NCBI C++ ToolKit
Classes | Macros | Typedefs | Enumerations | Enumerator | Functions | Variables
Macro language classes

! this is a hack to fool Tkit version skew protection defence so I can use a prebuilt version w/o ! having to change SV build environment ! remove once we don't have to jump through hoops to use variation_lib More...

+ Collaboration diagram for Macro language classes:

Classes

class  CMacroBioData
 The following asn-selectors are defined to be used in the FOR EACH statement: More...
 
class  IMacroBioDataIter
 IMacroBioDataIter - common interface of all iterators used in the editing macros The type of the iterator is defined by "foreach" selector in the macro. More...
 
struct  IMacroBioDataIter::STableToApply
 
class  CMacroBioData_FeatIterBase
 CMacroBioData_FeatIterBase - iterates over any type of features. More...
 
struct  SFeatInterval
 
class  CMacroBioData_FeatIntervalIter
 CMacroBioData_FeatIntervalIter - iterates over features within [|(left, right]|) intervals. More...
 
class  CMacroBioData_BioSourceIter
 CMacroBioData_BioSourceIter - iterates over all biosource descriptors and features in the seq-entry. More...
 
class  CMacroBioData_PubdescIter
 CMacroBioData_PubdescIter - iterates over all publication descriptors and features in the seq-entry. More...
 
class  CMacroBioData_PubdescIter::CSubmitblockIter
 
class  CMacroBioData_SeqdescIter
 CMacroBioData_SeqdescIter- iterates over all types of sequence descriptors. More...
 
class  CMacroBioData_MolInfoIter
 CMacroBioData_MolInfoIter - iterates over all molinfos in the seq-entry. More...
 
class  CMacroBioData_UserObjectIter
 CMacroBioData_UserObjectIter - iterates over all user objects in the seq-entry. More...
 
class  CMacroBioData_StructCommentIter
 CMacroBioData_StructCommentIter - iterates over all structured comments in the seq-entry. More...
 
class  CMacroBioData_DBLinkIter
 CMacroBioData_DBLinkIter - iterates over all DBlinks in the seq-entry. More...
 
class  CMacroBioData_AutodefOptsIter
 CMacroBioData_AutodefOptsIter - iterates over all AutodefOptions in the seq-entry. More...
 
class  CMacroBioData_SeqAlignIter
 CMacroBioData_SeqAlignIter - iterates over sequence alignments. More...
 
class  CMacroBioData_SeqIter
 CMacroBioData_SeqIter- iterates over sequences (na and aa) More...
 
class  CMacroBioData_SeqNAIter
 
class  CMacroBioData_SeqAAIter
 
class  CMacroBioData_SeqSetIter
 CMacroBioData_SeqSetIter- iterates over sets. More...
 
class  CMacroBioData_TSEntryIter
 CMacroBioData_TSEntryIterBase - iterator pointing to the top seq-entry. More...
 
class  CMacroCmdComposite
 implements special composite command, which does not call to its internal commands when run the very first time. More...
 
class  IEditMacroFunction
 Base class for any user function that performs editing operations on ASN.1 data. More...
 
class  IFunctionLog
 
class  CDiscrLog
 
class  CGeneralFuncLog
 
struct  SArgMetaData
 
class  CMacroFunction_TopLevel
 
class  CMacroStat
 CMacroStat - collecting statistics about a single macro. More...
 
class  CMacroStat::CMacroLog
 
class  IMacroEngine
 IMacroEngine. More...
 
class  CMacroEngine
 CMacroEngine. More...
 
struct  CMacroEngine::SKey_Less
 
class  IMacroFunctionContext
 
class  CMacroContextForEditing
 Defines the full set of macro functions. More...
 
class  CMacroContextForListing
 
class  CMacroResolver
 CMacroResolver Variable and function resolver Provides interfaces for: More...
 
class  CMacroEngineParallel
 CMacroEngineParallel. More...
 
struct  CMacroEngineParallel::SMacroInfo
 
class  CMacroParseException
 Macro exception. More...
 
class  CMacroDataException
 class CMacroExecException More...
 
class  CMacroExecException
 class CMacroExecException More...
 
class  CMQueryNodePreprocessor
 This class applies an operation to each node of the query tree to do necessary initialization (construction of user objects for tree nodes). More...
 
class  CMQueryNodeValue
 Subclass of the IQueryParseUserObject which is held as the user-defined object in each CQueryParseNode. More...
 
struct  CMQueryNodeValue::SResolvedField
 
class  CMQueryFunctionBase
 Query execution proxy class to add common operations and avoid modification of CQueryFunctionBase. More...
 
class  CMQueryFunctionValue
 Query execution function for simple atomic values. More...
 
class  CMQueryFunctionRTVar
 Query execution function for run-time variables. More...
 
class  CMQueryFunctionOps
 
class  CMQueryFunctionAssignment
 Query execution function for assignment operator. More...
 
class  CMQueryFunctionFunction
 Class implements functions calls in the do section of macro. More...
 
class  CMQueryFunctionDummy
 Default node processor. More...
 
class  IResolver
 Interface class for resolving entities during function execution. More...
 
class  CMacroExec
 Subclass of CQueryExec that adds: 1) Macro identifiers resolution 2) Where clause evaluation. More...
 
class  CMacroFunction_SwapQual
 
class  CMacroFunction_SwapRelFeatQual
 
class  CMacroFunction_SetStringQual
 
class  CMacroFunction_RemoveQual
 
class  CMacroFunction_EditStringQual
 
class  CMacroFunction_SetRelFeatQual
 
class  CMacroFunction_SetQual
 
class  CMacroFunction_AddDBLink
 
class  CMacroFunction_EditRelFeatQual
 
class  IOperateOnTwoQuals
 
class  CMacroFunction_ConvertStringQual
 
class  CMacroFunction_ConvertFeatQual
 
class  CMacroFunction_ConvertRNARelQual
 
class  CMacroFunction_ParseStringQual
 
class  CMacroFunction_ParseFeatQual
 
class  CMacroFunction_ParseRNARelQual
 
class  CMacroFunction_AddParsedText
 
class  CMacroFunction_AddParsedToFeatQual
 
class  CMacroFunction_ParsedText
 
class  CMacroFunction_ParsedTextFrom
 
class  CMacroFunction_ParseToStructComm
 
class  CMacroFunction_CopyStringQual
 
class  CMacroFunction_CopyFeatQual
 
class  CMacroFunction_CopyRNARelQual
 
class  CMacroFunction_RemoveOutside
 
class  CMacroFunction_RmvOutsideRelFeatQual
 
class  CMacroFunction_AddorSetContElement
 
class  CMacroFunction_AddorSetBsrcModifier
 
class  CMacroFunction_AddorSetGbQual
 
class  CMacroFunction_SetStructCommDb
 
class  CMacroFunction_SatelliteFields
 
class  CMacroFunction_SatelliteType
 
class  CMacroFunction_SatelliteName
 
class  CMacroFunction_MobileElementTypeFields
 
class  CMacroFunction_MobileElementType
 
class  CMacroFunction_MobileElementName
 
class  CMacroFunction_ApplyStrucVoucherPart
 
class  IMacroFunction< TData >
 Abstract base class for any user function which can be called from either the WHERE or DO clauses. More...
 
class  CMacroFunction_ModifyPrimerSeq
 
class  CMacroFunction_TrimJunkFromPrimers
 
class  CMacroFunction_FixIInPrimers
 
class  CMacroFunction_FixFormat
 
class  CMacroFunction_FixPubCaps
 
class  CMacroFunction_FixPubCapsTitle
 
class  CMacroFunction_FixPubCapsAuthor
 
class  CMacroFunction_FixPubCapsAffil
 
class  CMacroFunction_FixPubCapsAffilWithExcept
 
class  CMacroFunction_FixPubCapsAffilCountry
 
class  CMacroFunction_RemoveSegGaps
 
class  CMacroFunction_RemoveOrgName
 
class  CMacroFunction_MakeBoldXrefs
 
class  CMacroFunction_TrimTerminalNs
 
class  CMacroFunction_FixSpelling
 
class  CMacroFunction_RemoveSingleItemSet
 
class  CMacroFunction_Autodef
 
class  CMacroFunction_AutodefId
 
class  CMacroFunction_RefreshDefline
 
class  CMacroFunction_AutodefComplete
 
class  CMacroFunction_RenormalizeNucProtSet
 
class  CMacroFunction_CreateProteinFeats
 
class  CMacroFunction_DeltaSeqToRaw
 
class  CMacroFunction_UpdateProteinSeqs
 
class  CMacroFunction_FixProteinFormat
 
class  CMacroFunction_EditFeatLocation
 
class  CMacroFunction_SetBothPartials
 
class  CMacroFunction_RemoveBothPartials
 
class  CMacroFunction_Set5Partial
 
class  CMacroFunction_Set3Partial
 
class  CMacroFunction_Clear5Partial
 
class  CMacroFunction_Clear3Partial
 
class  CMacroFunction_ConvertLocStrand
 
class  CMacroFunction_ConvertLocType
 
class  CMacroFunction_Extend5Feature
 
class  CMacroFunction_Extend3Feature
 
class  CMacroFunction_RemoveAllFeatures
 
class  CMacroFunction_ApplyCDSFrame
 
class  CMacroFunction_ConvertFeature
 
class  CMacroFunction_ConvertCDS
 
class  CMacroFunction_RemoveGeneXref
 
class  CMacroFunction_ReplaceStopWithSelenocysteine
 
class  CMacroFunction_MakeLocation
 
class  CMacroFunction_MakeInterval
 
class  CMacroFunction_MakeWholeSeqInterval
 
class  CMacroFunction_MakePoint
 
class  CMacroFunction_ApplyFeature
 
class  CMacroFunction_ApplyCDS
 
class  CMacroFunction_ApplyRNA
 
class  CMacroFunction_ApplyGene
 
class  CMacroFunction_ApplyOtherFeature
 
class  CMacroFunction_LocPartialTest
 
class  CMacroFunction_LocEnd
 
class  CMacroFunction_LocationType
 
class  CMacroFunction_LocationSeqType
 
class  CMacroFunction_LocationDistConstraint
 
class  CUnculturedTool
 
class  CCulturedTool
 
class  CMacroFunction_PubFields
 
class  CMacroFunction_ApplyPublication
 
class  CMacroFunction_AuthorFix
 
class  CMacroFunction_MoveMiddleName
 
class  CMacroFunction_StripSuffix
 
class  CMacroFunction_TruncateMI
 
class  CMacroFunction_ReverseAuthNames
 
class  CMacroFunction_ISOJTALookup
 
class  CMacroFunction_LookupPub
 
class  CMacroFunction_SetPubTitle
 
class  CMacroFunction_SetPubAffil
 
class  CMacroFunction_SetPubAuthor
 
class  CMacroFunction_AddPubAuthor
 
class  CMacroFunction_AddAuthorList
 
class  CMacroFunction_SetPubJournal
 
class  CMacroFunction_SetPubVolIssuePages
 
class  CMacroFunction_SetPubDate
 
class  CMacroFunction_SetPubDateField
 
class  CMacroFunction_SetPubStatus
 
class  CMacroFunction_SetPubField
 
class  CMacroFunction_SetPubAffil_Depr
 
class  CMacroFunction_SetPubDate_Depr
 
class  CMacroFunction_FeatStrandednessConstraint
 
class  CMacroFunction_NumberOfFeatures
 
class  CMacroFunction_StringConstraints
 
class  CMacroFunction_StringFastConstraints
 
class  CMacroFunction_StringSlowConstraints
 
class  CMacroFunction_IsPresent
 
class  CMacroFunction_GetSeqdesc
 
class  CMacroFunction_GetSequence
 
class  CMacroFunction_FirstOrLastItem
 
class  CHugeMacroContext
 Stores the features of input data that are needed when data is processed in huge file mode. More...
 
class  CMacroLib
 CMacroLib - singleton. More...
 
class  CScanner
 Class for lexical tokens extraction from macro string. More...
 
struct  CScanner::SLocation
 
struct  CScanner::SData
 
struct  CScanner::SLexem
 
class  CMacroParser
 Class provides macro language interface for bulk bio-editing. More...
 
class  IMacroVar
 Abstract interface for variable representation. More...
 
struct  IMacroVar::SValue
 Variable value storage structure. More...
 
class  CMacroVarSimple
 derived classes for representation of specific variable types. More...
 
class  CMacroVarAsk
 Class for "ask" variable representation (i.e. More...
 
class  CMacroVarChoice
 Class for "choice" variable representation (i.e. More...
 
class  CMacroRep
 Class for parsed macro representation. More...
 
class  CRemoveTextOptions
 
class  CMQueryFunctionOps_BooleanBinary
 functor classes. More...
 
class  CMQueryFunctionOps_BooleanNot
 class CMQueryFunctionOps_BooleanNot More...
 
class  CMQueryFunctionOps_Comparison
 class CMQueryFunctionOps_Comparison More...
 
class  CMQueryFunctionOps_Like
 class CMQueryFunctionOps_Like More...
 
class  CMQueryFunctionOps_In
 class CMQueryFunctionOps_In More...
 
class  CMQueryFunctionOps_Between
 class CMQueryFunctionOps_Between More...
 

Macros

#define DECLARE_FUNC_CLASS(CL_NAME)
 Built-in functions. More...
 
#define DECLARE_FUNC_CLASS_WITH_ARGS(CL_NAME)
 
#define DECLARE_FUNC_CLASS_WITH_FNCNAME(CL_NAME)
 
#define DEFINE_MACRO_FUNCNAME(CL_NAME, FN_NAME)
 

Typedefs

using IMacroBioDataIter::STableToApply::TIndex = unordered_map< string, unsigned >
 
using IMacroBioDataIter::STableToApply::TPresent = vector< pair< string, bool > >
 true value for a key indicates that was present in the record More...
 
using IMacroBioDataIter::STableToApply::TTableValues = vector< string >
 
using CMacroBioData_PubdescIter::TPmidLookupMap = map< TEntrezId, CRef< objects::CPub > >
 
using CMacroBioData_PubdescIter::TDOILookupMap = map< string, CRef< objects::CPubdesc > >
 
using CMacroBioData_PubdescIter::ISOJTALookupMap = map< string, vector< string > >
 
using TChangedQuals = map< string, size_t >
 
using IEditMacroFunction::TParent = IMacroFunction< CIRef< IMacroBioDataIter > >
 
using IEditMacroFunction::TNodeValuesVec = vector< CRef< CMQueryNodeValue > >
 
typedef map< string, IEditMacroFunction *, SKey_LessCMacroEngine::TBuiltInFunctionsMap
 
typedef map< string, CRef< CMQueryNodeValue > > CMacroEngine::TRTVarsMap
 
typedef map< string, CObjectInfoCMacroEngine::TTempRTVarsMap
 
using IMacroFunctionContext::TBuiltInFunctionsMap = map< string, IEditMacroFunction *, PNocase >
 
typedef map< string, CRef< CMQueryNodeValue > > CMacroResolver::TRTVarsMap
 
typedef map< string, CObjectInfoCMacroResolver::TTempRTVarsMap
 
typedef list< SResolvedFieldCMQueryNodeValue::TObs
 
typedef vector< CRef< CMQueryNodeValue > > CMQueryFunctionOps::TUserArgs
 
typedef class CQueryExec CMacroExec::TBase
 
using CMacroFunction_AutodefId::TModifiers = objects::CAutoDefSourceDescription::TAvailableModifierVector
 
typedef objects::CSeqFeatData::ESubtype CMacroFunction_ConvertFeature::TFeatSubtype
 
using CMacroLib::TMacroNameMap = map< string, CRef< CMacroRep > >
 
using CMacroLib::TMacroLibrary = vector< CRef< CMacroRep > >
 
using CMacroLib::TStrSynList = map< string, list< string > >
 
typedef CQueryParseTree::TFunctionNames CMacroParser::TFunctionNamesList
 Type for the list of functions in Where/Do clauses. More...
 
typedef list< IMacroVar * > CMacroRep::TVariables
 Typedef vector of variables. More...
 
typedef list< TVariablesCMacroRep::TVarBlocks
 Typedef vector of blocks of variables. More...
 
using NMacroUtil::TVecFeatList = vector< CConstRef< objects::CSeq_feat > >
 
typedef SStaticPair< const char *, CMacroFunction_AuthorFix::EActionTypeTAuthorFixPair
 
typedef CStaticArrayMap< string, CMacroFunction_AuthorFix::EActionTypeTAuthorFixTypeMap
 
using NMacroUtil::TFeatLabelMap = SStaticPair< const char *, CLabel::ELabelType >
 
using NMacroUtil::TLabelTypeToNameMap = CStaticPairArrayMap< string, CLabel::ELabelType >
 

Enumerations

enum  CMacroBioData_BioSourceIter::ECollDateType { CMacroBioData_BioSourceIter::eCollDateType_NotSet , CMacroBioData_BioSourceIter::eAmbiguous_True , CMacroBioData_BioSourceIter::eAmbiguous_False }
 
enum  CMacroParseException::EErrCode {
  CMacroParseException::eParseKeywordExpected , CMacroParseException::eParseAsnSelectorExpected , CMacroParseException::eParseNamedAnnotExpected , CMacroParseException::eParseMacroNameExpected ,
  CMacroParseException::eParseVariableDefined , CMacroParseException::eParseVarDefinitionExpected , CMacroParseException::eParseUndefinedVariable , CMacroParseException::eParseIdentifierNameExpected ,
  CMacroParseException::eParseWrongVariableUsage , CMacroParseException::eParseIntegerExpected , CMacroParseException::eParseRangeInvalid , CMacroParseException::eParseThreadCountInvalid ,
  CMacroParseException::eParseAssignmentExpected , CMacroParseException::eParseAssignmentToConst , CMacroParseException::eParseLeftBraceExpected , CMacroParseException::eParseCommaOrRightBraceExpected ,
  CMacroParseException::eParseLeftParenthesisExpected , CMacroParseException::eParseRightParenthesisExpected , CMacroParseException::eParseLeftBracketExpected , CMacroParseException::eParseRightBracketExpected ,
  CMacroParseException::eParseWhereClauseExpected , CMacroParseException::eParseWhereClauseInvalid , CMacroParseException::eParseFunctionOrObjectNameExpected , CMacroParseException::eParseFunctionExpected ,
  CMacroParseException::eParseFunctionOrDoneExpected , CMacroParseException::eParseEndOfFunction , CMacroParseException::eParseNothingExpected , CMacroParseException::eParseSemicolonExpected ,
  CMacroParseException::eParseSeparatorExpected , CMacroParseException::eParseCommaExpected
}
 
enum  CMacroExecException::EErrCode {
  CMacroExecException::eInternalError , CMacroExecException::eWrongArguments , CMacroExecException::eFloatNotSupported , CMacroExecException::eIncorrectIdentifier ,
  CMacroExecException::eIncorrectNamedAnnot , CMacroExecException::eFunctionNotImplemented , CMacroExecException::eWrongFunctionScope , CMacroExecException::eInvalidQuery ,
  CMacroExecException::eIncorrectNodeType , CMacroExecException::eVarNotResolved , CMacroExecException::eInvalidData , CMacroExecException::eFileNotFound ,
  CMacroExecException::eMultipleEntries , CMacroExecException::eSynonymsNotFound
}
 
enum  CMQueryNodeValue::EType {
  CMQueryNodeValue::eNotSet , CMQueryNodeValue::eInt , CMQueryNodeValue::eFloat , CMQueryNodeValue::eBool ,
  CMQueryNodeValue::eString , CMQueryNodeValue::eStrings , CMQueryNodeValue::eObjects , CMQueryNodeValue::eRef
}
 
enum  CMacroFunction_EditStringQual::ESearchLoc { CMacroFunction_EditStringQual::eAnywhere , CMacroFunction_EditStringQual::eBeginning , CMacroFunction_EditStringQual::eEnd }
 
enum  CMacroFunction_ParseToStructComm::EFieldType { CMacroFunction_ParseToStructComm::eFieldValue , CMacroFunction_ParseToStructComm::eDbName , CMacroFunction_ParseToStructComm::eFieldName , CMacroFunction_ParseToStructComm::eFieldError }
 
enum  CMacroFunction_SatelliteFields::ESatelliteFieldType { CMacroFunction_SatelliteFields::eSatelliteType , CMacroFunction_SatelliteFields::eSatelliteName }
 
enum  CMacroFunction_MobileElementTypeFields::EMobileElemTFieldType { CMacroFunction_MobileElementTypeFields::eMobileElemTType , CMacroFunction_MobileElementTypeFields::eMobileElemTName }
 
enum  IMacroFunction< TData >::EScopeEnum { IMacroFunction< TData >::eWhere , IMacroFunction< TData >::eDo , IMacroFunction< TData >::eBoth }
 
enum  IMacroFunction< TData >::ENestedFunc { IMacroFunction< TData >::eNotNested , IMacroFunction< TData >::eNested }
 
enum  CMacroFunction_ModifyPrimerSeq::EModifyType { CMacroFunction_ModifyPrimerSeq::eTrimJunk , CMacroFunction_ModifyPrimerSeq::eFixI }
 
enum  CMacroFunction_FixPubCaps::EPubType {
  CMacroFunction_FixPubCaps::eTitle , CMacroFunction_FixPubCaps::eAuthor , CMacroFunction_FixPubCaps::eAffiliation , CMacroFunction_FixPubCaps::eAffilExceptAffilDiv ,
  CMacroFunction_FixPubCaps::eAffilCountry
}
 
enum  CMacroFunction_UpdateProteinSeqs::EMatch { CMacroFunction_UpdateProteinSeqs::eMatchNotSet , CMacroFunction_UpdateProteinSeqs::eMatchId , CMacroFunction_UpdateProteinSeqs::eMatchName }
 
