blastxml_format.cpp File Reference

Formatting of BLAST results in XML form, using the BLAST XML specification. More...

#include <ncbi_pch.hpp>
#include <objmgr/object_manager.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objmgr/util/sequence.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqalign/Dense_diag.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqalign/Std_seg.hpp>
#include <algo/blast/format/blastxml_format.hpp>
#include <algo/blast/format/blastfmtutil.hpp>
#include <objtools/align_format/showdefline.hpp>
#include <objtools/align_format/align_format_util.hpp>
#include <serial/objostrxml.hpp>
#include <algo/blast/api/version.hpp>
#include <algorithm>

Include dependency graph for blastxml_format.cpp:

Go to the source code of this file.

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Functions
	USING_SCOPE (objects)
	USING_SCOPE (blast)
	USING_SCOPE (align_format)
static bool	s_SerializeAndSplitBy (const CSerialObject &object, const char *tag, string &start_part, string &end_part, bool add_reference_dtd, bool add_xml_version)
	serialize givem object and split data by provided XML tag for futher manual integrationa More...
static int	s_GetTranslationFrame (bool plus_strand, int start, int end, int seq_length)
	Returns translation frame given the strand, alignment endpoints and total sequence length. More...
static void	s_SeqAlignSetToXMLHsps (list< CRef< CHsp > > &xhsp_list, const CSeq_align_set &alnset, CScope *scope, const CBlastFormattingMatrix *matrix, const ncbi::TMaskedQueryRegions *mask_info, int master_gentic_code, int slave_genetic_code)
	Creates a list of CHsp structures for the XML output, given a list of Seq-aligns. More...
static void	s_SeqAlignToXMLHit (CRef< CHit > &hit, const CSeq_align &align_in, CScope *scope, const CBlastFormattingMatrix *matrix, const ncbi::TMaskedQueryRegions *mask_info, bool ungapped, int master_gentice_code, int slave_genetic_code)
	Fill the CHit object in BLAST XML output, given an alignment and other information. More...
static const CSeq_id *	s_GetSubjectId (const CSeq_align &align)
	Retrieves subject Seq-id from a Seq-align. More...
static void	s_SeqAlignSetToXMLHits (list< CRef< CHit > > &hits, const CSeq_align_set &alnset, CScope *scope, const CBlastFormattingMatrix *matrix, const ncbi::TMaskedQueryRegions *mask_info, bool ungapped, int master_gentice_code, int slave_genetic_code, CNcbiOstream *out_stream)
	Fills the list of CHit objects, given a list of Seq-aligns. More...
static void	s_BlastXMLAddIteration (CBlastOutput &bxmlout, const CSeq_align_set *alnset, const CSeq_loc &seqloc, CScope *scope, const CBlastFormattingMatrix *matrix, const ncbi::TMaskedQueryRegions *mask_info, int index, int iteration, CStatistics &stat, bool is_ungapped, int master_gentice_code, int slave_genetic_code, const vector< string > &messages, CNcbiOstream *out_stream)
	Add an "iteration" to the BLAST XML report, corresponding to all alignments for a single query. More...
static void	s_SetBlastXMLParameters (CBlastOutput &bxmlout, const IBlastXMLReportData *data)
	Fills the parameters part of the BLAST XML output. More...
static void	s_BlastXMLGetStatistics (vector< CRef< CStatistics > > &stat_vec, const IBlastXMLReportData *data)
	Fills the search statistics part of the BLAST XML output for all queries. More...
static CReference::EPublication	s_GetBlastPublication (EProgram program)
	Given BLAST task, returns enumerated value for the publication to be referenced. More...
void	BlastXML_FormatReport (CBlastOutput &bxmlout, const IBlastXMLReportData *data, CNcbiOstream *out_stream, SBlastXMLIncremental *incremental_struct)
	Fills all fields in the data structure for a BLAST XML report. More...

Variables
ncbi::TMaskedQueryRegions	mask

Detailed Description

Formatting of BLAST results in XML form, using the BLAST XML specification.

