Application Framework
[CORELIB]

Collaboration diagram for Application Framework:


Classes

class  CAppException
 CAppException --. More...
class  CNcbiApplication
 CNcbiApplication --. More...
class  INcbiIdler
 Interface for application idler. More...
class  CDefaultIdler
 Default idler. More...
class  pair_base_member< Base, Member >
 Template used for empty base class optimization. More...
class  auto_ptr< X >
 auto_ptr -- More...
struct  Creater< X >
 Functor template for allocating object. More...
struct  Deleter< X >
 Functor tempate for deleting object. More...
struct  ArrayDeleter< X >
 Functor template for deleting array of objects. More...
struct  CDeleter< X >
 Functor template for the C language deallocation function, free(). More...
class  AutoPtr< X, Del >
 AutoPtr --. More...
class  AutoArray< X, Del >
 AutoArray --. More...
class  CRawPointer
 Helper address class. More...

Defines

#define HIDE_SAFE_BOOL_OPERATORS()
 Macro to hide all oprators with bool argument which may be used unintentially when second argument is of class having operator bool().
#define DECLARE_SAFE_BOOL_METHOD(Expr)
 Low level macro for declaring bool operator.
#define DECLARE_OPERATOR_BOOL(Expr)
 Declaration of safe bool operator from boolean expression.
#define DECLARE_OPERATOR_BOOL_PTR(Ptr)   DECLARE_OPERATOR_BOOL((Ptr) != 0)
 Declaration of safe bool operator from pointer expression.
#define DECLARE_OPERATOR_BOOL_REF(Ref)   DECLARE_OPERATOR_BOOL((Ref).NotNull())
 Declaration of safe bool operator from CRef<>/CConstRef<> expression.
#define NCBI_CTYPEFAKEBODY   { return See_the_standard_on_proper_argument_type_for_ctype_macros(c); }
#define ITERATE(Type, Var, Cont)   for ( Type::const_iterator Var = (Cont).begin(), NCBI_NAME2(Var,_end) = (Cont).end(); Var != NCBI_NAME2(Var,_end); ++Var )
 ITERATE macro to sequence through container elements.
#define NON_CONST_ITERATE(Type, Var, Cont)   for ( Type::iterator Var = (Cont).begin(); Var != (Cont).end(); ++Var )
 Non constant version of ITERATE macro.
#define ERASE_ITERATE(Type, Var, Cont)
 Non constant version with ability to erase current element, if container permits.
#define VECTOR_ERASE(Var, Cont)   (NCBI_NAME2(Var,_next) = (Cont).erase(Var))
 Use this macro inside body of ERASE_ITERATE cycle to erase from vector-like container.
#define REVERSE_ITERATE(Type, Var, Cont)   for ( Type::const_reverse_iterator Var = (Cont).rbegin(), NCBI_NAME2(Var,_end) = (Cont).rend(); Var != NCBI_NAME2(Var,_end); ++Var )
 ITERATE macro to reverse sequence through container elements.
#define NON_CONST_REVERSE_ITERATE(Type, Var, Cont)   for ( Type::reverse_iterator Var = (Cont).rbegin(); Var != (Cont).rend(); ++Var )
 Non constant version of REVERSE_ITERATE macro.
#define NCBI_DEPRECATED_CTOR(decl)   decl NCBI_DEPRECATED
 Macro used to mark a constructor as deprecated.

Typedefs

typedef unsigned int TSeqPos
 Type for sequence locations and lengths.
typedef int TSignedSeqPos
 Type for signed sequence position.

Enumerations

enum  ESwitch { eOff = 0, eOn, eDefault }
 Aux. More...
enum  EOwnership { eNoOwnership, eTakeOwnership }
 Which type of ownership between objects. More...
enum  ENullable { eNullable, eNotNullable }
 Whether a value is nullable. More...
enum  ESign { eNegative = -1, eZero = 0, ePositive = 1 }
 Whether a value is nullable. More...
enum  ERound { eTrunc, eRound }
 Whether to truncate/round a value. More...
enum  EFollowLinks { eIgnoreLinks, eFollowLinks }
 Whether to follow symbolic links (also known as shortcuts or aliases). More...
enum  EInterruptOnSignal { eInterruptOnSignal, eRestartOnSignal }
 Interrupt on signal mode. More...

Functions

INcbiIdlerGetIdler (EOwnership ownership=eNoOwnership)
 Return currently installed idler or NULL.
void SetIdler (INcbiIdler *idler, EOwnership ownership=eTakeOwnership)
 Set new idler and ownership.
void RunIdler (void)
 Execute currently installed idler if any.
char * strdup (const char *str)
 Supply string duplicate function, if one is not defined.
template<class T1, class T2>
END_NCBI_SCOPE BEGIN_STD_SCOPE
void 
swap (NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)
template<class P, class D>
void swap (NCBI_NS_NCBI::AutoPtr< P, D > &ptr1, NCBI_NS_NCBI::AutoPtr< P, D > &ptr2)
template<class Element, size_t Size>
size_t ArraySize (const Element(&)[Size])
static void * CRawPointer::Add (void *object, ssize_t offset)
 add offset to object reference (to get object's member)
static const void * CRawPointer::Add (const void *object, ssize_t offset)
static ssize_t CRawPointer::Sub (const void *first, const void *second)
 calculate offset inside object

Variables

const TSeqPos kInvalidSeqPos = ((TSeqPos) (-1))
 Define special value for invalid sequence position.


Define Documentation

#define DECLARE_OPERATOR_BOOL Expr   ) 
 

Value:

Declaration of safe bool operator from boolean expression.

Actual operator declaration will be: operator bool(void) const;

Definition at line 174 of file ncbimisc.hpp.

#define DECLARE_OPERATOR_BOOL_PTR Ptr   )     DECLARE_OPERATOR_BOOL((Ptr) != 0)
 

Declaration of safe bool operator from pointer expression.

Actual operator declaration will be: operator bool(void) const;

Definition at line 182 of file ncbimisc.hpp.

#define DECLARE_OPERATOR_BOOL_REF Ref   )     DECLARE_OPERATOR_BOOL((Ref).NotNull())
 

Declaration of safe bool operator from CRef<>/CConstRef<> expression.

Actual operator declaration will be: operator bool(void) const;

Definition at line 189 of file ncbimisc.hpp.

#define DECLARE_SAFE_BOOL_METHOD Expr   ) 
 

Value:

operator bool(void) const {                         \
        return (Expr);                                  \
    }
Low level macro for declaring bool operator.

Definition at line 165 of file ncbimisc.hpp.

#define ERASE_ITERATE Type,
Var,
Cont   ) 
 

Value:

for ( Type::iterator Var, NCBI_NAME2(Var,_next) = (Cont).begin();   \
          (Var = NCBI_NAME2(Var,_next)) != (Cont).end() &&              \
              (++NCBI_NAME2(Var,_next), true); )
Non constant version with ability to erase current element, if container permits.

Use only on containers, for which erase do not ruin other iterators into the container e.g., map, list, but NOT vector. See also VECTOR_ERASE

Definition at line 882 of file ncbimisc.hpp.

Referenced by CNCBlobStorage::x_DoBackgroundWork().

 
#define HIDE_SAFE_BOOL_OPERATORS  ) 
 

Value:

private:                                            \
    void operator<(bool) const;                         \
    void operator>(bool) const;                         \
    void operator<=(bool) const;                        \
    void operator>=(bool) const;                        \
    void operator==(bool) const;                        \
    void operator!=(bool) const;                        \
    void operator+(bool) const;                         \
    void operator-(bool) const;                         \
    public:
Macro to hide all oprators with bool argument which may be used unintentially when second argument is of class having operator bool().

All methods are simply declared private without body definition.

Definition at line 151 of file ncbimisc.hpp.

#define ITERATE Type,
Var,
Cont   )     for ( Type::const_iterator Var = (Cont).begin(), NCBI_NAME2(Var,_end) = (Cont).end(); Var != NCBI_NAME2(Var,_end); ++Var )
 

ITERATE macro to sequence through container elements.

Definition at line 871 of file ncbimisc.hpp.

