NCBI C++ ToolKit
Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 123456]
 Nbm
 Nctlib
 NdtlDtl – Diff Template Library
 Nimpl
 NJetBrains
 NmuNamespace for mathematical applications
 NncbiMagic spell ;-) needed for some weird compilers... very empiric
 NNImpl
 NNWinHook
 Nobjects
 Npcrecpp
 NPT
 Npython
 Npythonpp
 NrapidjsonMain RapidJSON namespace
 NTestUtil
 Nvalue_slice
 Nvariation
 Nvariation_ref
 NxmlXML library namespace
 NxsltXML library namespace
 C__bigint_struct
 C__bigint_struct_u
 C_Alloc_traits
 C_character_set_alias
 C_Const_traits
 C_Cor_Def
 C_cs_blkdesc
 C_cs_clientmsg
 C_cs_command
 C_cs_command_list
 C_cs_config
 C_cs_connection
 C_cs_context
 C_cs_datafmt
 C_cs_daterec
 C_cs_datetime
 C_cs_datetime4
 C_cs_dynamic
 C_cs_iodesc
 C_cs_locale
 C_cs_money
 C_cs_money4
 C_cs_numeric
 C_cs_objdata
 C_cs_objname
 C_cs_param
 C_cs_servermsg
 C_cs_varbinary
 C_cs_varchar
 C_csremote_proc
 C_ct_colinfo
 C_Cur_Aln
 C_Cur_Loc
 C_Cxl_Als
 C_Cxl_Los
 C_dblib_error_message
 C_DBREMOTE_PROC
 C_DBREMOTE_PROC_PARAM
 C_dheader
 C_drecord
 C_Fld_Mtf
 C_Gib_Scd
 C_Hashtable_iterator
 C_Hashtable_node
 C_hcattr
 C_hchk
 C_hdbc
 C_hdesc
 C_heattr
 C_henv
 C_hsattr
 C_hstmt
 C_Ht_iterator
 C_InputPeakStruct for holding a single peak
 C_MassMask
 C_MassPeak
 C_MODULEINFO
 C_nlm_mem_map
 C_Nonconst_traits
 C_pbcb
 C_PSIAlignedBlockThis structure keeps track of the regions aligned between the query sequence and those that were not purged
 C_PSIAlignmentTraitsAuxiliary structure to maintain information about two aligned regions between the query and a subject sequence
 C_PSIInternalPssmDataInternal representation of a PSSM in various stages of its creation and its dimensions
 C_PSIMsaInternal multiple alignment data structure used by the PSSM engine
 C_PSIMsaCellInternal data structure to represent a position in the multiple sequence alignment data structure
 C_PSIPackedMsaCompact version of PSIMsa structure
 C_PSIPackedMsaCellCompact version of the PSIMsaCell structure
 C_PSISequenceWeightsInternal data structure to keep computed sequence weights
 C_Qry_Seq
 C_Rcx_Ptl
 C_Rnd_Smp
 C_Seg_Cmp
 C_Seg_Gsm
 C_Seg_Nsm
 C_Seg_Ord
 C_Seq_Mtf
 C_sql_error
 C_sql_errors
 C_Stl_prime
 C_STLP_alloc_proxy
 C_STLP_Identity
 C_tds_bcpcoldata
 C_tds_compiletime_settingsA structure to hold all the compile-time settings
 C_tds_cursor
 C_tds_cursor_status
 C_tds_encodingInformation relevant to libiconv
 C_tds_errno_message_flags
 C_Thd_Cxe
 C_Thd_Gsm
 C_Thd_Tbl
 C_Thd_Tst
 CAaLookupBackboneCellStructure defining one cell of the compacted lookup table
 CAaLookupSmallboneCellStructure defining one cell of the small (i.e., use short) lookup table
 CAalookupTestFixtureA general lookup table for the test
 CAascanTestFixtureThe test fixture to use for all test cases in this file
 CAbstractLexer
 CAbstractParser
 CAbstractToken
 CAddRemoveIdEditAction
 CAddRemoveIdEditAction< false >
 CAdvancedProteinOptionsHandleFixture
 CAgeFunctor
 CAlertToId
 CALICORD
 CAlignedDM
 CAlignIdOrder
 CAlignLenOrder
 CAlignmentCollection
 CAlignmentDisplay
 CAlignmentFeature
 CAlignmentManager
 CAlignmentSet
 CAlignmentUtility
 CAlignSeqOrder
 CAllCutoffScores
 Calp
 Calp_data
 Calp_reg
 Calp_sim
 CAlphaInformation about the alphabet used by seg
 CAMatrix
 CAMatrix_base
 Cambchar
 CAnimationControls
 CAnnotateDialog
 CAnnotationEditorDialog