enum  CMacroFunction_ApplyCDSFrame::ECdsFrame { CMacroFunction_ApplyCDSFrame::eNotSet , CMacroFunction_ApplyCDSFrame::eBest , CMacroFunction_ApplyCDSFrame::eMatch }
 
enum class  ELocEndType { eStart , eStop }
 
enum  CMacroFunction_AuthorFix::EActionType {
  CMacroFunction_AuthorFix::eAuthorFixNotSet , CMacroFunction_AuthorFix::eMoveMiddleName , CMacroFunction_AuthorFix::eStripSuffix , CMacroFunction_AuthorFix::eReverseNames ,
  CMacroFunction_AuthorFix::eTruncateMI
}
 
enum  CMacroFunction_SetPubField::EPubFieldType { CMacroFunction_SetPubField::ePubField_Affil , CMacroFunction_SetPubField::ePubField_Date }
 
enum  CMacroFunction_StringConstraints::EStrConstrCase { CMacroFunction_StringConstraints::eNotSet , CMacroFunction_StringConstraints::eUpper , CMacroFunction_StringConstraints::eLower , CMacroFunction_StringConstraints::ePunct }
 
enum  CMacroFunction_StringConstraints::ELogicType { CMacroFunction_StringConstraints::eOR , CMacroFunction_StringConstraints::eAND }
 
enum  CScanner::EToken {
  CScanner::eTokenILLEGAL = -1 , CScanner::eTokenEOS = 0 , CScanner::eTokenKWMACRO , CScanner::eTokenKWVARS ,
  CScanner::eTokenKWFOR , CScanner::eTokenKWEACH , CScanner::eTokenKWFROM , CScanner::eTokenKWCHOICE ,
  CScanner::eTokenKWRANGE , CScanner::eTokenKWWHERE , CScanner::eTokenKWDO , CScanner::eTokenKWDONE ,
  CScanner::eTokenKWDOPARL , CScanner::eTokenKWPARLAUTO , CScanner::eTokenFUNCTION , CScanner::eTokenIDENT ,
  CScanner::eTokenASNSELECTOR , CScanner::eTokenNAMEDANNOT , CScanner::eTokenINTNUMBER , CScanner::eTokenFLOATNUMBER ,
  CScanner::eTokenSTRING , CScanner::eTokenASK , CScanner::eTokenBOOLCONST , CScanner::eTokenASSIGNMENT ,
  CScanner::eTokenLEFTPAREN , CScanner::eTokenRIGHTPAREN , CScanner::eTokenLEFTBRACKET , CScanner::eTokenRIGHTBRACKET ,
  CScanner::eTokenLEFTBRACE , CScanner::eTokenRIGHTBRACE , CScanner::eTokenCOMMA , CScanner::eTokenSEMICOLON ,
  CScanner::eTokenMINUS , CScanner::eTokenPLUS , CScanner::eTokenDOT , CScanner::eTokenMULT ,
  CScanner::eTokenDIV , CScanner::eTokenGREATER , CScanner::eTokenLESS , CScanner::eTokenNOTLESS ,
  CScanner::eTokenNOTGREATER , CScanner::eTokenNOTEQUAL , CScanner::eTokenCOMMENT
}
 
enum  CMacroParser::EParsingErrReportType { CMacroParser::eErrorLineAndColumn , CMacroParser::eErrorAbsolutePos }
 
enum  IMacroVar::EValueType {
  IMacroVar::eValueTypeString = 0 , IMacroVar::eValueTypeInt , IMacroVar::eValueTypeFloat , IMacroVar::eValueTypeBool ,
  IMacroVar::eValueTypeNotSet
}
 Type of stored value (not the type of variable) More...
 
enum  NMacroUtil::EStructVoucherPart { NMacroUtil::eSV_Coll , NMacroUtil::eSV_Inst , NMacroUtil::eSV_Specid , NMacroUtil::eSV_Error }
 
enum  NMacroUtil::EUnverifiedType {
  NMacroUtil::eUnVer_Organism , NMacroUtil::eUnVer_Features , NMacroUtil::eUnVer_Misassembled , NMacroUtil::eUnVer_Contaminant ,
  NMacroUtil::eUnVer_Unknown
}
 
enum  CRemoveTextOptions::EMatchType { CRemoveTextOptions::eNone = 0 , CRemoveTextOptions::eText , CRemoveTextOptions::eDigits , CRemoveTextOptions::eLetters }
 

Functions

 CMacroBioData::CMacroBioData (const objects::CSeq_entry_Handle &entry, CConstRef< objects::CSeq_submit > submit=CConstRef< objects::CSeq_submit >())
 
 CMacroBioData::~CMacroBioData ()
 
bool CMacroBioData::IsSetSeqSubmit (void) const
 
const objects::CSeq_submit & CMacroBioData::GetSeqSubmit (void) const
 
objects::CSeq_entry_Handle CMacroBioData::GetTSE () const
 
IMacroBioDataIterCMacroBioData::CreateIterator (const string &selector, const string &named_annot, const TSeqRange &range, CNcbiOstream *ostr=nullptr) const
 Create specific iterator as a subclass of IMacroBioDataIter. More...
 
IMacroBioDataIterCMacroBioData::CreateIterator (const string &selector, const string &named_annot, const SFeatInterval &feat_interval, CNcbiOstream *ostr=nullptr) const
 Create specific iterator as a subclass of IMacroBioDataIter. More...
 
static bool CMacroBioData::s_IsFeatSelector (const string &selector)
 
IMacroBioDataIterCMacroBioData::x_CreateNonFeatIterator (const string &selector) const
 
IMacroBioDataIterCMacroBioData::x_CreateFeatIterator (const string &selector, const string &named_annot, const TSeqRange &range) const
 
IMacroBioDataIterCMacroBioData::x_CreateFeatIterator (const string &selector, const string &named_annot, const SFeatInterval &feat_interval) const
 
objects::SAnnotSelector CMacroBioData::x_GetAnnotSelector (const string &selector, const string &named_annot) const
 
 CMacroBioData::CMacroBioData (const CMacroBioData &)
 
CMacroBioDataCMacroBioData::operator= (const CMacroBioData &)
 
virtual IMacroBioDataIter::~IMacroBioDataIter ()
 
virtual IMacroBioDataIterIMacroBioDataIter::Begin (void)=0
 
virtual IMacroBioDataIterIMacroBioDataIter::Next (void)=0
 
virtual bool IMacroBioDataIter::IsEnd (void) const =0
 
virtual bool IMacroBioDataIter::IsBegin (void)=0
 
virtual size_t IMacroBioDataIter::GetCount () const
 
virtual SConstScopedObject IMacroBioDataIter::GetScopedObject () const =0
 Dereferences the underlying iterator. More...
 
virtual string IMacroBioDataIter::GetBestDescr () const =0
 Used for logging. More...
 
virtual void IMacroBioDataIter::BuildEditedObject ()=0
 Creates a copy of the object that will be edited. More...
 
CObjectInfo IMacroBioDataIter::GetEditedObject ()
 
virtual void IMacroBioDataIter::RunEditCommand (CMacroCmdComposite *cmd_composite)=0
 Constructs and executes the editing command. More...
 
virtual void IMacroBioDataIter::RunDeleteCommand (CMacroCmdComposite *cmd_composite)=0
 Constructs and executes the delete command. More...
 
void IMacroBioDataIter::RunCommand (CRef< CCmdComposite > cmd, CMacroCmdComposite *cmd_composite)
 Method for executing a specific command. More...
 
bool IMacroBioDataIter::IntendToDelete () const
 
virtual void IMacroBioDataIter::SetToDelete (bool intent)
 
bool IMacroBioDataIter::IsModified () const
 
void IMacroBioDataIter::SetModified ()
 
bool IMacroBioDataIter::GetChoiceType (const string &field_name, string &choice_type) const
 returns choice type string for a given identifier field_name More...
 
virtual bool IMacroBioDataIter::IsDescriptor () const =0
 
virtual bool IMacroBioDataIter::IsFeature () const =0
 
virtual objects::CBioseq_Handle IMacroBioDataIter::GetBioseqHandle (void) const =0
 
virtual const vector< string > & IMacroBioDataIter::GetTaxnames () const
 
objects::CSeq_entry_Handle IMacroBioDataIter::GetSEH () const
 
bool IMacroBioDataIter::HasBeenCompleted () const
 
void IMacroBioDataIter::SetCompleted ()
 
bool IMacroBioDataIter::IsSetSeqSubmit (void) const
 
const objects::CSeq_submit & IMacroBioDataIter::GetSeqSubmit (void) const
 
void IMacroBioDataIter::SetSeqSubmit (const objects::CSeq_submit &submit)
 
void IMacroBioDataIter::SetOutputStream (CNcbiOstream *str)
 
bool IMacroBioDataIter::IsSetOutputStream () const
 
CNcbiOstreamIMacroBioDataIter::GetOutputStream () const
 
void IMacroBioDataIter::SetTableToApply (const string &file_name, size_t match_col, const string &delimiter, bool merge_de, bool split_firstcol, bool convert_multi, bool merge_firstcols, bool multiple_sp_only)
 
const stringIMacroBioDataIter::GetTableName () const
 
string IMacroBioDataIter::GetValueFromTable (size_t col)
 
bool IMacroBioDataIter::FindInTable (const CMQueryNodeValue::TObs &objs, bool case_sensitive=true)
 
bool IMacroBioDataIter::FindInTable (const vector< string > &strs, bool case_sensitive=true)
 
string IMacroBioDataIter::GetUnMatchedTableEntries (int &count)
 
void IMacroBioDataIter::SetHugeDataMode (bool value)
 
bool IMacroBioDataIter::IsHugeDataMode () const
 
auto & IMacroBioDataIter::RemoteUpdater ()
 
auto & IMacroBioDataIter::DOIUpdater ()
 
auto & IMacroBioDataIter::ISOJTAUpdater ()
 
bool IMacroBioDataIter::TopLevelObject () const
 
objects::CObject_id::TId & IMacroBioDataIter::MaxFeatureId ()
 
void IMacroBioDataIter::SetHugeContext (const shared_ptr< CHugeMacroContext > &context)
 
 IMacroBioDataIter::IMacroBioDataIter (const objects::CSeq_entry_Handle &entry)
 
virtual void IMacroBioDataIter::x_SetDefaultObjectInfo ()=0
 Initializes member variable m_CurIterOI. More...
 
void IMacroBioDataIter::x_Init ()
 
 IMacroBioDataIter::STableToApply::STableToApply (const string &file_name)
 
bool IMacroBioDataIter::STableToApply::SetTableToApply (const string &file_name, size_t match_col)
 
bool IMacroBioDataIter::STableToApply::GetValueFromTable (size_t col, string &value)
 
void IMacroBioDataIter::STableToApply::x_InitAndCheck (const string &file_name, size_t col)
 
bool IMacroBioDataIter::STableToApply::x_CacheColFromTable (size_t col)
 
 CMacroBioData_FeatIterBase::CMacroBioData_FeatIterBase (const objects::CSeq_entry_Handle &entry, const objects::SAnnotSelector &sel)
 
 CMacroBioData_FeatIterBase::CMacroBioData_FeatIterBase (const objects::CBioseq_Handle &bsh, const objects::SAnnotSelector &sel, const objects::CSeq_loc &loc)
 
virtual CMacroBioData_FeatIterBase::~CMacroBioData_FeatIterBase ()
 
virtual IMacroBioDataIterCMacroBioData_FeatIterBase::Begin (void)
 
virtual IMacroBioDataIterCMacroBioData_FeatIterBase::Next (void)
 
virtual bool CMacroBioData_FeatIterBase::IsEnd (void) const
 
virtual bool CMacroBioData_FeatIterBase::IsBegin (void)
 
virtual size_t CMacroBioData_FeatIterBase::GetCount () const
 
virtual SConstScopedObject CMacroBioData_FeatIterBase::GetScopedObject () const
 Dereferences the underlying iterator. More...
 
virtual string CMacroBioData_FeatIterBase::GetBestDescr () const
 Used for logging. More...
 
virtual void CMacroBioData_FeatIterBase::BuildEditedObject ()
 Creates a copy of the object that will be edited. More...
 
virtual void CMacroBioData_FeatIterBase::RunEditCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the editing command. More...
 
virtual void CMacroBioData_FeatIterBase::RunDeleteCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the delete command. More...
 
virtual bool CMacroBioData_FeatIterBase::IsDescriptor () const
 
virtual bool CMacroBioData_FeatIterBase::IsFeature () const
 
virtual objects::CBioseq_Handle CMacroBioData_FeatIterBase::GetBioseqHandle (void) const
 
virtual void CMacroBioData_FeatIterBase::SetToDelete (bool intent)
 
virtual const vector< string > & CMacroBioData_FeatIterBase::GetTaxnames () const
 
void CMacroBioData_FeatIterBase::SetCreateGeneralIdFlag ()
 
bool CMacroBioData_FeatIterBase::GetCreateGeneralIdFlag () const
 
virtual void CMacroBioData_FeatIterBase::x_SetDefaultObjectInfo ()
 Initializes member variable m_CurIterOI. More...
 
 CMacroBioData_FeatIterBase::CMacroBioData_FeatIterBase (const CMacroBioData_FeatIterBase &)
 
CMacroBioData_FeatIterBaseCMacroBioData_FeatIterBase::operator= (const CMacroBioData_FeatIterBase &)
 
 SFeatInterval::SFeatInterval (const TSeqRange &range, bool left=true, bool right=true)
 
 CMacroBioData_FeatIntervalIter::CMacroBioData_FeatIntervalIter (const objects::CBioseq_Handle &bsh, const objects::SAnnotSelector &sel, const SFeatInterval &feat_interval)
 
virtual CMacroBioData_FeatIntervalIter::~CMacroBioData_FeatIntervalIter ()
 
virtual IMacroBioDataIterCMacroBioData_FeatIntervalIter::Begin (void)
 
virtual IMacroBioDataIterCMacroBioData_FeatIntervalIter::Next (void)
 
virtual bool CMacroBioData_FeatIntervalIter::IsEnd (void) const
 
virtual bool CMacroBioData_FeatIntervalIter::IsBegin (void)
 
virtual SConstScopedObject CMacroBioData_FeatIntervalIter::GetScopedObject () const
 Dereferences the underlying iterator. More...
 
virtual string CMacroBioData_FeatIntervalIter::GetBestDescr () const
 Used for logging. More...
 
virtual void CMacroBioData_FeatIntervalIter::BuildEditedObject ()
 Creates a copy of the object that will be edited. More...
 
virtual void CMacroBioData_FeatIntervalIter::RunEditCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the editing command. More...
 
virtual void CMacroBioData_FeatIntervalIter::RunDeleteCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the delete command. More...
 
virtual bool CMacroBioData_FeatIntervalIter::IsDescriptor () const
 
virtual bool CMacroBioData_FeatIntervalIter::IsFeature () const
 
virtual objects::CBioseq_Handle CMacroBioData_FeatIntervalIter::GetBioseqHandle (void) const
 
virtual void CMacroBioData_FeatIntervalIter::x_SetDefaultObjectInfo ()
 Initializes member variable m_CurIterOI. More...
 
void CMacroBioData_FeatIntervalIter::x_StepToNextFeat ()
 
 CMacroBioData_FeatIntervalIter::CMacroBioData_FeatIntervalIter (const CMacroBioData_FeatIntervalIter &)
 
CMacroBioData_FeatIntervalIterCMacroBioData_FeatIntervalIter::operator= (const CMacroBioData_FeatIntervalIter &)
 
 CMacroBioData_BioSourceIter::CMacroBioData_BioSourceIter (const objects::CSeq_entry_Handle &entry)
 
virtual CMacroBioData_BioSourceIter::~CMacroBioData_BioSourceIter ()
 
virtual IMacroBioDataIterCMacroBioData_BioSourceIter::Begin (void)
 
virtual IMacroBioDataIterCMacroBioData_BioSourceIter::Next (void)
 
virtual bool CMacroBioData_BioSourceIter::IsEnd (void) const
 
virtual bool CMacroBioData_BioSourceIter::IsBegin (void)
 
virtual SConstScopedObject CMacroBioData_BioSourceIter::GetScopedObject () const
 Dereferences the underlying iterator. More...
 
virtual string CMacroBioData_BioSourceIter::GetBestDescr () const
 Used for logging. More...
 
virtual void CMacroBioData_BioSourceIter::BuildEditedObject ()
 Creates a copy of the object that will be edited. More...
 
virtual void CMacroBioData_BioSourceIter::RunEditCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the editing command. More...
 
virtual void CMacroBioData_BioSourceIter::RunDeleteCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the delete command. More...
 
virtual bool CMacroBioData_BioSourceIter::IsDescriptor () const
 
virtual bool CMacroBioData_BioSourceIter::IsFeature () const
 
virtual objects::CBioseq_Handle CMacroBioData_BioSourceIter::GetBioseqHandle (void) const
 
ECollDateType CMacroBioData_BioSourceIter::GetCollDateType () const
 
void CMacroBioData_BioSourceIter::SetCollDateType (bool ambiguous)
 
virtual void CMacroBioData_BioSourceIter::x_SetDefaultObjectInfo ()
 Initializes member variable m_CurIterOI. More...
 
const objects::CBioSource * CMacroBioData_BioSourceIter::x_GetBioSource ()
 
 CMacroBioData_BioSourceIter::CMacroBioData_BioSourceIter (const CMacroBioData_BioSourceIter &)
 
CMacroBioData_BioSourceIterCMacroBioData_BioSourceIter::operator= (const CMacroBioData_BioSourceIter &)
 
 CMacroBioData_PubdescIter::CMacroBioData_PubdescIter (const objects::CSeq_entry_Handle &entry)
 
virtual CMacroBioData_PubdescIter::~CMacroBioData_PubdescIter ()
 
virtual IMacroBioDataIterCMacroBioData_PubdescIter::Begin (void)
 
virtual IMacroBioDataIterCMacroBioData_PubdescIter::Next (void)
 
virtual bool CMacroBioData_PubdescIter::IsEnd (void) const
 
virtual bool CMacroBioData_PubdescIter::IsBegin (void)
 
virtual SConstScopedObject CMacroBioData_PubdescIter::GetScopedObject () const
 Dereferences the underlying iterator. More...
 
virtual string CMacroBioData_PubdescIter::GetBestDescr () const
 Used for logging. More...
 
virtual void CMacroBioData_PubdescIter::BuildEditedObject ()
 Creates a copy of the object that will be edited. More...
 
virtual void CMacroBioData_PubdescIter::RunEditCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the editing command. More...
 
virtual void CMacroBioData_PubdescIter::RunDeleteCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the delete command. More...
 
virtual bool CMacroBioData_PubdescIter::IsDescriptor () const
 
virtual bool CMacroBioData_PubdescIter::IsFeature () const
 
virtual objects::CBioseq_Handle CMacroBioData_PubdescIter::GetBioseqHandle (void) const
 
const TPmidLookupMapCMacroBioData_PubdescIter::GetPmidLookupMap () const
 
TPmidLookupMapCMacroBioData_PubdescIter::SetPmidLookupMap ()
 
TDOILookupMapCMacroBioData_PubdescIter::SetDOILookupMap ()
 
ISOJTALookupMapCMacroBioData_PubdescIter::SetISOJTALookupMap ()
 
virtual void CMacroBioData_PubdescIter::x_SetDefaultObjectInfo ()
 Initializes member variable m_CurIterOI. More...
 