Referenced by CTiwClient_Types::Activate(), CResolvedTypeSet::Add(), CSeqsRange::Add(), SChunkInfo::Add(), CAnnotPieces::Add(), CPdfDictionary::Add(), CSeqFetchQueue::Add(), CSeq_locFormatter::Add(), CCgiCookies::Add(), AddBioseq_setIds(), AddBioseqIds(), CQueueClientInfoList::AddClientInfo(), CProjectTreeBuilder::AddDatatoolSourcesDepends(), CRefArgs::AddDefinitions(), oligofar::CSeqIds::CSeqDef::AddIds(), CChainer::CChainerImpl::AddIfCompatible(), AddIntervals(), CMsvcPrjProjectContext::AdditionalLibraryDirectories(), CMsvcPrjProjectContext::AdditionalLinkerOptions(), AddLoc(), CDataContainerType::AddMembers(), CSelectionEvent::AddObjectSelection(), COStreamTextOStream::AddParagraph(), addProblems(), CSequenceInputStats::AddQueryBatch(), CHandleRange::AddRanges(), CTrOutputTrace::AddRowData(), CTrOutputStream::AddRowData(), CTSE_Default_Assigner::AddSeq_data(), CBioseq_Base_Info::AddSeq_descr(), CBioseq_Base_Info::AddSeqdesc(), CBuildDatabase::AddSequences(), CReadBlastApp::addSimpleTab(), AddSupport(), CTextUtil::AddWordFrequencies(), CBlastOptionsBuilder::AdjustProgram(), AgpRead(), CSplign::AlignSingleCompartment(), CDistMethods::AllFinite(), CTableNames::AllTableNames(), CMsvcConfigure::AnalyzeDefines(), AnalyzeDllData(), CLayout::Append(), CMsvcProjectMakefile::Append(), COMSSASearch::AppendSearch(), CQueue::AppendTags(), CSubjectRangesSet::ApplyRanges(), CSplignFormatter::AsAlignmentText(), CSpliced_seg::AsDiscSeg(), CSplignFormatter::AsExonTable(), CPluginArg::AsList(), CEUtils_IdGroupSet::AsQueryString(), CEUtils_IdGroup::AsQueryString(), CSplignFormatter::AsSeqAlignSet(), CInt_fuzz::AssignTranslated(), CEntrez2_id_list::AssignUids(), CWorkerNode::AsString(), CEditsSaver::Attach(), CProjectItem::Attach(), CBlobSplitterImpl::AttachToSkeleton(), CCleanup_imp::BasicCleanup(), BDB_batch_delete_recs(), CFileDBEngine::BeginTransaction(), BioTreeConvert2Container(), BioTreeConvertContainer2Dynamic(), BOOST_AUTO_TEST_CASE(), CDataMiningView::BroadcastVisibleRange(), BuildAln(), CSeqDBAliasNode::BuildFilterTree(), BuildGFF3Gap(), CProjectTreeBuilder::BuildOneProjectTree(), CProjectTreeBuilder::BuildProjectTree(), CCgiRequest::CalcChecksum(), CalcIdentity(), CComboChartDataSource::CalculateMinMax(), CAlnVec::CalculatePercentIdentity(), CSimpleScoringMethod::CalculateScores(), CQualityScoringMethod::CalculateScores(), CAlignShadow::CAlignShadow(), CEUtilsApp::CallEInfo(), CAlnPropertiesDlg::CAlnPropertiesDlg(), CTypesIteratorBase< Parent >::CanEnter(), CTypesIteratorBase< Parent >::CanSelect(), CAutoDefModifierCombo::CAutoDefModifierCombo(), CAutoDefSourceDescription::CAutoDefSourceDescription(), CBioseq_SplitInfo::CBioseq_SplitInfo(), CBlastHitMatrix::CBlastHitMatrix(), CBookmarkMgrDlg::CBookmarkMgrDlg(), CCgiEnvHolder::CCgiEnvHolder(), CChain::CChain(), CColorTableScoringModel::CColorTableScoringModel(), CComponentSearchJob::CComponentSearchJob(), CDB_ODBC_ConnParams::CDB_ODBC_ConnParams(), CDenseSegHit::CDenseSegHit(), CFeatCheckBrowser::CFeatCheckBrowser(), CFeatHistogramDS::CFeatHistogramDS(), CFeatureGraph::CFeatureGraph(), CFeatureSearchJob::CFeatureSearchJob(), CHandleRange::CHandleRange(), CSeq_loc::ChangeToPackedInt(), CFileSet::Check(), CFileModules::Check(), CDataTypeModule::Check(), CDiagFilter::Check(), CDiagFilter::CheckErrCode(), CDiagFilter::CheckFile(), CCodeGenerator::CheckFileNames(), COMSSASearch::CheckLibraryNameAndSize(), CReadBlastApp::CheckMissingRibosomalRNA(), CFileSet::CheckNames(), CFileModules::CheckNames(), CDataTypeModule::CheckNames(), CTreeMinimalSet< TNode, TSet, TNodeList >::CheckNodeList(), CSeq_align::CheckNumRows(), CPrimeNumberClient::CheckProgress(), CProjectsLstFileFilter::CheckProject(), CAltValidator::CheckTaxids(), CDataMemberContainerType::CheckType(), CUniSequenceDataType::CheckValue(), CEnumDataType::CheckValue(), CMultiDictionary::CheckWord(), CVisibleRangeEvent::Clamp(), CClassTypeInfoBase::ClassesById(), CClassTypeInfoBase::ClassesByName(), CLdsSearchDlg::CLdsSearchDlg(), CLocalHookSetBase::Clear(), CCgiCookies::Clear(), oligofar::CFeatMap::Clear(), CObjPool< TObjType, TObjFactory >::Clear(), CTL_CursorResultExpl::ClearFields(), CGeneModel::Clip(), CChain::ClipToCompleteAlignment(), CLoadLockBlob_ids::CLoadLockBlob_ids(), CloneContainer(), impl::CDriverContext::CloseAllConn(), CMsvcCombinedProjectMakefile::CMsvcCombinedProjectMakefile(), CMsvcPrjProjectContext::CMsvcPrjProjectContext(), CMsvcSite::CMsvcSite(), CMultiSeqInfo::CMultiSeqInfo(), CObjectList::CObjectList(), CLocMapper_Default::CollapseRanges(), CollectAttributes(), CollectDescriptors(), CollectDllsDepends(), CReadBlastApp::CollectFrameshiftedSeqs(), CChainer::CChainerImpl::CollectFShifts(), CReadBlastApp::collectPerfectHits(), CBlobSplitterImpl::CollectPieces(), CMsvcPrjFilesCollector::CollectResources(), CReadBlastApp::CollectRNAFeatures(), CMsvcPrjFilesCollector::CollectSources(), CSeq_loc_Mapper::CollectSynonyms(), CChain::CollectTrustedmRNAsProts(), CTableControl::ColumnDataToVisible(), CREnzyme::CombineIsoschizomers(), CFileDBEngine::CommitTransaction(), CModelCompare::CommonReadingFramePoint(), CCgiStatistics::Compose_Entries(), oligofar::CQueryHash::CompressFwd(), oligofar::CQueryHash::CompressRev(), CTextFsm< MatchType >::ComputeFail(), oligofar::CQueryHash::ComputeHasherWindowLength(), oligofar::CQueryHash::ComputeScannerWindowLength(), oligofar::CGuideSamFile::ComputeScore(), CMsvcConfigure::Configure(), CDBUniversalMapper::ConfigureFromRegistry(), CDBUDPriorityMapper::ConfigureFromRegistry(), CDBUDRandomMapper::ConfigureFromRegistry(), CICacheCF< CNetICacheClient >::ConfigureTimeStamp(), CSeqScores::ConstructSequenceAndMaps(), CTSE_Info::ContainsMatchingBioseq(), CTSE_ScopeInfo::ContainsMatchingBioseq(), CSynonymsSet::ContainsSynonym(), Convert_Entrezgene_Seq_loc_Genomic(), Convert_Entrezgene_Seq_loc_Product(), Convert_Entrezgene_Seq_loc_RefSeq(), Convert_Entrezgene_Seq_loc_Related(), Convert_Entrezgene_Set_Entrezgene(), Convert_Seq_align_Seq_id(), Convert_Seq_align_Seq_loc_Basic(), Convert_Seq_align_set_Seq_align(), Convert_Seq_align_set_Seq_loc(), Convert_Seq_annot_Seq_align(), Convert_Seq_annot_Seq_feat(), Convert_Seq_annot_Seq_graph(), Convert_Seq_annot_Seq_id(), Convert_Seq_annot_Seq_loc_All(), Convert_Seq_annot_Seq_loc_TotalRange(), Convert_Seq_feat_Seq_loc_dbxref_Loc(), Convert_SeqSubmit_Seq_entry(), ConvertDendiagToPairwiseAln(), CSeq_loc_Conversion_Set::ConvertEquiv(), CSeq_loc_Conversion::ConvertEquiv(), CArgDescriptions::ConvertKeys(), SMakeProjectT::ConvertLibDepends(), SMakeProjectT::ConvertLibDependsMacro(), CSeq_loc_Conversion_Set::ConvertMix(), CSeq_loc_Conversion::ConvertMix(), CPepXML::ConvertModifications(), CSeq_loc_Conversion_Set::ConvertPacked_int(), CSeq_loc_Conversion::ConvertPacked_int(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), CSeq_loc_Conversion::ConvertPacked_pnt(), CConfig::ConvertRegToTree(), ConvertSeqAlignToPairwiseAln(), ConvertSparseToPairwiseAln(), ConvertSplicedToPairwiseAln(), ConvertStdsegToPairwiseAln(), TMaskedQueryRegions::ConvertToCPacked_seqint(), SBDB_CacheStatistics::ConvertToRegistry(), SBDB_CacheUnitStatistics::ConvertToRegistry(), CRemoteBlast::ConvertToRemoteMasks(), CGenetic_codeTypeConverter::ConvertToString(), CopyContainer(), CTreeNode< TValue, TKeyGetter >::CopyFrom(), CBlobSplitterImpl::CopySkeleton(), CQueueDataBase::CountActiveJobs(), SChunkInfo::CountAnnotObjects(), CBlobSplitterImpl::CountAnnotObjects(), CAnnotPieces::CountAnnotObjects(), CountQueryCoverage(), CSeqMap::CountSegmentsOfType(), CPacked_seqint::CPacked_seqint(), CPluginManager< TClass >::CPluginManager(), CPriorityTree::CPriorityTree(), CProjectTreeFolders::CProjectTreeFolders(), CProSplignText::CProSplignText(), CQualityScoringPanel::CQualityScoringPanel(), CQueryDataPerChunk::CQueryDataPerChunk(), CRawSeqDBSource::CRawSeqDBSource(), SMakeProjectT::Create3PartyLibs(), CAnnotationASN1::CImplementationData::create_cdregion_feature(), CAnnotationASN1::CImplementationData::create_internal_feature(), CreateAnchoredAlnVec(), CEntrezDB::CreateAnnot_Genome(), CEntrezDB::CreateAnnot_Nuc_Prot(), CBlastAligner::CreateBlastAligners(), CProjBulderApp::CreateCheckList(), CDataContainerType::CreateClassInfo(), CMsvcConfigure::CreateConfH(), CPhrap_Contig::CreateContig(), CEnumDataType::CreateDefault(), SMakeProjectT::CreateDefines(), CreateDensegFromAnchoredAln(), CSeq_align::CreateDensegFromDisc(), CreateDensegFromPairwiseAln(), CSeq_align::CreateDensegFromStdseg(), CreateDllBuildTree(), CreateDllsList(), CProjBulderApp::CreateFeaturesAndPackagesFiles(), CProjectItemsTree::CreateFrom(), SMakeProjectT::CreateFullPathes(), SMakeProjectT::CreateIncludeDirs(), CBlobStorageNetCacheCF::CreateInstance(), CPluginManager< TClass >::CreateInstanceFromList(), CMsvcPrjProjectContext::CreateLibsList(), CAlignCleanup::CreatePairwiseFromMultiple(), CEntrezDB_GenomeProject::CreateProject(), CreateSplicedsegFromAnchoredAln(), CEnumDataType::CreateTypeInfo(), CResourceManager::CResourceManager(), CSeqDBIdSet_Vector::CSeqDBIdSet_Vector(), CSeqTableInfo::CSeqTableInfo(), CSeqTextFeatureList::CSeqTextFeatureList(), CSequenceSearchJob::CSequenceSearchJob(), CSniffReader::CSniffReader(), CSpellCheckDlg::CSpellCheckDlg(), CStdSegHit::CStdSegHit(), CTiwClient_Types::CTiwClient_Types(), CTrans_table::CTrans_table(), DDX_Browser(), DDX_CheckBrowser(), DDX_ComboBox(), CPluginReply::DecomposeRaw(), CHTML_area::DefinePolygon(), CMsvcPrjProjectContext::Defines(), CHomePageService::Delete(), impl::CDriverContext::DeleteAllConn(), CHMMParameters::SDetails::DeleteAllCreatedModels(), CUser_field::DeleteField(), CSelListModelImpl< Item >::DeleteItems(), CCgiSession_NetCache::DeleteSession(), CIdMapperConfig::DescribeContexts(), CEditsSaver::Detach(), CDataLoader::DetailsToChoice(), DFS::DFS(), CDiagRangeCollection::Diff(), CSeqGraphicDataSource::DisableScoringMethod(), CEventHandler::Dispatch(), CQueueWorkerNodeList::DisplaceWorkerNodeJobs(), CRemoveIdChecker::Do(), SMakeProjectT::DoResolveDefs(), CDiagPanel::draw(), CGlContainer::Draw(), CDataSource::DropAllTSEs(), DTDFileNameBase(), DTDPublicModuleName(), CComplexRelation::Dump(), CConvGraph::Dump(), CSimpleMakeFileContents::Dump(), CGuiRegistry::CReadView::DumpAll(), CThemeSet::DumpAll(), CObjectConverter::DumpDotGraph(), CAnnotationASN1::CImplementationData::DumpEvidence(), CProjBulderApp::DumpFiles(), CPackString::DumpStatistics(), DumpTaskInfo(), CAnnotCompareDS::DumpTextReport(), WSDLParser::EmbeddedElement(), CMaskedRangesVector::empty(), CExtraEncoder::Encode(), CPdf::EndDocument(), CLDS_FastaScanner::EntryFound(), CLDS_DatabaseHolder::EnumerateAliases(), CTar::EstimateArchiveSize(), CRowSelector::ExcludeRow(), CCodeGenerator::ExcludeTypes(), CQueue::ExecProject(), CAutoDefModifierCombo::ExpandByAnyPresent(), ExpandSupport(), CFileSet::ExternalResolve(), CTar::Extract(), CTitleExtractor::Extract(), CSeqDataExtractor::Extract(), COidExtractor::ExtractOID(), CDense_seg::ExtractRows(), CDense_seg::ExtractSlice(), CGlBitmapFont::FaceFromString(), CFeatureTypesParser::FeatTypesToString(), CNCBlobStorage::FillBlobIds(), CChainMembers::FillGaps(), CAlnMixSegments::FillUnalignedRegions(), CFilterSet::Filter(), CChainer::CChainerImpl::FilterOutChimeras(), FilterOutDllHostedProjects(), CChainer::CChainerImpl::FilterOutInferiorProtAlignmentsWithIncompatibleFShifts(), CSeq_annot_Finder::Find(), NStr::Find(), CWinMaskConfig::CIdSet_SeqId::find(), find_id(), FindBestChoice(), CDllResolver::FindCandidates(), CPluginManager< TClass >::FindClassFactory(), CComment_set::FindCommentRule(), CCyclicDepends::FindCycles(), CCyclicDepends::FindCyclesNew(), CEntryFormMenu::FindEntry(), CComment_rule::FindFieldRule(), FindFirstStart(), CProjectTreeFolders::FindFolder(), CMSResponse::FindHitSet(), CSampleLibraryObject::FindInPath(), CSeq_id_PDB_Tree::FindMatch(), CSeq_id_PDB_Tree::FindMatchStr(), CSeq_id_Patent_Tree::FindMatchStr(), CSeq_id_Giim_Tree::FindMatchStr(), CSeq_id_General_Tree::FindMatchStr(), COMSSASearch::FindMinMaxSearchSettingId(), COMSSASearch::FindMinMaxSpectrumNumber(), CUnimod::FindMod(), CCodeGenerator::FindModuleByName(), CTreeNode< TValue, TKeyGetter >::FindNodes(), CSeq_id_PDB_Tree::FindOrCreate(), CProjectTreeFolders::FindOrCreateFolder(), CTreeNode< TValue, TKeyGetter >::FindOrCreateNode(), CDataSource::FindSeq_feat_Lock(), CLDS_Query::FindSequences(), FindTextseq_id(), CEntrez2_docsum::FindValue(), CAbstractTCEditor::FireEditingCancelled(), CAbstractTCEditor::FireEditingFinished(), CReadBlastApp::fit_blast(), CChoiceDataType::FixTypeTree(), CDataMemberContainerType::FixTypeTree(), CNcbiTestTreeElement::FixUnitsOrder(), TestUtil::FlattenSeqAlignSet(), AbstractLexer::FlushCommentsTo(), ForEach(), ForEachGiRange(), CTSE_ScopeInfo::ForgetTSE_Lock(), CFlatNumberQVal::Format(), CGBSeqFormatter::FormatAccession(), CGenbankFormatter::FormatDBSource(), CGenbankFormatter::FormatFeature(), CGBSeqFormatter::FormatKeywords(), CGBSeqFormatter::FormatLocus(), CGeneModel::FrameShifts(), CResourcePool_Base< string, CNoLock, CResoursePool_NewClassFactory< string > >::FreeAll(), CRegistryFile::FromConfigFile(), CSnpMarkers::FromSeqAnnot(), CWsdlTypeStrings::GenerateClassCode(), CClassTypeStrings::GenerateClassCode(), CChoiceTypeStrings::GenerateClassCode(), CChoicePtrTypeStrings::GenerateClassCode(), CCodeGenerator::GenerateClientCode(), CCodeGenerator::GenerateCode(), CProjBulderApp::GenerateMacProjects(), CCodeGenerator::GenerateModuleCPP(), CCodeGenerator::GenerateModuleHPP(), CProjBulderApp::GenerateMsvcProjects(), GenerateSeed(), CProjBulderApp::GenerateSummary(), CWsdlTypeStrings::GenerateTypeCode(), CEnumTypeStrings::GenerateTypeCode(), CProjBulderApp::GenerateUnixProjects(), CFileCode::GenerateUserHPPCode(), CClassTypeStrings::GenerateUserHPPCode(), get_title(), CTSEAccessions::GetAccessions(), CBioseq_Handle::GetAccessSeq_id_Handle(), CQueueWorkerNodeListGuard::GetAffinities(), CSeqDBAliasNode::GetAliasFileValues(), CHitMatrixDataSource::GetAlignedIdsForParams(), CObjectIndex::GetAligns(), CArgs::GetAll(), CBookmarkManager::GetAllBookmarks(), CWindowManager::GetAllClients(), CGlBitmapFont::GetAllFaces(), CSelectionEvent::GetAllObjects(), CGlBitmapFont::GetAllSizes(), GetAllSwitchPoints(), CAlnVecMultiDataSource::GetAlnFromSeq(), CReadBlastApp::getAnnotComment(), CTSE_Info::GetAnnotIds(), CLDS_Object::GetAnnotInfo(), CReadBlastApp::getAnnotName(), CStudyLoader::GetAnnots(), CSeqUtils::GetAnnotSelector(), GetArgValue(), CCgiSession_NetCache::GetAttributeNames(), CReferenceItem::GetAuthNames(), CAutoDefSourceDescription::GetAvailableModifiers(), CQuerySet::GetBestRank(), CTSE_LockSet::GetBestTSEs(), CSeqDBVol::GetBioseq(), CMSBioseqSet::GetBioseqByOid(), CAlnMultiDSBuilder::GetBioseqHandles(), CLDS_Object::GetBioseqInfo(), CTSE_Split_Info::GetBioseqsIds(), CTSE_Info::GetBioseqsIds(), SAffinityInfo::GetBlacklistedJobs(), CGBDataLoader::GetBlobId(), CGBDataLoader::GetBlobs(), CDataSource_ScopeInfo::GetBlobs(), CDataSource::GetBlobs(), CReadBlastApp::getBounds(), CSplign::SAlignedCompartment::GetBox(), CUser_object::GetCategory(), CSplign::GetCds(), GetCdssForGene(), CCgiRequest::GetCGIEntriesStr(), CGroupCheckboxes::GetCheckList(), CWMDockContainer::GetChildPos(), CWMDockContainer::GetChildrenCount(), CMsvcSite::GetChoiceFor3PartyLib(), CMsvcSite::GetChoiceForLib(), CBlastDbDataLoader::GetChunk(), CGBDataLoader::GetChunks(), CDataLoader::GetChunks(), CBioseq::GetClosestDescriptor(), CHTMLPopupMenu::GetCodeHead(), CSeqportUtil_implementation::GetCodeIndexFromTo(), CHTMLPopupMenu::GetCodeItems(), CAlnMultiRenderer::GetColumnIndexByX(), CSeqDBImpl::GetColumnMetaData(), CPluginHandle_Impl::GetCommands(), GetCompartmentNum(), CDefaultLayout::GetCompleteLayout(), GetCompNum(), CBlastSeqVectorFromCSeq_data::GetCompressedPlusStrand(), CFeatShowPanel::GetConfigPanel(), CTableReader::GetConvertersNames(), NSnp::GetCreateTime(), CMsvcProjectMakefile::GetCustomBuildInfo(), CGBProject::GetData(), CLDS_DatabaseHolder::GetDatabase(), CDate_std::GetDate(), CDbtag::GetDBFlags(), CEntrezDB::GetDbName(), CEntrezDB::GetDbNames(), GetDefaultLogLocation(), CCgiApplication::GetDefaultLogPath(), CFileCode::GetDefineBase(), CShowBlastDeflineTest::GetDeflineInfo(), GetDeflineKeys(), CFeatList::GetDescriptions(), GetDllHost(), CBioseq_set_Info::GetEntryIndex(), CSearchResults::GetErrors(), CCompareSeq_locs::GetEvidenceString(), CGBDataLoader::GetExternalAnnotRecords(), CDataLoader::GetExternalAnnotRecords(), CProjectItemsTree::GetExternalDepends(), CGBDataLoader::GetExternalRecords(), CDataLoader::GetExternalRecords(), CSeqGraphicPane::GetFeatureNames(), CObjectIndex::GetFeatures(), CBioTreeFeatureList::GetFeatureValue(), CGuiRegistry::CReadView::GetField(), CGuiRegistry::GetField(), CReadBlastApp::getFromTo(), CChoiceDataType::GetFullCType(), oligofar::CSeqIds::CSeqDef::GetFullIdString(), CBlastQuerySourceBioseqSet::GetGeneticCodeId(), CSeq_feat::GetGeneXref(), GetGenomicBounds(), CBioseq_set::GetGenomicFromGenProdSet(), CReadBlastApp::getGenomicInterval(), CReadBlastApp::getGenomicLocation(), CSeqDBGiList::GetGiList(), CSeqDB::GetGis(), CReadBlastApp::getGIs(), CHistogramDlg::GetGraphColor(), CHitMatrixRenderer::GetGraphTypes(), CSplitter::GetHeights(), CGenetic_code::GetId(), CSeqDB_IdRemapper::GetIdList(), CDataLoader::GetIds(), CAlignModel::GetInDels(), CProjectItemsTree::GetInternalDepends(), CGuiRegistry::GetIntVec(), CRegistryData_File::GetKeys(), CDataLoader::GetLabel(), GetLabel(), CFeaturesPanelIR::GetLayoutHeight(), CFeaturesPanelIR::GetLayoutObjectSelection(), CBioTreeContainer::GetLeafCount(), GetLength(), CBlobSplitterImpl::GetLength(), CPacked_seqint::GetLength(), CReadBlastApp::getLenScore(), CMsvcSite::GetLibChoiceFor3PartyLib(), CMsvcSite::GetLibChoiceForLib(), CMsvcSite::GetLibChoiceIncludes(), CMsvcSite::GetLibInfo(), CGBReaderRequestResult::GetLoadedBlob_ids(), CDataSource::GetLoadedBlob_ids(), CReadBlastApp::GetLocMap(), CAnnotObject_Info::GetLocsTypes(), CReadBlastApp::getLocusTag(), GetLowestEvalue(), CAlnMultiView::GetMainObject(), CAnnotObject_Info::GetMaps(), CAlnMultiWidget::GetMarks(), CBioseq_set::GetMasterFromSegSet(), CDataSource::GetMatches(), CAutoDefModifierCombo::GetMaxInGroup(), CObjMemberSelector::GetMember(), CWindowManager::GetMenu(), CEntryFormMenu::GetMenuItems(), CAutoDefSourceGroup::GetModifiersPresentForAny(), CFileCode::GetModuleNames(), CSeq_annot_SplitInfo::GetName(), CGenetic_code::GetName(), CConnValidatorCoR::GetName(), CGBDataLoader::GetNamedAnnotAccessions(), CSeq_feat::GetNamedDbxref(), CSeq_feat::GetNamedQual(), CWMTemplateRegistry::GetNames(), CGen_code_table_imp::GetNcbieaa(), CGenetic_code::GetNcbieaa(), CSeqDBIdSet::GetNegativeList(), CRawSeqDBSource::GetNext(), CQueueWorkerNodeListGuard::GetNodes(), CQueueWorkerNodeList::GetNodes(), GetNonConsensusSpliceCount(), CQueueWorkerNodeList::GetNotifyList(), CBioseq_set::GetNucFromNucProtSet(), CAutoDefModifierCombo::GetNumUnique(), CMappedGraph::GetNumval(), CLayoutMatePair::GetObject(), CObjectIndex::GetObjects(), CLayoutMatePair::GetObjects(), CGwasTrack::GetObjects(), CTaxTreeBrowser::GetObjectSelection(), CSeqGraphicRenderer::GetObjectSelection(), CHitMatrixPane::GetObjectSelection(), CCrossPanelIR::GetObjectSelection(), CGuiRegistry::CReadView::GetOctetStringVec(), CGuiRegistry::GetOctetStringVec(), CMSResponse::GetOidsBelowThreshold(), oligofar::CSeqIds::GetOrdById(), GetOrganism(), CObjectIndex::GetOriginalIds(), CHandleRange::GetOverlappingRange(), CBlast4_parameters::GetParamByName(), CHMMParameters::SDetails::GetParameter(), CMasterContext::GetPartNumber(), CMsvcMetaMakefile::GetPchInfo(), CPluginRegistry::GetPlugin(), CPluginRegistry::GetPlugins(), CServer_ConnectionPool::GetPollAndTimerVec(), CSeqDBIdSet::GetPositiveList(), CWMDockContainer::GetPosToChildMap(), CMsHdf5::getPrecursorMzs(), CComplexRelation::GetProperty(), CReadBlastApp::GetProtName(), CSeq_feat::GetProtXref(), CRefArgs::GetQueryString(), CQueueDataBase::GetQueueNames(), CMaskedRangeSet::GetRanges(), CSelectionEvent::GetRangeSelectionAsLocs(), CNcbiTestApplication::GetRanTestsCount(), CGuiRegistry::GetRealVec(), CLDS_DataLoader::GetRecords(), CClassTypeInfoBase::GetRegisteredClassNames(), CObjectManager::GetRegisteredNames(), CComplexRelation::GetRelated(), CRelationTypeConverterAdapter::GetRelated(), CLDS_FindSeqIdFunc::GetResult(), CRemoteBlast::GetResultSet(), CReadBlastApp::GetRNAfeats(), CScheduler_MT::GetScheduledSeries(), CHitMatrixDataSource::GetScoreNames(), CStdSegHit::GetScoreValue(), CDiagHit::GetScoreValue(), CDenseSegHit::GetScoreValue(), CHitMatrixRenderer::GetSelectedHitElemsRect(), CAlnMultiWidget::GetSelectedIds(), CAlnMultiWidget::GetSelectedRows(), CProjectTree::GetSelectedViews(), CSeqTextPane::GetSelection(), CAlnSpanWidget::GetSelection(), CSelectionView::GetSelection(), CViewTaxTree::GetSelection(), CViewFlatfile::GetSelection(), CViewFeatTable::GetSelection(), CViewAlnTable::GetSelection(), CViewPhyloTree::GetSelection(), CViewGraphic::GetSelection(), CAlnMultiView::GetSelection(), CViewAnnotCompare::GetSelection(), CViewAlnSpanTable::GetSelection(), CStudyPreviewData::GetSelection(), CViewComposite::GetSelection(), CView::GetSelection(), CProjectTree::GetSelection(), CSeq_align::GetSeq_id(), GetSeq_idByType(), CAlnVecMultiDataSource::GetSeqFromAln(), CSeqDBImpl::GetSeqGI(), CShowBlastDefline::GetSeqIdList(), CShowBlastDefline::GetSeqIdListString(), CSeqDBVol::GetSeqIDs(), CTSE_Info::GetSeqMatch(), CStd_seg::GetSeqRange(), CSpliced_seg::GetSeqRange(), CSeq_align::GetSeqRange(), CStd_seg::GetSeqStart(), CStd_seg::GetSeqStop(), SNetScheduleAPIImpl::GetServerParams(), CElementaryMatching::CBoolVector::GetSetCount(), CMSRequest::GetSettingsById(), CGBenchServiceContext::GetSeviceNames(), CGen_code_table_imp::GetSncbieaa(), CGenetic_code::GetSncbieaa(), CHitMatrixDataSource::GetStdSegRange(), CTextUtil::GetStemFrequencies(), CSeq_loc_mix::GetStrand(), CPacked_seqint::GetStrand(), CSeq_id::GetStringDescr(), CGuiRegistry::GetStringVec(), CSettingsSet::GetStyleNames(), CPluginTaskManager::GetTaskCounts(), CT3Data::GetTaxFlags(), CBioseq::GetTaxId(), CSeqDBImpl::GetTaxIDs(), CTaxTreeDS_ObjMgr::GetTaxMap(), CSeqDBGiList::GetTiList(), GetTitle(), CAffinityDict::GetTokensIds(), CDataMiningService::GetToolNames(), CUIToolRegistry::GetToolNames(), CUIToolRegistry::GetTools(), CGen_code_table_imp::GetTransTable(), CGuideTree::GetTreeInfo(), CClusterer::GetTrees(), CDataSource::GetTSESetWithBioseqAnnots(), CDataSource::GetTSESetWithOrphanAnnots(), CThemeSet::GetTypeDescriptions(), CFeatTableDS::GetTypeNames(), CThemeSet::GetTypes(), CResolveIdDlg::GetUpdatedIds(), CEntrez2_docsum::GetValue(), CSerialItemContainer::GetValue(), CAlnMultiRenderer::GetVisibleColumns(), CViewAnnotCompare::GetVisibleRanges(), CSeqDB_IdRemapper::GetVolAlgos(), CSeqDBAliasNode::GetVolumeNames(), CSplitter::GetWidths(), CReadDispatcher::GetWriter(), CEnumDataType::GetXMLContents(), CDataValueTmpl< string >::GetXmlString(), CReadBlastApp::giMatch(), CGeneModel::GoodEnoughToBeAlternative(), CAlignGroup::GroupBySeqIds(), CAlignGroup::GroupBySequenceType(), CAlignGroup::GroupByStrand(), CProjBulderApp::Gui_ConfirmProjects(), impl::CDBHandlerStack::HandleExceptions(), CCleanupApp::HandleSeqEntry(), CStdSegHit::HasAlignment(), oligofar::CSeqIds::CSeqDef::HasAnyId(), CPluginArgSet::HasArgument(), CSearchResults::HasErrors(), CGuiRegistry::CReadView::HasField(), CGuiRegistry::HasField(), CReadBlastApp::hasGenomicInterval(), CReadBlastApp::hasGenomicLocation(), CSeqDBIsam::HashToOids(), CValidError_imp::HasIsoJTA(), TSearchMessages::HasMessages(), CValidError_imp::HasName(), TMaskedQueryRegions::HasNegativeStrandMasks(), CLayoutMatePair::HasObject(), CDataStore::HasObject(), CReverseObjectStore< TKey, TObject >::HasObject(), CReadBlastApp::hasProblems(), HasRawSequenceData(), CSeqMap::HasSegmentOfType(), CValidError_imp::HasTitle(), CSearchResults::HasWarnings(), CGBDataLoader::HaveCache(), HexToString(), CCrossPanelIR::HitTest(), CBioseq_ScopeInfo::IdString(), CBioseq_Info::IdString(), CCodeGenerator::IncludeAllMainTypes(), CChainer::CChainerImpl::IncludeWithIdenticals(), InframeFraction(), CSnpFilterUI::Init(), CAlignSeqTableModel::Init(), CAlnVecMultiDataSource::Init(), CSequenceSearchForm::Init(), CFeatureSearchForm::Init(), CEntrezSearchForm::Init(), CDeleteSeqFeatCommand::Init(), CSegmentedRangeCollection::insert(), CLayout::Insert(), CAlignResultsSet::Insert(), CQuerySet::Insert(), CAlnContainer::insert(), CSeqAlignContainer::insert(), CHandleRange::IntersectingWith(), CHandleRange::IntersectingWithSubranges(), CCDSInfo::Invariant(), InvertPartList(), CMsvcSite::Is3PartyLib(), CMsvcSite::Is3PartyLibWithChoice(), CDbtag::IsApprovedNoCase(), IsBlankStringList(), CPhrap_Contig::IsCircular(), CSeqportUtil_implementation::IsCodeAvailable(), CMsvcPrjProjectContext::IsConfigEnabled(), CCyclicDepends::IsCyclic(), CWMDockContainer::IsDocked(), CScheduler_MT::IsEmpty(), CValidError_bioseq::IsFlybaseDbxrefs(), IsGnomonConstructed(), CCyclicDepends::IsInAnyCycle(), CFormatGuess::IsInputRepeatMaskerWithoutHeader(), CMsvcSite::IsLibOk(), CMsvcSite::IsLibWithChoice(), CRefArgs::IsListedHost(), CLoadInfoSeq_ids::IsLoadedAccVer(), CLoadInfoSeq_ids::IsLoadedGi(), CQueueClientInfoList::IsMatchingClient(), CLayoutMatePair::IsPairSelected(), CSeqIdAlignBitmap< TSeqAlignSeqIdVec >::IsQueryAnchored(), CMsvcPrjProjectContext::IsRequiresOk(), CMod::isResidueSubset(), CSeq_loc_mix::IsSetStrand(), CPacked_seqint::IsSetStrand(), CAutoDefSourceDescription::IsTrickyHIV(), IsValid(), CChoice::ItemPathname(), LDS_TypeMapSearch(), CChainer::CChainerImpl::LeftRight(), CScoreVector< Key, Score >::Length2(), CRawScoreVector< Key, Score >::Length2(), CSeqDBVol::ListColumns(), CWriteDB_Impl::ListFiles(), CBlastQueryFilteredFrames::ListFrames(), CWriteDB_Impl::ListVolumes(), CSplitParser::Load(), CColumnScoringMethod::Load(), CColorTableMethod::Load(), CId2ReaderBase::LoadBlobs(), CReader::LoadBlobs(), CId2ReaderBase::LoadBlobSet(), CReader::LoadBlobSet(), CReader::LoadChunks(), LoadConfigInfoByNames(), CDataTool::LoadDefinitions(), CDataToolGeneratedSrc::LoadFrom(), CSeqGraphicConfig::LoadHistSettings(), CTemplateScoringMethod::LoadInfo(), CProjBulderApp::LoadProjectTags(), CTSE_Default_Assigner::LoadSequence(), CCgiSession_NetCache::LoadSession(), CUIToolRegistry::LoadSettings(), CUIToolRegistry::LoadTemplateToolsInfo(), CChainer::CChainerImpl::MakeChains(), MakeCompartment(), MakeCompartments(), CBlobSplitterImpl::MakeID2Chunk(), CBlobSplitterImpl::MakeID2SObjects(), CMappedGraph::MakeMappedGraphData(), CMSHits::MakeModString(), CMSHits::MakePepString(), CRebase::MakeREnzyme(), CBlobSplitterImpl::MakeSeq_annot(), CWig2tableApplication::MakeTable(), MapToLMBits(), CAlignMarkHandler::MarkRow(), CAlignMarkHandler::MarkSelectedRows(), CNodesToBitset< TNode, TSet, TNodeList >::MaskCopyNodes(), CMaskRegexp::Match(), CMaskFileName::Match(), CStringPairs< TContainer >::Merge(), MergePairwiseAlns(), CQueueWorkerNodeList::MergeWorkerNodes(), CTreeMinimalSet< TNode, TSet, TNodeList >::MinimalSet(), CBlastTabular::Modify(), CAlignShadow::Modify(), CTreeNode< TValue, TKeyGetter >::MoveSubnodes(), CEnumeratedTypeValues::NameToValue(), newickerror(), CCompareSeqRegions::NextComparisonGroup(), CSeqGraphicPane::NextPrevSplice(), CScoreVector< Key, Score >::Normalize(), CQueue::NotifyListeners(), NS_DecodeBitVector(), CGBenchToolMonitor::OnAbortJob(), CGBenchGUI::OnAddToHomePage(), CHitMatrixWidget::OnColorByScore(), CHomePageView::OnDelete(), CSeqGraphicPane::OnEditCopy(), CHomePageView::OnExecute(), CGBenchWorkspaceWindow::OnImportCurrent(), CGBenchWorkspaceWindow::OnNewViewDlg(), CGBenchToolMonitor::OnResumeJob(), CSeqTextWidget::OnScrollToSelection(), CProjectTree::OnShowHide(), CHomePageView::OnShowPopupMenu(), CGBenchToolMonitor::OnSuspendJob(), CGBenchToolMonitor::OnUpdateAbortJob(), CGBenchToolMonitor::OnUpdateResumeJob(), CProjectTree::OnUpdateShowHide(), CGBenchToolMonitor::OnUpdateSuspendJob(), CPhyloTreeWidget::OnUseSplines(), SCigarAlignment::operator()(), CLDS_FindSeqIdListFunctor::operator()(), CLDS_FindSeqIdFunctor::operator()(), CLDS_FindSeqIdFunc::operator()(), PIsExcludedByProjectMakefile::operator()(), CAlnSeqIdsExtract< TAlnSeqId >::operator()(), CPhyloTreeDataSource::tree_to_dynamic::operator()(), CTreeNonRedundantSet< TNode, TSet, TNodeList >::operator()(), CBioTreeConvert2ContainerFunc< TBioTreeContainer, TDynamicTree >::operator()(), CFeatureGraphProperties::operator+=(), operator<<(), CSeq_loc_CI::operator=(), CBioTreeFeatureDictionary::operator=(), CScoreVector< Key, Score >::operator=(), CRawScoreVector< Key, Score >::operator=(), CPluginArgSet::operator[](), CReadBlastApp::overlaps_na(), CReadBlastApp::overlaps_prot_na(), PairTreeTraceNode(), CSplitParser::Parse(), CStringPairs< TContainer >::Parse(), oligofar::COligoFarApp::ParseArg(), ParseAttributes(), CFastaMapper::ParseDefLine(), CDBUriConnParams::ParseParamPairs(), CBDB_ConfigStructureParser::ParseStructureLine(), SSnpFilter::Passes(), CEventProc::PerformActionOnSignal(), CEventProc::PerformConversions(), CGridCgiContext::PersistEntry(), PluginArgsAsStrs(), PluginInfoFromRegistry(), impl::CDriverContext::PopDefConnMsgHandler(), COMSSASearch::PopulateOidList(), CQueue::PrepareFields(), CProjSRCResolver::PrepereResolver(), CCompilerToolImpl::PreprocessorDefinitions(), CComments::Print(), CBlastTabularInfo::Print(), CSeqsRange::Print(), CVectorPrinter::Print(), CDiagFilter::Print(), CWNJobsWatcher::Print(), oligofar::CHashPopulator::Print(), CQueueClientInfoList::Print(), CVersion::Print(), CDataValueTmpl< string >::PrintASN(), CFileSet::PrintASN(), CFileModules::PrintASN(), CDataTypeModule::PrintASN(), CEnumDataType::PrintASN(), CComments::PrintASN(), CDataMemberContainerType::PrintASN(), CFileModules::PrintASNRefInfo(), CHTML_table::PrintBegin(), CFileSet::PrintDTD(), CFileModules::PrintDTD(), CDataTypeModule::PrintDTD(), CComments::PrintDTD(), CDataMemberContainerType::PrintDTDElement(), CEnumDataType::PrintDTDExtra(), CDataMemberContainerType::PrintDTDExtra(), CFileSet::PrintDTDModular(), CFileModules::PrintDTDModular(), CDataTypeModule::PrintDTDModular(), CNamespace::PrintFullName(), CCgiContext::PrintMsg(), CPostscript::PrintObject(), CBlastFormat::PrintPhiResult(), CDiagContext::PrintProperties(), CFileSet::PrintSampleDEF(), CFileModules::PrintSampleDEF(), CDataTypeModule::PrintSampleDEF(), CFileSet::PrintSpecDump(), CFileModules::PrintSpecDump(), CDataTypeModule::PrintSpecDump(), CEnumDataType::PrintSpecDumpExtra(), CDataMemberContainerType::PrintSpecDumpExtra(), SBDB_CacheStatistics::PrintStatistics(), SBDB_CacheUnitStatistics::PrintStatistics(), CAlignFormatUtil::PrintTildeSepLines(), CArgAllow_Strings::PrintUsageXml(), CArgAllow_Symbols::PrintUsageXml(), CArgDescriptions::PrintUsageXml(), COptChoice< T >::PrintValue(), COptFlags< T >::PrintValue(), CQueue::PrintWorkerNodeStat(), CFileModules::PrintXMLRefInfo(), CFileSet::PrintXMLSchema(), CFileModules::PrintXMLSchema(), CDataTypeModule::PrintXMLSchema(), CDataMemberContainerType::PrintXMLSchema(), CFileSet::PrintXMLSchemaModular(), CFileModules::PrintXMLSchemaModular(), CDataTypeModule::PrintXMLSchemaModular(), DFS::process_vertex(), CGlContainer::ProcessEvent(), CMzXML2hdf5Application::ProcessFiles(), CNetScheduleHandler::ProcessGetConfiguration(), CMsvcSite::ProcessMacros(), CNetScheduleHandler::ProcessMsgBatchSubmit(), CCgiRedirectApplication::ProcessRequest(), CNetScheduleHandler::ProcessStatusSnapshot(), CProsite::PSPatternToPCRE(), oligofar::CBatch::Purge(), CBlast_def_line_set::PutTargetGiFirst(), CNetScheduleAdmin::Query(), ReadContainer(), CPhrap_Read::ReadDS(), readGFF3(), readGFF3Gap(), ReadMap(), CHMMParameters::SDetails::ReadParameters(), CGff3Reader::ReadSeqEntry(), CProjectManager::RecordViewOpen(), CMsvcProjectMakefile::Redefine(), CNcbiTestApplication::ReEnableAllTests(), oligofar::CSeqIds::Register(), CClusterer::ReleaseTrees(), CCgiRedirectApplication::RemapEntries(), CAnnotPieces::Remove(), CEditsSaver::Remove(), CDir::Remove(), CGeneModel::RemoveExtraFShifts(), CChain::RemoveFshiftsFromUTRs(), CTextSelHandler::Render(), CLinearSelHandler::Render(), CLegendHandler::Render(), CBookmarksHandler::Render(), CAlignMarkHandler::Render(), CRegularGridRenderer::Render(), CAxisRenderer::Render(), CDefaultPolicy::RenderFeatureGrid(), CDefaultPolicy::RenderHairLineSelections(), CNSInfoRenderer::RenderQueueList(), CHTMLException::ReportExtra(), CProjBulderApp::ReportGeneratedFiles(), CReadBlastApp::reportProblems(), CProjBulderApp::ReportProjectWatchers(), CCgiSession_NetCache::Reset(), CGroupCheckboxes::Reset(), CTableReader::Reset(), CBioseq_Base_Info::ResetAnnot(), CDataSource_ScopeInfo::ResetHistory(), CBioseq_ScopeInfo::ResetId(), CBioseq_Info::ResetId(), CEditsSaver::ResetIds(), CCrossPanelIR::ResetObjectSelection(), CListPanel::resize(), SRelLoc::Resolve(), CSymResolver::Resolve(), CLDS_DataLoader::ResolveConflict(), CGBDataLoader::ResolveConflict(), CGuiRegistryUtil::ResolveFieldPolicy(), CPluginManager< TClass >::ResolveFile(), CCodeGenerator::ResolveImportRefs(), CFileSet::ResolveInAnyModule(), CFileModules::ResolveInAnyModule(), CExec::ResolvePath(), CProjSRCResolver::ResolveTo(), RestoreModelAttributes(), CChain::RestoreReasonableConfirmedStart(), TMaskedQueryRegions::RestrictToSeqInt(), CThreadPool_Impl::ResumeWork(), CChainer::CChainerImpl::RightLeft(), CScopeTransaction_Impl::RollBack(), CTableControl::RowDataToVisible(), CAlnMixSequences::RowsStartItsContsistencyCheck(), CSampleLibtestApplication::Run(), CSampleObjmgrApplication::Run(), CSampleObjectsApplication::Run(), CSampleLdsApplication::Run(), CBlastDemoApplication::Run(), CAlnBuildApp::Run(), CGBenchMonitorApp::Run(), CGBenchApp::Run(), CGridWorkerNode::Run(), CServer::Run(), CProjBulderApp::Run(), CFixMsHdf5Application::Run(), CNetScheduleCheck::Run(), CNSSubmitRemoteJobApp::Run(), CGi2TaxIdApp::Run(), CGuideTreeApplication::Run(), CBlastDBCmdApp::Run(), CTblastxApp::Run(), CRPSTBlastnApp::Run(), CRPSBlastApp::Run(), CBlastxApp::Run(), CBlastpApp::Run(), CAgpconvertApplication::Run(), CUpdateOmssaModApplication::Run(), CLocalFinderApp::Run(), CSplignSimple::Run(), CDemoContigAssemblyApp::Run(), CBl2Seq::RunEx(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), CTestTranscript_Orfs::RunTest(), CTestProtProd_Cdd::RunTest(), s_AddCoalescedLocations(), s_AddDefaultArgs(), s_AddDefaultArguments(), s_AddProjItemToDll(), s_AddSitesToAnnot(), s_AddToUniqueIdList(), s_AlignSet2Annot(), s_AllBlobsAreLoaded(), s_BuildMaskedRanges(), s_BuildResultsRemote(), s_BuildScoreList(), s_CalcCoverageCount(), s_CalculateStarts(), s_CheckIdLookup(), s_CheckUniqueValues(), s_Code_break(), s_CollapseProjectFolder(), s_CollectDatatoolIds(), s_CollectRelPathes(), s_CollectSeqIds(), s_Compare(), CSplign::s_ComputeStats(), s_ConvertBioseqs2TSeqLocVector(), s_ConvertBlastnMasks(), s_ConvertRelativePaths(), s_CountBlastDbDataLoaders(), s_CountIntervals(), CPsiBlastTestFixture::s_CountNumberUniqueGIs(), s_CoverageSeqLoc(), s_CreateAnnotView(), s_CreateBlastMask(), s_CreateSeqEntryHandleView(), s_DupIdsBioseq(), s_DupIdsRaw(), s_ExonDataToLoc(), s_ExonLen(), s_ExonToDenseg(), s_ExpandProjectFolder(), s_ExpandSubNodes(), s_ExtractFilteringAlgorithmIds(), s_ExtractKeys(), s_FindBestIdChoice(), s_FindDistAsMax(), s_FindDistAsMean(), s_FindEntryName(), s_FindMaxDistFromElem(), s_FindMean(), s_FindModelEvidanceUop(), s_FindOrfs(), s_FindSumDistFromElem(), s_Fingerprint_Dense_diag(), s_Fingerprint_Dense_seg(), s_Fingerprint_Int_graph(), s_Fingerprint_Packed_seg(), s_Fingerprint_Packed_seqint(), s_Fingerprint_Packed_seqpnt(), s_Fingerprint_Real_graph(), s_Fingerprint_Seq_align(), s_Fingerprint_Seq_align_set(), s_Fingerprint_Seq_feat(), s_Fingerprint_Seq_loc_equiv(), s_Fingerprint_Seq_loc_mix(), s_Fingerprint_Sparse_align(), s_Fingerprint_Sparse_seg(), s_Fingerprint_Spliced_exon(), s_Fingerprint_Spliced_seg(), s_Fingerprint_Std_seg(), s_FixInitials(), s_FlattenBioseqSet(), s_FormatErrors(), s_GetAlignmentContent(), s_GetAnnotContent(), s_GetAnnotName(), s_GetBlastScore(), s_GetContentLabel(), CCompareSeqRegions::s_GetGeneId(), s_GetGOText(), s_GetLabel(), s_GetNameForBioseq(), s_GetPlugins(), s_GetStringFromFormat(), s_GetTaxid(), s_GetText_PairwiseAlign(), s_GetUserObjectContent(), s_HasLocalIDs(), s_HasMisSpellFlag(), s_HasPub(), s_HasRawSequence(), s_ImportQueries(), s_InitalizeDllProj(), s_IsCDD(), s_IsEmpty(), s_IsJustQuotes(), s_IsJustUids(), s_IsLegalECNumber(), s_IsNumeric(), s_IsProducedByDatatool(), s_IsRefSeq(), s_IsTPA(), s_IsValidRpt_typeQual(), s_List2Set(), s_ListChanges(), s_ListProjectFolder(), s_LogSubmit(), s_MakeBioseqs(), s_MakeNewMasterSeq(), s_MapAllGis(), s_MapRangeData(), CQueryDataTestFixture::s_ObjMgr_QueryFactory_LocalDataFromBlastQueryVector(), CQueryDataTestFixture::s_ObjMgr_QueryFactory_LocalDataFromTSeqLocVector(), CQueryDataTestFixture::s_ObjMgrFree_QueryFactory_LocalDataFromBioseq_set(), s_ParseSubNodes(), s_PrintAccessions(), s_PrintIds(), s_PrintIds1(), s_PrintTSeqAlignSet(), s_ProcessErrorsFromReply(), s_QualVectorToNote(), s_ReadRanges(), s_ReportDependenciesStatus(), s_RestrictSeqLocs_Multiframe(), CAlignShadow::s_RunLengthDecode(), s_ScanRecursive(), s_ScopeProjectFolder(), s_SeqAlignSetToXMLHsps(), s_SeqAlignToBlastSeqLoc(), s_SeqDB_SeqIdIn(), s_SeqDB_TryPaths(), s_SeqDBMapNcbiNA8ToBlastNA8_Ranges(), s_SetAnyContentFromFields(), s_SetDeflineBits(), s_SetFieldsFromAnyContent(), s_SetIntervals(), s_SetQuals(), s_SetSearchParam(), s_SetupWithMultipleQueriesAndSubjects(), s_SplicedToDisc(), s_SplitAlignVectorBySubjects(), s_StringIsJustQuotes(), s_TestClustersAndTrees(), s_TestResultTree(), s_TestResultTreeContainer(), s_TestStdSegGaps(), s_TitleFromProtein(), s_TitleFromSegment(), CHitFilter< THit >::s_TrackHit(), s_TranslateAnchorToAlnCoords(), s_TranslatePairwise(), s_TranslatePairwiseToAlnCoords(), s_TSeqLocVectorToBioseqSet(), s_TSeqLocVectorToTSeqLocs(), s_UnpackUserField(), s_Validate(), s_VT_Descr(), s_WriteComment(), CThemePreviewMediator::Save(), CThemeMediator::Save(), CColorTableMethod::Save(), CSeqGraphicConfig::SaveHistSettings(), CReaderRequestResult::SaveLocksTo(), CUIToolRegistry::SaveSettings(), CBookmarkManager::SaveSettings(), COpenViewDlg::SaveSettings(), ScanForCpGs(), SelectCompartmentsHits(), CHitMatrixDataSource::SelectIds(), CCompareSeqRegions::SelectMatches(), CTaxon3::SendOrgRefList(), Seq_locs_Merge(), SeqDB_ReadGiList(), SeqDB_SplitQuoted(), SeqDB_VectorAssign(), SeqLocMapperToPairwiseAligns(), SeqLocRevCmp(), CRemoteAppRequestSB_Impl::Serialize(), CRemoteAppRequestMB_Impl::Serialize(), SSnpFilter::SerializeFrom(), SSnpFilter::SerializeTo(), CGuiRegistry::CReadWriteView::Set(), CGuiRegistry::Set(), CFlatfileBar::SetAccessions(), SAnnotSelector::SetAdaptiveTrigger(), CArgDescriptions::SetArgsType(), CBlastDatabaseArgs::SetArgumentDescriptions(), CPluginArg::SetBoolean(), CChain::SetConfirmedStartStopForCompleteProteins(), CAlnMultiModel::SetCurrentMethod(), CCrossPanelIR::SetDataSource(), CPluginArg::SetDouble(), CGridDebugContext::SetExecuteList(), CChainer::CChainerImpl::SetGenomicRange(), CEUtils_IdGroupSet::SetGroups(), CNetSchedule_AccessList::SetHosts(), CEUtils_IdGroup::SetIds(), CPluginArg::SetInputFile(), CPluginArg::SetInteger(), CPluginArg::SetList(), CBlobSplitterImpl::SetLoc(), CWriteDB_Impl::SetMaskData(), CAlnMultiModel::SetMasterRow(), CDefaultLayoutPolicy::SetNAAs(), CPluginArg::SetObject(), CSeqTableSetAnyObjField::SetObjectField(), CPluginArg::SetOutputFile(), CPluginArg::SetProject(), CSeqTextPane::SetRangeSelection(), CPhyloTreeWidget::SetScheme(), SetScores(), CPluginArg::SetSecretString(), CPhyloTreeDataSource::SetSelection(), CSeq_annot_SplitInfo::SetSeq_annot(), CAlignParam::SetSpliceSet(), CStatusBar1::SetStatusBar(), CPluginArg::SetString(), oligofar::CAligner::SetSubjectGuideTranscript(), CDisplaySeqalign::SetSubjectMasks(), CSeqTableLocColumns::SetTableKeyAndIndex(), CJob::SetTags(), CComboBox::SetType(), CListPanel::SetupColumns(), LinkHspTestFixture::setupCutoffScores(), LinkHspTestFixture::setupLinkHspInputTblastn(), setupQueryStructures(), CPhyloTreeWidget::SetUseDistances(), CAlnMultiModel::SetVisible(), CListPanel::SetWidth(), CSeqGraphicDemoUI::Show(), CPluginMgrDlg::Show(), CPostscript::ShowPage(), sIsViewApplicable(), CGlBitmapFont::SizeFromString(), CReadInSkipObjectHook< Object >::SkipObject(), SServerScanInfo::SkipServer(), CMsvcSite::SLibChoice::SLibChoice(), CBDB_Volumes::SortVolumes(), SourceFile::SourceFile(), CSeqDB_FilterTree::Specialize(), CChainer::CChainerImpl::SplitAlignmentsByStrand(), CBlobSplitterImpl::SplitBioseq(), SplitExon(), CBlobSplitterImpl::SplitPieces(), CTextUtil::SplitWordFrequencies(), sReadAA_I(), MzXmlReader::start_element(), CAlnMixSegment::StartItsConsistencyCheck(), CServer_ConnectionPool::StartListening(), CServer_ConnectionPool::StopListening(), CFeatureTypesParser::StringToFeatTypes(), StringToHex(), CNetScheduleSubmitter::SubmitJobBatch(), SubtractAlnRngCollections(), CMultiDictionary::SuggestAlternates(), CSimpleDictionary::SuggestAlternates(), CLDS_Manager::sx_CreateDB(), CTableNames::TableToName(), CBookmarksHandler::TC_NeedTooltip(), CDirTest::Test(), CDbTest::Test(), TestExonLength(), CFormatGuess::TestFormatAgp(), CFormatGuess::TestFormatAlignment(), CFormatGuess::TestFormatBed(), CFormatGuess::TestFormatBed15(), CFormatGuess::TestFormatFiveColFeatureTable(), CFormatGuess::TestFormatFlatFileSequence(), CFormatGuess::TestFormatNewick(), CFormatGuess::TestFormatPhrapAce(), CFormatGuess::TestFormatSnpMarkers(), CFormatGuess::TestFormatWiggle(), testNuclHitList(), CSplitCacheApp::TestSplit(), CGlBitmapFont::TextOut(), CAlignResultsSet::ToBestSeqAlignSet(), CQuerySet::ToBestSeqAlignSet(), CSplign::SAlignedCompartment::ToBuffer(), CColorTableScoringModel::ToMethod(), CAlignResultsSet::ToSeqAlignSet(), CQuerySet::ToSeqAlignSet(), CSnpMarkers::ToSeqAnnot(), TSearchMessages::ToString(), CNamespace::ToStringTo(), TotalScore(), CNSInfoCollector::TraverseNodes(), TreeReRoot(), CGeneModel::TrimEdgesToFrameInOtherAlignGaps(), CDllResolver::TryCandidate(), CResetIds_EditCommand::Undo(), CMemoryFileMap::UnmapAll(), CAlignMarkHandler::UnMarkSelected(), CQueueWorkerNodeList::UnregisterNode(), CHitMatrixRenderer::Update(), CFeatHistogramDS::Update(), CRegistryItemPanel::Update(), CPluginTable::Update(), CLDS_Object::UpdateBinaryASNObjects(), impl::CDriverContext::UpdateConnMaxTextImageSize(), impl::CDriverContext::UpdateConnTimeout(), CAlignRangeCollExtender< TColl >::UpdateIndex(), CWindowManager::UpdateMenu(), CAlnMultiModel::UpdateOnStyleChanged(), CToolMonitorModel::UpdateTable(), CWorkerNode::UpdateValidityTime(), CThemeConfigPanel2::UpdateWidgets(), CBlastQueryFilteredFrames::UseProteinCoords(), CSparse_seg::Validate(), CSeq_align::Validate(), CPluginArgDialog::Validate(), CValidError_imp::ValidateAuthorList(), CValidError_imp::ValidateCitations(), CValidError_imp::ValidateDbxref(), CValidError_feat::ValidateExceptText(), CValidError_feat::ValidateExtUserObject(), CValidError_feat::ValidateGene(), CValidError_feat::ValidateGoTerms(), CValidError_feat::ValidateLabelVal(), CValidError_feat::ValidateRptUnitVal(), CValidError_annot::ValidateSeqAnnot(), CEnumeratedTypeValues::ValueToName(), CSeqDBAtlas::Verify(), CProjBulderApp::VerifyArguments(), CProjectItemsTree::VerifyExternalDepends(), CSimpleDictionary::Write(), CSeq_annot_SNP_Info_Reader::Write(), CBinaryListBuilder::Write(), CBlastDbFormatter::Write(), CFastaOstream::Write(), IRegistry::Write(), CStackTrace::Write(), CCgiCookies::Write(), CSeq_id::WriteAsFasta(), oligofar::CMappedAlignment::WriteAsSam(), CSearch< LEGACY, NHITS >::WriteBioseqs(), CWriter::WriteBytes(), CClassCode::WriteConstructionCode(), WriteContainer(), CClassCode::WriteDestructionCode(), WriteEnvironment(), CId1FetchApp::WriteFastaIDs(), WriteMap(), CMsvcConfigure::WriteNcbiconfMsvcSite(), CFileCode::WriteSourceFile(), CFileCode::WriteUserFile(), CPdfObjectWriter::WriteXRef(), CNcbiTestApplication::x_ActualizeDeps(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), CDefaultLayoutPolicy::x_AddAlignmentsLayout(), CTSE_Info::x_AddAllFeaturesById(), CDefaultLayoutPolicy::x_AddAssnStudyFromGraph(), CDefaultLayoutPolicy::x_AddAssnStudyGraphsLayout(), CDefaultLayoutPolicy::x_AddAssnStudyLayout(), CBlastTabularInfo::x_AddDefaultFieldsToShow(), CDefaultLayoutPolicy::x_AddFeatCDSProduct_FeatsLayout(), CFeatureItem::x_AddFTableDbxref(), CFeatureItem::x_AddFTableExtQuals(), CWriteDB_IsamIndex::x_AddGis(), CFeatureItem::x_AddGoQuals(), CDefaultLayoutPolicy::x_AddHistogramsFromGraph(), CDefaultLayoutPolicy::x_AddHistogramsLayout(), CKeywordsItem::x_AddKeyword(), CAutoDefModifierCombo::x_AddOrgModString(), CDefaultLayoutPolicy::x_AddOtherFeaturesLayout(), CMergedPairwiseAln::x_AddPairwise(), CFeatureItem::x_AddQualsExt(), oligofar::CQueryHash::x_AddQuery(), CMultiAligner::x_AddRpsFreqsToCluster(), CDefaultLayoutPolicy::x_AddSeqGraphsLayout(), CDefaultLayoutPolicy::x_AddSNPsLayout(), CWriteDB_IsamIndex::x_AddStringIds(), CAutoDefModifierCombo::x_AddSubsourceString(), CNcbiTestTreeElement::x_AddToMustLeft(), CNcbiTestTreeElement::x_AddToMustRight(), CContextCommandService::x_AddToProject(), CWriteDB_IsamIndex::x_AddTraceIds(), CDataSource::x_AddTSEAnnots(), CDataSource::x_AddTSEBioseqAnnots(), CDataSource::x_AddTSEOrphanAnnots(), CScope_Impl::x_AddTSESetWithAnnots(), CSeqTextDataSource::x_AddVariationsFromFeature(), CAlnTableDS::x_AdjustColumns(), CSeq_loc_Mapper_Base::x_AdjustSeqTypesToProt(), CMultiAligner::x_AlignInClusters(), CGuiRegistry::CReadView::x_AppendToReadView(), CGuiRegistry::x_AppendToView(), x_ApplyCmd(), CDataLoaderPatcher::x_ApplyPatches(), CGridWorkerNode::x_AreMastersBusy(), x_Assign(), CNCMessageHandler::x_AssignCmdParams(), CGBDocument::x_AssignViewIndex(), CSplitParser::x_Attach(), CMultiAligner::x_AttachClusterTrees(), CBioseq_ScopeInfo::x_AttachTSE(), CPhyloTreeLabel::x_BestFont(), CTL_BCPInCmd::x_BlkSetHints(), CWriteDB_Impl::x_BuildDeflinesFromBioseq(), CObjectConverter::x_BuildGraph(), CAlnGraphic::x_BuildHtmlTable(), CWriteDB_ColumnIndex::x_BuildMetaData(), x_BuildRelations(), CBioseq_Info::x_CalcBioseqLength(), CSeqGraphicJob::x_CalcGeneHistogram(), CSeqGraphicJob::x_CalcGeneHistogram_Recursive(), CFeaturesPanelIR::x_CalcObjectRows_Recursive(), CDefaultPolicy::x_CalcObjectRows_Recursive(), CColumnScoringMethod::x_CalculateConsensusScores(), CSeq_loc::x_CalculateTotalRangeCheckId(), CNcbiTestApplication::x_CallUserFuncs(), CThreadPool_Impl::x_CancelExecutingTasks(), CScopeTransaction_Impl::x_CanCommitRollBack(), CCleanup_imp::x_ChangeGenBankBlocks(), CDiagFilter::x_Check(), CNCBlobStorage::x_CheckDBInitialized(), CShowBlastDefline::x_CheckForStructureLink(), CSeq_loc::x_CheckId(), CSeqDBVol::x_CheckVersions(), CAlignCleanup::x_Cleanup_AlignVec(), CAlignCleanup::x_Cleanup_AnchoredAln(), CElementaryMatching::x_CleanVolumes(), CGetFeature::x_Clear(), CHitMatrixDataSource::x_Clear(), CAlignedFeatureGraph::x_Clear(), CClipboard::x_Clear(), CHomePageService::x_Clear(), CCompoundRWRegistry::x_Clear(), CHitMatrixDataSource::x_ClearHits(), CFeaturesPanelIR::x_ClearSelection_Recursive(), CMemoryFileMap::x_Close(), CGBenchGUI::x_CloseAllSystemViews(), x_CollectMembers(), CPrimaryItem::x_CollectSegments(), CNCServerStat::x_CollectTo(), oligofar::CAligner::x_ColorspaceUpdatePenalty(), CRangeCollection< CPairwiseAln::TPos >::x_CombineWith(), CCleanup_imp::x_Common(), CValidError_bioseq::x_CompareStrings(), CPsiBlastInputClustalW::x_CopyQueryToMsa(), CValidError_align::x_CountBits(), CPhrap_Contig::x_CreateAlignAll(), CPhrap_Contig::x_CreateAlignOptimized(), CPhrap_Contig::x_CreateAlignPairs(), CMultiAligner::x_CreateBlastQueries(), CAlnMixMerger::x_CreateDenseg(), CHomePageView::x_CreateItems(), CFeatureGraph::x_CreateMapRanges(), CGBenchWorkspaceWindow::x_CreateNewViewSubmenu(), CWMTabControl::x_CreatePopupMenu(), CSeqGraphicWidget::x_CreatePopupMenu(), CPhrap_Contig::x_CreateSeq_align(), CStudyLoader::x_CreateSeqAnnots(), CStudyLoader::x_CreateSeqFtable(), CNetCacheServer::x_CreateStorages(), CDiagContext::x_CreateUID(), CEntrezSearchForm::x_DDX_DbName(), CSequenceSearchForm::x_DDX_MatchType(), CFeatureSearchForm::x_DDX_MatchType(), CAlgoPlugin_FindOrfs::x_DecodeGeneticCode(), x_DecodeGeneticCode(), CSeqGraphicDataSource::x_DeleteAllJobs(), CPhyloTreeLabel::x_DestroyFonts(), CTSE_ScopeInfo::x_DetachDS(), CBioseq_ScopeInfo::x_DetachTSE(), CShowBlastDefline::x_DisplayDefline(), CShowBlastDefline::x_DisplayDeflineTable(), CComponentSearchJob::x_DoSearch(), CCompartApp::x_DoWithExternalHits(), CWMCaptionPanel::x_DrawButtons(), CCrossPanelIR::x_DrawCrossAlignment(), CAxisRenderer::x_DrawHorzLabels(), CDefaultPolicy::x_DrawVariation(), CTSE_Info::x_DSAttachContents(), CTSE_Info::x_DSDetachContents(), CAppHitFilter::x_DumpOutput(), CEnvironmentRegistry::x_Empty(), CNcbiTestApplication::x_EnableAllTests(), CNcbiTestApplication::x_EnsureAllDeps(), CNcbiTestTreeElement::x_EnsureChildOrder(), CCompoundRWRegistry::x_Enumerate(), CCompoundRegistry::x_Enumerate(), CMemoryRegistry::x_Enumerate(), CEnvironmentRegistry::x_Enumerate(), CCompartApp::CCompartment::x_EvalExons(), CMRUCache::x_Exists(), CPsiBlastInputData::x_ExtractAlignmentData(), CPsiBlastInputClustalW::x_ExtractQueryFromMsa(), CQueue::x_FailJobs(), CNCBlobStorage::x_FillCacheFromDBPart(), CSeq_align_Mapper_Base::x_FillKnownStrands(), CCrossAlnDemoUI::x_FillLists(), CDisplaySeqalign::x_FillLocList(), x_FillObjects(), CRegistryDlg::x_FillTree(), CDataSource_ScopeInfo::x_FindBestTSE(), CDataSource::x_FindBestTSE(), CScope_Impl::x_FindBioseqInfo(), CBlastServices::x_FindDbInfoFromAvailableDatabases(), CSeq_id_PDB_Tree::x_FindInfo(), CSeq_id_Giim_Tree::x_FindInfo(), CMultiAligner::x_FindLocalInClusterHits(), CProjectFileWriter::x_FindParent(), CObjectConverter::x_FindRelationByName(), x_FindRSite(), CTSE_Info::x_FindSeq_feat(), CTracebackSearchTestFixture::x_FindUsedGis(), CProcessor_ID2::x_FixCompression(), CCleanup_imp::x_FixSuffix(), CGFFFormatter::x_FormatAttr(), CFtableFormatter::x_FormatQuals(), CNCBlobStorage::x_FreeBlobIdLocks(), CAlignedFeatureGraph::x_GatherCluster(), CDBSourceItem::x_GatherInfo(), CNCBlobStorage::x_GC_CleanDBPart(), CPhyloTreeLabel::x_GenerateLabel(), CAxisRenderer::x_GenerateLabels(), CScope::x_GetAccVer(), CHitMatrixDataSource::x_GetAlignedSeqIds(), CAlignFilter::x_GetAlignmentScore(), CProjectFileWriter::x_GetAnnotId(), CAlignmentSmear::x_GetAnnotName(), CAnnot_Collector::x_GetAnnotNames(), CSplignApp::x_GetBl2SeqHits(), CAlgoWebService::x_GetContentType(), x_GetConversions(), CAutoDefFeatureClause::x_GetDescription(), CODBC_Connection::x_GetDriverName(), CSeq_align_Mapper_Base::x_GetDstDendiag(), CSeq_align_Mapper_Base::x_GetDstDisc(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CSeq_align_Mapper_Base::x_GetDstStd(), CRemoteAppJob::x_GetEnv(), CId2ReaderBase::x_GetError(), x_GetFeatById(), x_GetFeatsById(), x_GetFeatsByXref(), CDefaultLayoutPolicy::x_GetFeaturesJob(), CWindowManager::x_GetFramedClients(), CScope::x_GetGi(), CProjectFileWriter::x_GetGi(), CDefaultLayoutPolicy::x_GetHistogramsJob(), CValidError_align::x_GetIds(), CDefaultPolicy::x_GetIntron(), CThemeConfigPanel2::x_GetItem(), CGuiRegistry::CReadView::x_GetKeys(), CAlnMultiDSBuilder::x_GetLinearAlignments(), CEntrez2ClientApp::x_GetLinkCounts(), CRuler::x_GetMaxNum(), CId2ReaderBase::x_GetMessageError(), CWindowManager::x_GetMoveFromFrameMenu(), CWindowManager::x_GetMoveHereMenu(), CSeq_align::x_GetNamedScore(), CSeq_align_Mapper_Base::x_GetPartialDenseg(), CBlastDBCmdApp::x_GetQueries(), CGBDataLoader::x_GetRecords(), CDataSource::x_GetRecords(), CAlignedFeatureGraph::x_GetRecsSortedByLength(), CDataSource_ScopeInfo::x_GetSeqMatch(), CDataSource::x_GetSeqMatch(), CBlastServices::x_GetSeqsFromReply(), CPrimaryItem::x_GetStrForPrimary(), CConfig::x_GetString(), CSettingsSet::x_GetStyleKey(), CScope_Impl::x_GetSynonyms(), CSeqDBVol::x_GetTaxDefline(), CDefaultPolicy::x_GetTitle(), CMenuBar::x_GetTooltip(), CProjectTree::x_GetTreeItemsMenu(), CScope_Impl::x_GetTSESetWithBioseqAnnots(), CClipboard::x_GetValueAt(), CSeqDBAliasNode::x_GetVolumeNames(), x_Glob(), CHitMatrixDataSource::x_GoodSeg(), CTSE_Info::x_HasIdObjects(), CSeq_align_Mapper_Base::x_HaveMixedSeqTypes(), CTextSelHandler::x_HitTest(), CLinearSelHandler::x_HitTest(), CAlignMarkHandler::x_HitTest(), CFlatGatherer::x_IdComments(), CFeatureItem::x_ImportQuals(), CDataSource::x_IndexAnnotTSEs(), CTSE_Info::x_IndexBioseq(), CDataSource::x_IndexSeqTSE(), CDataSource_ScopeInfo::x_IndexTSE(), CReferenceItem::x_Init(), CSeq_align_Mapper_Base::x_Init(), CFeatureTypesBrowser::x_Init(), CAnnotCompare_AlignDS::x_Init(), CSequenceDataTester::x_Init(), CSeq_annot_Info::x_InitAlignList(), CAlignMarkHandler::x_InitDeltaMap(), CSeq_annot_Info::x_InitFeatList(), CSeq_annot_Info::x_InitFeatTableKeys(), CSeq_annot_Info::x_InitGraphList(), CAnnot_CI::x_Initialize(), CSeq_loc_Mapper_Base::x_InitializeAlign(), CGBenchPluginInit::x_InitLDS(), CSeq_annot_Info::x_InitLocsList(), CSeqIdAlignBitmap< TSeqAlignSeqIdVec >::x_InitNucProtBitmaps(), CMultiAligner::x_InitParams(), CElementaryMatching::x_InitParticipationVector(), CGBenchApp::x_InitPlugins(), CGBenchGUI::x_InitSearchCommands(), CRangeCollection< CPairwiseAln::TPos >::x_IntersectWith(), CValidError_bioseq::x_IsDeltaLitOnly(), CBioseqContext::x_IsDeltaLitOnly(), CAutoDef::x_IsFeatureSuppressed(), CClassTypeStrings::x_IsNullWithAttlist(), CChoiceTypeStrings::x_IsNullWithAttlist(), CFeaturesPanelIR::x_IsObjectSelected(), x_IsOneMinusStrand(), CSeq_loc_Mapper_Base::x_IterateExonParts(), CAppHitFilter::x_IterateSeqAlignList(), CStatusBar1::x_Layout(), CMenu::x_Layout(), CThemeMediator::x_Load(), CFileLoader::x_LoadAGP(), CTSE_Split_Info::x_LoadChunks(), CLDSManageTable::x_LoadDataToView(), CExternalPluginInit::x_LoadExternalPlugins(), CSeqGraphicDemoUI::x_LoadFileSettings(), CSnpFilterUI::x_LoadFilter(), CThemeMediator::x_LoadFirst(), CSeqGraphicJob::x_LoadGWAS(), CGBenchApp::x_LoadPlugins(), CSeqGraphicUtilJob::x_LoadSegmentsSeqIDs(), CId2ReaderBase::x_LoadSeq_idBlob_idsSet(), CSeqGraphicJob::x_LoadSwitchPoints(), CWebPluginInit::x_LoadWebPlugin(), CAlgoWebServiceInit::x_LoadWebPlugins(), CCgiSampleApplication::x_LookAtArgs(), oligofar::CSeqScanner::x_MainLoop(), CFeaturesPanelIR::x_MainObjectIterator(), CMultiAligner::x_MakeFillerBlocks(), CTSE_Handle::x_MakeHandles(), CThemeConfigPanel2::x_MakeWidgets(), CTSE_Info::x_MapAnnotObject(), CSeq_annot_Info::x_MapAnnotObject(), CFeatureSearchJob::x_Match(), CDiagStrErrCodeMatcher::x_Match(), CReferenceItem::x_Matches(), CCleanup_imp::x_Merge(), CCleanup_imp::x_MergeAdjacentAnnots(), CGFFReader::x_MergeAttributes(), CMergeVolumes::x_MergeCandidates(), CAlnGraphic::x_MergeDifferentSeq(), CGFFReader::x_MergeRecords(), CSeqGraphicJob::x_MergeSeqSegments(), CGuiRegistry::x_MergeSite(), CAlnMixSegments::x_MinimizeGaps(), CCleanup_imp::x_MinimizePub(), CLDSManageTable::x_ModelToView(), CNetScheduleHandler::x_MonitorJob(), CCleanup_imp::x_MoveCodingRegionsToNucProtSets(), CCleanup_imp::x_MoveDbxrefs(), CCleanup_imp::x_MoveMapQualsToGeneMaploc(), CLocusItem::x_NameHasBadChars(), CSnpFilterUI::x_OnBtnDone(), CObjectListWidget::x_OnCmdCopy(), CSeqTextPane::x_OnCopy(), CCgiApplication::x_OnEvent(), CSequenceGotoDlg::x_OnGoto(), CBookmarksHandler::x_OnMousePush(), CSpellCheckDlg::x_OnNext(), CHairlineOptionsDlg::x_OnOK(), CPhyloTreeEdit::x_OnOK(), CPluginDlg::x_OnOK(), CSeqMarkerSetDlg::x_OnSet(), CViewValidator::x_OnSetSelection(), CViewTaxTree::x_OnSetSelection(), CViewFeatTable::x_OnSetSelection(), CViewPhyloTree::x_OnSetSelection(), CViewAnnotCompare::x_OnSetSelection(), CWMSplitter::x_OnShowPopupMenu(), CCache< TKey, TValue, THandler, TLock, TSize >::x_PackElementIndex(), CSplitQueryTestFixture::x_ParseConfigLine(), CNCBlobStorage::x_ParseTimestampParam(), CGFFReader::x_ParseV3Attributes(), CDataLoaderPatcher::x_PatchLockSet(), CScope_Impl::x_PopulateBioseq_HandleSet(), CAlnMultiDSBuilder::x_PreCreateSparseDataSource(), CSeq_loc_Mapper_Base::x_PreserveDestinationLocs(), CSeqDB_FilterTree::x_Print(), CDiagStrErrCodeMatcher::x_Print(), CArgDescriptions::x_PrintAliasesAsXml(), CBlastDBCmdApp::x_PrintBlastDatabaseInformation(), CBlastTabularInfo::x_PrintFieldNames(), CQueue::x_PrintJobStat(), CPdf::x_PrintPolygon(), CNetCacheServer::x_PrintServerStats(), CBlastTabularInfo::x_PrintSubjectAllAccessions(), CBlastTabularInfo::x_PrintSubjectAllGis(), CBlastTabularInfo::x_PrintSubjectAllSeqIds(), CBlastFormat::x_PrintTabularReport(), CXcompareAnnotsApplication::x_ProcessComparison(), CTar::x_ProcessEntry(), CMakeBlastDBApp::x_ProcessInputData(), CBlastOptionsBuilder::x_ProcessOptions(), CBlastDBCmdApp::x_ProcessSingleQuery(), x_RangesToSeq_loc(), CSeq_annot_SNP_Info_Reader::x_Read(), CNcbiTestApplication::x_ReadConfiguration(), CSplitQueryTestFixture::x_ReadQueryBoundsPerChunk(), CViewCompositeManager::x_RebuildMenu(), CViewTaxTree::x_RebuildObjectIndex(), CGlPaneWidgetChild::x_RegisterHandler(), CAlnMultiPane::x_RegisterHandler(), CBuildDatabase::x_ResolveGis(), CGFFReader::x_ResolveID(), CGFFReader::x_ResolveLoc(), CBuildDatabase::x_ResolveRemoteId(), CTSE_ScopeInfo::x_RestoreAdded(), CInstancedAligner::x_RunCleanup(), CLDSManageTable::x_SaveDataFromView(), CSearchFormBase::x_SavePatternType(), CElementaryMatching::x_Search(), CAnnot_Collector::x_SearchAll(), CFeatureSearchJob::x_SearchFeatures(), CAnnot_Collector::x_SearchLoc(), CAnnot_Collector::x_SearchMapped(), CAnnot_Collector::x_SearchMaster(), CAnnot_Collector::x_SearchSegments(), CTaxIdSet::x_SelectBestTaxid(), CFeaturesPanelIR::x_SelectByRect_Recursive(), CHistogramDlg::x_SelectGraph(), CBioseq::x_SeqLoc_To_DeltaExt(), CDefaultPolicy::x_SeqToProduct(), CBioseq_Base_Info::x_SetAnnot(), CTSE_Info::x_SetBioseqIds(), CSeqdesc_CI::x_SetChoices(), CThemeConfigPanel::x_SetItems(), CDefaultLayoutPolicy::x_SetNAAs(), CMasterContext::x_SetNumParts(), CBioseq_set_Info::x_SetObject(), CBioseq_Info::x_SetObject(), CThemeDlg::x_SetStates(), CEditStylesDlg::x_SetStates(), CConfigDlg::x_SetStates(), CThemeConfigPanel2::x_SetStyles(), CThemeConfigPanel::x_SetStyles(), CPhyloTreeEdit::x_Setup(), CSeq_align_Mapper_Base::x_SortSegs(), CSplitDataLoader::x_SplitAligns(), CTSE_Chunk_Info::x_SplitAttach(), CSplitDataLoader::x_SplitFeats(), CSplitDataLoader::x_SplitGraphs(), CSplign::x_SplitQualifyingHits(), CBlastFormat::x_SplitSeqAlign(), CNCMessageHandler::x_StartCommand(), CFeatureGraph::x_StartJob(), CFeature_table_reader_imp::x_StringIsJustQuotes(), CRangeCollection< CPairwiseAln::TPos >::x_Subtract(), CAlnMultiDSBuilder::x_TestAlignments(), CHitMatrixDataSource::x_TestAndSelectAligns(), x_TestGetFilteredQueryRegions(), x_TestGetSeqLocInfoVector(), CVecscreenTest::x_TestRangeList(), CVecscreenTest::x_TestSeqalign(), CSequenceDataTester::x_TestSingleSequence_Local(), x_ToBlastVec(), CHomePageService::x_ToUserObject(), CMergedPairwiseAln::x_TruncateOverlaps(), CTSE_Chunk_Info::x_TSEAttach(), CBioseq_Info::x_TSEDetachContents(), CDefaultLayoutPolicy::x_TurnRNA_CDS_Labels(), CDataSource::x_UnindexAnnotTSEs(), CDataSource_ScopeInfo::x_UnindexTSE(), CSelectionView::x_Update(), CTemplateDlg::x_Update(), CTSE_Chunk_Info::x_UpdateAnnotIndexContents(), CSnpFilterListDialog::x_UpdateBrowser(), CTrackCreatorUI::x_UpdateChoices(), CHitMatrixRenderer::x_UpdateGraphColor(), CScope_Impl::x_UpdateHandleSeq_id(), CFilterDlg::x_UpdateList(), CId2ReaderBase::x_UpdateLoadedSet(), CAlignMarkHandler::x_UpdateMarks(), CGBenchGUI::x_UpdateMRUMenu(), CSeq_annot_Info::x_UpdateName(), CAlnMultiWidget::x_UpdateOnSwitchMaster(), CPageHandler::x_UpdatePageTreeRoot(), CHitMatrixDataSource::x_UpdateScoreMap(), CGBenchGUI::x_UpdateSearchMenu(), CFeatTableDS::x_UpdateTypeHash(), CViewGraphic::x_UpdateVisRangeLayout(), CSelectionView::x_UpdateWidget(), CValidError_align::x_ValidateDendiag(), CMultiAligner::x_ValidateQueries(), CValidError_align::x_ValidateSegmentGap(), CValidError_align::x_ValidateSeqId(), CValidError_align::x_ValidateSeqLength(), CValidError_align::x_ValidateStd(), CValidError_align::x_ValidateStrand(), CScoringJob::x_WindowAvgScores(), CBlastFormat::x_WrapAlignmentInSeqAnnot(), CElementaryMatching::x_WriteIndexFile(), CXmlTagWriter::x_WriteTag(), CTextTagWriter::x_WriteTag(), CAlnGraphic::~CAlnGraphic(), CBlastQueryFilteredFrames::~CBlastQueryFilteredFrames(), CCgiApplication::~CCgiApplication(), CDriverManager::~CDriverManager(), CFileDeleteList::~CFileDeleteList(), CLDS_DatabaseHolder::~CLDS_DatabaseHolder(), CNcbiTestTreeElement::~CNcbiTestTreeElement(), CNCDBFileObjFactory< TFile >::~CNCDBFileObjFactory(), CObjectPool< C >::~CObjectPool(), CPluginManager< TClass >::~CPluginManager(), CPrefetchSequence::~CPrefetchSequence(), oligofar::CSamSource::~CSamSource(), oligofar::CScoringFactory::~CScoringFactory(), CSeq_id_Mapper::~CSeq_id_Mapper(), CShowBlastDefline::~CShowBlastDefline(), CTiwClient_Types::~CTiwClient_Types(), CVecscreen::~CVecscreen(), and CWebPlugin::~CWebPlugin().

