Include dependency graph for ct_nlmzip_trees.cpp:
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Classes | |
| struct | ct_data |
| struct | tree_desc |
Macros | |
| #define | MAX_BITS 15 |
| #define | MAX_BL_BITS 7 |
| #define | LENGTH_CODES 29 |
| #define | LITERALS 256 |
| #define | END_BLOCK 256 |
| #define | L_CODES (LITERALS+1+LENGTH_CODES) |
| #define | D_CODES 30 |
| #define | BL_CODES 19 |
| #define | STORED_BLOCK 0 |
| #define | STATIC_TREES 1 |
| #define | DYN_TREES 2 |
| #define | LIT_BUFSIZE 0x8000 |
| #define | REP_3_6 16 |
| #define | REPZ_3_10 17 |
| #define | REPZ_11_138 18 |
| #define | Freq fc.freq |
| #define | Code fc.code |
| #define | Dad dl.dad |
| #define | Len dl.len |
| #define | HEAP_SIZE (2*L_CODES+1) |
| #define | send_code(c, tree) Nlmzip_send_bits(tree[c].Code, tree[c].Len) |
| #define | d_code(dist) |
| #define | URMAX(a, b) (a >= b ? a : b) |
| #define | SMALLEST 1 |
| #define | pqremove(tree, top) |
| #define | smaller(tree, n, m) |
| #define | l_buf Nlmzip_inbuf /* overlay l_buf and Nlmzip_inbuf */ |
Typedefs | |
| typedef BEGIN_CTRANSITION_SCOPE struct ct_data | ct_data |
| typedef struct tree_desc | tree_desc |
Functions | |
| static void | init_block (void) |
| static void | pqdownheap (ct_data *, int) |
| static void | gen_bitlen (tree_desc *) |
| static void | gen_codes (ct_data *, int) |
| static void | build_tree (tree_desc *) |
| static void | scan_tree (ct_data *, int) |
| static void | send_tree (ct_data *, int) |
| static int | build_bl_tree (void) |
| static void | send_all_trees (int, int, int) |
| static void | compress_block (ct_data *, ct_data *) |
| static void | set_file_type (void) |
| void | Nlmzip_ct_init (ush *attr, int *methodp) |
| ulg | Nlmzip_flush_block (char *buf, ulg stored_len, int eof) |
| int | Nlmzip_ct_tally (int dist, int lc) |
Variables | |
| static int | extra_lbits [29] |
| static int | extra_dbits [30] |
| static int | extra_blbits [19] |
| static ct_data | dyn_ltree [(2 *(256+1+29)+1)] |
| static ct_data | dyn_dtree [2 *30+1] |
| static ct_data | static_ltree [(256+1+29)+2] |
| static ct_data | static_dtree [30] |
| static ct_data | bl_tree [2 *19+1] |
| static tree_desc | l_desc |
| static tree_desc | d_desc |
| static tree_desc | bl_desc |
| static unsigned short | bl_count [15+1] |
| static unsigned char | bl_order [19] |
| static int | heap [2 *(256+1+29)+1] |
| static int | heap_len |
| static int | heap_max |
| static unsigned char | depth [2 *(256+1+29)+1] |
| static unsigned char | length_code [258 - 3+1] |
| static unsigned char | dist_code [512] |
| static int | base_length [29] |
| static int | base_dist [30] |
| static unsigned char | flag_buf [(0x8000/8)] |
| static Uint4 | last_lit |
| static Uint4 | last_dist |
| static Uint4 | last_flags |
| static uch | flags |
| static uch | flag_bit |
| static ulg | opt_len |
| static ulg | static_len |
| static ulg | compressed_len |
| static ush * | file_type |
| static int * | file_method |
Macro Definition Documentation
◆ BL_CODES
| #define BL_CODES 19 |
Definition at line 120 of file ct_nlmzip_trees.cpp.
◆ Code
| #define Code fc.code |
Definition at line 161 of file ct_nlmzip_trees.cpp.
◆ d_code
| #define d_code | ( | dist | ) |
Definition at line 177 of file ct_nlmzip_trees.cpp.
◆ D_CODES
| #define D_CODES 30 |
Definition at line 117 of file ct_nlmzip_trees.cpp.
◆ Dad
| #define Dad dl.dad |
Definition at line 162 of file ct_nlmzip_trees.cpp.
◆ DYN_TREES
| #define DYN_TREES 2 |
Definition at line 125 of file ct_nlmzip_trees.cpp.
◆ END_BLOCK
| #define END_BLOCK 256 |
Definition at line 110 of file ct_nlmzip_trees.cpp.
◆ Freq
| #define Freq fc.freq |
Definition at line 160 of file ct_nlmzip_trees.cpp.
◆ HEAP_SIZE
| #define HEAP_SIZE (2*L_CODES+1) |
Definition at line 166 of file ct_nlmzip_trees.cpp.
◆ l_buf
| #define l_buf Nlmzip_inbuf /* overlay l_buf and Nlmzip_inbuf */ |
Definition at line 332 of file ct_nlmzip_trees.cpp.
◆ L_CODES
| #define L_CODES (LITERALS+1+LENGTH_CODES) |
Definition at line 114 of file ct_nlmzip_trees.cpp.
◆ Len
| #define Len dl.len |
Definition at line 163 of file ct_nlmzip_trees.cpp.
◆ LENGTH_CODES
| #define LENGTH_CODES 29 |
Definition at line 105 of file ct_nlmzip_trees.cpp.
◆ LIT_BUFSIZE
| #define LIT_BUFSIZE 0x8000 |
Definition at line 146 of file ct_nlmzip_trees.cpp.
◆ LITERALS
| #define LITERALS 256 |
Definition at line 108 of file ct_nlmzip_trees.cpp.
◆ MAX_BITS
| #define MAX_BITS 15 |
Definition at line 99 of file ct_nlmzip_trees.cpp.
◆ MAX_BL_BITS
| #define MAX_BL_BITS 7 |
Definition at line 102 of file ct_nlmzip_trees.cpp.
◆ pqremove
| #define pqremove | ( | tree, | |
| top | |||
| ) |
Definition at line 191 of file ct_nlmzip_trees.cpp.
◆ REP_3_6
| #define REP_3_6 16 |
Definition at line 152 of file ct_nlmzip_trees.cpp.
◆ REPZ_11_138
| #define REPZ_11_138 18 |
Definition at line 158 of file ct_nlmzip_trees.cpp.
◆ REPZ_3_10
| #define REPZ_3_10 17 |
Definition at line 155 of file ct_nlmzip_trees.cpp.
◆ send_code
Definition at line 171 of file ct_nlmzip_trees.cpp.
◆ smaller
Definition at line 202 of file ct_nlmzip_trees.cpp.
◆ SMALLEST
| #define SMALLEST 1 |
Definition at line 186 of file ct_nlmzip_trees.cpp.
◆ STATIC_TREES
| #define STATIC_TREES 1 |
Definition at line 124 of file ct_nlmzip_trees.cpp.
◆ STORED_BLOCK
| #define STORED_BLOCK 0 |
Definition at line 123 of file ct_nlmzip_trees.cpp.
◆ URMAX
Typedef Documentation
◆ ct_data
| typedef BEGIN_CTRANSITION_SCOPE struct ct_data ct_data |
◆ tree_desc
Function Documentation
◆ build_bl_tree()
Definition at line 800 of file ct_nlmzip_trees.cpp.
References BL_CODES, bl_desc, bl_order, bl_tree, build_tree(), d_desc, dyn_dtree, dyn_ltree, l_desc, Len, tree_desc::max_code, opt_len, and scan_tree().
Referenced by Nlmzip_flush_block().
◆ build_tree()
Definition at line 588 of file ct_nlmzip_trees.cpp.
References depth, tree_desc::dyn_tree, tree_desc::elems, Freq, gen_bitlen(), gen_codes(), heap, heap_len, heap_max, HEAP_SIZE, tree_desc::max_code, n, opt_len, pqdownheap(), pqremove, SMALLEST, static_len, tree_desc::static_tree, uch, and URMAX.
Referenced by build_bl_tree(), and Nlmzip_flush_block().
◆ compress_block()
Definition at line 866 of file ct_nlmzip_trees.cpp.
References base_dist, base_length, d_code, END_BLOCK, extra_dbits, extra_lbits, flag_buf, l_buf, last_lit, lc, length_code, LITERALS, Nlmzip_d_buf, Nlmzip_send_bits(), and send_code.
Referenced by Nlmzip_flush_block().
◆ gen_bitlen()
Definition at line 439 of file ct_nlmzip_trees.cpp.