Definition in file blastxml_format.cpp.

Function Documentation

BlastXML_FormatReport()

void BlastXML_FormatReport	(	CBlastOutput &	bxmlout,
		const IBlastXMLReportData *	data,
		CNcbiOstream *	out_stream,
		SBlastXMLIncremental *	incremental_struct
	)

Fills all fields in the data structure for a BLAST XML report.

Parameters

bxmlout	BLAST XML report data structure to fill [in] [out]
data	Data structure, from which all necessary information can be retrieved [in]
out_stream	Output stream for incremental output, ignore if NULL [out]

Definition at line 679 of file blastxml_format.cpp.

References CSeq_id::AsFastaString(), CBlastFormatUtil::BlastGetVersion(), bool, data, ERR_POST, Error(), eUnknown, CBioseq_Handle::GetBioseqCore(), CScope::GetBioseqHandle(), GetId(), GetLength(), GetSeqIdString(), CReference::GetString(), NStr::IntToString(), SBlastXMLIncremental::m_IterationNum, SBlastXMLIncremental::m_SerialXmlEnd, NCBI_THROW, NcbiEmptyString, NStr::NumericToString(), s_BlastXMLAddIteration(), s_BlastXMLGetStatistics(), s_GetBlastPublication(), s_SerializeAndSplitBy(), s_SetBlastXMLParameters(), CBlastOutput_Base::SetDb(), CBlastOutput_Base::SetProgram(), CBlastOutput_Base::SetQuery_def(), CBlastOutput_Base::SetQuery_ID(), CBlastOutput_Base::SetQuery_len(), CBlastOutput_Base::SetReference(), CBlastOutput_Base::SetVersion(), string, and CException::what().

s_BlastXMLAddIteration()

static void s_BlastXMLAddIteration ( CBlastOutput &  bxmlout, const CSeq_align_set *  alnset, const CSeq_loc &  seqloc, CScope *  scope, const CBlastFormattingMatrix *  matrix, const ncbi::TMaskedQueryRegions *  mask_info, int  index, int  iteration, CStatistics &  stat, bool  is_ungapped, int  master_gentice_code, int  slave_genetic_code, const vector< string > &  messages, CNcbiOstream *  out_stream  )

static

Add an "iteration" to the BLAST XML report, corresponding to all alignments for a single query.

Parameters

bxmlout	BLAST XML output object [in]
alnset	Set of aligments for a given query. [in]
seqloc	This query's Seq-loc. [in]
scope	Scope for retrieving sequences. [in]
matrix	ASCII-alphabet matrix for calculation of positives. [in]
mask_info	List of masking locations. [in]
index	This query's index [in]
stat	Search statistics for this query, already filled. [in]
is_ungapped	Is this an ungapped search? [in]
out_stream	Stream for incremental output, ignore if NULL [out]

Definition at line 532 of file blastxml_format.cpp.

References CSeq_id::AsFastaString(), bool, CBioseq_Handle::GetBioseqCore(), CScope::GetBioseqHandle(), GetId(), GetLength(), GetSeqIdString(), NcbiEmptyString, s_SeqAlignSetToXMLHits(), s_SerializeAndSplitBy(), and CBlastOutput_Base::SetIterations().

Referenced by BlastXML_FormatReport().

s_BlastXMLGetStatistics()

static void s_BlastXMLGetStatistics ( vector< CRef< CStatistics > > &  stat_vec, const IBlastXMLReportData *  data  )

static

Fills the search statistics part of the BLAST XML output for all queries.

Parameters

stat_vec	Vector of the CStatistics objects, to be filled. [in] [out]
data	Data structure, from which all necessary information can be retrieved [in]

Definition at line 629 of file blastxml_format.cpp.

References data, CStatistics_Base::SetDb_len(), CStatistics_Base::SetDb_num(), CStatistics_Base::SetEff_space(), CStatistics_Base::SetEntropy(), CStatistics_Base::SetHsp_len(), CStatistics_Base::SetKappa(), and CStatistics_Base::SetLambda().