 CMacroBioData_PubdescIter::CSubmitblockIter::CSubmitblockIter (CConstRef< objects::CSeq_submit > seqsubmit)
 
 CMacroBioData_PubdescIter::CSubmitblockIter::~CSubmitblockIter ()
 
bool CMacroBioData_PubdescIter::CSubmitblockIter::Processed () const
 
void CMacroBioData_PubdescIter::CSubmitblockIter::MarkProcessed ()
 
CRef< objects::CSubmit_block > CMacroBioData_PubdescIter::CSubmitblockIter::BuildEditedObject ()
 
const objects::CSubmit_block & CMacroBioData_PubdescIter::CSubmitblockIter::GetOrigSubmitBlock () const
 
objects::CSubmit_block & CMacroBioData_PubdescIter::CSubmitblockIter::GetEditedSubmitBlock () const
 
 CMacroBioData_PubdescIter::CMacroBioData_PubdescIter (const CMacroBioData_PubdescIter &)
 
CMacroBioData_PubdescIterCMacroBioData_PubdescIter::operator= (const CMacroBioData_PubdescIter &)
 
 CMacroBioData_SeqdescIter::CMacroBioData_SeqdescIter (const objects::CSeq_entry_Handle &entry)
 
virtual CMacroBioData_SeqdescIter::~CMacroBioData_SeqdescIter ()
 
virtual IMacroBioDataIterCMacroBioData_SeqdescIter::Begin (void)
 
virtual IMacroBioDataIterCMacroBioData_SeqdescIter::Next (void)
 
virtual bool CMacroBioData_SeqdescIter::IsEnd (void) const
 
virtual bool CMacroBioData_SeqdescIter::IsBegin (void)
 
virtual SConstScopedObject CMacroBioData_SeqdescIter::GetScopedObject () const
 Dereferences the underlying iterator. More...
 
virtual string CMacroBioData_SeqdescIter::GetBestDescr () const
 Used for logging. More...
 
virtual void CMacroBioData_SeqdescIter::BuildEditedObject ()
 Creates a copy of the object that will be edited. More...
 
virtual void CMacroBioData_SeqdescIter::RunEditCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the editing command. More...
 
virtual void CMacroBioData_SeqdescIter::RunDeleteCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the delete command. More...
 
virtual bool CMacroBioData_SeqdescIter::IsDescriptor () const
 
virtual bool CMacroBioData_SeqdescIter::IsFeature () const
 
virtual objects::CBioseq_Handle CMacroBioData_SeqdescIter::GetBioseqHandle (void) const
 
virtual void CMacroBioData_SeqdescIter::x_SetDefaultObjectInfo ()
 Initializes member variable m_CurIterOI. More...
 
string CMacroBioData_SeqdescIter::x_GetDescription (const string &descr_name) const
 
string CMacroBioData_SeqdescIter::x_GetSeqId () const
 
 CMacroBioData_SeqdescIter::CMacroBioData_SeqdescIter (const CMacroBioData_SeqdescIter &)
 
CMacroBioData_SeqdescIterCMacroBioData_SeqdescIter::operator= (const CMacroBioData_SeqdescIter &)
 
 CMacroBioData_MolInfoIter::CMacroBioData_MolInfoIter (const objects::CSeq_entry_Handle &entry)
 
virtual CMacroBioData_MolInfoIter::~CMacroBioData_MolInfoIter ()
 
virtual IMacroBioDataIterCMacroBioData_MolInfoIter::Begin (void)
 
virtual IMacroBioDataIterCMacroBioData_MolInfoIter::Next (void)
 
virtual bool CMacroBioData_MolInfoIter::IsEnd (void) const
 
virtual bool CMacroBioData_MolInfoIter::IsBegin (void)
 
virtual SConstScopedObject CMacroBioData_MolInfoIter::GetScopedObject () const
 Dereferences the underlying iterator. More...
 
virtual string CMacroBioData_MolInfoIter::GetBestDescr () const
 Used for logging. More...
 
virtual void CMacroBioData_MolInfoIter::BuildEditedObject ()
 Creates a copy of the object that will be edited. More...
 
virtual void CMacroBioData_MolInfoIter::RunEditCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the editing command. More...
 
virtual void CMacroBioData_MolInfoIter::RunDeleteCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the delete command. More...
 
virtual void CMacroBioData_MolInfoIter::x_SetDefaultObjectInfo ()
 Initializes member variable m_CurIterOI. More...
 
const objects::CMolInfo * CMacroBioData_MolInfoIter::x_GetMolInfo ()
 
 CMacroBioData_MolInfoIter::CMacroBioData_MolInfoIter (const CMacroBioData_MolInfoIter &)
 
CMacroBioData_MolInfoIterCMacroBioData_MolInfoIter::operator= (const CMacroBioData_MolInfoIter &)
 
 CMacroBioData_UserObjectIter::CMacroBioData_UserObjectIter (const objects::CSeq_entry_Handle &entry)
 
virtual CMacroBioData_UserObjectIter::~CMacroBioData_UserObjectIter ()
 
virtual IMacroBioDataIterCMacroBioData_UserObjectIter::Begin (void)
 
virtual IMacroBioDataIterCMacroBioData_UserObjectIter::Next (void)
 
virtual bool CMacroBioData_UserObjectIter::IsEnd (void) const
 
virtual bool CMacroBioData_UserObjectIter::IsBegin (void)
 
virtual SConstScopedObject CMacroBioData_UserObjectIter::GetScopedObject () const
 Dereferences the underlying iterator. More...
 
virtual string CMacroBioData_UserObjectIter::GetBestDescr () const
 Used for logging. More...
 
virtual void CMacroBioData_UserObjectIter::BuildEditedObject ()
 Creates a copy of the object that will be edited. More...
 
virtual void CMacroBioData_UserObjectIter::RunEditCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the editing command. More...
 
virtual void CMacroBioData_UserObjectIter::RunDeleteCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the delete command. More...
 
virtual void CMacroBioData_UserObjectIter::x_SetDefaultObjectInfo ()
 Initializes member variable m_CurIterOI. More...
 
 CMacroBioData_UserObjectIter::CMacroBioData_UserObjectIter (const CMacroBioData_UserObjectIter &)
 
CMacroBioData_UserObjectIterCMacroBioData_UserObjectIter::operator= (const CMacroBioData_UserObjectIter &)
 
 CMacroBioData_StructCommentIter::CMacroBioData_StructCommentIter (const objects::CSeq_entry_Handle &entry)
 
 CMacroBioData_StructCommentIter::~CMacroBioData_StructCommentIter ()
 
virtual IMacroBioDataIterCMacroBioData_StructCommentIter::Begin (void)
 
virtual IMacroBioDataIterCMacroBioData_StructCommentIter::Next (void)
 
virtual string CMacroBioData_StructCommentIter::GetBestDescr () const
 Used for logging. More...
 
void CMacroBioData_StructCommentIter::x_StepToNextStructComment ()
 
 CMacroBioData_StructCommentIter::CMacroBioData_StructCommentIter (const CMacroBioData_StructCommentIter &)
 
CMacroBioData_StructCommentIterCMacroBioData_StructCommentIter::operator= (const CMacroBioData_StructCommentIter &)
 
 CMacroBioData_DBLinkIter::CMacroBioData_DBLinkIter (const objects::CSeq_entry_Handle &entry)
 
 CMacroBioData_DBLinkIter::~CMacroBioData_DBLinkIter ()
 
virtual IMacroBioDataIterCMacroBioData_DBLinkIter::Begin (void)
 
virtual IMacroBioDataIterCMacroBioData_DBLinkIter::Next (void)
 
virtual string CMacroBioData_DBLinkIter::GetBestDescr () const
 Used for logging. More...
 
const objects::CUser_object * CMacroBioData_DBLinkIter::x_GetDBLink ()
 
 CMacroBioData_DBLinkIter::CMacroBioData_DBLinkIter (const CMacroBioData_DBLinkIter &)
 
CMacroBioData_DBLinkIterCMacroBioData_DBLinkIter::operator= (const CMacroBioData_DBLinkIter &)
 
 CMacroBioData_AutodefOptsIter::CMacroBioData_AutodefOptsIter (const objects::CSeq_entry_Handle &entry)
 
 CMacroBioData_AutodefOptsIter::~CMacroBioData_AutodefOptsIter ()
 
virtual IMacroBioDataIterCMacroBioData_AutodefOptsIter::Begin (void)
 
virtual IMacroBioDataIterCMacroBioData_AutodefOptsIter::Next (void)
 
virtual string CMacroBioData_AutodefOptsIter::GetBestDescr () const
 Used for logging. More...
 
const objects::CUser_object * CMacroBioData_AutodefOptsIter::x_GetAutodefOptions ()
 
 CMacroBioData_AutodefOptsIter::CMacroBioData_AutodefOptsIter (const CMacroBioData_AutodefOptsIter &)
 
CMacroBioData_AutodefOptsIterCMacroBioData_AutodefOptsIter::operator= (const CMacroBioData_AutodefOptsIter &)
 
 CMacroBioData_SeqAlignIter::CMacroBioData_SeqAlignIter (const objects::CSeq_entry_Handle &entry)
 
virtual CMacroBioData_SeqAlignIter::~CMacroBioData_SeqAlignIter ()
 
virtual IMacroBioDataIterCMacroBioData_SeqAlignIter::Begin (void)
 
virtual IMacroBioDataIterCMacroBioData_SeqAlignIter::Next (void)
 
virtual bool CMacroBioData_SeqAlignIter::IsEnd (void) const
 
virtual bool CMacroBioData_SeqAlignIter::IsBegin (void)
 
virtual SConstScopedObject CMacroBioData_SeqAlignIter::GetScopedObject () const
 Dereferences the underlying iterator. More...
 
virtual string CMacroBioData_SeqAlignIter::GetBestDescr () const
 Used for logging. More...
 
virtual void CMacroBioData_SeqAlignIter::BuildEditedObject ()
 Creates a copy of the object that will be edited. More...
 
virtual void CMacroBioData_SeqAlignIter::RunEditCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the editing command. More...
 
virtual void CMacroBioData_SeqAlignIter::RunDeleteCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the delete command. More...
 
virtual bool CMacroBioData_SeqAlignIter::IsDescriptor () const
 
virtual bool CMacroBioData_SeqAlignIter::IsFeature () const
 
virtual objects::CBioseq_Handle CMacroBioData_SeqAlignIter::GetBioseqHandle (void) const
 
virtual void CMacroBioData_SeqAlignIter::x_SetDefaultObjectInfo ()
 Initializes member variable m_CurIterOI. More...
 
 CMacroBioData_SeqAlignIter::CMacroBioData_SeqAlignIter (const CMacroBioData_SeqAlignIter &)
 
CMacroBioData_SeqAlignIterCMacroBioData_SeqAlignIter::operator= (const CMacroBioData_SeqAlignIter &)
 
virtual CMacroBioData_SeqIter::~CMacroBioData_SeqIter ()
 
static CMacroBioData_SeqIterCMacroBioData_SeqIter::s_MakeSeqIterator (const objects::CSeq_entry_Handle &entry, objects::CSeq_inst::EMol mol_type)
 
virtual IMacroBioDataIterCMacroBioData_SeqIter::Begin (void)
 
virtual IMacroBioDataIterCMacroBioData_SeqIter::Next (void)
 
virtual bool CMacroBioData_SeqIter::IsEnd (void) const
 
virtual bool CMacroBioData_SeqIter::IsBegin (void)
 
virtual SConstScopedObject CMacroBioData_SeqIter::GetScopedObject () const
 Dereferences the underlying iterator. More...
 
virtual string CMacroBioData_SeqIter::GetBestDescr () const
 Used for logging. More...
 
virtual void CMacroBioData_SeqIter::BuildEditedObject ()
 Creates a copy of the object that will be edited. More...
 
virtual void CMacroBioData_SeqIter::RunEditCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the editing command. More...
 
virtual void CMacroBioData_SeqIter::RunDeleteCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the delete command. More...
 
virtual bool CMacroBioData_SeqIter::IsDescriptor () const
 
virtual bool CMacroBioData_SeqIter::IsFeature () const
 
virtual objects::CBioseq_Handle CMacroBioData_SeqIter::GetBioseqHandle (void) const
 
const objects::CAutoDefOptions & CMacroBioData_SeqIter::GetAutodefOptions () const
 
objects::CAutoDefOptions & CMacroBioData_SeqIter::SetAutodefOptions ()
 
virtual void CMacroBioData_SeqIter::x_SetDefaultObjectInfo ()
 Initializes member variable m_CurIterOI. More...
 
 CMacroBioData_SeqIter::CMacroBioData_SeqIter (const objects::CSeq_entry_Handle &entry)
 
 CMacroBioData_SeqIter::CMacroBioData_SeqIter (const CMacroBioData_SeqIter &)
 
CMacroBioData_SeqIterCMacroBioData_SeqIter::operator= (const CMacroBioData_SeqIter &)
 
 CMacroBioData_SeqNAIter::CMacroBioData_SeqNAIter (const objects::CSeq_entry_Handle &entry)
 
virtual IMacroBioDataIterCMacroBioData_SeqNAIter::Begin (void)
 
virtual bool CMacroBioData_SeqNAIter::IsBegin (void)
 
 CMacroBioData_SeqAAIter::CMacroBioData_SeqAAIter (const objects::CSeq_entry_Handle &entry)
 
virtual IMacroBioDataIterCMacroBioData_SeqAAIter::Begin (void)
 
virtual bool CMacroBioData_SeqAAIter::IsBegin (void)
 
 CMacroBioData_SeqSetIter::CMacroBioData_SeqSetIter (const objects::CSeq_entry_Handle &entry)
 
virtual CMacroBioData_SeqSetIter::~CMacroBioData_SeqSetIter ()
 
virtual IMacroBioDataIterCMacroBioData_SeqSetIter::Begin (void)
 
virtual IMacroBioDataIterCMacroBioData_SeqSetIter::Next (void)
 
virtual bool CMacroBioData_SeqSetIter::IsEnd (void) const
 
virtual bool CMacroBioData_SeqSetIter::IsBegin (void)
 
virtual SConstScopedObject CMacroBioData_SeqSetIter::GetScopedObject () const
 Dereferences the underlying iterator. More...
 
virtual string CMacroBioData_SeqSetIter::GetBestDescr () const
 Used for logging. More...
 
virtual void CMacroBioData_SeqSetIter::BuildEditedObject ()
 Creates a copy of the object that will be edited. More...
 
virtual void CMacroBioData_SeqSetIter::RunEditCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the editing command. More...
 
virtual void CMacroBioData_SeqSetIter::RunDeleteCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the delete command. More...
 
virtual bool CMacroBioData_SeqSetIter::IsDescriptor () const
 
virtual bool CMacroBioData_SeqSetIter::IsFeature () const
 
virtual objects::CBioseq_Handle CMacroBioData_SeqSetIter::GetBioseqHandle (void) const
 
virtual void CMacroBioData_SeqSetIter::x_SetDefaultObjectInfo ()
 Initializes member variable m_CurIterOI. More...
 
 CMacroBioData_SeqSetIter::CMacroBioData_SeqSetIter (const CMacroBioData_SeqSetIter &)
 
CMacroBioData_SeqSetIterCMacroBioData_SeqSetIter::operator= (const CMacroBioData_SeqSetIter &)
 
 CMacroBioData_TSEntryIter::CMacroBioData_TSEntryIter (const objects::CSeq_entry_Handle &entry)
 
virtual CMacroBioData_TSEntryIter::~CMacroBioData_TSEntryIter ()
 
virtual IMacroBioDataIterCMacroBioData_TSEntryIter::Begin (void)
 
virtual IMacroBioDataIterCMacroBioData_TSEntryIter::Next (void)
 
virtual bool CMacroBioData_TSEntryIter::IsEnd (void) const
 
virtual bool CMacroBioData_TSEntryIter::IsBegin (void)
 
virtual SConstScopedObject CMacroBioData_TSEntryIter::GetScopedObject () const
 Dereferences the underlying iterator. More...
 
virtual string CMacroBioData_TSEntryIter::GetBestDescr () const
 Used for logging. More...
 
virtual void CMacroBioData_TSEntryIter::BuildEditedObject ()
 Creates a copy of the object that will be edited. More...
 
virtual void CMacroBioData_TSEntryIter::RunEditCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the editing command. More...
 
virtual void CMacroBioData_TSEntryIter::RunDeleteCommand (CMacroCmdComposite *cmd_composite)
 Constructs and executes the delete command. More...
 
virtual bool CMacroBioData_TSEntryIter::IsDescriptor () const
 
virtual bool CMacroBioData_TSEntryIter::IsFeature () const
 
virtual objects::CBioseq_Handle CMacroBioData_TSEntryIter::GetBioseqHandle (void) const
 
virtual void CMacroBioData_TSEntryIter::x_SetDefaultObjectInfo ()
 Initializes member variable m_CurIterOI. More...
 
 CMacroBioData_TSEntryIter::CMacroBioData_TSEntryIter (const CMacroBioData_TSEntryIter &)
 
CMacroBioData_TSEntryIterCMacroBioData_TSEntryIter::operator= (const CMacroBioData_TSEntryIter &)
 
 CMacroCmdComposite::CMacroCmdComposite (const string &label)
 
virtual IEditMacroFunction::~IEditMacroFunction ()
 Virtual destructor. More...
 
virtual void IEditMacroFunction::operator() (CMacroCmdComposite &cmd_composite, CIRef< IMacroBioDataIter > &data, CQueryParseTree::TNode &qnode) override
 Function operator. More...
 
bool IEditMacroFunction::SetQualStringValue (CObjectInfo &oi, const string &value)
 Functions make the action and collect statistics. More...
 
bool IEditMacroFunction::HasDataChanged () const
 
const CRef< IFunctionLog > & IEditMacroFunction::GetFunctionLog () const
 
 IEditMacroFunction::IEditMacroFunction (EScopeEnum func_scope)
 
virtual void IEditMacroFunction::x_InitCall (CIRef< IMacroBioDataIter > &data) override
 
virtual void IEditMacroFunction::x_SetUserObjects (CQueryParseTree::TNode &qnode) override
 Extracts the function arguments and initializes m_Result member. More...
 
virtual bool IEditMacroFunction::x_ValidArguments () const =0
 Tests the number and the type of function arguments. More...
 
virtual void IEditMacroFunction::x_ResetState ()
 Reset the state of member variables that are set directly/indirectly from function arguments. More...
 
virtual bool IEditMacroFunction::x_IsNestedFunctionReturnValid () const
 
void IEditMacroFunction::x_AssignReturnValue (const CObjectInfo &oi, const string &field_name)
 Assigns value to m_Result. It is mostly useful for functions used in the WHERE clause. More...
 
void IEditMacroFunction::x_AssignReturnValueFromContainer (const CObjectInfo &oi, const string &container, const string &field_name)
 
void IEditMacroFunction::x_GetObjectsFromRef (CMQueryNodeValue::TObs &objects, const size_t &index)
 
void IEditMacroFunction::x_GetOptionalArgs (string &delimiter, bool &remove_field, size_t &index)
 
void IEditMacroFunction::x_LogChangedQuals (const CRef< IFunctionLog > &log)
 
virtual IFunctionLog::~IFunctionLog ()
 
string IFunctionLog::Print () const
 
bool IFunctionLog::Merge (const IFunctionLog &log)
 
 IFunctionLog::IFunctionLog (const TChangedQuals &quals)
 
 IFunctionLog::IFunctionLog (const string &msg, size_t nr)
 
virtual string IFunctionLog::x_Print () const =0
 
 CDiscrLog::CDiscrLog (const TChangedQuals &quals)
 
virtual string CDiscrLog::x_Print () const
 
 CGeneralFuncLog::CGeneralFuncLog (const TChangedQuals &quals)
 
 CGeneralFuncLog::CGeneralFuncLog (const string &msg, size_t nr)
 
virtual string CGeneralFuncLog::x_Print () const
 
 SArgMetaData::SArgMetaData (const string &name, CMQueryNodeValue::EType type, bool opt)
 
 CMacroFunction_TopLevel::CMacroFunction_TopLevel (EScopeEnum func_scope)
 
virtual void CMacroFunction_TopLevel::TheFunction ()
 CMacroFunction_TopLevel It is the same as CMacroRep::m_TopFuncName. More...
 
static CTempString CMacroFunction_TopLevel::GetFuncName ()
 
virtual bool CMacroFunction_TopLevel::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroStat::CMacroStat ()
 
void CMacroStat::Reset ()
 reset the macro name, qualifier and iteration counts More...
 
const stringCMacroStat::CMacroLog::GetName () const
 
string CMacroStat::CMacroLog::GetLog () const
 
void CMacroStat::CMacroLog::SetName (const string &name)
 
void CMacroStat::CMacroLog::BuildReport (const string &rep)
 
void CMacroStat::CMacroLog::ClearAndBuildReport (const string &rep)
 
void CMacroStat::CMacroLog::AppendError (const string &errmsg)
 
const stringCMacroStat::CMacroLog::GetErrorLog () const
 
void CMacroStat::CMacroLog::Reset ()
 
const CMacroLogCMacroStat::GetMacroReport () const
 
void CMacroStat::AddToReport (const string &report)
 function gradually builds the log report More...
 
void CMacroStat::AddToErrorReport (const string &error)
 store encountered errors More...
 
void CMacroStat::GatherUnMatchedTableEntries (const string &report, const int count)
 Used when applying a table to the entry: it stores the values and number of table entries that were not matched during execution. More...
 
const vector< pair< string, int > > & CMacroStat::GetUnmatchedTableEntries () const
 
void CMacroStat::AddDataChanged (bool change)
 function to collect whether any data was changed during the execution of the macro More...
 
void CMacroStat::AddFunctionName (const string &func_name)
 function to collect DO function names to be used for processing reporting in huge file mode More...
 
const set< string > & CMacroStat::GetDOFunctionNames () const
 
void CMacroStat::LogStart (const string &macro_name)
 log start of macro execution More...
 
void CMacroStat::LogStop (bool status, const string &err_message)
 log end of macro execution this includes time of execution, status, count of changed qualifiers and an error message when applicable result also goes to the GBench status bar More...
 
long CMacroStat::GetExecutionTime () const
 
size_t CMacroStat::GetCounter () const
 
bool CMacroStat::HasDataUpdated () const
 
void CMacroStat::AddFunctionLog (const CRef< IFunctionLog > &log)
 
const vector< CRef< IFunctionLog > > & CMacroStat::GetFunctionsLog () const
 
 CMacroStat::CMacroStat (const CMacroStat &)
 
CMacroStatCMacroStat::operator= (const CMacroStat &)
 
virtual bool IMacroEngine::AppendToLibrary (const string &filename, CMacroLib::TMacroLibrary &lib)=0
 Parses a file containing macros and appends the results to a map. More...
 
virtual bool IMacroEngine::ReadAndParseMacros (const string &filename, vector< CRef< CMacroRep >> &macro_list)=0
 Parses a file containing macros and stores them in a list. More...
 
virtual CMacroRepIMacroEngine::Parse (const string &macro_text)=0
 Parses macro script into its binary representation. More...
 
virtual bool IMacroEngine::Exec (const CMacroRep &macro_rep, const CMacroBioData &data, CRef< CMacroCmdComposite > CmdComposite, bool throw_on_error=false, CNcbiOstream *ostream=nullptr)=0
 Executes a macro. More...
 
virtual const CMacroStatIMacroEngine::GetStatistics () const =0
 Gets the most recently executed macro statistics. More...
 
virtual IMacroEngine::~IMacroEngine ()
 
 CMacroEngine::CMacroEngine (bool lookup_synfile=false)
 Constructor. More...
 
 CMacroEngine::CMacroEngine (bool huge_file_mode, bool lookup_synfile=false)
 
virtual CMacroEngine::~CMacroEngine ()
 class CMacroEngine More...
 
bool CMacroEngine::AppendToLibrary (const string &filename, CMacroLib::TMacroLibrary &lib)
 Parses a file containing macros and appends the results to a map. More...
 
bool CMacroEngine::ReadAndParseMacros (const string &filename, vector< CRef< CMacroRep >> &macro_list)
 Parses a file containing macros and stores them in a list. More...
 
vector< stringCMacroEngine::GetSynonymFilenames (const vector< CRef< CMacroRep >> &macro_list) const
 Extracts synonym files present in the list of macros. More...
 