References bl_count, tree_desc::dyn_tree, tree_desc::extra_base, tree_desc::extra_bits, f(), heap, heap_max, HEAP_SIZE, Len, MAX_BITS, tree_desc::max_code, tree_desc::max_length, n, opt_len, static_len, and tree_desc::static_tree.
Referenced by build_tree().
◆ gen_codes()
Definition at line 542 of file ct_nlmzip_trees.cpp.
References bl_count, len, Len, MAX_BITS, n, and Nlmzip_bi_reverse().
Referenced by build_tree(), and Nlmzip_ct_init().
◆ init_block()
|
static |
Definition at line 364 of file ct_nlmzip_trees.cpp.
References BL_CODES, bl_tree, D_CODES, dyn_dtree, dyn_ltree, END_BLOCK, flag_bit, flags, L_CODES, last_dist, last_flags, last_lit, n, opt_len, and static_len.
Referenced by Nlmzip_ct_init(), and Nlmzip_flush_block().
◆ Nlmzip_ct_init()
Definition at line 938 of file ct_nlmzip_trees.cpp.
References base_dist, base_length, bl_count, compressed_len, D_CODES, dist_code, extra_dbits, extra_lbits, file_method, file_type, gen_codes(), init_block(), L_CODES, Len, length_code, LENGTH_CODES, MAX_BITS, n, Nlmzip_bi_reverse(), static_dtree, static_ltree, and uch.
Referenced by Nlmzip_Compress().
◆ Nlmzip_ct_tally()
Definition at line 1120 of file ct_nlmzip_trees.cpp.
References d_code, D_CODES, DIST_BUFSIZE, dyn_dtree, dyn_ltree, extra_dbits, flag_bit, flag_buf, flags, Freq, l_buf, last_dist, last_flags, last_lit, lc, length_code, LIT_BUFSIZE, LITERALS, Nlmzip_block_start, Nlmzip_d_buf, Nlmzip_level, Nlmzip_strstart, and uch.
Referenced by deflate_fast(), and Nlmzip_deflate().
◆ Nlmzip_flush_block()
Definition at line 1033 of file ct_nlmzip_trees.cpp.
References buf, build_bl_tree(), build_tree(), compress_block(), compressed_len, d_desc, dyn_dtree, dyn_ltree, DYN_TREES, file_type, flag_buf, flags, init_block(), l_desc, last_flags, tree_desc::max_code, Nlmzip_bi_windup(), Nlmzip_copy_block(), Nlmzip_send_bits(), opt_len, send_all_trees(), set_file_type(), static_dtree, static_len, static_ltree, STATIC_TREES, STORED_BLOCK, and UNKNOWN.
◆ pqdownheap()
Definition at line 396 of file ct_nlmzip_trees.cpp.
References heap, heap_len, and smaller.
Referenced by build_tree().
◆ scan_tree()
Definition at line 679 of file ct_nlmzip_trees.cpp.
References bl_tree, n, REP_3_6, REPZ_11_138, and REPZ_3_10.
Referenced by build_bl_tree().
◆ send_all_trees()
Definition at line 842 of file ct_nlmzip_trees.cpp.
References bl_order, bl_tree, dyn_dtree, dyn_ltree, Len, Nlmzip_send_bits(), and send_tree().
Referenced by Nlmzip_flush_block().
◆ send_tree()
Definition at line 736 of file ct_nlmzip_trees.cpp.
References bl_tree, n, Nlmzip_send_bits(), REP_3_6, REPZ_11_138, REPZ_3_10, and send_code.
Referenced by send_all_trees().
◆ set_file_type()
|
static |
Definition at line 920 of file ct_nlmzip_trees.cpp.
References BINARY, and file_type.
Referenced by Nlmzip_flush_block().
Variable Documentation
◆ base_dist
|
static |
Definition at line 327 of file ct_nlmzip_trees.cpp.
Referenced by compress_block(), and Nlmzip_ct_init().
◆ base_length
|
static |
Definition at line 324 of file ct_nlmzip_trees.cpp.
Referenced by compress_block(), CSeqDBVol::GetAmbigPartialSeq(), CMultAlign::InsertDashesInReads(), Nlmzip_ct_init(), s_Ncbi4naToNcbi2na(), s_SeqDBMapNA2ToNA4(), SeqDB_UnpackAmbiguities(), WriteDB_Ncbi2naToBinary(), WriteDB_Ncbi4naToBinary(), and CSeqDBVol::x_GetAmbigSeq().
◆ bl_count
|
static |
Definition at line 294 of file ct_nlmzip_trees.cpp.
Referenced by gen_bitlen(), gen_codes(), Nlmzip_ct_init(), and tr_static_init().
◆ bl_desc
|
static |
Definition at line 283 of file ct_nlmzip_trees.cpp.
Referenced by build_bl_tree().
◆ bl_order
|
static |
Definition at line 299 of file ct_nlmzip_trees.cpp.
Referenced by build_bl_tree(), and send_all_trees().
◆ bl_tree
|
static |
Definition at line 261 of file ct_nlmzip_trees.cpp.
Referenced by build_bl_tree(), init_block(), scan_tree(), send_all_trees(), and send_tree().
◆ compressed_len
|
static |
Definition at line 348 of file ct_nlmzip_trees.cpp.
Referenced by CChangePhyloTreeCommand::CChangePhyloTreeCommand(), CBDB_ExtBlobStore< TBV >::Flush(), Nlmzip_ct_init(), Nlmzip_flush_block(), and TKmerMethods< TKmerCounts >::SetParams().
◆ d_desc
|
static |
Definition at line 273 of file ct_nlmzip_trees.cpp.
Referenced by build_bl_tree(), and Nlmzip_flush_block().
◆ depth
|
static |
Definition at line 312 of file ct_nlmzip_trees.cpp.
Referenced by CDebugDumpViewer::Bpt(), build_tree(), CPrintTraversalNodeCallback::Call(), CSeqMap::CanResolveRange(), CGlTexture::CGlTexture(), CImage::CImage(), CTreeNode< TValue, TKeyGetterP >::CountNodes(), DTDParser::CreateEmbeddedName(), DTDElement::CreateEmbeddedName(), CSeq_loc_Mapper::CSeq_loc_Mapper(), CBlastOptions::DebugDump(), CSeqDB::DebugDump(), CSerialObject::DebugDump(), CBlastOptionsLocal::DebugDump(), CSeqDBAliasFile::DebugDump(), CSeqDB_BitSet::DebugDump(), CSeqDB_AliasMask::DebugDump(), CSeqDBImpl::DebugDump(), CSeqDBOIDList::DebugDump(), CDebugDumpable::DebugDumpFormat(), DebugDumpPairsCRefCRef(), DebugDumpPairsPtrCRef(), DebugDumpPairsPtrPtr(), DebugDumpPairsValuePtr(), DebugDumpRangeCRef(), DebugDumpRangeObj(), DebugDumpRangePtr(), CDebugDumpable::DebugDumpText(), CNCBlobStorage::DeleteBlobInfo(), CDemoApp::Dispatch(), CTaxFormat::DisplayLineageReport(), DTDParser::FixEmbeddedNames(), CImageUtil::FlipX(), CSeqUtils::GetAnnotSelector(), NSnpBins::GetBinSelector(), CDate_std::GetDate(), CSGUtils::GetFeatFetchDepth(), CObjectIStream::GetParentObjectPtr(), CObjectIStreamAsnBinary::GetTagPattern(), CImage::Init(), CObjectStack::IsKnownElement(), CDebugDumpContext::Log(), MapSeq_feat(), CObjectTypeInfo::MatchPattern(), mdb_page_merge(), CMessageListener_Stack::PopListener(), IMessageListener::PopListener(), CObjectStack::PushFrameLong(), CNCBlobStorage::ReadChunkData(), CImageIORaw::ReadImage(), CImageIO::ReadImageInfo(), CObjectIStreamXml::ReadName(), C5ColExportJob::Run(), CGffExportJob::Run(), CGtfExportJob::Run(), CDemoApp::Run(), CImageDemoApp::Run(), s_CheckDefClientConfig(), s_CollectClientConfigKeys(), s_SaveChunkMap(), bm::xor_scanner< BV >::search_best_xor_mask(), CSeqGraphicConfig::SetAnnotDepth(), CDemoApp::SetChoice(), CDemoApp::SetClass(), CDemoApp::SetContainer(), CSGGenBankDS::SetDepth(), CGenBankAsyncWriterEx< _Token >::SetDepth(), TMultiSourceFileSet< _enum, _options... >::SetDepth(), CImage::SetDepth(), CDemoApp::SetDispatch(), CDemoApp::SetPointer(), CDemoApp::SetPrimitive(), SAnnotSelector::SetResolveDepth(), CSeqUtils::SetResolveDepth(), CSGSegmentMapDS::SetSegmentLevel(), CObjectIStreamAsnBinary::SkipAnyContent(), TestSparseVectorGatherDecode(), CSimpleDesktopItem::UpdatePositions(), CCompositeDesktopItem::UpdatePositions(), CRootDesktopItem::UpdatePositions(), CDemoApp::WalkChoice(), CDemoApp::WalkClass(), CDemoApp::WalkContainer(), CDemoApp::WalkPointer(), CImageIORaw::WriteImage(), CAnnot_Collector::x_CollectSegments(), CSGSegmentMapDS::x_ConceptualToRealDepth(), CFeaturePanel::x_ConfigureSubtracks(), CAnnot_Collector::x_Initialize(), CSeq_loc_Mapper::x_InitializeSeqMap(), CSGSegmentSmearJob::x_LoadFromDeltaSeqs(), CTaxFormat::x_MapTaxInfoTemplate(), CSeqMap_CI::x_Push(), CAllOtherFeaturesTrack::x_ReinitFeatureTrack(), CAnnot_Collector::x_SearchSegments(), and x_ServiceName().