 CAnnotDataResolver
 CAnnotDataResolver< CSeq_align_Handle >
 CAnnotDataResolver< CSeq_feat_EditHandle >
 CAnnotDataResolver< CSeq_graph_Handle >
 CAnnotObjTrait
 CAnnotObjTrait< CSeq_align >
 CAnnotObjTrait< CSeq_feat >
 CAnnotObjTrait< CSeq_graph >
 CAnyType
 CApplyCDSFrame
 CAppResources
 Carray
 Carray_positive
 CArrayDeleterFunctor template for deleting array of objects
 CASNDataManager
 CASNInputContainerStream
 CASNIOTestApp
 CASNLexer
 CAsnMemoryRead
 CAsnMemoryWrite
 CASNParser
 CAtomCoord
 CAtomPntr
 CAtomSet
 CAtomStyle
 Cauto_ptrAuto_ptr –
 CAutoArrayAutoArray
 CAutoPtrAutoPtr
 CBadECNumberChar
 CBaseTagMapper
 CBCP_HOSTCOLINFO
 CBCP_HOSTFILEINFO
 Cbinary_functorTEMPLATE binary functor base struct
 CBioseqInfo
 CBioTreeBaseNodeBasic data contained in every bio-tree node
 CBitmapCharRec
 CBitmapFontRec
 CBitStream
 Cbitvec
 CBlast_AminoAcidCompositionRepresents the composition of an amino-acid sequence, in the ncbistdaa alphabet
 CBlast_CompositionWorkspaceWork arrays used to perform composition-based matrix adjustment
 CBLAST_DiagHashTrack initial word matches using hashing with chaining
 CBLAST_DiagTableStructure containing parameters needed for initial word extension
 CBlast_ExtendWordStructure for keeping initial word extension information
 CBlast_ForbiddenRangesAn instance of Blast_ForbiddenRanges is used by the Smith-Waterman algorithm to represent ranges in the database that are not to be aligned
 CBlast_GumbelBlkStructure to hold the Gumbel parameters (for FSC)
 CBlast_KarlinBlkStructure to hold the Karlin-Altschul parameters
 CBLAST_LetterProbRecords probability of letter appearing in sequence
 CBLAST_Matrix
 CBlast_MatrixInfoInformation about a amino-acid substitution matrix
 CBlast_MessageStructure to hold the a message from the core of the BLAST engine
 CBlast_RedoAlignCallbacksCallbacks used by Blast_RedoOneMatch and Blast_RedoOneMatchSmithWaterman routines
 CBlast_RedoAlignParamsA parameter block for the Blast_RedoOneMatch and Blast_RedoOneMatchSmithWaterman routines
 CBlast_ResCompIntermediate structure to store the composition of a sequence
 CBlast_ResFreqStores the letter frequency of a sequence or database
 CBlast_ScoreFreqHolds score frequencies used in calculation of Karlin-Altschul parameters for an ungapped search
 CBLAST_SequenceBlkStructure to hold a sequence
 CBlastAaLookupTableThe basic lookup table structure for blastp searches
 CBlastCompo_AlignmentWithin the composition adjustment module, an object of type BlastCompo_Alignment represents a distinct alignment of the query sequence to the current subject sequence
 CBlastCompo_GappingParamsParameters used to compute gapped alignments
 CBlastCompo_HeapA BlastCompo_Heap represents a collection of alignments between one query sequence and several matching subject sequences
 CBlastCompo_HeapRecordThe struct BlastCompo_HeapRecord data type is used below to define the internal structure of a BlastCompo_Heap (see below)
 CBlastCompo_MatchingSequenceA BlastCompo_MatchingSequence represents a subject sequence to be aligned with the query
 CBlastCompo_QueryInfoCollected information about a query
 CBlastCompo_SequenceDataBlastCompo_SequenceData - represents a string of amino acids or nucleotides
 CBlastCompo_SequenceRangeBlastCompo_SequenceRange - a struct whose instances represent a range of data in a sequence