CMacroRepCMacroEngine::Parse (const string &macro_text)
 Parses macro script into its binary representation. More...
 
bool CMacroEngine::Exec (const CMacroRep &macro_rep, const CMacroBioData &data, CRef< CMacroCmdComposite > CmdComposite, bool throw_on_error=false, CNcbiOstream *ostream=nullptr)
 Executes a macro. More...
 
bool CMacroEngine::GetStatus () const
 Get status of most recent command. More...
 
const stringCMacroEngine::GetErrorMessage () const
 Get error message in case previous command was unsuccessful. More...
 
Uint4 CMacroEngine::GetErrorLine () const
 Get error location in case previous command was unsuccessful. More...
 
Uint4 CMacroEngine::GetErrorColumn () const
 
const CMacroStatCMacroEngine::GetStatistics () const
 Gets the most recently executed macro statistics. More...
 
virtual CQueryParseTreeCMacroEngine::GetAssignmentWhereClause (int index) const
 get one of the "where" sub-clauses which are indentified by an index in the main parsed tree More...
 
virtual CRef< CMQueryNodeValueCMacroEngine::GetOrCreateRTVar (const string &name)
 Gets or creates run-time vars (used in assignment in Do clause) More...
 
virtual bool CMacroEngine::ExistRTVar (const string &name)
 Returns true if the run-time variable, identified by its name, was defined. More...
 
virtual void CMacroEngine::AddTmpRTVarObject (const string &name, CObjectInfo &oi)
 Temporary run-time variables used in evaluating subqueries in the DO section, used together with the Assignment Operator (CMQueryFunctionAssignment) More...
 
virtual bool CMacroEngine::GetTmpRTVarObject (const string &name, CObjectInfo &oi)
 
virtual void CMacroEngine::ResetTmpRTVarObjects ()
 
void CMacroEngine::SetRemoteUpdater (const shared_ptr< objects::edit::CRemoteUpdater > &updater)
 
void CMacroEngine::SetDOIUpdater (const shared_ptr< CDoiLookupWithCache > &updater)
 
void CMacroEngine::SetISOJTAUpdater (const shared_ptr< CISOJTALookupWithCache > &updater)
 
void CMacroEngine::SetHugeContext (const shared_ptr< CHugeMacroContext > &context)
 
bool CMacroEngine::x_AppendToLibrary (const string &filename, CMacroLib::TMacroLibrary &lib)
 
bool CMacroEngine::x_ResolveRTVar (const string &identifier, CMQueryNodeValue &v, const CQueryParseTree::TNode *parent)
 Gets the value of RT variable. More...
 
CRef< CMQueryNodeValueCMacroEngine::x_LocateRTVar (const string &identifier)
 Gets the pointer to RT variable. More...
 
virtual bool CMacroEngine::ResolveIdentifier (const string &identifier, CMQueryNodeValue &v, const CQueryParseTree::TNode *parent)
 Function resolves identifiers. More...
 
virtual void CMacroEngine::CallFunction (const string &name, CQueryParseTree::TNode &qnode)
 Function call the function specified by name, passing args as parameters and it can update nv as a result. More...
 
void CMacroEngine::x_ResetStatus (void)
 Reset status and error related private data. More...
 
void CMacroEngine::x_InitSetOfBuiltInFunctions (bool lookup_synfile)
 Define the list of functions that is recognized by the engine. More...
 
void CMacroEngine::x_InitStringConstraints (bool lookup_synfile)
 Define the list of functions used in string constraints. More...
 
IEditMacroFunctionCMacroEngine::x_ResolveFunctionName (const string &name) const
 Locates function by name. More...
 
void CMacroEngine::x_SetError (const string &message, Uint4 line=0, Uint4 column=0)
 Sets m_Status, error_message and its location. More...
 
void CMacroEngine::x_SetFunctions (CMacroParser &parser)
 Initializes do/where lists of functions in parser. More...
 
bool CMacroEngine::SKey_Less::operator() (const string &str1, const string &str2) const
 
virtual IMacroFunctionContext::~IMacroFunctionContext ()
 
IEditMacroFunctionIMacroFunctionContext::ResolveFunctionName (const string &name) const
 Return pointer to macro function identified by its name. More...
 
void IMacroFunctionContext::GetFunctionNames (CMacroParser::TFunctionNamesList &where_funcs, CMacroParser::TFunctionNamesList &do_funcs) const
 
 IMacroFunctionContext::IMacroFunctionContext ()
 
 CMacroContextForEditing::CMacroContextForEditing ()
 
void CMacroContextForEditing::x_InitSetOfBuiltInFunctions ()
 
 CMacroContextForListing::CMacroContextForListing ()
 
void CMacroContextForListing::x_InitSetOfBuiltInFunctions ()
 
 CMacroResolver::CMacroResolver (const CMacroRep &macro_rep, CIRef< IMacroBioDataIter > data_iter, CRef< CMacroCmdComposite > CmdComposite, CConstIRef< IMacroFunctionContext > context, CMacroStat &stat)
 
virtual bool CMacroResolver::ResolveIdentifier (const string &identifier, CMQueryNodeValue &val, const CQueryParseTree::TNode *parent)
 Resolve identifier and store the value in @val. More...
 
virtual void CMacroResolver::CallFunction (const string &name, CQueryParseTree::TNode &qnode)
 Function call the function specified by name, passing args as parameters and it can update nv as a result. More...
 
virtual CQueryParseTreeCMacroResolver::GetAssignmentWhereClause (int index) const
 Return the "where" sub-query from the DO-DONE section identified by the index in the main parsed tree. More...
 
virtual CRef< CMQueryNodeValueCMacroResolver::GetOrCreateRTVar (const string &name)
 Get or create run-time variable. More...
 
virtual bool CMacroResolver::ExistRTVar (const string &name)
 Return true if the run-time variable, identified by its name, is defined. More...
 
virtual void CMacroResolver::AddTmpRTVarObject (const string &name, CObjectInfo &oi)
 used together with the Assignment Operator (CMQueryFunctionAssignment) More...
 
virtual bool CMacroResolver::GetTmpRTVarObject (const string &name, CObjectInfo &oi)
 
virtual void CMacroResolver::ResetTmpRTVarObjects ()
 
bool CMacroResolver::x_ResolveRTVar (const string &identifier, CMQueryNodeValue &val, const CQueryParseTree::TNode *parent)
 Return the value of Run-Time (RT) variable. More...
 
CRef< CMQueryNodeValueCMacroResolver::x_LocateRTVar (const string &identifier)
 Return data associated with the RT variable based on its name. More...
 
 CMacroEngineParallel::CMacroEngineParallel ()
 
bool CMacroEngineParallel::AppendToLibrary (const string &filename, CMacroLib::TMacroLibrary &lib)
 Parse a file containing macros and append the results to the map that stores these macros. More...
 
bool CMacroEngineParallel::ReadAndParseMacros (const string &filename, vector< CRef< CMacroRep >> &macro_list)
 Parse a file containing macros and store them in a vector. More...
 
CMacroRepCMacroEngineParallel::Parse (const string &macro_text)
 Parse the macro script into its binary representation. More...
 
bool CMacroEngineParallel::Exec (const CMacroRep &macro_rep, const CMacroBioData &data, CRef< CMacroCmdComposite > CmdComposite, bool throw_on_error=false, CNcbiOstream *ostream=nullptr)
 Execute a macro. More...
 
bool CMacroEngineParallel::GetParsingStatus () const
 Get status of most recent command. More...
 
const stringCMacroEngineParallel::GetParsingErrorMessage () const
 Get error message in case previous command was unsuccessful. More...
 
Uint4 CMacroEngineParallel::GetParsingErrorLine () const
 Get error location in case previous command was unsuccessful. More...
 
Uint4 CMacroEngineParallel::GetParsingErrorColumn () const
 
const CMacroStatCMacroEngineParallel::GetStatistics () const
 Gets the most recently executed macro statistics. More...
 
void CMacroEngineParallel::SMacroInfo::Reset ()
 
void CMacroEngineParallel::SMacroInfo::SetError (const string &message, Uint4 line, Uint4 column)
 
bool CMacroEngineParallel::x_AppendToLibrary (const string &filename, CMacroLib::TMacroLibrary &lib)
 
void CMacroEngineParallel::x_SetFunctions (CMacroParser &parser)
 Initialize do/where lists of functions in parser. More...
 
unsigned CMacroEngineParallel::x_GetThreadCount (const CMacroRep &macro_rep, const CMacroBioData &data)
 
virtual const char * CMacroParseException::GetErrCodeString (void) const override
 
 CMacroParseException::NCBI_EXCEPTION_DEFAULT (CMacroParseException, CException)
 
virtual void CMacroDataException::ReportExtra (ostream &out) const override
 Constructor. More...
 
CConstRef< CSerialObjectCMacroDataException::GetData () const throw ()
 Returns the ASN.1 data that caused the error. More...
 
string CMacroDataException::GetDataAsString () const throw ()
 Returns the text encoded ASN.1 data that caused the error. More...
 
virtual void CMacroDataException::x_Assign (const CException &src) override
 
virtual const char * CMacroExecException::GetErrCodeString (void) const override
 
unsigned CMacroExecException::GetLineNo (void) const throw ()
 Returns the line number where error occurred. More...
 
void CMacroExecException::SetLineNo (unsigned lineNo) throw ()
 Sets the line number where error occurred. More...
 
unsigned CMacroExecException::GetColumnNo (void) const throw ()
 Returns the column number where error occurred. More...
 
void CMacroExecException::SetColumnNo (unsigned columnNo) throw ()
 Sets the column number where error occurred. More...
 
virtual void CMacroExecException::ReportExtra (ostream &out) const override
 
virtual void CMacroExecException::x_Assign (const CException &src) override
 
void ThrowCMacroExecException (const CDiagCompileInfo &info, CMacroExecException::EErrCode code, const string &message, const CQueryParseTree::TNode *treeNode, const CException *previous=nullptr)
 Throws CMacroExecException with the specified message and error location from the TNode. More...
 
ETreeTraverseCode CMQueryNodePreprocessor::operator() (CTreeNode< CQueryParseNode > &tr, int delta)
 Operator builds node values for each CQueryParseNode. More...
 
 CMQueryNodeValue::SResolvedField::SResolvedField (CObjectInfo parent, CObjectInfo field)
 
 CMQueryNodeValue::CMQueryNodeValue ()
 
 CMQueryNodeValue::CMQueryNodeValue (CQueryParseTree::TNode *n)
 
virtual void CMQueryNodeValue::Reset ()
 Reset user object (for reuse without reallocation) More...
 
bool CMQueryNodeValue::IsSimpleType () const
 
void CMQueryNodeValue::AssignFromObjectInfo (const CObjectInfo &objinfo)
 Assigns data from objinfo. It is used when storing evaluation result. More...
 
void CMQueryNodeValue::Dereference ()
 If it is a reference it is resolved to the first non reference type in the hierarchy. More...
 
void CMQueryNodeValue::SetDataType (EType dt)
 
EType CMQueryNodeValue::GetDataType () const
 
void CMQueryNodeValue::SetString (const string &data)
 Set/get underlying data type. More...
 
void CMQueryNodeValue::SetStrings (const vector< string > &data)
 
void CMQueryNodeValue::SetBool (bool data)
 
void CMQueryNodeValue::SetInt (Int8 data)
 
void CMQueryNodeValue::SetDouble (double data)
 
void CMQueryNodeValue::SetRef (CRef< CMQueryNodeValue > node)
 
void CMQueryNodeValue::SetObjects (const TObs &obs)
 
TObsCMQueryNodeValue::SetObjects (void)
 
void CMQueryNodeValue::SetNotSet ()
 
bool CMQueryNodeValue::AssignToRef (const CMQueryNodeValue &source)
 
const stringCMQueryNodeValue::GetString () const
 
const vector< string > & CMQueryNodeValue::GetStrings () const
 
bool CMQueryNodeValue::GetBool () const
 
Int8 CMQueryNodeValue::GetInt () const
 
double CMQueryNodeValue::GetDouble () const
 
const TObsCMQueryNodeValue::GetObjects () const
 
bool CMQueryNodeValue::IsString () const
 
bool CMQueryNodeValue::AreStrings () const
 
bool CMQueryNodeValue::IsBool () const
 
bool CMQueryNodeValue::IsInt () const
 
bool CMQueryNodeValue::IsDouble () const
 
bool CMQueryNodeValue::IsRef () const
 
bool CMQueryNodeValue::AreObjects () const
 
bool CMQueryNodeValue::IsNotSet () const
 
CQueryParseTree::TNodeCMQueryNodeValue::GetNode () const
 
CMacroExecCMQueryFunctionBase::GetContext ()
 class CMQueryFunctionBase More...
 
 CMQueryFunctionValue::CMQueryFunctionValue ()
 
virtual void CMQueryFunctionValue::Evaluate (CQueryParseTree::TNode &node)
 Calculates node values for constants and resolved identifiers. More...
 
virtual void CMQueryFunctionRTVar::Evaluate (CQueryParseTree::TNode &node)
 Function is a placeholder for run-time variable processing. More...
 
virtual CMQueryFunctionOps::~CMQueryFunctionOps ()
 
virtual void CMQueryFunctionOps::Evaluate (CQueryParseTree::TNode &node)=0
 Abstract node evaluation function. More...
 
void CMQueryFunctionOps::x_InitReferences (CQueryParseTree::TNode &node)
 Ininializes protected members to be used in derived classes. More...
 
bool CMQueryFunctionOps::x_ValidateAll (Uint4 number, CMQueryNodeValue::EType type)
 Checks the number and type of arguments. More...
 
bool CMQueryFunctionOps::x_Validate (Uint4 number, CMQueryNodeValue::EType type1, CMQueryNodeValue::EType type2)
 Checks the number of arguments, also their type should be one of the given types. More...
 
bool CMQueryFunctionOps::x_FindNotSet ()
 Find not set value. More...
 
bool CMQueryFunctionOps::x_IsCaseSensitive ()
 Gets case sensitiveness flag from environment. More...
 
void CMQueryFunctionOps::x_ProcessInvalidParams (CQueryParseTree::TNode &node)
 Throws exception for invalid number of types of arguments. More...
 
CRef< CMQueryNodeValueCMQueryFunctionOps::x_GetUserObject (CQueryParseTree::TNode &node)
 Gets user node value from CQueryParseTree node. More...
 
virtual void CMQueryFunctionAssignment::Evaluate (CQueryParseTree::TNode &node)
 Function implements the assignment operator. More...
 
virtual void CMQueryFunctionFunction::Evaluate (CQueryParseTree::TNode &node)
 Function implements functions calls in the do section of macro. More...
 
virtual void CMQueryFunctionDummy::Evaluate (CQueryParseTree::TNode &node)
 Function throws an exception about not implmented operation for the node. More...
 
virtual IResolver::~IResolver ()
 
virtual bool IResolver::ResolveIdentifier (const string &identifier, CMQueryNodeValue &vi, const CQueryParseTree::TNode *parent)=0
 
virtual void IResolver::CallFunction (const string &name, CQueryParseTree::TNode &qnode)=0
 
virtual CQueryParseTreeIResolver::GetAssignmentWhereClause (int index) const =0
 
virtual CRef< CMQueryNodeValueIResolver::GetOrCreateRTVar (const string &name)=0
 
virtual bool IResolver::ExistRTVar (const string &name)=0
 
virtual void IResolver::AddTmpRTVarObject (const string &name, CObjectInfo &oi)=0
 
virtual bool IResolver::GetTmpRTVarObject (const string &name, CObjectInfo &oi)=0
 
virtual void IResolver::ResetTmpRTVarObjects ()=0
 
 CMacroExec::CMacroExec ()
 
virtual CMacroExec::~CMacroExec ()
 
void CMacroExec::EvaluateTree (CQueryParseTree &Qtree, IResolver &resolver, bool query_tree, bool case_sensitive=false)
 Evaluates tree. More...
 
CRef< CMQueryNodeValueCMacroExec::GetOrCreateRTVar (const string &name)
 
bool CMacroExec::IsNotSetType () const
 Check/get functions result from the top node after calculation. More...
 
bool CMacroExec::IsBoolType () const
 
bool CMacroExec::GetBoolValue () const
 
bool CMacroExec::IsCaseSensitive () const
 Get function to access case sensitivity flag. More...
 
bool CMacroExec::PassIdentifierToResolver (const string &identifier, CMQueryNodeValue &NodeValue, const CQueryParseTree::TNode *parent)
 Identifier resolver function. More...
 
IResolverCMacroExec::GetResolver () const
 
virtual bool CMacroExec::ResolveIdentifier (const string &ident, bool &value)
 Stubs for virtual functions. More...
 
virtual bool CMacroExec::ResolveIdentifier (const string &ident, Int8 &value)
 
virtual bool CMacroExec::ResolveIdentifier (const string &ident, double &value)
 
virtual bool CMacroExec::ResolveIdentifier (const string &ident, string &value)
 
CRef< CMQueryNodeValueCMacroExec::x_GetTopUserNodeValue ()
 
void CMacroExec::x_Init ()
 class CMacroExec implementation More...
 
bool CMacroExec::x_EvaluateQueryTree (CQueryParseTree::TNode &node)
 
bool GetFieldsByName (CMQueryNodeValue::TObs *results, const CObjectInfo &oi_i, const string &field_name)
 Resolve existing dot qualified ASN.1 name (field_name) starting from the object information instance provided as a parameter (oi_i). More...
 
bool SetFieldsByName (CMQueryNodeValue::TObs *results, CObjectInfo &oi_i, const string &field_name)
 Resolve not necessarily existing dot qualified ASN.1 name (field_name) starting from the object information instance provided as a parameter (oi_i). More...
 
bool RemoveFieldByName (CMQueryNodeValue::SResolvedField &res_field)
 Remove the object information instance corresponding to field, using information about its parent node. More...
 
bool ResolveAndSetSimpleTypeValue (CObjectInfo &oi, const string &field_name, const CMQueryNodeValue &value, objects::edit::EExistingText existing_text=objects::edit::eExistingText_replace_old)
 Resolve dot qualified ASN.1 node_name using the object information instance provided as a parameter (oi) and sets node data. More...
 
bool SetSimpleTypeValue (CObjectInfo &oi, const CMQueryNodeValue &value, objects::edit::EExistingText existing_text=objects::edit::eExistingText_replace_old)
 Set single node data to the node specified by parameter of type CObjectInfo. More...
 
bool GetSimpleTypeValue (CObjectInfo &oi, const string &field_name, CMQueryNodeValue &value)
 Get single node data from the node specified by parameter of type CObjectInfo and additionally field field_name (set to empty string if oi is already at primitive value) More...
 
bool GetPrimitiveValue (const CObjectInfo &oi, CMQueryNodeValue &value)
 Get a primitive value from oi. More...
 
bool ResolveIdentToSimple (const CObjectInfo &oi, const string &identifier, CMQueryNodeValue &v)
 Resolve name to simple types value. More...
 
bool ResolveIdentToObjects (const CObjectInfo &oi, const string &identifier, CMQueryNodeValue &v)
 Resolve name to the list of objects. More...
 