◆ dist_code
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static |
Definition at line 321 of file ct_nlmzip_trees.cpp.
Referenced by Nlmzip_ct_init().
◆ dyn_dtree
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static |
Definition at line 246 of file ct_nlmzip_trees.cpp.
Referenced by build_bl_tree(), init_block(), Nlmzip_ct_tally(), Nlmzip_flush_block(), and send_all_trees().
◆ dyn_ltree
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static |
Definition at line 245 of file ct_nlmzip_trees.cpp.
Referenced by build_bl_tree(), init_block(), Nlmzip_ct_tally(), Nlmzip_flush_block(), and send_all_trees().
◆ extra_blbits
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static |
Definition at line 240 of file ct_nlmzip_trees.cpp.
◆ extra_dbits
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static |
Definition at line 233 of file ct_nlmzip_trees.cpp.
Referenced by compress_block(), Nlmzip_ct_init(), and Nlmzip_ct_tally().
◆ extra_lbits
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static |
Definition at line 226 of file ct_nlmzip_trees.cpp.
Referenced by compress_block(), and Nlmzip_ct_init().
◆ file_method
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static |
Definition at line 351 of file ct_nlmzip_trees.cpp.
Referenced by Nlmzip_ct_init().
◆ file_type
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static |
Definition at line 350 of file ct_nlmzip_trees.cpp.
Referenced by CBlastLMDBManager::CBlastEnv::CBlastEnv(), CFileDiagHandler::ComposeMessage(), CBlastLMDBManager::GetBlastEnv(), GetFileNameFromExistingLMDBFile(), GetLogFile(), CFileDiagHandler::GetLogFile(), CFileDiagHandler::GetLogStream(), CBlastLMDBManager::CBlastEnv::InitDbi(), Nlmzip_ct_init(), Nlmzip_flush_block(), CPhyExportPage::OnButton2Click(), CExportTreeDlg::OnSelectFileClick(), s_CreateHandler(), s_GetFileName(), set_file_type(), CFileDiagHandler::SetLogFile(), SetLogFile(), CFileDiagHandler::SetSubHandler(), CSaveFileHelper::ShowSaveDialog(), CFileDiagHandler::WriteMessage(), and CFileDiagHandler::x_GetHandler().
◆ flag_bit
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static |
Definition at line 343 of file ct_nlmzip_trees.cpp.
Referenced by init_block(), and Nlmzip_ct_tally().
◆ flag_buf
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static |
Definition at line 333 of file ct_nlmzip_trees.cpp.
Referenced by compress_block(), Nlmzip_ct_tally(), and Nlmzip_flush_block().
◆ flags
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static |
- Examples
- /home/coremake/doxygen/cxx/include/corelib/ncbimisc.hpp, and /home/coremake/doxygen/cxx/include/corelib/ncbistr.hpp.
Definition at line 342 of file ct_nlmzip_trees.cpp.
Referenced by _tWinMain(), CListeningSocket::Accept(), CAlnMixMatches::Add(), CAlnMixSequences::Add(), CAlnMix::Add(), CSeq_loc::Add(), CSeqFetchQueue::Add(), CUICommand::AddAccelerator(), CCommandArgDescriptions::AddCommand(), CArgDescriptions::AddDefaultKey(), CArgDescriptions::AddDefaultPositional(), CNetCacheKey::AddExtensions(), CArgDescriptions::AddExtra(), CFeatureTableReader_Imp::AddFeatQual(), CFeature_table_reader::AddFeatQual(), CArgDescriptions::AddFlag(), CScope::AddGC_Assembly(), CArgDescriptions::AddKey(), CWGSDb_Impl::AddMasterDescr(), CSeqSearch::AddNucleotidePattern(), CArgDescriptions::AddOpening(), CArgDescriptions::AddOptionalKey(), CArgDescriptions::AddOptionalPositional(), CMultipatternSearch::AddPattern(), CArgDescriptions::AddPositional(), CSAM_CIGAR_Formatter::AddRow(), AddStandardAlignmentScores(), CEnumeratedTypeValues::AddValue(), CTextUtil::AddWordFrequencies(), CUrl::Adjust(), CSeq_id::AdjustScore(), CBDB_File::Append(), xml::node::append_to_string(), CNWFormatter::AsDenseSeg(), CSplignFormatter::AsExonTable(), CArg_Ios::AsInputFile(), CArg_Ios::AsIOFile(), CObjectIStream::AsnIo::AsnIo(), CObjectOStream::AsnIo::AsnIo(), CArg_Ios::AsOutputFile(), CNWFormatter::AsSeqAlign(), CReadUtil::AsSeqId(), IRWRegistry::AssessImpact(), CStopWatch::AsSmartString(), CTimeSpan::AsSmartString(), variation_ref::CHgvsParser::AsVariationFeat(), CDirEntry::Backup(), BDB_RecoverEnv(), lmdb::txn::begin(), impl::binary_to_hex_string(), BOOST_AUTO_TEST_CASE(), BuildAln(), CSeqMap::CanResolveRange(), CArg_InputFile::CArg_InputFile(), CArg_IOFile::CArg_IOFile(), CArg_Ios::CArg_Ios(), CArg_OutputFile::CArg_OutputFile(), CArgDescMandatory::CArgDescMandatory(), CBedColumnData::CBedColumnData(), CBlastRPSInfo::CBlastRPSInfo(), CBlobOStream::CBlobOStream(), CBlobStoreStatic::CBlobStoreStatic(), CBlobWriter::CBlobWriter(), CByteStreamBuf::CByteStreamBuf(), CBZip2Compressor::CBZip2Compressor(), CBZip2Decompressor::CBZip2Decompressor(), CCgiContext::CCgiContext(), CCgiRequest::CCgiRequest(), CCgiEntries_Parser::CCgiRequestTFlagsToTFlags(), CCgiUserAgent::CCgiUserAgent(), CDatagramSocket::CDatagramSocket(), CDiagFileHandleHolder::CDiagFileHandleHolder(), CDll::CDll(), CEndpointKey::CEndpointKey(), CFastaBioseqSource::CFastaBioseqSource(), CFastaReader::CFastaReader(), CGff3LocationRecord::CGff3LocationRecord(), CGtfLocationRecord::CGtfLocationRecord(), check_flags(), CheckPairwiseAln(), CAlnMapPrinter::Chunks(), CTable2AsnValidator::Cleanup(), IRWRegistry::Clear(), CNetStorageObjectLoc::ClearLocatorFlags(), CListeningSocket::CListeningSocket(), NDirectNetStorageImpl::CObj::Clone(), CLZOCompressor::CLZOCompressor(), CLZODecompressor::CLZODecompressor(), CNamedPipeClient::CNamedPipeClient(), CNcbiRegistry::CNcbiRegistry(), NDirectNetStorageImpl::CObj::CObj(), CProjBulderApp::CollectDep(), CBDB_Transaction::Commit(), CBDB_RawFile::CompactEx(), CSeq_loc::Compare(), Compare(), CSDB_ConnectionParam::ComposeUrl(), CCgiApplication::ConfigureDiagFormat(), CONN_CreateEx(), CONN_SetFlags(), CUNIXSocket::Connect(), CSocket::Connect(), Convert_Container_Object(), Convert_Seq_align_ProjectItem(), Convert_Seq_align_set_ProjectItem(), Convert_Seq_feat_Seq_loc_dbxref_Loc(), Convert_Seq_id_Bioseq(), Convert_Seq_loc_Seq_id(), CFeatureGenerator::ConvertLocToAnnot(), CDirEntry::Copy(), CFile::Copy(), CDir::Copy(), CSymLink::Copy(), AbstractParser::CopyLineComment(), CDirEntry::CopyToDir(), CORE_SetLOGFormatFlags(), CBDB_RawFile::CountRecs(), CPoolBalancer::CPoolBalancer(), CDirectNetStorage::Create