NCBI C++ ToolKit
Namespaces | Classes | Macros | Typedefs | Enumerations | Enumerator | Functions | Variables
Application Framework
+ Collaboration diagram for Application Framework:

Namespaces

 ncbi
 Magic spell ;-) needed for some weird compilers... very empiric.
 

Classes

class  ncbi::CNcbiToolkit_LogMessage
 Logging message. More...
 
class  ncbi::INcbiToolkit_LogHandler
 Logging interface. More...
 
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  CBoolEnum< TEnum >
 Template used to replace bool type arguments with some strict equivalent. More...
 
struct  Creater< X >
 Functor template for allocating object. More...
 
struct  Deleter< X >
 Functor template 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...
 
struct  AutoPtr< X, Del >::SSafeBoolTag
 Bool operator for use in if() clause. More...
 
class  AutoArray< X, Del >
 AutoArray –. More...
 
struct  AutoArray< X, Del >::SSafeBoolTag
 Bool operator for use in if() clause. More...
 
struct  SThrowOnNull< TValue >
 
class  CNullable< TValue, TNullToValue >
 Template class allowing to store a value or null (unassigned) state. More...
 
class  CConstGIChecker< gi >
 a helper template to enforce constness of argument to GI_CONST macro More...
 
class  CRawPointer
 Helper address class. More...
 
class  CFastBuffer< KEmbeddedSize, TType >
 
class  CNcbiActionGuard
 CNcbiActionGuard class Executes registered callbacks on request or on destruction. More...
 
class  CNcbiActionGuard::CAction< TFunc >
 
class  CNcbiActionGuard::CAction_Base
 

Macros

#define NCBI_TOOLKIT_EXPORT
 
#define NCBI_ESWITCH_DEFINED
 
#define NCBI_EOWNERSHIP_DEFINED
 NCBI_ESWITCH_DEFINED. More...
 
#define DECLARE_SAFE_BOOL_METHOD(Expr)
 Support for safe bool operators. More...
 
#define DECLARE_OPERATOR_BOOL(Expr)   DECLARE_SAFE_BOOL_METHOD(Expr)
 Declaration of safe bool operator from boolean expression. More...
 
#define DECLARE_OPERATOR_BOOL_PTR(Ptr)   DECLARE_OPERATOR_BOOL((Ptr) != 0)
 Declaration of safe bool operator from pointer expression. More...
 
#define DECLARE_OPERATOR_BOOL_REF(Ref)   DECLARE_OPERATOR_BOOL((Ref).NotNull())
 Declaration of safe bool operator from CRef<>/CConstRef<> expression. More...
 
#define OVERRIDE_OPERATOR_BOOL(TAncestorClass, NewBoolExpr)
 Override the DECLARE_OPERATOR_BOOL, etc. More...
 
#define ITERATE_CONST(Cont)   NCBI_NS_NCBI::s_ITERATE_ConstRef(Cont)
 
#define ITERATE_BEGIN(Cont, Begin)
 
#define ITERATE_VAR(Type)   Type
 
#define ITERATE(Type, Var, Cont)
 ITERATE macro to sequence through container elements. More...
 
#define NON_CONST_ITERATE(Type, Var, Cont)
 Non constant version of ITERATE macro. More...
 
#define REVERSE_ITERATE(Type, Var, Cont)
 ITERATE macro to reverse sequence through container elements. More...
 
#define NON_CONST_REVERSE_ITERATE(Type, Var, Cont)
 Non constant version of REVERSE_ITERATE macro. More...
 
#define ERASE_ITERATE(Type, Var, Cont)
 Non-constant version with ability to erase current element, if container permits. More...
 
#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. More...
 
#define ITERATE_BOTH_BOOL_VALUES(BoolVar)   for( bool BoolVar##BOTH_BOOL_VALUES_DONE##__LINE__ = false, BoolVar = false; ! BoolVar##BOTH_BOOL_VALUES_DONE##__LINE__ ; BoolVar##BOTH_BOOL_VALUES_DONE##__LINE__ = BoolVar, BoolVar = true )
 The body of the loop will be run with Var equal to false and then true. More...
 
#define ITERATE_0_IDX(idx, up_to)   for( TSeqPos idx = 0; idx < up_to; ++idx )
 idx loops from 0 (inclusive) to up_to (exclusive) More...
 
#define ITERATE_SIMPLE(num_iters)   ITERATE_0_IDX( _dummy_idx_94768308_##__LINE__, num_iters )
 Just repeat the body of the loop num_iters times. More...
 
#define GI_CONST(gi)   (TGi(CConstGIChecker<gi>::value))
 
#define ZERO_GI   GI_CONST(0)
 
#define INVALID_GI   GI_CONST(-1)
 
#define GI_TO(T, gi)   (static_cast<T>(TIntId(gi)))
 Temporary macros to convert TGi to other types (int, unsigned etc.). More...
 
#define GI_FROM(T, value)   (TGi(static_cast<TIntId>(value)))
 
#define INT_ID_TO(T, id)   (static_cast<T>(id))
 Convert gi-compatible int to/from other types. More...
 
#define INT_ID_FROM(T, value)   (static_cast<TIntId>(value))
 
#define NCBI_DEPRECATED_CTOR(decl)   decl NCBI_DEPRECATED
 Macro used to mark a constructor as deprecated. More...
 
#define NCBI_DEPRECATED_CLASS   NCBI_DEPRECATED_CTOR(class)
 Macro used to mark a class as deprecated. More...
 
#define DECLARE_SAFE_FLAGS_TYPE(Enum, Typedef)   typedef underlying_type<Enum>::type Typedef
 
#define DECLARE_SAFE_FLAGS(Enum)   NCBI_EAT_SEMICOLON(safe_flags)
 

Typedefs

typedef char ncbi::TNcbiToolkit_XChar
 
typedef CNcbiApplication *(* ncbi::FNcbiApplicationFactory) (void)
 Provide means of creating custom CNcbiApplication object – to use the latter instead of "dummy" NCBI application. More...
 
typedef enum ENcbiSwitch ESwitch
 Aux. More...
 
typedef enum ENcbiOwnership EOwnership
 Ownership relations between objects. More...
 
typedef unsigned int TSeqPos
 Type for sequence locations and lengths. More...
 
typedef int TSignedSeqPos
 Type for signed sequence position. More...
 
typedef int TTaxId
 Type for Taxon1-name.taxid. More...
 
typedef int TGi
 Type for sequence GI. More...
 
typedef Int4 TIntId
 
typedef Uint4 TUintId
 
typedef TIntId TEntrezId
 TEntrezId type for entrez ids which require the same strictness as TGi. More...
 

Enumerations

enum  ncbi::CNcbiToolkit_LogMessage::ESeverity {
  ncbi::CNcbiToolkit_LogMessage::eInfo = 0, ncbi::CNcbiToolkit_LogMessage::eWarning, ncbi::CNcbiToolkit_LogMessage::eError, ncbi::CNcbiToolkit_LogMessage::eCritical,
  ncbi::CNcbiToolkit_LogMessage::eFatal, ncbi::CNcbiToolkit_LogMessage::eTrace
}
 Log message severity. More...
 
enum  CAppException::EErrCode {
  CAppException::eUnsetArgs, CAppException::eSetupDiag, CAppException::eLoadConfig, CAppException::eSecond,
  CAppException::eNoRegistry
}
 Error types that an application can generate. More...
 
enum  CNcbiApplication::EAppNameType { CNcbiApplication::eBaseName, CNcbiApplication::eFullName, CNcbiApplication::eRealName }
 
enum  CNcbiApplication::EPreparseArgs { CNcbiApplication::ePreparse_Continue, CNcbiApplication::ePreparse_Exit }
 Result of PreparseArgs() More...
 
enum  CNcbiApplication::EDisableArgDesc { CNcbiApplication::fDisableStdArgs = 0x01 }
 Disable argument descriptions. More...
 
enum  CNcbiApplication::EHideStdArgs {
  CNcbiApplication::fHideLogfile = 0x01, CNcbiApplication::fHideConffile = 0x02, CNcbiApplication::fHideVersion = 0x04, CNcbiApplication::fHideFullVersion = 0x08,
  CNcbiApplication::fHideDryRun = 0x10, CNcbiApplication::fHideHelp = 0x20, CNcbiApplication::fHideFullHelp = 0x40, CNcbiApplication::fHideXmlHelp = 0x80,
  CNcbiApplication::fHideAll = 0xFF
}
 Which standard flag's descriptions should not be displayed in the usage message. More...
 
enum  CNcbiApplication::EStdioSetup { CNcbiApplication::fDefault_SyncWithStdio = 0x01, CNcbiApplication::fDefault_CinBufferSize = 0x02, CNcbiApplication::fBinaryCin = 0x04, CNcbiApplication::fBinaryCout = 0x08 }
 Flags to adjust standard I/O streams' behaviour. More...
 
enum  CNcbiApplication::EExitMode { CNcbiApplication::eNoExits, CNcbiApplication::eExceptionalExits, CNcbiApplication::eAllExits }
 When to return a user-set exit code. More...
 
enum  ENcbiSwitch {
  eOff = 0, eOn, eDefault, eOff = 0,
  eOn, eDefault
}
 Aux. More...
 
enum  ENcbiOwnership { eNoOwnership, eTakeOwnership, eNoOwnership, eTakeOwnership }
 Ownership relations between objects. More...
 
enum  ENullable { eNullable, eNotNullable }
 Whether a value is nullable. More...
 
enum  ESign { eNegative = -1, eZero = 0, ePositive = 1 }
 Signedness of a value. 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  ENormalizePath { eNormalizePath, eNotNormalizePath }
 Whether to normalize a path. More...
 
enum  EInterruptOnSignal { eInterruptOnSignal, eRestartOnSignal }
 Interrupt on signal mode. More...
 
enum  ERetriable { eRetriable_No, eRetriable_Unknown, eRetriable_Yes }
 Can the action be retried? More...
 
enum  ENull { null = 0 }
 CNullable –. More...
 

Functions

void ncbi::NcbiToolkit_RegisterNcbiApplicationFactory (FNcbiApplicationFactory f)
 
void ncbi::NcbiToolkit_Init (int argc, const TNcbiToolkit_XChar *const *argv, const TNcbiToolkit_XChar *const *envp=NULL, INcbiToolkit_LogHandler *log_handler=NULL)
 Initialialize NCBI C++ Toolkit internal infrastructure: arguments, environment, diagnostics, logging. More...
 
void ncbi::NcbiToolkit_Fini (void)
 Release resources allocated for NCBI C++ Toolkit. More...
 
 ncbi::CNcbiToolkit_LogMessage::operator std::string (void) const
 Get the message the way it is formatted by the Toolkit. More...
 
std::string ncbi::CNcbiToolkit_LogMessage::Message (void) const
 Get text part of the message. More...
 
ESeverity ncbi::CNcbiToolkit_LogMessage::Severity (void) const
 Get message severity. More...
 
int ncbi::CNcbiToolkit_LogMessage::ErrCode (void) const
 Get error code. More...
 
int ncbi::CNcbiToolkit_LogMessage::ErrSubCode (void) const
 Get error subcode. More...
 
std::string ncbi::CNcbiToolkit_LogMessage::File (void) const
 Get file name in which message was originated. More...
 
size_t ncbi::CNcbiToolkit_LogMessage::Line (void) const
 Get line number in which message was originated. More...
 
const SDiagMessagencbi::CNcbiToolkit_LogMessage::GetNativeToolkitMessage (void) const
 Get all of the message's data – as provided natively by the Toolkit. More...
 
 ncbi::CNcbiToolkit_LogMessage::CNcbiToolkit_LogMessage (const SDiagMessage &msg)
 
virtual ncbi::CNcbiToolkit_LogMessage::~CNcbiToolkit_LogMessage (void)
 
 ncbi::CNcbiToolkit_LogMessage::CNcbiToolkit_LogMessage (const CNcbiToolkit_LogMessage &)
 
CNcbiToolkit_LogMessage & ncbi::CNcbiToolkit_LogMessage::operator= (const CNcbiToolkit_LogMessage &)
 
virtual ncbi::INcbiToolkit_LogHandler::~INcbiToolkit_LogHandler ()
 
virtual void ncbi::INcbiToolkit_LogHandler::Post (const CNcbiToolkit_LogMessage &msg)=0
 
INcbiIdlerGetIdler (EOwnership ownership=eNoOwnership)
 Return currently installed idler or NULL. More...
 
void SetIdler (INcbiIdler *idler, EOwnership ownership=eTakeOwnership)
 Set new idler and ownership. More...
 
void RunIdler (void)
 Execute currently installed idler if any. More...
 
NCBI_NORETURN void g_ThrowOnNull (void)
 
template<class TValue , class TNullToValue = SThrowOnNull<TValue>>
bool operator== (const CNullable< TValue, TNullToValue > &l, const CNullable< TValue, TNullToValue > &r)
 
template<class TValue , class TNullToValue = SThrowOnNull<TValue>>
bool operator!= (const CNullable< TValue, TNullToValue > &l, const CNullable< TValue, TNullToValue > &r)
 
char * strdup (const char *str)
 Supply string duplicate function, if one is not defined. More...
 
template<typename Type >
const Types_ITERATE_ConstRef (const Type &obj)
 
template<typename Type >
bool s_ITERATE_SameObject (const Type &obj1, const Type &obj2)
 
template<class T1 , class T2 >
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) More...
 
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 More...
 

Variables

const SDiagMessagencbi::CNcbiToolkit_LogMessage::m_Msg
 
 BEGIN_NCBI_NAMESPACE
 NCBI_EOWNERSHIP_DEFINED. More...
 
const TSeqPos kInvalidSeqPos = ((TSeqPos) (-1))
 Define special value for invalid sequence position. More...
 
 END_NCBI_NAMESPACE
 
 BEGIN_STD_NAMESPACE
 
 END_STD_NAMESPACE
 

Detailed Description

Macro Definition Documentation

#define DECLARE_OPERATOR_BOOL (   Expr)    DECLARE_SAFE_BOOL_METHOD(Expr)

Declaration of safe bool operator from boolean expression.

Actual operator declaration will be: operator TBoolType(void) const; where TBoolType is a typedef convertible to bool (member pointer).

Definition at line 191 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 198 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 205 of file ncbimisc.hpp.

#define DECLARE_SAFE_BOOL_METHOD (   Expr)
Value:
struct SSafeBoolTag { \
void SafeBoolTrue(SSafeBoolTag*) {} \
}; \
typedef void (SSafeBoolTag::*TBoolType)(SSafeBoolTag*); \
operator TBoolType() const { \
return (Expr)? &SSafeBoolTag::SafeBoolTrue: 0; \
} \
private: \
bool operator==(TBoolType) const; \
bool operator!=(TBoolType) const; \
public: \
friend struct SSafeBoolTag
bool
Definition: cgiapp.hpp:510
bool operator!=(const CNullable< TValue, TNullToValue > &l, const CNullable< TValue, TNullToValue > &r)
Definition: ncbimisc.hpp:727
bool operator==(const CNullable< TValue, TNullToValue > &l, const CNullable< TValue, TNullToValue > &r)
Definition: ncbimisc.hpp:721

Support for safe bool operators.

Low level macro for declaring safe bool operator.

Definition at line 172 of file ncbimisc.hpp.

#define DECLARE_SAFE_FLAGS (   Enum)    NCBI_EAT_SEMICOLON(safe_flags)

Definition at line 1289 of file ncbimisc.hpp.

#define DECLARE_SAFE_FLAGS_TYPE (   Enum,
  Typedef 
)    typedef underlying_type<Enum>::type Typedef

Definition at line 1288 of file ncbimisc.hpp.

#define ERASE_ITERATE (   Type,
  Var,
  Cont 
)
Value:
for ( ITERATE_VAR(Type::iterator) Var = ITERATE_BEGIN(Cont, begin), \
NCBI_NAME2(Var,_next) = Var; \
(Var = NCBI_NAME2(Var,_next)) != (Cont).end() && \
(++NCBI_NAME2(Var,_next), true); )
#define ITERATE_BEGIN(Cont, Begin)
Definition: ncbimisc.hpp:780
#define NCBI_NAME2(Name1, Name2)
Name concatenation macro with two names.
Definition: ncbistl.hpp:120
#define ITERATE_VAR(Type)
Definition: ncbimisc.hpp:791

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 823 of file ncbimisc.hpp.

Referenced by CDepthCollection::AddRange(), CleanSocketList(), CHttpCookies::Cleanup(), CSeq_annot_Info::ClearFeatIds(), impl::CDriverContext::CloseConnsForPool(), impl::CDriverContext::CloseOldIdleConns(), CombineCorrectionsAndIndels(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CCDSInfo::Cut(), CChainer::CChainerImpl::CutParts(), CSeq_loc_CI_Impl::DeleteRange(), CDbxrefPanel::DeleteTaxonRef(), CDisambiguator::Disambiguate(), CConnTest::ExtraCheckOnFailure(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), CDB_UserHandler_Deferred::Flush(), CServer_ConnectionPool::GetPollAndTimerVec(), CNCPeerControl::GetReadyForShutdown(), CGnomonEngine::GetScore(), impl::CDriverContext::MakePooledConnection(), CSeq_loc_Mapper_Base::Map(), CGnomonAnnotator_Base::MapAlignmentsToEditedContig(), MapAlignsToOrigContig(), CGnomonAnnotator_Base::MapModelsToOrigContig(), CFeatureGenerator::SImplementation::MaximizeTranslation(), CEditingActionDescUserObject::Modify(), CGraphOverlay::MoveTrackOut(), CConnTest::PostCheck(), CConnTest::PreCheck(), CGnomonAnnotator::Predict(), CID2CDDProcessor_Impl::ProcessPacket(), CID2SNPProcessor_Impl::ProcessPacket(), CID2WGSProcessor_Impl::ProcessPacket(), CNCBlobAccessor::Purge(), CFeatureGenerator::SImplementation::RecalculateExonIdty(), CNCPeriodicSync::ReConfig(), CAlignDistGraph::RemoveEquivs(), CSeq_feat::RemoveExt(), CNCPeerControl::RemoveSyncControl(), CObjectManager::RevokeDataLoaders(), s_OpenIndexDB(), s_ReadHeader(), CChainer::ScoreCDSes_FilterOutPoorAlignments(), CMergeTree::Search(), TraverseAndRunTestCases(), CSDBAPI::UpdateMirror(), CAnnot_Collector::x_AddPostMappings(), CNCMessageHandler::x_AssignCmdParams(), CMergeTree::x_FindBefores_Up_Iter(), CMergeTree::x_FindBefores_Up_Recur(), CGraphTrack::x_OnSettingsIconClicked(), CID2SNPProcessor_Impl::x_ProcessGetBlobId(), CFlatGatherer::x_RemoveDupComments(), and CGencollIdMapper::x_StripPseudoSeq().

#define GI_CONST (   gi)    (TGi(CConstGIChecker<gi>::value))
#define GI_FROM (   T,
  value 
)    (TGi(static_cast<TIntId>(value)))
#define GI_TO (   T,
  gi 
)    (static_cast<T>(TIntId(gi)))
#define INT_ID_FROM (   T,
  value 
)    (static_cast<TIntId>(value))

Definition at line 1030 of file ncbimisc.hpp.

Referenced by CSeq_id_Gibbsq_Tree::x_Get(), and CSeq_id_Gibbmt_Tree::x_Get().

#define INT_ID_TO (   T,
  id 
)    (static_cast<T>(id))

Convert gi-compatible int to/from other types.

Definition at line 1029 of file ncbimisc.hpp.

Referenced by CSeq_id_Handle::GetHash(), CSeq_id_Handle::operator<(), CSeq_id::Set(), CValidError_imp::ValidateCitations(), and CSeq_loc::x_CompareSingleId().

#define INVALID_GI   GI_CONST(-1)
#define ITERATE (   Type,
  Var,
  Cont 
)
Value:
for ( ITERATE_VAR(Type::const_iterator) \
Var = ITERATE_BEGIN(ITERATE_CONST(Cont), begin), \
NCBI_NAME2(Var,_end) = ITERATE_CONST(Cont).end(); \
Var != NCBI_NAME2(Var,_end); ++Var )
#define ITERATE_BEGIN(Cont, Begin)
Definition: ncbimisc.hpp:780
#define NCBI_NAME2(Name1, Name2)
Name concatenation macro with two names.
Definition: ncbistl.hpp:120
#define ITERATE_CONST(Cont)
Definition: ncbimisc.hpp:771
#define ITERATE_VAR(Type)
Definition: ncbimisc.hpp:791

ITERATE macro to sequence through container elements.

Definition at line 795 of file ncbimisc.hpp.