 CBlastCompressedAaLookupTableThe lookup table structure for protein searches using a compressed alphabet
 CBlastContextInfoThe context related information
 CBlastCoreAuxStructStructure to be passed to s_BlastSearchEngineCore, containing pointers to various preallocated structures and arrays
 CBlastDatabaseOptionsOptions used to create the ReadDBFILE structure Include database name and various information for restricting the database to a subset
 CBlastdbCopyApplication
 CBlastDiagnosticsReturn statistics from the BLAST search
 CBlastEffectiveLengthsOptionsOptions for setting up effective lengths and search spaces
 CBlastEffectiveLengthsParametersParameters for setting up effective lengths and search spaces
 CBlastEngineTestFixture
 CBLASTer
 CBlastExtensionOptionsOptions used for gapped extension These include: a
 CBlastExtensionParametersComputed values used as parameters for gapped alignments
 CBlastGapAlignStructStructure supporting the gapped alignment
 CBlastGapDPAuxiliary structure for dynamic programming gapped extension
 CBlastGappedCutoffsAll the gapped cutoff values that can change from context to context
 CBlastGappedStatsStructure containing hit counts from the gapped stage of a BLAST search
 CBlastGapSWAuxiliary structures for Smith-Waterman alignment with traceback
 CBlastHitListThe structure to contain all BLAST results for one query sequence
 CBlastHitSavingOptionsOptions used when evaluating and saving hits These include: a
 CBlastHitSavingParametersParameter block that contains a pointer to BlastHitSavingOptions and the values derived from it
 CBlastHSPStructure holding all information about an HSP
 CBlastHSPBestHitData
 CBlastHSPBestHitOptionsOptions for the Best Hit HSP collection algorithm
 CBlastHSPBestHitParamsKeeps parameters used in best hit algorithm
 CBlastHSPCollectorDataData structure used by the writer
 CBlastHSPCollectorParamsKeeps prelim_hitlist_size and HitSavingOptions together
 CBlastHSPCullingDataThe following are implementations for BlastHSPWriter ADT
 CBlastHSPCullingOptionsOptions for the HSP culling algorithm
 CBlastHSPCullingParamsKeeps parameters used in best hit algorithm
 CBlastHSPFilteringOptionsStructure containing the HSP filtering/writing options
 CBlastHSPLinkThe following structure is used in "link_hsps" to decide between two different "gapping" models
 CBlastHSPListThe structure to hold all HSPs for a given sequence after the gapped alignment
 CBlastHSPPipeADT definition of BlastHSPPipe
 CBlastHSPPipeInfoA wrap of data structure used to create a pipe
 CBlastHSPResultsThe structure to contain all BLAST results, for multiple queries
 CBlastHSPStreamDefault implementation of BlastHSPStream
 CBlastHSPStreamResultBatchStructure used to hold a collection of hits retrieved from the HSPStream
 CBlastHSPStreamResultsBatchArrayStructure to extract the contents of the BlastHSPStream for MT traceback processing
 CBlastHSPwOid
 CBlastHSPWriterADT definition of BlastHSPWriter
 CBlastHSPWriterInfoA wrap of data structure used to create a writer
 CBlastInitHitListStructure to hold all initial HSPs for a given subject sequence
 CBlastInitHSPStructure to hold the initial HSP information
 CBlastInitialWordOptionsOptions needed for initial word finding and processing
 CBlastInitialWordParametersParameter block that contains a pointer to BlastInitialWordOptions and the values derived from it
