlastFilteringOptionsToString(), SBlastFilterOptions::dustOptions, eBlastTypeBlastn, AutoPtr< X, Del >::get(), SBlastFilterOptions::mask_at_hash, NULL, SBlastFilterOptionsFree(), SBlastFilterOptions::segOptions, and util::strcmp().
BOOST_AUTO_TEST_CASE | ( | FilterOptionsFromStringDustMaskAtHash | ) |
Definition at line 1714 of file blastfilter_unit_test.cpp.
References BlastFilteringOptionsFromString(), BlastFilteringOptionsToString(), SBlastFilterOptions::dustOptions, eBlastTypeBlastn, AutoPtr< X, Del >::get(), SBlastFilterOptions::mask_at_hash, NULL, SBlastFilterOptionsFree(), and SBlastFilterOptions::segOptions.
BOOST_AUTO_TEST_CASE | ( | FilterOptionsFromStringSEGWithParams | ) |
Definition at line 1750 of file blastfilter_unit_test.cpp.
References BlastFilteringOptionsFromString(), BlastFilteringOptionsToString(), SBlastFilterOptions::dustOptions, eBlastTypeBlastp, AutoPtr< X, Del >::get(), SSegOptions::hicut, SSegOptions::locut, SBlastFilterOptions::mask_at_hash, NULL, SBlastFilterOptionsFree(), SBlastFilterOptions::segOptions, util::strcmp(), and SSegOptions::window.
BOOST_AUTO_TEST_CASE | ( | FilterOptionsToStringFromMaskAtHashOnly | ) |
Definition at line 1675 of file blastfilter_unit_test.cpp.
References BlastFilteringOptionsToString(), AutoPtr< X, Del >::get(), SBlastFilterOptions::mask_at_hash, and util::strcmp().
BOOST_AUTO_TEST_CASE | ( | FilterOptionsToStringFromNULL | ) |
Definition at line 1669 of file blastfilter_unit_test.cpp.
References BlastFilteringOptionsToString(), AutoPtr< X, Del >::get(), NULL, and util::strcmp().
BOOST_AUTO_TEST_CASE | ( | FilterOptionsToStringLargeData | ) |
Definition at line 1683 of file blastfilter_unit_test.cpp.
References BlastFilteringOptionsToString(), SBlastFilterOptions::dustOptions, AutoPtr< X, Del >::get(), SBlastFilterOptions::repeatFilterOptions, SDustOptionsFree(), SDustOptionsNew(), SRepeatFilterOptionsFree(), SRepeatFilterOptionsResetDB(), NStr::StartsWith(), and SDustOptions::window.
BOOST_AUTO_TEST_CASE | ( | FilterStringFalse | ) |
Definition at line 1877 of file blastfilter_unit_test.cpp.
References CBlastNucleotideOptionsHandle::GetDustFiltering(), CBlastOptionsHandle::GetMaskAtHash(), CBlastNucleotideOptionsHandle::GetWindowMaskerDatabase(), CBlastNucleotideOptionsHandle::GetWindowMaskerTaxId(), NULL, and CBlastOptionsHandle::SetFilterString().
BOOST_AUTO_TEST_CASE | ( | GetSeqLocInfoVector_AllPrograms | ) |
Definition at line 1994 of file blastfilter_unit_test.cpp.
References TestUtil::GetAllBlastProgramTypes(), CRandom::GetRand(), ITERATE, and x_TestGetSeqLocInfoVector().
BOOST_AUTO_TEST_CASE | ( | GetSeqLocInfoVector_EmptyMasks | ) |
Definition at line 1924 of file blastfilter_unit_test.cpp.
References Blast_GetSeqLocInfoVector(), BlastMaskLocNew(), CSeq_id_Base::e_Gi, eBlastTypeBlastn, GetNumberOfContexts(), ITERATE, mask, and U.
BOOST_AUTO_TEST_CASE | ( | GetSeqLocInfoVector_EmptyQueryIdVector | ) |
Definition at line 1913 of file blastfilter_unit_test.cpp.
References Blast_GetSeqLocInfoVector(), BlastMaskLocNew(), eBlastTypeBlastp, and mask.