 CMacroFunction_SwapQual::CMacroFunction_SwapQual (EScopeEnum func_scope)
 
virtual CMacroFunction_SwapQual::~CMacroFunction_SwapQual ()
 
virtual void CMacroFunction_SwapQual::TheFunction ()
 class CMacroFunction_SwapQual SwapQual(src_fieldname, dest_fieldname) Swaps the content of two fields. More...
 
static CTempString CMacroFunction_SwapQual::GetFuncName ()
 
static bool CMacroFunction_SwapQual::s_SwapFields (CObjectInfo &src, CObjectInfo &dest)
 
virtual bool CMacroFunction_SwapQual::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
bool CMacroFunction_SwapQual::x_DoFieldsExist (CObjectInfo oi, CMQueryNodeValue::TObs &result, size_t index)
 
bool CMacroFunction_SwapQual::x_SetFields (CObjectInfo oi, CMQueryNodeValue::TObs &result, size_t index)
 
bool CMacroFunction_SwapQual::x_SwapFields (CObjectInfo &src, CObjectInfo &dest)
 
void CMacroFunction_SwapQual::x_CopyFields (CMQueryNodeValue::TObs &src_objs, CMQueryNodeValue::TObs &dest_objs)
 
bool CMacroFunction_SwapQual::x_CopyFields (CObjectInfo &src, CObjectInfo &dest)
 
void CMacroFunction_SwapQual::x_SetField (CConstRef< CObject > &obj, const string &fieldname, CMQueryNodeValue::TObs &result)
 
 CMacroFunction_SwapRelFeatQual::CMacroFunction_SwapRelFeatQual (EScopeEnum func_scope)
 
virtual void CMacroFunction_SwapRelFeatQual::TheFunction ()
 class CMacroFunction_SwapRelFeatQual SwapFeatureQual([src_obj,] src_field, dest_feat_subtype, dest_field, update_mrna); More...
 
static CTempString CMacroFunction_SwapRelFeatQual::GetFuncName ()
 
virtual bool CMacroFunction_SwapRelFeatQual::x_ValidArguments (void) const
 Tests the number and the type of function arguments. More...
 
bool CMacroFunction_SwapRelFeatQual::x_DoDestFeatFieldsExist (const objects::CSeq_feat &src_feat, CMQueryNodeValue::TObs &result, const string &dest_feattype, const string &dest_field)
 
void CMacroFunction_SwapRelFeatQual::x_SetOrCreateDestFeatFields (const objects::CSeq_feat &src_feat, CMQueryNodeValue::TObs &result, size_t index)
 
 CMacroFunction_SetStringQual::CMacroFunction_SetStringQual (EScopeEnum func_scope)
 
virtual CMacroFunction_SetStringQual::~CMacroFunction_SetStringQual ()
 
virtual void CMacroFunction_SetStringQual::TheFunction ()
 class CMacroFunction_SetStringQual Expected Syntax: SetStringQual(field_name, newValue, existingtext_option, delimiter, remove_blank) The last two parameters are optional. More...
 
static CTempString CMacroFunction_SetStringQual::GetFuncName ()
 
virtual bool CMacroFunction_SetStringQual::x_ValidArguments (void) const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_SetStringQual::x_SetFields (CMQueryNodeValue::TObs &objs, const string &newValue, objects::edit::EExistingText existing_text, vector< string > &new_values)
 
void CMacroFunction_SetStringQual::x_SetNewPrimitiveValue (CObjectInfo &oi, const string &newValue, objects::edit::EExistingText existing_text, vector< string > &new_values)
 
 CMacroFunction_RemoveQual::CMacroFunction_RemoveQual (EScopeEnum func_scope)
 
virtual CMacroFunction_RemoveQual::~CMacroFunction_RemoveQual ()
 
virtual void CMacroFunction_RemoveQual::TheFunction ()
 class CMacroFunction_RemoveQual RemoveQual("genome"); or obj = PUB_AFFIL("sub"); RemoveQual(obj); More...
 
static CTempString CMacroFunction_RemoveQual::GetFuncName ()
 
static Int4 CMacroFunction_RemoveQual::s_RemoveFields (CIRef< IMacroBioDataIter > &dataiter, CMQueryNodeValue::TObs &objs)
 
virtual bool CMacroFunction_RemoveQual::x_ValidArguments (void) const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_EditStringQual::CMacroFunction_EditStringQual (EScopeEnum func_scope)
 
virtual CMacroFunction_EditStringQual::~CMacroFunction_EditStringQual ()
 
virtual void CMacroFunction_EditStringQual::TheFunction ()
 class CMacroFunction_EditStringQual Usage: EditStringQual(field_name|rt_obj, find_text, repl_text, location, case_sensitive, is_regex) More...
 
static bool CMacroFunction_EditStringQual::s_EditText (string &str, const string &find, const string &repl, ESearchLoc loc, bool case_sensitive, bool is_regex=false)
 
static ESearchLoc CMacroFunction_EditStringQual::s_GetLocFromName (const string &name)
 
static CTempString CMacroFunction_EditStringQual::GetFuncName ()
 
virtual bool CMacroFunction_EditStringQual::x_ValidArguments (void) const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_EditStringQual::x_EditFields (CMQueryNodeValue::TObs &resolved_objs, const string &find_txt, const string &repl_txt, ESearchLoc loc, bool case_sensitive, bool is_regex)
 
 CMacroFunction_SetRelFeatQual::CMacroFunction_SetRelFeatQual (EScopeEnum func_scope)
 
virtual void CMacroFunction_SetRelFeatQual::TheFunction ()
 class CMacroFunction_SetStringQual Expected Syntax: SetStringQual(field_name, newValue, existingtext_option, delimiter, remove_blank) The last two parameters are optional. More...
 
static CTempString CMacroFunction_SetRelFeatQual::GetFuncName ()
 
virtual bool CMacroFunction_SetRelFeatQual::x_ValidArguments (void) const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_SetQual::CMacroFunction_SetQual (EScopeEnum func_scope)
 
virtual void CMacroFunction_SetQual::TheFunction ()
 class CMacroFunction_SetQual SetQual(field_name, newValue) More...
 
static CTempString CMacroFunction_SetQual::GetFuncName ()
 
virtual bool CMacroFunction_SetQual::x_ValidArguments (void) const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_AddDBLink::CMacroFunction_AddDBLink (EScopeEnum func_scope)
 
virtual void CMacroFunction_AddDBLink::TheFunction ()
 Function implementation. More...
 
static CTempString CMacroFunction_AddDBLink::GetFuncName ()
 
virtual bool CMacroFunction_AddDBLink::x_ValidArguments (void) const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_EditRelFeatQual::CMacroFunction_EditRelFeatQual (EScopeEnum func_scope)
 
virtual void CMacroFunction_EditRelFeatQual::TheFunction ()
 class CMacroFunction_EditStringQual Usage: EditStringQual(field_name|rt_obj, find_text, repl_text, location, case_sensitive, is_regex) More...
 
virtual bool CMacroFunction_EditRelFeatQual::x_ValidArguments (void) const
 Tests the number and the type of function arguments. More...
 
virtual IOperateOnTwoQuals::~IOperateOnTwoQuals ()
 
void IOperateOnTwoQuals::ChangeFields (CMQueryNodeValue::TObs &src_objs, CMQueryNodeValue::TObs &dest_objs)
 
 IOperateOnTwoQuals::IOperateOnTwoQuals (EScopeEnum func_scope)
 
bool IOperateOnTwoQuals::x_GetSourceFields (CObjectInfo oi, size_t index, CMQueryNodeValue::TObs &result)
 
bool IOperateOnTwoQuals::x_GetDestFields (CObjectInfo oi, size_t index, CMQueryNodeValue::TObs &result)
 
string IOperateOnTwoQuals::x_GetSourceString (CObjectInfo &src)
 
virtual bool IOperateOnTwoQuals::x_ChangeFields (CObjectInfo &src, CObjectInfo &dest)=0
 
 CMacroFunction_ConvertStringQual::CMacroFunction_ConvertStringQual (EScopeEnum func_scope)
 
virtual CMacroFunction_ConvertStringQual::~CMacroFunction_ConvertStringQual ()
 
virtual void CMacroFunction_ConvertStringQual::TheFunction ()
 class CMacroFunction_ConvertStringQual ConvertStringQual(src_field, dst_field, capitalization, strip_name, existing_text_opt, delimiter) last parameter is optional The function will NOT delete the src_field. More...
 
static CTempString CMacroFunction_ConvertStringQual::GetFuncName ()
 
virtual bool CMacroFunction_ConvertStringQual::x_ValidArguments (void) const
 Tests the number and the type of function arguments. More...
 
string CMacroFunction_ConvertStringQual::x_GetSourceString (CObjectInfo &src)
 
virtual bool CMacroFunction_ConvertStringQual::x_ChangeFields (CObjectInfo &src, CObjectInfo &dest)
 
 CMacroFunction_ConvertFeatQual::CMacroFunction_ConvertFeatQual (EScopeEnum func_scope)
 
virtual void CMacroFunction_ConvertFeatQual::TheFunction ()
 class CMacroFunction_ConvertStringQual ConvertStringQual(src_field, dst_field, capitalization, strip_name, existing_text_opt, delimiter) last parameter is optional The function will NOT delete the src_field. More...
 
static CTempString CMacroFunction_ConvertFeatQual::GetFuncName ()
 
virtual bool CMacroFunction_ConvertFeatQual::x_ValidArguments (void) const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_ConvertRNARelQual::CMacroFunction_ConvertRNARelQual (EScopeEnum func_scope)
 
virtual void CMacroFunction_ConvertRNARelQual::TheFunction ()
 class CMacroFunction_ConvertStringQual ConvertStringQual(src_field, dst_field, capitalization, strip_name, existing_text_opt, delimiter) last parameter is optional The function will NOT delete the src_field. More...
 
static CTempString CMacroFunction_ConvertRNARelQual::GetFuncName ()
 
virtual bool CMacroFunction_ConvertRNARelQual::x_ValidArguments (void) const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_ParseStringQual::CMacroFunction_ParseStringQual (EScopeEnum func_scope)
 
virtual CMacroFunction_ParseStringQual::~CMacroFunction_ParseStringQual ()
 
virtual void CMacroFunction_ParseStringQual::TheFunction ()
 Function implementation. More...
 
static CTempString CMacroFunction_ParseStringQual::GetFuncName ()
 
virtual bool CMacroFunction_ParseStringQual::x_ValidArguments (void) const
 Tests the number and the type of function arguments. More...
 
string CMacroFunction_ParseStringQual::x_GetSourceString (CObjectInfo &src)
 
virtual bool CMacroFunction_ParseStringQual::x_ChangeFields (CObjectInfo &src, CObjectInfo &dest)
 
 CMacroFunction_ParseFeatQual::CMacroFunction_ParseFeatQual (EScopeEnum func_scope)
 
virtual void CMacroFunction_ParseFeatQual::TheFunction ()
 Function implementation. More...
 
static CTempString CMacroFunction_ParseFeatQual::GetFuncName ()
 
virtual bool CMacroFunction_ParseFeatQual::x_ValidArguments (void) const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_ParseRNARelQual::CMacroFunction_ParseRNARelQual (EScopeEnum func_scope)
 
virtual void CMacroFunction_ParseRNARelQual::TheFunction ()
 Function implementation. More...
 
static CTempString CMacroFunction_ParseRNARelQual::GetFuncName ()
 
virtual bool CMacroFunction_ParseRNARelQual::x_ValidArguments (void) const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_AddParsedText::CMacroFunction_AddParsedText (EScopeEnum func_scope)
 
virtual CMacroFunction_AddParsedText::~CMacroFunction_AddParsedText ()
 
virtual void CMacroFunction_AddParsedText::TheFunction ()
 Function implementation. More...
 
static CTempString CMacroFunction_AddParsedText::GetFuncName ()
 
virtual bool CMacroFunction_AddParsedText::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_AddParsedText::x_ParseFields (CMQueryNodeValue::TObs &dest_objs, const string &text_portion, objects::edit::EExistingText existing_text)
 
 CMacroFunction_AddParsedToFeatQual::CMacroFunction_AddParsedToFeatQual (EScopeEnum func_scope)
 
virtual void CMacroFunction_AddParsedToFeatQual::TheFunction ()
 Function implementation. More...
 
static CTempString CMacroFunction_AddParsedToFeatQual::GetFuncName ()
 
virtual bool CMacroFunction_AddParsedToFeatQual::x_ValidArguments (void) const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_ParsedText::CMacroFunction_ParsedText (EScopeEnum func_scope)
 
virtual CMacroFunction_ParsedText::~CMacroFunction_ParsedText ()
 
virtual void CMacroFunction_ParsedText::TheFunction ()
 Function implementation. More...
 
static CTempString CMacroFunction_ParsedText::GetFuncName ()
 
virtual bool CMacroFunction_ParsedText::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
bool CMacroFunction_ParsedText::x_GetSpecialField (const string &field, CMQueryNodeValue::TObs &objs, objects::CScope &scope)
 
CRef< objects::edit::CParseTextOptions > CMacroFunction_ParsedText::x_GetParseOptions (size_t start_index)
 
 CMacroFunction_ParsedTextFrom::CMacroFunction_ParsedTextFrom (EScopeEnum func_scope)
 
virtual void CMacroFunction_ParsedTextFrom::TheFunction ()
 Function implementation. More...
 
static CTempString CMacroFunction_ParsedTextFrom::GetFuncName ()
 
virtual bool CMacroFunction_ParsedTextFrom::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_ParseToStructComm::CMacroFunction_ParseToStructComm (EScopeEnum func_scope)
 
virtual void CMacroFunction_ParseToStructComm::TheFunction ()
 ParseToStructComment(text/src_field, structcomm_field ("fieldvalue"|"dbname"|"fieldname"), [fieldname,] capitalization, existing_text_opt, delimiter)) More...
 
static CTempString CMacroFunction_ParseToStructComm::GetFuncName ()
 
virtual bool CMacroFunction_ParseToStructComm::x_ValidArguments (void) const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_ParseToStructComm::x_SetFieldType (const string &strcomm_field)
 
 CMacroFunction_CopyStringQual::CMacroFunction_CopyStringQual (EScopeEnum func_scope)
 
virtual CMacroFunction_CopyStringQual::~CMacroFunction_CopyStringQual ()
 
virtual void CMacroFunction_CopyStringQual::TheFunction ()
 class CMacroFunction_CopyStringQual Expected syntax: CopyStringQual( src_field, dest_field, existingtext_opt, delimiter) the last parameter is optional src_field_name and dest_field_name are subfields of the same object Can not use this function to copy from taxname to protein description More...
 
static CTempString CMacroFunction_CopyStringQual::GetFuncName ()
 
virtual bool CMacroFunction_CopyStringQual::x_ValidArguments (void) const
 Tests the number and the type of function arguments. More...
 
virtual bool CMacroFunction_CopyStringQual::x_ChangeFields (CObjectInfo &src, CObjectInfo &dest)
 
 CMacroFunction_CopyFeatQual::CMacroFunction_CopyFeatQual (EScopeEnum func_scope)
 
virtual void CMacroFunction_CopyFeatQual::TheFunction ()
 class CMacroFunction_CopyStringQual Expected syntax: CopyStringQual( src_field, dest_field, existingtext_opt, delimiter) the last parameter is optional src_field_name and dest_field_name are subfields of the same object Can not use this function to copy from taxname to protein description More...
 
static CTempString CMacroFunction_CopyFeatQual::GetFuncName ()
 
virtual bool CMacroFunction_CopyFeatQual::x_ValidArguments (void) const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_CopyRNARelQual::CMacroFunction_CopyRNARelQual (EScopeEnum func_scope)
 
virtual void CMacroFunction_CopyRNARelQual::TheFunction ()
 class CMacroFunction_CopyStringQual Expected syntax: CopyStringQual( src_field, dest_field, existingtext_opt, delimiter) the last parameter is optional src_field_name and dest_field_name are subfields of the same object Can not use this function to copy from taxname to protein description More...
 
static CTempString CMacroFunction_CopyRNARelQual::GetFuncName ()
 
virtual bool CMacroFunction_CopyRNARelQual::x_ValidArguments (void) const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_RemoveOutside::CMacroFunction_RemoveOutside (EScopeEnum func_scope)
 
virtual CMacroFunction_RemoveOutside::~CMacroFunction_RemoveOutside ()
 
virtual void CMacroFunction_RemoveOutside::TheFunction ()
 RemoveOutsideStringQual(field_name(str/obj), before_match(b), left_del(str), rmv_left(b), after_match(b), right_del(str), rmv_right(b), case_insensitive(b), whole_word(b), update_mrna(b)) Last parameter is optional. More...
 
static CTempString CMacroFunction_RemoveOutside::GetFuncName ()
 
virtual bool CMacroFunction_RemoveOutside::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_RemoveOutside::x_RmvOutsideFields (CMQueryNodeValue::TObs &resolved_objs, const CRemoveTextOptions &options)
 
CRef< CRemoveTextOptionsCMacroFunction_RemoveOutside::x_GetRemoveTextOptions (size_t start_index) const
 
bool CMacroFunction_RemoveOutside::x_CheckArguments (size_t index) const
 
 CMacroFunction_RmvOutsideRelFeatQual::CMacroFunction_RmvOutsideRelFeatQual (EScopeEnum func_scope)
 
virtual void CMacroFunction_RmvOutsideRelFeatQual::TheFunction ()
 RmvOutsideRelatedFeatureQual(feat_type, field_name, before_match(b), left_del(str), rmv_left(b), after_match(b), right_del(str), rmv_right(b), case_insensitive(b), whole_word(b), update_mrna(b)) More...
 
static CTempString CMacroFunction_RmvOutsideRelFeatQual::GetFuncName ()
 
virtual bool CMacroFunction_RmvOutsideRelFeatQual::x_ValidArguments (void) const
 Tests the number and the type of function arguments. More...
 
virtual CMacroFunction_AddorSetContElement::~CMacroFunction_AddorSetContElement ()
 
virtual void CMacroFunction_AddorSetContElement::TheFunction ()
 Function implementation. More...
 
static bool CMacroFunction_AddorSetContElement::s_AddSrcOrgMod (objects::CBioSource &bsrc, int subtype, const string &value)
 
static bool CMacroFunction_AddorSetContElement::s_AddSrcSubSource (objects::CBioSource &bsrc, int subtype, const string &value)
 
static int CMacroFunction_AddorSetContElement::s_AddGBQualifier (objects::CSeq_feat &feat, const string &qual_name, const string &newValue)
 
 CMacroFunction_AddorSetContElement::CMacroFunction_AddorSetContElement (EScopeEnum func_scope, bool is_bsrc)
 
virtual bool CMacroFunction_AddorSetContElement::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_AddorSetContElement::x_AddBioSrcModifier (const string &subtype, const string &newValue)
 
 CMacroFunction_AddorSetBsrcModifier::CMacroFunction_AddorSetBsrcModifier (EScopeEnum func_scope)
 
static CTempString CMacroFunction_AddorSetBsrcModifier::GetFuncName ()
 
 CMacroFunction_AddorSetGbQual::CMacroFunction_AddorSetGbQual (EScopeEnum func_scope)
 
static CTempString CMacroFunction_AddorSetGbQual::GetFuncName ()
 
 CMacroFunction_SetStructCommDb::CMacroFunction_SetStructCommDb (EScopeEnum func_scope)
 
virtual void CMacroFunction_SetStructCommDb::TheFunction ()
 class CMacroFunction_SetStructCommDb SetStructCommDb(db_name, existing_text, delimiter, remove_blank) The last two parameters are optional More...
 
static CTempString CMacroFunction_SetStructCommDb::GetFuncName ()
 
static int CMacroFunction_SetStructCommDb::s_UpdateStructCommentDb (objects::CSeqdesc &seqdesc, const string &field, const string &db_name, objects::edit::EExistingText existing_text)
 
static int CMacroFunction_SetStructCommDb::s_UpdateStructCommentDb (objects::CUser_object &user, const string &field, const string &db_name, objects::edit::EExistingText existing_text)
 
static void CMacroFunction_SetStructCommDb::s_MoveSuffixToTheEnd (objects::CUser_object &user_object)
 
virtual bool CMacroFunction_SetStructCommDb::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
bool CMacroFunction_SetStructCommDb::x_MakeNewStructuredComment (const string &db_name, const string &kPrefix, const string &kSuffix)
 
virtual CMacroFunction_SatelliteFields::~CMacroFunction_SatelliteFields ()
 
virtual void CMacroFunction_SatelliteFields::TheFunction ()
 class CMacroFunction_SatelliteFields SATELLITE_NAME() SATELLITE_TYPE() More...
 
static string CMacroFunction_SatelliteFields::s_GetSatelliteType (const string &value)
 
static string CMacroFunction_SatelliteFields::s_GetSatelliteName (const string &value)
 
static string CMacroFunction_SatelliteFields::s_MakeSatellite (const string &type, const string &name)
 
 CMacroFunction_SatelliteFields::CMacroFunction_SatelliteFields (EScopeEnum func_scope, ESatelliteFieldType type)
 
virtual bool CMacroFunction_SatelliteFields::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_SatelliteType::CMacroFunction_SatelliteType (EScopeEnum func_scope)
 
static CTempString CMacroFunction_SatelliteType::GetFuncName ()
 
 CMacroFunction_SatelliteName::CMacroFunction_SatelliteName (EScopeEnum func_scope)
 
static CTempString CMacroFunction_SatelliteName::GetFuncName ()
 
virtual CMacroFunction_MobileElementTypeFields::~CMacroFunction_MobileElementTypeFields ()
 
virtual void CMacroFunction_MobileElementTypeFields::TheFunction ()
 class CMacroFunction_MobileElementTypeFields MOBILE_ELEMENTTYPE_NAME() MOBILE_ELEMENTTYPE_TYPE() More...
 
static string CMacroFunction_MobileElementTypeFields::s_GetMobileElemTType (const string &value)
 
static string CMacroFunction_MobileElementTypeFields::s_GetMobileElemTName (const string &value)
 
static string CMacroFunction_MobileElementTypeFields::s_MakeMobileElementT (const string &type, const string &name)
 
 CMacroFunction_MobileElementTypeFields::CMacroFunction_MobileElementTypeFields (EScopeEnum func_scope, EMobileElemTFieldType type)
 
virtual bool CMacroFunction_MobileElementTypeFields::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_MobileElementType::CMacroFunction_MobileElementType (EScopeEnum func_scope)
 
static CTempString CMacroFunction_MobileElementType::GetFuncName ()
 
 CMacroFunction_MobileElementName::CMacroFunction_MobileElementName (EScopeEnum func_scope)
 
static CTempString CMacroFunction_MobileElementName::GetFuncName ()
 
 CMacroFunction_ApplyStrucVoucherPart::CMacroFunction_ApplyStrucVoucherPart (EScopeEnum func_scope)
 
virtual void CMacroFunction_ApplyStrucVoucherPart::TheFunction ()
 class CMacroFunction_ApplyStrucVoucherPart ApplyStructVoucherPart(obj/voucher_type, part_name, newValue, existing_text, delimiter, remove_blank) Empty new values don't have any effect by default. More...
 
static CTempString CMacroFunction_ApplyStrucVoucherPart::GetFuncName ()
 
virtual bool CMacroFunction_ApplyStrucVoucherPart::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_ApplyStrucVoucherPart::x_ApplyPart (objects::COrgMod &orgmod, NMacroUtil::EStructVoucherPart part, const string &newValue, objects::edit::EExistingText existing_text)
 
void CMacroFunction_ApplyStrucVoucherPart::x_RemovePart (objects::COrgMod &orgmod, NMacroUtil::EStructVoucherPart part)
 
CRef< objects::COrgMod > CMacroFunction_ApplyStrucVoucherPart::x_AddNewQual (objects::COrgMod::TSubtype subtype, NMacroUtil::EStructVoucherPart part, const string &newValue)
 
 IMacroFunction< TData >::IMacroFunction (EScopeEnum func_scope)
 Constructor. More...
 
virtual IMacroFunction< TData >::~IMacroFunction ()
 Virtual destructor. More...
 
virtual void IMacroFunction< TData >::TheFunction ()=0
 Function implementation. More...
 
virtual void IMacroFunction< TData >::operator() (CMacroCmdComposite &cmd_composite, TData &data, CQueryParseTree::TNode &qnode)
 Function operator. More...
 