 CBlastIntervalTreeMain structure describing an interval tree
 CBlastKappa_GappingParamsContextData and data-structures needed to perform a gapped alignment
 CBlastKappa_SavedParametersA BlastKappa_SavedParameters holds the value of certain search parameters on entry to RedoAlignmentCore
 CBlastKappa_SequenceInfoBLAST-specific information that is associated with a BlastCompo_MatchingSequence
 CBlastLinkedHSPSetSimple doubly linked list of HSPs, used for calculating sum statistics
 CBlastLinkHSPParametersParameter block for linking HSPs with sum statistics
 CBlastMaskLocStructure for keeping the query masking information
 CBlastMBLookupTableThe lookup table structure used for Mega BLAST
 CBlastNaLookupTableThe basic lookup table structure for blastn searches
 CBlastNuclOptionsHandleFixture
 CBlastOffsetPairThis symbol enables the verbose option in makeblastdb and other BLAST+ search command line applications, as well as the option to submit searches to the test server in NCBI for remote BLAST searches #define _BLAST_DEBUG 1
 CBlastQueryInfoThe query related information
 CBlastRawCutoffsStructure holding raw cutoff and gap-x-drop values
 CBlastRPSAuxInfoInformation derived from RPS blast '.aux' file
 CBlastRPSFreqRatiosHeader
 CBlastRPSInfoThe RPS engine uses this structure to access all of the RPS blast related data (assumed to be collected in an implementation-specific manner)
 CBlastRPSLookupFileHeaderHeader of RPS blast '.loo' file
 CBlastRPSLookupTableThe basic lookup table structure for RPS blast searches
 CBlastRPSProfileHeaderHeader of RPS blast '.rps' file
 CBlastScoreBlkStructure used for scoring calculations
 CBlastScoringOptionsScoring options block Used to produce the BlastScoreBlk structure This structure may be needed for lookup table construction (proteins only), and for evaluating alignments
 CBlastScoringParametersScoring parameters block Contains scoring-related information that is actually used for the blast search
 CBlastSegOne sequence segment within an HSP
 CBlastSeqLocUsed to hold a set of positions, mostly used for filtering
 CBlastSeqSrcComplete type definition of Blast Sequence Source ADT
 CBlastSeqSrcGetSeqArgStructure used as the second argument to functions satisfying the GetSeqBlkFnPtr signature, associated with index-based implementations of the BlastSeqSrc interface
 CBlastSeqSrcIteratorComplete type definition of Blast Sequence Source Iterator
 CBlastSeqSrcNewInfoComplete type definition of the structure used to create a new BlastSeqSrc
 CBlastSeqSrcSetRangesArgStructure used as the argument to function SetRanges
 CBlastSmallNaLookupTableLookup table structure for blastn searches with small queries
 CblastStr
 CBlastUngappedCutoffsAll the ungapped cutoff values that can change from context to context
 CBlastUngappedDataStructure to hold ungapped alignment information
 CBlastUngappedStatsStructure containing hit counts from the ungapped stage of a BLAST search
 CBlock
 CBlockAligner
 CBlockAlignerOptionsDialog
 CBlockBoundaryAlgorithm
 CBlockEditingParams
 CBlockExtender
 CBlockFormater
 CBlockIntersector
 CBlockModel
 CBlockModelPair
 CBlockMultipleAlignment
 CBMARefinerInterface
 CBMARefinerOptions
 CBMARefinerOptionsDialog
 CBMAUtils
 CBond
 CBondStyle
 CBoundaryShapeEllipseBoundaryShapeEllipse
 Cbranch_chain
 Cbz_stream
 CbzFile