BOOST_AUTO_TEST_CASE | ( | LowerCaseMask_BothStrands | ) |
Definition at line 1100 of file blastfilter_unit_test.cpp.
References eNa_strand_both, and CBlastFilterTest::x_TestLowerCaseMaskWith().
BOOST_AUTO_TEST_CASE | ( | LowerCaseMask_BothStrands_Explicit | ) |
Definition at line 1118 of file blastfilter_unit_test.cpp.
References eNa_strand_both, and CBlastFilterTest::x_TestLowerCaseMaskWith().
BOOST_AUTO_TEST_CASE | ( | LowerCaseMask_MinusStrand | ) |
Definition at line 1094 of file blastfilter_unit_test.cpp.
References eNa_strand_minus, and CBlastFilterTest::x_TestLowerCaseMaskWith().
BOOST_AUTO_TEST_CASE | ( | LowerCaseMask_MinusStrand_Explicit | ) |
Definition at line 1112 of file blastfilter_unit_test.cpp.
References eNa_strand_minus, and CBlastFilterTest::x_TestLowerCaseMaskWith().
BOOST_AUTO_TEST_CASE | ( | LowerCaseMask_PlusStrand | ) |
Definition at line 1088 of file blastfilter_unit_test.cpp.
References eNa_strand_plus, and CBlastFilterTest::x_TestLowerCaseMaskWith().
BOOST_AUTO_TEST_CASE | ( | LowerCaseMask_PlusStrand_Explicit | ) |
Definition at line 1106 of file blastfilter_unit_test.cpp.
References eNa_strand_plus, and CBlastFilterTest::x_TestLowerCaseMaskWith().
BOOST_AUTO_TEST_CASE | ( | MaskNucleotideBothStrands | ) |
Definition at line 1389 of file blastfilter_unit_test.cpp.
References BlastMaskLocFree(), BlastMaskLocNew(), BlastSeqLocNew(), BlastSetUp_MaskQuery(), buffer, BlastQueryInfo::contexts, CBlastOptionsFactory::Create(), eBlastn, eBlastTypeBlastn, eNa_strand_both, CBlastOptionsHandle::GetOptions(), head, CTestObjMgr::Instance(), last(), BlastQueryInfo::last_context, NULL, BlastContextInfo::query_length, BlastMaskLoc::seqloc_array, BLAST_SequenceBlk::sequence, and setupQueryStructures().
BOOST_AUTO_TEST_CASE | ( | MaskProteinSequence | ) |
Definition at line 1344 of file blastfilter_unit_test.cpp.
References BlastMaskLocFree(), BlastMaskLocNew(), BlastSeqLocNew(), BlastSetUp_MaskQuery(), buffer, BlastQueryInfo::contexts, CBlastOptionsFactory::Create(), eBlastp, eBlastTypeBlastp, CBlastOptionsHandle::GetOptions(), head, CTestObjMgr::Instance(), last(), NULL, BlastContextInfo::query_length, BlastMaskLoc::seqloc_array, BLAST_SequenceBlk::sequence, and setupQueryStructures().
BOOST_AUTO_TEST_CASE | ( | MaskRestrictToInterval | ) |
Definition at line 1522 of file blastfilter_unit_test.cpp.
References BlastSeqLoc_RestrictToInterval(), BlastSeqLocNew(), SSeqRange::left, BlastSeqLoc::next, NULL, SSeqRange::right, and BlastSeqLoc::ssr.
BOOST_AUTO_TEST_CASE | ( | MergeOptionHandle | ) |
BOOST_AUTO_TEST_CASE | ( | OptionsHandleClear | ) |
Definition at line 1904 of file blastfilter_unit_test.cpp.
References CBlastNucleotideOptionsHandle::GetDustFiltering(), CBlastNucleotideOptionsHandle::GetRepeatFiltering(), CBlastNucleotideOptionsHandle::GetWindowMaskerDatabase(), CBlastNucleotideOptionsHandle::GetWindowMaskerTaxId(), NULL, and CBlastOptionsHandle::SetFilterString().