EScopeEnum IMacroFunction< TData >::GetFuncScope ()
 
ENestedFunc IMacroFunction< TData >::GetNestedState ()
 
const stringIMacroFunction< TData >::GetFuncReport () const
 Function extracts statistic from the object. More...
 
const stringIMacroFunction< TData >::GetErrorReport () const
 
void IMacroFunction< TData >::SetNestedState (ENestedFunc type)
 
virtual void IMacroFunction< TData >::x_InitCall (TData &data)=0
 
virtual void IMacroFunction< TData >::x_SetUserObjects (CQueryParseTree::TNode &qnode)=0
 
void IMacroFunction< TData >::x_LogFunction (CNcbiOstrstream &logstr)
 
void IMacroFunction< TData >::x_LogError (CNcbiOstrstream &logstr)
 
virtual CMacroFunction_ModifyPrimerSeq::~CMacroFunction_ModifyPrimerSeq ()
 
virtual void CMacroFunction_ModifyPrimerSeq::TheFunction ()
 Function implementation. More...
 
 CMacroFunction_ModifyPrimerSeq::CMacroFunction_ModifyPrimerSeq (EScopeEnum func_scope, EModifyType type)
 
virtual bool CMacroFunction_ModifyPrimerSeq::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_TrimJunkFromPrimers::CMacroFunction_TrimJunkFromPrimers (EScopeEnum func_scope)
 
 CMacroFunction_TrimJunkFromPrimers::~CMacroFunction_TrimJunkFromPrimers ()
 
static CTempString CMacroFunction_TrimJunkFromPrimers::GetFuncName ()
 
 CMacroFunction_FixIInPrimers::CMacroFunction_FixIInPrimers (EScopeEnum func_scope)
 
 CMacroFunction_FixIInPrimers::~CMacroFunction_FixIInPrimers ()
 
static CTempString CMacroFunction_FixIInPrimers::GetFuncName ()
 
 CMacroFunction_FixFormat::CMacroFunction_FixFormat (EScopeEnum func_scope)
 
virtual CMacroFunction_FixFormat::~CMacroFunction_FixFormat ()
 
virtual void CMacroFunction_FixFormat::TheFunction ()
 Function implementation. More...
 
static CTempString CMacroFunction_FixFormat::GetFuncName ()
 
static string CMacroFunction_FixFormat::s_FixLatLonFormat (objects::CBioSource &bsrc, const string &value)
 
static bool CMacroFunction_FixFormat::s_AddAltitudeToSubSourceNote (objects::CBioSource &bsrc, const string &value)
 
static string CMacroFunction_FixFormat::s_ConvertAltitudeToMeters (const string &value)
 
virtual bool CMacroFunction_FixFormat::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
virtual CMacroFunction_FixPubCaps::~CMacroFunction_FixPubCaps ()
 
virtual void CMacroFunction_FixPubCaps::TheFunction ()
 Function implementation. More...
 
static string CMacroFunction_FixPubCaps::s_FixCapitalizationInTitle (const string &title, bool first_is_upper, const objects::CSeq_entry_Handle &seh)
 
static Int4 CMacroFunction_FixPubCaps::s_FixCapitalizationInAuthor (objects::CName_std &auth_names)
 
static bool CMacroFunction_FixPubCaps::s_FixCapitalizationInElement (string &value, bool fix_abbrev, bool fix_short_words, bool cap_after_apostrophe)
 
static void CMacroFunction_FixPubCaps::s_FixCapitalizationInCountryString (string &country, bool punct_only)
 
static Int4 CMacroFunction_FixPubCaps::s_FixCapsInPubAffil (objects::CAffil &affil, bool punct_only)
 
static Int4 CMacroFunction_FixPubCaps::s_FixCapsInPubAffil_NoAffilDiv (objects::CAffil &affil, bool punct_only)
 
static Int4 CMacroFunction_FixPubCaps::s_FixCapsInPubAffil_Affil (objects::CAffil &affil, bool punct_only)
 
static Int4 CMacroFunction_FixPubCaps::s_FixCapsInPubAffil_Div (objects::CAffil &affil, bool punct_only)
 
static Int4 CMacroFunction_FixPubCaps::s_FixCapsInPubAffil_City (objects::CAffil &affil, bool punct_only)
 
static Int4 CMacroFunction_FixPubCaps::s_FixCapsInPubAffil_Street (objects::CAffil &affil, bool punct_only)
 
static Int4 CMacroFunction_FixPubCaps::s_FixCapsInPubAffil_Sub (objects::CAffil &affil, bool punct_only)
 
static Int4 CMacroFunction_FixPubCaps::s_FixCapsInPubAffil_Country (objects::CAffil &affil, bool punct_only)
 
 CMacroFunction_FixPubCaps::CMacroFunction_FixPubCaps (EScopeEnum func_scope, EPubType type)
 
virtual bool CMacroFunction_FixPubCaps::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_FixPubCaps::x_FixCapsInPubAffilCountry (objects::CAffil &affil, bool punct_only)
 
 CMacroFunction_FixPubCapsTitle::CMacroFunction_FixPubCapsTitle (EScopeEnum func_scope)
 
 CMacroFunction_FixPubCapsTitle::~CMacroFunction_FixPubCapsTitle ()
 
static CTempString CMacroFunction_FixPubCapsTitle::GetFuncName ()
 
 CMacroFunction_FixPubCapsAuthor::CMacroFunction_FixPubCapsAuthor (EScopeEnum func_scope)
 
 CMacroFunction_FixPubCapsAuthor::~CMacroFunction_FixPubCapsAuthor ()
 
static CTempString CMacroFunction_FixPubCapsAuthor::GetFuncName ()
 
 CMacroFunction_FixPubCapsAffil::CMacroFunction_FixPubCapsAffil (EScopeEnum func_scope)
 
 CMacroFunction_FixPubCapsAffil::~CMacroFunction_FixPubCapsAffil ()
 
static CTempString CMacroFunction_FixPubCapsAffil::GetFuncName ()
 
 CMacroFunction_FixPubCapsAffilWithExcept::CMacroFunction_FixPubCapsAffilWithExcept (EScopeEnum func_scope)
 
 CMacroFunction_FixPubCapsAffilWithExcept::~CMacroFunction_FixPubCapsAffilWithExcept ()
 
static CTempString CMacroFunction_FixPubCapsAffilWithExcept::GetFuncName ()
 
 CMacroFunction_FixPubCapsAffilCountry::CMacroFunction_FixPubCapsAffilCountry (EScopeEnum func_scope)
 
 CMacroFunction_FixPubCapsAffilCountry::~CMacroFunction_FixPubCapsAffilCountry ()
 
static CTempString CMacroFunction_FixPubCapsAffilCountry::GetFuncName ()
 
 CMacroFunction_RemoveSegGaps::CMacroFunction_RemoveSegGaps (EScopeEnum func_scope)
 
virtual CMacroFunction_RemoveSegGaps::~CMacroFunction_RemoveSegGaps ()
 
virtual void CMacroFunction_RemoveSegGaps::TheFunction ()
 Function implementation. More...
 
static bool CMacroFunction_RemoveSegGaps::s_RemoveSegGaps (objects::CSeq_align &align)
 
static CTempString CMacroFunction_RemoveSegGaps::GetFuncName ()
 
virtual bool CMacroFunction_RemoveSegGaps::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_RemoveOrgName::CMacroFunction_RemoveOrgName (EScopeEnum func_scope)
 
virtual CMacroFunction_RemoveOrgName::~CMacroFunction_RemoveOrgName ()
 
virtual void CMacroFunction_RemoveOrgName::TheFunction ()
 Function implementation. More...
 
static bool CMacroFunction_RemoveOrgName::s_RemoveOrgName (const objects::CBioSource &bsrc, string &field)
 
static CTempString CMacroFunction_RemoveOrgName::GetFuncName ()
 
virtual bool CMacroFunction_RemoveOrgName::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_MakeBoldXrefs::CMacroFunction_MakeBoldXrefs (EScopeEnum func_scope)
 
virtual CMacroFunction_MakeBoldXrefs::~CMacroFunction_MakeBoldXrefs ()
 
virtual void CMacroFunction_MakeBoldXrefs::TheFunction ()
 Function implementation. More...
 
static string CMacroFunction_MakeBoldXrefs::s_GetBarcodeId (const objects::CBioseq &bseq)
 
static bool CMacroFunction_MakeBoldXrefs::s_HasBarcodeDbXref (const objects::CBioseq &bseq, const string &barcode_id)
 
static CRef< objects::CDbtag > CMacroFunction_MakeBoldXrefs::s_MakeBarcodeDbXref (const string &barcode_id)
 
static CTempString CMacroFunction_MakeBoldXrefs::GetFuncName ()
 
virtual bool CMacroFunction_MakeBoldXrefs::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_TrimTerminalNs::CMacroFunction_TrimTerminalNs (EScopeEnum func_scope)
 
virtual void CMacroFunction_TrimTerminalNs::TheFunction ()
 Function implementation. More...
 
static CTempString CMacroFunction_TrimTerminalNs::GetFuncName ()
 
virtual bool CMacroFunction_TrimTerminalNs::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_FixSpelling::CMacroFunction_FixSpelling (EScopeEnum func_scope)
 
virtual void CMacroFunction_FixSpelling::TheFunction ()
 class CMacroFunction_FixSpelling Usage: FixSpelling(); More...
 
static void CMacroFunction_FixSpelling::s_SpellingFixes (CSerialObject &object, CNcbiOstrstream &oss)
 
static CTempString CMacroFunction_FixSpelling::GetFuncName ()
 
virtual bool CMacroFunction_FixSpelling::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_RemoveSingleItemSet::CMacroFunction_RemoveSingleItemSet (EScopeEnum func_scope)
 
virtual void CMacroFunction_RemoveSingleItemSet::TheFunction ()
 class CMacroFunction_RemoveSingleItemSet RemoveSingleItemSet(); More...
 
static short CMacroFunction_RemoveSingleItemSet::s_RemoveSingleItemSet (objects::CSeq_entry_Handle &seh)
 
static bool CMacroFunction_RemoveSingleItemSet::s_IsSingletonSet (const objects::CBioseq_set_Handle &bioseq_set)
 
static CTempString CMacroFunction_RemoveSingleItemSet::GetFuncName ()
 
virtual bool CMacroFunction_RemoveSingleItemSet::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_Autodef::CMacroFunction_Autodef (EScopeEnum func_scope)
 
virtual void CMacroFunction_Autodef::TheFunction ()
 class CMacroFunction_Autodef Autodef(clause_list_type, misc_feat_parse_rule, modifier1, modifier2, ...); More...
 
static CRef< CCmdCompositeCMacroFunction_Autodef::s_AutodefSeqEntry (const objects::CSeq_entry_Handle &seh, const objects::CAutoDefOptions &options)
 
static CRef< CCmdCompositeCMacroFunction_Autodef::s_AutodefSequence (const objects::CSeq_entry_Handle &seh, const objects::CBioseq_Handle &target, const objects::CAutoDefOptions &options)
 
static void CMacroFunction_Autodef::s_AutodefBioseqs (const objects::CSeq_entry_Handle &seh, objects::CAutoDefWithTaxonomy &autodef, objects::CAutoDefModifierCombo *mod_combo, CRef< CCmdComposite > composite_cmd)
 
static void CMacroFunction_Autodef::s_AutodefSets (const objects::CSeq_entry_Handle &seh, objects::CAutoDefWithTaxonomy &autodef, CRef< CCmdComposite > composite_cmd)
 
static void CMacroFunction_Autodef::s_AddAutodefOptions (const objects::CAutoDef &autodef, const objects::CBioseq_Handle &bsh, CRef< CCmdComposite > composite_cmd)
 
static CTempString CMacroFunction_Autodef::GetFuncName ()
 
static void CMacroFunction_Autodef::s_AutodefBioseqsNoTitle (const objects::CSeq_entry_Handle &seh, objects::CAutoDefWithTaxonomy &autodef, objects::CAutoDefModifierCombo *mod_combo, CRef< CCmdComposite > composite_cmd)
 
static void CMacroFunction_Autodef::s_AutodefSetsNoTitle (const objects::CSeq_entry_Handle &seh, objects::CAutoDefWithTaxonomy &autodef, CRef< CCmdComposite > composite_cmd)
 
virtual bool CMacroFunction_Autodef::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
virtual void CMacroFunction_Autodef::x_ResetState ()
 Reset the state of member variables that are set directly/indirectly from function arguments. More...
 
void CMacroFunction_Autodef::x_AddModifiersToOptions (objects::CAutoDefOptions &opts)
 
bool CMacroFunction_Autodef::x_IsRequested (const objects::CAutoDefAvailableModifier &modifier)
 
string CMacroFunction_Autodef::x_GetDescription ()
 
 CMacroFunction_AutodefId::CMacroFunction_AutodefId (EScopeEnum func_scope)
 
virtual void CMacroFunction_AutodefId::TheFunction ()
 class CMacroFunction_AutodefId AutodefId() More...
 
static void CMacroFunction_AutodefId::s_ConfigureAutodefOptionsForID (TModifiers &modifiers, objects::CSeq_entry_Handle seh)
 
static CTempString CMacroFunction_AutodefId::GetFuncName ()
 
bool CMacroFunction_AutodefId::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
static void CMacroFunction_AutodefId::s_SelectModifiersforAutodefID (objects::CAutoDef &autodef, TModifiers &modifiers, objects::CSeq_entry_Handle seh)
 
 CMacroFunction_RefreshDefline::CMacroFunction_RefreshDefline (EScopeEnum func_scope)
 
virtual void CMacroFunction_RefreshDefline::TheFunction ()
 RefreshDefline() More...
 
static CTempString CMacroFunction_RefreshDefline::GetFuncName ()
 
static CRef< CCmdCompositeCMacroFunction_RefreshDefline::s_RefreshDeflineCommand (const objects::CSeq_entry_Handle &seh)
 
bool CMacroFunction_RefreshDefline::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_AutodefComplete::CMacroFunction_AutodefComplete (EScopeEnum func_scope)
 
virtual void CMacroFunction_AutodefComplete::TheFunction ()
 class CMacroFunction_AutodefComplete AutodefComplete(misc_feat_parse_rule, modifier1, modifier2, ...) More...
 
static CTempString CMacroFunction_AutodefComplete::GetFuncName ()
 
bool CMacroFunction_AutodefComplete::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_AutodefComplete::x_AddModifiersToOptions (objects::CAutoDefOptions &opts)
 
bool CMacroFunction_AutodefComplete::x_IsRequested (const objects::CAutoDefAvailableModifier &modifier)
 
bool CMacroFunction_AutodefComplete::x_IsComplete (const objects::CBioseq_Handle bsh)
 
 CMacroFunction_RenormalizeNucProtSet::CMacroFunction_RenormalizeNucProtSet (EScopeEnum func_scope)
 
virtual void CMacroFunction_RenormalizeNucProtSet::TheFunction ()
 class CMacroFunction_RenormalizeNucProtSet RenormalizeNucProtSet(); More...
 
void CMacroFunction_RenormalizeNucProtSet::s_RenormalizeNucProtSets (objects::CSeq_entry_Handle seh, Int4 &count)
 
static CTempString CMacroFunction_RenormalizeNucProtSet::GetFuncName ()
 
bool CMacroFunction_RenormalizeNucProtSet::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_CreateProteinFeats::CMacroFunction_CreateProteinFeats (EScopeEnum func_scope)
 
virtual void CMacroFunction_CreateProteinFeats::TheFunction ()
 class CMacroFunction_CreateProteinFeats CreateProteinFeatures() More...
 
static CTempString CMacroFunction_CreateProteinFeats::GetFuncName ()
 
bool CMacroFunction_CreateProteinFeats::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_DeltaSeqToRaw::CMacroFunction_DeltaSeqToRaw (EScopeEnum func_scope)
 
virtual void CMacroFunction_DeltaSeqToRaw::TheFunction ()
 class CMacroFunction_DeltaSeqToRaw ConvertDeltaSeqToRaw() More...
 
static CTempString CMacroFunction_DeltaSeqToRaw::GetFuncName ()
 
static CRef< CCmdCompositeCMacroFunction_DeltaSeqToRaw::s_ConvertDeltaToRaw (objects::CSeq_entry_Handle seh, Int4 &count)
 
bool CMacroFunction_DeltaSeqToRaw::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_UpdateProteinSeqs::CMacroFunction_UpdateProteinSeqs (EScopeEnum func_scope)
 
virtual void CMacroFunction_UpdateProteinSeqs::TheFunction ()
 class CMacroFunction_UpdateProteinSeqs UpdateProteinSeqs(filename, "match_by_id|match_by_name") File should contain protein sequences in FASTA format More...
 
static CTempString CMacroFunction_UpdateProteinSeqs::GetFuncName ()
 
bool CMacroFunction_UpdateProteinSeqs::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_UpdateProteinSeqs::x_ReadUpdateSeqs (CNcbiIstream &istr)
 
EMatch CMacroFunction_UpdateProteinSeqs::x_GetMatchType ()
 
 CMacroFunction_FixProteinFormat::CMacroFunction_FixProteinFormat (EScopeEnum func_scope)
 
virtual CMacroFunction_FixProteinFormat::~CMacroFunction_FixProteinFormat ()
 
virtual void CMacroFunction_FixProteinFormat::TheFunction ()
 class CMacroFunction_FixProteinFormat FixProteinFormat() - removes organism names from protein names More...
 
static string CMacroFunction_FixProteinFormat::s_FixProteinNameFormat (const string &protein, const vector< string > &taxnames)
 
static CTempString CMacroFunction_FixProteinFormat::GetFuncName ()
 
virtual bool CMacroFunction_FixProteinFormat::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_FixProteinFormat::x_FixProteinNames (objects::CProt_ref &prot, const vector< string > &taxnames)
 
virtual CMacroFunction_EditFeatLocation::~CMacroFunction_EditFeatLocation ()
 
virtual void CMacroFunction_EditFeatLocation::TheFunction ()
 Function implementation. More...
 
virtual bool CMacroFunction_EditFeatLocation::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
bool CMacroFunction_EditFeatLocation::x_CheckInitFeature ()
 
void CMacroFunction_EditFeatLocation::x_RetranslateCDS (CNcbiOstrstream &log)
 
void CMacroFunction_EditFeatLocation::x_RetranslateCDSAdjustGene (const string &descr)
 
 CMacroFunction_EditFeatLocation::CMacroFunction_EditFeatLocation (EScopeEnum func_scope)
 
 CMacroFunction_SetBothPartials::CMacroFunction_SetBothPartials (EScopeEnum func_scope)
 
virtual void CMacroFunction_SetBothPartials::TheFunction ()
 class CMacroFunction_SetBothPartials SetBothEndsPartial("all"|"at-end", extend(boolean) [,retranslate_cds][,adjust_gene]) The first parameter is for feature selection use "at-end" to only apply to features whose both ends are at the end of sequence use extend = true, to extend to ends of sequence if partials are set More...
 
static bool CMacroFunction_SetBothPartials::s_SetBothEndsPartial (objects::CSeq_feat &feat, objects::CScope &scope, const string &descr, bool extend=false)
 
static CTempString CMacroFunction_SetBothPartials::GetFuncName ()
 
virtual bool CMacroFunction_SetBothPartials::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_RemoveBothPartials::CMacroFunction_RemoveBothPartials (EScopeEnum func_scope)
 
virtual void CMacroFunction_RemoveBothPartials::TheFunction ()
 class CMacroFunction_RemoveBothPartials RemoveBothEndsPartial("all"|"not-at-end" [,retranslate_cds][,adjust_gene]) First parameter specifies which features to select: "all" - all features, "not-at-end" - features whose both ends are not at the sequence ends More...
 
static bool CMacroFunction_RemoveBothPartials::s_RemoveBothPartials (objects::CSeq_feat &feat, objects::CScope &scope, const string &descr)
 
static CTempString CMacroFunction_RemoveBothPartials::GetFuncName ()
 
virtual bool CMacroFunction_RemoveBothPartials::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_Set5Partial::CMacroFunction_Set5Partial (EScopeEnum func_scope)
 
virtual void CMacroFunction_Set5Partial::TheFunction ()
 class CMacroFunction_Set5Partial SetPartialStart("all"|"at-end"|"bad-start"|"frame-not-one", extend(boolean) [,retranslate_cds][,adjust_gene]) More...
 
static bool CMacroFunction_Set5Partial::s_Set5EndPartial (objects::CSeq_feat &feat, objects::CScope &scope, const string &descr, bool extend5=false)
 
static CTempString CMacroFunction_Set5Partial::GetFuncName ()
 
virtual bool CMacroFunction_Set5Partial::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_Set3Partial::CMacroFunction_Set3Partial (EScopeEnum func_scope)
 
virtual void CMacroFunction_Set3Partial::TheFunction ()
 class CMacroFunction_Set3Partial SetPartialStop("all"|"at-end"|"bad-end", extend(boolean) [,retranslate_cds][,adjust_gene]) More...
 
static bool CMacroFunction_Set3Partial::s_Set3EndPartial (objects::CSeq_feat &feat, objects::CScope &scope, const string &descr, bool extend3=false)
 
static CTempString CMacroFunction_Set3Partial::GetFuncName ()
 
virtual bool CMacroFunction_Set3Partial::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_Clear5Partial::CMacroFunction_Clear5Partial (EScopeEnum func_scope)
 
virtual void CMacroFunction_Clear5Partial::TheFunction ()
 class CMacroFunction_Clear5Partial ClearPartialStart("all"|"not-at-end"|"good-start" [,retranslate_cds][,adjust_gene]) More...
 