 CC2DLayoutEngineClass C2DLayoutEngine defines the interface for a standard 2D layout engine
 CC2naCmp
 CC2naExpandToIupacna
 CC2naRevCmp
 CC2naReverse
 CC2naTo2naExpand
 CC2naTo4na
 CC2naTo8na
 CC2naToIupacna
 CC4naCmp
 CC4naRevCmp
 CC4naReverse
 CC4naTo2na
 CC4naTo2naExpand
 CC4naTo8na
 CC4naToIupacna
 CC5ColExporter
 CC5ColExporterFactory
 CC5ColExportJobC5ColExportJob
 CC5ColExportPage
 CC5ColExportParams
 CC5ColLoadManagerC5ColLoadManager
 CC5ColObjectLoaderC5ColObjectLoader
 CC8naCmp
 CC8naTo2na
 CC8naToIupacna
 CC_DriverMgr
 CC_FA_Storage
 CC_RA_Storage
 CC_SA_Storage
 CC_xDriverMgr
 CCAA
 CCAbstractProjectItem
 CCAbstractProjectItem_BaseCAbstractProjectItem_Base
 CCAccelTableCAccelTable - Accelerator Table
 CCAcceptRequest
 CCAccessionItem
 CCAccPatternCounterAccession naming patterns; find ranges for consequtive digits
 CCAccValidator
 CCAce2AsnApp
 CCAction_choiceCAction_choice
 CCAction_choice_BaseCAction_choice_Base
 CCActiveObject
 CCAdapterSearchApplication
 CCAdd_descriptor_list_actionCAdd_descriptor_list_action
 CCAdd_descriptor_list_action_BaseCAdd_descriptor_list_action_Base
 CCAdd_file_actionCAdd_file_action
 CCAdd_file_action_BaseCAdd_file_action_Base
 CCAddBioseqChecker
 CCAddCitSubForUpdate
 CCAddConstKeyword
 CCAddDefLineDlg
 CCAddDescr_EditCommand
 CCAddFeatChecker
 CCAddFeatureBetweenDlg
 CCAddFluComments
 CCAddIdChecker
 CCAddLocs_local
 CCAddQuickLaunchDlg
 CCAddSequences
 CCAddStructuredCommentKeyword
 CCAddToNodeSetCallback
 CCAddTranslExceptDlg
 CCAdjust_features_for_gaps_actionCAdjust_features_for_gaps_action
 CCAdjust_features_for_gaps_action_BaseCAdjust_features_for_gaps_action_Base
 CCAdjustForConsensusSplice
 CCAdminCmdProcessor
 CCAdvancedFileInputCAdvancedFileInput
 CCAECR_actionCAECR_action
 CCAECR_action_BaseCAECR_action_Base
 CCAECRDlg
 CCAECRParse_actionCAECRParse_action
 CCAECRParse_action_BaseCAECRParse_action_Base
 CCAffected_channelCAffected_channel
 CCAffected_channel_Base============================================ This section is mapped from module "pepXML" ================================================= channel recipient
 CCAffil.hpp User-defined methods of the data storage class
 CCAffil_BaseCAffil_Base
 CCAffilEditor
 CCAgpCompSpanSplitter
 CCAgpconvertApplication
 CCAgpConverter
 CCAgpErr
 CCAgpErrExCorrectly print multiple errors and warnings on consequitive lines; suppress undesired or higly repetitive messages; calculate total counts for each type of error
 CCAgpExporter
 CCAgpExporterFactory
 CCAgpExportJobCAgpExportJob
 CCAgpExportPage
 CCAgpExportParams
 CCAgpFastaComparator
 CCAgpLoaderCAgpLoader
 CCAgpLoadPage
 CCAgpLoadParams
 CCAgpObjectLoaderC5ColObjectLoader
 CCAgpReaderDetects scaffolds, object boundaries, errors that involve 2 consecutive lines, and is intended as a superclass for more complex readers
 CCAgpRenumber
 CCAgpRowA container for both the original string column values (Get*() methods) and the values converted to int, char, bool types (member variables)
 CCAgpToSeqEntryThis class is used to turn an AGP file into a vector of Seq-entry's
 CCAgpValidateApplication
 CCAgpValidateReader
 CCAgpWriteComponentIdMapper
 CCAgpwriteProcess
 CCAgressiveResizeStrategy
 CCAlgoAlignException
 CCAlgoAlignUtilException
 CCAlgorithm_typeCAlgorithm_type
 CCAlgorithm_type_BaseCAlgorithm_type_Base
 CCAlgoToolManagerBaseCAlgoToolManagerBase This is base class for simple algorithmic tool managers