Referenced by CFeatureTableReader::_AddProteinToSeqEntry(), CTabDelimitedValidator::_CheckHeader(), CFeatureTableReader::_CheckIfNeedConversion(), CTabDelimitedValidator::_OperateRows(), CTabDelimitedValidator::_ReportTab(), CTabDelimitedValidator::_ReportXML(), CSeqDBImpl::AccessionToOids(), SChunkInfo::Add(), CInt_fuzz::Add(), CAlnMix::Add(), CSeqFetchQueue::Add(), CResolvedTypeSet::Add(), CSeqsRange::Add(), CDBUDRandomMapper::Add(), CAnnotPieces::Add(), CPdfDictionary::Add(), CCgiCookies::Add(), CHttpCookies::Add(), CMultAlign::AddAlignment(), CAlignCollapser::AddAlignment(), CAlignDistGraph::AddAlignment(), CMiscSeqTableColumn::AddApplyObjectValue(), CBadResiduesException::SBadResiduePositions::AddBadIndexMap(), CLDS2_Database::AddBioseq(), AddBioseqToTable(), AddBioSourceToAttributes(), CSUCBlock::AddBlock(), CQueueClientInfoList::AddClientInfo(), AddColumnsToFeatureTable(), CCommandLineParser::AddCommand(), CEvidencePanel::AddCommand(), CBlkEdtFeatLocationPanel::AddCommand(), CStrandPanel::AddCommand(), CRevIntPanel::AddCommand(), CResyncPanel::AddCommand(), CPseudoPanel::AddCommand(), CExceptionPanel::AddCommand(), CExperimentPanel::AddCommand(), CEditInferencePanel::AddCommand(), CLDS2_Manager::AddDataDir(), CProjectTreeBuilder::AddDatatoolSourcesDepends(), CRefArgs::AddDefinitions(), CTMgr_ItemResolverRequest::AddDisplayTracks(), CMergeTree::AddEquiv(), CMergeTree::AddEquivs(), NAdapterSearch::CUnpairedAdapterDetector::AddExemplar(), AddFeatureToBioseq(), AddFeatureToSeqTable(), CSubmissionPrepMainPanel::AddField(), CWriteDB_GiMask::AddGiMask(), CWriteDB_GiMaskOffset::AddGIs(), CWriteDB_GiMaskIndex::AddGIs(), AddIdsFromSeqEntryToTable(), CChainer::CChainerImpl::AddIfCompatible(), CAlignRangeCollection< CAlignRange< TSeqPos > >::AddInsertions(), CSelectProjectOptions::AddItemsToWorkspace(), CMsvcPrjProjectContext::AdditionalIncludeDirectories(), CMsvcPrjProjectContext::AdditionalLibraryDirectories(), CMsvcPrjProjectContext::AdditionalLinkerOptions(), AddLocalIdUserObjects(), CHandleRangeMap::AddLocation(), CWGSDb_Impl::AddMasterDescr(), AddMiscColumnsToTable(), AddMissingCommonOrgMods(), AddMisspellsToReport(), CTrackContainer::AddNewTrack(), CObjectLoadingTask::AddObjects(), CSelectionEvent::AddObjectSelection(), AddObjsToReport(), CSourceRequirements::AddOneOfList(), CCommandLineParser::AddOption(), COStreamTextOStream::AddParagraph(), addProblems(), AddProblemsColumnToFeatureSeqTable(), CGBProjectHelper::AddProjectItemsFromRID(), CProjectService::AddProjectView(), CFeatureTableReader::AddProteins(), CCleanup::AddProteinTitle(), CNewCleanup_imp::AddProteinTitles(), AddProteinToSeqEntry(), CSequenceInputStats::AddQueryBatch(), CSegmentSmearGlyph::CSegMap::AddRanges(), CHandleRange::AddRanges(), CDensityMap< CntType >::AddRanges(), CSimpleMakeFileContents::AddReadyKV(), CFeatureGenePanel::AddReciprocicalXref(), CSAM_CIGAR_Formatter::AddRow(), CMasterSeqSegments::AddSegmentIds(), CExplicit_Mapper_Sequence_Info::AddSeq(), CTSE_Default_Assigner::AddSeq_data(), CBioseq_Base_Info::AddSeq_descr(), CImportFeatTable::AddSeqAnnotToSeqEntry(), CBioseq_Base_Info::AddSeqdesc(), AddSeqEntryToSeqEntry(), CSeq_loc_mix::AddSeqLoc(), CSAM_Formatter::CSAM_Headers::AddSequence(), CBuildDatabase::AddSequences(), CReadBlastApp::addSimpleTab(), CScoreBuilderBase::AddSplignScores(), AddStructuredCommentToAttributes(), AddSupport(), CValidErrorFormat::AddSuppression(), CCompareWithBiosample::AddTablePanel(), CThreadPool_Impl::AddTask(), CScoreBuilder::AddTracebacks(), CSourceRequirements::AddUniquenessList(), AddUserObjectFieldItems(), CProcessor::AddWGSMaster(), CTextUtil::AddWordFrequencies(), CUrl::Adjust(), CAlignmentAssistant::AdjustAlign(), CFeatGapInfo::AdjustForRelevantGapIntervals(), CBlastOptionsBuilder::AdjustProgram(), CTrackConfigManager::AdjustTrackOrder(), AdvancedStringCompare(), AgpRead(), CContigAssembly::Align(), AlignmentIsSupportedBySR(), CValidError_align::AlignmentScorePercentIdOk(), CSplign::AlignSingleCompartment(), CTrackConfigManager::AlignTrackConfig(), CLayoutGroup::AllChildrenSameType(), CDistMethods::AllFinite(), CTableNames::AllTableNames(), CAlnGraphic::AlnGraphicDisplay(), CMsvcConfigure::AnalyzeDefines(), AnalyzeDllData(), AnalyzeField(), CCyclicDepends::AnalyzeProjItem(), CCyclicDepends::AnalyzeProjItemNew(), CForeignContaminationScreenReportReader::AnnotateOrRemove(), CSymResolver::Append(), CMsvcProjectMakefile::Append(), CLayout::Append(), CReadBlastApp::append_misc_feature(), SNetScheduleExecutorImpl::AppendAffinityTokens(), COMSSASearch::AppendSearch(), CExpandGaps::apply(), CConvertSelectedGaps::apply(), CAddSequences::apply(), CRecomputeIntervals::apply(), CGroupExplode::apply(), CConvertGapsBySize::apply(), CRetranslateCDS::apply(), CEditSelectedGaps::apply(), CCombineAdjacentGaps::apply(), CRmvCddFeatDbxref::apply_to(), CPrefixAuthority::apply_to(), CDockManager::ApplyLayout(), CSubjectRangesSet::ApplyRanges(), SrcEditDialog::ApplySrcTableToSeqEntry(), ApplySrcTableToSeqEntry(), CAutoDefModifierCombo::AreFeatureClausesUnique(), CSplignFormatter::AsAlignmentText(), CSpliced_seg::AsDiscSeg(), CSplignFormatter::AsExonTable(), CPluginArg::AsList(), CEUtils_IdGroup::AsQueryString(), CEUtils_IdGroupSet::AsQueryString(), CFastaReader::AssembleSeq(), CNWFormatter::AsSeqAlign(), CSplignFormatter::AsSeqAlignSet(), CCompartmentAccessor< THit >::AsSeqAlignSet(), CInt_fuzz::AssignTranslated(), CEntrez2_id_list::AssignUids(), NSnpBins::CGeneMap::AsString(), NTweakExon::AsString(), CTime::AsString(), CTimeSpan::AsString(), variation::CVariationUtil::AsVariation(), variation::CVariationUtil::AsVariation_feats(), CAttachedHandles::Attach(), CSplitParser::Attach(), CEditsSaver::Attach(), variation::CVariationUtil::AttachProteinConsequences(), CBlobSplitterImpl::AttachToSkeleton(), CCompareWithBiosample::Authenticate(), CSequenceEditingEventHandler::Autodef(), CEditingBtnsPanel::AutodefOptions(), CDiscrepancyContext::AutofixAll(), CFieldChoicePanel::AutoMatch(), CFieldChoicePanel::AutoMatchCGP(), CFieldChoicePanel::AutoMatchDBLink(), CFieldChoicePanel::AutoMatchFeat(), CFieldChoicePanel::AutoMatchMisc(), CFieldChoicePanel::AutoMatchMolInfo(), CFieldChoicePanel::AutoMatchPub(), CFieldChoicePanel::AutoMatchRNA(), CGeneFinder::BadSeqLocSortOrderCStyle(), BDB_batch_delete_recs(), CMSAToolJob::BeforeRun(), CPdf::BeginDocument(), CFileDBEngine::BeginTransaction(), BelongToExon(), CBioSource::BiosampleDiffsOkForUpdate(), BioseqIndexData(), CSequesterSets::BioseqSetDescriptorPropagateUp(), BioseqSetDescriptorPropagateUp(), BioSourceFromImpFeat(), CCleanup::BioSrcFromFeat(), BioTreeAddFeatureToDictionary(), BioTreeContainerIsForest(), BioTreeConvert2Container(), BioTreeConvertContainer2Dynamic(), BioTreeConvertContainer2DynamicForest(), BioTreeConvertContainer2Tree(), BioTreeForestConvert2Container(), Blast_GetSeqLocInfoVector(), BOOST_AUTO_TEST_CASE(), CSelectionService::Broadcast(), BroadcastCommandToChildWindows(), CVisibleRangeService::BroadcastVisibleRange(), CAlnMixSegments::Build(), BuildAln(), BuildDBLinkValuesTableFromSeqEntry(), CSeqDBAliasNode::BuildFilterTree(), BuildGFF3Gap(), SNetStorage::SConfig::BuildImpl(), CProjectTreeBuilder::BuildOneProjectTree(), CProjectTreeBuilder::BuildProjectTree(), CCgiRequest::CalcChecksum(), CGraphUtils::CalcGraphLevels(), CDepthCollection::CalcStats(), CChain::CalculateDropLimits(), CComboChartDataSource::CalculateMinMax(), CAlnVec::CalculatePercentIdentity(), CQualityScoringMethod::CalculateScores(), CSimpleScoringMethod::CalculateScores(), CChainer::CChainerImpl::CalculateSpliceWeights(), CChain::CalculateSupportAndWeightFromMembers(), CAlignDistGraph::CAlignDistGraph(), CAlignMap::CAlignMap(), CAlignModel::CAlignModel(), CAlignShadow::CAlignShadow(), CEUtilsApp::CallEInfo(), CWorkerNodeCleanup::CallEventHandlers(), CAlnSpanVertModel::CAlnSpanVertModel(), CTypesIteratorBase< Parent >::CanEnter(), CTypesIteratorBase< Parent >::CanSelect(), CCgiResponse::CanSendTrailer(), CAutoDefModifierCombo::CAutoDefModifierCombo(), CAutoDefParsedRegionClause::CAutoDefParsedRegionClause(), CAutoDefSourceDescription::CAutoDefSourceDescription(), CBAMDataLoader_Impl::CBAMDataLoader_Impl(), CBioseq_SplitInfo::CBioseq_SplitInfo(), CBioseqIndex::CBioseqIndex(), CBioTreeSelection::CBioTreeSelection(), CBlastDbBioseqSource::CBlastDbBioseqSource(), CBlastHitMatrix::CBlastHitMatrix(), CBlastQueryFilteredFrames::CBlastQueryFilteredFrames(), CCgiEnvHolder::CCgiEnvHolder(), CChain::CChain(), CCriteriaSet_CalculateMemberships(), CCSRADataLoader_Impl::CCSRADataLoader_Impl(), CCSraDb_Impl::CCSraDb_Impl(), CDB_ODBC_ConnParams::CDB_ODBC_ConnParams(), CDDTypedAnnotDialog::CDDTypedAnnotDialog(), CDenseSegHit::CDenseSegHit(), CDiscRepItem::CDiscRepItem(), CdsTrnaOverlapStr(), CExonParameters::CExonParameters(), CFeatHistogramDS::CFeatHistogramDS(), CFeatureGraph::CFeatureGraph(), CGeneModelTrack::CGeneModelTrack(), CGeneFinder::CGeneSearchPlugin::CGeneSearchPlugin(), CGridTableSeqIds::CGridTableSeqIds(), CHandleRange::CHandleRange(), ChangeCountryColonToComma(), CReferenceItem::ChangeMedlineAuthorsToISO(), CSeqTable_multi_data::ChangeToBytes(), CSeqTable_multi_data::ChangeToCommon_bytes(), CSeqTable_multi_data::ChangeToCommon_string(), CWriteUtil::ChangeToPackedInt(), CSeq_loc::ChangeToPackedInt(), CSeqTable_multi_data::ChangeToString(), CFileModules::Check(), CDataTypeModule::Check(), CFileSet::Check(), CDiagFilter::Check(), check_no_overlaps(), CAlignCollapser::CheckAndInsert(), CheckAutoDefOptions(), CChainer::CChainerImpl::CheckCompatibility(), CheckDeflineMatches(), variation_ref::CVariationUtil::CheckExonBoundary(), variation::CVariationUtil::CheckExonBoundary(), CheckExpectedQuals(), CComment_rule::CheckFieldValue(), CCodeGenerator::CheckFileNames(), CheckForEmptySequences(), CValidError_bioseq::CheckForMultipleStructuredComments(), CValidError_bioseq::CheckForPubOnBioseq(), CConnTest::CheckFWConnections(), CComment_rule::CheckGeneralStructuredComment(), NTweakExon::CheckIdAndStrand(), COMSSASearch::CheckLibraryNameAndSize(), CheckLocalId(), CReadBlastApp::CheckMissingRibosomalRNA(), COrgMod::CheckMultipleVouchers(), CFileModules::CheckNames(), CDataTypeModule::CheckNames(), CFileSet::CheckNames(), CTreeMinimalSet< TNode, TSet, TNodeList >::CheckNodeList(), CSeq_align::CheckNumRows(), CheckPairwiseAln(), CCustomTree::CheckParent(), CPrimeNumberClient::CheckProgress(), CProjectsLstFileFilter::CheckProject(), CheckQual(), pub_report::CheckRefs(), CSourceRequirements::CheckSourceQuals(), CValidError_bioseq::CheckSoureDescriptor(), CAltValidator::CheckTaxids(), CReadBlastApp::CheckUniqLocusTag(), CUniSequenceDataType::CheckValue(), CMultiDictionary::CheckWord(), CCddInputData::CHit::CHit(), CId2ReaderBase::CId2ReaderBase(), CIgAnnotationInfo::CIgAnnotationInfo(), CCigar::CigarString(), CIndexedDb_New::CIndexedDb_New(), CIntronParameters::CIntronParameters(), CVisibleRange::Clamp(), CClassTypeInfoBase::ClassesById(), CClassTypeInfoBase::ClassesByName(), CLatLonCountryMap::CLatLonCountryMap(), CAlignCollapser::CleanSelfTranscript(), CHttpCookies::Cleanup(), CDiffList::CleanupAndMerge(), CGb_qual::CleanupAndRepairInference(), CLocalHookSetBase::Clear(), CBioTreeForest< BioTree >::Clear(), CObjPool< CRWLockHolder, THolderPoolFactory >::Clear(), CDeleteQueue< const CTSE_ScopeInfo *, CTSE_ScopeInternalLock >::Clear(), CCgiCookies::Clear(), NWinHook::COnExitProcess::ClearAll(), CTL_CursorResultExpl::ClearFields(), NSnp::ClinSigAsString(), CGeneModel::Clip(), CChain::ClipChain(), CChain::ClipLowCoverageUTR(), CAlignCollapser::ClipNotSupportedFlanks(), CChain::ClipToCompleteAlignment(), CLiteAlign::CLiteAlign(), CloneContainer(), CloneMenu(), CDockLayoutTree::CNode::CloneNode(), impl::CDriverContext::CloseAllConn(), impl::CDriverContext::CloseConnsForPool(), CLocalFileRestorer::CloseOpenViews(), CPhyloTreeDataSource::Clusterize(), CMatePairGlyph::CMatePairGlyph(), CMC3_CodingRegion< order >::CMC3_CodingRegion(), CGridCommandLineInterfaceApp::Cmd_GetQueueList(), CGridCommandLineInterfaceApp::Cmd_Replay(), CMsvcCombinedProjectMakefile::CMsvcCombinedProjectMakefile(), CMsvcPrjProjectContext::CMsvcPrjProjectContext(), CMsvcSite::CMsvcSite(), CMultiSeqInfo::CMultiSeqInfo(), CTraversalMerger::CNodeLabeler::CNodeLabeler(), CObjectList::CObjectList(), CObjMgr_QueryFactory::CObjMgr_QueryFactory(), CollapseDiscontinuitiesInUTR(), CDepthCollection::CollapseOnDepth(), CLocMapper_Default::CollapseRanges(), CDiscrepancyGroup::Collect(), CFileModules::CollectAllTypeinfo(), CDataTypeModule::CollectAllTypeinfo(), CFileSet::CollectAllTypeinfo(), CollectAttributes(), CollectBioSources(), CBam2Seq_graph::CollectCoverage(), pub_report::CollectDataArt(), CollectDescriptors(), CollectDllsDepends(), CMsvcPrjFilesCollector::CollectExtra(), CReadBlastApp::CollectFrameshiftedSeqs(), CProjBulderApp::CollectLibToLibDependencies(), CReadBlastApp::collectPerfectHits(), CBlobSplitterImpl::CollectPieces(), CBam2Seq_graph::CollectRawAccessCoverage(), CMsvcPrjFilesCollector::CollectResources(), CReadBlastApp::CollectRNAFeatures(), CollectSequencesByProjectID(), CMsvcPrjFilesCollector::CollectSources(), CScope_Mapper_Sequence_Info::CollectSynonyms(), CSeq_loc_Mapper_Base::CollectSynonyms(), CChain::CollectTrustedmRNAsProts(), CCodeGenerator::CollectTypes(), CwxTableListCtrl::ColumnModelToIndex(), CUnorderedSplitter::CombineAlignments(), CChainer::CChainerImpl::CombineCompatibleChains(), CREnzyme::CombineIsoschizomers(), CTableViewWithTextViewNav::CombineObjects(), IProjectViewFactory::CombineObjects(), SrcEditDialog::CombineTables(), CombineTables(), CPreBuildEventTool::CommandLine(), CPreBuildEventToolLibImpl::CommandLine(), CScopeTransaction_Impl::Commit(), CFileDBEngine::CommitTransaction(), CompareOrgModValue(), CmRNACDSLinker::CompleteHalfFormedXrefPairs(), CStructCommentFieldPanel::CompleteStructCommentFields(), CCgiStatistics::Compose_Entries(), CScatterPlotGlyph::ComputeAxisRange(), CClusterer::ComputeClusters(), CClusterer::ComputeClustersFromLinks(), TKmerMethods< TKmerCounts >::ComputeCounts(), CTextFsm< MatchType >::ComputeFail(), CScoreBuilderBase::ComputeScore(), CStringUtil::ConcatenateStrings(), CMsvcConfigure::Configure(), ConfigureAutodefForSeqEntry(), CCgiApplication::ConfigureDiagFormat(), CDBUDRandomMapper::ConfigureFromRegistry(), CDBUDPriorityMapper::ConfigureFromRegistry(), CDBUniversalMapper::ConfigureFromRegistry(), CICacheCF< CNetICacheClient >::ConfigureTimeStamp(), CReaderServiceConnector::Connect(), CFixGenericListCtrl::ConnectToControl(), CReadCmdExecutor::Consider(), CSequenceSearchForm::ConstructQuery(), COrfSearchForm::ConstructQuery(), CSeqScores::ConstructSequenceAndMaps(), variation::ContainsIupacNaAmbiguities(), ContainsLetters(), CTSE_Info::ContainsMatchingBioseq(), CTSE_ScopeInfo::ContainsMatchingBioseq(), CCountries::ContainsMultipleCountryNames(), CSynonymsSet::ContainsSynonym(), CConvertBioSrcToRptRegion::Convert(), CConvertProtToImp::Convert(), CConvertCDSToGene::Convert(), CConvertCDSToPseudoGene::Convert(), Convert_BioTreeContainer_Seq_id(), 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_GC_Assembly_Seq_id(), 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(), CBadResiduesException::SBadResiduePositions::ConvertBadIndexesToString(), CSeq_loc_Conversion::ConvertCdregion(), CSeq_loc_Conversion_Set::ConvertCdregion(), CSeq_inst::ConvertDeltaToRaw(), ConvertDendiagToPairwiseAln(), CCdsToMatPeptide::ConvertEach(), CSeq_loc_Conversion::ConvertEquiv(), CSeq_loc_Conversion_Set::ConvertEquiv(), CPepXML::ConvertFromOMSSA(), CCdsToMatPeptide::ConvertInner(), CArgDescriptions::ConvertKeys(), SMakeProjectT::ConvertLibDepends(), SMakeProjectT::ConvertLibDependsMacro(), CFeatureGenerator::ConvertLocToAnnot(), CSeq_loc_Conversion::ConvertMix(), CSeq_loc_Conversion_Set::ConvertMix(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CAuth_list::ConvertMlToStandard(), CPepXML::ConvertModifications(), CPepXML::ConvertMSHitSet(), CSeq_loc_Conversion::ConvertPacked_int(), CSeq_loc_Conversion_Set::ConvertPacked_int(), CSeq_loc_Conversion::ConvertPacked_pnt(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), ConvertRawToDeltaByNs(), CConfig::ConvertRegToTree(), ConvertSeqAlignToPairwiseAln(), CSeq_loc_Conversion::ConvertSimpleMix(), ConvertSparseToPairwiseAln(), ConvertSplicedToPairwiseAln(), ConvertStdsegToPairwiseAln(), TMaskedQueryRegions::ConvertToCPacked_seqint(), SBDB_CacheUnitStatistics::ConvertToRegistry(), SBDB_CacheStatistics::ConvertToRegistry(), CRemoteBlast::ConvertToRemoteMasks(), CDir::Copy(), CopyContainer(), CTable2AsnContext::CopyFeatureIdsToComments(), CTreeNode< TValue, TKeyGetter >::CopyFrom(), CReadBlastApp::CopyInfoFromGenesToProteins(), CopyMinusStrandData(), CBlobSplitterImpl::CopySequence(), CBlobSplitterImpl::CopySkeleton(), SChunkInfo::CountAnnotObjects(), CBlobSplitterImpl::CountAnnotObjects(), CAnnotPieces::CountAnnotObjects(), CMiscSeqTableColumn::CountConflicts(), CountInternalStopCodons(), CountQueryCoverage(), CSeqMap::CountSegmentsOfType(), SrcEditDialog::CountTableColumnConflicts(), CountTableColumnConflicts(), CPacked_seqint::CPacked_seqint(), CPluginManager< TClass >::CPluginManager(), CPriorityNode::CPriorityNode(), CPriorityTree::CPriorityTree(), CProjectTreeFolders::CProjectTreeFolders(), CProteinAlignText::CProteinAlignText(), CQueryDataPerChunk::CQueryDataPerChunk(), CQueryFactoryInfo::CQueryFactoryInfo(), CRawSeqDBSource::CRawSeqDBSource(), SMakeProjectT::Create3PartyLibs(), CAnnotationASN1::CImplementationData::create_cdregion_feature(), CAnnotationASN1::CImplementationData::create_internal_feature(), CAnnotationASN1::CImplementationData::create_ModelEvidence_user_object(), CreateAlignSetFromAnchoredAln(), CreateAlignSetFromPairwiseAln(), CreateAnchoredAlnVec(), CEntrezDB::CreateAnnot_Nuc_Prot(), CBlastAligner::CreateBlastAligners(), CRemoteBlastAligner::CreateBlastAligners(), CChainer::CChainerImpl::CreateChainsForPartialProteins(), CProjBulderApp::CreateCheckList(), CreateCompartmentAccessor(), CMsvcConfigure::CreateConfH(), CreateConfigurableFile(), CPhrap_Contig::CreateContig(), CLatLonTool::CreateControls(), CCountryConflict::CreateControls(), CBulkRna::CreateControls(), CBulkGene::CreateControls(), CBulkCDS::CreateControls(), CCompareWithBiosample::CreateControls(), CUnculTaxTool::CreateControls(), CRptTypePanel::CreateControls(), CAppOptionsDlg::CreateControls(), CBulkCountryEdit::CreateControls(), CncRNASubPanel::CreateControls(), CCDSGeneProtFieldNamePanel::CreateControls(), CRNAFieldNamePanel::CreateControls(), CCDSProductPanel::CreateControls(), CSubPrepIntroPanel::CreateControls(), CGenericPropsPanel::CreateControls(), CConvertCdsToMiscFeat::CreateControls(), CStructuredCommentPanel::CreateControls(), CFieldChoicePanel::CreateControls(), CSequencingTechnologyPanel::CreateControls(), CValidatorReportCfgDlg::CreateControls(), CGBQualPanel::CreateControls(), CSingleGbQualSubPanel::CreateControls(), CBulkRNAAddPanel::CreateControls(), CCDSTranslationPanel::CreateControls(), CBLASTSearchParamsPanel::CreateControls(), SrcEditDialog::CreateControls(), CTblEditDlg::CreateControls(), CDualRNAFieldNamePanel::CreateControls(), CQualApplyPanel::CreateControls(), CQualityScoringPanel::CreateControls(), CAlignRNAAddPanel::CreateControls(), SMakeProjectT::CreateDefines(), CreateDense_diagFromAnchoredAln(), CreateDensegFromAnchoredAln(), CreateDensegFromDendiag(), CAlignFormatUtil::CreateDensegFromDendiag(), CSeq_align::CreateDensegFromDisc(), CreateDensegFromPairwiseAln(), CSeq_align::CreateDensegFromStdseg(), CreateDllBuildTree(), CreateDllsList(), CEditingBtnsPanel::CreateFeature(), CSequenceEditingEventHandler::CreateFeature(), CProjBulderApp::CreateFeaturesAndPackagesFiles(), CProjectItemsTree::CreateFrom(), SMakeProjectT::CreateFullPathes(), SMakeProjectT::CreateIncludeDirs(), CGC_Assembly::CreateIndex(), CPluginManager< TClass >::CreateInstanceFromList(), CMsvcPrjProjectContext::CreateLibsList(), CSequence::CreateMsa(), SAppProjectT::CreateNcbiCToolkitLibs(), CGraphTrack::CreateOverlay(), CreatePackedsegFromAnchoredAln(), CreatePackedsegFromPairwiseAln(), CPhrap_Seq::CreatePadsFeat(), CAlignCleanup::CreatePairwiseFromMultiple(), STrackSettings::CreateProfileString(), CSeq_align::CreateRowSeq_loc(), CSeqUtils::CreateSeq_loc(), CBlastFormatUtil::CreateSeqAnnotFromSeqAlignSet(), CreateSparseAlign(), CTrackConfigManager::CreateTrackConfig(), CSeqTableGraphTrackFactory::CreateTracks(), CVarTrackFactory::CreateTracks(), CAggregateFeatureTrackFactory::CreateTracks(), CHapmapTrackFactory::CreateTracks(), CLDBlockTrackFactory::CreateTracks(), CGraphOverlayFactory::CreateTracks(), CBinsTrackFactory::CreateTracks(), CSnpTrackFactory::CreateTracks(), CEpigenomicsTrackFactory::CreateTracks(), CGeneModelFactory::CreateTracks(), CGraphTrackFactory::CreateTracks(), CFeatureTrackFactory::CreateTracks(), CAlignmentTrackFactory::CreateTracks(), CRemoteAppLauncher::CRemoteAppLauncher(), CSearchFormBase::CSearchFormBase(), CBl2Seq::CSearchResultSet2TSeqAlignVector(), CSeq_loc_Mapper::CSeq_loc_Mapper(), CSeqDBFileGiList::CSeqDBFileGiList(), CSeqDBIdSet_Vector::CSeqDBIdSet_Vector(), CSeqIdGuesser::CSeqIdGuesser(), CSeqLoc2BlastSeqLoc(), CSeqMap::CSeqMap(), CSequenceTrack::CSequenceTrack(), CSmallDNS::CSmallDNS(), CSniffReader::CSniffReader(), CStdSegHit::CStdSegHit(), CTableDataAlnSummary::CTableDataAlnSummary(), CTaxTreeDS_ObjMgr::CTaxTreeDS_ObjMgr(), CTempTrackProxy::CTempTrackProxy(), CTopLevelSeqEntryContext::CTopLevelSeqEntryContext(), CTrans_table::CTrans_table(), CTraversalCodeGenerator::CTraversalCodeGenerator(), CTraversalMerger::CTraversalMerger(), CTraversalPatternMatchCallback::CTraversalPatternMatchCallback(), CVDBGraphDataLoader_Impl::CVDBGraphDataLoader_Impl(), CWGSDataLoader_Impl::CWGSDataLoader_Impl(), CWriteDB_ConsolidateAliasFiles(), CWriteDB_CreateAliasFile(), CPluginReply::DecomposeRaw(), CHTML_area::DefinePolygon(), CMsvcPrjProjectContext::Defines(), impl::CDriverContext::DeleteAllConn(), CHMMParameters::SDetails::DeleteAllCreatedModels(), CSGGenBankDS::DeleteAllJobs(), DeleteBlastDb(), CUser_field::DeleteField(), CCmdFactory::DeleteGeneXRefs(), CSelListModelImpl< Item >::DeleteItems(), CCgiSession_NetCache::DeleteSession(), CSdbapiSimpleApp::DemoDynamicSql(), CSdbapiSimpleApp::DemoParamerizedSql(), CSdbapiSimpleApp::DemoStaticSql(), CSdbapiSimpleApp::DemoStoredProc(), CIdMapperConfig::DescribeContexts(), CEditsSaver::Detach(), CCigar::DetailedCigarString(), CDataLoader::DetailsToChoice(), CSubSource::DetectDateFormat(), DFS::DFS(), DictConvert2ContainerFeatureDict(), CDiagRangeCollection::Diff(), CDisambiguator::Disambiguate(), CEventHandler::Dispatch(), CDBConnectionFactory::DispatchServerName(), CTaxFormat::DisplayLineageReport(), CCigar::Distance(), CEquivRange::Distance(), DivvyUpAlignments(), CRemoveIdChecker::Do(), COpenViewManager::DoAsyncConversion(), DoCompartments(), SAppProjectT::DoCreate(), SLibProjectT::DoCreate(), SAsnProjectMultipleT::DoCreate(), SMsvcProjectT::DoCreate(), DoDiffsContainConflicts(), DoesApplyObjectMatchFieldConstraint(), DoesCodingRegionHaveTerminalCodeBreak(), CStringConstraint::DoesListMatch(), CConvertFeatDlg::DoesObjectAllQualsMatchFieldConstraint(), DoesObjectMatchFieldConstraint(), CSeqIdGuesser::DoesSeqMatchConstraint(), CStringConstraint::DoesTextMatch(), CStrWithURLRenderer::DoGetBestSize(), DoHighlightMotif(), pub_report::DoHydraSearch(), CPsiBlastApp::DoIterations(), CDeltaBlastApp::DoPsiBlastIterations(), SMakeProjectT::DoResolveDefs(), CMetaDataTest::DoTest(), CSampleTest::DoTest(), CFileLoadManager::DoTransition(), CStrWithURLRenderer::Draw(), CGlContainer::Draw(), CRenderingContext::DrawLineStrip(), CRenderingContext::DrawStrandIndicators(), CGraphOverlay::Drop(), CChainer::DropAlignmentInfo(), CDataSource::DropAllTSEs(), DTDFileNameBase(), DTDPublicModuleName(), CConvGraph::Dump(), CSimpleMakeFileContents::Dump(), CComplexRelation::Dump(), CSeq_id_int_Tree::Dump(), CBDB_FileDumperApp::Dump(), ILineError::Dump(), CLDS2_Database::Dump(), CSeq_id_Textseq_Tree::Dump(), CSeq_id_Local_Tree::Dump(), CSeq_id_General_Tree::Dump(), CSeq_id_Giim_Tree::Dump(), CSeq_id_Patent_Tree::Dump(), CSeq_id_PDB_Tree::Dump(), CLocksMonitor::SLocks::Dump(), CRegistryReadView::DumpAll(), DumpAnchoredAln(), ILineError::DumpAsXML(), CObjectConverter::DumpDotGraph(), CAnnotationASN1::CImplementationData::DumpEvidence(), CProjBulderApp::DumpFiles(), CLocksMonitor::DumpLocks(), DumpPairwiseAln(), DumpSeqEntries(), CPackString::DumpStatistics(), CDumpSysInfo::DumpSystemInfo(), CAnnotCompareDS::DumpTextReport(), CSequenceEditingEventHandler::Duplicate(), CAlignMap::EditedSequence(), CSequenceEditingEventHandler::EditStructuredCommentPrefixSuffix(), WSDLParser::EmbeddedElement(), CMaskedRangesVector::empty(), CExtraEncoder::Encode(), CLDS2_ObjectParser::EndBlob(), CPdf::EndDocument(), Entropy(), CRequestContext_PassThrough::Enumerate(), CTar::EstimateArchiveSize(), CID2WGSProcessor_Impl::ExcludedBlob(), CRowSelector::ExcludeRow(), CNetService::ExcludeServer(), CCodeGenerator::ExcludeTypes(), NAutomation::SNetScheduleService::ExecJobCounters(), SSingleQueueInfoToJson::ExecOn(), CNSTDatabase::ExecSP_GetAttributeNames(), CNSTDatabase::ExecSP_GetClientObjects(), CNSTDatabase::ExecSP_GetClients(), CNSTDatabase::ExecSP_GetGeneralDBInfo(), CNSTDatabase::ExecSP_GetStatDBInfo(), CNSTDatabase::ExecSP_GetUserObjects(), CNSTDatabase::ExecSP_GetUsers(), CAsyncObjConvert::Execute(), CPhyObjectLoader::Execute(), CFastaObjectLoader::Execute(), C5ColObjectLoader::Execute(), CAsyncObjConvert2::Execute(), CAssemblyObjectLoader::Execute(), CBedObjectLoader::Execute(), CVcfObjectLoader::Execute(), CAgpObjectLoader::Execute(), CWigObjectLoader::Execute(), CGffObjectLoader::Execute(), CRMObjectLoader::Execute(), CTextAlignObjectLoader::Execute(), CAsnObjectLoader::Execute(), CBLAST_DB_Dialog::CExecuteAsync_CreateItems::Execute(), CQueryImpl::Execute(), CNcbiActionGuard::ExecuteActions(), CMacroWorker::ExecuteMacros(), CQueryImpl::ExecuteSP(), CSeq_align::ExonLengthRange(), CAutoDefModifierCombo::ExpandByAnyPresent(), CCleanup::ExpandGeneToIncludeChildren(), ExpandSupport(), CAppDialogs::ExportDialog(), CSequenceEditingEventHandler::ExportStructuredCommentsTable(), CGeneModel::Extend(), CCyclicDepends::ExtendChains(), CFileSet::ExternalResolve(), CArchive::Extract(), CTar::Extract(), ExtractBioseq(), ExtractExtraIds(), CBlastDBExtractor::ExtractFasta(), CBlastDBExtractor::ExtractLeafCommonTaxonomicNames(), CBlastDBExtractor::ExtractLeafScientificNames(), CBlastDBExtractor::ExtractLeafTaxIds(), CBlastDBExtractor::ExtractLinksInteger(), CBlastDBExtractor::ExtractMaskingData(), CBlastDBExtractor::ExtractMembershipInteger(), CAnnotationASN1::ExtractModels(), CAlignFormatUtil::ExtractQuerySeqAlign(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), CDense_seg::ExtractRows(), CBlastDBExtractor::ExtractSeqData(), CDense_seg::ExtractSlice(), CBlastDBExtractor::ExtractTitle(), CTrackUtils::ExtractTrackConfig(), CGlBitmapFont::FaceFromString(), CDataTrackUtils::FeatSubtypes2TrackSubtypes(), FillReport(), CAlnMixSegments::FillUnalignedRegions(), CFilterSet::Filter(), CAlignCollapser::FilterAlignments(), CAlignDepthFilter::FilterBothRows(), CSeqAlignFilter::FilterByGiList(), CSeqAlignFilter::FilterByGiListFromFile(), CSeqAlignFilter::FilterBySeqDB(), CSGAlignmentJob::FilterDuplicatesAndBadReads(), CGeneSelector::FilterGenes(), CEntrez2Client::FilterIds(), CAlignDepthFilter::FilterOneRow(), CChainer::CChainerImpl::FilterOutChimeras(), FilterOutDllHostedProjects(), CChainer::CChainerImpl::FilterOutTandemOverlap(), CAlignFormatUtil::FilterSeqalignByEval(), CAlignFormatUtil::FilterSeqalignByPercentIdent(), CAlignFormatUtil::FilterSeqalignByScoreParams(), CNCSyncLog::Finalize(), CSeq_annot_Finder::Find(), CWinMaskUtil::CIdSet_SeqId::find(), SAccGuide::Find(), NStr::Find(), find_id(), CSrzPath::FindAccPath(), CFixedSeq_ids::FindAccVer(), CChainer::CChainerImpl::FindAltsForGeneSeeds(), FindAppropriateRule(), SrcEditDialog::FindBadColumns(), SrcEditDialog::FindBadRows(), FindBadRows(), FindBestChoice(), CAutoDef::FindBestModifierCombo(), CSelectTargetDlg::FindBioseq(), CDllResolver::FindCandidates(), FindChildWindowById(), CPluginManager< TClass >::FindClassFactory(), CUICommandRegistry::FindCommandByName(), CComment_set::FindCommentRule(), FindCompartments(), CChainer::CChainerImpl::FindContainedAlignments(), CCyclicDepends::FindCycles(), CCyclicDepends::FindCyclesNew(), CValidError_imp::FindEmbeddedScript(), CSeq_feat::FindExt(), CSeq_align::FindExt(), CComment_rule::FindFieldRuleRef(), FindFilesInDir(), FindFirstStart(), CProjectTreeFolders::FindFolder(), CChainer::CChainerImpl::FindGeneSeeds(), CFixedSeq_ids::FindGi(), CMSResponse::FindHitSet(), CSeq_loc_CI_Impl::FindInnerEquivSet(), CNCPeerControl::FindIPbyAlias(), CNCPeerControl::FindIPbyName(), CDocSum::FindItem(), CItem::FindItem(), CSeq_id_PDB_Tree::FindMatch(), CSeq_id_General_Tree::FindMatchStr(), CSeq_id_Giim_Tree::FindMatchStr(), CSeq_id_Patent_Tree::FindMatchStr(), CSeq_id_PDB_Tree::FindMatchStr(), COMSSASearch::FindMinMaxSearchSettingId(), COMSSASearch::FindMinMaxSpectrumNumber(), CCodeGenerator::FindModuleByName(), CTreeNode< TValue, TKeyGetter >::FindNodes(), FindNRuns(), FindNucInSeqEntry(), CSeq_id_PDB_Tree::FindOrCreate(), CProjectTreeFolders::FindOrCreateFolder(), CTreeNode< TValue, TKeyGetter >::FindOrCreateNode(), CNcbiApplication::FindProgramExecutablePath(), CObjectConverter::FindRelations(), CSeq_id_PDB_Tree::FindReverseMatch(), CValidError_align::FindSegmentGaps(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), CDataSource::FindSeq_feat_Lock(), SrcEditDialog::FindSeqIDColumn(), FindSeqIDColumn(), FindSeqTableColumnByName(), NAdapterSearch::CSimpleUngappedAligner::FindSingleBest(), CInternalStopFinder::FindStartsStops(), CInternalStopFinder::FindStartStopRanges(), COrf::FindStrongKozakUOrfs(), FindSubItem(), FindTextseq_id(), FindUnverified(), CEntrez2_docsum::FindValue(), CDocSum::FindValue(), CItem::FindValue(), CSeqDBAliasNode::FindVolumePaths(), CCgiStreamWrapperWriter::FinishChunkedTransfer(), pub_report::FirstOrLastAuthorMatches(), CReadBlastApp::fit_blast(), CBioSource::FixEnvironmentalSample(), FixGeneticCode(), FixHumanHost(), FixMedLineList(), CFeatureGenerator::SImplementation::FixOrderOfCrossTheOriginSeqloc(), CSubSource::FixSexQualifierValue(), FixTableAfterImport(), SrcEditDialog::FixTableAfterImport(), CChoiceDataType::FixTypeTree(), CNcbiTestTreeElement::FixUnitsOrder(), FlattenBioseqSet(), TestUtil::FlattenSeqAlignSet(), CSAM_Formatter::Flush(), AbstractLexer::FlushCommentsTo(), CFlatNumberQVal::Format(), CFlatGeneSynonymsQVal::Format(), CFlatCodeBreakQVal::Format(), CFlatPubSetQVal::Format(), CFlatSeqIdQVal::Format(), CFlatXrefQVal::Format(), CFlatModelEvQVal::Format(), CGBSeqFormatter::FormatAccession(), CReferenceItem::FormatAuthors(), CValidErrorFormat::FormatCompleteSubmitterReport(), CGenbankFormatter::FormatDBSource(), CGenbankFormatter::FormatGap(), CGBSeqFormatter::FormatGenomeProject(), CGenbankFormatter::FormatGenomeProject(), CGBSeqFormatter::FormatKeywords(), CBioTreeFormatLabel::FormatLabel(), CHTMLFormatterEx::FormatLocation(), CGBSeqFormatter::FormatLocus(), CHTMLFormatterEx::FormatProteinId(), CGBSeqFormatter::FormatReference(), CVecscreenRun::CFormatter::FormatResults(), CStringUtil::FormatStringsOccurrences(), CGeneModel::FrameShifts(), CResourcePool_Base< string, CNoLock, CResoursePool_NewClassFactory< string > >::FreeAll(), CRegistryFile::FromConfigFile(), CComplexRelation::FromUserObject(), g_FindDataFile(), g_GetWorkerNodeInfo(), CNWFormatter::SSegment::GapLength(), CSeq_align::GapLengthRange(), CSplitCDSwithTooManyXs::GapLocationsFromNs(), CRawSeqToDeltaByN::GapLocationsFromNs(), CGeneFinder::GeneMatchesXref(), CBlastAligner::GenerateAlignments(), CRemoteBlastAligner::GenerateAlignments(), CSplitSeqAlignMerger::GenerateAlignments(), CClientPseudoTypeStrings::GenerateClassCode(), CChoicePtrTypeStrings::GenerateClassCode(), CChoiceTypeStrings::GenerateClassCode(), CClassTypeStrings::GenerateClassCode(), CWsdlTypeStrings::GenerateClassCode(), CCodeGenerator::GenerateClientCode(), CTraversalNode::GenerateCode(), CCodeGenerator::GenerateCode(), CCodeGenerator::GenerateCombiningFile(), CFileCode::GenerateCPP(), CCodeGenerator::GenerateCvsignore(), CCodeGenerator::GenerateFileList(), CFileCode::GenerateHPP(), CProjBulderApp::GenerateMacProjects(), CCodeGenerator::GenerateModuleCPP(), CCodeGenerator::GenerateModuleHPP(), CProjBulderApp::GenerateMsvcProjects(), GenerateSeed(), CProjBulderApp::GenerateSummary(), CPhyloTreeDataSource::GenerateTooltipFormat(), CEnumTypeStrings::GenerateTypeCode(), CWsdlTypeStrings::GenerateTypeCode(), CProjBulderApp::GenerateUnixProjects(), CFileCode::GenerateUserCPPCode(), CClassTypeStrings::GenerateUserHPPCode(), CFileCode::GenerateUserHPPCode(), variation::CVariationUtil::CCdregionIndex::Get(), CScore_IndelToSplice::Get(), CScore_StartStopCodon::Get(), CScore_CdsInternalStops::Get(), CScore_EdgeExonInfo::Get(), CReadBlastApp::get_nucleotide_seq(), get_title(), CGC_AssemblyUnit::GetAccession(), CGC_Assembly::GetAccession(), CFeatGlyph::GetAccessoryLabel(), CBioseq_Handle::GetAccessSeq_id_Handle(), CCSRADataLoader_Impl::GetAccVer(), CSimpleProjectView::GetActiveObjects(), CTextView::GetActiveObjects(), CSeqDBAliasNode::GetAliasFileValues(), CSeq_align::GetAlignedBases(), CHitMatrixDataSource::GetAlignedIdsForParams(), CObjectIndex::GetAligns(), CArgs::GetAll(), CTrackUtils::GetAllDataKeys(), NSnp::GetAlleles(), CGlBitmapFont::GetAllFaces(), CFlatFileConfig::GetAllGenbankStrings(), CSelectionEvent::GetAllObjects(), CBLASTParams::GetAllRepeatLibs(), CGlBitmapFont::GetAllSizes(), GetAllSwitchPoints(), CScope_Impl::GetAllTSEs(), CAlnVecMultiDataSource::GetAlnFromSeq(), CSparseMultiDataSource::GetAlnFromSeq(), CAlignDistGraph::GetAndRemoveNearestPair(), CGnomonEngine::GetAnnot(), CFindRSites::GetAnnot(), CReadBlastApp::getAnnotComment(), CTSE_Info::GetAnnotIds(), CReadBlastApp::getAnnotName(), CEpigenomicsDS::GetAnnotNames(), CSGAlignmentJob::GetAnnotNames(), CSGFeatureJob::GetAnnotNames(), CSGSegmentSmearJob::GetAnnotNames(), CSGSeqGraphJob::GetAnnotNames(), CSGFeatureJob::GetAnnotNames_var(), CSeqUtils::GetAnnotSelector(), CFeatureSeqTableColumnBase::GetApplyObjects(), CGenomeProjectField::GetApplyObjects(), CProductColumn::GetApplyObjects(), CFieldHandler::GetApplyObjectsFromRelatedObjects(), CMiscSeqTableColumn::GetApplyObjectsValues(), CSequinDesktopView::GetAppSelection(), CTextView::GetAppSelection(), CNCServer::GetAppSetup(), CGC_Assembly::GetAssemblyUnits(), CAssemblyListPanel::GetAssmNameAndDesc(), CCgiSession_NetCache::GetAttributeNames(), GetAuthList(), CReferenceItem::GetAuthNames(), GetAuthorMatchStrings(), pub_report::GetAuthorsFromList(), GetAuthorsString(), GetAuthorString(), GetAvailableCriteria(), GetAvailableFields(), CSeqDBImpl::GetAvailableMaskAlgorithmDescriptions(), CAutoDefSourceDescription::GetAvailableModifiers(), GetBestBioseqLabel(), GetBestCdsForMrna(), GetBestGeneForCds(), GetBestGeneForMrna(), pub_report::GetBestId(), GetBestId(), GetBestMrnaForCds(), CQuerySet::GetBestRank(), CDefaultSynonymMapper::GetBestSynonym(), pub_report::GetBestTitle(), CTSE_LockSet::GetBestTSEs(), NSnpGui::GetBinLinks(), NSnpGui::GetBinTooltip(), CMolInfoFieldType::GetBiomolFromLabel(), CMolInfoFieldType::GetBiomolLabel(), GetBioProjectIDs(), CBioSource::GetBioprojectType(), GetBiosampleIDs(), CSeqDBVol::GetBioseq(), CMSBioseqSet::GetBioseqByOid(), CBiosampleChkApp::GetBioseqDiffs(), GetBioseqDiffs(), GetBioseqForSeqdesc(), CScope_Impl::GetBioseqHandle(), CShowBlastDefline::GetBioseqHandleDeflineAndId(), CAlnMultiDSBuilder::GetBioseqHandles(), CTSE_Split_Info::GetBioseqsIds(), CTSE_Info::GetBioseqsIds(), GetBioSource(), GetBioSourceFromDescr(), CAlignFormatUtil::GetBlastDbInfo(), CScoreBuilder::GetBlastScoreProtToNucl(), CScoreBuilder::GetBlastScoreSpliced(), CNCBlobStorage::GetBList(), SCacheInfo::GetBlob_idsSubkey(), CGBDataLoader::GetBlobId(), CGBDataLoader::GetBlobs(), CDataSource::GetBlobs(), CDataSource_ScopeInfo::GetBlobs(), CReadBlastApp::getBounds(), CSplign::SAlignedCompartment::GetBox(), CSeq_literal::GetBridgeability(), CUser_object::GetCategory(), CSeqGraphicConfig::GetCategoryConfig(), CSplign::GetCds(), CValidError_bioseq::CmRNACDSIndex::GetCDSFormRNA(), CSeqUtils::GetCdsMappingInfoFromRna(), CInternalStopFinder::GetCDSNucleotideSequence(), CConvertBadCdsAndRnaToMiscFeat::getCdsOverlap(), GetCdssForGene(), CCgiRequest::GetCGIEntries(), CFeatTree::GetChildrenTo(), CTempTrackProxy::GetChildTempTrack(), CMsvcSite::GetChoiceFor3PartyLib(), CMsvcSite::GetChoiceForLib(), CMolInfoFieldType::GetChoicesForField(), CSeqUtils::GetChrGI(), CSplitDataLoader::GetChunk(), CBlastDbDataLoader::GetChunk(), CLDS2_DataLoader::GetChunk(), CRemoteBlastDbDataLoader::GetChunks(), CVDBGraphDataLoader::GetChunks(), CWGSDataLoader::GetChunks(), CSNPDataLoader::GetChunks(), CBAMDataLoader::GetChunks(), CCSRADataLoader::GetChunks(), CGBDataLoader::GetChunks(), CDataLoader::GetChunks(), GetCitSubFromPub(), CFileCode::GetClasses(), CFileCode::GetClassNamespace(), CBioseq::GetClosestDescriptor(), CSeqportUtil_implementation::GetCodeIndexFromTo(), CAlignCollapser::GetCollapsedAlgnments(), CSeq_table::GetColumn(), CTableDataSeq_table::GetColumnCommonStrings(), CDataTrackUtils::GetColumnHeader(), CAlnMultiRenderer::GetColumnIndexByX(), CSeqDBImpl::GetColumnMetaData(), GetColumnRuleForFeatureSeqTable(), CFuseFeaturesDlg::GetCommand(), CRmDupFeaturesDlg::GetCommand(), CResolveIntersectingFeats::GetCommand(), CmRNAFromGeneCdsExon::GetCommand(), CtRNAFromGene::GetCommand(), CCdsFromGeneMrnaExon::GetCommand(), CGeneFeatFromOtherFeatDlg::GetCommand(), CExtendPartialFeatDlg::GetCommand(), CAddLinkageToGaps::GetCommand(), CConvertCdsToMiscFeat::GetCommand(), CCorrectGenesDialog::GetCommand(), CConvertFeatDlg::GetCommand(), CApplyRNAITSDlg::GetCommand(), CReplaceSectionPanel::GetCommand(), CReplaceEntirePubPanel::GetCommand(), CReplaceSingleFieldPanel::GetCommand(), CAuthorReplacePanel::GetCommand(), CFileDBEngine::GetCommands(), CVariationUtilities::GetCommonRepeatUnit(), CMolInfoFieldType::GetCompletenessFromLabel(), CMolInfoFieldType::GetCompletenessLabel(), CBlastSeqVectorFromCSeq_data::GetCompressedPlusStrand(), CObjectCoords::GetCoordinates(), CCountries::GetCorrectedCountryCapitalization(), CRangeCollection< TSeqPos >::GetCoveredLength(), NSnp::GetCreateTime(), CFlatFileViewContext::GetCurrentSelection(), CAsnViewContext::GetCurrentSelection(), CMsvcProjectMakefile::GetCustomBuildInfo(), CGBProject::GetData(), CBlastServices::GetDatabaseInfoLegacy(), CDate_std::GetDate(), CSeqDB::GetDate(), CDbtag::GetDBFlags(), CField_type::GetDBLinkFieldFromUserObject(), GetDBLinkIDs(), CEntrezDB::GetDbName(), CEntrezDB::GetDbNames(), CNetStorageGCDatabase::GetDBStructureVersion(), GetDefaultLogLocation(), CCgiApplication::GetDefaultLogPath(), CMetaRegistry::GetDefaultSearchPath(), CFileCode::GetDefineBase(), CShowBlastDeflineTest::GetDeflineInfo(), GetDeflineKeys(), NSNPVariationHelper::GetDeltas(), GetDeltaSeqForPosition(), CPkgManager::GetDependentPkgs(), CFeatList::GetDescriptions(), CEditObjectSeq_desc::GetDescriptorType(), GetDiscrepancyNames(), CSeqDB::GetDiskUsage(), CTaxon1::GetDisplayCommonName(), CLocusItem::GetDivision(), GetDllHost(), GetDocSumLabel(), CEditObjectSeq_desc::GetEditCommand(), CDiffList::GetEditDistance(), CDir::GetEntriesPtr(), CBioseq_set_Info::GetEntryIndex(), CAppEnvHolder::GetEnv(), CSeq_loc_CI_Impl::GetEquivSet(), CSeq_loc_CI_Impl::GetEquivSetsCount(), CBlastKmerResults::GetErrors(), CSearchResults::GetErrors(), CSearchResults::GetErrorStrings(), CCompareSeq_locs::GetEvidenceString(), GetExonPartialness(), CFeatureGenerator::SImplementation::GetExonStructure(), CPhyloTree::GetExplicitlySelectedIDs(), CGBDataLoader::GetExternalAnnotRecords(), CDataLoader::GetExternalAnnotRecords(), CProjectItemsTree::GetExternalDepends(), CLDS2_DataLoader::GetExternalRecords(), CGBDataLoader::GetExternalRecords(), CDataLoader::GetExternalRecords(), CMsvcProjectMakefile::GetExtraFiles(), CSGUtils::GetFeatFetchDepth(), CValidator::CCacheImpl::GetFeatFromCacheMulti(), CCreateFeat::GetFeatLabel(), CMacroUtil::GetFeatSubtype(), CDataTrackUtils::GetFeatSubtypes(), CAutoDefFeatureClause_Base::GetFeatureClausePhrases(), CBioseq_Info::GetFeatureFetchPolicy(), CValidErrorFormat::GetFeatureIdLabel(), CSeqGraphicPane::GetFeatureNames(), CObjectIndex::GetFeatures(), CBioTreeFeatureList::GetFeatureValue(), CRegistryReadView::GetField(), CGuiRegistry::GetField(), GetFieldDiffs(), GetFieldFromWizardObject(), CComment_set::GetFieldNames(), CUser_object::GetFieldRef(), CUser_field::GetFieldRef(), CUser_field::GetFieldsMap(), GetFieldValueAsString(), CWGSDataLoader_Impl::GetFileInfoByGi(), CWGSDataLoader_Impl::GetFileInfoByProtAcc(), CAgpFastaComparator::CTmpSeqVecStorage::GetFileName(), CGCClient_GetAssemblyBySequenceRequest::GetFilterDisplayName(), GetFilteredRedundantGis(), GetFilteredRedundantSeqids(), CBl2Seq::GetFilteredSubjectRegions(), CGeneModelFeatJob::GetFilters(), GetFirstGBQualMatch(), CSeq_loc_mix::GetFirstLoc(), CFeat_qual_choice::GetFirstStringMatch(), COrgName::GetFlatName(), variation::GetFocusLocusIDs(), CSubSrcQual::GetFormatErrors(), CGenericStructuredCommentColumn::GetFromComment(), CGbQualColumn::GetFromFeat(), CSatelliteTypeNameColumn::GetFromFeat(), CGeneRefColumn::GetFromFeat(), CDbXrefColumn::GetFromFeat(), CCodonsRecColumn::GetFromFeat(), CAntiCodonColumn::GetFromFeat(), CTagPeptideColumn::GetFromFeat(), CReadBlastApp::getFromTo(), CGC_Assembly::GetFullAssemblies(), CNCBlobStorage::GetFullBlobsList(), CChoiceDataType::GetFullCType(), TaxClient::GetFullLineage(), CConnTest::GetFWConnections(), CGapAnalysis::GetGapLengthSummary(), CFastaOstream::GetGapModText(), CNetStorageGCDatabase::GetGCCandidates(), GetGcodeForInternalStopErrors(), GetGcodeForName(), CLabelRna::GetGenBankId(), GetGeneForFeature(), CParse::GetGenes(), CBLASTParams::GetGeneticCodeByLabel(), CBlastQuerySourceBioseqSet::GetGeneticCodeId(), CBLASTParams::GetGeneticCodeLabel(), CBLASTParams::GetGeneticCodeLabels(), CSeq_feat::GetGeneXref(), CProteinAlignText::GetGenomicBounds(), CBioseq_set::GetGenomicFromGenProdSet(), CReadBlastApp::getGenomicInterval(), CReadBlastApp::getGenomicLocation(), CCSRADataLoader_Impl::GetGi(), GetGIForSeqId(), CSeqIdListSet::GetGiList(), CSeqLocListSet::GetGiList(), CSeqDBGiList::GetGiList(), CReadBlastApp::getGIs(), CSeqDB::GetGis(), CwxHistogramDlg::GetGraphColor(), CHitMatrixRenderer::GetGraphTypes(), CDbvarClinicalAsstSorter::GetGroupIdx(), CDbvarValidationSorter::GetGroupIdx(), CSeqGraphicPane::GetHitMarker(), CGeneMarkerGlyph::GetHTMLActiveAreas(), CTrackContainer::GetHTMLActiveAreas(), CBinsGlyph::GetHTMLActiveAreas(), CLayoutGroup::GetHTMLActiveAreas(), CLinkedFeatsGroup::GetHTMLActiveAreas(), CFeatGlyph::GetHTMLActiveAreas(), CHistogramGlyph::GetHTMLActiveAreas(), CTableDataSNP::GetHtmlValue(), CHttpHeaders::GetHttpHeader(), CGenetic_code::GetId(), GetId(), CSplign::SAlignedCompartment::GetIdentity(), GetIdField(), CSeqDB_IdRemapper::GetIdList(), CWGSResolver_GiRangeFile::GetIdRanges(), CWGSResolver_AccRangeFile::GetIdRanges(), CDemoApp::GetIds(), CWGSDataLoader_Impl::GetIds(), CDataLoader::GetIds(), CCSRADataLoader_Impl::GetIds(), CSeqIdGuesser::GetIdStrings(), CValidator::CCacheImpl::GetIdToBioseq(), CIdentifiersPanel::GetIdXrefs(), CPubField::GetImprint(), CCigar::GetInDels(), CGeneModel::GetInDels(), CProjectItemsTree::GetInternalDepends(), CTableDataSNP::GetIntValue(), CRegistryReadView::GetIntVec(), CAppExplorerDataObject::GetItems(), CMRUList< string >::GetItems(), CFlatFileViewContext::GetItemSelection(), CPubField::GetJournal(), CInfluenzaSet::GetKey(), CAutoDef::GetKeywordPrefix(), CPub_equiv::GetLabel(), CBioseq::GetLabel(), CSourceModParser::GetLabel(), GetLabel(), CSeq_featHandler::GetLabel(), CEntrezgene_SetHandler::GetLabel(), CVariationHandler::GetLabel(), CAuth_list::GetLabelV2(), CAlignDistGraph::GetLastAlignEquivs(), CNCBlobStorage::GetLatestBlobExpire(), CBioTreeContainer::GetLeafCount(), CSeqDBImpl::GetLeafTaxIDs(), CSeqDB::GetLeafTaxIDs(), CGraphTrack::GetLegend(), CPacked_seqint::GetLength(), CBlobSplitterImpl::GetLength(), GetLength(), CCddInputData::CHit::GetLength(), CReadBlastApp::getLenScore(), CMsvcSite::GetLibChoiceFor3PartyLib(), CMsvcSite::GetLibChoiceForLib(), CMsvcSite::GetLibChoiceIncludes(), CMsvcSite::GetLibInfo(), GetLineSize(), CLinkage_evidence::GetLinkageEvidence(), GetLinkedIdsForMember(), CGuiObjectInfoVariant::GetLinks(), CGuiObjectInfoVariation::GetLinks(), CVecscreenRun::GetList(), CServer_ConnectionPool::GetListenerPorts(), CLocationListCtrl::GetListIdStrForSeqId(), CGBReaderRequestResult::GetLoadedBlob_ids(), CDataSource::GetLoadedBlob_ids(), CCSRADataLoader::SLoaderParams::GetLoaderName(), CWGSDataLoader::GetLoaderNameFromArgs(), CVDBGraphDataLoader::GetLoaderNameFromArgs(), CBAMDataLoader::GetLoaderNameFromArgs(), GetLocalGeneByLocus(), variation::CVariationUtil::CVariantPropertiesIndex::GetLocationProperties(), CValidError_bioseq::GetLocFromSeq(), CReadBlastApp::GetLocMap(), CSeqUtils::GetLocPlacements(), CAnnotObject_Info::GetLocsTypes(), CReadBlastApp::getLocusTag(), CDiffList::GetLongestCommonSubstring(), GetLowestEvalue(), CAnnotMapping_Info::GetMappedSeq_align(), CAnnotObject_Info::GetMaps(), CSeqGraphicPane::GetMarkerNum(), CSeqGraphicPane::GetMarkers(), CAlnMultiWidget::GetMarks(), CSeqDBAliasNode::GetMaskList(), CSeqVecSeqInfoSrc::GetMasks(), CSeqDbSeqInfoSrc::GetMasks(), CRemoteBlast::GetMasks(), CAlignFormatUtil::GetMasterCoverage(), CBioseq_set::GetMasterFromSegSet(), CWGSDb_Impl::GetMasterGi(), CGeneModelFactory::GetMatchedAnnots(), ILayoutTrackFactory::GetMatchedAnnots(), CDataSource::GetMatches(), CSeq_id_Mapper::GetMatchingHandlesStr(), CWord_substitution::GetMatchLens(), CHistogramGlyph::GetMax(), CAutoDefModifierCombo::GetMaxInGroup(), CDictionaryUtil::GetMetaphone(), CHistogramGlyph::GetMin(), CAutoDefFeatureClause_Base::GetMiscRNAElements(), GetMiscTableFromSeqEntry(), GetMismatchOrMissingOrgRefReport(), CSourceModParser::GetModAllowedValues(), CSourceModParser::GetModAllowedValuesAsOneString(), GetModelEvidenceUserObject(), CAutoDefSourceGroup::GetModifiersPresentForAny(), CSourceModParser::GetMods(), CFileCode::GetModuleNames(), CMolInfoFieldType::GetMolFromLabel(), GetMolInfo(), CMolInfoFieldType::GetMolLabel(), variation::CVariationUtil::GetMolType(), CValidError_bioseq::CmRNACDSIndex::GetmRNAForCDS(), GetmRNAforCDS(), GetMrnasForGene(), CProjectTreeView::GetMultiple(), CAsnCache::GetMultipleBlobs(), CAsnCache::GetMultipleEntries(), CAsnCache::GetMultipleRaw(), CGenetic_code::GetName(), CSeq_annot_SplitInfo::GetName(), CConnValidatorCoR::GetName(), CGBDataLoader::GetNamedAnnotAccessions(), CTableDataValidateParams::GetNamedBoolField(), CSeq_feat::GetNamedDbxref(), CSeq_feat::GetNamedQual(), CBioSource::GetNameValPairs(), CNAUtils::GetNATrackInfo(), CGenetic_code::GetNcbieaa(), CGen_code_table_imp::GetNcbieaa(), CSeqDBIdSet::GetNegativeList(), GetNewProteinId(), CSplitCDSwithTooManyXs::GetNewProtId(), CSplitCDSwithTooManyXs::GetNewProtIdFromExistingProt(), CRawSeqDBSource::GetNext(), COrgName::GetNomenclature(), GetNonConsensusSpliceCount(), CBioseq::GetNonLocalId(), CBioseq_set::GetNucFromNucProtSet(), GetNumberOfViewedBioseqs(), CGridTableSeqIds::GetNumberRows(), CAutoDefModifierCombo::GetNumUnique(), CMappedGraph::GetNumval(), CMatePairGlyph::GetObject(), CTextDescriptorField::GetObjects(), CDBLinkField::GetObjects(), CStructuredCommentField::GetObjects(), CMatePairGlyph::GetObjects(), CLinkedFeatsGroup::GetObjects(), CObjectIndex::GetObjects(), CDiscrepancyCore::GetObjects(), CCrossPanelIR::GetObjectSelection(), CSelectionVisitor::GetObjectSelection(), CHitMatrixPane::GetObjectSelection(), CTaxTreeBrowser::GetObjectSelection(), CMSResponse::GetOidsBelowThreshold(), CBlastServices::GetOrganismSpecificRepeatsDatabases(), CTable2AsnContext::GetOrgName(), CObjectIndex::GetOriginalIds(), CVDBGraphDataLoader_Impl::GetOrphanAnnotRecords(), CSNPDataLoader_Impl::GetOrphanAnnotRecords(), CSelectionEvent::GetOther(), CHandleRange::GetOverlappingRange(), CBlast4_parameters::GetParamByName(), CHMMParameters::SDetails::GetParameter(), CMacroUtil::GetParentEntryForBioSource(), CMasterContext::GetPartNumber(), CMsvcMetaMakefile::GetPchInfo(), CNCDistributionConf::GetPeerServers(), CSeqDBIdSet::GetPositiveList(), CVDBGraphDataLoader_Impl::GetPossibleAnnotNames(), CBAMDataLoader_Impl::GetPossibleAnnotNames(), CCSRAFileInfo::GetPossibleAnnotNames(), CCSRADataLoader_Impl::GetPossibleAnnotNames(), CWGSResolver_DL::GetPrefixes(), CWGSResolver_Proc::GetPrefixes(), GetPrimerSetNameValues(), GetPrimerSetSeqValues(), GetProductName(), CProductStringBuilder::GetProductString(), CBLASTParams::GetProgramByLabel(), CBLASTParams::GetProgramLabels(), CWorkspaceFolder::GetProject(), CProjectFolder::GetProjectFolder(), GetProjectID(), CProjectFolder::GetProjectItem(), CProjBulderApp::GetProjectTreeInfo(), CComplexRelation::GetProperty(), CGeneModel::GetProtein(), CDiscrepancyContext::GetProteinId(), CCleanup::GetProteinName(), GetProteinWeights(), CReadBlastApp::GetProtName(), CSeq_feat::GetProtXref(), CCleanup::GetPubdescLabels(), CPubField::GetPubTitle(), GetPubTitleAndAuthors(), CNCBlobAccessor::GetPurgeData(), CRefArgs::GetQueryString(), CEUtils_Request::GetQueryString(), CUrlArgs::GetQueryString(), CGridCgiContext::GetQueryStringEntryValue(), SNetScheduleAPIImpl::GetQueueParams(), CClonePlacementGlyph::GetRange(), CLinkedFeatsGroup::GetRange(), CFeatGlyph::GetRange(), CHistogramGlyph::GetRange(), CSeqUtils::GetRangeCollection(), CMaskedRangeSet::GetRanges(), CSelectionEvent::GetRangeSelectionAsLocs(), CNcbiTestApplication::GetRanTestsCount(), CRegistryReadView::GetRealVec(), CmRNACDSLinker::GetReferencedmRNA_CDS(), CProjectView::GetReflectionInfo(), CBAMDataLoader_Impl::GetRefSeqBlobId(), CClassTypeInfoBase::GetRegisteredClassNames(), CObjectManager::GetRegisteredNames(), CSeqFeatData::GetRegulatoryClass(), CComplexRelation::GetRelated(), CRelationTypeConverterAdapter::GetRelated(), GetRelatedFeatureApplyObjects(), GetRelatedFeatures(), CFeatureSeqTableColumnBase::GetRelatedGeneApplyObjects(), CGC_AssemblyUnit::GetReleaseId(), CGC_Assembly::GetReleaseId(), CBLASTParams::GetRepeatLib(), GetReplacementSeqIds(), CBioSource::GetRepliconName(), CGC_Assembly::GetRepliconTypeLocRole(), CGridCgiContext::GetRequestEntryValue(), CRemoteBlast::GetResultSet(), GetReverseComplement(), GetRmCultureNotesCommand(), CReadBlastApp::GetRNAfeats(), CConvertBadCdsAndRnaToMiscFeat::getRnaOverlap(), CPhyloTreeWidget::GetRotateLabels(), CGridTableSeqIds::GetRowLabelValue(), CTableSelectionBioTreeContainer::GetRows(), CSpliced_exon::GetRowSeq_insertions(), CScheduler_MT::GetScheduledSeries(), CGnomonEngine::GetScore(), CHitMatrixDataSource::GetScoreNames(), CDiagHit::GetScoreValue(), CDenseSegHit::GetScoreValue(), CStdSegHit::GetScoreValue(), CBlastQuerySourceBioseqSet::GetSegmentInfo(), CValidatorReportCfgDlg::GetSelected(), CAssemblyListPanel::GetSelectedAssemblies(), CPhyloTree::GetSelectedBoundary(), CHitMatrixRenderer::GetSelectedHitElemsRect(), CPhyloTree::GetSelectedIDs(), CAlnMultiWidget::GetSelectedIds(), CTextPanelContext::GetSelectedObjects(), CAlnMultiWidget::GetSelectedRows(), CTableViewWithTextViewNav::GetSelection(), CAlnSpanWidget::GetSelection(), CSeqTextPane::GetSelection(), CProjectView::GetSelection(), CCrossAlignView::GetSelection(), CDotMatrixView::GetSelection(), CAlignSpanView::GetSelection(), CMPCrossAlignView::GetSelection(), CPhyTreeView::GetSelection(), CViewGraphic::GetSelection(), CFeatTableView::GetSelection(), CMultiAlignView::GetSelection(), CSelectionView::GetSelection(), CSequinDesktopView::GetSelection(), CSimpleProjectView::GetSelection(), CGridWidget::GetSelection(), CTableSelectionBioTreeContainer::GetSelection(), CTextView::GetSelection(), CSNPTableView::GetSelection(), CSeq_align::GetSeq_id(), GetSeq_idByType(), CAlignFormatUtil::GetSeqAlignCoverageParams(), CAlignFormatUtil::GetSeqAlignSetCalcParams(), CRemoteBlast::GetSeqAlignSets(), CSeqTextDataSource::GetSeqData(), CAlignFormatUtil::GetSeqDescrString(), GetSeqEntryForPubdesc(), GetSeqEntryForSeqdesc(), GetSeqFeatHandleForBadLocFeature(), CAlnVecMultiDataSource::GetSeqFromAln(), CSparseMultiDataSource::GetSeqFromAln(), CShowBlastDefline::GetSeqIdList(), CShowBlastDefline::GetSeqIdListString(), GetSeqIdProblems(), CAsnCache::GetSeqIds(), CSeqDBVol::GetSeqIDs(), CValidError_bioseq::GetSeqLen(), CDensegGraphicDataSource::GetSeqLength(), CTSE_Info::GetSeqMatch(), CStd_seg::GetSeqRange(), CSparse_seg::GetSeqRange(), CSpliced_seg::GetSeqRange(), CSeq_align::GetSeqRange(), CStd_seg::GetSeqStart(), CSparse_seg::GetSeqStart(), CStd_seg::GetSeqStop(), CSparse_seg::GetSeqStop(), CSeqTextDataSource::GetSeqString(), GetSeqTableForSrcQualFromSeqEntry(), GetSeqTableFromSeqEntry(), CBioseq_Info::GetSequenceClass(), CDataLoader::GetSequenceLength(), CMolinfo_field::GetSequenceQualFromBioseq(), CDataLoader::GetSequenceState(), CDataLoader::GetSequenceType(), CDBUDRandomMapper::GetServer(), SNetScheduleAPIImpl::GetServerParams(), CElementaryMatching::CBoolVector::GetSetCount(), CVarTrackFactory::GetSettings(), CAllOtherFeaturesTrackFactory::GetSettings(), CGraphOverlayFactory::GetSettings(), CTraceGraphTrackFactory::GetSettings(), CSegmentMapTrackFactory::GetSettings(), CSnpTrackFactory::GetSettings(), CSequenceTrackFactory::GetSettings(), CGraphTrackFactory::GetSettings(), CSixFramesTransTrackFactory::GetSettings(), CFeatureTrackFactory::GetSettings(), CAlignmentTrackFactory::GetSettings(), CMSRequest::GetSettingsById(), CBamFileInfo::GetShortSeqBlobId(), CBAMDataLoader_Impl::GetShortSeqBlobId(), CMatePairGlyph::GetSignature(), CSeqDBGiList::GetSiList(), CGenetic_code::GetSncbieaa(), CGen_code_table_imp::GetSncbieaa(), GetSortedFeatList(), CDictionaryUtil::GetSoundex(), GetSourceDescriptors(), GetSourceFields(), CUnorderedSplitter::GetSplitIdList(), CGuiObjectInfoSeq_align::GetSRAReadStatus(), GetSrcQual(), CPubField::GetStatus(), CHitMatrixDataSource::GetStdSegRange(), CTextUtil::GetStemFrequencies(), CSeq_loc_mix::GetStrand(), CPacked_seqint::GetStrand(), CMolInfoFieldType::GetStrandFromLabel(), CMolInfoFieldType::GetStrandLabel(), CSeq_id::GetStringDescr(), CWriteUtil::GetStringForModelEvidence(), CCommentItem::GetStringForRefTrack(), CCommentItem::GetStringForTPA(), CTableDataGBProject::GetStringValue(), CTableDataGCAssembly::GetStringValue(), CTableDataSNP::GetStringValue(), CRegistryReadView::GetStringVec(), GetStructuredCommentFields(), CComment_rule::GetStructuredCommentPrefix(), CSettingsSet::GetStyleNames(), CAlignFormatUtil::GetSubjectsNumber(), CGC_Sequence::GetSubmitterName(), CUnculturedTool::GetSuggestedCorrection(), CGeneFinder::GetSuppressionCheckGeneRef(), CGencollIdMapper::GetSynonyms(), CGC_Sequence::GetSynonymSeq_id(), GetTargetedLocusNameConsensus(), CFileLoadManager::GetTask(), CBamUILoadManager::GetTask(), CT3Data::GetTaxFlags(), CGC_Assembly::GetTaxId(), CBioseq::GetTaxId(), CDataLoader::GetTaxId(), CAlignFormatUtil::GetTaxidForSeqid(), CSeqDBImpl::GetTaxIDs(), CSeqDB::GetTaxIDs(), CTaxTreeDS_ObjMgr::GetTaxMap(), GetTaxonTag(), CMolInfoFieldType::GetTechFromLabel(), CMolInfoFieldType::GetTechLabel(), CSeq_feat::GetTempExceptionTextSet(), GetTerminalPartialness(), CReportObject::GetTextObjectDescription(), CSeqDBGiList::GetTiList(), CTitle::GetTitle(), GetTitle(), CFixTitleCap::getTitle(), CBlastQuerySourceBioseqSet::GetTitle(), CNcbiTestApplication::GetToFixTestsCount(), CUIToolRegistry::GetToolNames(), CDataMiningService::GetToolNames(), CUIToolRegistry::GetTools(), CGuiObjectInfoPrimer::GetToolTip(), CGuiObjectInfoClone::GetToolTip(), CGuiObjectInfoVariant::GetToolTip(), CGuiObjectInfoVariation::GetToolTip(), CGuiObjectInfoSeq_feat::GetToolTip(), CGuiObjectInfoSeq_align::GetToolTip(), CSegmentGlyph::GetTooltip(), CTranslationGlyph::GetTooltip(), CGuiObjectInfoRegionFeature::GetToolTip(), CGeneMarkerGlyph::GetTooltip(), CGuiObjectInfoSeqFeature::GetToolTip(), CLinkedFeatsGroup::GetTooltip(), CHistogramGlyph::GetTooltip(), CMolInfoFieldType::GetTopologyFromLabel(), CMolInfoFieldType::GetTopologyLabel(), CScoreBuilder::GetTraceback(), CTrackConfigManager::GetTrackDisplayOptions(), CBinsDS::GetTrackNames(), CSGHapmapDS::GetTrackNames(), CLDBlockDS::GetTrackNames(), CTrackConfigManager::GetTrackTypes(), CGen_code_table_imp::GetTransTable(), CClusterer::GetTrees(), CAutoDefFeatureClause_Base::GetTrnaIntergenicSpacerClausePhrases(), CDataSource::GetTSESetWithBioseqAnnots(), CDataSource::GetTSESetWithOrphanAnnots(), CResolvedTypeSet::GetType(), CTaxon1::GetTypeMaterial(), CFeatTableDS::GetTypeNames(), CAlignFormatUtil::GetUniqSeqCoverage(), CArgAllow_Symbols::GetUsage(), CArgAllow_String::GetUsage(), CArgAllow_Int8s::GetUsage(), CArgAllow_Doubles::GetUsage(), CMsvcMetaMakefile::GetUsePchThroughHeader(), CGBBlockField::GetVals(), CDBLinkField::GetVals(), CStructuredCommentField::GetVals(), CPubField::GetVals(), CGenbankKeywordField::GetVals(), CBankITCommentField::GetVals(), CStructCommFieldValuePair::GetVals(), CStructCommFieldName::GetVals(), CSrcTablePrimerColumn::GetValsFromBioSource(), CEntrez2_docsum::GetValue(), CItem::GetValue(), CGridTableSeqIds::GetValue(), CInferencePanel::GetValue(), COrgModQual::GetValue(), CSubSrcQual::GetValue(), CEditingActionFeatAnticodon::GetValue(), GetValueFromTable(), CDBLinkTableCommandConverter::GetValuesTableFromSeqEntry(), CStructuredCommentCommandConverter::GetValuesTableFromSeqEntry(), CFeatureTableCommandConverter::GetValuesTableFromSeqEntry(), CMultAlign::GetVariationAlignList(), CVariationUtilities::GetVariationRefAlt(), CVariationUtilities::GetVariationType(), CGBProjectHandle::GetViewSettings(), CAlnMultiRenderer::GetVisibleColumns(), CAlignSpanView::GetVisibleRanges(), CSearchResults::GetWarningStrings(), CSequenceSearchForm::GetWidget(), COrfSearchForm::GetWidget(), CSubmissionPrepMainPanel::GetWizardSrcTypeFromName(), CTextUtil::GetWordFrequencies(), CReadDispatcher::GetWriter(), CEnumDataType::GetXMLContents(), CReadBlastApp::giMatch(), CAlignGroup::GroupBySeqIds(), CAlignGroup::GroupBySequenceType(), CAlignGroup::GroupByStrand(), CAlignGroup::GroupByTaxIds(), GroupInDels(), CGencollIdMapper::Guess(), CObjectIStreamAsnBinary::GuessDataType(), CObjectIStream::GuessDataType(), CSubPrep_panel::GuessWizardTypefromSeqEntry(), CProjBulderApp::Gui_ConfirmProjects(), NWinHook::CApiHookMgr::HackModuleOnLoad(), CToMultiExHandler::HandleAll(), CDB_UserHandler_Deferred::HandleAll(), impl::CDBHandlerStack::HandleExceptions(), CGene::HarborsRange(), CStdSegHit::HasAlignment(), HasAmplifiedWithSpeciesSpecificPrimerNote(), CPluginArgSet::HasArgument(), HasAssemblyOrNullGap(), HasAuthor(), HasBadGenomeAssemblyName(), CValidError_bioseq::HasBadWGSGap(), HasBoolField(), CPsiBlastIterationState::HasConverged(), HasCultureCollectionForATCCStrain(), CProjItem::HasDataspecDependency(), CSeq_loc_CI_Impl::HasEquivBreak(), CBlastKmerResults::HasErrors(), CSearchResults::HasErrors(), CRegistryReadView::HasField(), CGuiRegistry::HasField(), CSeqDB_FilterTree::HasFilter(), HasGeneIdXref(), CReadBlastApp::hasGenomicInterval(), CReadBlastApp::hasGenomicLocation(), CSeqDBIsam::HashToOids(), CSeqDBImpl::HashToOids(), CBamLoadOptionPanel::HasIndexFile(), HasIntField(), CPostProcessUtils::HasIntronOffset(), CValidError_imp::HasIsoJTA(), CWGSBioseqUpdater_Base::HasMasterId(), TSearchMessages::HasMessages(), HasMisSpellFlag(), CFeatureGenerator::SImplementation::HasMixedGenomicIds(), HasMod(), CValidError_imp::HasName(), TMaskedQueryRegions::HasNegativeStrandMasks(), CLocationEditPolicy::HasNulls(), CMatePairGlyph::HasObject(), CReverseObjectStore< TKey, TObject >::HasObject(), CLinkedFeatsGroup::HasObject(), CNCPeerControl::HasPeerInThrottle(), CT3Data::HasPlastids(), CReadBlastApp::hasProblems(), HasRawSequenceData(), HasRepairedIDs(), CGC_Sequence::HasRole(), CSeqMap::HasSegmentOfType(), CSeq_feat::HasSeqFeatXref(), HasStrainForATCCCultureCollection(), HasStringField(), CBioSource::HasSubtype(), CValidError_imp::HasTitle(), CTrackUtils::HasTrack(), CChain::HasTrustedEvidence(), HasUnculturedNotes(), HasUnpubWithoutTitle(), COrg_ref::HasValidVariety(), CBlastKmerResults::HasWarnings(), CSearchResults::HasWarnings(), CGBDataLoader::HaveCache(), NWinHook::CHookedFunctions::HaveHookedFunctions(), SCommandLineParserImpl::Help(), SCommandLineParserImpl::HelpOnCommand(), CAlignFormatUtil::HitListToHspList(), CCellHyperlinks::HitTest(), CCrossPanelIR::HitTest(), CAlignFormatUtil::HspListToHitList(), CAlignFormatUtil::HspListToHitMap(), CBioseq_Info::IdString(), CBioseq_ScopeInfo::IdString(), CCodeGenerator::IncludeAllMainTypes(), IndexABioseq(), CAsnSubCacheCreateApplication::IndexNewBlobsInSubCache(), InframeFraction(), variation::InheritParentAttributes(), CAlignSeqTableModel::Init(), CSeqScores::Init(), CAlnVecMultiDataSource::Init(), CApplyGCode::Init(), CSuppressGenes::Init(), CTableDataGCAssembly::Init(), CRemoveGeneXrefs::Init(), CTableDataSeq_table::Init(), CLocAndGCodePanel::Init(), CTableDataBioTreeContainer::Init(), CLocationPanel::Init(), CRemoveFeaturesDlg::Init(), CCorrectIntervalOrder::Init(), CAlnGraphic::Init(), CAgpconvertApplication::Init(), CPrimeCacheApplication::Init(), CTextTableModel::Init(), CLorentz::Init(), CGapStatsApplication::Init(), CColorTableScoringPanel::Init(), CSDBAPI::Init(), CSGAlignmentDS::InitAlignScoreCache(), InitAlnStats(), CID2SNPProcessor_Impl::InitContext(), CID2WGSProcessor_Impl::InitContext(), CSeq_align_Mapper_Base::InitExon(), CAutoDefModifierCombo::InitFromOptions(), CAutoDefOptions::InitFromUserObject(), CSequenceTrack::InitHTMLActiveArea(), PT::CProject::Initialize(), CTaxonCache::Initialize(), CNCPeriodicSync::Initialize(), CNCBlobStorage::Initialize(), CIdMapperConfig::Initialize(), CMsvcConfigure::InitializeFrom(), CMsvcSite::InitializeLibChoices(), CLayoutTrack::InitIconTextures(), CSeqportUtil_implementation::InitIndexCodeName(), CNCDistributionConf::InitMirrorConfig(), CAutoDefModifierCombo::InitOptions(), InitSplicedsegFromPairwiseAln(), CwxTrackSettingsDlg::InitTrackTypes(), CViewGraphic::InitView(), CPhyTreeView::InitView(), CTextView::InitView(), CEditObjViewDlgModal::InitWidget(), CAlnContainer::insert(), CQuerySet::Insert(), CAlignResultsSet::Insert(), CSegmentedRangeCollection::insert(), CLayout::Insert(), CMultAlign::InsertDashesInBase(), CMultAlign::InsertDashesInReads(), CSeq_loc_CI_Impl::InsertRange(), InterpretMrnaException(), CHandleRange::IntersectingWith(), CHandleRange::IntersectingWith_NoStrand(), CHandleRangeMap::IntersectingWithMap(), CHandleRange::IntersectingWithSubranges(), CLayoutGroup::Intersects(), CCddInputData::CHit::IntersectWith(), CSeq_align::IntronLengthRange(), CMsvcSite::Is3PartyLib(), CMsvcSite::Is3PartyLibWithChoice(), CFormatGuess::IsAllComment(), CGene::IsAllowedAlternative(), CProjBulderApp::IsAllowedProjectTag(), IsAllRptUnitSeqChars(), CGene::IsAlternative(), IsAppropriateRule(), CDbtag::IsApprovedNoCase(), CTMS_SupportedAssemblies_Client::IsAssemblySupported(), pub_report::IsAuthorInList(), IsBlankStringList(), IsCapInitialsCorrect(), CPhrap_Contig::IsCircular(), IsCitSubMissingAffiliation(), CSeqportUtil_implementation::IsCodeAvailable(), CSubSource::IsCollectionDateAfterTime(), IsCommonName(), CMsvcPrjProjectContext::IsConfigEnabled(), CFeatGlyph::IsConsensus(), IsContinuous(), IsCrossKingdom(), CCyclicDepends::IsCyclic(), IsElectronicJournal(), CValidError_bioseq::IsEmblOrDdbj(), CStructuredCommentField::IsEmpty(), CScheduler_MT::IsEmpty(), CCddInputData::CHit::IsEmpty(), CSDB_ConnectionParam::IsEmpty(), CAutoDefFeatureClause::IsEndogenousVirusSourceFeature(), CAutoDefFeatureClause::IsExonWithNumber(), CConvertBadCdsAndRnaToMiscFeat::IsExtendableLeft(), IsExtendableLeft(), CConvertBadCdsAndRnaToMiscFeat::IsExtendableRight(), IsExtendableRight(), CAutoDefOptions::IsFeatureSuppressed(), CValidError_bioseq::IsFlybaseDbxrefs(), CVariationNormalization::isFullyShifted(), CValidError_bioseq::IsGenbank(), IsGeneInXref(), IsGeneLocationOk(), CCleanup::IsGeneXrefUnnecessary(), CAlignFormatUtil::IsGiList(), IsGnomonConstructed(), CAlnMixMatch::IsGood(), CCyclicDepends::IsInAnyCycle(), CSeq_loc_CI_Impl::IsInEquivSet(), CFormatGuess::IsInputRepeatMaskerWithoutHeader(), SNetServiceImpl::IsInService(), CScoreLookup::IsIntegerScore(), CVariationUtilities::IsIntronicVariation(), CMsvcSite::IsLibOk(), CMsvcSite::IsLibWithChoice(), CFormatGuess::IsLineGvf(), CFormatGuess::IsLineHgvs(), CLinks::IsLink(), CRefArgs::IsListedHost(), CWriteUtil::IsLocationOrdered(), CSequenceEditingEventHandler::IsLocationSelected(), CEditingBtnsPanel::IsLocationSelectedAa(), CEditingBtnsPanel::IsLocationSelectedNa(), CGencollIdMapper::IsLocInAGap(), variation::IsLRG(), CAutoDefFeatureClause::IsLTR(), CValidError_bioseq::IsMaster(), CQueueClientInfoList::IsMatchingClient(), IsMatchingIdMissing(), IsMicroSatellite(), CCleanup::IsMinPub(), IsMissingRequiredClone(), IsMixedAlignment(), CGeneFinder::IsMixedStrand(), IsmRnaQualsPresent(), IRegistry::IsNameSection(), CMatePairGlyph::IsPairSelected(), CRptTypePanel::IsParseable(), IsProducedByDatatool(), CMsvcSite::IsProvided(), IsPseudo(), IsPubInSet(), CDiscrepancyContext::IsPubMed(), IsRBS(), CVariationUtilities::IsReferenceCorrect(), CValidError_bioseq::IsRefSeq(), CDiscrepancyContext::IsRefseq(), CSGSequenceDS::IsRefSeqGene(), variation::IsRefSeqGene(), CMsvcPrjProjectContext::IsRequiresOk(), variation::IsRightPartial(), IsSegmentSubtype(), CValidError_bioseq::IsSelfReferential(), IsSeqDescInList(), CSeq_loc_mix::IsSetStrand(), CPacked_seqint::IsSetStrand(), CConvertBadCdsAndRnaToMiscFeat::IsShortrRNA(), IsShortrRNA(), NSnp::IsSnpKnown(), CVariation_ref::IsSNV(), CGeneModel::IsSubAlignOf(), CCountries::IsSubstringOfStringInList(), CTrackContainer::IsTrackNameUsed(), IsTransgenic(), CAutoDefSourceDescription::IsTrickyHIV(), CValidError_bioseq::IsTSAAccession(), CSeqEntrySource::IsUnverified(), IsUnverifiedFeature(), IsUnverifiedMisassembled(), IsUnverifiedOrganism(), CComment_rule::IsValid(), CGenomeProjectField::IsValid(), CRptUnitRangeColumn::IsValid(), CRptUnitSeqColumn::IsValid(), CSatelliteTypeNameColumn::IsValid(), CCountries::IsValid(), IsValid(), CSrcTableGenomeColumn::IsValid(), CSrcTableOriginColumn::IsValid(), CSGAlignmentDS::IsValidDNAScoringMethod(), CSmallDNS::IsValidIP(), CSGAlignmentDS::IsValidProteinScoringMethod(), CGb_qual::IsValidRptTypeValue(), CRequestContext::IsValidSessionID(), CSubSource::IsValidSexQualifierValue(), CValidError_bioseq::IsWGS(), CValidError_bioseq::IsWGSAccession(), CValidError_bioseq::IsWGSMaster(), CNetService::Iterate(), CTextJoiner< num_prealloc, TIn, TOut >::Join(), CUser_field::SFieldNameChain::Join(), JoinCompartment(), NStr::Justify(), CGene::LargeCdsOverlap(), C2DLayoutEngine::Layout(), CRawScoreVector< Key, Score >::Length2(), CScoreVector< Key, Score >::Length2(), CAlignFormatUtil::LimitSeqalignByHsps(), CAgpRow::LinkageEvidencesToString(), CSeqDBVol::ListColumns(), CWriteDB_Volume::ListFiles(), CWriteDB_Impl::ListFiles(), CBlastQueryFilteredFrames::ListFrames(), CFeatureTypePanel::ListPresentFeaturesFirst(), CStructFieldValuePanel::ListStructCommentFields(), CWriteDB_Impl::ListVolumes(), CStringHistory::Load(), CColorTableMethod::Load(), CSplitParser::Load(), CColumnScoringMethod::Load(), CMatrixScoringMethod::Load(), CBamRefSeqInfo::LoadAlignChunk(), CSGAlignmentDS::LoadAlignFeats(), CCSRARefSeqInfo::LoadAnnotAlignChunk(), CCSRARefSeqInfo::LoadAnnotMainChunk(), CCSRARefSeqInfo::LoadAnnotMainSplit(), CCompoundRWRegistry::LoadBaseRegistries(), CProcessor_AnnotInfo::LoadBlob(), CId2ReaderBase::LoadBlobs(), CReader::LoadBlobs(), CId2ReaderBase::LoadBlobSet(), CReader::LoadBlobSet(), CId2ReaderBase::LoadChunks(), CReader::LoadChunks(), LoadConfigInfoByNames(), CPhyloTreeScheme::LoadCurrentSettings(), CCompareWithBiosample::LoadData(), CFeaturePanel::LoadDefaultTracks(), CDataTool::LoadDefinitions(), CProjBulderApp::LoadDepGraph(), CDataToolGeneratedSrc::LoadFrom(), CRemoteBlast::LoadFromArchive(), CTempTrackProxy::LoadFromRegistry(), CFastaObjectLoader::LoadFromStream(), CId1Reader::LoadGiSeq_ids(), CTemplateScoringMethod::LoadInfo(), CDockManager::LoadLayout(), CBamRefSeqInfo::LoadMainChunk(), CPkgManager::LoadPackages(), CProjectTask::LoadProjects(), CProjBulderApp::LoadProjectTags(), CGridCgiContext::LoadQueryStringTags(), LoadScope(), CId2ReaderBase::LoadSeq_idBlob_ids(), CReader::LoadSeq_idTaxId(), CTSE_Default_Assigner::LoadSequence(), CReader::LoadSequenceLength(), LoadSequencesToScope(), CReader::LoadSequenceType(), CCgiSession_NetCache::LoadSession(), CUIToolRegistry::LoadSettings(), CHistParamsManager::LoadSettings(), CDiscrepancyDlg::LoadSettings(), CReader::LoadStates(), CMultiReader::LoadTemplate(), CUIToolRegistry::LoadTemplateToolsInfo(), CStdAnnotTypes::LoadTypes(), CAutoAddDesc::LocateDesc(), CFieldChoicePanel::LooksLikeHeader(), CBlastAsyncFormatThread::Main(), CMergeTreeThread::Main(), CSeqDBDemo_Thread::Main(), CWig2tableApplication::MakeAnnot(), SNetScheduleAPIImpl::MakeAuthString(), COrf::MakeCDSAnnot(), CChainer::CChainerImpl::MakeChains(), COrgName::MakeCommon(), COrg_ref::MakeCommon(), CBioSource::MakeCommonExceptOrg(), MakeCompartment(), MakeCompartments(), CSeq_loc_Conversion::MakeDstMix(), MakeEntryForDeltaConversion(), MakeFileName(), CFeatureTableReader::MakeGap(), CWig2tableApplication::MakeGraph(), CBlobSplitterImpl::MakeID2Chunk(), CBlobSplitterImpl::MakeID2SObjects(), CSeq_loc_CI_Impl::MakeLoc(), MakeMailReportPostReport(), CMappedGraph::MakeMappedGraphData(), CMSHits::MakeModString(), CMSHits::MakePepString(), impl::CDriverContext::MakePooledConnection(), CFeatureTableCommandConverter::MakeProblemsColumn(), CRebase::MakeREnzyme(), CScoreUniqSeqCoverage::MakeScore(), CBam2Seq_graph::MakeSeq_annot(), CBlobSplitterImpl::MakeSeq_annot(), CInfluenzaSet::MakeSet(), CWig2tableApplication::MakeTable(), CGBProjectHandle::MakeUniqueDataLoaderLabel(), CGBProjectHandle::MakeUniqueFolderLabel(), MakeWrongCap(), CIdMapperComposite::Map(), CSeq_loc_Mapper_Base::Map(), MapAlignsToOrigContig(), CCDSInfo::MapFromEditedToOrig(), CCDSInfo::MapFromOrigToEdited(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), MapOneModelToOrigContig(), MapToLMBits(), SChainMember::MarkIncludedForChain(), SChainMember::MarkPostponedForChain(), CAlignMarkHandler::MarkRow(), CAlignMarkHandler::MarkSelectedRows(), SChainMember::MarkUnwantedCopiesForChain(), CNodesToBitset< TNode, TSet, TNodeList >::MaskCopyNodes(), CMaskRegexp::Match(), CVisibleRange::Match(), CMaskFileName::Match(), CCigar::Matches(), CReferenceItem::Matches(), CBlob_Annot_Info::Matches(), CDirEntry::MatchesMask(), CSelectionEvent::MatchLocWithId(), CAlignFormatUtil::MatchSeqInSeqList(), CStringMatching::MatchString(), CNCBlobStorage::MeasureDB(), CHttpHeaders::Merge(), Merge(), CStringPairs< TExtraValuesMap >::Merge(), CTreeAlignMerger::Merge_AllAtOnce(), CTreeAlignMerger::Merge_Dist(), CTreeAlignMerger::Merge_Pairwise(), CEquivRangeBuilder::MergeAbuttings(), CCdsToMatPeptide::MergeConvert(), CCleanup::MergeDupBioSources(), MergePairwiseAlns(), CAlignSort::MergeSortedFiles(), CTrackConfigManager::MergeTrackConfig(), ILineError::Message(), CDepthCollection::MinDepthForRange(), CTreeMinimalSet< TNode, TSet, TNodeList >::MinimalSet(), CNCPeerControl::MirrorProlong(), CNCPeerControl::MirrorRemove(), CNCPeerControl::MirrorUpdate(), CNCPeerControl::MirrorWrite(), CNetScheduleNotificationHandler::MkBaseGETCmd(), SNetScheduleExecutorImpl::MkSETAFFCmd(), CBlastTabular::Modify(), CAlignShadow::Modify(), CNewCleanup_imp::MoveCitationQuals(), CCleanup::MoveFeatToProtein(), CTreeNode< TValue, TKeyGetter >::MoveSubnodes(), CGraphOverlay::MoveTrackOut(), CEnumeratedTypeValues::NameToValue(), NCBITEST_AUTO_INIT(), CMAViewManager::NeedAnchorPanel(), CSequenceTrack::NeedTooltip(), CGridCommandLineInterfaceApp::NetScheduleSanityCheck(), newickerror(), CPhyloTreeDataSource::NewNode(), CCompareSeqRegions::NextComparisonGroup(), CAlignCompare::NextGroup(), CSeqGraphicPane::NextPrevSplice(), impl::CDriverContext::NofConnections(), CScoreVector< Key, Score >::Normalize(), CWGSDb_Impl::NormalizePathOrAccession(), NS_ValidateClasses(), SGridWorkerNodeImpl::OfflineRun(), CInfluenzaSet::OkToMakeSet(), CCleanup::OkToPromoteNpPub(), CMrnaMatchInfo::OkWithoutCds(), CObjectListWidgetSel::OnAddAccessionClick(), CSubPrep_panel::OnAddSequenceBtnClick(), CColorTableScoringPanel::OnApply(), CMatchFeatureTableDlg::OnAutomatchTableIdClick(), CDataMiningPanel::OnAutorun(), CAlignmentTrack::OnChangeProjectedFeats(), CDiscrepancyDlg::OnClick(), CHitMatrixWidget::OnColorByScore(), CNetCacheServerListener::OnConnected(), CSeqTextPane::OnCopy(), CDiscrepancyDlg::OnDblClk(), CBioseqEditor::OnDeleteSelection(), CValidateFrame::OnDone(), CProjectTreePanel::OnEnableDisable(), CAppPackagesDlg::OnEnablePkg(), OneRowOk(), CSNPGridEvtExt::OnEventLinkout(), CSNPGridEvtExt::OnEventUpdateLinkout(), CPhyloTreeWidget::OnExportSelection(), CFeatTableWidget::OnFilter(), CSubmitBlockDlg::OnImportBtnClick(), CCDSTranslationPanel::OnImportCdsProteinHyperlinkClicked(), CTblEditDlg::OnImportTableClick(), CDiscrepancyDlg::OnJobNotification(), CProjectTreePanel::OnLoadProject(), SrcEditDialog::OnLoadqualsClick(), CwxSeqMarkerSetDlg::OnOkClick(), CAssemblyTrackingPanel::OnPopulateBtnClick(), CProjectTreePanel::OnProjectTableView(), CRelaxedLookupDlg::OnPubTextDClick(), CProjectTreePanel::OnRemove(), CProjectTreePanel::OnRemoveProject(), CValidatorReportCfgDlg::OnReportBtnClick(), CPhyloTreeWidget::OnRotateLabels(), CMacroEdit_dlg::OnRun(), CSeqGraphicWidget::OnSavePdf(), CSeqTextWidget::OnScrollToSelection(), CProjectTreePanel::OnUnLoadProject(), CProjectTreePanel::OnUpdateCopy(), CProjectTreePanel::OnUpdateCut(), CProjectTreePanel::OnUpdateLoadProject(), CProjectTreePanel::OnUpdateProjectTableView(), CProjectTreePanel::OnUpdateRemove(), CProjectTreePanel::OnUpdateRemoveProject(), CProjectTreePanel::OnUpdateUnLoadProject(), CPhyloTreeWidget::OnUseSplines(), CPipeHandle::Open(), CBAMDataLoader_Impl::OpenBAMFiles(), SCigarAlignment::operator()(), CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::operator()(), CPsiBlastAlignmentProcessor::operator()(), CAlignSort::SAlignExtractor::operator()(), CSorterByMultiCols::operator()(), CBioTreeConvert2ContainerFunc< TBioTreeContainer, TDynamicTree >::operator()(), PIsExcludedByProjectMakefile::operator()(), SBlobInserter::operator()(), CTreeNonRedundantSet< TNode, TSet, TNodeList >::operator()(), CTreeConvert2ContainerFunc< TBioTreeContainer, TTreeType >::operator()(), CTreeConvertSelected2ContainerFunc< TBioTreeContainer, TTreeType >::operator()(), CTreeConvertNonSingleChild2ContainerFunc< TBioTreeContainer, TTreeType >::operator()(), visitor_stringmatch_query::operator()(), CFeedbackTextArrayPrinter::operator()(), visitor_paste_subtree::operator()(), CTreeConvert2ContainerPartialFunc< TBioTreeContainer, TTreeType >::operator()(), AlignLenOrder::operator()(), operator+(), operator<<(), CRawScoreVector< Key, Score >::operator=(), CTempTrackProxy::operator=(), CScoreVector< Key, Score >::operator=(), CBioTreeFeatureDictionary::operator=(), CFeatTree::operator=(), CPluginArgSet::operator[](), CDUpdater::OssToDefline(), CAgpConverter::OutputBioseqs(), CAgpConverter::OutputOneFileForEach(), CDiscrepancyContext::OutputText(), CDiscrepancyContext::OutputXML(), CReadBlastApp::overlaps_na(), CReadBlastApp::overlaps_prot_na(), PackedSeqLocToMaskedQueryRegions(), CCustomTree::Paint(), PairTreeTraceNode(), CSplitParser::Parse(), CHttpCookie::Parse(), CSeq_id_General_Str_Info::Parse(), CStringPairs< TExtraValuesMap >::Parse(), CCgiApplication::ParseAcceptHeader(), SCommandLineParserImpl::ParseAndValidate(), ParseAttributes(), CFastaReader::ParseDefLine(), CFastaMapper::ParseDefLine(), CAgpRow::ParseGapCols(), CFastaReader::ParseGapLine(), CHttpRetryContext::ParseHeader(), CHttpHeaders::ParseHttpHeader(), CGb_qual::ParseInferenceString(), CDBUriConnParams::ParseParamPairs(), CSGConfigUtils::ParseProfileString(), SSNP_Info::ParseSeq_feat(), STrackSettings::ParseSettings(), CBDB_ConfigStructureParser::ParseStructureLine(), CNcbiApplogApp::ParseToken(), SSnpFilter::Passes(), PT::CProjectFolder::Paste(), PatchTargetSequence(), CMakefilePatch::PatchTreeMakefiles(), CChangePhyloPropertyCmd::PerformEdit(), CChangePhyloExpandCollapseCmd::PerformEdit(), CChangePhyloPropertyCmd::PerformFeatureDictEdit(), CChainer::CChainerImpl::PlaceAllYouCan(), impl::CDriverContext::PopDefConnMsgHandler(), CAlignCompare::SAlignment::PopulateBoundariesMap(), CAdjustFeaturesForGaps::PopulateFeatureList(), CGBQualPanel::PopulateGBQuals(), CLocationListCtrl::PopulateIdListFromScope(), CDescPlacementPanel::PopulateLocationChoices(), CSrcModListPanel::PopulateModifiers(), COMSSASearch::PopulateOidList(), CDDTypedAnnotDialog::PopulatePredefinedSitesMap(), CWordPairIndexer::PopulateWordPairIndex(), CAppPopup::PopupURL(), CConnTest::PostCheck(), CConnTest::PreCheck(), CGnomonAnnotator::Predict(), CPrefetchSeqDescr::PrefetchSeqDescr(), CDisplaySeqalign::PrepareBlastUngappedSeqalign(), CDisplaySeqalign::PrepareBlastUngappedSeqalignEx(), CDisplaySeqalign::PrepareBlastUngappedSeqalignEx2(), CProjSRCResolver::PrepareResolver(), CCompilerToolImpl::PreprocessorDefinitions(), CBlast_SAM_Formatter::Print(), CWNJobWatcher::Print(), CComments::Print(), CDepthCollection::Print(), CMaskWriterSeqLoc::Print(), CMaskWriterTabular::Print(), CMaskWriterBlastDbMaskInfo::Print(), CSeqsRange::Print(), CTabularFormatter_AllSeqIds::Print(), CBlastTabularInfo::Print(), CQueueClientInfoList::Print(), CSeq_annot_SplitInfo::Print(), CDiagFilter::Print(), CTabularFormatter_MismatchPositions::Print(), CTabularFormatter_GapRanges::Print(), CTabularFormatter_AlignId::Print(), CTabularFormatter_BestPlacementGroup::Print(), CJob::Print(), CTabularFormatter_ExonIntrons::Print(), CTabularFormatter_SeqChrom::Print(), CTabularFormatter_SeqClone::Print(), CTabularFormatter_AssemblyInfo::Print(), CTabularFormatter_NearestGap::Print(), CAlignDistGraph::Print(), CArgDescriptions::CPrintUsageXml::PrintArguments(), CBlastFormatUtil::PrintAsciiPssm(), CChoiceDataType::PrintASN(), CFileModules::PrintASN(), CDataTypeModule::PrintASN(), CEnumDataType::PrintASN(), CFileSet::PrintASN(), CDataMemberContainerType::PrintASN(), CFileModules::PrintASNRefInfo(), CHTMLPageStat::PrintBegin(), CHTML_table::PrintBegin(), PrintBioseqXML(), CNetService::PrintCmdOutput(), PrintCompartments(), CMSResponse::PrintCSV(), CAlignFormatUtil::PrintDbReport(), CScoreLookup::PrintDictionary(), CBiosampleChkApp::PrintDiffs(), CFileModules::PrintDTD(), CDataTypeModule::PrintDTD(), CFileSet::PrintDTD(), CFileModules::PrintDTDModular(), CDataTypeModule::PrintDTDModular(), CFileSet::PrintDTDModular(), CBlastFormatterApp::PrintFormattedOutput(), CNamespace::PrintFullName(), CChoiceDataType::PrintJSONSchema(), CFileModules::PrintJSONSchema(), CDataTypeModule::PrintJSONSchema(), CEnumDataType::PrintJSONSchema(), CFileSet::PrintJSONSchema(), CDataMemberContainerType::PrintJSONSchema(), CMaskWriterInt::PrintMasks(), COMSSABase::PrintMods(), CCgiContext::PrintMsg(), CGridCommandLineInterfaceApp::PrintNetScheduleStats(), CPhyTreeFormatter::PrintNexusTree(), CBlastFormat::PrintOneResultSet(), CBlastFormat::PrintPhiResult(), CDiagContext::PrintProperties(), CNetScheduleAdmin::PrintQueueInfo(), CHttpSessionApp::PrintResponse(), PrintSAM(), PrintSAMHeader(), CFileModules::PrintSampleDEF(), CDataTypeModule::PrintSampleDEF(), CFileSet::PrintSampleDEF(), CFileModules::PrintSpecDump(), CDataTypeModule::PrintSpecDump(), CFileSet::PrintSpecDump(), CEnumDataType::PrintSpecDumpExtra(), CDataMemberContainerType::PrintSpecDumpExtra(), CNCActiveSyncControl::PrintState(), SBDB_CacheUnitStatistics::PrintStatistics(), SBDB_CacheStatistics::PrintStatistics(), CColumnValidatorRegistry::PrintSupported(), CBiosampleChkApp::PrintTable(), PrintTabular(), CAlignFormatUtil::PrintTildeSepLines(), CPdfArray::PrintTo(), CPdfDictionary::PrintTo(), CNCStat::PrintToSocket(), CDiscRepArgDescriptions::PrintUsage(), CCommandArgDescriptions::PrintUsage(), CArgAllow_Symbols::PrintUsageXml(), CArgAllow_String::PrintUsageXml(), CArgAllow_Strings::PrintUsageXml(), CArgAllow_Int8s::PrintUsageXml(), CArgAllow_Doubles::PrintUsageXml(), CRegexpTemplateTester::PrintVars(), CFileModules::PrintXMLRefInfo(), CUniSequenceDataType::PrintXMLSchema(), CFileModules::PrintXMLSchema(), CDataTypeModule::PrintXMLSchema(), CFileSet::PrintXMLSchema(), CDataMemberContainerType::PrintXMLSchema(), CFileModules::PrintXMLSchemaModular(), CDataTypeModule::PrintXMLSchemaModular(), CFileSet::PrintXMLSchemaModular(), CObjectsSniffer::Probe(), CObjectsSniffer::ProbeASN1_Bin(), CObjectsSniffer::ProbeText(), CGetStatisticsProcessor::Process(), CProcessor_ExtAnnot::Process(), DFS::process_vertex(), CBiosampleStatusReport::ProcessBioseq(), CBiosampleChkApp::ProcessBioseqForUpdate(), CSplitCacheApp::ProcessBlob(), CReadBlastApp::ProcessCDD(), CDataTool::ProcessData(), CMsvcConfigure::ProcessDefine(), CProjectTreeBuilder::ProcessDir(), WSDLParser::ProcessEndpointTypes(), CSplitCacheApp::ProcessEntry(), CGlContainer::ProcessEvent(), CBam2GraphApp::ProcessFile(), ProcessForTrimAndSplitUpdates(), CID2WGSProcessor_Impl::ProcessGetChunks(), CCgiApplication::ProcessHelpRequest(), CMsvcSite::ProcessMacros(), CESearchParser< T >::ProcessMessages(), CBiosampleChkApp::ProcessOneDirectory(), CCgiSessionSampleApplication::ProcessRequest(), CCgiRedirectApplication::ProcessRequest(), ProcessSeqEntryAnnot(), CSplitCacheApp::ProcessSeqId(), CTLSHandler::ProcessSeqSubmit(), CBiosampleChkApp::ProcessSeqSubmit(), CTLSHandler::ProcessSet(), CBiosampleChkApp::ProcessSet(), CCgiApplication::ProcessVersionRequest(), ProjectExon_newlogic(), ProjectExon_oldlogic(), ProjectExons(), CApplyRNAITSDlg::Propagate_RNAITSList(), CCustomTree::PropagateCheck(), PropagateDBLink(), PropagateDescriptor(), CNewCleanup_imp::ProtSeqBC(), CAlignFormatUtil::PruneSeqalign(), CAlignFormatUtil::PruneSeqalignAll(), PsiBlastComputePssmFromAlignment(), CCDSInfo::PStop(), CCleanup::PubAlreadyInSet(), CNewCleanup_imp::PubSetBC(), CBDB_Cache::Purge(), CGBDataLoader::PurgeCache(), CBiosampleChkApp::PushToRecord(), CMessageListenerBase::PutProgress(), CBlast_def_line_set::PutTargetGiFirst(), CBioTreeAttrReader::Read(), CDistanceMatrix::Read(), CGFFReader::Read(), NSnpBins::ReadAnnotDesc(), CObjectIStreamAsn::ReadBitString(), ReadContainer(), CNCPeerControl::ReadCurState(), CPhrap_Read::ReadDS(), ReadEnvironment(), ReadMap(), CHMMParameters::SDetails::ReadParameters(), CHgvsReader::ReadSeqAnnot(), CFeature_table_reader::ReadSequinFeatureTables(), CNCPeerShutdown::ReadyForShutdown(), CSeq_entry::ReassignConflictingIds(), CFeatureGenerator::SImplementation::RecalculateExonIdty(), CFeatureGenerator::SImplementation::RecomputePartialFlags(), CNCPeriodicSync::ReConfig(), RecursiveSummary(), RecursiveText(), RecursiveXML(), CMsvcProjectMakefile::Redefine(), CNcbiTestApplication::ReEnableAllTests(), RefreshDeflineCommand(), CUICommandRegistry::RegisterCommand(), CTextPanel::RegisterCommands(), CCachedSequence::RegisterIds(), CPluginManager< TClass >::RegisterWithEntryPoint(), CNCPeriodicSync::ReInitialize(), CSatelliteTypeNameColumn::RelaxedMatch(), CInfoManager::ReleaseAllLoadLocks(), CInfoRequestor::ReleaseAllUsedInfos(), CInfoCache_Base::ReleaseInfos(), NWinHook::CModuleInstance::ReleaseModules(), CClusterer::ReleaseTrees(), CDBLinkTableCommandConverter::RemapColumnName(), CCgiRedirectApplication::RemapEntries(), variation::CVariationUtil::RemapToAnnotatedTarget(), CFileObsolete::Remove(), CEditsSaver::Remove(), CAnnotPieces::Remove(), CBDB_Cache::Remove(), CDir::Remove(), CRemoveSet::remove_set(), CRemoveSet::remove_sets_from_set(), CSimpleB2SWrapper::RemoveAllDataLoaders(), CAutoRegistrar::RemoveAllDataLoaders(), CdBlaster::RemoveAllDataLoaders(), RemoveAllDataLoaders(), RemoveBioseq(), CCmdFactory::RemoveCitations(), CDiagContextThreadData::RemoveCollectGuard(), RemoveCountryColon(), CScope_Impl::RemoveDataLoader(), CCleanup::RemoveDupBioSource(), CAlignDistGraph::RemoveEquivs(), CSeq_feat::RemoveExceptText(), CCommentItem::RemoveExcessNewlines(), CChain::RemoveFshiftsFromUTRs(), CServer_ConnectionPool::RemoveListener(), CWorkerNodeCleanup::RemoveListeners(), CAlignCollapser::RemoveNotSupportedIntronsFromTranscript(), CProjectTask::RemoveProjects(), CSeq_feat::RemoveQualifier(), RemoveStrain(), CCleanup::RemoveUnseenTitles(), CTextSelHandler::Render(), CAxisRenderer::Render(), CAlignMarkHandler::Render(), CLinearSelHandler::Render(), CRegularGridRenderer::Render(), CCleanup::RenormalizeNucProtSets(), CFileHandleDiagHandler::Reopen(), CSeq_annot_Info::ReorderFtable(), CCleanup::RepackageProteins(), CCleanup::RepairXrefs(), CChainer::CChainerImpl::ReplacePseudoGeneSeeds(), CChainer::CChainerImpl::ReplicatePStops(), pub_report::ReportAuthorDiff(), CValidError_bioseq::ReportBadAssemblyGap(), CTable2AsnValidator::ReportErrors(), CHTMLException::ReportExtra(), CProjBulderApp::ReportGeneratedFiles(), CReadBlastApp::reportProblems(), CProjBulderApp::ReportProjectWatchers(), pub_report::ReportSeqIds(), pub_report::ReportTitleDiff(), ReportTranslationErrors(), CPhyTreeFormatter::RerootTree(), CCleanup::RescueSiteRefPubs(), CCgiSession_NetCache::Reset(), CBioseq_Base_Info::ResetAnnot(), CDataSource_ScopeInfo::ResetHistory(), CBioseq_Info::ResetId(), CBioseq_ScopeInfo::ResetId(), CEditsSaver::ResetIds(), CMenuService::ResetMenuBar(), CCrossPanelIR::ResetObjectSelection(), CSymResolver::Resolve(), SRelLoc::Resolve(), CLDS2_DataLoader::ResolveConflict(), CGBDataLoader::ResolveConflict(), CMsvcSite::ResolveDefine(), CRegistryReadView::ResolveField(), CPluginManager< TClass >::ResolveFile(), CGeneFinder::ResolveGeneObjectId(), CID2WGSProcessor_Impl::ResolveGi(), CFeatureFilter::ResolveIdentifier(), ResolveIdentToObjects(), CCodeGenerator::ResolveImportRefs(), CFileModules::ResolveInAnyModule(), CFileSet::ResolveInAnyModule(), CExec::ResolvePath(), CID2WGSProcessor_Impl::ResolveProtAcc(), ResolveSuppliedBioSampleAccession(), CProjSRCResolver::ResolveTo(), RestoreModelAttributes(), RestoreOriginalHits(), CChain::RestoreReasonableConfirmedStart(), TMaskedQueryRegions::RestrictToSeqInt(), CThreadPool_Impl::ResumeWork(), CSequenceEditingEventHandler::ResynchronizePartials(), ReverseComplementLocation(), CScopeTransaction_Impl::RollBack(), CFileDBEngine::RollbackTransaction(), CwxTableListCtrl::RowDataToVisible(), CAlnMixSequences::RowsStartItsContsistencyCheck(), CRMBlastnApp::Run(), CSampleLibtestApplication::Run(), CSampleBasicApplication::Run(), CGi2TaxIdApp::Run(), CNSSubmitRemoteJobApp::Run(), CAlignTabExportJob::Run(), CGtfExportJob::Run(), CLocalFinderApp::Run(), CSdbapiTest::Run(), CGffExportJob::Run(), CDiscRepApp::Run(), CFetchGBProjectApp::Run(), CSampleObjectsApplication::Run(), CMkIndexApplication::Run(), CGeneModelDemoApp::Run(), CRunTestApplication::Run(), CHttpSessionApp::Run(), CWiggleExportJob::Run(), CNetScheduleControl::Run(), CObjConvProfile::Run(), CDemoContigAssemblyApp::Run(), CFastaExportJob::Run(), CGuideTreeApplication::Run(), CBlastnApp::Run(), CBlastpApp::Run(), CBlastxApp::Run(), CTblastnApp::Run(), CTblastxApp::Run(), CIgBlastpApp::Run(), CSeqDescrRetrievalJob::Run(), CAgpFastaComparator::Run(), CSplignApp::Run(), CRPSBlastApp::Run(), CRPSTBlastnApp::Run(), CBlastDemoApplication::Run(), CSplignSimple::Run(), CBlastDBCmdApp::Run(), CDeltaBlastApp::Run(), CSampleObjmgrApplication::Run(), CProjBulderApp::Run(), CMultiApplication::Run(), CSampleLds2Application::Run(), CAlnBuildApp::Run(), CNetBlastSubmittingJob::Run(), CAlnTestApp::Run(), CGumbelParamsApplication::Run(), CDownloadJob::Run(), CAsnCacheTestApplication::Run(), CSeedTopApp::Run(), CDemoApp::Run(), CTbl2AsnApp::Run(), CDataLoadingAppTask::Run(), CIdfetchApplication::Run(), CNetBlastMonitoringJob::Run(), CAgpconvertApplication::Run(), CSeedTop::Run(), CNgAlignApp::Run(), CMergeyApp::Run(), SGridWorkerNodeImpl::Run(), CIgBlastnApp::Run(), CDiscrepancyReportJob::Run(), CTLSApp::Run(), CSeqAnnotSplicerApp::Run(), CFeatCompareJob_Align::Run(), CAsnSubCacheCreateApplication::Run(), CSeqDBDemo_Threaded::Run(), CXcompareAnnotsApplication::Run(), CFeatCompareJob_Location::Run(), CEditingBtnsPanel::RunMacroWithReport(), CGapStatsApplication::RunNoCatch(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), CTestProtProd_Cdd::RunTest(), CTestBlastp_All::RunTest(), CTestSingleAln_All::RunTest(), CTestTranscript_Orfs::RunTest(), CDiscrepancyDlg::RunTests(), s_AddCoalescedLocations(), s_AddGraphToMap(), variation_ref::CVariationUtil::s_AddIntronicOffsets(), variation::CVariationUtil::s_AddIntronicOffsets(), s_AddMasterDescr(), s_AddProjItemToDll(), s_AddPubmedLinksRow(), s_AddSeqTitleToPssm(), s_AddSitesToAnnot(), s_AddTopLevelGenomicLinks(), s_AddToUniqueIdList(), s_AlignIdsFromEquivList(), s_AlignSet2Annot(), s_AlignToSeqRanges(), CIgBlast::s_AppendResults(), s_AreLinkedToDifferentFeats(), s_AreThereOtherCDSForThisProduct(), variation::CVariationUtil::s_AttachGeneIDdbxref(), s_AuthListEmpty(), s_BuildAlignDataSource(), s_BuildArchiveAll(), s_BuildGetSeqRequest(), s_BuildMaskedRanges(), s_BuildResultsRemote(), s_BuildScoreList(), s_CalcCoverageCount(), s_CalcDevs(), s_CalcMean(), variation_ref::CVariationUtil::s_CalcPrecursorVariationCodon(), variation::CVariationUtil::s_CalcPrecursorVariationCodon(), s_CalcStdDev(), s_CalculateStarts(), s_CallExtensionProjectItemAttached(), s_CallExtensionProjectItemCreated(), s_CallExtensionProjectItemDetached(), s_CheckDataStatus(), s_CheckEndlessRecursion(), s_CheckIdLookup(), s_CheckMatches(), s_CheckQuals_cdregion(), s_CheckTraceMateAlign(), s_CheckUniqueValues(), s_ChoiceType(), s_CitMatches(), s_Code_break(), variation_ref::CVariationUtil::s_CollapseAmbiguities(), variation::CVariationUtil::s_CollapseAmbiguities(), s_CollapseProjectFolder(), s_CollectAllLeaves(), s_CollectCollidingIDs_Entry(), s_CollectDatatoolIds(), s_CollectRelPathes(), s_CollectSeqIds(), s_CombineDustMasksWithUserProvidedMasks(), s_CompareFtables(), s_CompareOverlapping(), s_Complement(), s_ComposeCodonRecognizedStr(), CSplign::s_ComputeStats(), s_ContainsOffset(), s_ConvertBioseqs2TSeqLocVector(), s_ConvertBlastnMasks(), s_ConvertRelativePaths(), s_ConvertSubjects2TSeqLocVector(), s_ConvertToBlastQueries(), NAdapterSearch::CSimpleUngappedAligner::s_CoordSetToMapIndex(), CMacroFunction_PubFields::s_CopyResolvedObjs(), s_CountAccessions(), s_CountBlastDbDataLoaders(), s_CountDisabledItems(), s_CountIntervals(), CPsiBlastTestFixture::s_CountNumberUniqueGIs(), s_CoverageSeqLoc(), s_CreateAliasFilePriv(), s_CreateBlastMask(), s_CreateFeedbackRequest(), s_CreateHistCommentString(), s_CreateNameToQualsMap(), s_CreateSubtypeValueToNameMap(), s_CreateThirdPartyLibsInstallMakefile(), s_CutDensegSegment(), s_DensegHasAccessionWithZeroVersion(), s_DetermineComponentType(), s_DivvyUpAlignments_ProcessAnnot(), s_DivvyUpAlignments_ProcessAnnot_Dendiag(), s_DivvyUpAlignments_ProcessAnnot_Denseg(), s_DoesBioseqRecurse(), s_DoFatalAbort(), s_DoParseGet2JobResponse(), s_DupIdsBioseq(), s_DupIdsRaw(), s_EditFolder(), s_ExonLen(), s_ExonToDenseg(), s_ExpandProjectFolder(), s_ExpandSubNodes(), s_Extract(), s_ExtractBlastDefline(), s_ExtractKeys(), s_ExtractSeqidsAndRanges(), s_FeatureHasEvidenceOrInferenceQuals(), s_FieldHasNonBlankValue(), s_FillAlignVector(), s_FillMaskLocFromBlastResults(), variation::CVariationUtil::s_FindAssertedLiteral(), s_FindBestIdChoice(), s_FindBlastDbDataLoaderName(), variation::CVariationUtil::s_FindConsequenceForPlacement(), s_FindDistAsMax(), s_FindDistAsMean(), s_FindEntryName(), variation::CVariationUtil::s_FindFirstLiteral(), s_FindGaps(), s_FindLocalId(), s_FindMaxDistFromElem(), s_FindMean(), s_FindModelEvidanceUop(), s_FindOrfs(), s_FindSeparator(), s_FindServerSlot(), s_FindSumDistFromElem(), s_FindUserObjectTypeRecursive_helper(), 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_FirstPubMatchesSecond(), s_FixBioseqDeltas(), CUpdateSeq_Input::s_FixCollidingIDs_Bioseq(), CMacroFunction_FixProteinFormat::s_FixProteinNameFormat(), s_FlattenLoc(), s_FormatErrors(), s_FormatJournal(), s_FormatPatent(), s_FormatSecondaryAccessions(), s_GCSeqsToSeqLocs(), s_GeneCommentaryToLocations(), s_GenerateTitle(), s_GetAlignmentContent(), s_GetAlignmentLength(), s_GetAlignmentMismatches(), s_GetAlignmentSpans_Exon(), s_GetAlignmentSpans_Interval(), s_GetAlignmentSpans_Intron(), s_GetAlignmentTooltip(), s_GetAlignNames(), CMixedStrands::s_GetAlignVector(), s_GetAlnMapplingLocs(), s_GetAltRefFromInst(), s_GetAnnotContent(), s_GetAnnotId(), s_GetAnnotName(), s_GetAssemblyInfo(), s_GetAuthorsString(), CMacroWorker::s_GetAutofixMacroRep(), s_GetBestSynonym(), s_GetBlastScore(), s_GetCdregionContentLabel(), s_GetCdregionLabel(), s_GetCdsSequence(), s_GetCitIds(), s_GetClipLoc(), s_GetConcatenatedExon(), s_GetContentLabel(), s_GetCountIdentityMismatch(), s_GetDBTree(), s_GetDisplayLabel(), s_GetEncodeValues(), s_GetFeatureContentLabelExtras(), s_GetFeatureKeyLinkLocation(), s_GetFeaturesForRange(), s_GetFieldAt(), s_GetFilteredRedundantGis(), s_GetFirstBioseqName(), s_GetGapCount(), s_GetGbValue(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetGeneID(), CCompareSeqRegions::s_GetGeneId(), s_GetGeneticCode(), s_GetGeneWeight(), s_GetGOText(), s_GetIdBase(), s_GetIdLabel(), s_GetImpLabel(), s_GetInstCodeFromBioSource(), s_GetLabel(), s_GetLinkFeatureKey(), s_GetLiteralLength(), CMacroWorker::s_GetMacroSteps(), s_GetMaskLoc(), s_GetMaskSeqLoc(), s_GetModelEvidance(), s_GetMrnaProteinLink(), s_GetNAAlignNames(), s_GetNameForBioseq(), s_GetNumFrameshifts(), s_GetNumFromLatLonToken(), s_GetOverlap(), s_GetPrefixForStructuredComment(), s_GetProductName(), s_GetProteinName(), CUnculturedTool::s_GetRank(), s_GetRnaRefLabel(), s_GetSeqIds(), s_GetSeqsFromReply(), s_GetSpecificHostFromBioSource(), s_GetSplicedSegIdentityMismatch(), s_GetSpliceSite(), s_GetStrand(), s_GetStrForStructuredComment(), s_GetSupportTotal(), s_GetSynHandle(), s_GetTaxid(), s_GetTaxId(), s_GetTitle(), s_GetUncoveredLength(), s_GetUngapLoc(), s_GetUnsavedProjects(), s_GetUserObjectContent(), s_GetWeight(), s_GetWGSMasterDescr(), s_GiInCSeq_hist_ids(), s_GoodDigits(), s_GoodLetters(), s_HasGenBankId(), s_HasLocalIDs(), s_HasMatchingGBMod(), s_HasMobileElementForInterval(), s_HasOrgMod(), s_HasPub(), s_HasRawSequence(), s_HasSubSourceNote(), s_HastRNAXref(), s_IdxFindBestIdChoice(), s_ImportDatabase(), s_ImportQueries(), NAdapterSearch::CSimpleUngappedAligner::s_IndexWord(), s_InitalizeDllProj(), s_InitConstants(), s_Initialize(), s_InsertInUnnamedGroup(), s_IntersectionLength(), s_IsAllCaps(), s_IsAllDigits(), s_IsAllDigitsOrPeriods(), s_IsAllowedMethod(), s_IsAllowedOrigin(), s_IsBioSample(), s_IsCDD(), s_IsCitSub(), s_IsConWithGaps(), s_IsCopyNumberMethod(), s_IsDouble(), variation::CVariationUtil::s_IsInstStrandFlippable(), s_IsJustUids(), s_IsLeaf(), s_IsLegalECNumber(), s_IsLOH(), s_IsMatchById(), s_IsNumeric(), s_IsOrdered(), s_IsRefSeqGene(), s_IsRelated(), s_IsSelenocysteine(), s_IsSetWeight(), s_IsTPA(), s_IsUnspecified(), s_IsUsingRemoteBlastDbDataLoader(), s_JoinLinkableStrs(), s_JoinNumbers(), CReaderRequestResult::s_KeyBlobIds(), s_LayoutValueToStr(), s_List2Set(), s_ListChanges(), s_ListHasFeature(), s_ListProjectFolder(), s_Load_Packed_seqint(), s_LoadTempTrackRecursive(), s_MakeBioseqs(), s_MakeCommonStringList(), s_MakeGroupsForUniqueValues(), s_MakeNewMasterSeq(), s_MakeTopHitsId(), s_MapAllGis(), s_MapSingleAA(), s_MapSlaveFeatureToMaster(), s_MaskQuerySeq(), s_Match_id(), s_MatchOrgname(), s_MergeRangeList(), s_NeedFeatureClause(), s_NeedsFlattening(), s_NsAreGaps(), s_NumGiToStringGiList(), CQueryDataTestFixture::s_ObjMgr_QueryFactory_LocalDataFromBlastQueryVector(), CQueryDataTestFixture::s_ObjMgr_QueryFactory_LocalDataFromTSeqLocVector(), CQueryDataTestFixture::s_ObjMgrFree_QueryFactory_LocalDataFromBioseq_set(), s_OkToAddFeature(), s_OssToDefline(), s_ParseQueueInfo(), s_ParseReadJobResponse(), s_ParseSubNodes(), s_PopulateScores(), s_PopulateScoreSet(), s_PopulateValuesArray(), s_PrintAccessions(), s_PrintIds(), s_PrintIds1(), s_PrintTree(), s_PrintTSeqAlignSet(), s_ProcessAlignSet(), s_ProcessErrorsFromReply(), s_ProjectFolderClone(), s_ProjectItemGetDescr(), s_ProjectItemSetDescr(), s_PromoteSingletonSetsInSet(), s_QualVectorToNote(), s_QuoteSpawnArg(), s_RangeVector2BlastSeqLoc(), s_ReadPerClientConfig(), s_ReadServerParams(), s_RemoveAliasComponents(), s_RemoveDependentItems(), s_Render_Feat_Evidence(), s_Render_PairwiseAlign(), s_RenderAccList(), CMacroFunction_RenormalizeNucProtSet::s_RenormalizeNucProtSets(), s_ReplaceGIs(), s_ReplaceListFromQuals(), s_ReportDependenciesStatus(), s_ResolveIdentOICommon(), s_RestrictSeqLocs_Multiframe(), s_RetainEmptyAnnot(), s_Reverse(), s_ReverseComplement(), CUpdateSeq_Input::s_RunBlast2AASeq(), CUpdateSeq_Input::s_RunBlast2NASeq(), CHitFilter< THit >::s_RunGreedy(), CAlignShadow::s_RunLengthDecode(), s_SameIds(), s_SaveDbMap(), s_SaveToSmartClient(), s_ScanRecursive(), s_ScopeProjectFolder(), s_ScoreAlignments(), s_ScoreFromEquivList(), s_Seq_align_Seq_loc(), s_SeqAlignInSet(), s_SeqAlignSetToXMLHsps(), s_SeqAlignToBlastSeqLoc(), s_SeqAlignToXMLHit(), s_SeqDB_DBExists(), s_SeqDB_SeqIdIn(), s_SeqDB_TryPaths(), s_SeqLoc2MaskedSubjRanges(), s_SeqMapForHandle(), s_SetAnyContentFromFields(), s_SetBlastXMLSearch(), s_SetChildrenFeatureIds(), s_SetDeflineBits(), s_SetDeflineLeafs(), s_SetFieldsFromAnyContent(), s_SetIntervals(), s_SetQuals(), s_SetReplaces(), s_SetSearchParam(), s_SetTrnaProduct(), s_SetupWithMultipleQueriesAndSubjects(), CIgBlast::s_SortResultsByEvalue(), s_SplicedToDisc(), s_Split(), s_SplitAlignVectorBySubjects(), s_StrictIsoJta(), s_StringIsJustQuotes(), s_Test_Extremes(), s_Test_Interval(), s_Test_Subset(), s_TestCalc(), s_TestClustersAndTrees(), s_TestClusterTree(), s_TestFeatureDict(), s_TestNode(), s_TestResultAlignment(), s_TestResultClusters(), s_TestResultTree(), s_TestResultTreeContainer(), s_TestStdSegGaps(), s_TestTree(), s_TestTreeContainer(), s_TitleEndsInOrganism(), s_TitleFromBioSource(), s_TitleFromSegment(), s_TitleMatch(), CHitFilter< THit >::s_TrackHit(), s_TranslateAnchorToAlnCoords(), s_TranslatePairwise(), s_TranslatePairwiseToAlnCoords(), s_TSeqLocVectorToBioseqSet(), s_TSeqLocVectorToTSeqLocs(), s_UniformAlignId(), s_UnpackContainerField(), s_UnpackUserField(), s_UseFastaReaderDeflines(), s_Validate(), s_ValueOkForQual(), s_VerifyTree(), s_VT_Descr(), s_WordsToJsonArray(), s_WriteComment(), s_WriteHeader(), s_WriteInt4List(), s_WriteUint4List(), CAlignCompare::SAlignment::SAlignment(), CPub_equiv::SameCitation(), impl::CDriverContext::SatisfyPoolMinimum(), CStringHistory::Save(), CColorTableMethod::Save(), CNcbiResourceInfoFile::SaveFile(), CDockManager::SaveLayout(), CReaderRequestResult::SaveLocksTo(), CGenBankLoadOptionPanel::SaveMruAccessions(), CCacheWriter::SaveSeq_idBlob_ids(), CSeqGraphicConfig::SaveSettings(), CProjectService::SaveSettings(), CUIToolRegistry::SaveSettings(), CHistParamsManager::SaveSettings(), CItemSelectionPanel::SaveSettings(), CFileLoadManager::SaveSettings(), CExportTableDlg::SaveTable(), SrcEditDialog::SaveTableFile(), SaveTableFile(), CwxTableListCtrl::SaveTableSettings(), CTempTrackProxy::SaveToRegistry(), CFileLoadMRUList::SaveToStrings(), SaveWallModel(), SBlocks::SBlocks(), ScanForCpGs(), SChunkAnnots::SChunkAnnots(), CCigar::Score(), CMergeTree::Score(), CPctIdentScorer::ScoreAlignments(), CPctCoverageScorer::ScoreAlignments(), CExpansionScorer::ScoreAlignments(), CWeightedIdentityScorer::ScoreAlignments(), CHangScorer::ScoreAlignments(), COverlapScorer::ScoreAlignments(), CClippedScorer::ScoreAlignments(), CCommonComponentScorer::ScoreAlignments(), NSNPWebServices::Search(), CSeqSearch::Search(), CMultAlign::SelectAligns(), CTableDataBioTreeContainer::SelectFeatures(), CHitMatrixDataSource::SelectIds(), CCompareSeqRegions::SelectMatches(), CSelectionVisitor::SelectSelection(), CTableDataBioTreeContainer::SelectSeqIds(), impl::CDB_Params::SemiShallowClone(), CRemoteAppRequest::Send(), CTaxon3::SendNameList(), CTaxon3::SendOrgRefList(), CCachedTaxon3::SendOrgRefList(), CCachedTaxon3_impl::SendOrgRefList(), CRelaxedLookupDlg::SendQuery(), CTaxon3::SendTaxidList(), Seq_locs_Merge(), SeqAlignSetConvert(), SeqDB_ReadGiList(), SeqDB_SplitQuoted(), SeqDB_VectorAssign(), SeqEntryFromSeqSubmit(), CInvertProcess::SeqEntryProcess(), CSeqDBImpl::SeqidToOids(), SeqLocAllowed(), CNewCleanup_imp::SeqLocBC(), SeqLocMapperToPairwiseAligns(), CNewCleanup_imp::SeqLocMixBC(), SeqLocPartialCheck(), SeqLocPrintUseBestID(), SeqTableFromAssemblyFields(), CSeqTextDataSource::SequencePosToSourcePos(), Serialize< string, float >(), SSnpFilter::SerializeFrom(), SSnpFilter::SerializeTo(), CRegistryWriteView::Set(), CSeq_id::Set(), CGuiRegistry::Set(), SAnnotSelector::SetAdaptiveTrigger(), CServer_ConnectionPool::SetAllActive(), CArgDescriptions::SetArgsType(), CPsiBlastArgs::SetArgumentDescriptions(), CBlastDatabaseArgs::SetArgumentDescriptions(), CHistogramGlyph::SetAxisRange(), CBamCoverageGraphPanel::SetBamFiles(), CChain::SetBestPlacement(), CValidError_bioseq::CmRNACDSIndex::SetBioseq(), CReadDispatcher::SetBlobState(), CPluginArg::SetBoolean(), CSuspectAddConstraint::SetChoices(), CStringConstraintPanel::SetChoices(), CMacroAdvStringConstraintPanel< T >::SetChoices(), CAdvStringConstraintPanel< T >::SetChoices(), CMacroStringConstraintPanel::SetChoices(), CAgpConverter::SetChromosomesInfo(), CCitationsPanel::SetCitations(), CAlnMultiRenderer::SetColumnsByStyle(), CAgpConverter::SetComponentsBioseqSet(), CChain::SetConfirmedStartStopForCompleteProteins(), CChain::SetConsistentCoverage(), CTMgr_ClientInfo::SetContext(), CTwoPartQualPanel::SetControlledList(), CGBQualSemicontrolledTextPanel::SetControlledList(), SetCultureCollectionFromStrain(), CAlnMultiModel::SetCurrentMethod(), CCrossPanelIR::SetDataSource(), CSearchControl::SetDictionary(), CPluginArg::SetDouble(), CPhyloTree::SetExplicitlySelected(), CFieldHandlerNamePanel::SetFieldNames(), CUser_field::SetFieldRef(), CChainer::CChainerImpl::SetFlagsForChains(), CTabularFormatter::SetFormat(), CFastaReader::SetGapLinkageEvidences(), CChainer::CChainerImpl::SetGenomicRange(), CRemoteBlast::SetGIList(), CNewCleanup_imp::SetGlobalFlags(), CClassTypeInfo::SetGlobalHook(), CChoiceTypeInfo::SetGlobalHook(), CEUtils_IdGroupSet::SetGroups(), CNetScheduleAccessList::SetHosts(), CEUtils_IdGroup::SetIds(), CPluginArg::SetInputFile(), CMultiAligner::SetInputMSAs(), CBLASTToolManager::SetInputObjects(), CPluginArg::SetInteger(), CMRUList< string >::SetItems(), CISOJTALookupDlg::SetJournalList(), CPhyloTree::SetLeavesExplicitlySelected(), CPluginArg::SetList(), CBlobSplitterImpl::SetLoc(), CSeqGraphicPane::SetMarkers(), CWriteDB_Impl::SetMaskData(), CWGSDb_Impl::SetMasterDescr(), CDir::SetMode(), CUIToolRegistry::SetMRUToolNames(), CBlastDbSet::SetNegativeGiList(), CRemoteBlast::SetNegativeGIList(), COrgName::SetNomenclature(), CPluginArg::SetObject(), CSeqTableSetAnyObjField::SetObjectField(), CWiggleExporter::SetObjects(), CFastaAlignExporter::SetObjects(), CAlignTabExporter::SetObjects(), CFlatFileExporter::SetObjects(), CGtfExporter::SetObjects(), CAgpExporter::SetObjects(), CFastaExporter::SetObjects(), CGffExporter::SetObjects(), C5ColExporter::SetObjects(), CObjectListWidgetSel::SetObjects(), CConversionResultPanel::SetObjects(), CCrossPanelIR::SetObjectSelection(), CHitMatrixPane::SetObjectSelection(), CChain::SetOpenForPartialyAlignedProteins(), SetOrgMod(), CPluginArg::SetOutputFile(), CwxPhyloEditDlg::SetParams(), CwxPhyloSettingsDlg::SetParams(), variation::CVariationUtil::SetPlacementProperties(), CBlastDbSet::SetPositiveGiList(), CPluginArg::SetProject(), CRelaxedLookupDlg::SetPubdesc(), CMultiAligner::SetQueries(), CMultiAlignerTest::SetQuerySeqlocs(), CSeqTextPane::SetRangeSelection(), variation_ref::CVariationUtil::SetReferenceSequence(), CSearch< LEGACY, NHITS >::SetResult(), CCgiResponse::SetRetryContext(), CPhyloTreeWidget::SetRotateLabels(), CPhyloTreeWidget::SetScheme(), SetScores(), CPluginArg::SetSecretString(), CAlnMultiWidget::SetSelectedIds(), CDesktopCanvas::SetSelectedObjects(), CTextPanelContext::SetSelectedObjects(), CTaxTreeBrowser::SetSelectedUids(), CPhyloTree::SetSelectionIDs(), CPhyloSaveSelectiondlg::SetSelections(), CSeq_annot_SplitInfo::SetSeq_annot(), CwxTableListCtrl::SetSorterByColumns(), CSubmissionPrepMainPanel::SetSourceType(), CPluginArg::SetString(), CDisplaySeqalign::SetSubjectMasks(), SetSubsource(), CValidErrorFormat::SetSuppressionRules(), CSeqTableLocColumns::SetTableKeyAndIndex(), CBlast_def_line::SetTaxIds(), CTrackConfigManager::SetTrackConfig(), CValidError_imp::Setup(), LinkHspTestFixture::setupCutoffScores(), CGeneFinder::CGeneSearchPlugin::setUpFeatureIterator(), LinkHspTestFixture::setupLinkHspInputTblastn(), CPssmInputTestData::SetupQueryAlignedWithInternalGaps(), setupQueryStructures(), CPhyloTreeWidget::SetUseDistances(), CAuthorizedAccessPanel::SetUser_object(), CRefGeneTrackingPanel::SetUser_object(), CGridTableSeqIds::SetValue(), CAlnMultiModel::SetVisible(), sFilenameSetToString(), sGetCdsProductName(), NStr::ShellEncode(), CwxTableListCtrl::ShiftSorting(), CReadBlastApp::short_proteins(), CCleanup::ShouldStripPubSerial(), ShowFatal(), ShowOrgRef(), CGlBitmapFont::SizeFromString(), pub_report::CSkipPubUnpublishedHook::SkipObject(), pub_report::CSkipPubJournalHook::SkipObject(), CLDS2_AnnotType_Hook::SkipObject(), CReadInSkipObjectHook< Object >::SkipObject(), CLDS2_Annot_Hook::SkipObject(), SServerScanInfo::SkipServer(), SkipWeasel(), CMsvcSite::SLibChoice::SLibChoice(), CAlignCompare::SAlignment::Slice(), CEquivRangeBuilder::SliceOnQuery(), CEquivRangeBuilder::SliceOnSubjt(), CSelListModelImpl< Item >::SLM_SelectItems(), SLoadTokens::SLoadTokens(), CAlignSort::SortAlignments(), SortGBQuals(), CAlignFormatUtil::SortHitByTotalScoreDescending(), SortPrimerHitByMismatchAscending(), CAlignFormatUtil::SortSeqalignForSortableFormat(), CBDB_Volumes::SortVolumes(), SourceFile::SourceFile(), CSeqTextDataSource::SourcePosToSequencePos(), CSeqDB_FilterTree::Specialize(), CBlobSplitterImpl::Split(), CChainer::CChainerImpl::SplitAlignmentsByStrand(), CBlobSplitterImpl::SplitBioseq(), CTraversalNode::SplitByVarName(), CEquivRangeBuilder::SplitIntersections(), CSeq_align::SplitOnLongDiscontinuity(), CBlobSplitterImpl::SplitPieces(), CAlignFormatUtil::SplitSeqalignByMolecularType(), CAnchoredAln::SplitStrands(), CTextUtil::SplitWordFrequencies(), sPrepareSeqAlign(), sReadAA_I(), CAlnMixSegment::StartItsConsistencyCheck(), CServer_ConnectionPool::StartListening(), CTextSelHandler::STGH_GetMouseOverFeatureSubtypes(), CTextSelHandler::STGH_GetSelectedFeatureSubtypes(), CServer_ConnectionPool::StopListening(), CReadBlastApp::StoreBlast(), StrictlyContainedInDels(), CAlignFormatUtil::StringGiToNumGiList(), CSuspect_rule::StringMatchesSuspectProductRule(), CDirEntry::StringToMode(), CSeqDBIsam::StringToOids(), CGridCommandLineInterfaceApp::SubmitJob_Batch(), CNetScheduleSubmitter::SubmitJobBatch(), SubtractAlnRngCollections(), CSimpleDictionary::SuggestAlternates(), CMultiDictionary::SuggestAlternates(), CDiscrepancyCase_SOURCE_QUALS::Summarize(), CDiscrepancyCase_FEATURE_COUNT::Summarize(), CDiscrepancyCase_CITSUBAFFIL_CONFLICT::Summarize(), CDiscrepancyCase_INCONSISTENT_BIOSOURCE::Summarize(), CSuspect_rule::SummarizeConstraintSet(), SummarizeIdProblems(), CSuspect_rule::SummarizeStringConstraint(), sUpdateAll(), sx_AddSplitIds(), sx_AllDigits(), sx_Assign(), sx_ComesBefore(), CRequestContext::sx_GetContextFieldsMask(), sx_GetSize(), CNcbiEncrypt::sx_InitKeyMap(), sx_IsNABlobId(), CTableNames::TableToName(), CSeq_entry_EditHandle::TakeAllAnnots(), TaxonomyLookupCommand(), CDbTest::Test(), CDirTest::Test(), TestBulkSpecificHostFixList(), CCompareWithBiosample::TestCookie(), CFormatGuess::TestFormatAgp(), CFormatGuess::TestFormatAlignment(), CFormatGuess::TestFormatBed(), CFormatGuess::TestFormatBed15(), CFormatGuess::TestFormatFiveColFeatureTable(), CFormatGuess::TestFormatFlatFileSequence(), CFormatGuess::TestFormatNewick(), CFormatGuess::TestFormatPhrapAce(), CFormatGuess::TestFormatSnpMarkers(), CFormatGuess::TestFormatVcf(), CFormatGuess::TestFormatWiggle(), CFastaExporterFactory::TestInputObjects(), CGtfExporterFactory::TestInputObjects(), CAsnExporterFactory::TestInputObjects(), CFlatFileExporterFactory::TestInputObjects(), CAlignTabExporterFactory::TestInputObjects(), CFastaAlignExporterFactory::TestInputObjects(), CPhyExporterFactory::TestInputObjects(), CAgpExporterFactory::TestInputObjects(), C5ColExporterFactory::TestInputObjects(), CGffExporterFactory::TestInputObjects(), CWiggleExporterFactory::TestInputObjects(), testNuclHitList(), CTestAction::TestOID(), CSplitCacheApp::TestSplit(), CSplitCacheApp::TestSplitBlob(), CGlBitmapFont::TextOut(), CCigar::ToAlign(), CQuerySet::ToBestSeqAlignSet(), CAlignResultsSet::ToBestSeqAlignSet(), CSplign::SAlignedCompartment::ToBuffer(), CSplitCDSwithTooManyXs::TooManyXs(), CQuerySet::ToSeqAlignSet(), CAlignResultsSet::ToSeqAlignSet(), CTraversalSpecFileParser::CDescFileNode::ToString(), TSearchMessages::ToString(), CNamespace::ToStringTo(), CTable2AsnValidator::TotalErrors(), TotalFrameShift(), CHandleRangeMap::TotalRangeIntersectingWith(), TotalRawScore(), TotalScore(), CBLASTParams::ToUserObject(), CComplexRelation::ToUserObject(), CIndexedDb_New::TraceNames(), CIndexedDb_New::TraceVolumes(), CNGAlignPanel::TransferDataFromWindow(), CFeatureCreateDialog::TransferDataFromWindow(), CSingleAssemblyTrackingPanel::TransferDataToWindow(), CImportMacros_dlg::TransferDataToWindow(), CSingleRefGeneTrackLocPanel::TransferDataToWindow(), CCrossRefFeatsDlg::TransferDataToWindow(), CCitationsPanel::TransferDataToWindow(), CUserFieldListPanel::TransferDataToWindow(), CFilterDialog::TransferDataToWindow(), CDbxrefPanel::TransferDataToWindow(), CStructuredCommentPanel::TransferDataToWindow(), CSequencingTechnologyPanel::TransferDataToWindow(), CCDSTranslationPanel::TransferDataToWindow(), CRemarksAndSerialNumberPanel::TransferDataToWindow(), CMatchFeatureTableDlg::TransferDataToWindow(), CLocationPanel::TransferDataToWindow(), CObjectListWidgetSel::TransferDataToWindow(), CSourceOtherPanel::TransferFromOrgRef(), CGBQualStringListValidator::TransferToWindow(), CCodonsStringListValidator::TransferToWindow(), CUserFieldStringListValidator::TransferToWindow(), CFeatureGenerator::SImplementation::TransformProteinAlignToTranscript(), CSeqTranslator::Translate(), CSeqTranslator::TranslateToProtein(), TraverseAndRunTestCases(), CNSInfoCollector::TraverseNodes(), TreeConvert2Container(), TreeConvert2ContainerPartial(), TreeConvertNonSingleChild2Container(), TreeConvertSelected2Container(), TreeReRoot(), CChainer::CChainerImpl::TrimAlignmentsIncludedInDifferentGenes(), TrimEntry(), CSplignTrim::TrimHolesToCodons(), TruncateToCDS(), CDllResolver::TryCandidate(), TryToSanitizeHtml(), TSeqLocVector2Bioseqs(), TSeqLocVector2Packed_seqint(), CResetIds_EditCommand::Undo(), CCodeGenerator::UndoGenerateCode(), NWinHook::CHookedFunctions::UnHookAllFuncs(), CProjectTask::UnLoadProjects(), CMemoryFileMap::UnmapAll(), CAlignMarkHandler::UnMarkSelected(), CHitMatrixRenderer::Update(), CEntrezSearchForm::Update(), CFeatureSearchForm::Update(), CFeatHistogramDS::Update(), CDiscrepancyContext::Update_Bioseq_set_Stack(), CDiscrepancyDlg::UpdateButtons(), CSeqTableGridPanel::UpdateColumnChoices(), impl::CDriverContext::UpdateConnMaxBlobSize(), impl::CDriverContext::UpdateConnTimeout(), CSearchFormBase::UpdateContexts(), CLDS2_Manager::UpdateData(), CProjBulderApp::UpdateDepGraph(), PT::CProjectFolder::UpdateDisabledItems(), COrg_ref::UpdateFromTable(), CAlignRangeCollExtender< TAlnRngColl >::UpdateIndex(), CValidateFrame::UpdateList(), CwxMarkerInfoDlg::UpdateMarker(), CRecentToolList::UpdateMenu(), CQuickLaunchList::UpdateMenu(), CSDBAPI::UpdateMirror(), CPhyloTree::UpdateNodesMapping(), PT::CProjectFolder::UpdateProjectItems(), CQualApplyPanel::UpdateQualChoices(), CSelectionVisitor::UpdateSelection(), CSeqTableInfo::UpdateSeq_feat(), CSeqTableLocColumns::UpdateSeq_loc(), CGeneModelConfig::UpdateSettings(), CwxTableListCtrl::UpdateSortIcons(), CScoreLookup::UpdateState(), CDiscrepancyDlg::UpdateTestList(), UpdateToBestId(), CBioSource::UpdateWithBioSample(), CProjBulderApp::UseAbsolutePath(), CBlastQueryFilteredFrames::UseProteinCoords(), CTable2AsnValidator::Validate(), CSpliced_seg::Validate(), CSparse_seg::Validate(), CMolTypeValidator::Validate(), CValidError_imp::Validate(), CSeq_align::Validate(), CCddInputData::CHitSegment::Validate(), CGumbelParamsOptions::Validate(), CCddInputData::CHit::Validate(), NTweakExon::Validate(), CMultiAlignerOptions::Validate(), CValidError_imp::ValidateAuthorList(), CValidError_bioseq::ValidateBioseqContext(), CValidError_imp::ValidateBioSource(), CValidError_imp::ValidateBioSourceForSeq(), CValidError_feat::ValidateCDSPartial(), CValidError_bioseq::ValidateCDSUTR(), CValidError_imp::ValidateCitations(), CValidError_bioseq::ValidateCollidingGenes(), CValidError_bioseq::ValidateCompleteGenome(), CValidError_desc::ValidateDblink(), CValidError_imp::ValidateDbxref(), CValidError_bioseq::ValidateDelta(), CValidError_bioseq::ValidateDupOrOverlapFeats(), CValidError_feat::ValidateExceptText(), CValidError_feat::ValidateExtUserObject(), CValidError_feat::ValidateFeatCit(), CValidError_feat::ValidateGene(), CValidError_feat::ValidateGeneXRef(), CValidError_feat::ValidateGoTerms(), CValidError_bioseq::ValidateHistory(), CValidError_bioseq::ValidateIDSetAgainstDb(), CValidError_feat::ValidateImp(), CValidError_feat::ValidateLabelVal(), CSeqDB::ValidateMaskAlgorithms(), CValidError_bioseq::ValidateMultiIntervalGene(), CValidError_bioseq::ValidateMultipleGeneOverlap(), CValidError_imp::ValidateMultipleTaxIds(), CValidError_feat::ValidateNonImpFeat(), CAsnvalApp::ValidateOneDirectory(), CValidError_imp::ValidateOrgModVoucher(), CValidError_imp::ValidatePCRReactionSet(), CValidError_feat::ValidateRptUnitVal(), CValidError_bioseq::ValidateSegRef(), CValidError_align::ValidateSeqAlign(), CValidError_annot::ValidateSeqAnnot(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_bioseq::ValidateSeqFeatContext(), CValidError_bioseq::ValidateSeqGap(), CValidError_bioseq::ValidateSeqId(), CValidError_bioseq::ValidateSeqParts(), CValidError_feat::ValidateTrnaCodons(), CValidError_desc::ValidateUser(), CValidError_bioseq::ValidateWGSMaster(), CEnumeratedTypeValues::ValueToName(), CMultAlign::Variations(), CLinkage_evidence::VecToString(), CArgAllow_Symbols::Verify(), CArgAllow_String::Verify(), CArgAllow_Int8s::Verify(), CArgAllow_Doubles::Verify(), CProjectTreeBuilder::VerifyBuildOrder(), CProjectItemsTree::VerifyExternalDepends(), SMakeProjectT::VerifyLibDepends(), VisitAllSeqSets(), CSeqDBAliasNode::WalkNodes(), CDemoApp::WalkPrimitive(), CCountries::WasValid(), CPluginManager< TClass >::WillExtendCapabilities(), NStr::WrapList(), CBlastDbFormatter::Write(), CSeq_annot_SNP_Info_Reader::Write(), CBlastDB_SeqFormatter::Write(), CStackTrace::Write(), CSimpleDictionary::Write(), IRegistry::Write(), CMakeNode::Write(), CMakeProperty::Write(), CMakeProject::Write(), CCgiCookies::Write(), CBinaryListBuilder::Write(), CFastaOstream::Write(), CUCSCRegionWriter::WriteAnnot(), CBedWriter::WriteAnnot(), CNCServer::WriteAppSetup(), CSeq_id::WriteAsFasta(), CSearch< LEGACY, NHITS >::WriteBioseqs(), CObjectOStreamAsn::WriteBitString(), CNCBlobStorage::WriteBlobList(), CAsnSubCacheCreateApplication::WriteBlobsInSubCache(), CNCBlobStorage::WriteBlobStat(), CWriter::WriteBytes(), CFtableWriteHook::WriteChoiceVariant(), CClassCode::WriteConstructionCode(), WriteContainer(), CNCBlobStorage::WriteDbInfo(), CClassCode::WriteDestructionCode(), WriteEnvironment(), CId1FetchApp::WriteFastaIDs(), CHttpFormData::WriteFormData(), CCgiResponse::WriteHeader(), CId1FetchApp::WriteHistoryTable(), WriteMap(), CWriteDB_GiMaskData::WriteMask(), CStyledTextOStream::WriteMultiLineText(), CMsvcConfigure::WriteNcbiconfMsvcSite(), CPageHandler::WritePages(), CCacheWriter::WriteSeq_ids(), CWriteDB_Volume::WriteSequence(), CNCDistributionConf::WriteSetup(), CFileCode::WriteSourceFile(), CFileCode::WriteSpecRefs(), CFileCode::WriteUserFile(), CPdfObjectWriter::WriteXRef(), CSimpleProjectView::x_ActivateTextView(), CNcbiTestApplication::x_ActualizeDeps(), CFlatSeqLoc::x_Add(), CSeqMap::x_Add(), CIdMapperGCAssembly::x_AddAliasMappings(), CAlnTableDS::x_AddAlign(), CNgAlignApp::x_AddAligners(), CSeq_annot_Info::x_AddAlignKeys(), CPhrap_Contig::x_AddAlignRanges(), CTSE_Info::x_AddAllFeaturesById(), CReferenceItem::x_AddAuthors(), CPhrap_Contig::x_AddBaseSegFeats(), CGC_Assembly_Parser::x_AddBioseq(), CTraversalMerger::x_AddCallersToTier(), CLinkUtils::x_AddDbxrefFeatureLinks(), CBlastTabularInfo::x_AddDefaultFieldsToShow(), CNewCleanup_imp::x_AddEnvSamplOrMetagenomic(), CProductStringBuilder::x_AddExon(), CDllResolver::x_AddExtraDllPath(), CFeat_CI::x_AddFeatures(), CFeatureTrack::x_AddFeaturesLayout(), CNgAlignApp::x_AddFilters(), CFeatureItem::x_AddFTableBiosrcQuals(), CFeatureItem::x_AddFTableCdregionQuals(), CFeatureItem::x_AddFTableDbxref(), CFeatureItem::x_AddFTableExtQuals(), CFeatureItem::x_AddFTableGeneQuals(), CFeatureItem::x_AddFTableProtQuals(), CFeatureItem::x_AddFTableQuals(), CBulkOtherAddPanel::x_AddGeneQuals(), CAlignOtherAddPanel::x_AddGeneQuals(), CWriteDB_IsamIndex::x_AddGis(), CFeatureItem::x_AddGoQuals(), CGBDocument::x_AddItems(), CGuiObjectInfoSeq_feat::x_AddLocationRows(), CIdMapperScope::x_AddMappings(), CBuildDatabase::x_AddMasksForSeqId(), CAutoDefModifierCombo::x_AddMinicircle(), CAutoDef::x_AddMiscRNAFeatures(), CNewCleanup_imp::x_AddNonCopiedQual(), CAutoDefModifierCombo::x_AddOrgModString(), CMergedPairwiseAln::x_AddPairwise(), CFastaReader::x_AddPairwiseAlignments(), CSourceFeatureItem::x_AddPcrPrimersQuals(), CDBSourceItem::x_AddPIRBlock(), CAnnot_Collector::x_AddPostMappingsCvt(), CFeatureItem::x_AddProductIdQuals(), SWGSCreateInfo::x_AddProducts(), CFeatureItem::x_AddQualCdsProduct(), CFeatureItem::x_AddQualDbXref(), CFeatureItem::x_AddQualExceptions(), CSourceQualifiersReader::x_AddQualifiers(), CFeatureItem::x_AddQualProtActivity(), CFeatureItem::x_AddQualProtEcNumber(), CBulkOtherAddPanel::x_AddQuals(), CFeatureItem::x_AddQuals(), CSourceFeatureItem::x_AddQuals(), CAlignOtherAddPanel::x_AddQuals(), CFeatureItem::x_AddQualSeqfeatNote(), CFeatureItem::x_AddQualsExt(), CFeatureItem::x_AddQualsGene(), CFeatureItem::x_AddQualsProt(), CFeatureItem::x_AddQualsRegion(), CFeatureItem::x_AddQualsRna(), CFeatureItem::x_AddQualsVariation(), CPhrap_Contig::x_AddReadLocFeats(), CConvertFeatureBase::x_AddRnaDestinationConversionOptions(), CMultiAligner::x_AddRpsFreqsToCluster(), CFeatureItem::x_AddRptTypeQual(), CNgAlignApp::x_AddScorers(), CSnpTrack::x_AddSnpsLayout(), CDBSourceItem::x_AddSPBlock(), CNCStat::x_AddStats(), CSrvStat::x_AddStats(), CWriteDB_IsamIndex::x_AddStringIds(), CAutoDefModifierCombo::x_AddSubsourceString(), CPhrap_Read::x_AddTagFeats(), CPhrap_Contig::x_AddTagFeats(), CNcbiTestTreeElement::x_AddToMustLeft(), CNcbiTestTreeElement::x_AddToMustRight(), CDescPlacementPanel::x_AddToStrings(), CWriteDB_IsamIndex::x_AddTraceIds(), CAutoDef::x_AddtRNAAndOther(), CDataSource::x_AddTSEAnnots(), CDataSource::x_AddTSEBioseqAnnots(), CDataSource::x_AddTSEOrphanAnnots(), CScope_Impl::x_AddTSESetWithAnnots(), CGuiObjectInfoSeq_align::x_AddUserObject(), CSeqTextDataSourceInterval::x_AddVariationsFromFeature(), CBlastDBAliasApp::x_AddVDBsToAliasFile(), CSeq_loc_Mapper::x_AddVirtualBioseq(), x_AdjustAnchorDirection(), CAlnTableDS::x_AdjustColumns(), CSeq_loc_Mapper_Base::x_AdjustSeqTypesToProt(), CNgAligner::x_Align_Impl(), CMultiAligner::x_AlignClusterQueries(), CMultiAligner::x_AlignFillerBlocks(), CMultiAligner::x_AlignInClusters(), CMultiAligner::x_AlignMSAs(), CMultiAligner::x_AlignProfileProfileUsingHit(), CQuerySet::x_AlreadyContains(), CAdjustForConsensusSplice::x_AlsoAdjustmRNA(), CIgBlast::x_AnnotateDomain(), CIgBlast::x_AnnotateV(), CFlatGatherer::x_AnnotComments(), CTraversalPatternMatchCallback::x_AnyPatternMatches(), CArchive::x_Append(), CTar::x_Append(), CTraversalMerger::CNodeLabeler::x_AppendDirectNodeLabel(), CTrackConfigManager::x_AppendKeyDisplayOptions(), CTraversalMerger::CNodeLabeler::x_AppendNodeLabelRecursively(), CRegistryReadView::x_AppendToReadView(), CMakeBadSpecificHostTable::x_AppendToTable(), CGuiRegistry::x_AppendToView(), CFastaReader::x_ApplyAllMods(), x_ApplyCmd(), CSourceModParser::x_ApplyGenomeProjectsDBMods(), CSourceModParser::x_ApplyMods(), CDataLoaderPatcher::x_ApplyPatches(), CSourceModParser::x_ApplyTPAMods(), SGridWorkerNodeImpl::x_AreMastersBusy(), CCleanupAlignmentsToolManager::x_AreSelfAlignmentsOnly(), variation_ref::CHgvsParser::x_AsHgvsExpression(), variation::CHgvsParser::x_AsHgvsExpression(), variation::CHgvsParser::x_AsHgvsInstExpression(), x_Assign(), CFeatTree::x_AssignParents(), CFeatTree::x_AssignParentsByOverlap(), CGBDocument::x_AssignViewIndex(), variation::CVariationUtil::x_AsVariation(), variation::CVariationUtil::x_AsVariation_ref(), CSplitParser::x_Attach(), CMultiAligner::x_AttachClusterTrees(), CProjectViewBase::x_AttachToProject(), CBioseq_ScopeInfo::x_AttachTSE(), CDiscRepApp::x_Autofix(), CCleanupApp::x_BasicAndExtended(), CAutoDefModifierCombo::x_BioSourceHasOrgMod(), CAutoDefModifierCombo::x_BioSourceHasSubSrc(), CTL_BCPInCmd::x_BlkSetHints(), CBl2Seq::x_BuildAncillaryData(), CWriteDB_Impl::x_BuildDeflinesFromBioseq(), CSeqFormatter::x_Builder(), CObjectConverter::x_BuildGraph(), CVecscreen::x_BuildHtmlBar(), CAlnGraphic::x_BuildHtmlTable(), CDumpASNIndex::x_BuildIndexAndSeqIdInfo(), CInlineLayout::x_BuildLayout1Row(), CSeqDBImpl::x_BuildMaskAlgorithmList(), CWriteDB_ColumnIndex::x_BuildMetaData(), CTraversalCodeGenerator::x_BuildNameToASNMap(), CVecscreen::x_BuildNonOverlappingRange(), x_BuildRelations(), CBlobCacher::x_CacheMetaRec(), CGapStatsApplication::x_CalcAllGapLens(), CTabularFormatter_BiggestGapBases::x_CalcBiggestGap(), CBioseq_Info::x_CalcBioseqLength(), CPhyTreeCalc::x_CalcDivergenceMatrix(), CSGCalcFeatHistJob::x_CalcFeatHistRecursive(), CLinkedFeatsGroup::x_CalcIntervals(), CScoringJob::x_CalculateAlignmentScores(), CAlignDistGraph::x_CalculateAllDistances(), CColumnScoringMethod::x_CalculateConsensusScores(), CAlignDistGraph::x_CalculateOneDistance(), CSeq_loc::x_CalculateTotalRangeCheckId(), CNcbiTestApplication::x_CallUserFuncs(), CTSE_Split_Info::x_CanAddBioseq(), CClusterer::x_CanAddElem(), CThreadPool_Impl::x_CancelExecutingTasks(), CScopeTransaction_Impl::x_CanCommitRollBack(), CClusterer::x_CanJoinClusters(), CFileLoadWizard::x_CanLeavePage(), CFileLoadManager::x_CanLeavePage(), CNewCleanup_imp::x_CanRemoveGenbankBlockSource(), CGencollIdMapper::x_CanSeqMeetSpec(), CReferenceItem::x_CapitalizeTitleIfNecessary(), CInfoCache_Base::x_Check(), CInfoCache< KeyType, DataType >::x_Check(), CMacroFunction_StringConstraints::x_CheckConstraintObjects(), CDiagFilter::x_CheckErrCode(), CReportEntry::x_CheckExonGap(), CDiagFilter::x_CheckFile(), CCDSTranslationProblems::x_CheckForRaggedEnd(), CBioseqContext::x_CheckForShowComments(), CShowBlastDefline::x_CheckForStructureLink(), CValidError_bioseq::x_CheckGeneralIDs(), CSeq_loc::x_CheckId(), CFeatureGenerator::SImplementation::x_CheckInconsistentDbxrefs(), CDiagFilter::x_CheckLocation(), CValidError_bioseq::x_CheckOrigProteinAndTranscriptIds(), CValidError_imp::x_CheckPackedInt(), CCgiUserAgent::x_CheckPattern(), CNCActiveSyncControl::x_CheckSlotOurSync(), CNCActiveSyncControl::x_CheckSlotTheirSync(), CSeqDBVol::x_CheckVersions(), CSourceFieldNamePanel::x_ChooseTextQualifier(), CBlobCacher::x_CleanOrphanRecs(), CDBAPI_Cache::x_CleanOrphantBlobs(), CFeatureItem::x_CleanQuals(), CNCActiveSyncControl::x_CleanSyncObjects(), CAlignCleanup::x_Cleanup_AlignVec(), CAlignCleanup::x_Cleanup_AnchoredAln(), CNewCleanup_imp::x_CleanupGenbankBlock(), CElementaryMatching::x_CleanVolumes(), CGetFeature::x_Clear(), CClipboard::x_Clear(), CHitMatrixDataSource::x_Clear(), CAlignedFeatureGraph::x_Clear(), CCompoundRWRegistry::x_Clear(), CScope_Impl::x_ClearCacheOnNewData(), CScope_Impl::x_ClearCacheOnRemoveSeqId(), CHitMatrixDataSource::x_ClearHits(), CSubPrep_panel::x_ClearWizardSpecificData(), CTraversalNode::x_CloneWithoutCallers(), CMemoryFileMap::x_Close(), CGBDocument::x_CloseProjectItemViews(), CNewCleanup_imp::x_CollapseSet(), CDataSource::x_CollectBioseqs(), CAnnot_Collector::x_CollectMapped(), x_CollectMembers(), CPrimaryItem::x_CollectSegments(), CAnnot_Collector::x_CollectSegments(), CRangeCollection< TSeqPos >::x_CombineWith(), x_CompareConsecutiveIntervals(), CRegexpTemplateTester::x_CompareLines(), CValidError_bioseq::x_CompareStrings(), CElementaryMatching::x_CompartPair(), CSeqDBOIDList::x_ComputeFilters(), CFeaturePanel::x_ConfigureSubtracks_Recursive(), CFeaturePanel::x_ConfigureTracks(), CAlnMixSegments::x_ConsolidateGaps(), CQuerySet::x_ContainsAlignment(), CTSE_Chunk_Info::x_ContainsFeatType(), CSeq_align_Mapper_Base::x_ConvertSegment(), CSplitDblinkQuals::x_ConvertStrsToStrs(), CSplitDblinkQuals::x_ConvertStrToStrs(), CConvertFeatureBase::x_ConvertToCDS(), CWriteDB_Impl::x_CookIds(), CFlatGatherer::x_CopyCDSFromCDNA(), CGC_Assembly_Parser::x_CopyData(), CPsiBlastInputClustalW::x_CopyQueryToMsa(), CValidError_bioseq::x_CountAdjacentNs(), CMergeTree::x_CountChildLinks(), CMergeTree::x_CountChildNodes(), CFeatureTrack::x_CountFeats_recursive(), CDeltaBlastTestFixture::x_CountNumberUniqueIds(), CSeq_id_Resolver__LRG::x_Create(), CPhrap_Contig::x_CreateAlignAll(), CPhrap_Contig::x_CreateAlignOptimized(), CPhrap_Contig::x_CreateAlignPairs(), CMultiAligner::x_CreateBlastQueries(), CAsn2FlatApp::x_CreateCancelBenchmarkCallback(), CFeatureGenerator::SImplementation::x_CreateCdsFeature(), CWGSSeqIterator::x_CreateChunk(), CSGFeatureJob::x_CreateCloneFeature(), CProjectTreePanel::x_CreateDataObject(), CAlnMixMerger::x_CreateDenseg(), CPhrapReader::x_CreateDesc(), CSeqDesktopPanel::x_CreateEditor(), CTextPanel::x_CreateEditor(), CFeatureGenerator::SImplementation::x_CreateGeneFeature(), CGFFReader::x_CreateGeneFeatures(), CFeature_table_reader_imp::x_CreateGenesFromCDSs(), CHitMatrixDataSource::x_CreateIds(), CLDBlockTrack::x_CreateLayout(), CHapmapTrack::x_CreateLayout(), CFeatureGraph::x_CreateMapRanges(), CTraversalCodeGenerator::x_CreateNode(), CSGAlignStatJob::x_CreatePileUpGraphs(), CAlnMultiWidget::x_CreatePopupMenu(), CSeqGraphicWidget::x_CreatePopupMenu(), CNGAlignJob::x_CreateProjectItems(), CTaxTreeToolJob::x_CreateProjectItems(), CBLASTSeqToolJob::x_CreateProjectItems(), CProSplignJob::x_CreateProjectItems(), CMSAToolJob::x_CreateProjectItems(), CCleanupAlignmentsJob::x_CreateProjectItems(), CGroupAlignmentsJob::x_CreateProjectItems(), CMergeAlignmentsJob::x_CreateProjectItems(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CBamLoadingJob::x_CreateProjectItems(), CFindOverlapJob::x_CreateProjectItems(), CCleanupJob::x_CreateProjectItems(), CSrcEditJob::x_CreateProjectItems(), CSplignJob::x_CreateProjectItems(), CWindowMaskerJob::x_CreateProjectItems(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), SWGSCreateInfo::x_CreateProtSet(), CObjConvProfile::x_CreateRelatedMap(), CSelectProjectOptions::x_CreateSeparateProjects(), CPhrap_Contig::x_CreateSeq_align(), CNgAlignApp::x_CreateSequenceSet(), CRunToolDlg::x_CreateToolItems(), CGeneModelFactory::x_CreateTracksWithFilters(), CDiagContext::x_CreateUID(), CReferenceItem::x_CreateUniqueStr(), CPhyTreeCalc::x_CreateValidAlign(), CReportTrim::x_CutDensegSegment(), CVectorTrimPanel::x_CutDensegSegment(), CBlastDB_SeqFormatter::x_DataRequired(), COrfSearchJob::x_DecodeGeneticCode(), CProjectServiceTestJob::x_DeleteItems(), CBlobCacher::x_DelFileAndRetryCreate(), CBioseq_ScopeInfo::x_DetachTSE(), CShowBlastDefline::x_DisplayDefline(), CShowBlastDefline::x_DisplayDeflineTableBody(), CShowBlastDefline::x_DisplayDeflineTableTemplate(), CTraversalPatternMatchCallback::x_DoAttachment(), CValidError_imp::x_DoBarcodeTests(), CNCMessageHandler::x_DoCmd_Health(), CNCMessageHandler::x_DoCmd_SyncStart(), CImportFeatTable::x_DoImportFeaturesFromFile(), CServer::x_DoRun(), CSNPSearchJob::x_DoSearch(), CComponentSearchJob::x_DoSearch(), CCpgSearchJob::x_DoSearch(), COrfSearchJob::x_DoSearch(), CSequenceSearchJob::x_DoSearch(), CSelectionVisitor::x_DoSelection(), CMergeTree::x_Dot_Edges(), CMergeTree::x_Dot_Nodes(), CTraversalMerger::x_DoTier(), CCompartApp::x_DoWithExternalHits(), CDownloadJob::x_DownloadAndExtract(), CTranslationGlyph::x_Draw(), CScatterPlotGlyph::x_Draw(), CGeneMarkerGlyph::x_Draw(), CSegmentGlyph::x_Draw(), CMatePairGlyph::x_Draw(), CClonePlacementGlyph::x_Draw(), CLayoutGroup::x_Draw(), CHistogramGlyph::x_Draw(), CAlnStatGlyph::x_DrawBarGraph(), CLinkedFeatsGroup::x_DrawChildrenOnParent(), CCrossPanelIR::x_DrawCrossAlignment(), CAlnStatGlyph::x_DrawDensityTable(), CLinkedFeatsGroup::x_DrawFeatureBar(), CAxisRenderer::x_DrawHorzLabels(), CLinkedFeatsGroup::x_DrawLabels(), CAlignGlyph::x_DrawMultiAlign(), CAlignGlyph::x_DrawNonConsensusSpliceSites(), CAlignGlyph::x_DrawNoScoreAlign(), CFeatGlyph::x_DrawProjectedRuler(), CFeatGlyph::x_DrawRuler(), CCrossPanelIR::x_DrawSequence(), CTSE_Info::x_DSAttachContents(), CTSE_Info::x_DSDetachContents(), CAppHitFilter::x_DumpOutput(), CAppPackagesDlg::x_DumpPkgInfo(), CId2ReaderBase::x_DumpReply(), CAsnSubCacheCreateApplication::x_EliminateIdsAlreadyInCache(), CEnvironmentRegistry::x_Empty(), CTrackContainer::x_Empty(), CNcbiTestApplication::x_EnableAllTests(), CBuildDatabase::x_EndBuild(), CDB_Exception::x_EndOfWhat(), CNcbiTestApplication::x_EnsureAllDeps(), CNcbiTestTreeElement::x_EnsureChildOrder(), CEntropyCalculator::x_Entropy(), CEnvironmentRegistry::x_Enumerate(), CMemoryRegistry::x_Enumerate(), CCompoundRegistry::x_Enumerate(), CCompoundRWRegistry::x_Enumerate(), CCompartApp::CCompartment::x_EvalExons(), CSGSwitchPointJob::x_Execute(), CSGCalcFeatHistJob::x_Execute(), CNewCleanup_imp::x_ExtendSingleGeneOnMrna(), CPsiBlastInputData::x_ExtractAlignmentData(), CPrimeCacheApplication::x_ExtractAndIndex(), CPrimeCacheApplication::x_ExtractDelta(), CArchive::x_ExtractEntry(), CBlastFormatterApp::x_ExtractQueries(), CPsiBlastInputClustalW::x_ExtractQueryFromMsa(), CRemoteBlast::x_ExtractQueryIds(), CTableDataValidateJob::x_FetchAll(), CSnpJob::x_FetchGraphs(), CAsnSubCacheCreateApplication::x_FetchMissingBlobs(), CGencollIdMapper::x_FillChromosomeIds(), CShowBlastDefline::x_FillDeflineAndId(), CDisplaySeqalign::x_FillInserts(), CSeq_align_Mapper_Base::x_FillKnownStrands(), CLocationPanel::x_FillList(), CSrcModListPanel::x_FillList(), CDisplaySeqalign::x_FillLocList(), CSDB_ConnectionParam::x_FillLowerParams(), CSDB_ConnectionParam::x_FillParamMap(), CProSplignJob::x_FilterCompartments(), CNAUtils::x_FilterNAIds(), CVectorScreen::x_FindAccession(), CMergeTree::x_FindAfters(), CMergeTree::x_FindAfters_Up(), variation::CHgvsParser::x_FindAssertedSequence(), CTblEditDlg::x_FindBadImportColumns(), CMergeTree::x_FindBefores(), CMergeTree::x_FindBefores_Up_Iter(), CMergeTree::x_FindBefores_Up_Recur(), CDataSource_ScopeInfo::x_FindBestTSE(), CDataSource::x_FindBestTSE(), CScope_Impl::x_FindBioseqInfo(), CGencollIdMapper::x_FindChromosomeSequence(), CBlastServices::x_FindDbInfoFromAvailableDatabases(), CIgBlast::x_FindDJAln(), CSeq_id_Giim_Tree::x_FindInfo(), CSeq_id_PDB_Tree::x_FindInfo(), CMinPanelContainer::x_FindItemByPanel(), CMergeTree::x_FindLeafs(), CVectorScreen::x_FindLocalId(), CMultiAligner::x_FindLocalInClusterHits(), CConvertFeatureBase::x_FindOption(), variation::CVariationUtil::x_FindOrCreateLiteral(), CProjectFileWriter::x_FindParent(), CGencollIdMapper::x_FindParentSequence(), CTaxon2_data::x_FindPropertyConst(), CMultiAligner::x_FindQueryClusters(), CMetaRegistry::x_FindRegistry(), CObjectConverter::x_FindRelationByName(), CMultiAligner::x_FindRPSHits(), x_FindRSite(), CTSE_Info::x_FindSeq_feat(), CValidError_feat::x_FindStartOfGap(), CVectorScreen::x_FindTypeGeneral(), CTracebackSearchTestFixture::x_FindUsedGis(), CSeqDBAliasNode::x_FindVolumePaths(), CSequenceAmbigTrimmer::x_FindWhereToTrim(), CUnorderedSplitter::x_FixAlignment(), CUpdateSeq_Input::x_FixCollidingIDs_Bioseq(), CProcessor_ID2::x_FixCompression(), CSequenceUpdater::x_FixIDInNewEntry(), CSeq_loc_Mapper_Base::x_ForceSeqTypes(), CGuiObjectInfoClone::x_FormatAccessionLinks(), CCIGAR_Formatter::x_FormatAlignmentRows(), CDisplaySeqalign::x_FormatAlnHSPLinks(), CDisplaySeqalign::x_FormatDefLinesHeader(), CShowBlastDefline::x_FormatDeflineTableLine(), CDisplaySeqalign::x_FormatDynamicFeaturesInfo(), CValidErrorFormat::x_FormatECNumberForSubmitterReport(), CFeatureItem::x_FormatGOQualCombined(), CAlnGraphic::x_FormatGraphOverview(), CDBSourceItem::x_FormatPDBSource(), CFtableFormatter::x_FormatQuals(), CAlignFilter::x_FuncCall(), CSequenceUpdater::x_FuseProtFeatsForCDS(), CFlatGatherer::x_GatherCDSReferences(), CAlignedFeatureGraph::x_GatherCluster(), CDBSourceItem::x_GatherInfo(), CContigItem::x_GatherInfo(), CVersionItem::x_GatherInfo(), CGenomeProjectItem::x_GatherInfo(), CKeywordsItem::x_GatherInfo(), CAccessionItem::x_GatherInfo(), CReferenceItem::x_GatherInfo(), CFlatGatherer::x_GatherReferences(), CReferenceItem::x_GatherRemark(), CFlatGatherer::x_GatherSourceFeatures(), CGenbankGatherer::x_GatherTLS(), CGenbankGatherer::x_GatherTSA(), CGenbankGatherer::x_GatherWGS(), CProSplignJob::x_GenerateCompartments(), CTraversalCodeGenerator::x_GenerateHeaderFile(), CAxisRenderer::x_GenerateLabels(), CTraversalCodeGenerator::x_GenerateSourceFile(), CMatchTabulate::x_GetAccessionVersion(), CScope::x_GetAccVer(), CHitMatrixDataSource::x_GetAlignedSeqIds(), CApplyRNAITSDlg::x_GetAlignments(), CNAUtils::x_GetAllGIs(), CSeqDBVol::x_GetAmbigSeq(), CFlatGatherer::x_GetAnnotDescStrucCommentFromBioseqHandle(), CProjectFileWriter::x_GetAnnotId(), CSeq_entry_Info::x_GetAnnotIds(), CAlignmentSmear::x_GetAnnotName(), CAnnot_Collector::x_GetAnnotNames(), CAssemblyInfo::x_GetAssmInfo(), CBamUILoadManager::x_GetBamRefSeqs(), CPkgManager::x_GetBasePkgs(), CFastaOstream::x_GetBestId(), CWriteDB_Impl::x_GetBioseqBinaryHeader(), CSeq_entry_Info::x_GetBioseqsIds(), CSplignApp::x_GetBl2SeqHits(), CID2CDDProcessor_Impl::x_GetBlobId(), CSeqGraphicPane::x_GetCachedTipId(), CConvertFeatureBase::x_GetCDSProduct(), CDensegGraphicDataSource::x_GetCigarStr(), CInstancedAligner::x_GetCleanupInstances(), CClonePlacementGlyph::x_GetCloneEnds(), CCreateGeneModelTask::x_GetCommand(), CCommandArgDescriptions::x_GetCommandGroupIndex(), CCorrectGenesDialog::x_GetConstrainedList(), CQueryImpl::x_GetContext(), CProjectTreePanel::x_GetContextMenu(), CBamUILoadManager::x_GetCSraRefSeqs(), CAlgoToolManagerBase::x_GetDataLocker(), CSubSource::x_GetDateTokens(), CCommonComponentScorer::x_GetDeltaExtCompList(), CAutoDefFeatureClause::x_GetDescription(), CInstancedAligner::x_GetDistanceInstances(), x_GetDivisionProc(), CNcbiEncrypt::x_GetDomainKeys(), CODBC_Connection::x_GetDriverName(), CSeq_align_Mapper_Base::x_GetDstDendiag(), CSeq_align_Mapper_Base::x_GetDstDenseg(), CSeq_align_Mapper_Base::x_GetDstDisc(), CSeq_align_Mapper_Base::x_GetDstPacked(), CSeq_align_Mapper_Base::x_GetDstSparse(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CSeq_align_Mapper_Base::x_GetDstStd(), CId2ReaderBase::x_GetError(), CAutoDefFeatureClause::x_GetExonDescription(), CWriteDB_Impl::x_GetFastaReaderDeflines(), CAutoDef::x_GetFeatureClauseProductEnding(), CDisplaySeqalign::x_GetFeatureInfo(), CAutoDefFeatureClause::x_GetFeatureTypeWord(), CSeqDBVol::x_GetFilteredHeader(), CGeneGroup::x_GetFirstFeat(), CLinkedFeatsGroup::x_GetFirstFeat(), CFeat_qual_choice::x_GetFirstGBQualMatch(), CFeat_qual_choice::x_GetFirstGBQualMatchConstraintName(), CAsn2FlatApp::x_GetGenbankCallback(), CAdjustFeaturesForGaps::x_GetGenesForFeatures(), CProjectFileWriter::x_GetGi(), CScope::x_GetGi(), CAutoDef::x_GetHumanSTRFeatureClauses(), x_GetId(), CGencollIdMapper::x_GetIdFromSeqAndSpec(), CValidError_align::x_GetIds(), CPubField::x_GetImprintField(), variation_ref::CHgvsParser::x_GetInstData(), variation_ref::CHgvsParser::x_GetInstLength(), variation::CHgvsParser::x_GetInstLength(), CRegistryReadView::x_GetKeys(), CFeat_qual_choice::x_GetLegalQualName(), CGC_Sequence::x_GetLength(), CAlnMultiDSBuilder::x_GetLinearAlignments(), CEntrez2ClientApp::x_GetLinkCounts(), CFeatureGenerator::SImplementation::SMapper::x_GetLocFromSplicedExons(), CAlnMultiWidget::x_GetMatchingHiddenRows(), CRuler::x_GetMaxNum(), CAlnStatGlyph::x_GetMaxTotal(), CId2ReaderBase::x_GetMessageError(), CDensegGraphicDataSource::x_GetMismatchStr(), CDeflineGenerator::x_GetModifiers(), x_GetMolLocTypeUserObj(), CSeq_align::x_GetNamedScore(), CNAUtils::x_GetNAMetaData(), CTableDataBioTreeContainer::x_GetNodeFeature(), CBlastDbDataLoader::x_GetOid(), CAutoDefFeatureClause::x_GetOperonSubfeatures(), CBioSource::x_GetOrgModNameValPairs(), CUpdateMultipleSeq_Input::x_GetOriginalId(), CAlignGlyph::x_GetOverrideColor(), CSeq_align_Mapper_Base::x_GetPartialDenseg(), CSDB_ConnectionParam::x_GetPassword(), CAutoDefFeatureClause::x_GetProductName(), CSmartFileTextToolbar::x_GetProject_Path(), CTSE_Split_Info::x_GetRecords(), CGBDataLoader::x_GetRecords(), CDataSource::x_GetRecords(), CAlignedFeatureGraph::x_GetRecsSortedByLength(), CGencollIdMapper::x_GetRole(), CApplyRNAITSDlg::x_GetRow(), CAlnMultiRenderer::x_GetRowTooltip(), CWGSSeqIterator::x_GetSeq_inst(), CHitMatrixDataSource::x_GetSeqAlignIds(), CSeqDBImpl::x_GetSeqGI(), CCommonComponentScorer::x_GetSeqHistCompList(), CDataSource_ScopeInfo::x_GetSeqMatch(), CDataSource::x_GetSeqMatch(), CSeqTechDlg::x_GetSeqTechUserFromSeqEntry(), CSubPrep_panel::x_GetSequenceLengths(), SrcEditDialog::x_GetSourceTableChoices(), CBamUILoadManager::x_GetSrzRefSeqs(), CCorrectRNAStrandDlg::x_GetStatusSMART(), CPrimaryItem::x_GetStrForPrimary(), CConfig::x_GetString(), CSettingsSet::x_GetStyleKey(), CGC_Assembly::x_GetSubmitterId(), CBioSource::x_GetSubtypeNameValPairs(), CClonePlacementGlyph::x_GetSupportTypeForNonPrototypeEnds(), CScope_Impl::x_GetSynonyms(), CSeqDBVol::x_GetTaxDefline(), CDumpASNIndex::x_GetTaxId(), CMatePairGlyph::x_GetTitle(), CScope_Impl::x_GetTSESetWithBioseqAnnots(), CCreateGeneModelTask::x_GetUpdatedGeneCommand(), CCommonComponentScorer::x_GetUserCompList(), CClipboard::x_GetValueAt(), CSrcTablePrimerColumn::x_GetValues(), CViewGraphic::x_GetViewSettingsFromParams(), CDbTest::x_GetVolumeList(), CDirTest::x_GetVolumeList(), x_Glob(), CHitMatrixDataSource::x_GoodSeg(), CCreateGeneModelTask::x_Group_By_GeneID(), CIdMapperTestApp::x_HandleAlignments(), CDB_UserHandler::x_HandleAll(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CIdMapperTestApp::x_HandleFeatures(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CAgpconvertApplication::x_HandleTaxArgs(), CValidError_bioseq::x_HasCitSub(), CLayoutGroup::x_HasExpandedChildren(), CValidError_bioseq::x_HasGap(), CTSE_Info::x_HasIdObjects(), CJournalPanel::x_HasIsoJtaTitle(), CFeatureItem::x_HasMethodtRNAscanSE(), CSingleFeatValidator::x_HasNamedQual(), CValidError_feat::x_HasNonReciprocalXref(), CSetTransgSrcDesc::x_HasTransgenicSubtype(), CAutoDefModifierCombo::x_HasTypeStrainComment(), CSequenceTrack::x_HasVisibleRsite(), CSeq_align_Mapper_Base::x_HaveMixedSeqTypes(), CSeq_align_Mapper_Base::x_HaveMixedStrand(), CTextSelHandler::x_HitTest(), CLinearSelHandler::x_HitTest(), CAlignMarkHandler::x_HitTest(), CFlatGatherer::x_IdComments(), CHistogramBinning::x_IdentifyClusters(), CFeatureItem::x_ImportQuals(), CDataSource::x_IndexAnnotTSEs(), CTSE_Info::x_IndexBioseq(), CDataSource::x_IndexSeqTSE(), CDataSource_ScopeInfo::x_IndexTSE(), CTaxonTextCompleter::x_Init(), CSequenceDataTester::x_Init(), NSnpBins::CGeneMap::x_Init(), CAnnotCompare_AlignDS::x_Init(), CReferenceItem::x_Init(), CSeq_align_Mapper_Base::x_Init(), CCmdLineBlastXMLReportData::x_Init(), CFeatList::x_Init(), CCgiRequest::x_Init(), CPhyTreeCalc::x_InitAlignDS(), CSeq_annot_Info::x_InitAlignList(), CwxAnnotConfigDlg::x_InitAnnotList(), CTaxFormat::x_InitBlastNameTaxInfo(), CNcbiTestApplication::x_InitCommonParserVars(), CCmdLineBlastXML2ReportData::x_InitDB(), CAlignMarkHandler::x_InitDeltaMap(), CSeq_annot_Info::x_InitFeatKeys(), CSeq_annot_Info::x_InitFeatList(), CSeq_annot_Info::x_InitFeatTableKeys(), CFeatureCreateDialog::x_InitFeatTypes(), CElementaryMatching::x_InitFilteringVector(), CSeq_loc_Mapper::x_InitGCAssembly(), CSeq_loc_Mapper::x_InitGCSequence(), CSixFramesTransTrack::x_InitGeneticCodeName(), CSeq_annot_Info::x_InitGraphKeys(), CSeq_annot_Info::x_InitGraphList(), CAnnot_CI::x_Initialize(), CSeqTableInfo::x_Initialize(), CAnnot_Collector::x_Initialize0(), CSeq_loc_Mapper_Base::x_InitializeAlign(), CAgpConverter::x_InitializeCopyOfTemplate(), CSearchDatabase::x_InitializeDb(), CHistogramBinning::x_InitializeHistogramAlgo(), CSeq_loc_Mapper::x_InitializeSeqMapDown(), CAnnotType_Index::x_InitIndexTables(), CTaxFormat::x_InitLineageMetaData(), CSeq_annot_Info::x_InitLocsKeys(), CSeq_annot_Info::x_InitLocsList(), CDisplayMacros_dlg::x_InitMacroList(), CWGSFileInfo::x_InitMasterDescr(), CTSE_Chunk_Info::x_InitObjectIndexList(), CMultiAligner::x_InitParams(), CElementaryMatching::x_InitParticipationVector(), CRemoteBlast::x_InitQueries(), CBioseqIndex::x_InitSource(), CSeq_loc_Mapper_Base::x_InitSpliced(), CTaxFormat::x_InitTaxInfoMap(), CFeaturePanel::x_InitTrackIcons(), CTrackConfigManager::x_InitTrackManager(), CFeatureCheckPanel::x_InitTree(), CAlignSpanView::x_InitWidget(), variation_ref::CHgvsParser::x_InstToString(), CTL_CursorResult::x_InvalidateDescriptors(), CAgpconvertApplication::x_IsAnySimpleSubsourceArgSet(), CGeneModelFeatJob::x_IsCCDS(), CCommentItem::x_IsCommentEmpty(), CGeneModelFeatJob::x_IsDbref(), CBioseqContext::x_IsDeltaLitOnly(), CValidError_bioseq::x_IsDeltaLitOnly(), CSeq_align_Mapper_Base::x_IsEmpty(), CMergeTree::x_IsEventualChildOf(), CDisplaySeqalign::x_IsGeneInfoAvailable(), CMatchTabulate::x_IsGoodGloballyReciprocalBest(), CAutoDef::x_IsHumanSTR(), CGencollIdMapper::x_IsLoc_Int_InAGap(), CGeneModelFeatJob::x_IsncRNA(), CGeneModelFeatJob::x_IsnpcGene(), CChoiceTypeStrings::x_IsNullWithAttlist(), CClassTypeStrings::x_IsNullWithAttlist(), CGencollIdMapper::x_IsParentSequence(), CDiscrepancyContext::x_IsPseudo(), CNewCleanup_imp::x_IsPubContentBad(), CValidError_bioseq::x_IsRangeGap(), CSeqTechDlg::x_IsSpecialTech(), CBlastAppArgs::x_IssueWarningsForIgnoredOptions(), CSeq_loc_Mapper_Base::x_IsSynonym(), CSeq_loc_Mapper::x_IsUCSCRandomChr(), CUser_object::x_IsUnverifiedType(), CSeq_loc_Mapper_Base::x_IterateExonParts(), CAppHitFilter::x_IterateSeqAlignList(), CClusterer::x_JoinClustElem(), CClusterer::x_JoinClusters(), CAddFeatureBetweenDlg::x_ListFeatures(), CBulkOtherAddPanel::x_ListFeatures(), CAlignOtherAddPanel::x_ListFeatures(), CLDS2_DataLoader::x_LoadBlobs(), CTSE_Split_Info::x_LoadChunks(), CSGAnnotJob::x_LoadCoverageGraph(), CRequestContext::x_LoadEnvContextProperties(), CNgAlignApp::x_LoadExternalSequences(), CSeqGraphicConfig::x_LoadFeatSettings(), CSGSegmentSmearJob::x_LoadFromNA(), CLDBlockJob::x_LoadFtable(), CFileLoader::x_LoadGff(), CPkgManager::x_LoadPackage(), CAppPackagesDlg::x_LoadPkgList(), CBamRefSeqInfo::x_LoadRangesCov(), CCSRARefSeqInfo::x_LoadRangesStat(), CId2ReaderBase::x_LoadSeq_idBlob_idsSet(), CTraceGraphTrack::x_LoadSettings(), CSegmentMapTrack::x_LoadSettings(), CSnpTrack::x_LoadSettings(), CGraphOverlay::x_LoadSettings(), CGraphTrack::x_LoadSettings(), CSequenceTrack::x_LoadSettings(), CFeatureTrack::x_LoadSettings(), CEpigenomicsTrack::x_LoadSettings(), CAlignmentTrack::x_LoadSettings(), CSixFramesTransTrack::x_LoadSettings(), CFeatureSearchForm::x_LoadSettings(), CFeaturePanel::x_LoadSettings(), CSourceQualifiersReader::x_LoadSourceQualifiers(), CTaxFormat::x_LoadTaxTree(), CAgpconvertApplication::x_LoadTemplate(), CScoreMethodsDlg::x_LoadTools(), CLDS2_DataLoader::x_LoadTSE(), CAsnSubCacheCreateApplication::x_LocateBlobsInCache(), CNcbiApplication::x_LogOptions(), CCgiSampleApplication::x_LookAtArgs(), CFeatTree::x_LookupParentByRef(), CAutodefJob::x_MakeChanges(), NSnpGui::x_MakeClinVarLink(), CMultiAligner::x_MakeClusterResidueFrequencies(), CMultiAligner::x_MakeFillerBlocks(), CTSE_Handle::x_MakeHandles(), CSnpJob::x_MakeHistogramFromFtable(), CTreeAlignMerger::x_MakeMergeableGroups(), CAutoDefOptions::x_MakeModifierList(), CTreeAlignMerger::x_MakeSeqAlign(), CGencollIdMapper::x_MakeSpecForSeq(), CAutoDefOptions::x_MakeSuppressedFeatures(), NSnpGui::x_MakeVarVuLink(), CMappingRange::x_Map_Fuzz(), CSeq_annot_Info::x_MapAnnotObject(), CTSE_Info::x_MapAnnotObject(), CSeq_annot_Info::x_MapFeatIds(), CFeatureGenerator::SImplementation::x_MapFeature(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CPhyTreeFormatter::x_MarkLeavesBySeqId(), CFeatureSearchJob::x_Match(), CDiagStrErrCodeMatcher::x_Match(), CValidError_bioseq::x_MatchesOverlappingFeaturePartial(), CAlnMixMerger::x_Merge(), CTreeAlignMerger::x_Merge_Dist_Impl(), CMergeAligner::x_MergeAlignments(), CGFFReader::x_MergeAttributes(), CMergeVolumes::x_MergeCandidates(), CAlnGraphic::x_MergeDifferentSeq(), CCleanup::x_MergeDupOrgNames(), CCleanup::x_MergeDupOrgRefs(), CFlatGatherer::x_MergeEqualBioSources(), CVecscreen::x_MergeLowerRankSeqalign(), CSeqTextView::x_MergeObjects(), CViewGraphic::x_MergeObjects(), CFeatTableView::x_MergeObjects(), CGFFReader::x_MergeRecords(), CVecscreen::x_MergeSeqalign(), CMergeAligner::x_MergeSeqAlignSet(), CInversionMergeAligner::x_MergeSeqAlignSet(), CTable2AsnContext::x_MergeSeqDescr(), CSGSegmentMapJob::x_MergeSeqSegments(), CInstancedAligner::x_MinCoverageCheck(), CAlnMixSegments::x_MinimizeGaps(), CNewCleanup_imp::x_MovedNamedValuesInStrain(), CSpaceShrinker::x_MoveNextRecord(), CNewCleanup_imp::x_MoveNPTitle(), CNewCleanup_imp::x_MovePopPhyMutPub(), CMultiAligner::x_MultiAlignClusters(), CLocusItem::x_NameHasBadChars(), CFeatureTrack::x_NeedHighlight(), CSequenceAmbigTrimmer::x_NormalizeVecTrimRules(), COligoSpecificityCheck::x_NW_alignment(), x_OkayToAddKeyword(), CGraphOverlay::x_OnAllJobsFinished(), CFeaturePanel::x_OnColorIconClicked(), CFeatureTrack::x_OnContentIconClicked(), CSixFramesTransTrack::x_OnContentIconClicked(), CObjectListWidget::x_OnCopy(), CFeaturePanel::x_OnDecorationIconClicked(), CCgiApplication::x_OnEvent(), CSixFramesTransTrack::x_OnGeneticIconClicked(), CHapmapTrack::x_OnIconClicked(), CBinsTrack::x_OnIconClicked(), CSnpTrack::x_OnIconClicked(), CSegmentMapTrack::x_OnJobCompleted(), CFeaturePanel::x_OnLabelIconClicked(), CGeneModelTrack::x_OnLayoutIconClicked(), CFeaturePanel::x_OnLayoutIconClicked(), CAlignmentTrack::x_OnLayoutIconClicked(), CFeatureTrack::x_OnLayoutIconClicked(), CAlignmentTrack::x_OnScoreIconClicked(), CSeqTextView::x_OnSetSelection(), CCrossAlignView::x_OnSetSelection(), CDotMatrixView::x_OnSetSelection(), CMultiAlignView::x_OnSetSelection(), CPhyTreeView::x_OnSetSelection(), CViewGraphic::x_OnSetSelection(), CFeatTableView::x_OnSetSelection(), CSixFramesTransTrack::x_OnSettingIconClicked(), CGraphTrack::x_OnSettingsIconClicked(), CFeaturePanel::x_OnSizeIconClicked(), CProjectTask::x_OpenProjects(), CDiscRepApp::x_OutputMacro(), CDisplaySeqalign::x_OutputSeq(), CCache< TKey, TValue, THandler, TLock, TSize >::x_PackElementIndex(), CSplitQueryTestFixture::x_ParseConfigLine(), CDiscRepApp::x_ParseDirectory(), SDiagMessage::x_ParseExtraArgs(), CGFFReader::x_ParseFeatRecord(), CLDS2_Manager::x_ParseFile(), CGC_Assembly_Parser::x_ParseGCAssembly(), CGC_Assembly_Parser::x_ParseGCSequence(), CSplitParser::x_ParseLocation(), CNAUtils::x_ParseNAMetaData(), CTraversalSpecFileParser::x_ParseOutputClassNameClause(), CSeedTop::x_ParsePattern(), CAlignFilter::x_ParseTree_Flatten(), CGFFReader::x_ParseV3Attributes(), CString_constraint::x_PartialCompare(), CDataLoaderPatcher::x_PatchLockSet(), CTraversalPatternMatchCallback::x_PatternMatches(), CSGAnnotJob::x_PercentileButNotMax(), CCorrectRNAStrandDlg::x_PopulateAccessionList(), CScope_Impl::x_PopulateBioseq_HandleSet(), CObjectListWidgetSel::x_PopulateGroups(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CRNAPanel::x_PopulateTranscriptID(), CTaxTreeBrowser::x_PopulateTree(), CArgDescriptions::x_PostCheck(), CNewCleanup_imp::x_PostProcessing(), CAlignSpanView::x_PreAttachToProject(), CAlnMultiDSBuilder::x_PreCreateSparseDataSource(), CFlatGatherer::x_PrepareAnnotDescStrucComment(), CDisplaySeqalign::x_PrepareRowData(), CNCActiveSyncControl::x_PrepareSyncByBlobs(), CSpaceShrinker::x_PrepareToShrink(), CSeq_loc_Mapper_Base::x_PreserveDestinationLocs(), CDiagStrErrCodeMatcher::x_Print(), CMergeTree::x_Print(), CSeqDB_FilterTree::x_Print(), CArgDescriptions::x_PrintAliasesAsXml(), CBlastDBCmdApp::x_PrintBlastDatabaseInformation(), CNetScheduleHandler::x_PrintCmdRequestStart(), CTablePrinter::x_PrintColumnNames(), CArgDescriptions::x_PrintComment(), CTablePrinter::x_PrintDashes(), CScoreLookup::x_PrintDictionaryEntry(), CDisplaySeqalign::x_PrintDynamicFeatures(), CMultiAlnPrinter::x_PrintFastaPlusGaps(), CBlastTabularInfo::x_PrintFieldNames(), CGapStatsApplication::x_PrintHistogram(), CProjectServiceTestJob::x_PrintItems(), CTaxFormat::x_PrintLineage(), CNgAlignApp::x_PrintNoHitList(), CNCMessageHandler::x_PrintRequestStart(), CGapStatsApplication::x_PrintSeqsForGapLengths(), CBlastFormat::x_PrintStructuredReport(), CBlastTabularInfo::x_PrintSubjectAllAccessions(), CBlastTabularInfo::x_PrintSubjectAllGis(), CBlastTabularInfo::x_PrintSubjectAllSeqIds(), CBlastTabularInfo::x_PrintSubjectBlastNames(), CBlastTabularInfo::x_PrintSubjectCommonNames(), CBlastTabularInfo::x_PrintSubjectSciNames(), CBlastTabularInfo::x_PrintSubjectSuperKingdoms(), CBlastTabularInfo::x_PrintSubjectTaxIds(), CGapStatsApplication::x_PrintSummaryView(), CBlastFormat::x_PrintTabularReport(), CNCStat::x_PrintUnstructured(), CSrvStat::x_PrintUnstructured(), CBlastFormat::x_PrintXML2Report(), CAgpFastaComparator::x_Process(), CPrimeCacheApplication::x_Process_Ids(), CExportStrategy::x_Process_Query(), CExportStrategy::x_Process_SearchDb(), CAnnotObject_Info::x_ProcessAlign(), CCddInputData::x_ProcessAlignments(), CDiscRepApp::x_ProcessAll(), CBinsTrack::x_ProcessBinsJobResult(), CXcompareAnnotsApplication::x_ProcessComparison(), CProSplignJob::x_ProcessCompartment(), CBlast_SAM_Formatter::x_ProcessCustomSpec(), CIgBlast::x_ProcessDGeneResult(), CTar::x_ProcessEntry(), CDiscRepApp::x_ProcessFile(), CId2ReaderBase::x_ProcessGetBlobId(), CID2SNPProcessor_Impl::x_ProcessGetChunks(), CNetScheduleHandler::x_ProcessGetConfiguration(), CId2ReaderBase::x_ProcessGetSeqIdSeqId(), CMakeBlastDBApp::x_ProcessInputData(), CGeneModelFeatJob::x_ProcessLandMarkFeatures(), CSeq_loc_CI_Impl::x_ProcessLocation(), CMakeBlastDBApp::x_ProcessMaskData(), CNetScheduleHandler::x_ProcessMsgQueue(), CCleanupApp::x_ProcessOneDirectory(), CBlastOptionsBuilder::x_ProcessOneOption(), CBlastOptionsBuilder::x_ProcessOptions(), CSplignApp::x_ProcessPair(), CCorrectRNAStrandDlg::x_ProcessRNAStrandLine(), CFilterColumnsDlg::x_ProcessSelectionPattern(), CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile(), CCDSTranslationProblems::x_ProteinHasTooManyXs(), CTraversalCodeGenerator::x_PruneEmptyNodes(), CAlignFilter::x_Query_Op(), CRemoteBlast::x_QueryMaskingLocationsToNetwork(), x_RangesToSeq_loc(), CSeq_annot_SNP_Info_Reader::x_Read(), CNcbiRegistry::x_Read(), CUpdateSeq_Input::x_ReadAccession(), CUpdateAlign::x_ReadAlign(), CArchive::x_ReadAndProcess(), CNCMessageHandler::x_ReadAuthMessage(), CNcbiTestApplication::x_ReadConfiguration(), CSeqAlignFilter::x_ReadExtraGis(), CQueueDataBase::x_ReadIniFileQueueClassDescriptions(), CQueueDataBase::x_ReadIniFileQueueDescriptions(), CAppHitFilter::x_ReadInputHits(), CQueueDataBase::x_ReadLinkedSections(), CNCActiveHandler::x_ReadPeerVersion(), CSplitQueryTestFixture::x_ReadQueryBoundsPerChunk(), CFastaReader::x_ReadSegSet(), CCgiEntryReaderContext::x_ReadURLEncodedEntry(), CNgAlignApp::x_RecurseSeqEntry(), CTabularFormatter_DiscStrand::x_RecurseStrands(), CGencollIdMapper::x_RecursiveSeqFix(), CGlWidgetPane::x_RegisterHandler(), CNewCleanup_imp::x_RemovePopPhyBioSource(), CNewCleanup_imp::x_RemovePopPhyMolInfo(), CScheduler_MT::x_RemoveTaskImpl(), CSequenceTrack::x_RenderContent(), CGlyphContainer::x_RenderContent(), CFeaturePanel::x_RenderFeatureGrid(), CFeaturePanel::x_RenderHairLineSelections(), CTextSelHandler::x_RenderSelectedFeatures(), CPlainTextItem::x_RenderText(), SrcEditDialog::x_RepopulateAddQualList(), CValidError_bioseq::x_ReportDuplicatePubLabels(), CValidError_imp::x_ReportInvalidFuzz(), CSDB_ConnectionParam::x_ReportOverride(), CValidError_align::x_ReportSegmentGaps(), CValidError_desc::x_ReportStructuredCommentErrors(), CSeqFormatter::x_RequireData(), CNewCleanup_imp::x_RescueMolInfo(), CSelectionPanel::x_ResetSelObjects(), CSelectionPanel::x_ResetTargetChoice(), CBuildDatabase::x_ResolveFromSource(), CBuildDatabase::x_ResolveGis(), CGFFReader::x_ResolveID(), CGFFReader::x_ResolveLoc(), CBuildDatabase::x_ResolveRemoteId(), CMacroEngine::x_ResolveRTVar(), CTrackConfigManager::x_ResolveSubTracks(), CTSE_ScopeInfo::x_RestoreAdded(), CWorkspaceAutoSaver::x_RestoreWorkspace(), CBlastFormat::x_ReverseQuery(), CFlatFeatureRetrieveJob::x_Run(), CNWAligner::x_Run(), CSplign::x_Run(), CInstancedAligner::x_RunAligner(), CInstancedAligner::x_RunCleanup(), CPsiBlastApp::x_RunLocalPsiBlastIterations(), CInversionMergeAligner::x_RunMerger(), CSplign::x_RunOnCompartment(), CQuickLaunchList::x_Save(), COligoSpecificityCheck::x_SavePrimerInfo(), CTSE_ScopeInfo::x_SaveRemoved(), CAlignmentTrack::x_SaveSettings(), CFeatureSearchForm::x_SaveSettings(), CFeaturePanel::x_SaveSettings(), CElementaryMatching::x_Search(), CMergeTree::x_Search_Iter(), CAnnot_Collector::x_SearchAll(), CFeatureSearchJob::x_SearchFeatures(), CAnnot_Collector::x_SearchLoc(), CAnnot_Collector::x_SearchMapped(), CAnnot_Collector::x_SearchMaster(), CNAUtils::x_SearchNAIds(), CAnnot_Collector::x_SearchObjects(), CAnnot_Collector::x_SearchRange(), CAnnot_Collector::x_SearchSegments(), CSequenceSearchJob::x_SearchSequence(), CAnnot_Collector::x_SearchTSE2(), CTaxIdSet::x_SelectBestTaxid(), CCleanupAlignmentsToolManager::x_SelectCompatibleInputObjects(), CMergeAlignmentsToolManager::x_SelectCompatibleInputObjects(), CGroupAlignmentsToolManager::x_SelectCompatibleInputObjects(), CSrcEditTool::x_SelectCompatibleInputObjects(), CCreateGeneModelToolManager::x_SelectCompatibleInputObjects(), CwxHistogramDlg::x_SelectGraph(), CSelectionControl::x_SelectItems(), CHitMatrixGraph::x_SelectTest(), CAlignGroup::x_SeparateByTaxId(), CNewCleanup_imp::x_SeqFeatCDSGBQualBC(), CApplyRNAITSDlg::x_SeqIdsAlignedWith(), variation_ref::CHgvsParser::x_SeqIdToHgvsHeader(), CFeatureItem::x_SeqIdWriteForTable(), CBioseq::x_SeqLoc_To_DeltaExt(), CMemoryRegistry::x_Set(), CBioseq_Base_Info::x_SetAnnot(), CTSE_Info::x_SetBioseqIds(), CDeflineGenerator::x_SetBioSrc(), CIgBlast::x_SetChainType(), CSeqdesc_CI::x_SetChoices(), CAgpConverter::x_SetChromosomeNameInSourceSubtype(), CFeatureGenerator::SImplementation::x_SetComment(), CHttpSession::x_SetCookies(), CBioseqContext::x_SetDataFromUserObjects(), CWGSSeqIterator::x_SetDelta(), CMultiAligner::x_SetDomainHits(), CFeatureGenerator::SImplementation::x_SetExceptText(), CId2ReaderBase::x_SetExclude_blobs(), CReportEntry::x_SetFeature(), CSeqTableSetExt::x_SetField(), CBlastTabularInfo::x_SetFieldsToShow(), CSNPDbFeatIterator::x_SetFilter(), CDeflineGenerator::x_SetFlags(), CGapsEditor::x_SetGapParameters(), CFeatTree::x_SetGeneRecursive(), CBlastDBExtractor::x_SetGi(), CBlastDBExtractor::x_SetGi2AccMap(), CBlastDBExtractor::x_SetGi2SeqIdMap(), CBlastDBExtractor::x_SetGi2TitleMap(), CHitMatrixRenderer::x_SetGraphs(), CBioseqContext::x_SetId(), CCDSTranslationPanel::x_SetLocationForProtein(), CAutoDefOptions::x_SetModifierList(), CMasterContext::x_SetNumParts(), CBioseq_set_Info::x_SetObject(), CBioseq_Info::x_SetObject(), CFeatureCheckPanel::x_SetSelections(), CAgpToSeqEntry::x_SetSeqGap(), CSourceItem::x_SetSource(), CBlastTabularInfo::x_SetSubjectIds(), CAutoDefOptions::x_SetSuppressedFeatures(), CBlastTabularInfo::x_SetTaxInfo(), CBlastTabularInfo::x_SetTaxInfoAll(), CBioseqContext::x_SetTaxname(), CDeflineGenerator::x_SetTitleFromBioSrc(), CDeflineGenerator::x_SetTitleFromGPipe(), CDeflineGenerator::x_SetTitleFromSegSeq(), CDeflineGenerator::x_SetTitleFromWGS(), CDataLoadersUtil::x_SetupASNCacheDataLoader(), CDataLoadersUtil::x_SetupBlastDataLoader(), CIgBlast::x_SetupDbSearch(), CIgBlast::x_SetupDJSearch(), CDataLoadersUtil::x_SetupLDS2DataLoader(), CIgBlast::x_SetupNoOverlapDSearch(), BlastdbCopyApplication::x_ShouldCopyPIGs(), BlastdbCopyApplication::x_ShouldParseSeqIds(), CMappingObjectLoader::x_ShowMappingDlg(), CGenbankFormatter::x_SmartWrapQuals(), x_SortByCount(), CMacroParser::x_SortParseTree(), COligoSpecificityCheck::x_SortPrimerHit(), CInversionMergeAligner::x_SplitAlignmentsByStrand(), CSplitDataLoader::x_SplitAligns(), CTSE_Chunk_Info::x_SplitAttach(), CUnorderedSplitter::x_SplitDeltaExt(), CSplitDataLoader::x_SplitFeats(), CGff2Record::x_SplitGffAttributes(), CTreeAlignMerger::x_SplitGlobalUnique(), CSplitDataLoader::x_SplitGraphs(), CTraversalCodeGenerator::x_SplitNodesByVar(), CAlignCompare::x_SplitOnOverlaps(), CSplign::x_SplitQualifyingHits(), CSplitDblinkQuals::x_SplitQuals(), CBlastFormat::x_SplitSeqAlign(), CFeatureGraph::x_StartJob(), CDiagContext::x_StartRequest(), CNCActiveSyncControl::x_StartScanSlots(), CReferenceItem::x_StringIsJustCapitalLetters(), CFeature_table_reader_imp::x_StringIsJustQuotes(), CSearch_func::x_StringMayContainPlural(), CUnorderedSplitter::x_StripDistantAlignments(), CGencollIdMapper::x_StripPseudoSeq(), x_SubAndSort(), x_SubNoSort(), CRangeCollection< TSeqPos >::x_Subtract(), CAttribTableColumnIdPanel::x_TableReaderCommon(), CAlnMultiDSBuilder::x_TestAlignments(), CSeqTest::x_TestAllCdregions(), CHitMatrixDataSource::x_TestAndSelectAlign(), CHitMatrixDataSource::x_TestAndSelectAligns(), x_TestGetFilteredQueryRegions(), x_TestGetSeqLocInfoVector(), CBlastFilterTest::x_TestLowerCaseMaskWith(), CVecscreenTest::x_TestRangeList(), CVecscreenTest::x_TestSeqalign(), CSequenceDataTester::x_TestSingleSequence_Local(), x_TitleFromChromosome(), x_ToBlastVec(), CValidError_bioseq::x_TranscriptIDsMatch(), CBDB_Cache::x_TruncateDB(), CMergedPairwiseAln::x_TruncateOverlaps(), CFormatGuessEx::x_TryBed(), CHistogramBinning::x_TryForEvenBins(), CFormatGuessEx::x_TryGff2(), CFormatGuessEx::x_TryGff3(), CFormatGuessEx::x_TryGtf(), CIdResolver::x_TryProcessLRG(), CTSE_Chunk_Info::x_TSEAttach(), CBioseq_Info::x_TSEDetachContents(), CDataSource::x_UnindexAnnotTSEs(), CDataSource_ScopeInfo::x_UnindexTSE(), CTSE_Info::x_UnmapAnnotObjects(), CSeq_annot_Info::x_UnmapFeatIds(), CFlatGatherer::x_UnorderedComments(), CEnvironmentRegistry::x_Unset(), CFlatGatherer::x_UnverifiedComment(), CTSE_Chunk_Info::x_UpdateAnnotIndexContents(), CBLASTSearchOptionsPanel::x_UpdateDBCombo(), CMakeProfileDBApp::x_UpdateDelta(), CSubPrep_panel::x_UpdateFeatureStatus(), CUserFieldListPanel::x_UpdateFields(), CSequenceSearchForm::x_UpdateFileList(), CCreateGeneModelTask::x_UpdateGeneOnSequence(), CHitMatrixRenderer::x_UpdateGraphColor(), CScope_Impl::x_UpdateHandleSeq_id(), COrfSearchForm::x_UpdateKozak(), CGraphOverlay::x_UpdateLegend(), CAssemblyListPanel::x_UpdateListPanel(), CId2ReaderBase::x_UpdateLoadedSet(), CSeqGraphicWidget::x_UpdateMarkerInfo(), CAlignMarkHandler::x_UpdateMarks(), CSeq_annot_Info::x_UpdateName(), CAlnMultiWidget::x_UpdateOnSwitchMaster(), CConvertFeatDlg::x_UpdateOptions(), CPageHandler::x_UpdatePageTreeRoot(), CApplyRNAITSDlg::x_UpdatePartials(), CFeatureCreateDialog::x_UpdateQualifiers(), CwxGridTableAdapter::x_UpdateRenderers(), CHitMatrixDataSource::x_UpdateScoreMap(), CAutodefFeatClausePanel::x_UpdateSuppressedFeatureTypeList(), CFeatTableDS::x_UpdateTypeHash(), CAssignColumnValueDlg::x_UpdateValues(), CViewGraphic::x_UpdateVisRangeLayout(), CWindowManager::x_UpdateWindowsMenu(), CValidError_bioseq::x_ValidateAbuttingUTR(), CMakeProfileDBApp::x_ValidateCd(), CValidError_bioseq::x_ValidateCDSmRNAmatch(), CValidError_align::x_ValidateDendiag(), CSingleFeatValidator::x_ValidateExtUserObject(), CSingleFeatValidator::x_ValidateFeatCit(), CValidError_feat::x_ValidateGbQual(), CSingleFeatValidator::x_ValidateGbQual(), CValidError_bioseq::x_ValidateGeneCDSmRNACounts(), CValidError_feat::x_ValidateGeneId(), CSingleFeatValidator::x_ValidateGeneId(), CSingleFeatValidator::x_ValidateGoTerms(), CCddInputData::x_ValidateHits(), CMultiAligner::x_ValidateInputMSAs(), CAlgoToolManagerBase::x_ValidateInputObjects(), CValidError_bioseq::x_ValidateLocusTagGeneralMatch(), CPkgManager::x_ValidatePackage(), CMultiAligner::x_ValidateQueries(), CValidError_align::x_ValidateSeqId(), CValidError_align::x_ValidateSeqLength(), CValidError_align::x_ValidateStd(), CValidError_align::x_ValidateStrand(), CValidError_bioseq::x_ValidateStructuredCommentContext(), CAgpConverter::x_VerifyComponents(), CNCActiveSyncControl::x_WaitForExecutingTasks(), CApplyRNAITSDlg::x_WasPropagatedTo(), CScoringJob::x_WindowAvgScores(), CNCMessageHandler::x_WriteFullBlobsList(), CElementaryMatching::x_WriteIndexFile(), CFastaOstream::x_WriteSeqIds(), CTextTagWriter::x_WriteTag(), CXmlTagWriter::x_WriteTag(), CFlatXrefQVal::x_XrefInGeneXref(), CForeignContaminationScreenReportReader::xCheckLen(), xf_IsDeltaLitOnly(), CSeqSubSplitter::xFlattenSeqEntry(), CSrcWriter::xGatherGi(), SIdCompare::xGetGeneralId(), CWiggleReader::xMakeGraph(), CWiggleReader::xMakeTable(), CSeqSubSplitter::xMergeSeqDescr(), xSetScores(), CForeignContaminationScreenReportReader::xTrimData(), CForeignContaminationScreenReportReader::xTrimExt(), CAnnotWriterApp::xTryProcessSeqAlignSet(), CDepthCollection::ZeroFill(), CAlnGraphic::~CAlnGraphic(), CAsnBioContextContainer::~CAsnBioContextContainer(), CBlastQueryFilteredFrames::~CBlastQueryFilteredFrames(), CCgiApplication::~CCgiApplication(), CGridHyperlinks::CColHyperlinks::~CColHyperlinks(), CDriverManager::~CDriverManager(), CFileDeleteList::~CFileDeleteList(), CGridHyperlinks::~CGridHyperlinks(), CCddInputData::CHit::~CHit(), CMergeTree::~CMergeTree(), CNcbiTestTreeElement::~CNcbiTestTreeElement(), CObjectPool< C >::~CObjectPool(), CPhyloTreePane::~CPhyloTreePane(), CPluginManager< TClass >::~CPluginManager(), CPrefetchSequence::~CPrefetchSequence(), CPssmInputWithSingleCD::~CPssmInputWithSingleCD(), CRootTextItem::~CRootTextItem(), CSeq_id_Mapper::~CSeq_id_Mapper(), CShowBlastDefline::~CShowBlastDefline(), CStrWithUrlContainer::~CStrWithUrlContainer(), CVecscreen::~CVecscreen(), CwxTableListCtrl::~CwxTableListCtrl(), and CDB_Exception::SParams::~SParams().