static bool CMacroFunction_Clear5Partial::s_Clear5EndPartial (objects::CSeq_feat &feat, objects::CScope &scope, const string &descr)
 
static CTempString CMacroFunction_Clear5Partial::GetFuncName ()
 
virtual bool CMacroFunction_Clear5Partial::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_Clear3Partial::CMacroFunction_Clear3Partial (EScopeEnum func_scope)
 
virtual void CMacroFunction_Clear3Partial::TheFunction ()
 class CMacroFunction_Clear3Partial ClearPartialStop("all"|"not-at-end"|"good-end" [,retranslate_cds][,adjust_gene]) More...
 
static bool CMacroFunction_Clear3Partial::s_Clear3EndPartial (objects::CSeq_feat &feat, objects::CScope &scope, const string &descr)
 
static CTempString CMacroFunction_Clear3Partial::GetFuncName ()
 
virtual bool CMacroFunction_Clear3Partial::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_ConvertLocStrand::CMacroFunction_ConvertLocStrand (EScopeEnum func_scope)
 
virtual void CMacroFunction_ConvertLocStrand::TheFunction ()
 class CMacroFunction_ConvertLocStrand ConvertLocationStrand(from_strand, to_strand [,retranslate_cds][,adjust_gene]) from_strand can be one of {any, plus, minus, unknown, both} to_strand can be one of {plus, minus, unknown, both, reverse} More...
 
static objects::ENa_strand CMacroFunction_ConvertLocStrand::s_GetStrandFromString (const string &str)
 
static bool CMacroFunction_ConvertLocStrand::s_ConvertLocationStrand (objects::CSeq_feat &feat, objects::CScope &scope, const string &str_from, const string &str_to)
 
static CTempString CMacroFunction_ConvertLocStrand::GetFuncName ()
 
virtual bool CMacroFunction_ConvertLocStrand::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_ConvertLocType::CMacroFunction_ConvertLocType (EScopeEnum func_scope)
 
virtual void CMacroFunction_ConvertLocType::TheFunction ()
 class CMacroFunction_ConvertLocType ConvertLocationType("join"|"order"|"single-interval" [,retranslate_cds][,adjust_gene]) More...
 
static bool CMacroFunction_ConvertLocType::s_ConvertLocationType (objects::CSeq_feat &feat, objects::CScope &scope, const string &descr)
 
static CTempString CMacroFunction_ConvertLocType::GetFuncName ()
 
virtual bool CMacroFunction_ConvertLocType::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_Extend5Feature::CMacroFunction_Extend5Feature (EScopeEnum func_scope)
 
virtual void CMacroFunction_Extend5Feature::TheFunction ()
 class CMacroFunction_Extend5Feature - extends the feature ends to the respective end of the sequence ExtendFeatToSeqStart([retranslate_cds][,adjust_gene]) More...
 
static CTempString CMacroFunction_Extend5Feature::GetFuncName ()
 
virtual bool CMacroFunction_Extend5Feature::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_Extend3Feature::CMacroFunction_Extend3Feature (EScopeEnum func_scope)
 
virtual void CMacroFunction_Extend3Feature::TheFunction ()
 class CMacroFunction_Extend3Feature - extends the feature ends to the respective end of the sequence ExtendFeatToSeqStop([retranslate_cds][,adjust_gene]) More...
 
static CTempString CMacroFunction_Extend3Feature::GetFuncName ()
 
virtual bool CMacroFunction_Extend3Feature::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_RemoveAllFeatures::CMacroFunction_RemoveAllFeatures (EScopeEnum func_scope)
 
virtual void CMacroFunction_RemoveAllFeatures::TheFunction ()
 class CMacroFunction_RemoveAllFeatures RemoveAllFeatures(); More...
 
static CTempString CMacroFunction_RemoveAllFeatures::GetFuncName ()
 
virtual bool CMacroFunction_RemoveAllFeatures::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_ApplyCDSFrame::CMacroFunction_ApplyCDSFrame (EScopeEnum func_scope)
 
virtual CMacroFunction_ApplyCDSFrame::~CMacroFunction_ApplyCDSFrame ()
 
virtual void CMacroFunction_ApplyCDSFrame::TheFunction ()
 class CMacroFunction_ApplyCDSFrame ApplyCDSFrame("best"|"match") More...
 
static bool CMacroFunction_ApplyCDSFrame::s_SetCDSFrame (objects::CSeq_feat &cds, ECdsFrame frame_type, objects::CScope &scope)
 
static objects::CCdregion::TFrame CMacroFunction_ApplyCDSFrame::s_FindMatchingFrame (const objects::CSeq_feat &cds, objects::CScope &scope)
 
static ECdsFrame CMacroFunction_ApplyCDSFrame::s_GetFrameFromName (const string &name)
 
static CTempString CMacroFunction_ApplyCDSFrame::GetFuncName ()
 
virtual bool CMacroFunction_ApplyCDSFrame::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_ConvertFeature::CMacroFunction_ConvertFeature (EScopeEnum func_scope)
 
virtual CMacroFunction_ConvertFeature::~CMacroFunction_ConvertFeature ()
 
virtual void CMacroFunction_ConvertFeature::TheFunction ()
 class CMacroFunction_ConvertFeature ConvertFeature(feat_type); ConvertFeature(feat_type, subtype) // subtype can be used for specifying type of bond, ncRNA class or type of site ConvertFeature(feat_type, create_on_protein) // when the feat_type is region, create_on_protein is of bool type ConvertCDSToFeature(feat_type, rem_mRNA, rem_gene, rem_transcript_id); ConvertCDSToFeature(feat_type, subtype, rem_mRNA, rem_gene, rem_transcript_id); ConvertCDSToFeature(feat_type, create_on_protein, rem_mRNA, rem_gene, rem_transcript_id); More...
 
static CTempString CMacroFunction_ConvertFeature::GetFuncName ()
 
virtual bool CMacroFunction_ConvertFeature::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_ConvertFeature::x_SetConvertOptions (CRef< CConvertFeatureBase > converter)
 
 CMacroFunction_ConvertCDS::CMacroFunction_ConvertCDS (EScopeEnum func_scope)
 
 CMacroFunction_ConvertCDS::~CMacroFunction_ConvertCDS ()
 
static CTempString CMacroFunction_ConvertCDS::GetFuncName ()
 
virtual bool CMacroFunction_ConvertCDS::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_RemoveGeneXref::CMacroFunction_RemoveGeneXref (EScopeEnum func_scope)
 
virtual CMacroFunction_RemoveGeneXref::~CMacroFunction_RemoveGeneXref ()
 
virtual void CMacroFunction_RemoveGeneXref::TheFunction ()
 class CMacroFunction_RemoveGeneXref RemoveGeneXref(suppressing_type, necessary_type); suppressing_type = {"any", "suppressing", "nonsuppressing"} necessary_type = {"any", "necessary", "unnecessary"} More...
 
static bool CMacroFunction_RemoveGeneXref::s_GeneXrefMatchesSuppression (const objects::CGene_ref &gene, objects::EGene_xref_suppression_type suppr_type)
 
static bool CMacroFunction_RemoveGeneXref::s_GeneXrefMatchesNecessary (const objects::CGene_ref &gene, const objects::CSeq_feat &feat, objects::CScope &scope, objects::EGene_xref_necessary_type necessary_type)
 
static CTempString CMacroFunction_RemoveGeneXref::GetFuncName ()
 
virtual bool CMacroFunction_RemoveGeneXref::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_ReplaceStopWithSelenocysteine::CMacroFunction_ReplaceStopWithSelenocysteine (EScopeEnum func_scope)
 
virtual CMacroFunction_ReplaceStopWithSelenocysteine::~CMacroFunction_ReplaceStopWithSelenocysteine ()
 
virtual void CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction ()
 class CMacroFunction_ReplaceStopWithSelenocysteine ReplaceSelenocysteineStops(); Replace all stops with selenocysteine (U) if the codon is TGA and the product name contains "seleno" More...
 
static CTempString CMacroFunction_ReplaceStopWithSelenocysteine::GetFuncName ()
 
virtual bool CMacroFunction_ReplaceStopWithSelenocysteine::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
CRef< objects::CSeq_loc > CMacroFunction_ReplaceStopWithSelenocysteine::x_GetProteinLoc (const objects::CSeq_id &prot_id, TSeqPos pos) const
 
virtual CMacroFunction_MakeLocation::~CMacroFunction_MakeLocation ()
 
virtual void CMacroFunction_MakeLocation::TheFunction ()
 Function implementation. More...
 
virtual bool CMacroFunction_MakeLocation::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
bool CMacroFunction_MakeLocation::x_SetCurrentBioseq ()
 class CMacroFunction_MakeLocation Generates different type of seq-loc objects More...
 
void CMacroFunction_MakeLocation::x_HandleNegativeCoordinates (size_t index)
 
objects::ENa_strand CMacroFunction_MakeLocation::x_GetStrand (const string &str)
 
 CMacroFunction_MakeLocation::CMacroFunction_MakeLocation (EScopeEnum func_scope)
 
 CMacroFunction_MakeInterval::CMacroFunction_MakeInterval (EScopeEnum func_scope)
 
virtual void CMacroFunction_MakeInterval::TheFunction ()
 class CMacroFunction_MakeInterval MakeInterval(from, to, partial5(bool), partial3(bool), "plus"|"minus") More...
 
static CTempString CMacroFunction_MakeInterval::GetFuncName ()
 
virtual bool CMacroFunction_MakeInterval::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_MakeWholeSeqInterval::CMacroFunction_MakeWholeSeqInterval (EScopeEnum func_scope)
 
virtual void CMacroFunction_MakeWholeSeqInterval::TheFunction ()
 class CMacroFunction_MakeWholeSeqInterval MakeWholeSeqInterval(partial5, partial3, "plus" | "minus") More...
 
static CTempString CMacroFunction_MakeWholeSeqInterval::GetFuncName ()
 
virtual bool CMacroFunction_MakeWholeSeqInterval::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_MakePoint::CMacroFunction_MakePoint (EScopeEnum func_scope)
 
virtual void CMacroFunction_MakePoint::TheFunction ()
 class CMacroFunction_MakePoint MakePoint(point(integer), partial5, partial3, strand) More...
 
static CTempString CMacroFunction_MakePoint::GetFuncName ()
 
virtual bool CMacroFunction_MakePoint::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
virtual void CMacroFunction_ApplyFeature::TheFunction ()
 Function implementation. More...
 
virtual bool CMacroFunction_ApplyFeature::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
bool CMacroFunction_ApplyFeature::x_SetLocation (size_t index)
 
bool CMacroFunction_ApplyFeature::x_ShouldAddRedundant (size_t index)
 class CMacroFunction_ApplyFeature Generates different types of apply feature commands More...
 
void CMacroFunction_ApplyFeature::x_SetAdditionalFields (size_t index)
 
 CMacroFunction_ApplyFeature::CMacroFunction_ApplyFeature (EScopeEnum func_scope)
 
 CMacroFunction_ApplyCDS::CMacroFunction_ApplyCDS (EScopeEnum func_scope)
 
virtual void CMacroFunction_ApplyCDS::TheFunction ()
 ApplyCDS(protein_name, protein_description, frame("best"|1|2|3), location(object), add_redundant(bool), add_mRNA(bool) [,qualifier_name][,qualifier_value]) qualifier_name should be specified by its asn path, relative to the CDS Seq-feat. More...
 
static CTempString CMacroFunction_ApplyCDS::GetFuncName ()
 
virtual bool CMacroFunction_ApplyCDS::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_ApplyRNA::CMacroFunction_ApplyRNA (EScopeEnum func_scope)
 
virtual void CMacroFunction_ApplyRNA::TheFunction ()
 ApplyRNA(type, rna_name, location(object), add_redundant(bool) [,qualifier_name][,qualifier_value]) qualifier_name should be specified by its asn path, relative to the Seq-feat Type of RNA can be one of: preRNA, mRNA, tRNA, rRNA, ncRNA, tmRNA, miscRNA. More...
 
static CTempString CMacroFunction_ApplyRNA::GetFuncName ()
 
virtual bool CMacroFunction_ApplyRNA::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_ApplyGene::CMacroFunction_ApplyGene (EScopeEnum func_scope)
 
virtual void CMacroFunction_ApplyGene::TheFunction ()
 class CMacroFunction_ApplyGene ApplyGene(location [,qualifier_name][,qualifier_value]) Different from ApplyFeature() function as it always applies a gene to the sequence Used mostly together with ApplyCDS/ApplyRNA/ApplyFeature functions to create an additional gene More...
 
static CTempString CMacroFunction_ApplyGene::GetFuncName ()
 
virtual bool CMacroFunction_ApplyGene::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_ApplyOtherFeature::CMacroFunction_ApplyOtherFeature (EScopeEnum func_scope)
 
virtual void CMacroFunction_ApplyOtherFeature::TheFunction ()
 CMacroFunction_ApplyOtherFeature ApplyFeature(type, name, location, add_redundant(bool) [,qualifier_name][,qualifier_value]) Example: ApplyFeature("data.prot.name", "new protein", location, true, "data.prot.processed", "preprotein") ApplyFeature("data.psec-str", "helix", location, false) ApplyFeature("data.imp.key", "misc_feature", location, true); ApplyFeature("data.gene.locus", "", location, true, "data.gene.desc", "gene description") More...
 
static CTempString CMacroFunction_ApplyOtherFeature::GetFuncName ()
 
virtual bool CMacroFunction_ApplyOtherFeature::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_LocPartialTest::CMacroFunction_LocPartialTest (EScopeEnum func_scope, ELocEndType testcase)
 
virtual void CMacroFunction_LocPartialTest::TheFunction ()
 Function implementation. More...
 
virtual bool CMacroFunction_LocPartialTest::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_LocEnd::CMacroFunction_LocEnd (EScopeEnum func_scope, ELocEndType testcase)
 
virtual void CMacroFunction_LocEnd::TheFunction ()
 Function implementation. More...
 
virtual bool CMacroFunction_LocEnd::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_LocationType::CMacroFunction_LocationType (EScopeEnum func_scope)
 
virtual void CMacroFunction_LocationType::TheFunction ()
 class CMacroFunction_LocationType - obtain information about the type of location ISLOCATIONTYPE(loc_type) - returns true if type of location is loc_type parameter "loc_type" can be one of: "single-interval", "ordered", "joined" More...
 
static CTempString CMacroFunction_LocationType::GetFuncName ()
 
virtual bool CMacroFunction_LocationType::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
bool CMacroFunction_LocationType::x_Match (const objects::CSeq_loc &loc, const objects::CLocation_constraint &loc_cons)
 
 CMacroFunction_LocationSeqType::CMacroFunction_LocationSeqType (EScopeEnum func_scope, const objects::ESeqtype_constraint &seq_type=objects::eSeqtype_constraint_any)
 
virtual void CMacroFunction_LocationSeqType::TheFunction ()
 Function implementation. More...
 
static objects::CSeq_loc * CMacroFunction_LocationSeqType::s_GetLocation (const string &field_name, CIRef< IMacroBioDataIter > iter)
 
virtual bool CMacroFunction_LocationSeqType::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_LocationDistConstraint::CMacroFunction_LocationDistConstraint (EScopeEnum func_scope, ELocEndType testcase)
 
virtual void CMacroFunction_LocationDistConstraint::TheFunction ()
 Function implementation. More...
 
virtual bool CMacroFunction_LocationDistConstraint::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CUnculturedTool::CUnculturedTool ()
 
 CUnculturedTool::CUnculturedTool (const objects::CBioSource &bsrc)
 
 CUnculturedTool::~CUnculturedTool ()
 
void CUnculturedTool::SetBioSource (const objects::CBioSource &bsrc)
 
string CUnculturedTool::GetSuggestedCorrection (void)
 
void CUnculturedTool::CorrectBioSource (objects::CBioSource &bsrc, bool &converted_note, bool &removed_note_sp, bool &removed_note_univ)
 
static string CUnculturedTool::s_MakeUnculturedName (const string &taxname, const string &suffix=kEmptyStr)
 
static string CUnculturedTool::s_GetRank (CRef< objects::CT3Reply > reply)
 
static bool CUnculturedTool::s_IsAmbiguous (CRef< objects::CT3Reply > reply)
 
static bool CUnculturedTool::s_OrganismNotFound (CRef< objects::CT3Reply > reply)
 
static string CUnculturedTool::s_GetSuggestion (CRef< objects::CT3Reply > reply)
 
static bool CUnculturedTool::s_CompareOrgnameLineage (CRef< objects::CT3Reply > reply, const string &lineage)
 
static void CUnculturedTool::s_AddEnvironmentalSample (objects::CBioSource &bsrc)
 
static bool CUnculturedTool::s_OkToTaxFix (const string &taxname)
 
static bool CUnculturedTool::s_IsUnculturedName (const string &taxname)
 
static bool CUnculturedTool::s_HasTaxId (const objects::CBioSource &bsrc)
 
void CUnculturedTool::x_Reset ()
 
bool CUnculturedTool::x_ShouldLookupTaxname (void)
 
string CUnculturedTool::x_GetCorrection ()
 
string CUnculturedTool::x_StandardFixes ()
 
CRef< objects::CT3Reply > CUnculturedTool::x_GetReply (const string &standard_taxname)
 
bool CUnculturedTool::x_CheckSuggestedFix (string &suggestion)
 
string CUnculturedTool::x_TryRankFix (CRef< objects::CT3Reply > reply, string &name)
 
void CUnculturedTool::x_ConvertNote (objects::CBioSource &biosource, const char *note_list[], const string &new_note)
 
 CUnculturedTool::CUnculturedTool (const CUnculturedTool &)
 
CUnculturedToolCUnculturedTool::operator= (const CUnculturedTool &)
 
 CCulturedTool::CCulturedTool ()
 
 CCulturedTool::CCulturedTool (const objects::CBioSource &bsrc)
 
 CCulturedTool::~CCulturedTool ()
 
void CCulturedTool::SetBioSource (const objects::CBioSource &bsrc)
 
void CCulturedTool::CorrectBioSource (objects::CBioSource &bsrc, bool &remove_note)
 
bool CCulturedTool::x_RemoveIfFoundSubSourceNote (objects::CBioSource &bsrc, const char *note_list[])
 
bool CCulturedTool::x_RemoveIfFoundOrgModNote (objects::CBioSource &bsrc, const char *note_list[])
 
 CCulturedTool::CCulturedTool (const CCulturedTool &)
 
CCulturedToolCCulturedTool::operator= (const CCulturedTool &)
 
 CMacroFunction_PubFields::CMacroFunction_PubFields (EScopeEnum func_scope, objects::EPublication_field field)
 
virtual CMacroFunction_PubFields::~CMacroFunction_PubFields ()
 
virtual void CMacroFunction_PubFields::TheFunction ()
 Function implementation. More...
 
static void CMacroFunction_PubFields::s_GetObjectsFromTitle (const CObjectInfo &title, CMQueryNodeValue::TObs &objs)
 
static void CMacroFunction_PubFields::s_GetObjectsFromImprint (const CObjectInfo &imp, const string &field_name, CMQueryNodeValue::TObs &objs)
 
static void CMacroFunction_PubFields::s_GetObjectsFromDate (const CObjectInfo &date, const string &field_name, CMQueryNodeValue::TObs &objs)
 
static void CMacroFunction_PubFields::s_GetObjectsFromAffil (const CObjectInfo &affil, const string &field_name, CMQueryNodeValue::TObs &objs)
 
static void CMacroFunction_PubFields::s_GetObjectsFromAuthListNames (const CObjectInfo &names, const string &field_name, CMQueryNodeValue::TObs &objs)
 
static void CMacroFunction_PubFields::s_GetObjectsFromPersonID (const CObjectInfo &names, const string &field_name, CMQueryNodeValue::TObs &objs)
 
static void CMacroFunction_PubFields::s_CopyResolvedObjs (const CMQueryNodeValue::TObs &objs_from, CMQueryNodeValue::TObs &objs_to)
 
static string CMacroFunction_PubFields::s_GetStatus (const objects::CPubdesc &pubdesc)
 
static bool CMacroFunction_PubFields::s_IsUnpublished (const string &citation)
 
static CPubFieldType::EPubFieldStatus CMacroFunction_PubFields::s_GetStatusEnum (const objects::CPub &pub)
 
static bool CMacroFunction_PubFields::s_IsPubFieldFnc (const string &fn_name)
 
virtual bool CMacroFunction_PubFields::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
virtual void CMacroFunction_PubFields::x_ResetState ()
 Reset the state of member variables that are set directly/indirectly from function arguments. More...
 