 CCAlgoToolManagerParamsPanelCAlgoToolManagerParamsPanel
 CCAli
 CCAliasBaseAlias wrapper templates
 CCAliasRefTypeStrings
 CCAliasTest
 CCAliasTypeInfo
 CCAliasTypeInfoFunctions
 CCAliasTypeStrings
 CCAliCreator
 CCAlign_annotCAlign_annot
 CCAlign_annot_BaseCAlign_annot_Base
 CCAlign_annot_setCAlign_annot_set
 CCAlign_annot_set_BaseCAlign_annot_set_Base
 CCAlign_CICAlign_CI
 CCAlign_defCAlign_def
 CCAlign_def_BaseCAlign_def_Base
 CCAlign_statsCAlign_stats
 CCAlign_stats_BaseCAlign_stats_Base
 CCAlignCigarScore
 CCAlignCleanupClass CAlignCleanup implements an alignment cleanup utility based on the C++ alignment manager
 CCAlignCollapser
 CCAlignCommon
 CCAlignCompare
 CCAlignDataSource
 CCAlignDataSourceException
 CCAlignDepthFilter
 CCAlignDistGraph
 CCAlignedFeatureGraphCFeatureGraph
 CCAlignedGisClass to contain the gis of the aligned sequences
 CCAlignFilterCAlignFilter exposes a query language for inspecting properties and scores placed on Seq-align objects
 CCAlignFindContext
 CCAlignFormatUtilThis class contains misc functions for displaying BLAST results
 CCAlignGlyph
 CCAlignGroup
 CCAlignInfo
 CCAlignMap
 CCAlignMarkHandlerCAlignMarkHandler manages handling and editing of marks on alignments
 CCAlignmentBasedRowSelector
 CCAlignmentConfigFile Description:
 CCAlignmentItem
 CCAlignmentRefiner
 CCAlignmentSmear
 CCAlignmentTrackCAlignmentTrack
 CCAlignmentTrackFactoryCAlignmentTrackFactory
 CCAlignModel
 CCAlignMultipleDemoAppDerive our application class from CwxNCBIApp and use it together with standard CNCBIwxApplication
 CCAlignMultipleDemoDlg
 CCAlignNeedlemanWunschPanel
 CCAlignPackageDeclare the Package Object
 CCAlignProjectItemExtension
 CCAlignRangeCAlignRange Represents an element of pairwise alignment of two sequences
 CCAlignRangeCollectionClass CAlignRangeCollection<TAlignRange> represent a sorted collection of TAlignRange
 CCAlignRangeCollException
 CCAlignRangeCollExtenderCAlignRangeCollExtender this is an adapter for a collection that perfroms some of the operations faster due to an additional index built on top of the collection
 CCAlignResultsSet
 CCAlignRow
 CCAlignRowGraphContCAlignRowGraphCont
 CCAlignSeqTableModelCAlignSeqTableModel
 CCAlignShadow
 CCAlignSmearGlyph
 CCAlignSort
 CCAlignSpanViewCAlignSpanView
 CCAlignSpanViewFactoryCAlignSpanViewFactory
 CCAlignStrandSorterCAlignStrandSorter is a sorter used to sort alignments based on alignment strand
 CCAlignTabExporter
 CCAlignTabExporterFactory
 CCAlignTabExportJobCAlignTabExportJob
 CCAlignTabExportPage
 CCAlignTabExportPage2
 CCAlignTabExportParams
 CCAliPiece
 CCAliToSeq_align
 CCAllOtherFeaturesTrackFile Description:
 CCAllOtherFeaturesTrackFactoryCAllOtherFeaturesTrackFactory
 CCAlnAsnReaderHelper class for reading seq-align objects from a CObjectIStream
 CCAlnBuildApp
 CCAlnChunkSegmentCAlnChunkSegment - IAlnSegment implementation for CAlnMap::CAlnChunk
 CCAlnContainerCSeq_align container
 CCAlnContentEvtHandler
 CCAlnError
 CCAlnException
 CCAlnGraphic
 CCAlnIdMapContainer mapping seq-aligns to vectors of participating seq-ids
 CCAlnMap
 CCAlnMapPrinter
 CCAlnMix
 CCAlnMixMatch
 CCAlnMixMatches
 CCAlnMixMerger
 CCAlnMixSegment
 CCAlnMixSegments
 CCAlnMixSeq
 CCAlnMixSequences
 CCAlnMixStarts
 CCAlnMrgApp
 CCAlnMrgTaskProgressCallback
 CCAlnMultiCGIApplication