BOOST_AUTO_TEST_CASE | ( | OptionsHandleNotClear | ) |
Definition at line 1897 of file blastfilter_unit_test.cpp.
References CBlastNucleotideOptionsHandle::GetDustFiltering(), CBlastNucleotideOptionsHandle::GetRepeatFiltering(), and CBlastOptionsHandle::SetFilterString().
BOOST_AUTO_TEST_CASE | ( | RepeatsAndDustFilter | ) |
Definition at line 704 of file blastfilter_unit_test.cpp.
References Blast_FindDustFilterLoc(), Blast_FindRepeatFilterLoc(), Compare(), eSame, fCompareOverlapping, CTestObjMgr::Instance(), mask, CBlastNucleotideOptionsHandle::SetDustFiltering(), and CBlastNucleotideOptionsHandle::SetRepeatFiltering().
BOOST_AUTO_TEST_CASE | ( | RepeatsFilter | ) |
Definition at line 508 of file blastfilter_unit_test.cpp.
References Blast_FindRepeatFilterLoc(), eNa_strand_both, CTestObjMgr::Instance(), ITERATE, mask, and CBlastNucleotideOptionsHandle::SetRepeatFiltering().
BOOST_AUTO_TEST_CASE | ( | RepeatsFilter_NoHitsFound | ) |
Definition at line 805 of file blastfilter_unit_test.cpp.
References Blast_FindRepeatFilterLoc(), eNa_strand_both, CTestObjMgr::Instance(), mask, CBlastNucleotideOptionsHandle::SetRepeatFiltering(), and CBlastNucleotideOptionsHandle::SetRepeatFilteringDB().
BOOST_AUTO_TEST_CASE | ( | RepeatsFilter_OnSeqInterval | ) |
Definition at line 604 of file blastfilter_unit_test.cpp.
References Blast_FindDustFilterLoc(), Blast_FindRepeatFilterLoc(), eNa_strand_both, CTestObjMgr::Instance(), ITERATE, mask, CBlastNucleotideOptionsHandle::SetDustFiltering(), and CBlastNucleotideOptionsHandle::SetRepeatFiltering().
BOOST_AUTO_TEST_CASE | ( | RepeatsFilterWithMissingParameter | ) |
Definition at line 836 of file blastfilter_unit_test.cpp.
References Blast_FindRepeatFilterLoc(), CTestObjMgr::Instance(), and CBlastOptionsHandle::SetFilterString().
BOOST_AUTO_TEST_CASE | ( | RestrictLowerCaseMask | ) |
Definition at line 874 of file blastfilter_unit_test.cpp.
References CSeq_interval_Base::CanGetStrand(), CSeq_id::Compare(), CSeq_id_Base::e_Gi, CSeq_id::e_YES, CSeqLocInfo::eFrameNotSet, eNa_strand_plus, ITERATE, CSeq_id::Match(), compile_time_bits::range(), TMaskedQueryRegions::RestrictToSeqInt(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetStrand(), and CSeq_interval_Base::SetTo().
BOOST_AUTO_TEST_CASE | ( | SegFilter | ) |
Definition at line 468 of file blastfilter_unit_test.cpp.
References BlastSeqLocFree(), BlastSetUp_Filter(), BlastQueryInfo::contexts, CBlastOptionsFactory::Create(), eBlastp, eSeg, CBlastOptionsHandle::GetOptions(), CBlastOptions::GetProgramType(), CTestObjMgr::Instance(), SSeqRange::left, BlastSeqLoc::next, NULL, BlastContextInfo::query_length, SSeqRange::right, SBlastFilterOptionsFree(), SBlastFilterOptionsNew(), BLAST_SequenceBlk::sequence, and setupQueryStructures().
BOOST_AUTO_TEST_CASE | ( | TestBlastSeqLocCombine_MergeElems | ) |
Definition at line 2076 of file blastfilter_unit_test.cpp.
References BlastSeqLocCombine(), BlastSeqLocFree(), ITERATE, SSeqRange::left, mask, BlastSeqLoc::next, NULL, SSeqRange::right, s_RangeVector2BlastSeqLoc(), and BlastSeqLoc::ssr.