(), lmdb::env::create(), CDir::Create(), NDirectNetStorageImpl::SContext::Create(), SNetStorageRPC::Create(), CNetStorage::Create(), SDirectNetStorageImpl::Create(), CreateAnchoredAlnFromAln(), CCgiApplication::CreateContextWithFlags(), CCgi2RCgiApp::CreateContextWithFlags(), CCgiApplication::CreateContextWithFlags_Default(), CBDB_RawFile::CreateCursor(), CGeneModel::CreateGeneModelFromAlign(), CGeneModel::CreateGeneModelsFromAligns(), CSQLITE_HandleFactory::CreateObject(), CDir::CreatePath(), CSparseRowHandle::CreateSegmentIterator(), CAlnVecRowHandle::CreateSegmentIterator(), CAlnVecMultiDataSource::CreateSegmentIterator(), CAlnVecGraphicDataSource::CreateSegmentIterator(), CFeatureTableReader_Imp::CreateSeqFeat(), CFeature_table_reader::CreateSeqFeat(), CBDB_Env::CreateTxn(), CRegexp::CRegexp(), CSeq_annot_CI::CSeq_annot_CI(), CSeq_id::CSeq_id(), CSeqEntryIndex::CSeqEntryIndex(), CSimpleBlobStore::CSimpleBlobStore(), CSocket::CSocket(), CSplitQueryTestFixture::CSplitQueryTestFixture(), CSQLITE_Connection::CSQLITE_Connection(), CSysLog::CSysLog(), CTimeFormat::CTimeFormat(), CUNIXListeningSocket::CUNIXListeningSocket(), CUNIXSocket::CUNIXSocket(), lmdb::cursor_del(), lmdb::cursor_put(), CVersionInfo::CVersionInfo(), CxBlobWriter::CxBlobWriter(), CZipCompressor::CZipCompressor(), CZipDecompressor::CZipDecompressor(), Daemonize(), CCurrentProcess::Daemonize(), CProcess::Daemonize(), lmdb::dbi_flags(), lmdb::dbi_open(), lmdb::dbi_put(), DBLB_GetServer(), CLZOCompression::DecompressBlock(), CLZOCompression::DecompressBlockStream(), CCgiRequest::Deserialize(), CNCBINode::DoAppendChild(), NStr::DoubleToString(), DSOCK_CreateEx(), dumpit(), IRegistry::Empty(), IRegistry::EnumerateEntries(), CSynRegistryToIRegistry::EnumerateEntries(), IRegistry::EnumerateInSectionComments(), CSynRegistryToIRegistry::EnumerateInSectionComments(), IRegistry::EnumerateSections(), CSynRegistryToIRegistry::EnumerateSections(), lmdb::env_copy(), lmdb::env_copy_fd(), lmdb::env_get_flags(), lmdb::env_open(), lmdb::env_set_flags(), ErrSetOptFlags(), CLZOCompression::EstimateCompressionBufferSize(), CGffObjectLoader::Execute(), SDirectNetStorageImpl::Exists(), CDirectNetStorageByKey::Exists(), SDirectNetStorageByKeyImpl::Exists(), CNetStorageByKey::Exists(), CwxTableListCtrl::ExportTableControlToCSV(), CTar::Extract(), ExtractStorageFlags(), CFindRSites::Find(), find_firstassertedchar(), FindBlastDBs(), CCompoundRegistry::FindByContents(), CCompoundRWRegistry::FindByContents(), FindFiles(), FindFiles2(), FindFilesInDir(), CFeatureGenerator::SImplementation::FixOrderOfCrossTheOriginSeqloc(), CNcbiDiag::ForceImportantFlags(), CCurrentProcess::Fork(), CProcess::Fork(), CCurrentProcess::ForkForExec(), CFlatStringQVal::Format(), CFlatNumberQVal::Format(), CFlatBondQVal::Format(), CFlatGeneQVal::Format(), CFlatSiteQVal::Format(), CFlatStringListQVal::Format(), CFlatOrgModQVal::Format(), CFlatSubSourceQVal::Format(), CFlatXrefQVal::Format(), CFlatGoQVal::Format(), CFlatProductNamesQVal::Format(), CFlatFileConfig::FromArguments(), CFlatFileGenerator::Generate(), CDeflineGenerator::GenerateDefline(), CEnumTypeStrings::GenerateTypeCode(), CSynRegistry::CInclude::Get(), CFeatImporter::Get(), IRegistry::Get(), CSynRegistryToIRegistry::Get(), GetAccessionForGi(), GetAccessionForId(), CSeqUtils::GetAccessionPlacements(), CSeqUtils::GetAccessionPlacementsMsec(), CScope_Impl::GetAccVer(), CScope::GetAccVer(), CScope_Impl::GetAccVers(), GetAlignmentFromStream(), CAlnMap::GetAlnChunks(), CSeqUtils::GetAnnotSelector(), CWGSSeqIterator::GetAnnotSet(), CWGSProteinIterator::GetAnnotSet(), CWGSSeqIterator::GetBioseq(), CWGSScaffoldIterator::GetBioseq(), CWGSProteinIterator::GetBioseq(), CStatement::GetBlobOStream(), CResultSet::GetBlobOStream(), CCursor::GetBlobOStream(), CStatement::GetBlobWriter(), CCursor::GetBlobWriter(), IRegistry::GetBool(), CWGSSeqIterator::GetChunk(), CWGSSeqIterator::GetChunkData(), CVDBGraphDataLoader_Impl::GetChunkOnce(), IRegistry::GetComment(), CSynRegistryToIRegistry::GetComment(), CSNPDbSeqIterator::GetCoverageAnnot(), GetDateErrorDescription(), SAnnotSelector::GetDefaultAdaptiveDepthFlags(), IRegistry::GetDouble(), CBioseqEditor::GetEditFlags(), IRegistry::GetEncryptedString(), CDir::GetEntries(), CDir::GetEntriesPtr(), CSNPDbSeqIterator::GetEntry(), CSNPDbSeqIterator::GetFeatAnnot(), SNetStorageRPC::GetFlags(), CBamFileAlign::GetFlags(), CBamAlignIterator::GetFlags(), CScope_Impl::GetGi(), CScope::GetGi(), GetGiForAccession(), GetGiForId(), CSeqUtils::GetGiPlacements(), CScope_Impl::GetGis(), CWGSSeqIterator::GetId(), CWGSScaffoldIterator::GetId(), CWGSProteinIterator::GetId(), SSeqIdRange::const_iterator::GetID(), CWGSSeqIterator::GetIds(), CWGSScaffoldIterator::GetIds(), CWGSProteinIterator::GetIds(), CScope::GetIds(), CScope_Impl::GetIds(), IRegistry::GetInt(), GetLabel(), CScope::GetLabel(), CScope_Impl::GetLabel(), CSeq_id::GetLabel(), ICitationBase::GetLabel(), CPub::GetLabel(), CPub_equiv::GetLabel(), CPub_set::GetLabel(), CScope_Impl::GetLabels(), CAuth_list::GetLabelV1(), CCit_art::GetLabelV1(), CCit_book::GetLabelV1(), CCit_gen::GetLabelV1(), CCit_let::GetLabelV1(), CCit_proc::GetLabelV1(), CCit_sub::GetLabelV1(), CMedline_entry::GetLabelV1(), CAuth_list::GetLabelV2(), CAuthor::GetLabelV2(), CCit_art::GetLabelV2(), CCit_book::GetLabelV2(), CCit_gen::GetLabelV2(), CCit_jour::GetLabelV2(), CCit_let::GetLabelV2(), CCit_pat::GetLabelV2(), CCit_proc::GetLabelV2(), CCit_sub::GetLabelV2(), CId_pat::GetLabelV2(), CMedline_entry::GetLabelV2(), CRegexp_loc::GetLoc(), CRegexp::GetMatch(), CSeqEntrySource::GetNext(), CBlobBookmarkImpl::GetOStream(), CRemoteQFB::GetOStream(), CQueryBlobImpl::GetOStream(), CQuery::CField::GetOStream(), CBlobBookmark::GetOStream(), CHandleRange::GetOverlappingRange(), CSNPDbSeqIterator::GetOverviewAnnot(), CSNPDbSeqIterator::GetOverviewGraph(), GetPackedFeatAnnot(), CTimeFormat::GetPredefined(), CWGSSeqIterator::GetQualityAnnot(), CReaderBase::GetReader(), CComplexRelation::GetRelated(), CBasicRelation::GetRelated(), CRelationTypeConverterAdapter::GetRelated(), CSplignSimple::GetResultsAsAln(), CAlnVecRow::GetRowStatistics(), CWGSSeqIterator::GetSeq_descr(), CWGSScaffoldIterator::GetSeq_descr(), CWGSProteinIterator::GetSeq_descr(), CWGSSeqIterator::GetSeq_entry(), CWGSScaffoldIterator::GetSeq_entry(), CWGSProteinIterator::GetSeq_entry(), CWGSSeqIterator::GetSeq_entryData(), CSNPDbFeatIterator::GetSeq_feat(), CWGSSeqIterator::GetSeq_inst(), CAlnMap::GetSeqChunks(), CGffBaseColumns::GetSeqId(), CSeq_id::GetSeqIdString(), CGffBaseColumns::GetSeqLoc(), GetSeqLocFromStream(), CScope::GetSequenceHash(), CScope_Impl::GetSequenceHash(), CScope_Impl::GetSequenceHashes(), CScope::GetSequenceLength(), CScope_Impl::GetSequenceLength(), CScope_Impl::GetSequenceLengths(), CScope::GetSequenceState(), CScope_Impl::GetSequenceState(), CScope_Impl::GetSequenceStates(), CScope::GetSequenceType(), CScope_Impl::GetSequenceType(), CScope_Impl::GetSequenceTypes(), CCSraShortReadIterator::GetShortBioseq(), CBamAlignIterator::GetShortSeq_id(), CWGSSeqIterator::GetSplitInfo(), CSNPDbSeqIterator::GetSplitInfoAndVersion(), CWGSSeqIterator::GetSplitInfoAndVersion(), CWGSSeqIterator::GetSplitInfoData(), CWGSSeqIterator::GetSplitInfoDataAndVersion(), CTextUtil::GetStemFrequencies(), CNetStorageObjectLoc::GetStorageAttrFlags(), IRegistry::GetString(), CSNPDbSeqIterator::GetTableFeatAnnots(), CScope::GetTaxId(), CScope_Impl::GetTaxId(), CScope_Impl::GetTaxIds(), GetTitle(), IRegistry::GetValue(), CWGSClient::GetWGSData(), CTextUtil::GetWordFrequencies(), CAlignGroup::GroupBySeqIds(), CAlignGroup::GroupBySequenceType(), IRegistry::HasEntry(), CSeqMap::HasSegmentOfType(), CWGSSeqIterator::HasSeq_descr(), CWGSScaffoldIterator::HasSeq_descr(), CWGSProteinIterator::HasSeq_descr(), CHTMLHelper::HTMLAttributeEncode(), CHTMLHelper::HTMLEncode(), CHTMLHelper::HTMLJavaScriptEncode(), HTTP_CreateConnector(), HTTP_CreateConnectorEx(), HTTP_CreateTunnel(), HTTP_CreateTunnelEx(), CSeq_id::IdentifyAccession(), CNcbiRegistry::IncludeNcbircIfAllowed(), CSplitContentIndex::IndexChunkContent(), variation::CVariationUtil::InferNAfromAA(), inflateSync(), CCgi2RCgiApp::Init(), CPsgClientApp::Init(), SThrottleParams::SIOFailureThreshold::Init(), init_block(), CGff2Record::InitializeFeature(), CGffBaseColumns::InitializeFeature(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::insert(), CAlignRangeCollection< CAlignRange< TSeqPos > >::insert(), CBDB_File::Insert(), NStr::Int8ToString(), CSeq_loc::Intersect(), NStr::IntToString(), CArg_Ios::IosMode(), IsBlobSuppressed(), IsBlobWithdrawn(), CCgiUserAgent::IsBot(), IsHistorySuppressed(), CRegexp::IsMatch(), IRegistry::IsNameEntry(), IRegistry::IsNameSection(), CBamAlignIterator::IsSecondary(), IsSeqAnnotChoiceSelected(), IsSeqIdChoiceSelected(), CAlignRangeCollection< CAlignRange< TSeqPos > >::IsSet(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::IsSet(), CValidator::IsValidDbxref(), CBDB_Env::JoinEnv(), CStdPoolOfThreads::KillAllThreads(), CUNIXListeningSocket::Listen(), CListeningSocket::Listen(), CMetaRegistry::Load(), CDll::Load(), CFastaObjectLoader::LoadAlignsFromStream(), CSNPSeqInfo::LoadAnnotBlob(), CCompoundRWRegistry::LoadBaseRegistries(), CWGSFileInfo::LoadBlob(), CSNPSeqInfo::LoadBlob(), CFastaObjectLoader::LoadFromStream(), CCSRAFileInfo::LoadReadsBlob(), CFileLock::Lock(), LOG_ComposeMessage(), NStr::LongToString(), LSOCK_AcceptEx(), LSOCK_CreateEx(), LSOCK_CreateUNIX(), main(), CSeq_loc_Mapper_Base::Map(), IRWRegistry::MaybeSet(), mbedtls_mpi_gen_prime_ncbicxx_2_28_3(), mbedtls_ssl_check_cert_usage_ncbicxx_2_28_3(), mbedtls_x509_crt_verify_info_ncbicxx_2_28_3(), mbedtls_x509_crt_verify_ncbicxx_2_28_3(), mbedtls_x509_crt_verify_restartable_ncbicxx_2_28_3(), mbedtls_x509_crt_verify_with_profile_ncbicxx_2_28_3(), mdb_cursor_del(), mdb_cursor_put(), mdb_dbi_flags(), mdb_dbi_open(), mdb_del0(), mdb_env_copy2(), mdb_env_copyfd2(), mdb_env_cwalk(), mdb_env_map(), mdb_env_open(), mdb_env_open2(), mdb_env_sync(), mdb_env_write_meta(), mdb_fopen(), mdb_node_add(), mdb_node_move(), mdb_page_new(), mdb_page_search(), mdb_page_search_root(), mdb_page_split(), mdb_put(), mdb_txn_begin(), mdb_txn_renew0(), CAlnMixMerger::Merge(), CAlnMix::Merge(), CSeq_loc::Merge(), MergePairwiseAlns(), SNetStorageRPC::MkObjectRequest(), IRegistry::Modified(), CDirEntry::MoveToDir(), mz_zip_extract_archive_file_to_heap(), mz_zip_extract_archive_file_to_heap_v2(), mz_zip_reader_extract_file_iter_new(), mz_zip_reader_extract_file_to_callback(), mz_zip_reader_extract_file_to_cfile(), mz_zip_reader_extract_file_to_file(), mz_zip_reader_extract_file_to_heap(), mz_zip_reader_extract_file_to_mem(), mz_zip_reader_extract_file_to_mem_no_alloc(), mz_zip_reader_extract_iter_new(), mz_zip_reader_extract_to_callback(), mz_zip_reader_extract_to_cfile(), mz_zip_reader_extract_to_file(), mz_zip_reader_extract_to_heap(), mz_zip_reader_extract_to_mem(), mz_zip_reader_extract_to_mem_no_alloc(), mz_zip_reader_init(), mz_zip_reader_init_cfile(), mz_zip_reader_init_file(), mz_zip_reader_init_file_v2(), mz_zip_reader_init_internal(), mz_zip_reader_init_mem(), mz_zip_reader_locate_file(), mz_zip_reader_locate_file_v2(), mz_zip_reader_read_central_dir(), mz_zip_string_equal(), mz_zip_validate_archive(), mz_zip_validate_file(), mz_zip_validate_file_archive(), mz_zip_validate_mem_archive(), mz_zip_writer_init_cfile(), mz_zip_writer_init_file_v2(), mz_zip_writer_init_from_reader_v2(), mz_zip_writer_init_heap_v2(), mz_zip_writer_init_v2(), NcbiLog_UpdateOnFork(), CSDBAPI::NewBlobStore(), CDatabase::NewBlobStore(), Nlm_MemGet(), Nlmzip_ct_tally(), Nlmzip_flush_block(), Nlmzip_lm_init(), NStr::NumericToString(), CMoreTableColsDlg::OnColTableLeftDown(), CProjectTreePanel::OnDragOver(), CProjectTreePanel::OnDrop(), CProjectTreePanel::OnEndDrag(), CMapControl::OnKeyDown(), CwxTreeCtrlEx::OnLeftDown(), CPhyloSaveSelectiondlg::OnLeftDown(), CTrackListCtrl::OnLeftDown(), wxCheckedListCtrl::OnMouseEvent(), CwxTreeCtrl::OnMouseMove(), lmdb::env::open(), SDirectNetStorageByKeyImpl::Open(), CBDB_Env::Open(), CFileIO::Open(), CNamedPipeHandle::Open(), CNamedPipeClient::Open(), SNetStorageByKeyRPC::Open(), CNetStorageByKey::Open(), CDirectNetStorageByKey::Open(), MSerial_Format_AsnText::operator()(), MSerial_Format_Json::operator()(), MSerial_Format_Xml::operator()(), CMetaRegistry::SKey::operator<(), operator<<(), CDiscrepancyProductImpl::OutputText(), CDiscrepancyProductImpl::OutputXML(), CCustomTree::Paint(), CJsonNode::ParseArray(), ParseAttributes(), CSeq_id::ParseFastaIds(), CSeq_id::ParseIDs(), CJsonNode::ParseJSON(), CJsonNode::ParseObject(), pcre_dfa_exec(), pcre_exec(), PIPE_CreateConnector(), CValidError_imp::PostBadDateError(), CNCBINode::Print(), CVersionAPI::Print(), CDataType::PrintASNTypeComments(), CVersionAPI::PrintJson(), CBlastFormat::PrintOneResultSet(), CBlastFormat::PrintPhiResult(), PrintSAMUnaligned(), CHTMLText::PrintString(), CArgDesc::PrintXml(), CVersionAPI::PrintXml(), CProjectTreeBuilder::ProcessDir(), CTAbleValApp::ProcessOneFile(), ProductToSource(), PromoteCdregion(), PromoteFeatures(), CNCActiveHandler::ProxyWrite(), CGFFReader::Read(), IRWRegistry::Read(), CRmReader::Read(), ReadFasta(), ReadFastaQueries(), ReadFastaSeqsFromFile(), ReadMsa(), ReadPhrap(), CFeatureTableReader::ReadProtein(), CFeature_table_reader::ReadSequinFeatureTable(), CFeatureTableReader_Imp::ReadSequinFeatureTable(), CFeature_table_reader::ReadSequinFeatureTables(), RecursiveSummary(), RecursiveText(), RecursiveXML(), CMetaRegistry::Reload(), CNcbiApplicationAPI::ReloadConfig(), CNetStorage::Relocate(), CNetStorageByKey::Relocate(), SNetStorageObjectRPC::Relocate(), CDirectNetStorageObject::Relocate(), NDirectNetStorageImpl::CObj::Relocate(), CNetStorageByKey::Remove(), CDirEntry::Remove(), CDir::Remove(), CDirEntry::RemoveEntry(), CDirEntry::Rename(), CFileHandleDiagHandler::Reopen(), CFileDiagHandler::Reopen(), CAsyncDiagHandler::Reopen(), CTeeDiagHandler::Reopen(), CException::Report(), CExceptionReporterStream::Report(), CException::ReportAll(), CExceptionReporter::ReportDefault(), CExceptionReporter::ReportDefaultEx(), CHTMLException::ReportExtra(), CException::ReportStd(), CException::ReportThis(), CJsonNode::Repr(), CThreadPool_Impl::RequestExclusiveExecution(), CThreadPool::RequestExclusiveExecution(), CThreadPool_Impl::RequestSuspend(), CArgDescriptions::ResetMiscFlags(), SRelLoc::Resolve(), CSeqMap::ResolvedRangeIterator(), CGffExportJob::Run(), CGtfExportJob::Run(), CThread::Run(), CMultiApplication::Run(), CBlastDbCheckApplication::Run(), CFeatImportApp::Run(), CMultipatternApp::Run(), CDemoApp::Run(), CAce2AsnApp::Run(), CBDB_Env::RunBackgroundWriter(), CBDB_Env::RunCheckpointThread(), s_Accept(), s_AddEntry(), s_CheckCompressionFlags(), s_CheckGZipHeader(), s_CheckLZOHeader(), s_Close(), s_CollectAllLeaves(), CSplign::s_ComputeStats(), s_Connect(), s_CopyAttrs(), s_Create(), s_CreateConnector(), s_CreateHttpConnector(), s_CreateListening(), s_CreateOnTop(), s_Daemonize(), s_DirCreate(), s_FastaStringToBioseq(), s_FormatFlagsToFlags(), s_GeneCommentaryToLocations(), CPsgClientApp::s_GetCommand(), s_GetContentLabel(), s_GetFileSystemInfo(), s_GetFlags(), s_GetImpLabel(), s_GetLabel(), s_GetProteinName(), s_GetRealCompileFlags(), s_GetRealMatchFlags(), s_GetRnaRefLabel(), s_GetRnaRefLabelFromComment(), s_GetTopology(), s_GetTypeLabel(), s_GetVariationLabel(), s_HTMLEncode(), s_IdLabel(), s_Init(), s_IsNameSectionSymbol(), s_IsNote(), s_KeyUsageSynopsis(), s_MemAllocator(), SUvNgHttp2_Session< SH2S_Session >::s_OnData(), SUvNgHttp2_Session< SH2S_Session >::s_OnHeader(), s_OpenLogFiles(), s_OrganelleName(), s_PrintBase10Uint8(), s_Repr_Array(), s_Repr_Object(), s_Repr_Value(), s_SeqLocToTotalRangesInfoMapByStrand(), s_SetCloexec(), s_SetDiagPostAllFlags(), s_SetDiagPostFlag(), s_SetFlags(), s_SetNonblock(), s_SetStorageFlags(), s_SocketConnectorBuilder(), s_Test_Extremes(), s_Test_Interval(), s_TestForOverlapEx(), s_TitleFromProtein(), s_TitleFromSegment(), s_TranslateBlobStoreFlags(), s_TranslateToAlnCoords(), s_UnsetDiagPostFlag(), s_WriteGZipHeader(), s_WriteLZOHeader(), NStr::Sanitize(), xml::document::save_to_file(), xml::document::save_to_stream(), xml::document::save_to_string(), xml::node::save_to_string(), xml::document::save_to_string_canonical(), SDiagMessage::SDiagMessage(), CGetSeqLocFromStringHelper::Seq_loc_Add(), CGetSeqLocFromStringHelper_ReadLocFromText::Seq_loc_Add(), Seq_loc_Add(), Seq_loc_Merge(), Seq_loc_Subtract(), Seq_locs_Merge(), CSeq_id::Set(), CRegexp_loc::Set(), IRWRegistry::Set(), CRegexp::Set(), CSDB_ConnectionParam::Set(), lmdb::env::set_flags(), SAnnotSelector::SetAdaptiveDepthFlags(), CFastaOstream::SetAllFlags(), CNcbiApplicationAPI::SetAppFlags(), IRWRegistry::SetComment(), CDelayBuffer::SetData(), SAnnotSelector::SetDefaultAdaptiveDepthFlags(), CObjectConverter::SetDefaultFlags(), SetDiagPostAllFlags(), SetDiagTraceAllFlags(), SetDiagUserAndHost(), CAsnElementItem::SetEditFlags(), CFlatFileTextItem::SetEditFlags(), CNCBINode::SetExceptionFlags(), CObjectOStream::SetFailFlags(), CObjectIStream::SetFailFlags(), CObjectOStream::SetFailFlagsNoError(), CLDS2_Manager::SetFastaFlags(), CSoapServerApplication::SetFaultPostFlags(), CFlatFileConfig::SetFlags(), CFeatureGenerator::SetFlags(), CNetICacheClient::SetFlags(), CExceptionArgs_Base::SetFlags(), SSeqMapSelector::SetFlags(), CSeqMap_CI::SetFlags(), CSeqref::SetFlags(), CPromote::SetFlags(), CSAM_Formatter::SetFlags(), CFastaOstreamComp::SetFlags(), CArchive::SetFlags(), CCompression::SetFlags(), CTar::SetFlags(), CAsyncWriteCache::SetFlags(), CSQLITE_Connection::SetFlags(), CTimeFormat::SetFormat(), MSerial_Flags::SetFormatFlags(), CObjectOStream::SetFormattingFlags(), CObjectOStreamXml::SetFormattingFlags(), CHttpSession_Base::SetHttpFlags(), CFeatureGenerator::SetIntronStitchThresholdFlags(), CNetStorageObjectLoc::SetLocatorFlags(), CAlnUserOptions::SetMergeFlags(), CArgDescriptions::SetMiscFlags(), CDirEntry::SetMode(), CDir::SetMode(), CDirEntry::SetModeEntry(), IRegistry::SetModifiedFlag(), variation::CVariationUtil::SetPlacementProperties(), CCgiApplication::SetRequestFlags(), SetSeqAnnotChoiceMask(), SetSeqIdChoiceMask(), CLDS2_Database::SetSQLiteFlags(), CNetStorageObjectLoc::SetStorageAttrFlags(), CLayoutTrack::SetTrackAttr(), CBioseq_ScopeInfo::SetUnresolved(), CSplitCacheApp::SetupCache(), IRWRegistry::SetValue(), CBDB_CheckPointThread::SetWorkFlag(), pythonpp::SMethodDef::SMethodDef(), SOCK_CreateConnectorEx(), SOCK_CreateEx(), SOCK_CreateInternal(), SOCK_CreateOnTopEx(), SOCK_CreateOnTopInternal(), SOCK_CreateUNIX(), SourceToProduct(), NStr::Split(), NStr::SplitByPattern(), SRelLoc::SRelLoc(), sRunTest(), SSeqIdRange::SSeqIdRange(), ssl_pick_cert(), CBDB_Cache::StartPurgeThread(), SPSG_ThrottleParams::SThreshold::SThreshold(), NStr::StringToDouble(), NStr::StringToInt(), NStr::StringToNonNegativeInt(), NStr::StringToNumeric(), CSeq_loc::Subtract(), sUpdateCase(), SWGSCreateInfo::SWGSCreateInfo(), sx_AddMasterDescr(), CParam< TDescription >::sx_IsSetFlag(), sx_SetOverviewName(), tdefl_compress_lz_codes(), tdefl_compress_mem_to_heap(), tdefl_compress_mem_to_mem(), tdefl_compress_mem_to_output(), tdefl_init(), tds7_send_auth(), tds_answer_challenge(), tds_answer_challenge_ntlmv2(), tds_ntlm_handle_next(), tds_parse_conf_section(), tds_process_col_fmt(), tds_put_data_info(), tds_put_data_info_length(), tds_put_params(), tds_readpassphrase(), tds_submit_query_params(), TestForOverlapEx(), TestSimpleAlignment(), TestSparseIt(), CCgiEntries_Parser::TFlagsToCCgiRequestTFlags(), CObjectIStream::ThrowError1(), CObjectOStream::ThrowError1(), tinfl_decompress_mem_to_callback(), tinfl_decompress_mem_to_heap(), tinfl_decompress_mem_to_mem(), CJson_ConstNode::ToString(), CSeqTranslator::Translate(), CPaintSequence::TranslateCDS(), CBamRawAlignIterator::TryGetFlags(), CBamFileAlign::TryGetFlags(), CBamAlignIterator::TryGetFlags(), lmdb::txn_begin(), NStr::UInt8ToString(), NStr::UInt8ToString_DataSize(), NStr::UIntToString(), NStr::ULongToString(), IRWRegistry::Unset(), CGff2Record::UpdateFeature(), URL_Connect(), URL_ConnectEx(), UTIL_PrintableStringEx(), CAlignRangeCollection< CAlignRange< TSeqPos > >::Validate(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::Validate(), CValidError_imp::ValidateDbxref(), CSubSource::ValidateLatLonCountry(), CAlignRangeCollection< CAlignRange< TSeqPos > >::ValidateRanges(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::ValidateRanges(), CCassBlobTaskLoadBlob::Wait1(), CCassStatusHistoryTaskGetPublicComment::Wait1(), NStr::Wrap(), CFlatItemFormatter::Wrap(), NStr::WrapList(), SDiagMessage::Write(), IRegistry::Write(), CJson_Document::Write(), CChecksum::WriteHexSum(), x509_crt_merge_flags_with_cb(), x509_crt_verify_chain(), x509_crt_verify_name(), x509_crt_verify_restartable_ca_cb(), x509_crt_verifycrl(), IFlatQVal::x_AddFQ(), CSeqSearch::x_AddNucleotidePattern(), CSeqSearch::x_AddPattern(), SWGSCreateInfo::x_AddProducts(), CFeatureTableReader_Imp::x_AddQualifierToFeature(), CFeatureItem::x_AddQualsProt(), x_AdjustAnchorDirection(), CTimeSpan::x_AsSmartString_Precision(), CTimeSpan::x_AsSmartString_Smart_Big(), CTimeSpan::x_AsSmartString_Smart_Small(), IRegistry::x_CheckFlags(), CSQLITE_Connection::x_CheckFlagsValidity(), CAlignCleanup::x_Cleanup_AlignVec(), CAlignCleanup::x_Cleanup_AnchoredAln(), CEnvironmentRegistry::x_Clear(), CTwoLayerRegistry::x_Clear(), CCompoundRWRegistry::x_Clear(), CNcbiRegistry::x_Clear(), CAnnot_Collector::x_CollectSegments(), CAlnMap::x_CompareAdjacentSegTypes(), CBlastFormat::x_ConfigCShowBlastDefline(), CWGSSeqIterator::x_CreateEntry(), CWGSScaffoldIterator::x_CreateEntry(), CFeatureTableReader_Imp::x_CreateGenesFromCDSs(), CNetStorageHandler::x_CreateObjectStream(), CArg_Ios::x_CreatePath(), CGroupAlignmentsJob::x_CreateProjectItems(), CMergeAlignmentsJob::x_CreateProjectItems(), SWGSCreateInfo::x_CreateProtSet(), x_DataToGiData(), CBDB_RawFile::x_DB_CPut(), CBDB_RawFile::x_DB_Fetch(), CBDB_RawFile::x_DB_Put(), CBDB_RawFile::x_DBC_Fetch(), CBioseqIndex::x_DefaultSelector(), CNetStorageHandler::x_DetectMetaDBNeedOnCreate(), CNetStorageHandler::x_DetectMetaDBNeedOnGetObjectInfo(), CNetStorageHandler::x_DetectMetaDBNeedUpdate(), CFeatureSearchJob::x_DoSearch(), CBioseq_Base_Info::x_DoUpdate(), CBioseq_Info::x_DoUpdate(), CBioseq_set_Info::x_DoUpdate(), CSeq_entry_Info::x_DoUpdate(), CSeq_annot_SNP_Info::x_DoUpdate(), CTSE_Info::x_DoUpdate(), CTSE_Info_Object::x_DoUpdate(), CCompoundRegistry::x_Empty(), CTwoLayerRegistry::x_Empty(), CCompoundRWRegistry::x_Empty(), CSynRegistryToIRegistry::x_Empty(), CEnvironmentRegistry::x_Enumerate(), CMemoryRegistry::x_Enumerate(), CCompoundRegistry::x_Enumerate(), CTwoLayerRegistry::x_Enumerate(), CCompoundRWRegistry::x_Enumerate(), CSeqSearch::x_ExpandPattern(), CBDB_File::x_Fetch(), x_FindRSite(), CAlnVecRow::x_ForEachAlnSeg(), CFeatureItem::x_FormatGOQualCombined(), CFeatureItem::x_FormatNoteQual(), CSourceFeatureItem::x_FormatNoteQual(), CFeatureItem::x_FormatQual(), CSourceFeatureItem::x_FormatQual(), CDeflineItem::x_GatherInfo(), CEnvironmentRegistry::x_Get(), CCompoundRegistry::x_Get(), CTwoLayerRegistry::x_Get(), CCompoundRWRegistry::x_Get(), CAlnVecRow::x_GetAlignmentTooltip_Helper(), CAlnMap::x_GetChunks(), CCompoundRegistry::x_GetComment(), CTwoLayerRegistry::x_GetComment(), CCompoundRWRegistry::x_GetComment(), CNcbiRegistry::x_GetComment(), CDBPoolBalancer::x_GetFlags(), x_GetLabel_Content(), x_GetLabel_Type(), CCit_art::x_GetLabelV2(), CAuthor::x_GetLabelV2(), CNetStorageHandler::x_GetObject(), CMultiAlignView::x_GetRowSeqLoc(), CWGSSeqIterator::x_GetSegmentsWithExplicitGaps(), CSAM_CIGAR_Formatter::x_GetSeqIdString(), CNetStorageHandler::x_GetStorageParams(), x_Glob(), CEnvironmentRegistry::x_HasEntry(), CMemoryRegistry::x_HasEntry(), CCompoundRegistry::x_HasEntry(), CTwoLayerRegistry::x_HasEntry(), CCompoundRWRegistry::x_HasEntry(), CSeq_id::x_IdentifyAccession(), variation::CVariationUtil::x_InferNAfromAA(), CCgiRequest::x_Init(), CDll::x_Init(), CBlastRPSInfo::x_Init(), CSeq_annot_CI::x_Initialize(), CSeqMasterIndex::x_Initialize(), CAgpConverter::x_InitializeCopyOfTemplate(), CFeatureTableReader_Imp::x_InitId(), CBlastFastaInputSource::x_InitInputReader(), CCgiRequest::x_InitRequestContext(), CCgiContext::x_InitSession(), CDockContainer::x_InstantiateNode(), CSeqSearch::x_IsAllowMismatch(), CSeqSearch::x_IsExpandPattern(), CSeqSearch::x_IsJustTopStrand(), CMetaRegistry::x_Load(), CFileLoader::x_LoadGff(), CGBProjectTool::x_LoadGffData(), seqmasks_io_fixture::x_LoadMaskedBioseq(), CAlnPrinterFixture::x_LoadSequences(), CDataSource::x_LockTSE(), CRegexp::x_Match(), x_MatchStrand(), x_mdb_txn_begin(), x_MergeAndSort(), x_MergeNoSort(), x_MergeRanges(), CEnvironmentRegistry::x_Modified(), CCompoundRegistry::x_Modified(), CTwoLayerRegistry::