Referenced by BlastXML_FormatReport().

s_GetBlastPublication()

static CReference::EPublication s_GetBlastPublication ( EProgram  program )

static

Given BLAST task, returns enumerated value for the publication to be referenced.

Parameters

program

BLAST task [in]

Returns

What publication to reference?

Definition at line 653 of file blastxml_format.cpp.

References CReference::eCompBasedStats, eDeltaBlast, CReference::eDeltaBlast, CReference::eGappedBlast, eMapper, CReference::eMaxPublications, eMegablast, CReference::eMegaBlast, CReference::ePhiBlast, ePHIBlastn, ePHIBlastp, and ePSIBlast.

Referenced by BlastXML_FormatReport().

s_GetSubjectId()

static const CSeq_id* s_GetSubjectId ( const CSeq_align &  align )

static

Retrieves subject Seq-id from a Seq-align.

Parameters

align

Seq-align object [in]

Returns

Subject Seq-id for this Seq-align.

Definition at line 431 of file blastxml_format.cpp.

References CSeq_align_Base::C_Segs::GetDendiag(), CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetIds(), CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::GetStd(), CSeq_align_Base::C_Segs::IsDendiag(), CSeq_align_Base::C_Segs::IsDenseg(), CSeq_align_Base::C_Segs::IsStd(), and NULL.

Referenced by s_SeqAlignSetToXMLHits().

s_GetTranslationFrame()

static int s_GetTranslationFrame ( bool  plus_strand, int  start, int  end, int  seq_length  )

static

Returns translation frame given the strand, alignment endpoints and total sequence length.

Parameters

plus_strand	Is this position on a forward strand? [in]
start	Starting position, in 1-offset coordinates. [in]
end	Ending position in 1-offset coordinates [in]
seq_length	Total length of sequence [in]

Returns

Frame number.

Definition at line 86 of file blastxml_format.cpp.

Referenced by s_SeqAlignSetToXMLHsps().

s_SeqAlignSetToXMLHits()

static void s_SeqAlignSetToXMLHits ( list< CRef< CHit > > &  hits, const CSeq_align_set &  alnset, CScope *  scope, const CBlastFormattingMatrix *  matrix, const ncbi::TMaskedQueryRegions *  mask_info, bool  ungapped, int  master_gentice_code, int  slave_genetic_code, CNcbiOstream *  out_stream  )

static

Fills the list of CHit objects, given a list of Seq-aligns.

Parameters

hits	List of CHit objects to fill [in] [out]
alnset	Seq-align-set object containing a list of sequence alignments. [in]
scope	Scope for retrieving sequences. [in]
matrix	ASCII-alphabet matrix for calculation of positives. [in]
mask_info	List of masking locations. [in]
ungapped	Is this an ungapped search? [in]

Definition at line 453 of file blastxml_format.cpp.

References bool, eEncoding_Ascii, eNoOwnership, CSeq_align_set_Base::Get(), CSeq_id::Match(), s_GetSubjectId(), s_SeqAlignToXMLHit(), CSeq_align_set_Base::Set(), CSeq_align_Base::SetSegs(), and string.

Referenced by s_BlastXMLAddIteration().

s_SeqAlignSetToXMLHsps()

static void s_SeqAlignSetToXMLHsps ( list< CRef< CHsp > > &  xhsp_list, const CSeq_align_set &  alnset, CScope *  scope, const CBlastFormattingMatrix *  matrix, const ncbi::TMaskedQueryRegions *  mask_info, int  master_gentic_code, int  slave_genetic_code  )

static

Creates a list of CHsp structures for the XML output, given a list of Seq-aligns.

Parameters

xhsp_list	List of CHsp's to populate [in] [out]
alnset	Set of alignments to get data from [in]
scope	Scope for retrieving sequences [in]
matrix	256x256 matrix for calculating positives for a protein search. NULL is passed for a nucleotide search.
mask_info	Masking locations [in]

Definition at line 108 of file blastxml_format.cpp.