BOOST_AUTO_TEST_CASE | ( | TestBlastSeqLocCombine_MergeIdenticals | ) |
Definition at line 2103 of file blastfilter_unit_test.cpp.
References BlastSeqLocCombine(), BlastSeqLocFree(), ITERATE, SSeqRange::left, mask, BlastSeqLoc::next, NULL, SSeqRange::right, s_RangeVector2BlastSeqLoc(), and BlastSeqLoc::ssr.
BOOST_AUTO_TEST_CASE | ( | TestBlastSeqLocCombine_NoMerging | ) |
Definition at line 2134 of file blastfilter_unit_test.cpp.
References BlastSeqLocCombine(), BlastSeqLocFree(), ITERATE, SSeqRange::left, mask, BlastSeqLoc::next, NULL, SSeqRange::right, s_RangeVector2BlastSeqLoc(), and BlastSeqLoc::ssr.
BOOST_AUTO_TEST_CASE | ( | TestBlastSeqLocListReverse | ) |
Definition at line 2163 of file blastfilter_unit_test.cpp.
References BlastSeqLocFree(), BlastSeqLocListReverse(), ITERATE, SSeqRange::left, mask, BlastSeqLoc::next, NULL, SSeqRange::right, s_RangeVector2BlastSeqLoc(), and BlastSeqLoc::ssr.
BOOST_AUTO_TEST_CASE | ( | TestGetFilteredQueryRegions_BothStrandsOneQuery | ) |
Test the conversion of a BlastMaskLoc internal structure to the TSeqLocInfoVector type, used in formatting.
Definition at line 864 of file blastfilter_unit_test.cpp.
References eNa_strand_both, and x_TestGetFilteredQueryRegions().
BOOST_AUTO_TEST_CASE | ( | TestGetFilteredQueryRegions_MinusStrandsOneQuery | ) |
Definition at line 870 of file blastfilter_unit_test.cpp.
References eNa_strand_minus, and x_TestGetFilteredQueryRegions().
BOOST_AUTO_TEST_CASE | ( | TestGetFilteredQueryRegions_PlusStrandsOneQuery | ) |
Definition at line 867 of file blastfilter_unit_test.cpp.
References eNa_strand_plus, and x_TestGetFilteredQueryRegions().
BOOST_AUTO_TEST_CASE | ( | TestGetTaxIdWithWindowMaskerSupport | ) |
Definition at line 2187 of file blastfilter_unit_test.cpp.
References set< Key, Compare >::empty(), set< Key, Compare >::end(), set< Key, Compare >::find(), and GetTaxIdWithWindowMaskerSupport().
BOOST_AUTO_TEST_CASE | ( | TSeqLocVector2Packed_seqint_TestEmptyInput | ) |
Definition at line 442 of file blastfilter_unit_test.cpp.
References ctll::empty(), CRef< C, Locker >::Empty(), and TSeqLocVector2Packed_seqint().
BOOST_AUTO_TEST_CASE | ( | TSeqLocVector2Packed_seqint_TestIntervals | ) |
Definition at line 379 of file blastfilter_unit_test.cpp.
References CSeq_id_Base::e_Gi, i, input(), ITERATE, CSimpleOM::NewScope(), and TSeqLocVector2Packed_seqint().
BOOST_AUTO_TEST_CASE | ( | TSeqLocVector2Packed_seqint_TestNoIntervals | ) |
Definition at line 413 of file blastfilter_unit_test.cpp.
References CSeq_id_Base::e_Gi, GI_CONST, i, input(), ITERATE, CSeq_id::Match(), CSimpleOM::NewScope(), CSeq_loc::SetWhole(), and TSeqLocVector2Packed_seqint().
BOOST_AUTO_TEST_CASE | ( | WindowMasker | ) |
Definition at line 540 of file blastfilter_unit_test.cpp.
References Blast_FindWindowMaskerLoc(), eNa_strand_both, CTestObjMgr::Instance(), ITERATE, mask, and CBlastNucleotideOptionsHandle::SetWindowMaskerTaxId().