#define ITERATE_0_IDX (   idx,
  up_to 
)    for( TSeqPos idx = 0; idx < up_to; ++idx )
#define ITERATE_BEGIN (   Cont,
  Begin 
)
Value:
"rvalue container in *ITERATE"), (Cont).Begin())
CBeginInfo Begin(C &obj)
Get starting point of object hierarchy.
Definition: iterator.hpp:958
#define NCBI_ASSERT_EXPR(expr, mess)
Definition: ncbidbg.hpp:129
bool s_ITERATE_SameObject(const Type &obj1, const Type &obj2)
Definition: ncbimisc.hpp:776

Definition at line 780 of file ncbimisc.hpp.

#define ITERATE_BOTH_BOOL_VALUES (   BoolVar)    for( bool BoolVar##BOTH_BOOL_VALUES_DONE##__LINE__ = false, BoolVar = false; ! BoolVar##BOTH_BOOL_VALUES_DONE##__LINE__ ; BoolVar##BOTH_BOOL_VALUES_DONE##__LINE__ = BoolVar, BoolVar = true )

The body of the loop will be run with Var equal to false and then true.

The seemlingly excessive complexity of this macro is to get around a couple of limitations: * A bool only has two states, so it's not possible to represent the complete state space of (first iteration, second iteration, done) without another variable. * The variables declared in a for-loop's first part must be of the same type, so the other variable has to be a bool instead of something more convenient such as as a loop-counter.

Definition at line 841 of file ncbimisc.hpp.

Referenced by BOOST_AUTO_TEST_CASE().

#define ITERATE_CONST (   Cont)    NCBI_NS_NCBI::s_ITERATE_ConstRef(Cont)

Definition at line 771 of file ncbimisc.hpp.

#define ITERATE_SIMPLE (   num_iters)    ITERATE_0_IDX( _dummy_idx_94768308_##__LINE__, num_iters )

Just repeat the body of the loop num_iters times.

Definition at line 849 of file ncbimisc.hpp.

Referenced by CAsn2FlatApp::x_CreateCancelBenchmarkCallback(), and CBaseCountItem::x_GatherInfo().

#define ITERATE_VAR (   Type)    Type

Definition at line 791 of file ncbimisc.hpp.

#define NCBI_DEPRECATED_CLASS   NCBI_DEPRECATED_CTOR(class)

Macro used to mark a class as deprecated.

See also
NCBI_DEPRECATED_CTOR

Definition at line 1124 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 1118 of file ncbimisc.hpp.

#define NCBI_EOWNERSHIP_DEFINED

NCBI_ESWITCH_DEFINED.

Definition at line 82 of file ncbimisc.hpp.

#define NCBI_ESWITCH_DEFINED

Definition at line 56 of file ncbimisc.hpp.

#define NCBI_TOOLKIT_EXPORT

Definition at line 66 of file ncbi_toolkit_impl.hpp.

#define NON_CONST_ITERATE (   Type,
  Var,
  Cont 
)
Value:
for ( ITERATE_VAR(Type::iterator) Var = ITERATE_BEGIN(Cont, begin); \
Var != (Cont).end(); ++Var )
#define ITERATE_BEGIN(Cont, Begin)
Definition: ncbimisc.hpp:780
#define ITERATE_VAR(Type)
Definition: ncbimisc.hpp:791

Non constant version of ITERATE macro.

Definition at line 802 of file ncbimisc.hpp.