 CCAlnMultiCGIExceptionNumber of gradient colors in alignment
 CCAlnMultiDSBuilder
 CCAlnMultiHeaderCAlnMultiHeader
 CCAlnMultiHeaderHandlerCAlnMultiHeaderHandler
 CCAlnMultiModelClass CAlnMultiModel - represents a visual model of an alignment
 CCAlnMultiModelFactoryCAlnMultiModelFactory - a factory to separate creation of the model from widget
 CCAlnMultiPaneClass CAlnMultiPane
 CCAlnMultiRendererClass CAlnMultiRenderer - renders multiple alignment represented by IAlnMultiRendererContext (the Model)
 CCAlnMultiWidgetClass CAlnMultiWidget
 CCAlnPos_CI
 CCAlnPropertiesDlgCwxAlnPropertiesDlg
 CCAlnReaderClass CAlnReader supports importing a large variety of text-based alignment formats into standard data structures
 CCAlnRowStateCAlnRowState - implements state management for Align Row
 CCAlnScoringMethodSelector
 CCAlnSeqIdDefault IAlnSeqId implementation based on CSeq_id_Handle
 CCAlnSeqIdConverterDefault seq-id converter
 CCAlnSeqIdsExtractIAlnSeqId extracting functor
 CCAlnSpanSettingsDlg
 CCAlnSpanVertModel
 CCAlnSpanWidget
 CCAlnStatConfig
 CCAlnStatGlyph
 CCAlnStatsHelper class which collects seq-align statistics: seq-ids participating in alignments and rows, potential anchors etc
 CCAlnSummaryView
 CCAlnSummaryViewFactoryCAlnSummaryViewFactory
 CCAlnTableDS
 CCAlnTableWidget
 CCAlnTestApp
 CCAlnUserOptionsOptions for different alignment manager operations
 CCAlnVec
 CCAlnVecGraphicDataSourceCAlnVecGraphicDataSource - implementation of CAlnGraphicDataSource for CAlnVec-based alignments
 CCAlnVecIteratorCAlnVecIterator - IAlnSegmentIterator implementation for CAlnMap::CAlnChunkVec
 CCAlnVecMultiDataSourceCAlnVecMultiDataSource - implementation of IAlnMultiDataSource for CAlnVec-based alignments
 CCAlnVecPrinter
 CCAlnVecRowClass CAlnVecRow - implementation of IAlignRow for CAlnVec-based alignments
 CCAlnVecRowHandleCAlnVecRowHandle is inherited from IAlignRowHandle and represents a row of CAlnVec-based alignment
 CCAlnVwrApp
 CCAlternate_conformation_idCAlternate_conformation_id
 CCAlternate_conformation_id_BaseCAlternate_conformation_id_Base
 CCAlternate_conformation_idsCAlternate_conformation_ids
 CCAlternate_conformation_ids_BaseAn alternate conformation id is optionally associated with each coordinate
 CCAlternative_proteinCAlternative_protein
 CCAlternative_protein_BaseOther protein in search database that contains peptide
 CCAltitudePanel
 CCAltValidator
 CCAlwaysFailMockBlastSeqSrcMock BlastSeqSrc implementation which always fails
 CCAmbigDataBuilderEncode ambiguities in blast database format
 CCAmbiguiousTypes
 CCAmbiguityContext
 CCAmbiguousRegionAmbiguous portion of a sequence
 CCAminoacid_modificationCAminoacid_modification
 CCAminoacid_modification_BaseModified aminoacid, static or variable
 CCAminoAcidCharToSymbol
 CCAnalysis_resultCAnalysis_result
 CCAnalysis_result_BaseCAnalysis_result_Base
 CCAnalysis_summaryCAnalysis_summary
 CCAnalysis_summary_BaseSummary of analysis subjected to run(s)
 CCAnalysis_timestampCAnalysis_timestamp
 CCAnalysis_timestamp_BaseReference for analysis applied to current run (time corresponds with analysis_summary/, id corresponds with analysis_result/)
 CCAnalysisProcess
 CCAnalysisProcessFactory
 CCAnalysisWorkflow
 CCAnalyzeShiftApp
 CCAnchoredAlnQuery-anchored alignment can be 2 or multi-dimentional
 CCAnisotropic_temperature_factorsCAnisotropic_temperature_factors