#define NCBI_CTYPEFAKEBODY   { return See_the_standard_on_proper_argument_type_for_ctype_macros(c); }
 

Definition at line 707 of file ncbimisc.hpp.

#define NCBI_DEPRECATED_CTOR decl   )     decl NCBI_DEPRECATED
 

Macro used to mark a constructor as deprecated.

The correct syntax for this varies from compiler to compiler: older versions of GCC (prior to 3.4) require NCBI_DEPRECATED to follow any relevant constructor declarations, but some other compilers (Microsoft Visual Studio 2005, IBM Visual Age / XL) require it to precede any relevant declarations, whether or not they are for constructors.

Definition at line 959 of file ncbimisc.hpp.

#define NON_CONST_ITERATE Type,
Var,
Cont   )     for ( Type::iterator Var = (Cont).begin(); Var != (Cont).end(); ++Var )
 

Non constant version of ITERATE macro.

Definition at line 875 of file ncbimisc.hpp.

Referenced by CWindowManager::ActivateClients(), CNcbiTable< TValue, TRow, TColumn >::AddColumn(), CProjectTreeBuilder::AddDatatoolSourcesDepends(), CScope_Impl::AddDefaults(), TSearchMessages::AddMessageAllQueries(), CAutoDefSourceGroup::AddQual(), CAutoDefModifierCombo::AddQual(), CScoreBuilder::AddScore(), CAutoDefModifierCombo::AddSource(), AgpRead(), AnalyzeDllData(), CReadBlastApp::AnalyzeSeqs(), CReadBlastApp::AnalyzeSeqsViaBioseqs(), CProjectItem::Attach(), CBlobSplitterImpl::AttachToSkeleton(), CCleanup_imp::BasicCleanup(), Blast_FindDustFilterLoc(), Blast_FindWindowMaskerLoc(), CAlignFormatUtil::BlastPrintError(), BOOST_AUTO_TEST_CASE(), CDataMiningView::BroadcastVisibleRange(), BuildGoodProtSeq(), CAlnMixSequences::BuildRows(), CAlnVecRow::CAlnVecRow(), CChainMembers::CChainMembers(), CColorTableScoringModel::CColorTableScoringModel(), CFlagsFormatter::CFlagsFormatter(), CSeq_loc::ChangeToMix(), CQueueDataBase::CheckExecutionTimeout(), CWNJobsWatcher::CheckInfinitLoop(), CServer_ConnectionPool::Clean(), CleanDoubleQuote(), CDBServiceMapperCoR::CleanExcluded(), CWriteDB_PackedBuffer< BLOCK >::Clear(), CSparseAlignment::Clear(), CEventHandler::CPostQueue::Clear(), CObjectIndex::Clear(), CPluginTaskQueue::Clear(), CUsedTlsBases::ClearAll(), CPluginArgSet::ClearObjects(), CAlnMultiModel::ClearRows(), CHit::Clone(), CGBenchWorkspaceWindow::CloseClients(), CGBenchGUI::CloseSystemView(), impl::CDriverContext::CloseUnusedConnections(), SChainMember::CollectContainedAlignments(), CSeqDBAliasNode::CompleteAliasFileValues(), CSeqMatch::CompNcbi8na(), CDBServiceMapperCoR::ConfigureFromRegistry(), CSeq_align_Mapper::Convert(), CSeq_align_Mapper_Base::Convert(), ConvertAuthorContainerMlToStd(), ConvertDoubleQuotes(), COMSSASearch::CopyHitsets(), CReadBlastApp::CopyInfoFromGenesToProteins(), COMSSASearch::CopySettings(), COMSSASearch::CopySpectra(), CPluginHandle_Impl::CPluginHandle_Impl(), CBlastAligner::CreateBlastAligners(), CSeqMap::CSeqMap(), CSeqScores::CSeqScores(), CUser_field::DeleteField(), CProjectItem::Detach(), CTreeNode< TValue, TKeyGetter >::DetachNode(), CPluginManager< TClass >::DetachResolver(), CProjectManager::DetachView(), CViewComposite::Dispatch(), CMultEditCommand::Do(), CMytestApplication::DoProcessFeatureGeneOverlap(), SMakeProjectT::DoResolveDefs(), CTestActionList::DoTest(), CTSE_LockSet::Drop(), CChainer::CChainerImpl::DropAlignmentInfo(), CDataSource::DropAllTSEs(), CBDB_FileDumperApp::Dump(), CServer_ConnectionPool::Erase(), CDBServiceMapperCoR::Exclude(), CEditAction_UpdateIds::Execute(), CEditCommand_Defline::Execute(), CDeleteSeqFeatCommand::Execute(), CChangeSeqFeatCommand::Execute(), CAutoDefModifierCombo::ExpandByAnyPresent(), ExtractChunks(), CObjMgr_QueryFactory::ExtractScopes(), CObjMgr_QueryFactory::ExtractUserSpecifiedMasks(), CQueryFilter::FilterAlignments(), CGBReaderCacheManager::FindCache(), CProjectFolder::FindChildFolder(), CChainer::CChainerImpl::FindContainedAlignments(), CChainer::CChainerImpl::FindMultiplyIncluded(), CLDS_CoreObjectsReader::FindObjectInfo(), CGBWorkspace::FindProjectHandle(), CPluginArgForm::FindWidget(), CLinearWizardData::Finish(), CTableControl::FireFocusCellChanged(), CAbstractTableModel::FireTableChanged(), CDefaultSelectionModel::FireValueChanged(), CTaxIdSet::FixTaxId(), CSeq_loc_mix::FlipStrand(), CPacked_seqint::FlipStrand(), CMultiWriter::Flush(), CQueue::FlushTags(), CResourcePool_Base< string, CNoLock, CResoursePool_NewClassFactory< string > >::Forget(), CTSE_ScopeInfo::ForgetTSE_Lock(), CMergeAligner::GenerateAlignments(), CInstancedAligner::GenerateAlignments(), CFileCode::GenerateCode(), CProjBulderApp::GenerateMsvcProjects(), CGBDataLoader::GetBlobs(), CDataSource::GetBlobs(), CDataLoader::GetBlobs(), CExtensionRegistry::GetExtension(), CExtensionRegistry::GetExtensionPoints(), CExtensionPoint::GetExtensions(), CGuiRegistry::GetKeys(), GetProjectHandles(), CMaskedRangeSet::GetRanges(), CProjectTree::GetSelectedProjectFolders(), CProjectTree::GetSelectedProjectIds(), CProjectTree::GetSelectedProjects(), CProjectTree::GetSelectedViews(), CProjectTree::GetSelectedWMClients(), CHTML_tr::GetTextLength(), CFlagsFormatter::GetWidget(), CFlagsFormatter::GetWidgetByArg(), CTextUtil::GetWordFrequencies(), CSplitter::handle(), impl::CDBExceptionStorage::Handle(), CDeleteSeqFeatCommand::Init(), CAlnMixSequences::InitExtraRowsStartIts(), CAlnMixSequences::InitRowsStartIts(), CLDS_Object::IsObject(), CProjectTree::IsProjectsSelected(), CGraphContainer::Layout(), CFeatureGraph::Layout(), CAlignRowGraphCont::Layout(), CWindowManager::LayoutToUserObject(), LDS_LoadTSE(), CChainer::CChainerImpl::LeftRight(), CSeqUtils::LinkFeatures(), CGBProjectHandle::Load(), LoadedChunksPacket(), COpenViewDlg::LoadGroupSettings(), CHitList::MakeCanonical(), CChainer::CChainerImpl::MakeChains(), CChainer::CChainerImpl::MakeOneStrandChains(), CReadBlastApp::match_na(), CHitList::MatchOverlappingSubHits(), CCpGIslands::MergeIslesWithin(), CTreeMinimalSet< TNode, TSet, TNodeList >::MinimalSet(), CGraphContainer::NeedTooltip(), CAlignedFeatureGraph::NeedTooltip(), CInt_fuzz::Negate(), CScoreVector< Key, Score >::Normalize(), CRawScoreVector< Key, Score >::Normalize(), CWorkerNodeJobWatchers::Notify(), CQueueDataBase::NotifyListeners(), CSeq_align::OffsetRow(), CGBenchGUI::OnBeforeClientClosed(), CGBenchWorkspaceWindow::OnCloseAllViews(), CProjectTree::OnCloseProjects(), CHistogramDlg::OnColorBtnChanged(), CProjectTree::OnCopy(), CProjectTree::OnMerge(), CGBenchWorkspaceWindow::OnNewViewDlg(), CProjectTree::OnRemove(), CGBenchGUI::OnSaveProject(), CGBenchGUI::OnSaveProjectAs(), CProjectTree::OnUpdateCopy(), CGBenchGUI::OnUpdateSaveProject(), CGBenchGUI::OnUpdateSaveProjectAs(), CViewComposite::OnVisibleRangeChanged(), CScoreVector< Key, Score >::operator *=(), CRawScoreVector< Key, Score >::operator *=(), impl::SUnLock::operator()(), CAlnPos_CI::operator++(), CAlnPos_CI::operator--(), CScoreVector< Key, Score >::operator/=(), CRawScoreVector< Key, Score >::operator/=(), CTreeNode< TValue, TKeyGetter >::operator=(), CPluginArgSet::operator[](), CSeq_entry::Parentize(), CSeq_entry::ParentizeOneLevel(), CHTML_table::PrintBegin(), CNCBINode::PrintChildren(), CHTML_tr::PrintChildren(), CNCBlobStorage::PrintStat(), CScoreVector< Key, Score >::ProbNormalize(), CRawScoreVector< Key, Score >::ProbNormalize(), ProductToSource(), CQueueDataBase::Purge(), CGBDataLoader::PurgeCache(), CBlast_def_line_set::PutTargetGiFirst(), CSplitQueryTestFixture::QuerySplitter_BlastnMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastnSingleQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxSingleQueryMultiChunk(), readGFF3(), CGff3Reader::ReadSeqEntry(), CProjectManager::RecordViewClose(), CProjectItem::Refresh(), CReaderRequestResult::ReleaseLocks(), CReverseObjectStore< TKey, TObject >::ReleaseObject(), CProjectManager::ReleaseWorkspace(), CCDSInfo::Remap(), CGeneModel::Remap(), CWMDockContainer::Remove(), CGlContainer::Remove(), CObjectIndex::Remove(), CFilterSet::Remove(), CBDB_Transaction::Remove(), CCompoundRegistry::Remove(), CSeriesBase::RemoveAllArrays(), CTreeNode< TValue, TKeyGetter >::RemoveAllSubNodes(), CPluginArgSet::RemoveArgument(), CLDS_DatabaseHolder::RemoveDatabase(), TSearchMessages::RemoveDuplicates(), CExtensionRegistry::RemoveExtension(), CExtensionPoint::RemoveExtension(), CExtensionRegistry::RemoveExtensionPoint(), CBioTreeFeatureList::RemoveFeature(), CReadBlastApp::RemoveInterim2(), CEnvironmentRegistry::RemoveMapper(), CTreeNode< TValue, TKeyGetter >::RemoveNode(), CAutoDefSourceGroup::RemoveQual(), CAutoDefModifierCombo::RemoveQual(), CBioseq_Base_Info::RemoveSeqdesc(), CGraphContainer::Render(), CGraphPanel::Render(), COMSSASearch::RenumberSearchSettingId(), COMSSASearch::RenumberSpectrumNumber(), CReadBlastApp::reportProblems(), CAlnMixMerger::Reset(), CMergeBitsetBlob< BV >::Reset(), CReadDispatcher::ResetCaches(), CDataSource_ScopeInfo::ResetDS(), CHitMatrixGraph::ResetGlyphSelection(), CScope_Impl::ResetHistory(), CSeq_loc_mix::ResetStrand(), CPacked_seqint::ResetStrand(), CListPanel::resize(), CNcbiTable< TValue, TRow, TColumn >::Resize(), CDense_seg::Reverse(), CChainer::CChainerImpl::RightLeft(), CFileDBEngine::RollbackTransaction(), CAlnMixSequences::RowsStartItsContsistencyCheck(), CEditBioseqSampleApp::Run(), CMergeVolumes::Run(), CSplign::Run(), s_AdjustIds(), s_Attach(), s_CheckEmptyLists(), s_CollapseProjectFolder(), s_FindProjectItemInFolder(), s_FixSeqData(), s_GetOrCreateFolder(), s_GetScopeFromProjectItem(), CSeqFeatData::s_InitLegalQuals(), CSeqFeatData::s_InitMandatoryQuals(), s_PurgeTrees(), s_RemoveFolder(), s_RemoveItem(), s_ReplaceCtrlAsInTitle(), s_ReplaceItem(), s_ReplaceProvidedSeqIdsForRequestedSeqIds(), s_ReplaceUforT(), s_SplitAlignVectorBySubjects(), CWMTemplateRegistry::SaveCustomTemplates(), CDBUDRandomMapper::ScalePreference(), CChainer::CChainerImpl::ScoreCdnas(), CHitMatrixGraph::SelectGlyph(), CPluginArgForm::SetArgs(), CColorTableScoringModel::SetBackColors(), CFlagsFormatter::SetCallback(), CHitGlyph::SetColorIndex(), CListPanelData::SetCols(), CTSE_ScopeInfo::SetEditTSE(), CBioTreeFeatureList::SetFeature(), CUser_object::SetFieldRef(), CColorTableScoringModel::SetForeColors(), CSeq_feat::SetGeneXref(), CHitMatrixRenderer::SetGraphColor(), CTrOutputSeqTable::SetHdrData(), CSeq_loc::SetId(), CBlastAppArgs::SetOptions(), SJS_Request::SetParamFields(), CDBUDRandomMapper::SetPreference(), CDBServiceMapperCoR::SetPreference(), CClusterer::SetPrototypes(), CSeq_feat::SetProtXref(), CSearchResultSet::SetRID(), CViewComposite::SetSelection(), CViewComposite::SetSelectionService(), CSeq_loc_mix::SetStrand(), CPacked_seqint::SetStrand(), SetUpCommandLineArguments(), CAlnMultiRenderer::SetVisibleColumns(), CSplitter::show(), CAppJobDispatcher::ShutDown(), CProjectManager::ShutDown(), CGBenchServiceContext::ShutDown(), CReadBlastApp::simple_overlaps(), CWriteDB_PackedSemiTree::Sort(), CReadBlastApp::SortSeqs(), SourceToProduct(), CBlobSplitterImpl::SplitPieces(), CSeq_align_set::SwapRows(), CSeq_align::SwapRows(), CColorTableScoringModel::SwitchForeBackColors(), sx_Del(), CScheduler_MT::TaskExecuted(), CMytestApplication::TestFeatureGeneOverlap(), NStr::ToLower(), NStr::ToUpper(), CScoreVector< Key, Score >::TrimCount(), CScoreVector< Key, Score >::TrimLength(), CThemeSet::Uncache(), CEditAction_UpdateIds::Unexecute(), CEditCommand_Defline::Unexecute(), CDeleteSeqFeatCommand::Unexecute(), CChangeSeqFeatCommand::Unexecute(), CDllResolver::Unload(), CPluginTable::Update(), CProjectManager::UpdateAllViews(), CGraphPanel::UpdateLimits(), CSymbolGuard::UpdateSymbols(), CConnValidatorCoR::Validate(), CFlagsFormatter::ViewToModel(), CPluginArgForm::ViewToModel(), CFlatItemFormatter::Wrap(), CMultiWriter::Write(), CTSE_Split_Info::x_AddAnnotPlace(), CTSE_Split_Info::x_AddAssemblyInfo(), CTSE_Split_Info::x_AddBioseqPlace(), CTSE_Split_Info::x_AddDescInfo(), CClipboard::x_AddFlavor(), CDefaultLayoutPolicy::x_AddGWAS_Layout(), CDefaultLayoutPolicy::x_AddHapMapLayout(), CDefaultLayoutPolicy::x_AddHistogramsLayout(), CGBProjectTool::x_AddItem(), CSerialBrowserTree::x_AddLeaf(), CDefaultLayoutPolicy::x_AddOtherFeaturesLayout(), CSeqSearch::x_AddPattern(), CTSE_Split_Info::x_AddSeq_data(), CNgAligner::x_Align_Impl(), CScoringJob::x_AllocBuffer(), CGBenchGUI::x_AtLeastOneSelProjectLoaded(), CBlastOptionsRemote::x_AttachValue(), CScoringJob::x_CalculateAlignmentScores(), CNCBlobStorage::x_CheckPartsMinBlobId(), CSeqDBVol::x_CheckVersions(), CCompoundRegistry::x_ChildLockAction(), CQueueDataBase::x_CleanParamMap(), CCleanup_imp::x_CleanupExcept_text(), CHomePageService::x_Clear(), CScope_Impl::x_ClearAnnotCache(), CSparseMultiDataSource::x_ClearHandles(), CAlnVecMultiDataSource::x_ClearHandles(), CGBenchGUI::x_CloseAllSystemViews(), CPromote::x_CopyCdregionToRNA(), CGBenchWorkspaceWindow::x_CreateManageDataSourcesSubmenu(), CGBenchWorkspaceWindow::x_CreateNewViewSubmenu(), CContextCommandService::x_CreateOneProject(), CGBenchWorkspaceWindow::x_CreateSearchSubmenu(), CContextCommandService::x_CreateSeparateProjects(), CGBenchWorkspaceWindow::x_CreateToolsSubmenu(), CHomePageService::x_Delete(), CProjectTree::x_DeleteItem(), CWinManagerApp::x_Destroy(), CWMDockContainer::x_DestroyDock(), CGBDocument::x_DetachAllViewers(), CGBDocument::x_DetachAllViews(), CTSE_ScopeInfo::x_DetachDS(), CBDB_Transaction::x_DetachFromFiles(), CScopeTransaction_Impl::x_DoFinish(), CComponentSearchJob::x_DoSearch(), CBioseq_set_Info::x_DoUpdate(), CBioseq_Base_Info::x_DoUpdate(), CMenu::x_DrawItems(), CBioseq_set_Info::x_DSAttachContents(), CBioseq_Base_Info::x_DSAttachContents(), CBioseq_set_Info::x_DSDetachContents(), CBioseq_Base_Info::x_DSDetachContents(), CCleanup_imp::x_ExpandCombinedQuals(), x_FillObjects(), CWMDockContainer::x_FindChild(), CMultiAligner::x_FindConstraints(), CProjectTree::x_FindItemByLabel(), CSessionManagementThread::x_FindSession(), CNcbiTable< TValue, TRow, TColumn >::x_Free(), CNCBlobStorage::x_GC_CollectPartsStatistics(), CSeq_loc_Mapper_Base::x_GetMappedSeq_loc(), CBlastServices::x_GetPartsFromReply(), CProjectTree::x_GetSelectedItems(), CGBenchWorkspaceWindow::x_GetSelectedUserTypes(), CDefaultLayoutPolicy::x_GetSpecificNaasJob(), CListPanel::x_HandleColHeaderClick(), CSeqGraphicPane::x_Handlers_handle(), CGlPaneWidgetChild::x_Handlers_handle(), CAlnMultiPane::x_Handlers_handle(), CCrossAlnPane::x_Handlers_handle(), x_HitToConstraints(), CSeq_annot_Info::x_InitAlignKeys(), CSeq_annot_Info::x_InitAlignList(), CSeq_annot_Info::x_InitFeatKeys(), CSeq_annot_Info::x_InitFeatList(), CGBenchApp::x_InitGBenchService(), CSeq_annot_Info::x_InitGraphKeys(), CSeq_annot_Info::x_InitGraphList(), CSeq_annot_Info::x_InitLocsList(), CGuideTree::x_InitTreeLabels(), CAlnMultiRenderer::x_InvalidateRows(), CWNJobsWatcher::x_KillNode(), CBlastPrelimSearch::x_LaunchMultiThreadedSearch(), CAxisRenderer::x_LayoutLabels(), CTSE_Split_Info::x_LoadAnnot(), CTSE_Split_Info::x_LoadAssembly(), CTSE_Split_Info::x_LoadBioseq(), CAppHitFilter::x_LoadConstraints(), CBlastDbDataLoader::x_LoadData(), CTSE_Split_Info::x_LoadDescr(), CTSE_Split_Info::x_LoadSeq_entry(), CTSE_Split_Info::x_LoadSequence(), CWMTemplateRegistry::x_LoadTemplates(), CProjectManager::x_LoadWorkspace(), CAlnMixMerger::x_Merge(), CAlnGraphic::x_MergeDifferentSeq(), CGFFReader::x_MergeRecords(), CAlnGraphic::x_MergeSameSeq(), CMultiAligner::x_MultiAlignClusters(), CService_Impl::x_NotifyObservers(), CSnpFilterUI::x_OnBtnExport(), CTimerUI::x_OnChangeTimers(), CTabControl::x_OnCloseTab(), CRWLockHolder::x_OnLockAcquired(), CRWLockHolder::x_OnLockReleased(), CTabControl::x_OnTabSelected(), CSeq_loc_Mapper_Base::x_OptimizeSeq_loc(), CQueueDataBase::x_OptimizeStatusMatrix(), CBioseq_set_Info::x_ParentAttach(), CBioseq_set_Info::x_ParentDetach(), CGFFReader::x_PlaceAlignment(), CSeq_loc_Mapper_Base::x_PreserveDestinationLocs(), CId2FetchApp::x_ProcessRequest(), CBlastDBCmdApp::x_ProcessSearchRequest(), CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile(), CPromote::x_PromoteFeatures(), CQueueDataBase::x_PurgeUnconditional(), x_RangesToSeq_loc(), CContextCommandService::x_RegisterPluggableOperations(), CViewComposite::x_ReleaseViews(), CMetaRegistry::x_Reload(), CGBWorkspace::x_RemoveFromFolder(), CAppJobDispatcher::x_RemoveJobRecord(), CHitMatrixGraph::x_RenderHits(), CHitMatrixGraph::x_RenderPath(), CHitMatrixGraph::x_RenderSelection(), CAlnMultiRenderer::x_ResetRowListMap(), CWriteDB_Impl::x_ResetSequenceData(), CSimpleBandedAligner::x_RunBanded(), CGBenchGUI::x_SaveProjects(), CSequenceSearchJob::x_SearchSequence(), CHitMatrixGraph::x_SelectByPoint(), CHitMatrixGraph::x_SelectByRect(), CBioseq_Base_Info::x_SetAnnot(), CBuildDatabase::x_SetLinkAndMbit(), CSeq_align::x_SetNamedScore(), CBioseq_set_Info::x_SetObject(), CSplign::x_SetPattern(), CFlatfileParagraph::x_SetText(), CSplitDataLoader::x_SplitAnnot(), CSplitDataLoader::x_SplitSet(), x_TestAlignmentQuerySubjStrandCombinations(), CSeqFormatter::x_Transform(), CTSE_Split_Info::x_TSEAttach(), CBioseq_set_Info::x_TSEAttachContents(), CBioseq_Base_Info::x_TSEAttachContents(), CBioseq_set_Info::x_TSEDetachContents(), CBioseq_Base_Info::x_TSEDetachContents(), CSeq_id_PDB_Tree::x_Unindex(), CSeq_id_Giim_Tree::x_Unindex(), CGlPaneWidgetChild::x_UnregisterHandler(), CAlnMultiPane::x_UnregisterHandler(), CTSE_Split_Info::x_UpdateAnnotIndex(), CBioseq_set_Info::x_UpdateAnnotIndexContents(), CBioseq_Base_Info::x_UpdateAnnotIndexContents(), CMenu::x_UpdateItems(), CAlignMarkHandler::x_UpdateSelection(), CSelListModelImpl< Item >::x_ViewsUpdateItemRange(), CSelListModelImpl< Item >::x_ViewsUpdateItems(), CFastaOstream::x_WriteSeqTitle(), impl::CDBExceptionStorage::~CDBExceptionStorage(), CEventHandler::~CEventHandler(), CHitList::~CHitList(), CLinearWizardData::~CLinearWizardData(), CMultiSeqInfo::~CMultiSeqInfo(), CNSTagMap::~CNSTagMap(), CPluginManager< TClass >::~CPluginManager(), CEventHandler::CPostQueue::~CPostQueue(), CQueryFactoryInfo::~CQueryFactoryInfo(), CQueueWorkerNodeList::~CQueueWorkerNodeList(), CSafeStaticGuard::~CSafeStaticGuard(), CSeqFormatter::~CSeqFormatter(), CSyncQueue_ConstAccessGuard< Type, Container >::~CSyncQueue_ConstAccessGuard(), CTabControl::~CTabControl(), CTreeItemBrowser::~CTreeItemBrowser(), CTreeNode< TValue, TKeyGetter >::~CTreeNode(), CTSE_Split_Info::~CTSE_Split_Info(), SIdAnnotObjs::~SIdAnnotObjs(), SNetServiceImpl::~SNetServiceImpl(), and SRotatedFontCachePurger::~SRotatedFontCachePurger().