BOOST_AUTO_TEST_CASE | ( | WindowMasker_NoHitsFound | ) |
Definition at line 820 of file blastfilter_unit_test.cpp.
References Blast_FindRepeatFilterLoc(), eNa_strand_both, CTestObjMgr::Instance(), mask, and CBlastNucleotideOptionsHandle::SetWindowMaskerTaxId().
BOOST_AUTO_TEST_CASE | ( | WindowMasker_OnSeqInterval | ) |
Definition at line 758 of file blastfilter_unit_test.cpp.
References Blast_FindDustFilterLoc(), Blast_FindWindowMaskerLoc(), eNa_strand_both, CTestObjMgr::Instance(), ITERATE, mask, CBlastNucleotideOptionsHandle::SetDustFiltering(), and CBlastNucleotideOptionsHandle::SetWindowMaskerTaxId().
BOOST_AUTO_TEST_CASE | ( | WindowMaskerAndDustFilter | ) |
Definition at line 731 of file blastfilter_unit_test.cpp.
References Blast_FindDustFilterLoc(), Blast_FindWindowMaskerLoc(), Compare(), eSame, fCompareOverlapping, CTestObjMgr::Instance(), mask, CBlastNucleotideOptionsHandle::SetDustFiltering(), and CBlastNucleotideOptionsHandle::SetWindowMaskerTaxId().
BOOST_AUTO_TEST_CASE | ( | WindowMaskerWithMissingParameter | ) |
Definition at line 849 of file blastfilter_unit_test.cpp.
References Blast_FindWindowMaskerLoc(), CTestObjMgr::Instance(), and CBlastOptionsHandle::SetFilterString().
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static |
Definition at line 73 of file blastfilter_unit_test.cpp.
References BlastSeqLocNew(), ITERATE, and NULL.
Referenced by BOOST_AUTO_TEST_CASE().
void setupQueryInfoForOffsetTranslation | ( | CBlastQueryInfo & | query_info | ) |
Definition at line 1561 of file blastfilter_unit_test.cpp.
References CScope::AddDefaults(), BlastQueryInfoGetQueryLength(), CBlastOptionsFactory::Create(), eBlastTypeBlastx, eBlastx, CBlastOptionsHandle::GetOptions(), CBlastOptions::GetProgramType(), CBlastOptions::GetStrandOption(), GI_CONST, i, CTestObjMgr::Instance(), len, prog, SetupQueryInfo(), and CSeq_loc::SetWhole().
Referenced by BOOST_AUTO_TEST_CASE().
void setupQueryStructures | ( | TSeqLocVector & | query_vector, |
const CBlastOptions & | kOpts, | ||
BLAST_SequenceBlk ** | query_blk, | ||
BlastQueryInfo ** | qinfo | ||
) |
Definition at line 448 of file blastfilter_unit_test.cpp.
References CBlastOptions::GetProgramType(), CBlastOptions::GetStrandOption(), ITERATE, prog, CBlastQueryInfo::Release(), SetupQueries(), and SetupQueryInfo().
Referenced by BOOST_AUTO_TEST_CASE().
Definition at line 154 of file blastfilter_unit_test.cpp.
Referenced by CBlastFilterTest::x_TestLowerCaseMaskWith().
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static |
Definition at line 309 of file blastfilter_unit_test.cpp.
References Blast_FindDustFilterLoc(), first(), CTestObjMgr::Instance(), IsReverse(), ITERATE, mask, and query_test().
Referenced by BOOST_AUTO_TEST_CASE().
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static |
Definition at line 91 of file blastfilter_unit_test.cpp.
References CPacked_seqint::AddInterval(), BLAST_ContextToFrame(), Blast_GetSeqLocInfoVector(), Blast_ProgramNameFromType(), BlastMaskLocNew(), BlastSeqLocNew(), context, eBlastTypeBlastn, CSeqLocInfo::eFrameNotSet, TestUtil::GenerateRandomSeqid_Gi(), GetNumberOfContexts(), ITERATE, SSeqRange::left, mask, NULL, offsets, SSeqRange::right, and BlastSeqLoc::ssr.
Referenced by BOOST_AUTO_TEST_CASE().