x_Modified(), CCompoundRWRegistry::x_Modified(), CSynRegistryToIRegistry::x_Modified(), SDiagMessage::x_NewWrite(), NStr::x_NumericToString(), SDiagMessage::x_OldWrite(), CBDB_Env::x_Open(), CArg_InputFile::x_Open(), CArg_OutputFile::x_Open(), CArg_IOFile::x_Open(), CDiscRepApp::x_Output(), CAlnReader::x_ParseAndValidateSeqIds(), CCgiUserAgent::x_ParseToken(), CAlnSpanVertModel::x_PopulateRows(), CPrimeCacheApplication::x_Process_Fasta(), CDiscRepApp::x_ProcessAll(), CNetStorageHandler::x_ProcessCreate(), CNetStorageHandler::x_ProcessExists(), CMacroApplySrcTablePanel::x_ProcessFirstLine(), CFastaDeflineReader::x_ProcessIDs(), CCgiRequest::x_ProcessInputStream(), CSplignApp::x_ProcessPair(), CFeatureTableReader_Imp::x_ProcessQualifier(), CCgiRequest::x_ProcessQueryString(), x_PutData(), x_RangesToSeq_loc(), IRWRegistry::x_Read(), CCompoundRWRegistry::x_Read(), CNcbiRegistry::x_Read(), CFeature_table_reader::x_ReadFeatureTable(), CUpdateSeq_Input::x_ReadUpdateSeq_Fasta(), CMacroFunction_UpdateProteinSeqs::x_ReadUpdateSeqs(), CUpdateMultipleSeq_Input::x_ReadUpdateSeqs_Fasta(), CMetaRegistry::x_Reload(), CAlnVecRow::x_RenderAlign(), CAlnVecRow::x_RenderInserts(), CAlnVecRow::x_RenderUnaligned(), CAlignRangeCollection< CAlignRange< TSeqPos > >::x_ResetFlags(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_ResetFlags(), CFlatFileRetrieveJob::x_Run(), CAnnot_Collector::x_SearchSegments(), CEnvironmentRegistry::x_Set(), CMemoryRegistry::x_Set(), CTwoLayerRegistry::x_Set(), CCompoundRWRegistry::x_Set(), CCgiRequest::x_SetClientIpProperty(), CMemoryRegistry::x_SetComment(), CTwoLayerRegistry::x_SetComment(), CCompoundRWRegistry::x_SetComment(), CDeflineGenerator::x_SetFlags(), CAlignRangeCollection< CAlignRange< TSeqPos > >::x_SetFlags(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::x_SetFlags(), CDeflineGenerator::x_SetFlagsIdx(), SWGSCreateInfo::x_SetId(), CEnvironmentRegistry::x_SetModifiedFlag(), CCompoundRegistry::x_SetModifiedFlag(), CTwoLayerRegistry::x_SetModifiedFlag(), CCompoundRWRegistry::x_SetModifiedFlag(), CSynRegistryToIRegistry::x_SetModifiedFlag(), CTSE_Info_Object::x_SetNeedUpdate(), CSeq_entry_Info::x_SetNeedUpdateContents(), CBioseq_Base_Info::x_SetNeedUpdateParent(), CTSE_Info_Object::x_SetNeedUpdateParent(), CBDB_FileDumper::x_SetQuoteFlags(), CAlnMap::x_SetRawSegType(), CAlnMap::x_SetRawSegTypes(), CFeatureTableReader_Imp::x_SetupSeqFeat(), CAlnMap::x_SkipType(), NStr::x_StringToNumeric(), x_SubAndSort(), x_SubNoSort(), x_TitleFromChromosome(), CSysLog::x_TranslateFlags(), CMemoryRegistry::x_Unset(), CTwoLayerRegistry::x_Unset(), CCompoundRWRegistry::x_Unset(), CSeq_entry_Info::x_Update(), CTSE_Info_Object::x_Update(), CNetStorageHandler::x_ValidateWriteMetaDBAccess(), CAlnReader::x_VerifyAlignmentInfo(), NStr::x_VerifyFloatLimits(), NStr::x_VerifyIntLimits(), CAlignFormatUtil::x_WrapOutputLine(), CBDB_File::x_Write(), CResultSet::xGetBlobOStream(), CFeatImportApp::xGetImporterFlags(), CGff2Record::xInitFeatureData(), CGffBaseColumns::xInitFeatureLocation(), CAnnotWriterApp::xInitWriter(), CGff2Record::xMigrateAttributes(), CMultiReaderApp::xProcessAlignment(), CMultiReader::xReadGFF3(), CMultiReader::xReadGTF(), xTryTextFile(), CGff2Record::xUpdateFeatureData(), and zlibCompileFlags().
◆ heap
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Definition at line 307 of file ct_nlmzip_trees.cpp.
Referenced by build_tree(), BZ2_hbMakeCodeLengths(), gen_bitlen(), HEAP_AddRef(), HEAP_Alloc(), HEAP_AttachFast(), HEAP_Base(), HEAP_Copy(), HEAP_Create(), HEAP_Destroy(), HEAP_Detach(), HEAP_Free(), HEAP_FreeFast(), HEAP_Idle(), HEAP_Next(), HEAP_Serial(), HEAP_Size(), HEAP_Trim(), HEAP_Used(), HEAP_Walk(), LBSM_GetConfig(), LBSM_GetVersion(), LBSM_LookupHost(), LBSM_LookupService(), LBSM_LookupServiceEx(), LBSM_Shmem_Attach(), LBSM_Shmem_Destroy(), LBSM_Shmem_Detach(), LBSM_Shmem_Update(), LBSMD_GetConfig(), LBSMD_GetHostParameter(), pqdownheap(), s_FillResultsFromCompoHeaps(), s_GetHeapCopy(), s_GetLocalHostAddress(), s_GetNextInfo(), s_HEAP_Collect(), s_HEAP_Find(), s_HEAP_Free(), s_HEAP_Link(), s_HEAP_Take(), s_HEAP_Walk(), s_LookupHost(), s_Shmem_Attach(), s_VerifyChecksum(), and x_HEAP_Walk().
◆ heap_len
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Definition at line 308 of file ct_nlmzip_trees.cpp.
Referenced by build_tree(), and pqdownheap().
◆ heap_max
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Definition at line 309 of file ct_nlmzip_trees.cpp.
Referenced by build_tree(), and gen_bitlen().
◆ l_desc
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Definition at line 263 of file ct_nlmzip_trees.cpp.
Referenced by build_bl_tree(), and Nlmzip_flush_block().
◆ last_dist
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Definition at line 340 of file ct_nlmzip_trees.cpp.
Referenced by init_block(), and Nlmzip_ct_tally().
◆ last_flags
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Definition at line 341 of file ct_nlmzip_trees.cpp.
Referenced by init_block(), Nlmzip_ct_tally(), and Nlmzip_flush_block().
◆ last_lit
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Definition at line 339 of file ct_nlmzip_trees.cpp.
Referenced by compress_block(), init_block(), and Nlmzip_ct_tally().
◆ length_code
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Definition at line 315 of file ct_nlmzip_trees.cpp.
Referenced by compress_block(), Nlmzip_ct_init(), and Nlmzip_ct_tally().
◆ opt_len
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Definition at line 345 of file ct_nlmzip_trees.cpp.
Referenced by build_bl_tree(), build_tree(), gen_bitlen(), bm::improve_gap_levels(), init_block(), and Nlmzip_flush_block().
◆ static_dtree
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Definition at line 258 of file ct_nlmzip_trees.cpp.
Referenced by Nlmzip_ct_init(), and Nlmzip_flush_block().
◆ static_len
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Definition at line 346 of file ct_nlmzip_trees.cpp.
Referenced by build_tree(), gen_bitlen(), init_block(), and Nlmzip_flush_block().
◆ static_ltree
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Definition at line 253 of file ct_nlmzip_trees.cpp.
Referenced by Nlmzip_ct_init(), and Nlmzip_flush_block().