#define NON_CONST_REVERSE_ITERATE Type,
Var,
Cont   )     for ( Type::reverse_iterator Var = (Cont).rbegin(); Var != (Cont).rend(); ++Var )
 

Non constant version of REVERSE_ITERATE macro.

Definition at line 896 of file ncbimisc.hpp.

Referenced by CNCBlobStorage::IsBlobExists(), CNCBlobStorage::ReadBlobCoords(), CNCBlobStorage::ReadBlobKey(), CNCBlobStorage::x_DoBackgroundWork(), CCleanup_imp::x_RemoveEmptyTitles(), and CCleanup_imp::x_RemoveMultipleTitles().

#define REVERSE_ITERATE Type,
Var,
Cont   )     for ( Type::const_reverse_iterator Var = (Cont).rbegin(), NCBI_NAME2(Var,_end) = (Cont).rend(); Var != NCBI_NAME2(Var,_end); ++Var )
 

ITERATE macro to reverse sequence through container elements.

Definition at line 892 of file ncbimisc.hpp.

Referenced by CCompoundRegistry::FindByContents(), CThreadPool_Impl::FinishThreads(), impl::CDBHandlerStack::HandleExceptions(), impl::CDBHandlerStack::PostMsg(), CCompoundRegistry::x_Empty(), CCompoundRWRegistry::x_Enumerate(), CCompoundRegistry::x_Enumerate(), CEnvironmentRegistry::x_Get(), CCompoundRegistry::x_Modified(), and CEnvironmentRegistry::x_Set().

#define VECTOR_ERASE Var,
Cont   )     (NCBI_NAME2(Var,_next) = (Cont).erase(Var))
 

Use this macro inside body of ERASE_ITERATE cycle to erase from vector-like container.

Plain erase() call would invalidate Var_next iterator and would make the cycle controlling code to fail.

Definition at line 889 of file ncbimisc.hpp.


Typedef Documentation

typedef unsigned int TSeqPos
 

Type for sequence locations and lengths.

Use this typedef rather than its expansion, which may change.

Definition at line 903 of file ncbimisc.hpp.

typedef int TSignedSeqPos
 

Type for signed sequence position.

Use this type when and only when negative values are a possibility for reporting differences between positions, or for error reporting -- though exceptions are generally better for error reporting. Use this typedef rather than its expansion, which may change.

Definition at line 915 of file ncbimisc.hpp.


Enumeration Type Documentation

enum EFollowLinks
 

Whether to follow symbolic links (also known as shortcuts or aliases).

Enumerator:
eIgnoreLinks 
eFollowLinks 

Definition at line 127 of file ncbimisc.hpp.

enum EInterruptOnSignal
 

Interrupt on signal mode.

On UNIX some functions can be interrupted by a signal and EINTR errno value. We can restart or cancel its execution.

Enumerator:
eInterruptOnSignal  Cancel operation if interrapted by a signal.
eRestartOnSignal  Restart operation if interrupted by a signal.

Definition at line 137 of file ncbimisc.hpp.

enum ENullable
 

Whether a value is nullable.

Enumerator:
eNullable  Value can be null.
eNotNullable  Value cannot be null.

Definition at line 105 of file ncbimisc.hpp.

enum EOwnership
 

Which type of ownership between objects.

Can be used to specify ownership relationship between objects. For example, specify if a CSocket object owns the underlying SOCK object.

Enumerator:
eNoOwnership  No ownership relationship.
eTakeOwnership  An object can take ownership of another.

Definition at line 98 of file ncbimisc.hpp.

enum ERound
 

Whether to truncate/round a value.

Enumerator:
eTrunc  Value must be truncated.
eRound  Value must be rounded.

Definition at line 120 of file ncbimisc.hpp.

enum ESign
 

Whether a value is nullable.

Enumerator:
eNegative  Value is negative.
eZero  Value is zero.
ePositive  Value is positive.

Definition at line 112 of file ncbimisc.hpp.

enum ESwitch
 

Aux.

enum to set/unset/default various features

Enumerator:
eOff 
eOn 
eDefault 

Definition at line 77 of file ncbimisc.hpp.


Function Documentation

const void * CRawPointer::Add const void *  object,
ssize_t  offset
[inline, static, inherited]
 

Definition at line 936 of file ncbimisc.hpp.

void * CRawPointer::Add void *  object,
ssize_t  offset
[inline, static, inherited]
 

add offset to object reference (to get object's member)

Definition at line 930 of file ncbimisc.hpp.

Referenced by CSequenceOfTypeInfo::Data(), EndOf(), and CSequenceOfTypeInfo::NextNode().

template<class Element, size_t Size>
size_t ArraySize const   Element(&)[Size]  )  [inline]
 

Definition at line 992 of file ncbimisc.hpp.

INcbiIdler* GetIdler EOwnership  ownership = eNoOwnership  ) 
 

Return currently installed idler or NULL.

Update idler ownership according to the flag.

Definition at line 1215 of file ncbiapp.cpp.

References s_IdlerWrapper.

void RunIdler void   ) 
 

Execute currently installed idler if any.

Definition at line 1227 of file ncbiapp.cpp.

References s_IdlerWrapper.

void SetIdler INcbiIdler idler,
EOwnership  ownership = eTakeOwnership
 

Set new idler and ownership.

Definition at line 1221 of file ncbiapp.cpp.

References s_IdlerWrapper.

char* strdup const char *  str  ) 
 

Supply string duplicate function, if one is not defined.

Definition at line 2434 of file ncbistr.cpp.

References malloc().

ssize_t CRawPointer::Sub const void *  first,
const void *  second
[inline, static, inherited]
 

calculate offset inside object

Definition at line 942 of file ncbimisc.hpp.

template<class P, class D>
void swap NCBI_NS_NCBI::AutoPtr< P, D > &  ptr1,
NCBI_NS_NCBI::AutoPtr< P, D > &  ptr2
[inline]
 

Definition at line 977 of file ncbimisc.hpp.

template<class T1, class T2>
END_NCBI_SCOPE BEGIN_STD_SCOPE void swap NCBI_NS_NCBI::pair_base_member< T1, T2 > &  pair1,
NCBI_NS_NCBI::pair_base_member< T1, T2 > &  pair2
[inline]
 

Definition at line 968 of file ncbimisc.hpp.

Referenced by __WORKAROUND_RENAME(), oligofar::CGuideSamFile::AddHit(), CIdMapper::AddMapping(), oligofar::CAligner::Align(), CCleanup_imp::BasicCleanup(), bNNItopSwitch(), bNNIupdateAverages(), oligofar::CGuideSamFile::C_Key::C_Key(), CCommentItem::CCommentItem(), oligofar::CHit::CHit(), CIntron::CIntron(), CModelCompare::CodingCompatibleOneCDS(), CModelCompare::CodingCompatibleTwoCDS(), oligofar::CHit::ComputeGeometry(), CSeq_loc_Conversion::ConvertInterval(), CProSplignText::CProSplignText(), CAnnotationASN1::CImplementationData::create_cdregion_feature(), CRgbaColorTable::CRgbaColorTable(), oligofar::CQuery::Export(), CDense_seg::ExtractSlice(), oligofar::CSpacialRanges::FindContaining(), oligofar::CSpacialRanges::FindOverlapping(), FindStartsStops(), CImageUtil::FlipX(), CImageUtil::FlipY(), oligofar::CFaDiceApp::GeneratePair(), CAlnVecMultiDataSource::GetAlnFromSeq(), CHitElemGlyph::GetDistPixels(), CDictionaryUtil::GetEditDistance(), CHitMatrixRenderer::GetSelectedHitElemsRect(), CAlnVecMultiDataSource::GetSeqFromAln(), GetVector(), COptArg< pair< T, T > >::Handle(), oligofar::CSnpDbCreator::Insert(), CAlignRange< Position >::IsAbutting(), CHitList::MakeCanonical(), CPhyloTreeDataSource::MoveNode(), StyleManager::MoveUserAnnotation(), NNItopSwitch(), NNIupdateAverages(), ProjectCDS::operator()(), xml::impl::ait_impl::operator=(), ParseAttributes(), oligofar::CSamSource::ParseSamLine(), CDefaultLayoutPolicy::PrepareData(), CDefaultPolicy::PreparePolicy(), oligofar::CFilter::ProcessMatch(), CHitElemGlyph::Render(), CDense_seg::Reverse(), oligofar::Reverse(), s_LoadGuide(), xml::document::save_to_file(), CBl2Seq::SetInterruptCallback(), CRgbaColorTable::SetMaxColor(), CRgbaColorTable::SetMinColor(), CAlignShadow::SetStrand(), CSeqDB_BitSet::Swap(), xml::node_set::const_iterator::swap(), xml::node_set::iterator::swap(), xml::node::const_iterator::swap(), xml::node::iterator::swap(), xml::attributes::swap(), xml::attributes::attr::swap(), xml::attributes::const_iterator::swap(), xml::attributes::iterator::swap(), xml::node::swap(), CCheckBrowser::swap(), xml::document::swap(), array_set< T, Cmp >::swap(), array_map< K, V, Cmp, kCapacityIncrement >::swap(), CSimpleBufferT< T, ResizeStrategy >::swap(), CNcbiMatrix< T >::Swap(), CAnnotObject_Ref::Swap(), CAnnotMapping_Info::Swap(), CSeq_id_Handle::Swap(), CWeakRef< CQueue >::Swap(), CConstRef< CSeq_loc >::Swap(), CRef< CQueueItem >::Swap(), AutoArray< CS_INT >::Swap(), AutoPtr< CNcbiOstrstream >::Swap(), pair_base_member< convert_to_string_type, value_type >::Swap(), hashtable< _Val, _Key, _HF, _ExK, _EqK, _All >::swap(), CScoreVector< Key, Score >::Swap(), CRawScoreVector< Key, Score >::Swap(), multiset< Key, Compare, Allocator >::swap(), set< ETranslationFrame >::swap(), CDense_seg::SwapRows(), CNcbiMatrix< T >::SwapRows(), CColorTableScoringModel::SwitchForeBackColors(), CGlBitmapFont::TextOut(), CMatrix4< T >::Transpose(), CMatrix3< T >::Transpose(), oligofar::CMappedAlignment::ValidateConsistency(), CSeqSearch::x_AddPattern(), CLayoutPWAlign::x_CalcIntervals(), CDefaultPolicy::x_DrawAlignment(), CSeq_align_Mapper_Base::x_Init(), CFeaturesPanelIR::x_IsIntersects(), CSeqDBAliasNode::x_ReadLine(), CDefaultPolicy::x_RenderAveragableScores(), CTraceGraph::x_RenderConfGraph(), CTraceGraph::x_RenderContour(), CTraceGraph::x_RenderCurveSegment(), CHitMatrixGraph::x_RenderEventHandler(), CAlnVecRow::x_RenderIcons(), CTraceGraph::x_RenderIntensityGraphs(), CDefaultPolicy::x_RenderNonAveragableScores(), CSeqGraphicPane::x_RenderRectSelHandler(), CRuler::x_RenderScale(), IPhyloTreeRenderer::x_RenderSelection(), CMouseZoomHandler::x_RenderZoomRect(), IPhyloTreeRenderer::x_SelectByRect(), CCommentItem::x_SetSkip(), CNCMMReserve::x_SortChunkPtrs(), CSeqVector_CI::x_SwapCache(), x_TestAlignmentQuerySubjStrandCombinations(), and CSeqGraphicRenderer::ZoomOnRange().


Variable Documentation

const TSeqPos kInvalidSeqPos = ((TSeqPos) (-1))
 

Define special value for invalid sequence position.

Definition at line 906 of file ncbimisc.hpp.

Referenced by SAlignment_Segment::AddRow(), BOOST_AUTO_TEST_CASE(), CSeqMap::CanResolveRange(), CFastaReader::CloseMask(), CSeq_loc_Conversion::CombineWith(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), CSeq_loc_Conversion::ConvertPacked_pnt(), CSeq_loc_Conversion::ConvertPos(), CBlobSplitterImpl::CopyDescr(), CBlobSplitterImpl::CopySequence(), CSeqMap_CI::CSeqMap_CI(), CSeq_loc::GetCircularLength(), CFastaReader::GetCurrentPos(), CSeqMap::GetLength(), SAlignment_Segment::SAlignment_Row::GetSegStart(), CScope_Impl::GetSeq_featHandle(), CSeq_loc_Mapper_Base::GetSequenceLength(), CSeq_loc_mix::GetStart(), CSeq_loc::GetStart(), CPacked_seqpnt::GetStart(), CPacked_seqint::GetStart(), CSeq_loc_mix::GetStop(), CSeq_loc::GetStop(), CPacked_seqpnt::GetStop(), CPacked_seqint::GetStop(), CGapItem::HasEstimatedLength(), SSNP_Info::NoMore(), CFastaReader::OpenMask(), CPhrap_Seq::ReadData(), CFastaReader::ReadOneSeq(), s_LocationsOverlap(), s_PrematureStopCodon(), CSeqMap::SetRegionInChunk(), TestForOverlap64(), CFastaOstream::Write(), CSeqMap::x_Add(), CSeqMap::x_AddEnd(), CPhrap_Read::x_AddQualityFeat(), CSeq_loc_Mapper_Base::x_CheckSeqTypes(), CFastaReader::x_CloseMask(), CSeq_align_Mapper_Base::x_ConvertSegment(), CSeq_align_Mapper::x_ConvertSegmentCvt(), CSeq_align_Mapper_Base::x_FillKnownStrands(), CSeqMap::x_FindSegment(), CFlatGatherer::x_GatherCDSReferences(), CSeqMap::x_GetChunkToLoad(), CSeq_align_Mapper_Base::x_GetDstDendiag(), CSeq_align_Mapper_Base::x_GetDstStd(), CSeq_loc_Mapper_Base::x_GetMappedSeq_loc(), CSeqMap::x_GetSegmentLength(), CPsiBlastInputData::x_GetSubjectSequence(), CSeq_loc_Mapper_Base::x_InitializeLocs(), CSeq_loc_Mapper::x_InitializeSeqMap(), CSeqMap::x_LoadObject(), CSeq_loc_Mapper_Base::x_NextMappingRange(), CFastaReader::x_OpenMask(), CSeq_loc_Mapper_Base::x_PreserveDestinationLocs(), CSeqMap::x_ResolveSegmentLength(), CSeqMap::x_ResolveSegmentPosition(), CSeqMap_CI::x_Select(), and CSeqMap::x_SetChanged().


Generated on Mon Nov 9 15:25:49 2009 for NCBI C++ ToolKit by  doxygen 1.4.6
Modified on Mon Nov 09 15:48:47 2009 by modify_doxy.py rev. 173732