References CDense_seg::Assign(), CreateDensegFromDendiag(), CSeq_align::CreateDensegFromStdseg(), CSeq_align::CreateTranslatedDensegFromNADenseg(), CDisplaySeqalign::eN, eNa_strand_minus, CDisplaySeqalign::eX, CSeq_align_set_Base::Get(), CSeq_align::GetAlignLength(), CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CSeq_align_Base::C_Segs::GetDenseg(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CSeq_align::GetSeqStart(), CSeq_align::GetSeqStop(), CSeq_align::GetSeqStrand(), CDense_seg_Base::GetStrands(), CSeq_align::GetTotalGapCount(), CBlastFormatUtil::GetWholeAlnSeqStrings(), i, CSeq_align_Base::C_Segs::IsDendiag(), CBioseq_Handle::IsNa(), CDense_seg_Base::IsSetStrands(), CSeq_align_Base::C_Segs::IsStd(), ITERATE, min(), NcbiEmptyString, CRef< C, Locker >::Reset(), CDense_seg::Reverse(), s_GetTranslationFrame(), and tmp.

Referenced by s_SeqAlignToXMLHit().

s_SeqAlignToXMLHit()

static void s_SeqAlignToXMLHit ( CRef< CHit > &  hit, const CSeq_align &  align_in, CScope *  scope, const CBlastFormattingMatrix *  matrix, const ncbi::TMaskedQueryRegions *  mask_info, bool  ungapped, int  master_gentice_code, int  slave_genetic_code  )

static

Fill the CHit object in BLAST XML output, given an alignment and other information.

Parameters

hit	CHit object to fill [in] [out]
align_in	Sequence alignment [in]
scope	Scope for retrieving sequences [in]
matrix	ASCII-alphabet matrix for calculation of positives [in]
mask_info	List of masking locations [in]
ungapped	Is this an ungapped search? [in]

Definition at line 357 of file blastxml_format.cpp.

References _ASSERT, CSeq_id::AsFastaString(), eGetId_Best, CSeq_align_set_Base::Get(), CScope::GetBioseqHandle(), CShowBlastDefline::GetBioseqHandleDeflineAndId(), CSeq_align_Base::C_Segs::GetDisc(), GetId(), CAlignFormatUtil::GetLabel(), GetLength(), CSeq_align_Base::GetSegs(), CSeq_id_Handle::GetSeqId(), CSeq_align_Base::C_Segs::IsDisc(), NcbiEmptyString, CDisplaySeqalign::PrepareBlastUngappedSeqalign(), CRef< C, Locker >::Reset(), and s_SeqAlignSetToXMLHsps().

Referenced by s_SeqAlignSetToXMLHits().

s_SerializeAndSplitBy()

static bool s_SerializeAndSplitBy ( const CSerialObject &  object, const char *  tag, string &  start_part, string &  end_part, bool  add_reference_dtdi = false, bool  add_xml_versioni = false  )

static

serialize givem object and split data by provided XML tag for futher manual integrationa

Definition at line 771 of file blastxml_format.cpp.

References eEncoding_Ascii, eNoOwnership, eSerialVerifyData_No, string, and tag.

Referenced by BlastXML_FormatReport(), and s_BlastXMLAddIteration().

s_SetBlastXMLParameters()

static void s_SetBlastXMLParameters ( CBlastOutput &  bxmlout, const IBlastXMLReportData *  data  )

static

Fills the parameters part of the BLAST XML output.

Parameters

bxmlout	BLAST XML output object [in] [out]
data	Data structure, from which all necessary information can be retrieved [in]

Definition at line 599 of file blastxml_format.cpp.

References data, NcbiEmptyString, CParameters_Base::SetExpect(), CParameters_Base::SetFilter(), CParameters_Base::SetGap_extend(), CParameters_Base::SetGap_open(), CParameters_Base::SetMatrix(), CBlastOutput_Base::SetParam(), CParameters_Base::SetPattern(), CParameters_Base::SetSc_match(), CParameters_Base::SetSc_mismatch(), str(), and val.