void CMacroFunction_PubFields::x_GetPubFieldObjectFromPub (const CObjectInfo &pub_oi, CMQueryNodeValue::TObs &objs)
 
void CMacroFunction_PubFields::x_GetObjectsForPubField_Cit (const objects::CPub &pub, const CObjectInfo &pub_var, CMQueryNodeValue::TObs &objs)
 
void CMacroFunction_PubFields::x_GetObjectsForPubField_Title (const objects::CPub &pub, const CObjectInfo &pub_var, CMQueryNodeValue::TObs &objs)
 
void CMacroFunction_PubFields::x_GetObjectsForPubField_SerialNumber (const objects::CPub &pub, const CObjectInfo &pub_var, CMQueryNodeValue::TObs &objs)
 
void CMacroFunction_PubFields::x_GetObjectsForPubField_Journal (const objects::CPub &pub, const CObjectInfo &pub_var, CMQueryNodeValue::TObs &objs)
 
void CMacroFunction_PubFields::x_GetObjectsForPubField_VolIssuePage (const objects::CPub &pub, const CObjectInfo &pub_var, CMQueryNodeValue::TObs &objs)
 
void CMacroFunction_PubFields::x_GetObjectsForPubField_Date (const objects::CPub &pub, const CObjectInfo &pub_var, CMQueryNodeValue::TObs &objs)
 
void CMacroFunction_PubFields::x_GetObjectsForPubField_AffilField (const objects::CPub &pub, const CObjectInfo &pub_var, CMQueryNodeValue::TObs &objs)
 
void CMacroFunction_PubFields::x_GetObjectsForPubField_PMID (objects::CPub &pub, const CObjectInfo &pub_var, CMQueryNodeValue::TObs &objs)
 
void CMacroFunction_PubFields::x_GetObjectsForPubField_Authors (const objects::CPub &pub, const CObjectInfo &pub_var, CMQueryNodeValue::TObs &objs)
 
void CMacroFunction_PubFields::x_GetPubFieldObjectFromSubmitBlock (const CObjectInfo &block_oi, CMQueryNodeValue::TObs &objs)
 
string CMacroFunction_PubFields::x_GetPubStatus (const CObjectInfo &pubdesc_oi)
 
static string CMacroFunction_PubFields::x_GetStatus (const objects::CPub &pub)
 
 CMacroFunction_ApplyPublication::CMacroFunction_ApplyPublication (EScopeEnum func_scope, objects::CPub::E_Choice pub_type)
 
virtual CMacroFunction_ApplyPublication::~CMacroFunction_ApplyPublication ()
 
virtual void CMacroFunction_ApplyPublication::TheFunction ()
 Function implementation. More...
 
virtual bool CMacroFunction_ApplyPublication::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
virtual CMacroFunction_AuthorFix::~CMacroFunction_AuthorFix ()
 
virtual void CMacroFunction_AuthorFix::TheFunction ()
 Function implementation. More...
 
static const stringCMacroFunction_AuthorFix::GetDescription (EActionType fix_type)
 
static EActionType CMacroFunction_AuthorFix::GetActionType (const string &descr)
 
static bool CMacroFunction_AuthorFix::s_MoveMiddleToFirst (objects::CName_std &name)
 
static bool CMacroFunction_AuthorFix::s_TruncateMiddleInitials (objects::CName_std &name)
 
static bool CMacroFunction_AuthorFix::s_FixInitials (objects::CName_std &name)
 
static bool CMacroFunction_AuthorFix::s_ReverseAuthorNames (objects::CName_std &name)
 
static string CMacroFunction_AuthorFix::s_GetFirstNameInitials (const string &first_name)
 
static string CMacroFunction_AuthorFix::s_InsertInitialPeriods (const string &orig)
 
static string CMacroFunction_AuthorFix::s_GetFirstNameInitialsWithoutStops (const string &first_name)
 
static void CMacroFunction_AuthorFix::s_BuildName (const string &firstname, const string &mid_initials, const string &lastname, const string &suffix, objects::CName_std &name)
 
 CMacroFunction_AuthorFix::CMacroFunction_AuthorFix (EScopeEnum func_scope, EActionType type)
 
virtual bool CMacroFunction_AuthorFix::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
int CMacroFunction_AuthorFix::x_MakeAuthorChanges (objects::CAuth_list &auth_list)
 
 CMacroFunction_MoveMiddleName::CMacroFunction_MoveMiddleName (EScopeEnum func_scope)
 
 CMacroFunction_MoveMiddleName::~CMacroFunction_MoveMiddleName ()
 
static CTempString CMacroFunction_MoveMiddleName::GetFuncName ()
 
 CMacroFunction_StripSuffix::CMacroFunction_StripSuffix (EScopeEnum func_scope)
 
 CMacroFunction_StripSuffix::~CMacroFunction_StripSuffix ()
 
static CTempString CMacroFunction_StripSuffix::GetFuncName ()
 
 CMacroFunction_TruncateMI::CMacroFunction_TruncateMI (EScopeEnum func_scope)
 
 CMacroFunction_TruncateMI::~CMacroFunction_TruncateMI ()
 
static CTempString CMacroFunction_TruncateMI::GetFuncName ()
 
 CMacroFunction_ReverseAuthNames::CMacroFunction_ReverseAuthNames (EScopeEnum func_scope)
 
 CMacroFunction_ReverseAuthNames::~CMacroFunction_ReverseAuthNames ()
 
static CTempString CMacroFunction_ReverseAuthNames::GetFuncName ()
 
 CMacroFunction_ISOJTALookup::CMacroFunction_ISOJTALookup (EScopeEnum func_scope)
 
virtual void CMacroFunction_ISOJTALookup::TheFunction ()
 Function implementation. More...
 
static CTempString CMacroFunction_ISOJTALookup::GetFuncName ()
 
virtual bool CMacroFunction_ISOJTALookup::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_ISOJTALookup::x_LookupTitleInJournal (objects::CCit_jour &journal)
 
bool CMacroFunction_ISOJTALookup::x_HasIsoJtaTitle (const objects::CTitle &title) const
 
const stringCMacroFunction_ISOJTALookup::x_GetIsoJtaTitle (const objects::CTitle &title) const
 
vector< stringCMacroFunction_ISOJTALookup::x_FindIsoJtaTitle (const string &title)
 
 CMacroFunction_LookupPub::CMacroFunction_LookupPub (EScopeEnum func_scope)
 
 CMacroFunction_LookupPub::~CMacroFunction_LookupPub ()
 
virtual void CMacroFunction_LookupPub::TheFunction ()
 Function implementation. More...
 
static CTempString CMacroFunction_LookupPub::GetFuncName ()
 
static CRef< objects::CPub > CMacroFunction_LookupPub::s_GetArticleFromEntrezById (TEntrezId pmid, bool asn_format=false)
 
virtual bool CMacroFunction_LookupPub::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_SetPubTitle::CMacroFunction_SetPubTitle (EScopeEnum func_scope)
 
 CMacroFunction_SetPubTitle::~CMacroFunction_SetPubTitle ()
 
virtual void CMacroFunction_SetPubTitle::TheFunction ()
 class CMacroFunction_SetPubTitle SetPubTitle(title_object, newValue, existingtext_option, delimiter, remove_blank) The last two parameters are optional More...
 
static CTempString CMacroFunction_SetPubTitle::GetFuncName ()
 
virtual bool CMacroFunction_SetPubTitle::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_SetPubTitle::x_SetTitleInPubdesc (objects::CPubdesc &pubdesc, const string &value)
 
void CMacroFunction_SetPubTitle::x_SetTitleInSubmitBlock (objects::CSubmit_block &submit_block, const string &value)
 
 CMacroFunction_SetPubAffil::CMacroFunction_SetPubAffil (EScopeEnum func_scope)
 
 CMacroFunction_SetPubAffil::~CMacroFunction_SetPubAffil ()
 
virtual void CMacroFunction_SetPubAffil::TheFunction ()
 CMacroFunction_SetPubAffil SetPubAffil("affil", new_value, existing_text, delimiter, remove_blank) SetPubAffil("city", new_value, existing_text, delimiter, remove_blank) The last two parameters are optional. More...
 
static CTempString CMacroFunction_SetPubAffil::GetFuncName ()
 
virtual bool CMacroFunction_SetPubAffil::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_SetPubAffil::x_SetAffilField (objects::CAuth_list &auth_list, const string &field, const string &value, objects::edit::EExistingText existing_text)
 
void CMacroFunction_SetPubAffil::x_RemoveAffilField (objects::CAuth_list &auth_list, const string &field)
 
 CMacroFunction_SetPubAuthor::CMacroFunction_SetPubAuthor (EScopeEnum func_scope)
 
virtual void CMacroFunction_SetPubAuthor::TheFunction ()
 class CMacroFunction_SetPubAuthor SetPubAuthorName(author_object, field_name, newValue, existingtext_option, delimiter, remove_blank) More...
 
static CTempString CMacroFunction_SetPubAuthor::GetFuncName ()
 
virtual bool CMacroFunction_SetPubAuthor::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_SetPubAuthor::x_SetAuthorInPubdesc (objects::CPubdesc &pubdesc, const string &field, const CMQueryNodeValue &value, objects::edit::EExistingText existing_text)
 
void CMacroFunction_SetPubAuthor::x_SetNewAuthor (objects::CAuth_list &auth_list, const string &field, const CMQueryNodeValue &value)
 
 DECLARE_FUNC_CLASS_WITH_FNCNAME (CMacroFunction_SetPubAuthorMI)
 
 CMacroFunction_AddPubAuthor::CMacroFunction_AddPubAuthor (EScopeEnum func_scope)
 
virtual void CMacroFunction_AddPubAuthor::TheFunction ()
 class CMacroFunction_AddPubAuthors AddAuthor(last_name, first_name, middle initial, suffix, existingtext_option) More...
 
static CTempString CMacroFunction_AddPubAuthor::GetFuncName ()
 
virtual bool CMacroFunction_AddPubAuthor::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_AddPubAuthor::x_AddAuthorInPubdesc (objects::CPubdesc &pubdesc, objects::edit::EExistingText existing_text)
 
void CMacroFunction_AddPubAuthor::x_AddAuthor (objects::CAuth_list &auth_list, objects::edit::EExistingText existing_text)
 
 CMacroFunction_AddAuthorList::CMacroFunction_AddAuthorList (EScopeEnum func_scope)
 
virtual void CMacroFunction_AddAuthorList::TheFunction ()
 class CMacroFunction_AddAuthorList AddAuthorList(author_list, remove_blank) The only option for it is to overwrite existing values The last parameter is optional More...
 
static CTempString CMacroFunction_AddAuthorList::GetFuncName ()
 
virtual bool CMacroFunction_AddAuthorList::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_AddAuthorList::x_AddAuthorListInPubdesc (objects::CPubdesc &pubdesc)
 
 CMacroFunction_SetPubJournal::CMacroFunction_SetPubJournal (EScopeEnum func_scope)
 
 CMacroFunction_SetPubJournal::~CMacroFunction_SetPubJournal ()
 
virtual void CMacroFunction_SetPubJournal::TheFunction ()
 class CMacroFunction_SetPubJournal SetPubJournal(newValue, existingtext_option, delimiter, remove_blank) The last two parameters are optional More...
 
static CTempString CMacroFunction_SetPubJournal::GetFuncName ()
 
virtual bool CMacroFunction_SetPubJournal::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_SetPubJournal::x_SetJournalInPubdesc (objects::CPubdesc &pubdesc, const string &value, objects::edit::EExistingText existing_text)
 
void CMacroFunction_SetPubJournal::x_RemoveJournalInPubdesc (objects::CPubdesc &pubdesc)
 
 CMacroFunction_SetPubVolIssuePages::CMacroFunction_SetPubVolIssuePages (EScopeEnum func_scope, const string &field)
 
 CMacroFunction_SetPubVolIssuePages::~CMacroFunction_SetPubVolIssuePages ()
 
virtual void CMacroFunction_SetPubVolIssuePages::TheFunction ()
 Function implementation. More...
 
virtual bool CMacroFunction_SetPubVolIssuePages::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_SetPubVolIssuePages::x_SetVolIssuePagesInPubdesc (objects::CPubdesc &pubdesc, const string &value, objects::edit::EExistingText existing_text)
 
void CMacroFunction_SetPubVolIssuePages::x_RemoveVolIssuePagesInPubdesc (objects::CPubdesc &pubdesc)
 
 CMacroFunction_SetPubDate::CMacroFunction_SetPubDate (EScopeEnum func_scope)
 
 CMacroFunction_SetPubDate::~CMacroFunction_SetPubDate ()
 
virtual void CMacroFunction_SetPubDate::TheFunction ()
 SetPubDate(year, month, date) OR SetPubDate(date_str) The only option is to overwrite. More...
 
static CTempString CMacroFunction_SetPubDate::GetFuncName ()
 
virtual bool CMacroFunction_SetPubDate::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_SetPubDate::x_AddDate (CMQueryNodeValue::TObs &objs)
 
 CMacroFunction_SetPubDateField::CMacroFunction_SetPubDateField (EScopeEnum func_scope)
 
 CMacroFunction_SetPubDateField::~CMacroFunction_SetPubDateField ()
 
virtual void CMacroFunction_SetPubDateField::TheFunction ()
 SetPubDateField(date_field, new_value, remove_blank) More...
 
static CTempString CMacroFunction_SetPubDateField::GetFuncName ()
 
virtual bool CMacroFunction_SetPubDateField::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_SetPubDateField::x_AddDateField (CMQueryNodeValue::TObs &objs)
 
void CMacroFunction_SetPubDateField::x_RemoveDateField (CMQueryNodeValue::TObs &objs)
 
 CMacroFunction_SetPubStatus::CMacroFunction_SetPubStatus (EScopeEnum func_scope)
 
 CMacroFunction_SetPubStatus::~CMacroFunction_SetPubStatus ()
 
virtual void CMacroFunction_SetPubStatus::TheFunction ()
 SetPubStatus(value) More...
 
static CTempString CMacroFunction_SetPubStatus::GetFuncName ()
 
static bool CMacroFunction_SetPubStatus::s_SetStatus (objects::CPubdesc &pubdesc, const string &value)
 
virtual bool CMacroFunction_SetPubStatus::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
static bool CMacroFunction_SetPubStatus::x_SetStatus (objects::CPub &pub, CPubFieldType::EPubFieldStatus status)
 
virtual CMacroFunction_SetPubField::~CMacroFunction_SetPubField ()
 
virtual void CMacroFunction_SetPubField::TheFunction ()
 Function implementation. More...
 
 CMacroFunction_SetPubField::CMacroFunction_SetPubField (EScopeEnum func_scope, EPubFieldType pub_field)
 
virtual bool CMacroFunction_SetPubField::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_SetPubField::x_SetPubFieldInPub (CObjectInfo &pub_oi)
 
void CMacroFunction_SetPubField::x_SetObjects_Date (objects::CPub &pub, CObjectInfo &pub_var)
 
void CMacroFunction_SetPubField::x_SetObjects_Affil (objects::CPub &pub, CObjectInfo &pub_var)
 
 CMacroFunction_SetPubAffil_Depr::CMacroFunction_SetPubAffil_Depr (EScopeEnum func_scope)
 
 CMacroFunction_SetPubAffil_Depr::~CMacroFunction_SetPubAffil_Depr ()
 
 CMacroFunction_SetPubDate_Depr::CMacroFunction_SetPubDate_Depr (EScopeEnum func_scope)
 
 CMacroFunction_SetPubDate_Depr::~CMacroFunction_SetPubDate_Depr ()
 
 CMacroFunction_FeatStrandednessConstraint::CMacroFunction_FeatStrandednessConstraint (EScopeEnum func_scope)
 
virtual CMacroFunction_FeatStrandednessConstraint::~CMacroFunction_FeatStrandednessConstraint ()
 
virtual void CMacroFunction_FeatStrandednessConstraint::TheFunction ()
 class CMacroFunction_FeatStrandednessConstraint Checks for the strandedness of all features ISSTRAND_OF_FEATURES(strandedness) - accepts one parameter, a string corresponding to Feature-strandedness-constraint, except "any" More...
 
static CTempString CMacroFunction_FeatStrandednessConstraint::GetFuncName ()
 
virtual bool CMacroFunction_FeatStrandednessConstraint::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
objects::EFeature_strandedness_constraint CMacroFunction_FeatStrandednessConstraint::x_GetStrandednessFromName (const string &strand_name)
 
bool CMacroFunction_FeatStrandednessConstraint::x_Match (const objects::CBioseq_Handle &bsh, objects::EFeature_strandedness_constraint strandedness)
 
 CMacroFunction_NumberOfFeatures::CMacroFunction_NumberOfFeatures (EScopeEnum func_scope)
 
virtual CMacroFunction_NumberOfFeatures::~CMacroFunction_NumberOfFeatures ()
 
virtual void CMacroFunction_NumberOfFeatures::TheFunction ()
 Function implementation. More...
 
static int CMacroFunction_NumberOfFeatures::s_GetFeatTypeCount (const objects::CBioseq_Handle &bsh, const string &feat_type)
 returns the number of features of type feat_type present on the bioseq More...
 
static CTempString CMacroFunction_NumberOfFeatures::GetFuncName ()
 
virtual bool CMacroFunction_NumberOfFeatures::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
virtual CMacroFunction_StringConstraints::~CMacroFunction_StringConstraints ()
 
virtual void CMacroFunction_StringConstraints::TheFunction ()
 Function implementation. More...
 
static bool CMacroFunction_StringConstraints::s_IsStringMatching (const string &fn_name)
 
static bool CMacroFunction_StringConstraints::s_IsSynonymFile (const string &str)
 
 CMacroFunction_StringConstraints::CMacroFunction_StringConstraints (EScopeEnum func_scope, const string &type, EStrConstrCase testcase=eNotSet, ELogicType op_type=eOR)
 
virtual bool CMacroFunction_StringConstraints::x_ValidArguments () const
 checks whether the arguments number and their type is good and sets the m_Modifier flag in case of a modifier More...
 
virtual void CMacroFunction_StringConstraints::x_ResetState ()
 Reset the state of member variables that are set directly/indirectly from function arguments. More...
 
virtual bool CMacroFunction_StringConstraints::x_IsNestedFunctionReturnValid () const
 
void CMacroFunction_StringConstraints::x_SetModifierFlag ()
 
void CMacroFunction_StringConstraints::x_BuildStringConstraint (void)
 builds a new string constraint to later match with the value of the field More...
 
void CMacroFunction_StringConstraints::x_BuildCaseStringConstraint (void)
 
void CMacroFunction_StringConstraints::x_BuildNoCaseStringConstraint (void)
 
bool CMacroFunction_StringConstraints::x_CheckStringConstraint (const CObjectInfo &oi)
 
bool CMacroFunction_StringConstraints::x_CheckConstraintPrimitive (const string &field)
 
bool CMacroFunction_StringConstraints::x_CheckConstraintContainer (const string &container, const string &subtype)
 
bool CMacroFunction_StringConstraints::x_CheckConstraintWithinClass (const CObjectInfo &obj, const string &subtype)
 
bool CMacroFunction_StringConstraints::x_CheckConstraintObjects (const CMQueryNodeValue::TObs &objs)
 
bool CMacroFunction_StringConstraints::x_CheckAuthorNames (const CObjectInfo &obj)
 
virtual CRef< objects::CWord_substitution > CMacroFunction_StringConstraints::x_ReadSynonymsFor (const string &filename, const string &phrase)=0
 
 CMacroFunction_StringFastConstraints::CMacroFunction_StringFastConstraints (EScopeEnum func_scope, const string &type, EStrConstrCase testcase=eNotSet, ELogicType op_type=eOR)
 
virtual CRef< objects::CWord_substitution > CMacroFunction_StringFastConstraints::x_ReadSynonymsFor (const string &filename, const string &phrase)
 
 CMacroFunction_StringSlowConstraints::CMacroFunction_StringSlowConstraints (EScopeEnum func_scope, const string &type, EStrConstrCase testcase=eNotSet, ELogicType op_type=eOR)
 
virtual CRef< objects::CWord_substitution > CMacroFunction_StringSlowConstraints::x_ReadSynonymsFor (const string &filename, const string &phrase)
 
 CMacroFunction_IsPresent::CMacroFunction_IsPresent (EScopeEnum func_scope)
 
virtual void CMacroFunction_IsPresent::TheFunction ()
 Function implementation. More...
 
static CTempString CMacroFunction_IsPresent::GetFuncName ()
 
virtual bool CMacroFunction_IsPresent::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
void CMacroFunction_IsPresent::x_IsSimpleTypePresent (const string &field_name)
 
void CMacroFunction_IsPresent::x_IsContainerElementPresent (const string &container, const string &field_name)
 
 CMacroFunction_GetSeqdesc::CMacroFunction_GetSeqdesc (EScopeEnum func_scope, objects::CSeqdesc::E_Choice type)
 
virtual void CMacroFunction_GetSeqdesc::TheFunction ()
 Function implementation. More...
 
virtual bool CMacroFunction_GetSeqdesc::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_GetSequence::CMacroFunction_GetSequence (EScopeEnum func_scope)
 
virtual void CMacroFunction_GetSequence::TheFunction ()
 Function implementation. More...
 
virtual bool CMacroFunction_GetSequence::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CMacroFunction_FirstOrLastItem::CMacroFunction_FirstOrLastItem (EScopeEnum func_scope, bool first_item)
 
virtual void CMacroFunction_FirstOrLastItem::TheFunction ()
 Function implementation. More...
 
virtual bool CMacroFunction_FirstOrLastItem::x_ValidArguments () const
 Tests the number and the type of function arguments. More...
 
 CHugeMacroContext::CHugeMacroContext ()=default
 
 CHugeMacroContext::CHugeMacroContext (objects::edit::CHugeAsnReader &reader)
 
void CHugeMacroContext::CacheTaxnames (objects::edit::CHugeAsnReader &reader)
 
const vector< string > & CHugeMacroContext::GetTaxnames () const
 
 CMacroLib::CMacroLib ()
 Constructors are private to make the class a singleton. More...
 
 CMacroLib::CMacroLib (const CMacroLib &)
 
CMacroLibCMacroLib::operator= (const CMacroLib &)
 
static CMacroLibCMacroLib::GetInstance ()
 
bool CMacroLib::AppendToLibrary (const string &filename)
 Function parses the file with macros and stores the results internally in a map. More...
 
bool CMacroLib::AppendToLibrary (const vector< string > &filenames)
 
void CMacroLib::GetMacroNames (vector< string > &macro_names) const
 Function builds a list of macro names in the library to use for example in the toolbar. More...
 
const TMacroLibraryCMacroLib::GetMacros () const
 Returns all macros in the library. More...
 
CMacroRepCMacroLib::GetMacroRep (const string &macro_name) const