Referenced by CFeatureTableReader::_MergeCDSFeatures_impl(), CDockManager::ActivateClients(), CReportNode::Add(), CLDS2_Database::AddAnnot(), CNcbiTable< TValue, TRow, TColumn >::AddColumn(), CSourceRequirements::AddColumnsToSeqTable(), CProjectTreeBuilder::AddDatatoolSourcesDepends(), CScope_Impl::AddDefaults(), AddEmptyProteinFeatureToProtein(), AddGenbankKeyword(), CChainer::CChainerImpl::AddIfCompatible(), CSeq_gap::AddLinkageEvidence(), AddLinkageEvidence(), AddLocalIdUserObjects(), TSearchMessages::AddMessageAllQueries(), AddMiscColumnsToTable(), CCleanup::AddMissingMolInfo(), CObjectLoadingTask::AddObjects(), AddObjsToReport(), CSeq_feat::AddOrReplaceQualifier(), CCleanup::AddPartialToProteinTitle(), CGBProjectHelper::AddProjectItemsFromRID(), CAutoDefSourceGroup::AddQual(), CAutoDefModifierCombo::AddQual(), AddRBS(), CSimpleMakeFileContents::AddReadyKV(), CFeatureGenePanel::AddReciprocicalXref(), CSourceRequirements::AddRequirement(), CObjectList::AddRow(), SAccGuide::AddRule(), CScoreBuilder::AddScore(), CScoreBuilderBase::AddScore(), AddSeqdescToSeqEntryRecursively(), CSeq_loc_mix::AddSeqLoc(), CAutoDefModifierCombo::AddSource(), AddSubFieldReport(), CValidErrorFormat::AddSuppression(), AddTitle(), CSrcTablePrimerColumn::AddToBioSource(), CGenericStructuredCommentColumn::AddToComment(), CDockManager::AddToDefaultLocation(), CGbQualColumn::AddToFeature(), CProtRefColumn::AddToFeature(), CScoreBuilder::AddTracebacks(), CTrackContainer::AddTracks(), AddUserObjectFieldItems(), AddValueToTable(), CFeatureGenerator::SImplementation::AdjustAlignment(), NTweakExon::AdjustBiostops(), variation_ref::CVariationUtil::AdjustDelinsToInterval(), AdjustForCDSPartials(), CFeatGapInfo::AdjustForRelevantGapIntervals(), AdjustProteinFeature(), CFeatGapInfo::AdjustProteinSeq(), CTrackConfigManager::AdjustTrackOrder(), AgpRead(), CContigAssembly::Align(), AlignModelToSeqalign(), CTrackConfigManager::AlignTrackConfig(), CVariationNormalization::AlterToDelIns(), AnalyzeDllData(), AnalyzeFieldReport(), CReadBlastApp::AnalyzeSeqs(), CReadBlastApp::AnalyzeSeqsViaBioseqs(), CLayoutGroup::Append(), CReadBlastApp::append_misc_feature(), CConvertSelectedGaps::apply(), CEditSelectedGaps::apply(), CMRnaForCDS::apply_to(), CMultiReader::ApplyAdditionalProperties(), CSourceModParser::ApplyAllMods(), CTable2AsnContext::ApplyCreateDate(), CTable2AsnContext::ApplyCreateUpdateDates(), ApplyReplacementIds(), CProSplign::AssignGeneticCode(), CItemsInfo::AssignItemsTags(), SNSCommandArguments::AssignValues(), variation::CVariationUtil::AsVariation_feats(), CAttachedHandles::Attach(), variation::CHgvsParser::AttachHgvs(), variation::CVariationUtil::AttachProteinConsequences(), variation::CVariationUtil::AttachSeq(), CBlobSplitterImpl::AttachToSkeleton(), CDiscrepancyContext::AutofixAll(), AutofixBiosrc(), AutofixProductNames(), Blast_FindDustFilterLoc(), Blast_FindWindowMaskerLoc(), Blast_Message2TSearchMessages(), BlastHitList2SeqAlign_OMF(), CAlignFormatUtil::BlastPrintError(), BOOST_AUTO_TEST_CASE(), CMPCrossAlignView::BroadcastVisibleRange(), CAlnMixSegments::Build(), BuildAln(), BuildGoodProtSeq(), CSimpleLayout::BuildLayout(), CColumnLayout::BuildLayout(), COverlayLayout::BuildLayout(), CProjectTreeBuilder::BuildProjectTree(), CAlnMixSequences::BuildRows(), CEquivRangeBuilder::CalcMatches(), CSGAlignmentDS::CalculateAlignmentScore(), CDiffList::CalculateOffsets(), CChainer::CChainerImpl::CalculateSpliceWeights(), CChain::CalculateSupportAndWeightFromMembers(), CAlignSort::CAlignSort(), CAppJobDispatcher::CancelAllJobs(), Canonicalize(), CChain::CChain(), CChainMembers::CChainMembers(), CCommentItem::CCommentItem(), CComponentSearchJob::CComponentSearchJob(), CCriteriaSet_CalculateMemberships(), CCSraDb_Impl::CCSraDb_Impl(), CFeatureSearchJob::CFeatureSearchJob(), CConvertSetTypeDlg::ChangeNotify(), ChangeNucId(), variation_ref::CVariationUtil::ChangeToDelins(), variation::CVariationUtil::ChangeToDelins(), CSeqTable_sparse_index::ChangeToIndexes(), CSeqTable_sparse_index::ChangeToIndexes_delta(), CSeqTable_multi_data::ChangeToInt_delta(), CSeqTable_multi_data::ChangeToInt_scaled(), CSeq_loc::ChangeToMix(), CSeqTable_multi_data::ChangeToReal_scaled(), variation::CVariationUtil::CheckAmbiguitiesInLiterals(), CheckConnectsTimeout(), CWorkspaceAutoSaver::CheckCrash(), CWNJobWatcher::CheckForInfiniteLoop(), CConnTest::CheckFWConnections(), CLatLonCountryMap::CLatLonCountryMap(), CleanDoubleQuote(), CDBServiceMapperCoR::CleanExcluded(), CSparseAlignment::Clear(), CObjectIndex::Clear(), CWriteDB_PackedBuffer< BLOCK >::Clear(), CTraversalNode::Clear(), CUsedTlsBases::ClearAll(), CDB_UserHandler::ClearExceptions(), ClearFocus(), CCleanup::ClearInternalPartials(), CPluginArgSet::ClearObjects(), CObjectList::ClearRows(), CFeatureGenerator::SImplementation::ClearScores(), CHit::Clone(), CWriteDB_Volume::Close(), impl::CDriverContext::CloseUnusedConnections(), CObjMgr_QueryFactory::CObjMgr_QueryFactory(), NTweakExon::CollapseNonframeshiftting(), CAlignCollapser::CollapsIdentical(), CDiscrepancyGroup::Collect(), CollectProteins(), CollectSequencesByProjectID(), CReadBlastApp::CollectSimpleSeqs(), CUnorderedSplitter::CombineAlignments(), CTableViewWithTextViewNav::CombineObjects(), IProjectViewFactory::CombineObjects(), CSequenceEditingEventHandler::CombineSelectedGenesIntoPseudogenes(), CSeqDBAliasNode::CompleteAliasFileValues(), CSeqMatch::CompNcbi8na(), CClusterer::ComputeClusters(), CSeqDBAliasNode::ComputeMasks(), CDBServiceMapperCoR::ConfigureFromRegistry(), CSeq_align_Mapper::Convert(), CSeq_align_Mapper_Base::Convert(), ConvertAuthorContainerMlToStd(), CSeq_inst::ConvertDeltaToRaw(), ConvertDoubleQuotes(), CSeq_loc_Conversion_Set::ConvertInterval(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CGapsEditor::ConvertNs2Gaps(), NTweakExon::ConvertOverlapsToGaps(), ConvertRegulatoryFeature(), ConvertToReverseComplement(), CRemoteUpdater::ConvertToStandardAuthors(), ConvertToStandardAuthors(), COMSSASearch::CopyHitsets(), CReadBlastApp::CopyInfoFromGenesToProteins(), CopyNode(), COMSSASearch::CopySettings(), COMSSASearch::CopySpectra(), CObjectOStreamAsnBinary::CopyString(), CorrectIntervalOrder(), CVariationUtilities::CorrectRefAllele(), CBlastAligner::CreateBlastAligners(), CRemoteBlastAligner::CreateBlastAligners(), CChainer::CChainerImpl::CreateChainsForPartialProteins(), CDataSourcesPage::CreateControls(), CConvertSetTypeDlg::CreateControls(), CreateDense_diagFromAnchoredAln(), CreateDllBuildTree(), CGC_Assembly::CreateHierarchy(), CSequence::CreateMsa(), CGraphTrack::CreateOverlay(), CViewManagerService::CreateViewInstanceByFingerprint(), CEditObjectSeq_feat::CreateWindowImpl(), CSeqMap::CSeqMap(), CSeqScores::CSeqScores(), CSequenceSearchJob::CSequenceSearchJob(), CStringMatching::CStringMatching(), CTablePrinter::CTablePrinter(), CTraversalPatternMatchCallback::CTraversalPatternMatchCallback(), CTraversalNode::CUserCall::CUserCall(), CVDBGraphDb_Impl::CVDBGraphDb_Impl(), CTrackContainer::DeleteAllJobs(), CUser_field::DeleteField(), SrcEditDialog::DeleteTableRow(), DeleteTableRow(), CRawSeqToDeltaByN::DeltaSeqToRaw(), CSelectionVisitor::DeSelectObject(), CMPCrossAlignView::DestroyView(), CAttachedHandles::Detach(), CTreeNode< TValue, TKeyGetter >::DetachNode(), CPluginManager< TClass >::DetachResolver(), CMultEditCommand::Do(), COpenViewManager::DoAsyncConversion(), CMytestApplication::DoProcessFeatureGeneOverlap(), SMakeProjectT::DoResolveDefs(), CTestActionList::DoTests(), COpenViewManager::DoTransition(), CMAViewManager::DoTransition(), CGraphOverlay::Drop(), CTSE_LockSet::Drop(), CChainer::DropAlignmentInfo(), CDataSource::DropAllTSEs(), CBDB_FileDumperApp::Dump(), CLDS2_ObjectParser::EndBlob(), CServer_ConnectionPool::Erase(), CDBServiceMapperCoR::Exclude(), CProjBulderApp::ExcludeProjectsByTag(), CAsyncObjConvert::Execute(), CChangeUnindexedObjectCommand< T >::Execute(), CGBObjectLoader::Execute(), CAsyncObjConvert2::Execute(), CBedObjectLoader::Execute(), CAgpObjectLoader::Execute(), CWigObjectLoader::Execute(), CGffObjectLoader::Execute(), CLBLASTObjectLoader::Execute(), CDumpSequences_wRanges::Execute(), CNCPeerControl::ExecuteSlice(), CTrackContainer::ExpandAll(), CAutoDefModifierCombo::ExpandByAnyPresent(), CReportNode::Export(), CAppDialogs::ExportDialog(), CNewCleanup_imp::ExtendedCleanupSeqSubmit(), CObjMgr_QueryFactory::ExtractScopes(), ExtractSupportModels(), CObjMgr_QueryFactory::ExtractUserSpecifiedMasks(), CCddInputData::CHit::FillData(), FillShortColumns(), CQueryFilter::FilterAlignments(), CAlignCollapser::FilterAlignments(), CGeneSelector::FilterGenes(), CChainer::CChainerImpl::FilterOutSimilarsWithLowerScore(), SrcEditDialog::FindBadColumns(), CGBReaderCacheManager::FindCache(), CWorkspaceFolder::FindChildFolderById(), CProjectFolder::FindChildFolderByTitle(), CWorkspaceFolder::FindChildFolderByTitle(), FindCompartments(), CChainer::CChainerImpl::FindContainedAlignments(), CGBProjectHandle::FindDataLoaderByLabel(), CSeq_feat::FindExt(), CSeq_align::FindExt(), CChainer::CChainerImpl::FindGenes(), CProSplign::FindGlobalAlignment(), FindMultiplyIncluded(), CFeatureTableReader::FindOpenReadingFrame(), CObjectConverter::FindRelations(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), CLocalFileRestorer::FindSMARTPrjTextView(), CProjectService::FindView(), CProjectService::FindViews(), FixCapitalization(), CCleanup::FixGeneXrefSkew(), FixMoltype(), CFeatureGenerator::SImplementation::FixOrderOfCrossTheOriginSeqloc(), CGb_qual::FixRptTypeValue(), FixTableAfterImport(), SrcEditDialog::FixTableAfterImport(), CTaxIdSet::FixTaxId(), CPacked_seqint::FlipStrand(), CSeq_loc_mix::FlipStrand(), variation::CVariationUtil::FlipStrand(), CMultiWriter::Flush(), CJob::Flush(), CDiagContext::FlushMessages(), CPairwiseAln::ForceGenomicCoords(), CWorkspaceFolder::ForEachProject(), CProjectFolder::ForEachProjectItem(), CResourcePool_Base< string, CNoLock, CResoursePool_NewClassFactory< string > >::Forget(), CTSE_ScopeInfo::ForgetTSE_Lock(), CTabularFormatter::Format(), CGenbankFormatter::FormatComment(), CGenbankFormatter::FormatFeature(), CGBSeqFormatter::FormatReference(), CBLASTParams::FromUserObject(), CMergeTreeAligner::GenerateAlignments(), CInversionMergeAligner::GenerateAlignments(), CMergeAligner::GenerateAlignments(), CBlastAligner::GenerateAlignments(), CInstancedAligner::GenerateAlignments(), CRemoteBlastAligner::GenerateAlignments(), CSplitSeqAlignMerger::GenerateAlignments(), CFileCode::GenerateCode(), CProjBulderApp::GenerateMsvcProjects(), CVDBObjectCacheBase::Get(), CMiscSeqTableColumn::GetApplyObjectsValues(), CAppTaskService::GetBackgroundedTasks(), CRemoteBlastDbDataLoader::GetBlobs(), CGBDataLoader::GetBlobs(), CDataSource::GetBlobs(), CDataLoader::GetBlobs(), CTrackContainer::GetChildContainerTrack(), CTempTrackProxy::GetChildTempTrack(), CRemoteBlastDbDataLoader::GetChunks(), CAlignCollapser::GetCollapsedAlgnments(), CLowerQuals::GetCommand(), CAddLinkageToGaps::GetCommand(), CAdjustFeaturesForGaps::GetCommand(), CConvertFeatDlg::GetCommand(), CRemoveTextInsideStrDlg::GetCommand(), CApplyRNAITSDlg::GetCommand(), CAuthorReplacePanel::GetCommand(), CDensityMap< CntType >::GetDensityMap(), GetDustMasks_SkipNs(), CExtensionRegistry::GetExtension(), CExtensionRegistry::GetExtensionPoints(), CExtensionPoint::GetExtensions(), CViewManagerService::GetFactories(), CSeqTextDataSource::GetFeatureData(), CSeqTextDataSource::GetFeaturesAtPosition(), CGraphOverlay::GetHTMLActiveAreas(), CGlyphContainer::GetHTMLActiveAreas(), IEditingActionDescJournal::GetImprintOrCitgen(), GetItemsByBiosource(), CSelectFeatures::GetMainObject(), CNetBLASTUIDataSource::GetMenu(), CMergeBitsetBlob< BV >::GetMergeBuffer(), GetMiscTableFromSeqEntry(), GetNumOfObjects(), CDiscrepancyCore::GetObjects(), CProjectService::GetObjProjects(), CAlignCollapser::GetOnlyOtherAlignments(), CTable2AsnContext::GetOrgRef(), GetOrgRefs(), CProjectService::GetProjectTreePanel(), CMaskedRangeSet::GetRanges(), CCSRADataLoader_Impl::GetReadsFileInfo(), CNCPeerControl::GetReadyForShutdown(), CCSraRefSeqIterator::GetRefBioseq(), CCSRADataLoader_Impl::GetRefSeqInfo(), CRemoteBlast::GetResultSet(), CAppTaskService::GetRunningTasksCount(), CProjectTreePanel::GetSelectedProjectIds(), CEditPubDlg::GetSelectedPub(), CViewGraphic::GetSelection(), CProjectTreeView::GetSelection(), CSrcEditPanel::GetSeqEntryHandle(), CGroupExplode::GetSeqFeats(), CStructuredCommentPanel::GetStructuredCommentRules(), CSeqTextDataSource::GetSubtypesForAlternatingExons(), CGencollIdMapper::GetSynonyms(), GetTaxIdWithWindowMaskerSupport(), CTimeReporter::GetTime(), CSeqTextDataSource::GetToolTipForSourcePos(), CBulkCmdDlg::GetTopLevelSeqEntryAndProcessor(), CValidateFrame::GetTopSeqAndSeqSubmit(), CTrackUtils::GetTrackSettingsSetSelection(), CViewManagerService::GetTypeDescriptors(), CDbtag::GetUrl(), CSeqTextDataSource::GetVariations(), GetViewObjects(), CTextUtil::GetWordFrequencies(), CAlignGroup::GroupByLikeTaxIds(), CAlignGroup::GroupByTaxIds(), CLayoutGroup::HitTest(), CSeqGraphicConfig::IgnoreFeatureStrand(), CVariation::Index(), CColorTableScoringPanel::Init(), CAlnMixSequences::InitExtraRowsStartIts(), PT::CProjectFolder::Initialize(), PT::CWorkspace::Initialize(), CNCPeerControl::Initialize(), CNCSyncLog::Initialize(), CIdMapperConfig::Initialize(), CLayoutTrack::InitIconTextures(), CAlnMixSequences::InitRowsStartIts(), CAlnContainer::insert(), CLayoutGroup::InsertAft(), CMultAlign::InsertDashesInBase(), CSeq_loc_CI_Impl::InsertRange(), CPoolOfThreads_ForServer::KillAllThreads(), CStdPoolOfThreads::KillAllThreads(), CAlignRowGraphCont::Layout(), CGraphContainer::Layout(), CFeatureGraph::Layout(), C2DLayoutEngine::Layout(), CChainer::CChainerImpl::LeftRight(), CSeqUtils::LinkFeatures(), CmRNACDSLinker::LinkSelectedFeatures(), CGBProjectHandle::Load(), CCSRARefSeqInfo::LoadAnnotPileupChunk(), LoadedChunksPacket(), CFastaObjectLoader::LoadFromStream(), CAsnObjectLoader::LoadFromStream(), CDockManager::LoadLayout(), CNGAlignParams::LogDump(), main(), CHitList::MakeCanonical(), CMakeCdrProds::MakeCdrProds(), CChainer::CChainerImpl::MakeChains(), CTable2AsnContext::MakeGenomeCenterId(), CBlobSplitterImpl::MakeID2Chunk(), CCleanup::MakeSmallGenomeSet(), CGnomonAnnotator_Base::MapModelsToEditedContig(), CGnomonAnnotator_Base::MapModelsToOrigContig(), SChainMember::MarkIncludedForChain(), SChainMember::MarkPostponedForChain(), SChainMember::MarkUnwantedCopiesForChain(), MarkUnwantedLowSupportIntrons(), CReadBlastApp::match_na(), CHitList::MatchOverlappingSubHits(), CStringMatching::MatchString(), CFeatureGenerator::SImplementation::MaximizeTranslation(), CTraversalNode::Merge(), CTreeAlignMerger::Merge_AllAtOnce(), CTreeAlignMerger::Merge_Pairwise(), CCpGIslands::MergeIslesWithin(), CTable2AsnContext::MergeWithTemplate(), CTreeMinimalSet< TNode, TSet, TNodeList >::MinimalSet(), CEditingActionDescLocalId::Modify(), CEditingActionDescComment::Modify(), CGraphOverlay::MoveTrackOut(), CMAViewManager::NeedAnchorPanel(), CGraphContainer::NeedTooltip(), CAlignedFeatureGraph::NeedTooltip(), CInt_fuzz::Negate(), CAlignCompare::NextGroup(), CRawScoreVector< Key, Score >::Normalize(), CScoreVector< Key, Score >::Normalize(), NormalizeUnknownLengthGaps(), CProcessor::OffsetAllGis(), CSeq_align::OffsetRow(), CUnculTaxTool::OnApply(), CAddFeatureBetweenDlg::OnApplyButton(), CScoreMethodsDlg::OnButton1Click(), CTblEditDlg::OnClearTableClick(), CHitMatrixWidget::OnColorByScore(), CwxHistogramDlg::OnColourpickerctrl1ColourPickerChanged(), CMinPanelContainer::OnContextMenu(), CEditingBtnsPanel::OnDataChange(), CDiscrepancyDlg::OnDblClk(), CStructuredCommentPanel::OnDelete(), CProjectTreePanel::OnEnableDisable(), SrcEditDialog::OnExportQualsClick(), CBLAST_DB_Dialog::OnInitDialog(), CGraphContainer::OnMouseEvents(), CAlnPropertiesDlg::OnOkClick(), CUnculTaxTool::OnRefreshBtn(), CProjectTreePanel::OnRemove(), CAuthorNamesPanel::OnReplaceAllAuthors(), CAuthorNamesPanel::OnReplaceSameAuthors(), CMinPanelContainer::OnRestoreWindow(), CEditingBtnsPanel::OnReverseAuthorNamesClick(), CSelectTargetDlg::OnSelTargetAcceptClick(), CFeaturePanel::OnTrackInitFinished(), CViewGraphic::OnViewReleased(), CMPCrossAlignView::OnVisibleRangeChanged(), CAppDialogs::OpenViewlDialog(), CRawScoreVector< Key, Score >::operator*=(), CScoreVector< Key, Score >::operator*=(), CAlnPos_CI::operator++(), CAlnPos_CI::operator--(), CRawScoreVector< Key, Score >::operator/=(), CScoreVector< Key, Score >::operator/=(), CTreeNode< TValue, TKeyGetter >::operator=(), CPluginArgSet::operator[](), CSeqDBVol::OptimizeGiLists(), OverlapsSameAccessionAlignment::OverlapsSameAccessionAlignment(), CSeq_entry::Parentize(), CSeq_entry::ParentizeOneLevel(), CDiscrepancyContext::Parse(), ParseTitlesToNewSeqEntries(), PT::CProjectFolder::Paste(), PatchTargetSequence(), CChangePhyloPropertyCmd::PerformEdit(), CChangePhyloExpandCollapseCmd::PerformEdit(), CMessageListener_Stack::Post(), CConnTest::PostCheck(), CRemoteUpdater::PostProcessPubs(), CConnTest::PreCheck(), CGnomonAnnotator::Predict(), CDisplaySeqalign::PrepareBlastUngappedSeqalignEx2(), CAppTaskService::PreShutDownService(), CHTML_table::PrintBegin(), CNCBINode::PrintChildren(), printed_ranges(), printGFF3(), CBlastFormat::PrintPhiResult(), CRawScoreVector< Key, Score >::ProbNormalize(), CScoreVector< Key, Score >::ProbNormalize(), CReadDispatcher::Process(), CReadBlastApp::processAnnot(), subfuse::CSubmissionCollector::ProcessFile(), CAsnvalApp::ProcessSeqSubmit(), ProductToSource(), ProjectExon_oldlogic(), CLayoutGroup::PropagateRelatedSelection(), CNewCleanup_imp::ProtSeqBC(), CBlockingQueue< TRequest >::Put(), CBlast_def_line_set::PutTargetGiFirst(), CSplitQueryTestFixture::QuerySplitter_BlastnMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastnSingleQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxMultiQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxSingleQueryMultiChunk(), CMuscleTool::QuickLaunch(), CSplignTool::QuickLaunch(), CKalignTool::QuickLaunch(), CMafftTool::QuickLaunch(), CGlimmerReader::Read(), CGFFReader::Read(), readGFF3(), readGFF3Gap(), CLocalFileRestorer::ReadObjectFromFile(), CHgvsReader::ReadSeqAnnot(), CSeq_entry::ReassignConflictingIds(), CAdjustFeaturesForGaps::RecalculateGapIntervals(), CFeatureGenerator::SImplementation::RecalculateScores(), CAutoDefWithTaxonomy::RegeneratePopsetTitles(), CAutoDef::RegenerateSequenceDefLines(), CViewManagerService::RegisterFactory(), CReverseObjectStore< TKey, TObject >::ReleaseObject(), CTSE_ScopeInfo::ReleaseUsedTSEs(), CCDSInfo::Remap(), CGeneModel::Remap(), CFeatIdRemapper::RemapIds(), CSeq_align::RemapToLoc(), CGlContainer::Remove(), CLayoutGroup::Remove(), CBDB_Transaction::Remove(), CFilterSet::Remove(), CCompoundRegistry::Remove(), CRemoveSet::remove_sets_from_set(), CSeriesBase::RemoveAllArrays(), CProjectFolder::RemoveAllChildItems(), CDockLayoutTree::CNode::RemoveAllChildren(), CTreeNode< TValue, TKeyGetter >::RemoveAllSubNodes(), CPluginArgSet::RemoveArgument(), CWorkspaceFolder::RemoveChildFolder(), CProjectFolder::RemoveChildFolder(), CProjectFolder::RemoveChildItem(), CMinPanelContainer::RemoveClient(), CGBDocument::RemoveDataLoader(), RemoveDbxref(), TSearchMessages::RemoveDuplicates(), CSeq_feat::RemoveExt(), CExtensionPoint::RemoveExtension(), CExtensionRegistry::RemoveExtension(), CExtensionRegistry::RemoveExtensionPoint(), CSeq_annot_Info::RemoveFeatId(), CBioTreeFeatureList::RemoveFeature(), CGene::RemoveGeneFromOtherGenesSets(), CBioseq_Info::RemoveId(), CReadBlastApp::RemoveInterim2(), CEnvironmentRegistry::RemoveMapper(), CCleanup::RemoveNcbiCleanupObject(), CTreeNode< TValue, TKeyGetter >::RemoveNode(), CWorkspaceFolder::RemoveProject(), CAutoDefSourceGroup::RemoveQual(), CAutoDefModifierCombo::RemoveQual(), RemoveRowsFromTable(), CBioseq_Base_Info::RemoveSeqdesc(), CGnomonAnnotator::RemoveShortHolesAndRescore(), RemoveSpaces(), CWriteDB_Volume::RenameSingle(), CGraphContainer::Render(), CGraphPanel::Render(), CSeqTextDataSource::RenderFeatureExtras(), CSeqGraphicPane::RenderPdf(), CPhyloSelectionSetMgr::RenumberClusterIDs(), COMSSASearch::RenumberSearchSettingId(), COMSSASearch::RenumberSpectrumNumber(), variation_ref::RepackageAssertedSequence(), variation::RepackageAssertedSequence(), CRegexpUtil::ReplaceRange(), CChainer::CChainerImpl::ReplicatePStops(), CReadBlastApp::reportProblems(), pub_report::CUnpublishedReport::ReportUnpublished(), CPhyTreeFormatter::RerootTree(), CMergeBitsetBlob< BV >::Reset(), CAlnMixMerger::Reset(), CReadDispatcher::ResetCaches(), CScope_Impl::ResetDataAndHistory(), CDataSource_ScopeInfo::ResetDS(), CSubmissionPrepMainPanel::ResetFieldsInUse(), CHitMatrixGraph::ResetGlyphSelection(), CScope_Impl::ResetHistory(), ResetLinkageEvidence(), CSeq_align::ResetNamedScore(), ResetOrgname(), SNetServerPoolImpl::ResetServerConnections(), CPacked_seqint::ResetStrand(), CSeq_loc_mix::ResetStrand(), CNcbiTable< TValue, TRow, TColumn >::Resize(), CPluginManager< TClass >::ResolveFile(), CGeneFinder::ResolveGeneXref(), RestoreOriginalHits(), RevComp(), CDense_seg::Reverse(), ReverseComplement(), ReverseComplementCDRegion(), ReverseComplementLocation(), CGeneModel::ReverseComplementModel(), CObjectManager::RevokeAllDataLoaders(), CChainer::CChainerImpl::RightLeft(), CFileDBEngine::RollbackTransaction(), CAlnMixSequences::RowsStartItsContsistencyCheck(), CDemoSeqQaApp::Run(), CSampleNetScheduleClient::Run(), CTestCompartApplication::Run(), CSeqSubSplitter::Run(), CSeqDescrRetrievalJob::Run(), CGumbelParamsApplication::Run(), CId2FetchApp::Run(), CMergeVolumes::Run(), CDeltaBlast::Run(), CVectorScreen::Run(), CFeatureLoadingJob::Run(), CCompartmentFinder< THit >::Run(), CSplign::Run(), CEditBioseqSampleApp::Run(), CFeatCompareJob_Align::Run(), CSeqDBDemo_Threaded::Run(), CAsn2Asn::RunAsn2Asn(), CMacroFlowEditor::RunScriptStandalone(), variation_ref::CVariationUtil::s_AddIntronicOffsets(), s_AddSeqLocMix(), s_BalanceTasks(), s_BLAST_OneSubjectResults2CSeqAlign(), s_BuildAlignDataSource(), s_CheckEmptyLists(), s_CleanSeqAlign(), s_CollapseProjectFolder(), s_CollectCollidingIDs_Entry(), CUpdateSeq_Input::s_ConvertDeltaToRawEntry(), variation::CVariationUtil::s_ConvertInstOffsetsToPlacementOffsets(), CSeq_loc_Conversion::s_ConvertToMix(), s_Create5ColFeatTable(), s_CreateItems(), s_DeleteOldestSockets(), s_DivvyUpAlignments_ProcessAnnot_Dendiag(), s_ExtendEntriesFromAlignments(), s_ExtractSeqIds(), variation_ref::CVariationUtil::s_FactorOutLocsInPlace(), variation::CVariationUtil::s_FactorOutPlacements(), s_FindOrfs(), s_FindProjectTreePanel(), s_FindTrackProxy(), CUpdateSeq_Input::s_FixCollidingIDs_Annot(), CUpdateSeq_Input::s_FixCollidingIDs_Entry(), s_FixZeroVersions(), CSeq_id_Resolver::s_Get(), s_GetMinLocalSyncedRecordNo(), s_GetOrCreateFolder(), s_GetPartsFromReply(), s_InitializeStructuredCommentRules(), s_InitializeViews(), CSeqFeatData::s_InitLegalQuals(), CSeqFeatData::s_InitMandatoryQuals(), CSeqFeatData::s_InitXrefAllowedSubtypesTable(), CSeqFeatData::s_InitXrefProhibitedSubtypesTable(), s_IsReadyForShutdown(), s_IsValidException(), s_ItemsToViews(), s_MakeLittleEndian(), s_MakePackedInt2(), CHitFilter< THit >::s_MergeAbutting(), s_OldGetTaxIdWithWindowMaskerSupport(), s_ProcessInstitutionCollectionCodeLine(), s_ProcessOrgRefMapLine(), variation_ref::CVariationUtil::s_PropagateLocsInPlace(), s_PurgeTrees(), variation_ref::CVariationUtil::s_Remap(), s_RemoveAnnot(), s_RemoveAnnotsFromEntry(), s_RemoveFolder(), s_RemoveItem(), s_ReplaceCtrlAsInTitle(), s_ReplaceFeatureIdXref(), s_ReplaceUforT(), s_ResetExecTime(), variation_ref::CVariationUtil::s_ResolveIntronicOffsets(), s_RoundScores(), s_SeqLocToRangeInfoMap(), s_SeqLocToRangeInfoMapByStrand(), s_SeqLocToTotalRangesInfoMapByStrand(), s_SetFieldAt(), CSequenceUpdater::s_Shift_CDSCodeBreaks(), s_SplitAlignVectorBySubjects(), CGBDocument::Save(), CGBProjectHandle::SaveViewSettings(), CDBUDRandomMapper::ScalePreference(), CBlastScorer::ScoreAlignments(), CPctIdentScorer::ScoreAlignments(), CPctCoverageScorer::ScoreAlignments(), CExpansionScorer::ScoreAlignments(), CWeightedIdentityScorer::ScoreAlignments(), CHangScorer::ScoreAlignments(), COverlapScorer::ScoreAlignments(), CGPipeAlignmentScorer::ScoreAlignments(), CClippedScorer::ScoreAlignments(), CCommonComponentScorer::ScoreAlignments(), CChainer::CChainerImpl::ScoreCdnas(), CMergeTree::Search(), CHitMatrixGraph::SelectGlyph(), CSelectionVisitor::SelectSelection(), CNewCleanup_imp::SeqLocBC(), CLayoutGroup::Set(), SetAllSocksRunnable(), CSourceModParser::SetAllUnused(), SetAuthList(), SetAuthorNames(), SetBiomol(), CTSE_Info::SetBioseqUpdater(), SetChromosome(), CHitGlyph::SetColorIndex(), CGlyphContainer::SetCommentGlyphs(), SetCommon(), SetCompleteness(), CChainer::CChainerImpl::SetConfirmedStartStopForProteinAlignments(), SetDbxref(), SetDiv(), CTSE_ScopeInfo::SetEditTSE(), SetEnvSampleFixAmplifiedPrimers(), CSourceRequirements::SetExamples(), CBioTreeFeatureList::SetFeature(), CUser_object::SetFieldRef(), CUser_field::SetFieldRef(), CSeq_loc_mix::SetFirstLoc(), CChainer::CChainerImpl::SetFlagsForChains(), SetFocus(), CTabularFormatter::SetFormat(), SetGcode(), CTabularFormatter::SetGencoll(), CSeq_feat::SetGeneXref(), SetGenome(), CHitMatrixRenderer::SetGraphColor(), CGlyphContainer::SetHighlights(), CSeqGraphicPane::SetHorizontal(), CGenetic_code::SetId(), CSeq_loc::SetId(), CPubField::SetImprint(), CGlyphContainer::SetLabelGlyphs(), CGraphTrack::SetLayout(), SetLineage(), SetLinkageType(), SetLinkageTypeLinkedRepeat(), SetLinkageTypeScaffold(), CAlnMultiModel::SetMasterRow(), SetMGcode(), SetMolinfoForProtein(), CTableDataValidateParams::SetNamedBoolField(), CBlastAppArgs::SetOptions(), CBlastAppArgs::SetOptionsForSavedStrategy(), SetOrgMod(), SetOrigin(), SetPGcode(), CDBServiceMapperCoR::SetPreference(), CDBUDRandomMapper::SetPreference(), CCleanup::SetProteinName(), CClusterer::SetPrototypes(), CSeq_feat::SetProtXref(), CPubField::SetPubTitle(), variation_ref::CVariationUtil::SetReferenceSequence(), SetRefGeneTrackingStatus(), CSearchResultSet::SetRID(), CSelectionVisitor::SetSelectedObjectSig(), CMPCrossAlignView::SetSelection(), CPacked_seqint::SetStrand(), CSeq_loc_mix::SetStrand(), SetSubSource(), SetTargetedLocusName(), SetTaxname(), SetTaxon(), SetTech(), CEditingBtnsPanel::SetTextViewBackgroundColour(), CFixTitleCap::setTitle(), SetTitleName(), CTrackConfigManager::SetTrackConfig(), SetTransgenic(), SetUpCommandLineArguments(), CDBLinkField::SetVal(), CEditingActionDescJournal::SetValue(), variation::CVariationUtil::SetVariantProperties(), CReadBlastApp::short_proteins(), CTrackContainer::ShowAll(), CAppJobDispatcher::ShutDown(), CReadBlastApp::simple_overlaps(), CWriteDB_PackedSemiTree::Sort(), CMergedPairwiseAln::SortInsertions(), SortSeqDescr(), CReadBlastApp::SortSeqs(), SourceToProduct(), CBlobSplitterImpl::SplitPieces(), CSeqUtils::StringToRange(), NTweakExon::SubsumeMicroIntervals(), CDiscrepancyCase_COUNT_RRNAS::Summarize(), CDiscrepancyCase_SOURCE_QUALS::Summarize(), CDiscrepancyCase_DUP_DEFLINE::Summarize(), CDiscrepancyCase_COUNT_TRNAS::Summarize(), CDiscrepancyCase_COMMENT_PRESENT::Summarize(), CDiscrepancyCase_TITLE_AUTHOR_CONFLICT::Summarize(), CDiscrepancyCase_DUPLICATE_LOCUS_TAGS::Summarize(), CDiscrepancyCase_MISMATCHED_COMMENTS::Summarize(), CDiscrepancyContext::Summarize(), CDiscrepancyCase_FEATURE_COUNT::Summarize(), CDiscrepancyCase_CITSUBAFFIL_CONFLICT::Summarize(), CDiscrepancyCase_SUBMITBLOCK_CONFLICT::Summarize(), CDiscrepancyCase_INCONSISTENT_MOLINFO_TECH::Summarize(), CDiscrepancyCase_INCONSISTENT_DBLINK::Summarize(), CDiscrepancyCase_INCONSISTENT_STRUCTURED_COMMENTS::Summarize(), CDiscrepancyCase_GENE_PRODUCT_CONFLICT::Summarize(), SummarizeTaxnameConflict(), CSeq_align_set::SwapRows(), CSeq_align::SwapRows(), CRfamTool::sx_GetModel(), sx_PopLastNewPtrMultiple(), CGuiCoreHelper::Sync(), CScheduler_MT::TaskExecuted(), TestCollidingAccessionFixes(), CMytestApplication::TestFeatureGeneOverlap(), CMultiAlignViewFactory::TestInputObjects(), CDiscrepancyContext::TestString(), CMacroFunction_ModifyPrimerSeq::TheFunction(), CMacroFunction_ApplyPublication::TheFunction(), CMacroFunction_FixFormat::TheFunction(), CMacroFunction_FixPubCaps::TheFunction(), CMacroFunction_SetStringQual::TheFunction(), CMacroFunction_EditStringQual::TheFunction(), CMacroFunction_ApplyOtherFeature::TheFunction(), NStr::ToLower(), NStr::ToUpper(), CFeatureGenePanel::TransferDataFromWindow(), CRemarksAndSerialNumberPanel::TransferDataFromWindow(), CtmRNASubPanel::TransferDataToWindow(), CPublicationTypePanel::TransferDataToWindow(), CSubPrep_panel::TransferDataToWindow(), CUserFieldStringListValidator::TransferFromWindow(), CFeatureGenerator::SImplementation::TransformProteinAlignToTranscript(), TransformSeqAnnots(), TranslateCDSCommand(), CSeqTranslator::TranslateToProtein(), CChainer::CChainerImpl::TrimAlignmentsIncludedInDifferentGenes(), CScoreVector< Key, Score >::TrimCount(), CScoreVector< Key, Score >::TrimLength(), TryToSanitizeHtmlList(), CChangeUnindexedObjectCommand< T >::Unexecute(), CDllResolver::Unload(), CFeaturePanel::Update(), CLayoutGroup::Update(), CPhyloTreePane::UpdateDataSource(), PT::CRoot::UpdateDataSources(), CCleanup::UpdateECNumbers(), CSNPFeatureParams::UpdateLabelPos(), CGraphPanel::UpdateLimits(), CAlnMultiModel::UpdateOnStyleChanged(), UpdateOrgInformation(), CRemoteUpdater::UpdatePubReferences(), CSelectionVisitor::UpdateSelection(), CGraphOverlay::UpdateSource(), CSymbolGuard::UpdateSymbols(), UpgradeSeqLocId(), CNewCleanup_imp::UserObjectBC(), CConnValidatorCoR::Validate(), CPkgManager::ValidatePackages(), CFlatItemFormatter::Wrap(), CMultiWriter::Write(), CTimeReporter::Write(), CTabularFormatter::WriteHeader(), CAlignmentTrack::x_AddAlignFeat_Recursive(), CAlignmentTrack::x_AddAlignFeatLayout(), CAlignmentTrack::x_AddAlignmentLayout(), CTSE_Split_Info::x_AddAnnotPlace(), CTSE_Split_Info::x_AddAssemblyInfo(), CTSE_Split_Info::x_AddBioseqPlace(), CGeneModelTrack::x_AddCDSmRNA_SNPLayout(), CGeneModelTrack::x_AddCDSProduct_FeatsLayout(), CTSE_Split_Info::x_AddDescInfo(), CGeneModelTrack::x_AddFeatProductLayout(), CFeatureTrack::x_AddFeaturesLayout(), CClipboard::x_AddFlavor(), CEpigenomicsTrack::x_AddGraphs(), CGBProjectTool::x_AddItem(), CGBDocument::x_AddItems(), CGeneModelTrack::x_AddLandMarkFeaturesLayout(), CNewCleanup_imp::x_AddNcbiCleanupObject(), CSeqSearch::x_AddPattern(), CDBSourceItem::x_AddPDBBlock(), CDBSourceItem::x_AddPIRBlock(), CDBSourceItem::x_AddPRFBlock(), CFeatureItem::x_AddRptUnitQual(), CSatelliteColumn::x_AddSatelliteName(), CSatelliteColumn::x_AddSatelliteType(), CSegmentMapTrack::x_AddSegmentMapLayout(), CTSE_Split_Info::x_AddSeq_data(), CConvertSetTypeDlg::x_AddSet(), CSixFramesTransTrack::x_AddTranslations(), CMSAToolJob::x_AddTreeProjectItem(), CTSE_Split_Info::x_AddUsedMemory(), x_AdjustListPair(), CFeatGapInfo::x_AdjustOrigLabel(), CSeq_loc_Mapper_Base::x_AdjustSeqTypesToProt(), CNgAligner::x_Align_Impl(), CScoringJob::x_AllocBuffer(), CIgBlast::x_AnnotateD(), CIgBlast::x_AnnotateDJ(), CIgBlast::x_AnnotateJ(), CSourceModParser::x_ApplyMods(), CMiscSeqTable::x_ApplyRowToEntry(), CSrcTablePrimerColumn::x_ApplyStringToPrimerSet(), CCreateGeneModelTask::x_AssignIDsAndCrossLinkFeats(), CCreateGeneModelTask::x_AssignIDsAndUpdateGenes(), CMultiAligner::x_AssignRPSResFreqs(), CId2ReaderBase::x_AssignSerialNumbers(), CGBDocument::x_AttachDataLoaders(), CSequenceUpdater::x_AttachFeaturesToNewSeq(), CBlastOptionsRemote::x_AttachValue(), CBlastQuerySourceOM::x_AutoDetectGeneticCodes(), CAutogeneratedCleanup::x_BasicCleanupBioseq_annot(), CAutogeneratedCleanup::x_BasicCleanupBioseq_annot_E_E_data_ftable(), CAutogeneratedCleanup::x_BasicCleanupBioseq_descr_descr(), CAutogeneratedCleanup::x_BasicCleanupBioseq_inst_inst_ext_ext_map_map(), CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot(), CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E_data_ftable(), CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E_data_graph_ETC(), CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E_data_seq_table_seq_table_columns_ETC(), CAutogeneratedCleanup::x_BasicCleanupBioseqSet_annot_E_E_desc_desc_ETC(), CAutogeneratedCleanup::x_BasicCleanupBioseqSet_descr_descr_ETC(), CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set(), CAutogeneratedCleanup::x_BasicCleanupBioseqSet_seq_set_E_E_seq_seq_inst_inst_ext_ext_delta_delta_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqAnnot_data_ftable(), CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set_set_annot(), CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set_set_annot_E_E_data_ftable(), CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set_set_seq_set(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_cit_cit_article_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_cit_cit_book_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_cit_cit_journal_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_cit_cit_medline_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_cit_cit_patent_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_cit_cit_proc_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_cit_cit_pub_E_E_equiv_equiv(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_cit_cit_pub_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_dbxref_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_exts(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_exts_E_E_data(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_exts_E_E_data_E_E_data_fields(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_exts_E_E_data_E_E_data_objects(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_inference_E_E_basis_basis_accessions_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_inference_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_E_E_protein_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_support_support_model_evidence_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_mod_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_mod_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_hybrid_hybrid(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_subtype_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_cdregion_cdregion_code_break_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_clone_clone_clone_seq_clone_seq_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_dendiag_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_disc_disc(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_sparse_sparse_rows_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_spliced_spliced_exons_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_num_num_ref_ref_aligns_aligns_segs_std_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_pub_pub_num_num_ref_ref_aligns_aligns_segs_disc_disc_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_pub_pub_pub_pub1778_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_rna_rna_ext_gen_gen_quals_quals_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_E_E_syn_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_activity_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_E_E_name_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_txorg_txorg_orgname_orgname_name_hybrid_hybrid_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_consequence(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_instance_instance_delta_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_data_set_variations(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_ext_data_E_E_data_fields_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_ext_data_E_E_data_objects_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_locs_E_E_location_location_equiv_equiv(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_locs_E_E_location_location_mix_mix(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_ext_locs_E_E_location_location_packed_int_packed_int_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_location_location_equiv_equiv_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_article_article_title_title_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_equiv_equiv(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_authors_authors_names_std_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_man_man_cit_cit_imp_imp_history_history_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_pub_pub_patent_patent_priority_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_E_E_data_data_variation_variation_somatic_origin_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqFeat_xref_ETC(), CAutogeneratedCleanup::x_BasicCleanupSeqSubmit_data_annots(), CAutogeneratedCleanup::x_BasicCleanupSeqSubmit_data_annots_E_E_data_ftable(), CAutogeneratedCleanup::x_BasicCleanupSeqSubmit_data_entrys(), CNewCleanup_imp::x_BioseqSetGenBankEC(), CNewCleanup_imp::x_BothStrandBC(), CSelectionService::x_Broadcast(), CSparseAln::x_Build(), CInlineLayout::x_BuildLayout1Row(), CInlineLayout::x_BuildLayoutMultiRows(), CBinsGlyph::x_BuildNonEmptyBinList(), CGeneMarkerGlyph::x_BuildSignatures(), CBLAST_DB_Dialog::x_BuildTreeItems(), CSequenceEditingEventHandler::x_CacheSelectedLocations(), CScoringJob::x_CalculateAlignmentScores(), CFeatureGraph::x_CancelJobs(), CCmdPropagateFeat::x_CdsMapCodeBreaks(), CSequenceUpdater::x_ChangeIDInFeature(), CSeqDBVol::x_CheckVersions(), CCompoundRegistry::x_ChildLockAction(), CAlignCleanup::x_Cleanup_AlignVec(), CAlignCleanup::x_Cleanup_AnchoredAln(), CNewCleanup_imp::x_CleanupECNumberList(), CScope_Impl::x_ClearAnnotCache(), CScope_Impl::x_ClearCacheOnNewData(), CAlnVecMultiDataSource::x_ClearHandles(), CSparseMultiDataSource::x_ClearHandles(), CSeqGraphicPane::x_ClearMarkers(), CElementaryMatching::x_CompartPair(), CSeq_align_Mapper::x_ConvertAlignCvt(), CAlgoToolManagerBase::x_ConvertInputObjects(), CTaxon1::x_ConvertOrgrefProps(), CPromote::x_CopyCdregionToRNA(), CProjectService::x_CreateDocuments(), CSGFeatureJob::x_CreateFeature_Recursive(), CGeneModelFeatJob::x_CreateFeaturesWithFilter(), CSGAlignmentJob::x_CreateGeneModels(), CGeneModelFeatJob::x_CreateGeneModels(), CSGAnnotJob::x_CreateHistFromGraph(), CProSplignTool::x_CreateLoadingJob(), CSplignTool::x_CreateLoadingJob(), CCddInputData::x_CreateMsa(), CNGAlignJob::x_CreateProjectItems(), CBLASTSeqToolJob::x_CreateProjectItems(), CCleanupAlignmentsJob::x_CreateProjectItems(), CMergeAlignmentsJob::x_CreateProjectItems(), CGroupAlignmentsJob::x_CreateProjectItems(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CBamLoadingJob::x_CreateProjectItems(), CTreeBuilderJob::x_CreateProjectItems(), CSplignJob::x_CreateProjectItems(), CWindowMaskerJob::x_CreateProjectItems(), CTraversalNode::x_DepthFirst(), CGBDocument::x_DetachDataLoaders(), CTSE_ScopeInfo::x_DetachDS(), CBDB_Transaction::x_DetachFromFiles(), CDisplaySeqalign::x_DoFills(), CScopeTransaction_Impl::x_DoFinish(), CAdjustFeaturesForGaps::x_DoGroup(), CSNPSearchJob::x_DoSearch(), CComponentSearchJob::x_DoSearch(), CEntrezSearchJob::x_DoSearch(), COrfSearchJob::x_DoSearch(), CTraversalMerger::x_DoTier(), CBioseq_Base_Info::x_DoUpdate(), CBioseq_set_Info::x_DoUpdate(), CMatePairGlyph::x_Draw(), CBioseq_Base_Info::x_DSAttachContents(), CBioseq_set_Info::x_DSAttachContents(), CBioseq_Base_Info::x_DSDetachContents(), CBioseq_set_Info::x_DSDetachContents(), CAsnSubCacheCreateApplication::x_EliminateIdsAlreadyInCache(), CSGAlignmentJob::x_Execute(), CSGFeatureJob::x_Execute(), CSGAlignScoringJob::x_Execute(), CBatchFeatJob::x_Execute(), CNewCleanup_imp::x_ExpandCombinedQuals(), CIgBlast::x_ExtendAlign(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupBioseq_annot(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupBioseq_inst_inst_ext_ext_map_map(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupBioseqSet_annot(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupBioseqSet_annot_E_E_desc_desc_ETC(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupBioseqSet_seq_set(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupBioseqSet_seq_set_E_E_seq_seq_descr_descr_ETC(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqAnnot_data_ftable(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqEntry_set_set_annot(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqEntry_set_set_seq_set(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_biosrc_biosrc_org_org_orgname_orgname_name_hybrid_hybrid(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_gene_ETC(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_E_E_data_data_txinit_txinit_protein_ETC(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqFeat_xref_ETC(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqSubmit_data_annots(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupSeqSubmit_data_entrys(), CFeatureTrack::x_ExtracGlyphs_Recursive(), CSnpJob::x_FetchGraphs(), CCddInputData::x_FillHitsData(), CSeqDBVol::x_FilterHasId(), CBLAST_DB_Dialog::x_FilterItems(), CHttpCookies::x_Find(), CTblEditDlg::x_FindBadImportColumns(), CMultiAligner::x_FindConstraints(), CMultiAligner::x_FindDomainHits(), CMinPanelContainer::x_FindItemByPos(), CTimeReporter::x_FindOrCreate(), CTaxon2_data::x_FindProperty(), CMultiAligner::x_FindQueryClusters(), CwxAbstractTableModel::x_FireTableChanged(), CVariationUtilities::x_FixAlleles(), CFlatGatherer::x_FlushComments(), CNcbiTable< TValue, TRow, TColumn >::x_Free(), CSequenceUpdater::x_FuseProtFeatsForCDS(), CDBSourceItem::x_GatherInfo(), CContigItem::x_GatherInfo(), CNewCleanup_imp::x_GeneOntologyTermsBC(), CProSplignJob::x_GenerateCompartments(), CTraversalCodeGenerator::x_GenerateHeaderFile(), CTraversalCodeGenerator::x_GenerateSourceFile(), CSGAlignmentJob::x_GetAlignments(), COrgName::x_GetAttribFlag(), COrgName::x_GetAttribValue(), CCreateGeneModelTask::x_GetCommand(), CGBProject::x_GetContainingFolder(), CTMgr_AnnotCounts::x_GetCount(), CInstancedAligner::x_GetDistanceInstances(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CSeqDBVol::x_GetHdrAsn1(), CPublicationTypePanel::x_GetMainPub(), CSeq_loc_Mapper_Base::x_GetMappedSeq_loc(), CNAUtils::x_GetNAEntrezLinks(), CNAUtils::x_GetNAMetaData(), CObjectListWidgetSel::x_GetObjectList(), CGeneFeatFromOtherFeatDlg::x_GetSelectedFeats(), CEditingBtnsPanel::x_GetSelectedLocations(), CCorrectGenesDialog::x_GetSelectedPair(), CEditingBtnsPanel::x_GetSelectedSeq(), CSequenceUpdater::x_GetSeqAnnot_WithoutCDS(), CCreateGeneModelTask::x_GetUpdatedGeneCommand(), CFlatGatherer::x_GiveOneResidueIntervalsBogusFuzz(), CCreateGeneModelTask::x_Group_By_GeneID(), CCreateGeneModelTask::x_GroupGenes(), CIdMapperTestApp::x_HandleAlignments(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CEditObjectSeq_feat::x_HandleCdsProduct(), CIdMapperTestApp::x_HandleFeatures(), CGlWidgetPane::x_Handlers_handle(), CInversionMergeAligner::x_HandleSingleStrandMerging(), x_HitToConstraints(), CGC_Assembly::x_Index(), variation::CVariationUtil::x_InferNAfromAA(), CGencollIdMapper::x_Init(), CSeq_annot_Info::x_InitAlignKeys(), CSeq_annot_Info::x_InitAlignList(), CNcbiTestApplication::x_InitCommonParserVars(), CSeq_annot_Info::x_InitFeatKeys(), CSeq_annot_Info::x_InitFeatList(), CFeatureTrack::x_InitGlyphs_Recursive(), CSeq_annot_Info::x_InitGraphKeys(), CSeq_annot_Info::x_InitGraphList(), CAgpConverter::x_InitializeAndCheckCopyOfTemplate(), CAgpConverter::x_InitializeCopyOfTemplate(), CLinks::x_InitLinkPtrs(), CSeq_annot_Info::x_InitLocsList(), CBLASTToolManager::x_InitProjectParams(), CAlgoToolManagerBase::x_InitProjectParams(), CPhyTreeFormatter::x_InitTreeFeatures(), CPhyTreeFormatter::x_InitTreeLabels(), CAlnSpanVertModel::x_InsertIntrons(), CAlnMultiRenderer::x_InvalidateRows(), CClusterer::x_JoinClustElem(), CClusterer::x_JoinClusters(), CWNJobWatcher::x_KillNode(), CBlastPrelimSearch::x_LaunchMultiThreadedSearch(), CLayeredLayout::x_LayerByPos(), CLayeredLayout::x_LayerBySize(), CAlignedFeatureGraph::x_Layout(), CAxisRenderer::x_LayoutLabels(), CGBProjectHandle::x_LinkChildFolders(), CMetaRegistry::x_Load(), CFileLoader::x_LoadAGP(), CTSE_Split_Info::x_LoadAnnot(), CTSE_Split_Info::x_LoadAssembly(), CTSE_Split_Info::x_LoadBioseqs(), CAppHitFilter::x_LoadConstraints(), CSplitDataLoader::x_LoadData(), CBlastDbDataLoader::x_LoadData(), CTSE_Split_Info::x_LoadDescr(), CTSE_Split_Info::x_LoadSeq_entry(), CSGSeqGraphJob::x_LoadSeqTable(), CTSE_Split_Info::x_LoadSequence(), CSequenceTrack::x_LoadSettings(), CAsnSubCacheCreateApplication::x_LocateBlobsInCache(), CMacroFunction_AuthorFix::x_MakeAuthorChanges(), CAutodefJob::x_MakeChanges(), CCSraDb_Impl::x_MakeRefSeq_ids(), CFeaturePanel::x_MakeTopLevelTracks(), CFeatureGenerator::SImplementation::x_MapFeature(), CSequenceUpdater::x_MappedFeature_ChangeId(), CSequenceUpdater::x_MappedFeature_ThroughAlign(), CPhyTreeFormatter::x_MarkLeavesBySeqId(), CGenbankFormatter::x_Medline(), CAlnMixMerger::x_Merge(), CTreeAlignMerger::x_Merge_Dist_Impl(), CMergeAligner::x_MergeAlignments(), CAlnGraphic::x_MergeDifferentSeq(), CVecscreen::x_MergeLowerRankSeqalign(), CMultiAlignView::x_MergeObjects(), CGFFReader::x_MergeRecords(), CAlnGraphic::x_MergeSameSeq(), CMergeAligner::x_MergeSeqAlignSet(), CInversionMergeAligner::x_MergeSeqAlignSet(), CAlnMixSegments::x_MinimizeGaps(), CProjectServiceTestJob::x_ModifyItems(), CNewCleanup_imp::x_MoveNpDBlinks(), CNewCleanup_imp::x_MoveNpPub(), CNewCleanup_imp::x_MoveNpSrc(), CNewCleanup_imp::x_MovePopPhyMutPub(), CMultiAligner::x_MultiAlignClusters(), SGridWorkerNodeImpl::x_NotifyJobWatchers(), CGraphTrack::x_OnJobCompleted(), CGraphOverlay::x_OnLayoutChanged(), CGraphTrack::x_OnLayoutChanged(), CAlignmentTrack::x_OnLayoutPolicyChanged(), CRWLockHolder::x_OnLockAcquired(), CRWLockHolder::x_OnLockReleased(), CGraphTrack::x_OnSettingsIconClicked(), CSeq_loc_Mapper_Base::x_OptimizeSeq_loc(), CCache< TKey, TValue, THandler, TLock, TSize >::x_PackElementIndex(), CBioseq_set_Info::x_ParentAttach(), CBioseq_set_Info::x_ParentDetach(), CGFFReader::x_PlaceAlignment(), CGFFReader::x_PlaceFeature(), CNewCleanup_imp::x_PostProcessing(), CAnnotCompareView::x_PreAttachToProject(), CDotMatrixView::x_PreAttachToProject(), CBinsJob::x_PreFetchFtable(), CSeq_loc_Mapper_Base::x_PreserveDestinationLocs(), CDisplaySeqalign::x_PrintFeatures(), CGencollIdMapper::x_PrioritizeIds(), CPrimeCacheApplication::x_Process_Fasta(), CExportStrategy::x_Process_Query(), CIgBlast::x_ProcessDGeneResult(), CIgBlast::x_ProcessDJResult(), CGeneModelFeatJob::x_ProcessLandMarkFeatures(), CSplignApp::x_ProcessPair(), CId2FetchApp::x_ProcessRequest(), CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile(), CPromote::x_PromoteFeatures(), variation_ref::CVariationUtil::x_ProtToPrecursor(), x_RangesToSeq_loc(), CDiscRepApp::x_ReadFile(), CIdMapperTestApp::x_RecurseMapSeqAligns(), CProjectTreePanel::x_RefreshProjectTables(), CGlWidgetPane::x_RegisterHandler(), CFeatureTrack::x_RegroupFeats(), CTrackContainer::x_ReinitSubtracks(), CYieldingRWLock::x_ReleaseLock(), CMetaRegistry::x_Reload(), CGFFReader::x_RemapGeneRefs(), CFlatGatherer::x_RemoveBogusFuzzFromIntervals(), CGencollIdMapper::x_RemoveHiddenAccessions(), CSequenceUpdater::x_RemoveNewIDInFeature(), CNewCleanup_imp::x_RemovePopPhyBioSource(), CNewCleanup_imp::x_RemovePopPhyMolInfo(), CSeqGraphicPane::x_Render(), CHitMatrixGraph::x_RenderHits(), CHitMatrixGraph::x_RenderPath(), CHitMatrixGraph::x_RenderSelection(), CProjectViewBase::x_ReportInvalidInputData(), CAlnMultiRenderer::x_ResetRowListMap(), CWriteDB_Impl::x_ResetSequenceData(), CTrackConfigManager::x_ResolveSubTracks(), CNWAligner::x_Run(), CSplign::x_Run(), CInstancedAligner::x_RunCleanup(), CSplign::x_RunOnCompartment(), CScheduler_MT::x_SchedQueueChanged(), CIgBlast::x_ScreenByAlignLength(), CMergeTree::x_Search_Recur(), CFeatureSearchJob::x_SearchFeatures(), CSequenceSearchJob::x_SearchSequence(), CHitMatrixGraph::x_SelectByPoint(), CHitMatrixGraph::x_SelectByRect(), CProSplignTool::x_SelectCompatibleInputObjects(), CFindOverlapTool::x_SelectCompatibleInputObjects(), CMergeTool::x_SelectCompatibleInputObjects(), CSplignTool::x_SelectCompatibleInputObjects(), CCleanupTool::x_SelectCompatibleInputObjects(), CAutodefToolManager::x_SelectCompatibleInputObjects(), CNGAlignTool::x_SelectCompatibleInputObjects(), ILayoutPolicy::x_SeparateObjects(), CMacroFunction_ApplyFeature::x_SetAdditionalFields(), CBioseq_Base_Info::x_SetAnnot(), CIgBlast::x_SetAnnotation(), CTSE_Split_Info::x_SetBioseqUpdater(), CMacroFunction_ConvertFeature::x_SetConvertOptions(), CSeqTableSetExt::x_SetField(), CBuildDatabase::x_SetLinkAndMbit(), CNewCleanup_imp::x_SetMolInfoTechFromGenBankBlock(), CSeq_align::x_SetNamedScore(), CBioseq_set_Info::x_SetObject(), CColumnLayout::x_SetObjectPos(), CLayeredLayout::x_SetObjectPos(), CSequenceUpdater::x_SetOldIDInFeatures(), CNewCleanup_imp::x_SetPartialsForProtein(), CSplign::x_SetPattern(), CVariationUtilities::x_SetReference(), CPubField::x_SetStatus(), CSuspectProductRulesEditor::x_SetUpTSEandUnDoManager(), CSequenceEditingEventHandler::x_SetUpTSEandUnDoManager(), CVariationNormalization_base< T >::x_Shift(), CMappingObjectLoader::x_ShowMappingDlg(), CWindowManagerService::x_ShowToolBar(), CWorkbench::x_ShutDownServices(), CGenbankFormatter::x_SmartWrapQuals(), CSGFeatureJob::x_SortFeature_recursive(), CSGFeatureJob::x_SortFeatures(), COligoSpecificityTemplate::x_SortHit(), COligoSpecificityCheck::x_SortPrimerHit(), CSplitDataLoader::x_SplitAnnot(), CTraversalCodeGenerator::x_SplitNodesByVar(), CSplitDataLoader::x_SplitSet(), CFlatGatherer::x_SubtractFromFocus(), x_TestAlignmentQuerySubjStrandCombinations(), CNewCleanup_imp::x_tRNACodonEC(), CTraversalPatternMatchCallback::x_TryToAttachPattern(), CTraversalPatternMatchCallback::x_TryToDeprecatePatternMatchers(), CTSE_Split_Info::x_TSEAttach(), CBioseq_Base_Info::x_TSEAttachContents(), CBioseq_set_Info::x_TSEAttachContents(), CBioseq_Base_Info::x_TSEDetachContents(), CBioseq_set_Info::x_TSEDetachContents(), CSeq_id_Giim_Tree::x_Unindex(), CSeq_id_PDB_Tree::x_Unindex(), CSeq_annot_Info::x_UnmapAnnotObjects(), CGlWidgetPane::x_UnregisterHandler(), CDataMiningService::x_UnRegisterTools(), CCompoundRWRegistry::x_Unset(), CTSE_Split_Info::x_UpdateAnnotIndex(), CBioseq_Base_Info::x_UpdateAnnotIndexContents(), CNamedGroup::x_UpdateBoundingBox(), CSequenceTrack::x_UpdateBoundingBox(), CGraphOverlay::x_UpdateBoundingBox(), CMatePairGlyph::x_UpdateBoundingBox(), CGraphTrack::x_UpdateBoundingBox(), CLayoutGroup::x_UpdateBoundingBox(), CGlyphContainer::x_UpdateComments(), CGlyphContainer::x_UpdateCommentTargetPos(), CTSE_Split_Info::x_UpdateFeatIdIndex(), CCreateGeneModelTask::x_UpdateGeneOnSequence(), CSeqAlignFilter::x_UpdateGiInSeqalign(), CId2ReaderBase::x_UpdateLoadedSet(), CAlnSpanVertModel::x_UpdateLocs(), CAlignMarkHandler::x_UpdateSelection(), CGraphOverlay::x_UpdateTrackSettings(), CValidError_bioseq::x_ValidateCDSmRNAmatch(), CSelListModelImpl< Item >::x_ViewsUpdateItemRange(), CSelListModelImpl< Item >::x_ViewsUpdateItems(), CNCMessageHandler::x_WriteFullBlobsList(), CSeqSubSplitter::xFlattenSeqEntry(), CSeqSubSplitter::xFlattenSeqEntrys(), CMultiReaderApp::xProcessAgp(), CRemoteUpdater::xUpdatePubReferences(), impl::CDBExceptionStorage::~CDBExceptionStorage(), CEventHandler::~CEventHandler(), CFastaOstreamComp::~CFastaOstreamComp(), CHitList::~CHitList(), CMergeTree::~CMergeTree(), CMultiSeqInfo::~CMultiSeqInfo(), CPluginManager< TClass >::~CPluginManager(), CEventHandler::CPostQueue::~CPostQueue(), CQueryFactoryInfo::~CQueryFactoryInfo(), CSafeStaticGuard::~CSafeStaticGuard(), CSyncQueue_ConstAccessGuard< Type, Container, Traits >::~CSyncQueue_ConstAccessGuard(), CTempString_Storage::~CTempString_Storage(), CTreeNode< TValue, TKeyGetter >::~CTreeNode(), CTSE_Split_Info::~CTSE_Split_Info(), CUICommandRegistry::~CUICommandRegistry(), SIdAnnotObjs::~SIdAnnotObjs(), SNetServerPoolImpl::~SNetServerPoolImpl(), and SRotatedFontCachePurger::~SRotatedFontCachePurger().

#define NON_CONST_REVERSE_ITERATE (   Type,
  Var,
  Cont 
)
Value:
for ( ITERATE_VAR(Type::reverse_iterator) \
Var = ITERATE_BEGIN(Cont, rbegin); \
Var != (Cont).rend(); ++Var )
#define ITERATE_BEGIN(Cont, Begin)
Definition: ncbimisc.hpp:780
#define ITERATE_VAR(Type)
Definition: ncbimisc.hpp:791

Non constant version of REVERSE_ITERATE macro.

Definition at line 814 of file ncbimisc.hpp.

Referenced by CAlnMixMatches::Add(), CHandleRange::AddRange(), CNCSyncLog::GetEventsList(), impl::CDriverContext::MakeConnection(), impl::CDriverContext::MakePooledConnection(), CSeq_loc_mix::SetLastLoc(), CSplign::x_Run(), and CFeature_table_reader_imp::x_UpdatePointStrand().

#define OVERRIDE_OPERATOR_BOOL (   TAncestorClass,
  NewBoolExpr 
)
Value:
using TAncestorClass::TBoolType; \
using TAncestorClass::SSafeBoolTag; \
operator TBoolType() const { \
return (NewBoolExpr)? & SSafeBoolTag::SafeBoolTrue : 0; \
}

Override the DECLARE_OPERATOR_BOOL, etc.

from an ancestor class. This is needed because sometimes you can't just use DECLARE_OPERATOR_BOOL due to cases such as the ancestor class being privately inherited from.

Definition at line 212 of file ncbimisc.hpp.

#define REVERSE_ITERATE (   Type,
  Var,
  Cont 
)
Value:
for ( ITERATE_VAR(Type::const_reverse_iterator) \
Var = ITERATE_BEGIN(ITERATE_CONST(Cont), rbegin), \
NCBI_NAME2(Var,_end) = ITERATE_CONST(Cont).rend(); \
Var != NCBI_NAME2(Var,_end); ++Var )
#define ITERATE_BEGIN(Cont, Begin)
Definition: ncbimisc.hpp:780
#define NCBI_NAME2(Name1, Name2)
Name concatenation macro with two names.
Definition: ncbistl.hpp:120
#define ITERATE_CONST(Cont)
Definition: ncbimisc.hpp:771
#define ITERATE_VAR(Type)
Definition: ncbimisc.hpp:791

ITERATE macro to reverse sequence through container elements.

Definition at line 807 of file ncbimisc.hpp.