Referenced by BlastXML_FormatReport().

USING_SCOPE() [1/3]

USING_SCOPE

(

align_format

)

USING_SCOPE() [2/3]

USING_SCOPE

(

blast

)

USING_SCOPE() [3/3]

USING_SCOPE

(

objects

)

Variable Documentation

mask

ncbi::TMaskedQueryRegions mask

Examples

/home/coremake/doxygen/cxx/include/corelib/ncbistr.hpp.

Definition at line 59 of file blastxml_format.cpp.

Referenced by _mm_addsub_pd(), _mm_addsub_ps(), _mm_blend_ps(), _mm_blendv_epi8(), _mm_blendv_pd(), _mm_blendv_ps(), _mm_cvtps_pi8(), _mm_maskmove_si64(), _mm_maskmoveu_si128(), _mm_test_all_zeros(), _mm_test_mix_ones_zeros(), _PHIBlastFindHitsShort(), _PHIGetRightOneBits(), CMask::Add(), CWGSMasterDescrSetter::AddChunksToWait(), CWGSMasterDescrSetter::AddChunkToWait(), CMask::AddExclusion(), CWriteDB_GiMask::AddGiMask(), AddMasterDescr(), CRequestContext::AddPassThroughProperty(), CArgDescriptions::AddStdArguments(), CCommandArgDescriptions::AddStdArguments(), CWGSMasterSupport::AddWGSMaster(), bm::bvector< Alloc >::and_bit_no_check(), CAgpErr::AppliesTo(), compile_time_bits::bitset_traits< _Ty, _Size, u_type >::assemble_mask(), CSeqDB_BitSet::AssignBitRange(), bm::avx2_andnot_arr_2_mask(), bm::avx2_bit_block_gather_scatter(), bm::avx2_bit_block_xor(), bm::avx2_bit_find_first(), bm::avx2_bit_find_first_diff(), bm::avx2_bit_to_gap(), bm::avx2_cmpge_u16(), bm::avx2_cmpge_u32(), bm::avx2_gap_bfind(), bm::avx2_lower_bound_scan_u32(), bm::avx2_set_block_bits(), bm::avx2_set_block_bits3(), bm::avx2_xor_arr_2_mask(), bm::avx512_andnot_arr_2_mask(), bm::avx512_xor_arr_2_mask(), bm::bit_block_and(), bm::bit_block_and_2way(), bm::bit_block_and_3way(), bm::bit_block_and_5way(), bm::bit_block_and_or_2way(), bm::bit_block_any_range(), bm::bit_block_is_all_one_range(), bm::bit_block_sub(), bm::bit_block_sub_2way(), bm::bit_block_sub_3way(), bm::bit_block_sub_5way(), bm::bit_block_xor(), bit_convert_to_gap(), CSeqMaskerUtil::BitCount(), Blast_FindRepeatFilterLoc(), Blast_FindWindowMaskerLoc(), Blast_GetSeqLocInfoVector(), BLAST_MainSetUp(), BlastHashLookupIndexQueryExactMatches(), BlastResCompStr(), BlastSeqLoc_RestrictToInterval(), bm::block_init_digest0(), BOOST_AUTO_TEST_CASE(), BVImportTest(), bm::calc_block_digest0(), CalcBeginMask(), CalcEndMask(), CGlAttrGuard::CGlAttrGuard(), bm::check_zero_digest(), CDirEntry::CheckAccess(), bm::bvector_mini< A >::clear_bit(), CWriteDB_LMDB::SKeyValuePair::cmp_key(), CSeqDBAliasNode::ComputeMasks(), ComputeTableIndexIncremental(), TMaskedQueryRegions::ConvertToCPacked_seqint(), DeBruijn::CReadHolder::CopyBits(), CountNs(), CountNucleotides(), compile_time_bits::bitset_traits< _Ty, _Size, u_type >::ct_set(), compile_time_bits::const_bitset< static_cast< size_t >(eTestNames::max_test_names), eTestNames >::ct_set(), CWGSMasterDescrSetter::CWGSMasterDescrSetter(), dbnextrow(), dbreadtext(), bm::digest_mask(), DoAnchoredScan(), CSeqMasker::DoMask(), ecp_mod_koblitz(), xml::impl::epimpl::epimpl(), xml::event_parser::event_parser(), CPipe::ExecWait(), CTar::Extract(), bm::sparse_vector< Val, BV >::extract(), bm::sparse_vector< Val, BV >::extract_planes(), CBlastDBExtractor::ExtractFasta(), CBlastDBExtractor::ExtractSeqData(), CNCBlobStorage::FindBlob(), CSampleLibraryObject::FindInPath(), flip_bit(), FNV_hash(), bm::for_each_bit_blk(), bm::bit_out< TEncoder >::gamma(), bitvec< unsigned int >::get(), bm::bit_in< TDecoder >::get_bit(), bm::bvector_mini< A >::get_next(), get_pkcs_padding(), bm::base_sparse_vector< Val, BV, MAX_SIZE >::get_slice_mask(), get_zeros_and_len_padding(), get_zeros_padding(), CNCBlobStorage::GetBList(), CGBDataLoader_Native::GetBlobs(), GetDefaultLogLocation(), CCgiApplication::GetDefaultLogPath(), CDir::GetEntries(), CDir::GetEntriesPtr(), CAgpErr::GetErrorMessage(), CBlastQuerySourceOM::GetMaskedRegions(), CSeqDBAliasNode::GetMaskList(), CSeqVecSeqInfoSrc::GetMasks(), CRemoteBlast::GetMasks(), CSparseGraph::GetMissingRegions(), CGBDataLoader_Native::GetOrphanAnnotRecordsNA(), CSnpBitfield1_2::GetWeight(), CSnpBitfield2::GetWeight(), TMaskedQueryRegions::HasNegativeStrandMasks(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::import_char_slice(), bm::bvector< Alloc >::inc(), inflate_table(), CInputStreamSource::InitArgs(), CSeqportUtil_implementation::InitMasks(), bm::sparse_vector< Val, BV >::insert_value_no_null(), bm::bvector_mini< A >::is_bit_true(), bm::is_digest_one_range(), CGridCommandLineInterfaceApp::IsOptionAccepted(), CComponentIDToolApp::IsOptionAccepted(), CGridCommandLineInterfaceApp::IsOptionExplicitlySet(), CComponentIDToolApp::IsOptionExplicitlySet(), CGridCommandLineInterfaceApp::IsOptionSet(), CComponentIDToolApp::IsOptionSet(), LBSM_LookupService(), LBSM_LookupServiceEx(), CAgpRow::LinkageEvidenceFlagsToString(), CReadDispatcher::LoadBlobs(), CId2ReaderBase::LoadBlobs(), CReader::LoadBlobs(), CWGSMasterDescrSetter::Loaded(), LZCNTTest(), mark_fd(), MarkUsed(), CPathHook::Match(), CBlob_Info::Matches(), CDirEntry::MatchesMask(), NStr::MatchesMask(), mbedtls_clz(), mbedtls_ct_memcpy_if_eq_ncbicxx_2_28_8(), mbedtls_ct_mpi_uint_cond_assign_ncbicxx_2_28_8(), mbedtls_ct_size_mask_lt(), mbedtls_ct_uint_if_ncbicxx_2_28_8(), mbedtls_ssl_decrypt_buf_ncbicxx_2_28_8(), CGlState::MergeStates(), mgf_mask(), NcbiGetHostIfConfEx(), NcbiIPv6Subnet(), NcbiIPv6Suffix(), NcbiIsInIPv6Network(), CSubjectMap_Factory_Base::NewSequenceInit(), DeBruijn::LargeInt< precision >::oahash(), odbc_set_string_flag(), DeBruijn::IntegerTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::cast_from_other::operator()(), CPipeHandle::Poll(), CPipe::Poll(), poly1305_compute_mac(), CGlRender::PolygonStipple(), CGlRenderDebug::PolygonStipple(), CGlState::PolygonStipple(), CRenderVector::PolygonStipple(), CSparseKmerCounts::PreCount(), bm::sparse_vector_scanner< SV, S_FACTOR >::prepare_and_sub_aggregator(), CMaskWriterBlastDbMaskInfo::Print(), CMaskWriterFasta::Print(), CMaskWriterInt::Print(), CMaskWriterSeqLoc::Print(), CMaskWriterTabular::Print(), CMaskWriterInt::PrintMasks(), CNCActiveSyncControl::PrintState(), bm::aggregator< BV >::process_bit_blocks_and(), bm::aggregator< BV >::process_bit_blocks_sub(), bm::random_subset< BV >::process_word(), CTbl2AsnApp::ProcessOneDirectory(), CTAbleValApp::ProcessOneDirectory(), psa_key_slot_clear_bits(), psa_key_slot_get_flags(), psa_key_slot_set_bits_in_flags(), psa_key_slot_set_flags(), CGlRender::PushAttrib(), CGlRenderDebug::PushAttrib(), CRenderVector::PushAttrib(), bm::bit_out< TEncoder >::put_bits(), CObjectIStreamAsn::ReadBitString(), CObjectIStreamAsnBinary::ReadBitString(), CObjectIStreamXml::ReadBitString(), CObjectIStreamJson::ReadCustomBytes(), CMask::Remove(), CFileObsolete::Remove(), CMask::RemoveExclusion(), CSparseKmerCounts::Reset(), compile_time_bits::const_bitset< static_cast< size_t >(eTestNames::max_test_names), eTestNames >::reset(), CPluginManager_DllResolver::ResolveFile(), TMaskedQueryRegions::RestrictToSeqInt(), subfuse::CSubfuseApp::Run(), CTLSApp::Run(), s_AddMask(), s_AddWordHit(), s_BlastNaHashScanSubject_Any(), s_BlastNaScanSubject_Any(), s_BlastSmallNaScanSubject_Any(), s_ConvertBlastnMasks(), s_ConvertToBlastQueries(), s_CreateWordArray(), s_FillMaskLocFromBlastResults(), s_FindHitProbability(), s_FindHitsLong(), s_FindNumIdentical(), s_FindPrefixAndSuffixPos(), s_GetBlastnMask(), s_GetMaskSeqLoc(), s_GuessProgram(), s_HexDumpText(), s_IncludeDefline_MaskFilter(), s_IsGoodDescr(), s_LenOf(), s_LenOfL(), CBinaryRangeCacheWithLock< Position, Value >::s_MakeRange(), s_MaskingTest(), s_MatchesMask(), s_MatchExcludeMask(), s_MBCountWordsInSubject_16_1(), s_MBScanSubject_Any(), s_ModeToTar(), s_NaHashLookupCountWordsInSubject_16_1(), s_PHIGetLongPattern(), s_PHIGetShortPattern(), s_TestMaskingLimits(), NAdapterSearch::s_Translate(), SERV_PrintFirewallPorts(), bm::miniset< A, N >::set(), bm::bvmini< N >::set(), compile_time_bits::const_bitset< static_cast< size_t >(eTestNames::max_test_names), eTestNames >::set(), bitvec< unsigned int >::set(), bm::bvector_mini< A >::set_bit(), bm::bvector< Alloc >::set_bit_conditional_impl(), bm::bvector< Alloc >::set_bit_no_check(), bm::sparse_vector< Val, BV >::set_value_no_null(), CRemoteBlast::SetDbFilteringAlgorithmId(), CRemoteBlast::SetDbFilteringAlgorithmKey(), CGridJobBatchSubmitter::SetJobMask(), CGridClient::SetJobMask(), CPdfObject::SetLineDashStyle(), CBlastInputSourceConfig::SetLowercaseMask(), CTar::SetMask(), CArchive::SetMask(), CJob::SetMask(), CBDB_BufferManager::SetNullBit(), CAlnRowState::SetRowState(), SetSeqAnnotChoiceMask(), SetSeqIdChoiceMask(), SetupQueries_OMF(), bm::sse2_andnot_arr_2_mask(), bm::sse2_bit_block_xor(), bm::sse2_bit_find_first(), bm::sse2_bit_find_first_diff(), bm::sse2_lower_bound_scan_u32(), bm::sse2_xor_arr_2_mask(), bm::sse42_bit_block_xor(), bm::sse42_bit_find_first(), bm::sse42_bit_find_first_diff(), bm::sse42_cmpge_u32(), SSeqLoc::SSeqLoc(), ssl_bitmask_check(), ssl_bitmask_set(), ssl_parse_encrypted_pms(), StringToCode(), TestBlockToGAP(), CBDB_BufferManager::TestNullBit(), TestSignedSparseVectorSerial(), TestSparseVector_XOR_Scanner(), TestSparseVectorSerial(), Uint8ToBytes(), bm::update_block_digest0(), UTIL_MatchesMask(), UTIL_MatchesMaskEx(), CAsnvalApp::ValidateOneDirectory(), bm::widx_to_digest_mask(), CRegexp::WildcardToRegexp(), CBlastDB_SeqFormatter::Write(), CObjectOStreamAsn::WriteBitString(), CObjectOStreamAsnBinary::WriteBitString(), CObjectOStreamJson::WriteBitString(), CObjectOStreamXml::WriteBitString(), CNCBlobStorage::WriteBlobList(), CObjectOStreamJson::WriteCustomBytes(), CNCBlobStorage::WriteDbInfo(), CWriteDB_GiMaskData::WriteMask(), CSeqdesc_CI::x_AddChoice(), CNcbiApplicationAPI::x_AddDefaultArgs(), CTar::x_Append(), CSQLITE_Connection::x_CheckFlagsValidity(), CElementaryMatching::x_CleanVolumes(), CSeqDBOIDList::x_ComputeFilters(), seqmasks_io_fixture::x_ConvertMasks(), CWriteDB_OidList::x_CreateBitMap(), CNCMessageHandler::x_DoCmd_GetConfig(), CString_constraint::x_DoesSingleStringMatchConstraint(), CWGSMasterDescrSetter::x_GetActualExistingDescrMask(), CBioseq_Base_Info::x_GetExistingDescrMask(), CGBDataLoader_Native::x_GetRecords(), CRequestContext::x_LoadEnvContextProperties(), seqmasks_io_fixture::x_LoadMaskedBioseq(), CGBDataLoader_Native::x_MakeContentMask(), x_MatchesMask(), CGlState::x_MergeFlag(), x_NameMatch(), CPipeHandle::x_Poll(), CId2ReaderBase::x_ProcessGetBlobId(), CAsn2FastaApp::x_ProcessISubdirectory(), CCleanupApp::x_ProcessOneDirectory(), CTar::x_ReadAndProcess(), CSeqdesc_CI::x_RemoveChoice(), CBioseq_Base_Info::x_SearchFirstDesc(), CSNPDbFeatIterator::x_SetFilter(), CRemoteBlast::x_SetOneParam(), CMenuItem::x_SetState(), CIgBlast::x_SetupCRegionSearch(), CIgBlast::x_SetupDbSearch(), CIgBlast::x_SetupDJSearch(), CIgBlast::x_SetupNoOverlapDSearch(), NFast::x_sse_ConvertBuffer(), x_TestGetFilteredQueryRegions(), x_TestGetSeqLocInfoVector(), CBlastFilterTest::x_TestLowerCaseMaskWith(), CBDB_Cache::x_TruncateDB(), CSeqDBDemo_Thread::x_UseOID(), and bm::xor_bit_block().