Referenced by CDockManager::ApplyLayout(), BOOST_AUTO_TEST_CASE(), CBlobSplitterImpl::CopySkeleton(), CCompoundRegistry::FindByContents(), FindCompartments(), CThreadPool_Impl::FinishThreads(), CScore_IndelToSplice::Get(), CMatePairGlyph::GetHTMLActiveAreas(), CSeq_loc_mix::GetLastLoc(), CProductStringBuilder::GetProductString(), impl::CDBHandlerStack::HandleExceptions(), impl::CDBHandlerStack::HandleMessage(), CCompoundRWRegistry::LoadBaseRegistries(), CDockManager::LoadLayout(), impl::CDBHandlerStack::PostMsg(), CDBServiceMapperCoR::RecordServer(), s_MatchPattern(), CRequestContext::SelectLastSessionID(), CHttpCookies::sx_RevertDomain(), CProductStringBuilder::x_AddExon(), CArchive::x_Append(), CTar::x_Append(), CCompoundRegistry::x_Empty(), CCompoundRegistry::x_Enumerate(), CCompoundRWRegistry::x_Enumerate(), CTraversalCodeGenerator::x_GenerateHeaderFile(), CTraversalCodeGenerator::x_GenerateSourceFile(), CEnvironmentRegistry::x_Get(), CDrawTextOStream::x_GetStyles(), CCompoundRegistry::x_Modified(), CMergeTree::x_Search_Iter(), 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 832 of file ncbimisc.hpp.

Referenced by CDepthCollection::AddRange(), CSeq_annot_Info::ClearFeatIds(), CCDSInfo::Cut(), CSeq_loc_CI_Impl::DeleteRange(), CDbxrefPanel::DeleteTaxonRef(), CConnTest::ExtraCheckOnFailure(), CDB_UserHandler_Deferred::Flush(), CGnomonEngine::GetScore(), CEditingActionDescUserObject::Modify(), CGraphOverlay::MoveTrackOut(), CNCPeriodicSync::ReConfig(), and CGraphTrack::x_OnSettingsIconClicked().

#define ZERO_GI   GI_CONST(0)

Definition at line 1021 of file ncbimisc.hpp.

Referenced by AccessionToKey(), CSeqDB::AccessionToOids(), HitDistributor::addBatch(), BOOST_AUTO_TEST_CASE(), CAlignFormatUtil::BuildUserUrl(), CCachedSequence::CCachedSequence(), CheckAccession(), CBlastDBExtractor::ExtractAccession(), CBlastDBExtractor::ExtractGi(), ExtractGi(), CBlastDBExtractor::ExtractMembershipInteger(), CBlastDBExtractor::ExtractSeqId(), CBlastDBExtractor::ExtractTitle(), CID1Client::FetchEntry(), SeqTreeAsnizer::fillAsnSeqTreeNode(), FindGi(), CHTMLFormatterEx::FormatModelEvidence(), CGenbankFormatter::FormatSequence(), CEmblFormatter::FormatVersion(), CGenbankFormatter::FormatVersion(), FullBlobs(), CAltValidator::GetAccDataFromObjMan(), CDefaultSynonymMapper::GetBestSynonym(), NSnpGui::GetBinLinks(), CSeqDBVol::GetBioseq(), CShowBlastDefline::GetBioseqHandleDeflineAndId(), GetCommonTax(), CAlignFormatUtil::GetDbType(), CAsnCache_DataLoader::GetGi(), CDUpdater::getGi(), CID2WGSProcessor_Impl::GetGi(), CSeq_id_Handle::GetGi(), CDataLoader::GetGi(), CScope_Impl::GetGi(), CWGSSeqIterator::GetGi(), CWGSProteinIterator::GetGi(), CSeqDBVol::GetGiBounds(), CSeqDBImpl::GetGiBounds(), GetGiForAccession(), GetGiForId(), GetGIForSeqId(), CAlignFormatUtil::GetGiForSeqIdList(), CSeq_id_Gi_Tree::GetGiHandle(), CSeqIdListSet::GetGiList(), CSeqLocListSet::GetGiList(), CScope_Impl::GetGis(), CWGSSeqIterator::GetGiSeq_id(), CWGSProteinIterator::GetGiSeq_id(), CAlignFormatUtil::GetGraphiscLink(), GetId(), CLocationListCtrl::GetIdFromForm(), GetLabel(), CAlignFormatUtil::GetLinkoutUrl(), CWGSDb_Impl::GetMasterGi(), GetMasterGIFromSeqAlign(), CGBDataLoader::GetSatSatkey(), CAlignFormatUtil::GetSeqLinkoutInfo(), CIdMapperApp::GetSourceHandle(), TaxClient::GetTaxIDForSeqId(), TaxTreeData::GetTaxIDForSequence(), CGeneMarkerGlyph::GetTooltip(), CBinsGlyph::GetTooltip(), GiFootPrint::GiFootPrint(), CWGSSeqIterator::HasGi(), CWGSProteinIterator::HasGi(), CUser_object::CRefGeneTrackingAccession::IsSetGI(), CId1Reader::LoadGiBlob_ids(), CPubseqReader::LoadGiHash(), CId1Reader::LoadGiSeq_ids(), CPubseqReader::LoadGiSeq_ids(), CPubseqReader::LoadSeq_idAccVer(), CId1Reader::LoadSeq_idGi(), CPubseqReader::LoadSeq_idInfo(), CUser_object::CRefGeneTrackingAccession::MakeAccessionField(), CUser_object::CRefGeneTrackingAccession::MakeAccessionFromUserField(), CAltValidator::SGiVerLenTaxid::MatchesVersion_HasAllData(), CSeqDB::PigToBioseq(), CMSResponse::PrintCSV(), CAltValidator::ProcessQueue(), CBlast_def_line_set::PutTargetGiFirst(), CGiCache::RecordKnown(), CValidError_annot::ReportLocationGI0(), CWGSGiIterator::Reset(), CGi2TaxIdApp::Run(), COMSSA::Run(), CId1FetchApp::Run(), CTestProtProd_EntrezNeighbors::RunTest(), s_AddOtherRelatedInfoLinks(), s_CheckQuals_cdregion(), s_GetBestSynonym(), s_GetCachedDescription(), s_GetFeatureKeyLinkLocation(), s_GetFullLinkoutUrl(), s_GetGi(), s_GetLinkFeatureKey(), s_GetLinkoutUrl(), s_GetModelEvidance(), s_HtmlWrapModelEvidenceName(), s_IdXrefsNotReciprocal(), s_TestDatabase(), SDIRecord::SDIRecord(), SeqDB_ReadMemoryGiList(), CSeqDB::SeqidToBioseq(), CAlignFormatUtil::SetCustomLinksTypes(), CBlastDBExtractor::SetSeqId(), CAltValidator::SGiVerLenTaxid::SGiVerLenTaxid(), CDUpdater::update(), CSeqTableLocColumns::UpdateSeq_loc(), CValidError_bioseq::ValidateDeltaLoc(), CValidError_bioseq::ValidateHistory(), CValidError_bioseq::ValidateIDSetAgainstDb(), CValidError_bioseq::ValidateSeqId(), CBlastDB_FastaFormatter::Write(), CBlastDB_BioseqFormatter::Write(), CId1FetchApp::WriteHistoryTable(), CFeatureItem::x_AddQualProteinId(), CAlnGraphic::x_BuildHtmlTable(), CTaxTreeToolJob::x_CreateProjectItems(), CShowBlastDefline::x_DisplayDefline(), CShowBlastDefline::x_DisplayDeflineTableBody(), CDisplaySeqalign::x_DisplaySequenceIDForQueryAnchored(), CShowBlastDefline::x_FillDeflineAndId(), CDisplaySeqalign::x_FillSeqid(), CProjectFileWriter::x_FindParent(), CShowBlastDefline::x_FormatDeflineTableLine(), CAlnGraphic::x_FormatGraphOverview(), CDisplaySeqalign::x_FormatOneDynamicFeature(), CAlnGraphic::x_GetAlnInfo(), CProjectFileWriter::x_GetAnnotId(), CCreateGeneModelTask::x_GetCommand(), CShowBlastDefline::x_GetDeflineInfo(), CDisplaySeqalign::x_GetFeatureInfo(), CProjectFileWriter::x_GetGi(), CScope::x_GetGi(), CSeqDBImpl::x_GetSeqGI(), CValidError_bioseq::x_IdXrefsNotReciprocal(), CSequenceDataTester::x_Init(), CNAUtils::x_Init(), CWGSGiIterator::x_Init(), CDisplaySeqalign::x_InitDefLinesHeader(), CSFTranslationJob::x_InitGeneticCode(), CShowBlastDefline::x_InitLinkOutInfo(), CDisplaySeqalign::x_InitSeqUrl(), CTaxFormat::x_InitTaxInfoMap(), CDisplaySeqalign::x_MapDefLine(), CNAUtils::x_NAIdMatchesGI(), CDisplaySeqalign::x_PrepareRowData(), CDisplaySeqalign::x_PrintDefLine(), CDisplaySeqalign::x_PrintDynamicFeatures(), CBuildDatabase::x_ResolveGis(), CBuildDatabase::x_ResolveRemoteId(), COligoSpecificityCheck::x_SavePrimerInfo(), CCleanupApp::x_SeqIdToGiNumber(), CBlastDBExtractor::x_SetGi(), CId1Reader::x_SetParams(), and CSeq_annot_SNP_Info_Reader::x_Write().

Typedef Documentation

typedef enum ENcbiOwnership EOwnership

Ownership relations between objects.

Can be used to define or transfer ownership of objects. For example, specify if a CSocket object owns its underlying SOCK object.

typedef enum ENcbiSwitch ESwitch

Aux.

enum to set/unset/default various features.

typedef CNcbiApplication*(* ncbi::FNcbiApplicationFactory) (void)

Provide means of creating custom CNcbiApplication object – to use the latter instead of "dummy" NCBI application.

Note
It is an esoteric feature that is very rarely used.

Definition at line 77 of file ncbi_toolkit_impl.hpp.

typedef TIntId TEntrezId

TEntrezId type for entrez ids which require the same strictness as TGi.

Definition at line 1011 of file ncbimisc.hpp.

typedef int TGi

Type for sequence GI.

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

Definition at line 998 of file ncbimisc.hpp.

typedef Int4 TIntId

Definition at line 999 of file ncbimisc.hpp.

Definition at line 49 of file ncbi_toolkit_impl.hpp.

typedef unsigned int TSeqPos

Type for sequence locations and lengths.

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

Definition at line 855 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 867 of file ncbimisc.hpp.

typedef int TTaxId

Type for Taxon1-name.taxid.

Definition at line 870 of file ncbimisc.hpp.

typedef Uint4 TUintId

Definition at line 1000 of file ncbimisc.hpp.

Enumeration Type Documentation

Enumerator
eBaseName 

per GetProgramDisplayName

eFullName 

per GetProgramExecutablePath(eIgnoreLinks)

eRealName 

per GetProgramExecutablePath(eFollowLinks)

Definition at line 335 of file ncbiapp.hpp.

Disable argument descriptions.

Call with a bit flag set if you do not want std AND user cmd.line args to be parsed. Note that by default the parsing of cmd.line args are enabled.

Enumerator
fDisableStdArgs 

(-logfile, -conffile, -version etc)

Definition at line 388 of file ncbiapp.hpp.

Error types that an application can generate.

These error conditions are checked for and caught inside AppMain().

Enumerator
eUnsetArgs 

Command-line argument description not found.

eSetupDiag 

Application diagnostic stream setup failed.

eLoadConfig 

Registry data failed to load from config file.

eSecond 

Second instance of CNcbiApplication is prohibited.

eNoRegistry 

Registry file cannot be opened.

Definition at line 87 of file ncbiapp.hpp.

When to return a user-set exit code.

Enumerator
eNoExits 

never (stick to existing logic)

eExceptionalExits 

when an (uncaught) exception occurs

eAllExits 

always (ignoring Run's return value)

Definition at line 565 of file ncbiapp.hpp.

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

Enumerator
eIgnoreLinks 

Do not follow symbolic links.

eFollowLinks 

Follow symbolic links.

Definition at line 135 of file ncbimisc.hpp.

Which standard flag's descriptions should not be displayed in the usage message.

Do not display descriptions of the standard flags such as the -h, -logfile, -conffile, -version flags in the usage message. Note that you still can pass them in the command line.

Enumerator
fHideLogfile 

Hide log file description.

fHideConffile 

Hide configuration file description.

fHideVersion 

Hide version description.

fHideFullVersion 

Hide full version description.

fHideDryRun 

Hide dryrun description.

fHideHelp 

Hide help description.

fHideFullHelp 

Hide full help description.

fHideXmlHelp 

Hide XML help description.

fHideAll 

Hide all standard argument descriptions.

Definition at line 401 of file ncbiapp.hpp.

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 interrupted by a signal.

eRestartOnSignal 

Restart operation if interrupted by a signal.

Definition at line 152 of file ncbimisc.hpp.

Ownership relations between objects.

Can be used to define or transfer ownership of objects. For example, specify if a CSocket object owns its underlying SOCK object.

Enumerator
eNoOwnership 

No ownership is assumed.

eTakeOwnership 

An object can take ownership of another.

eNoOwnership 
eTakeOwnership 

No ownership assumed.

An object can take ownership of another

Definition at line 99 of file ncbimisc.hpp.

Aux.

enum to set/unset/default various features.

Enumerator
eOff 
eOn 
eDefault 
eOff 
eOn 
eDefault 

Definition at line 70 of file ncbimisc.hpp.

Whether to normalize a path.

Enumerator
eNormalizePath 

Normalize a path.

eNotNormalizePath 

Do not normalize a path.

Definition at line 142 of file ncbimisc.hpp.

enum ENull

CNullable –.

A value whith 'unassigned' state.Define "null" pointer value.

Enumerator
null 

Definition at line 630 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 113 of file ncbimisc.hpp.

Result of PreparseArgs()

Enumerator
ePreparse_Continue 

Continue application execution.

ePreparse_Exit 

Exit the application with zero exit code.

Definition at line 373 of file ncbiapp.hpp.

enum ERetriable

Can the action be retried?

Enumerator
eRetriable_No 

It makes no sense to retry the action.

eRetriable_Unknown 

It is unknown if the action can succeed if retried.

eRetriable_Yes 

It makes sense to try again.

Definition at line 159 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 128 of file ncbimisc.hpp.

Log message severity.

Enumerator
eInfo 

Informational message.

eWarning 

Warning message.

eError 

Error message.

eCritical 

Critical error message.

eFatal 

Fatal error.

eTrace 

Trace message.

Definition at line 102 of file ncbi_toolkit.hpp.

enum ESign

Signedness of a value.

Enumerator
eNegative 

Value is negative.

eZero 

Value is zero.

ePositive 

Value is positive.

Definition at line 120 of file ncbimisc.hpp.

Flags to adjust standard I/O streams' behaviour.

Enumerator
fDefault_SyncWithStdio 

Use compiler-specific default as pertains to the synchronizing of "C++" Cin/Cout/Cerr streams with their "C" counterparts.

fDefault_CinBufferSize 

Use compiler-specific default of Cin buffer size.

fBinaryCin 

treat standard input as binary

fBinaryCout 

treat standard output as binary

Definition at line 418 of file ncbiapp.hpp.

Function Documentation

void * CRawPointer::Add ( void *  object,
ssize_t  offset 
)
inlinestatic

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

Definition at line 1046 of file ncbimisc.hpp.

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

const void * CRawPointer::Add ( const void *  object,
ssize_t  offset 
)
inlinestatic

Definition at line 1052 of file ncbimisc.hpp.

template<class Element , size_t Size>
size_t ArraySize ( const   Element(&)[Size])
inline
CNcbiToolkit_LogMessage::CNcbiToolkit_LogMessage ( const SDiagMessage msg)
protected

Definition at line 64 of file ncbi_toolkit.cpp.

ncbi::CNcbiToolkit_LogMessage::CNcbiToolkit_LogMessage ( const CNcbiToolkit_LogMessage )
private
int CNcbiToolkit_LogMessage::ErrCode ( void  ) const

Get error code.

Definition at line 101 of file ncbi_toolkit.cpp.

References SDiagMessage::m_ErrCode, and ncbi::CNcbiToolkit_LogMessage::m_Msg.

int CNcbiToolkit_LogMessage::ErrSubCode ( void  ) const

Get error subcode.

Definition at line 106 of file ncbi_toolkit.cpp.

References SDiagMessage::m_ErrSubCode, and ncbi::CNcbiToolkit_LogMessage::m_Msg.

string CNcbiToolkit_LogMessage::File ( void  ) const

Get file name in which message was originated.

Definition at line 119 of file ncbi_toolkit.cpp.

References SDiagMessage::m_File, and ncbi::CNcbiToolkit_LogMessage::m_Msg.

NCBI_NORETURN void g_ThrowOnNull ( void  )

Definition at line 859 of file ncbiexpt.cpp.

References NCBI_THROW.

Referenced by SThrowOnNull< TValue >::operator()().

INcbiIdler* GetIdler ( EOwnership  ownership = eNoOwnership)

Return currently installed idler or NULL.

Update idler ownership according to the flag.

Definition at line 1651 of file ncbiapp.cpp.

References CSafeStatic< T, Callbacks >::Get(), and CIdlerWrapper::GetIdler().

const SDiagMessage & CNcbiToolkit_LogMessage::GetNativeToolkitMessage ( void  ) const

Get all of the message's data – as provided natively by the Toolkit.

Definition at line 80 of file ncbi_toolkit.cpp.

References ncbi::CNcbiToolkit_LogMessage::m_Msg.

size_t CNcbiToolkit_LogMessage::Line ( void  ) const

Get line number in which message was originated.

Definition at line 124 of file ncbi_toolkit.cpp.

References SDiagMessage::m_Line, and ncbi::CNcbiToolkit_LogMessage::m_Msg.

string CNcbiToolkit_LogMessage::Message ( void  ) const

Get text part of the message.

Definition at line 111 of file ncbi_toolkit.cpp.

References kEmptyStr, SDiagMessage::m_Buffer, SDiagMessage::m_BufferLen, ncbi::CNcbiToolkit_LogMessage::m_Msg, and string.

void ncbi::NcbiToolkit_Fini ( void  )

Release resources allocated for NCBI C++ Toolkit.

See also
NcbiToolkit_Init

Definition at line 257 of file ncbi_toolkit.cpp.

References kNcbiToolkit_Finalized, NULL, and s_NcbiToolkit.

void ncbi::NcbiToolkit_Init ( int  argc,
const TNcbiToolkit_XChar *const argv,
const TNcbiToolkit_XChar *const envp = NULL,
INcbiToolkit_LogHandler log_handler = NULL 
)

Initialialize NCBI C++ Toolkit internal infrastructure: arguments, environment, diagnostics, logging.

Note
This function may be called only once – and, before calling any other C++ Toolkit function.
Parameters
argcArgument count [argc in a regular main(argc, argv)].
argvArgument vector [argv in a regular main(argc, argv)].
envpEnvironment pointer [envp in a regular main(argc, argv, envp)]; a null pointer (the default) corresponds to the standard system array (environ on most Unix platforms).
log_handlerHandler for diagnostic messages that are emitted by the C++ Toolkit code
See also
INcbiToolkit_LogHandler, NcbiToolkit_Fini
void ncbi::NcbiToolkit_RegisterNcbiApplicationFactory ( FNcbiApplicationFactory  f)

Definition at line 267 of file ncbi_toolkit.cpp.

References f().

ncbi::CNcbiToolkit_LogMessage::operator std::string ( void  ) const

Get the message the way it is formatted by the Toolkit.

template<class TValue , class TNullToValue = SThrowOnNull<TValue>>
bool operator!= ( const CNullable< TValue, TNullToValue > &  l,
const CNullable< TValue, TNullToValue > &  r 
)

Definition at line 727 of file ncbimisc.hpp.

References operator==().

CNcbiToolkit_LogMessage& ncbi::CNcbiToolkit_LogMessage::operator= ( const CNcbiToolkit_LogMessage )
private
template<class TValue , class TNullToValue = SThrowOnNull<TValue>>
bool operator== ( const CNullable< TValue, TNullToValue > &  l,
const CNullable< TValue, TNullToValue > &  r 
)
virtual void ncbi::INcbiToolkit_LogHandler::Post ( const CNcbiToolkit_LogMessage msg)
pure virtual
void RunIdler ( void  )

Execute currently installed idler if any.

Definition at line 1663 of file ncbiapp.cpp.

References CSafeStatic< T, Callbacks >::Get(), and CIdlerWrapper::RunIdler().

template<typename Type >
const Type& s_ITERATE_ConstRef ( const Type obj)
inline

Definition at line 767 of file ncbimisc.hpp.

template<typename Type >
bool s_ITERATE_SameObject ( const Type obj1,
const Type obj2 
)
inline

Definition at line 776 of file ncbimisc.hpp.

void SetIdler ( INcbiIdler idler,
EOwnership  ownership = eTakeOwnership 
)

Set new idler and ownership.

Definition at line 1657 of file ncbiapp.cpp.

References CSafeStatic< T, Callbacks >::Get(), and CIdlerWrapper::SetIdler().

CNcbiToolkit_LogMessage::ESeverity CNcbiToolkit_LogMessage::Severity ( void  ) const
char* strdup ( const char *  str)

Supply string duplicate function, if one is not defined.

Definition at line 5264 of file ncbistr.cpp.

References result, and size.

ssize_t CRawPointer::Sub ( const void *  first,
const void *  second 
)
inlinestatic

calculate offset inside object

Definition at line 1058 of file ncbimisc.hpp.

template<class T1 , class T2 >
void swap ( NCBI_NS_NCBI::pair_base_member< T1, T2 > &  pair1,
NCBI_NS_NCBI::pair_base_member< T1, T2 > &  pair2 
)
inline

Definition at line 1356 of file ncbimisc.hpp.

Referenced by __WORKAROUND_RENAME(), CInt_fuzz::Add(), CLinks::AddLink(), CIdMapper::AddMapping(), CTableAnnotDataSource::AddSeqLoc(), CTSE_ScopeInfo::AddUsedTSE(), variation_ref::CVariationUtil::AdjustDelinsToInterval(), AlignFNog(), AlignModelToSeqalign(), CFastaReader::AssembleSeq(), xml::document::assign(), xml::node::assign(), bisection(), bNNItopSwitch(), BOOST_AUTO_TEST_CASE(), CCommentItem::CCommentItem(), CCSraDb_Impl::CCSraDb_Impl(), CFixedBlob_ids::CFixedBlob_ids(), CFixedSeq_ids::CFixedSeq_ids(), CFlatSeqLoc::CFlatSeqLoc(), CSeqTable_multi_data::ChangeToBit(), CSeqTable_multi_data::ChangeToBytes(), CSeqTable_multi_data::ChangeToInt1(), CSeqTable_multi_data::ChangeToInt2(), CSeqTable_multi_data::ChangeToInt4(), CSeqTable_multi_data::ChangeToInt8(), CSeqTable_multi_data::ChangeToInt_delta(), CSeqTable_multi_data::ChangeToInt_scaled(), CSeqTable_multi_data::ChangeToReal(), CSeqTable_multi_data::ChangeToReal_scaled(), CSeqTable_multi_data::ChangeToString(), CSplicedAligner::CheckPreferences(), CAlignCollapser::ClipNotSupportedFlanks(), CREnzyme::CombineIsoschizomers(), dtl::Diff< elem, sequence, comparator >::composeUnifiedHunks(), CClusterer::ComputeClusters(), DeBruijn::CDBGraphDigger::ConnectTwoNodes(), CSeq_loc_Conversion::ConvertInterval(), CProteinAlignText::CProteinAlignText(), CAnnotationASN1::CImplementationData::create_packed_int_seqloc(), CAlignmentAssistant::CreateFeature(), CProtSeqlocHelper::CreateSeqloc(), CDeltaHelper::CreateSSR(), CRgbaColorTable::CRgbaColorTable(), CSegmentGlyph::CSegmentGlyph(), lmdb::cursor::cursor(), CPaintSequence::CutSelection(), lmdb::dbi::dbi(), CAlignmentAssistant::DeleteSelection(), CAlignGlyph::DrawPWAlignElem(), CPaintAlignment::DrawTextCell(), CPaintSequence::DrawTextCell(), lmdb::env::env(), CCmdChangeBioseqId::Execute(), CDense_seg::ExtractSlice(), CAlignCollapser::FillGapsInAlignmentAndAddToGenomicGaps(), FindCompartments(), FindFGapIntronNog(), FindIGapIntrons(), CFeatureGenerator::SImplementation::FixOrderOfCrossTheOriginSeqloc(), CImage::Flip(), CImageUtil::FlipX(), FrAlign(), FrAlignFNog1(), CPaintAlignment::GetAlignSelection(), CAlnVecMultiDataSource::GetAlnFromSeq(), CSparseMultiDataSource::GetAlnFromSeq(), CCSraRefSeqIterator::GetAlnOverStarts(), CHitElemGlyph::GetDistPixels(), CDictionaryUtil::GetEditDistance(), CFeatureGenerator::SImplementation::GetExonStructure(), CPaintAlignment::GetFeatWholeRange(), CParse::GetGenes(), CTSE_Handle::GetGenesByRef(), CBulkLocationPanel::GetLocForBioseq(), CSeqUtils::GetLocPlacements(), GetRandomSegment(), CHitMatrixRenderer::GetSelectedHitElemsRect(), CPaintAlignment::GetSelection(), CPaintSequence::GetSelection(), CAlnVecMultiDataSource::GetSeqFromAln(), CSparseMultiDataSource::GetSeqFromAln(), IAlnGraphicDataSource::GetSeqString(), GetTerminalPartialness(), CTranslationGlyph::GetTooltip(), GetVector(), GlbAlign(), IEditingActionFeat::GoToOrigFeature(), IEditingActionFeat::GoToProtFeature(), hunt(), huntExtreme(), CSeqScores::Init(), dtl::Diff< elem, sequence, comparator >::init(), CAlignRange< Position >::IsAbutting(), CLinks::IsLink(), LclAlign(), CAlnVecRow::LTH_OnLayoutChanged(), CHitList::MakeCanonical(), CNWFormatter::MakeSegments(), CPosMapper::Map(), mbedtls_mpi_safe_cond_swap_ncbicxx_2_4_2(), CPhyloTreeDataSource::MoveNode(), StyleManager::MoveUserAnnotation(), newtonRaphson(), SNetServiceIterator_RandomPivot::Next(), CDistMethods::NjTree(), NNItopSwitch(), CAlignmentAssistant::OnAddAlignCDS(), CAlignmentAssistant::OnAddAlignOther(), CAlignmentAssistant::OnAddAlignRNA(), CStringConstraintSelect::OnApply(), CPaintSequence::OnCopy(), CSuspectProductRulesEditor::OnDeleteRules(), DeBruijn::CDBGraphDigger::OneStepBranchExtend(), CMacroListPanel_Obs::OnMoveDownItem(), CMacroListPanel::OnMoveDownItem(), CMacroListPanel_Obs::OnMoveUpItem(), CMacroListPanel::OnMoveUpItem(), CAssemblyTrackingPanel::OnPopulateBtnClick(), CLocationListCtrl::OnSortClick(), CPhyTreeCalc::CDistMatrix::operator()(), xml::impl::ait_impl::operator=(), xml::attributes::operator=(), xml::node_set::iterator::operator=(), CVersion::operator=(), xml::node_set::const_iterator::operator=(), xml::attributes::iterator::operator=(), xml::attributes::const_iterator::operator=(), xml::node::iterator::operator=(), xml::document::operator=(), xml::node::const_iterator::operator=(), lmdb::env::operator=(), lmdb::txn::operator=(), xml::node::operator=(), lmdb::dbi::operator=(), lmdb::cursor::operator=(), SSparseIndex::Optimize(), CDense_seg::OrderAdjacentGaps(), CPaintAlignment::Paint(), CPaintSequence::Paint(), ParseAttributes(), CSeqGlyph::PointInRect(), CTabularFormatter_AlignStart::Print(), CTabularFormatter_AlignEnd::Print(), ProjectExons(), readGFF3(), CHitElemGlyph::Render(), CFindASN1Dlg::ReplaceLinebreaks(), CSuspectProductRulesEditor::ReplaceRule(), CChain::RestoreReasonableConfirmedStart(), CDense_seg::Reverse(), DeBruijn::CDBGraphDigger::SContig::ReverseComplement(), ReverseComplementLocation(), CXcompareAnnotsApplication::Run(), s_GetAlnMapplingLocs(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetNeighborhoodLocs(), s_GetRowData(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetStartAndStopCodonsLocs(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetUTRLocs(), s_MakeRandomDeflineSet(), s_PartialAtGapOrNs(), s_PopulateUserObject(), s_PrepareTrackPane(), s_PrintLocAsJavascriptArray(), s_RCUMoveGPMarkers(), s_SetIntervals(), s_SwapRows(), s_TestForOverlapEx(), xml::document::save_to_file(), xml::document::save_to_stream(), xml::document::save_to_string(), CChain::SetConfirmedStartStopForCompleteProteins(), CBlastPrelimSearch::SetInterruptCallback(), CRgbaColorTable::SetMaxColor(), CRgbaColorTable::SetMinColor(), CSeqMarkHandler::SetRange(), CAlignShadow::SetStrand(), DeBruijn::CKmerCountTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::Swap(), CRawScoreVector< Key, Score >::Swap(), SNetServiceImpl::CTry::Swap(), set< ETranslationFrame >::swap(), CNcbiMatrix< T >::Swap(), xml::attributes::swap(), CScoreVector< Key, Score >::Swap(), CSeqDB_BitSet::Swap(), CSimpleBufferT< char >::swap(), xml::document::swap(), xml::node_set::iterator::swap(), multiset< Key, Compare, Allocator >::swap(), xml::attributes::attr::swap(), pair_base_member< convert_to_string_type, value_type >::Swap(), xml::attributes::iterator::swap(), hashtable< _Val, _Key, _HF, _ExK, _EqK, _All >::swap(), xml::node_set::const_iterator::swap(), xml::attributes::const_iterator::swap(), AutoPtr< CNcbiOstrstream >::Swap(), DeBruijn::CReadHolder::Swap(), AutoArray< CS_INT >::Swap(), xml::node::swap(), xml::node::iterator::swap(), xml::node::const_iterator::swap(), CEditingActionFlatFile::SwapContext(), CEditingActionSeqid::SwapContext(), IEditingActionDesc::SwapContext(), IEditingActionBiosource::SwapContext(), IEditingActionFeat::SwapContext(), IEditingAction::SwapContext(), IEditingActionInst::SwapContext(), IEditingActionDescPub::SwapContext(), CEditingActionDescPubTitle::SwapContext(), IEditingActionDescAffil::SwapContext(), IEditingActionDescAuthors::SwapContext(), CEditingActionDescAuthorNameList::SwapContext(), CStd_seg::SwapRows(), CNcbiMatrix< T >::SwapRows(), CDense_seg::SwapRows(), CObjectIStreamAsyncIterator< TRoot >::sx_ClearGarbageAndParse(), CObjectIStreamAsyncIterator< TRoot, TChild >::sx_ClearGarbageAndParse(), sx_PopLastNewPtrMultiple(), CGlBitmapFont::TextOut(), CGlTextureFont::TextOut(), CMacroFunction_MakeInterval::TheFunction(), CLocationListCtrl::TransferDataFromWindow(), ProjectCDS::transform_align(), RemoveTrailingNs::transform_model(), CPaintSequence::TranslateCDS(), CAlignmentAssistant::TranslateLocations(), CNcbiMatrix< T >::Transpose(), CMatrix3< T >::Transpose(), CMatrix4< T >::Transpose(), CChainer::CChainerImpl::TrimAlignmentsIncludedInDifferentGenes(), lmdb::txn::txn(), CWGSResolver_GiRangeFile::Update(), CWGSResolver_AccRangeFile::Update(), CPrintSetupDlg::UpdateMargins(), CFarPointerSeq::ValidateAlignment(), CAlignRangeCollection< CAlignRange< TSeqPos > >::ValidateRanges(), VariBandAlign(), CFeature_table_reader_imp::x_AddIntervalToFeature(), CSeqSearch::x_AddPattern(), CLocationListCtrl::x_AddRow(), variation::CVariationUtil::x_AdjustDelinsToInterval(), CFeatTree::x_AssignGenes(), CFeatTree::x_AssignParentsByOverlap(), CLayoutPWAlign::x_CalcIntervals(), CAlignGlyph::x_CalcIntervals(), CScoringJob::x_CalculateAlignmentScores(), CFeatureGraph::x_Create(), CInversionMergeAligner::x_CreateDiscAlignment(), CNaSeqlocHelper::x_CreateSeqloc(), CAlignGlyph::x_DrawAlignRowSequence(), CFeatGlyph::x_DrawFeatureBar(), CAlignGlyph::x_DrawGaps(), CAlignGlyph::x_DrawInternalUnalignedRegions(), CAlignGlyph::x_DrawMultiAlign(), CFeatGlyph::x_DrawProjectedRuler(), CTranslationGlyph::x_DrawSequence(), CAlignGlyph::x_DrawUnalignedRowSequence(), IEditingActionFeat::x_FindGeneForFeature(), CAlnVecRow::x_ForEachAlnSeg(), CAlnVecRow::x_GetAlignmentTooltip_Helper(), CBoundaryShapeTri::x_GetArc(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CSeq_align_Mapper_Base::x_GetDstStd(), CLinks::x_GetLink(), CGuiObjectInfoSeq_feat::x_GetProductSequence(), CCommonComponentScorer::x_GetSeqHistCompList(), CGuiObjectInfoSeq_feat::x_GetSplicedSeqTitle(), CSeq_align_Mapper_Base::x_Init(), CSparse_CI::x_InitSegment(), CPairwise_CI::x_InitSegment(), CTranslationGlyph::x_Intersecting(), CValidError_bioseq::x_IsPartialAtSpliceSiteOrGap(), CAuthorNamesPanel::x_MoveRowUp(), CNCMMSizePool::x_NewEmptySet(), variation::CHgvsParser::x_PlacementCoordsToStr(), CAlnSpanVertModel::x_PopulateRows(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CAlignFilter::x_Query_Range(), CAlignGlyph::x_RenderAveragableScores(), CTraceGraph::x_RenderConfGraph(), CTraceGlyph::x_RenderConfGraph(), CTraceGraph::x_RenderContour(), CTraceGraph::x_RenderCurveSegment(), CTraceGlyph::x_RenderCurveSegment(), CHitMatrixGraph::x_RenderEventHandler(), CAlnVecRow::x_RenderIcons(), CAlnVecRow::x_RenderIconStrand(), CTraceGraph::x_RenderIntensityGraphs(), CTraceGlyph::x_RenderIntensityGraphs(), CAlignGlyph::x_RenderNonAveragableScores(), CSeqGraphicPane::x_RenderRectSelHandler(), CRuler::x_RenderScale(), IPhyloTreeRender::x_RenderSelection(), CMouseZoomHandler::x_RenderZoomRect(), IPhyloTreeRender::x_SelectByRect(), CNewCleanup_imp::x_SeqIntervalBC(), CCommentItem::x_SetSkip(), CNCMMReserve::x_SortChunkPtrs(), CSeqVector_CI::x_SwapCache(), x_TestAlignmentQuerySubjStrandCombinations(), CFeatTrim::x_TrimLocation(), CObjectIStreamAsyncIterator< TRoot >::CData::x_UpdateFuturesQueue(), CAlnSpanVertModel::x_UpdateMetaData(), CPsiBlastInputClustalW::x_ValidateQueryInMsa(), CGff3FlybaseWriter::xAssignAlignmentDensegTarget(), CGff3Writer::xAssignAlignmentDensegTarget(), CSeqGraphicRenderer::ZoomOnRange(), CSafeStaticGuard::~CSafeStaticGuard(), and CUnlockedTSEsGuard::~CUnlockedTSEsGuard().

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 1365 of file ncbimisc.hpp.

CNcbiToolkit_LogMessage::~CNcbiToolkit_LogMessage ( void  )
protectedvirtual

Definition at line 69 of file ncbi_toolkit.cpp.

virtual ncbi::INcbiToolkit_LogHandler::~INcbiToolkit_LogHandler ( )
inlinevirtual

Definition at line 162 of file ncbi_toolkit.hpp.

Variable Documentation

BEGIN_NCBI_NAMESPACE

NCBI_EOWNERSHIP_DEFINED.

Definition at line 109 of file ncbimisc.hpp.

BEGIN_STD_NAMESPACE

Definition at line 1352 of file ncbimisc.hpp.

END_NCBI_NAMESPACE

Definition at line 1350 of file ncbimisc.hpp.

END_STD_NAMESPACE

Definition at line 1397 of file ncbimisc.hpp.

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

Define special value for invalid sequence position.

Definition at line 858 of file ncbimisc.hpp.

Referenced by SAlignment_Segment::AddRow(), BOOST_AUTO_TEST_CASE(), BuildGoodByteGraph(), CSeqMap::CanResolveRange(), CBamRawAlignIterator::CBamRawAlignIterator(), CCSraDb_Impl::CCSraDb_Impl(), CFastaReader::CloseMask(), CBam2Seq_graph::CollectCoverage(), CBam2Seq_graph::CollectEstimatedCoverage(), CBam2Seq_graph::CollectRawAccessCoverage(), CSeq_loc_Conversion::CombineWith(), CSeq_loc_Conversion_Set::ConvertInterval(), CSeq_loc_Conversion::ConvertPacked_pnt(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), CSeq_loc_Conversion::ConvertPos(), CBlobSplitterImpl::CopyDescr(), CBlobSplitterImpl::CopySequence(), CBlobSplitterImpl::CopySkeleton(), CreateDense_diagFromAnchoredAln(), CreatePackedsegFromAnchoredAln(), CreatePackedsegFromPairwiseAln(), CDense_seg::CreateRowSeq_interval(), CSeqMap::CSeqMap(), CSeqMap_CI::CSeqMap_CI(), CSNPDbPageIterator::CSNPDbPageIterator(), SBamIndexRefIndex::EstimateDataSizeByAlnStartPos(), CInternalStopFinder::FindStartStopRanges(), CSparseAln::GetAlnSeqString(), CSeq_loc::GetCircularLength(), CResolveIntersectingFeats::GetCommand(), CFastaReader::GetCurrentPos(), CSeq_align_Mapper_Base::GetDstAlign(), NSnpBins::GetEntry(), CIntronOffsetHelper::GetIntronOffset(), CSeqMap::GetLength(), CBlobSplitterImpl::GetLength(), CID2WGSProcessor_Impl::GetLength(), CBamRefSeqIterator::GetLength(), CRegexp_loc::GetLoc(), CCSraAlignIterator::GetMatchAlign(), CBamAlignIterator::GetMatchAlign(), GetOverlappingFeatures(), CAnnotObject_Less::GetRangeOpen(), CBamDb::GetRefSeqLength(), CBamAlignIterator::SAADBImpl::GetRefSeqPos(), SRepeatRegion::GetRptLength(), CBamRawAlignIterator::GetSegments(), SAlignment_Segment::SAlignment_Row::GetSegStart(), CScope_Impl::GetSeq_featHandle(), CCSraRefSeqIterator::GetSeqLength(), CAsnCache_DataLoader::GetSequenceLength(), CScope_Mapper_Sequence_Info::GetSequenceLength(), CBlastDbDataLoader::GetSequenceLength(), CSRADataLoader::GetSequenceLength(), CWGSDataLoader_Impl::GetSequenceLength(), CDefault_Mapper_Sequence_Info::GetSequenceLength(), CSraRun::GetSequenceLength(), CGBDataLoader::GetSequenceLength(), CDataSource::GetSequenceLength(), CDataLoader::GetSequenceLength(), CScope_Impl::GetSequenceLength(), CCSRADataLoader_Impl::GetSequenceLength(), CTestMapperSeqInfo::GetSequenceLength(), CScope_Impl::GetSequenceLengths(), CDataLoader::GetSequenceLengths(), CPacked_seqpnt::GetStart(), CSeq_loc_mix::GetStart(), CPacked_seqint::GetStart(), CSeq_loc::GetStart(), CPacked_seqpnt::GetStop(), CSeq_loc_mix::GetStop(), CPacked_seqint::GetStop(), CSeq_loc::GetStop(), CLocalBlastDbAdapter::GetTaxId(), IBlastDbAdapter::GetTaxId(), CPhrap_Seq::GetUnpaddedPos(), CGapItem::HasEstimatedLength(), InitSplicedsegFromPairwiseAln(), CLoadLockLength::IsFound(), variation::IsPureFuzzPoint(), CUser_object::CRefGeneTrackingAccession::IsSetFrom(), CUser_object::CRefGeneTrackingAccession::IsSetTo(), CCSRAFileInfo::IsValidReadId(), CReader::LoadLengths(), CReader::LoadSequenceLength(), LoadSequencesToScope(), CUser_object::CRefGeneTrackingAccession::MakeAccessionField(), CUser_object::CRefGeneTrackingAccession::MakeAccessionFromUserField(), CBamIndex::MakeEstimatedCoverageAnnot(), CFeatureTableReader::MakeGap(), CBlobSplitterImpl::MakeID2Chunk(), CMappingRange::Map_Range(), SSNP_Info::NoMore(), CFastaReader::OpenMask(), CRepeatToFeat::operator()(), CAnnotObject_Less::operator()(), CAnnotObject_LessReverse::operator()(), OutOfRange(), CGeneFinder::CGeneSearchPlugin::postProcessDiffAmount(), CRepeatLibrary::Read(), CPhrap_Seq::ReadData(), CFastaReader::ReadOneSeq(), CStd_seg::RemapToLoc(), CSNPDbPageIterator::Reset(), CSNPDbGraphIterator::Reset(), CDemoApp::Run(), s_GetTopology(), s_LocationsOverlap(), s_PrematureStopCodon(), CFeatureGenerator::s_ProjectRNA(), s_SeqLocToTotalRangesInfoMapByStrand(), s_ShouldRemoveRef(), s_TestForOverlapEx(), CCacheWriter::SaveSequenceLength(), CCSraAlignIterator::Select(), CSNPDbPageIterator::Select(), CSNPDbGraphIterator::Select(), CSeqMap::SetRegionInChunk(), CGeneFinder::CGeneSearchPlugin::setUpFeatureIterator(), TestForOverlapEx(), TestStrongKozakUorfs(), CValidError_feat::ValidateRptUnitRangeVal(), CFastaOstreamComp::Write(), CFastaOstream::Write(), variation::CHgvsParser::x_abs_pos(), CSeqMap::x_Add(), CPhrap_Contig::x_AddAlignRanges(), CPhrap_Contig::x_AddBaseSegFeats(), CSeq_loc_Mapper_Base::x_AddConversion(), CSeqMap::x_AddEnd(), CGapAnalysis::x_AddGapsFromBases(), CPhrap_Read::x_AddQualityFeat(), CSeq_loc_Mapper_Base::x_AdjustSeqTypesToProt(), CSeq_loc_Mapper_Base::x_CheckSeqTypes(), CFastaReader::x_CloseMask(), CSeq_align_Mapper_Base::x_ConvertSegment(), CSeq_align_Mapper::x_ConvertSegmentCvt(), CNaSeqlocHelper::x_CreateSeqloc(), CSeqMap::x_FindSegment(), variation_ref::CHgvsParser::x_fuzzy_pos(), variation::CHgvsParser::x_fuzzy_pos(), CFlatGatherer::x_GatherCDSReferences(), CSeqMap::x_GetChunkToLoad(), CSeq_align_Mapper_Base::x_GetDstDendiag(), CSeq_align_Mapper_Base::x_GetDstDenseg(), CSeq_align_Mapper_Base::x_GetDstPacked(), CSeq_align_Mapper_Base::x_GetDstStd(), CAnnotObject_Less::x_GetExtremes(), CSeq_loc_Mapper_Base::x_GetMappedSeq_loc(), CSeq_align_Mapper_Base::x_GetPartialDenseg(), CWGSSeqIterator::x_GetQualityAnnot(), CSeqMap::x_GetSegmentLength(), CPsiBlastInputData::x_GetSubjectSequence(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper::x_InitGCSequence(), CSeq_loc_Mapper_Base::x_InitializeLocs(), CSeq_align_Mapper_Base::x_IsEmpty(), CSeqMap::x_LoadObject(), CBamRefSeqInfo::x_LoadRangesCov(), CBamRefSeqInfo::x_LoadRangesStat(), variation_ref::CHgvsParser::x_location(), variation::CHgvsParser::x_location(), CSeq_loc_Mapper_Base::x_MapInterval(), CSeq_loc_Mapper_Base::x_MapNextRange(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CSNPDbPageIterator::x_Next(), CSNPDbGraphIterator::x_Next(), CBioseqGaps_CI::x_Next(), CSeq_loc_Mapper_Base::x_NextMappingRange(), CFastaReader::x_OpenMask(), CSeq_loc_Mapper_Base::x_PreserveDestinationLocs(), CId2ReaderBase::x_ProcessGetSeqIdSeqId(), CSeqMap::x_ResolveSegmentLength(), CSeqMap::x_ResolveSegmentPosition(), CSeqMap_CI::x_Select(), CSeqMap::x_SetChanged(), and CIntronOffsetHelper::x_SetDeltaItemOffset().

const SDiagMessage& ncbi::CNcbiToolkit_LogMessage::m_Msg
private
Modified on Sun Dec 17 15:53:43 2017 by modify_doxy.py rev. 546573