 CCAnisotropic_temperature_factors_BaseCAnisotropic_temperature_factors_Base
 CCAnnot_CICAnnot_CI
 CCAnnot_Collector
 CCAnnot_descrCAnnot_descr
 CCAnnot_descr_BaseCAnnot_descr_Base
 CCAnnot_idCAnnot_id
 CCAnnot_id_BaseCAnnot_id_Base
 CCAnnotationASN1
 CCAnnotCompare
 CCAnnotCompare_AlignDSCAnnotCompare_AlignDS
 CCAnnotCompare_LocationDSCAnnotCompare_LocationDS
 CCAnnotCompareDSCAnnotCompareDS
 CCAnnotCompareViewCAnnotCompareView
 CCAnnotCompareViewFactoryCAnnotCompareViewFactory
 CCAnnotCompareWidgetCAnnotCompareWidget
 CCAnnotConfigUtils
 CCAnnotdescCAnnotdesc
 CCAnnotdesc_BaseCAnnotdesc_Base
 CCAnnotExceptionAnnotation iterators exceptions
 CCAnnotMapperExceptionSeq-loc and seq-align mapper exceptions
 CCAnnotMapping_Info
 CCAnnotMappingCollector
 CCAnnotMetaDataData structure for holding meta information for an annotaion
 CCAnnotMetaDataJobCAnnotMetaDataJob
 CCAnnotMetaDataJobResultCAnnotMetaDataJobResult
 CCAnnotName
 CCAnnotObject_Info
 CCAnnotObject_Less
 CCAnnotObject_LessReverse
 CCAnnotObject_Ref
 CCAnnotObject_SplitInfo
 CCAnnotObjectType_Less
 CCAnnotPieces
 CCAnnotReadConfig
 CCAnnotSearchLimitException
 CCAnnotType_Index
 CCAnnotTypes_CI
 CCAnnotWriteConfig
 CCAnnotWriterApp
 CCAntiCodonColumn
 CCAntigenic
 CCAnyContentDataType
 CCAnyContentFunctions
 CCAnyContentObjectSerializable object that stores any combination of parsable data
 CCAnyContentTypeStrings
 CCAnyIntron
 CCAnyTypeChoice
 CCAnyTypeClassInfo
 CCAnyTypeSource
 CCApadCApad
 CCApad_BaseCApad_Base
 CCApp
 CCAppDialogs
 CCAppendModToOrg
 CCAppendModToOrgDlg
 CCAppExceptionCAppException
 CCAppExplorerDataObjectCAppExplorerDataObject - wxDataObject for use with CAppExplorerService
 CCAppHitFilter
 CCAppHitFilterException
 CCAppInfoClass CAppInfo defines an interface for application registration information
 CCAppJobCAppJob - default implementation of IAppJob that could be used as a base class
 CCAppJobDispatcherCAppJobDispatcher
 CCAppJobErrorCAppJobError Default implementation for IAppJobError - encapsulates a text error message
 CCAppJobEventTranslatorCAppJobEventTranslator Standard Listener that generates notification events
 CCAppJobExceptionIAppJobListener Interface for components that need to be notified about changes in Jobs
 CCAppJobExecuteUnit
 CCAppJobNotificationCAppJobNotification Notification send by CAppJobEventTranslator
 CCAppJobProgressCAppJobProgress Default implementation for IAppJobProgress - the class encapsulates a text message and a numeric value indicating the progress of the task normalized in [0.0, 1.0] range (0.0 - just started, 1.0 - 100% done)
 CCAppJobTaskCAppJobTask CAppJobTask is an adapter that allows for running IAppJobs as Tasks in App Task Service
 CCAppJobTestApplicationCAppJobTestApplication
 CCAppJobTextResultCAppJobTextResult Default implementation for result object - encapsulates a text error message
 CCApply_actionCApply_action
 CCApply_action_BaseCApply_action_Base
 CCApply_feature_actionCApply_feature_action
 CCApply_feature_action_BaseCApply_feature_action_Base
 CCApply_table_actionCApply_table_action
 CCApply_table_action_BaseCApply_table_action_Base
 CCApply_table_extra_dataCApply_table_extra_data
 CCApply_table_extra_data_BaseCApply_table_extra_data_Base
 CCApplyEditconvertPanel
 CCApplyIndexerComments
 CCApplyObject
 CCApplyRNAITSDlg
 CCApplySubpanel
 CCAppNWA
 CCAppNWAException
 CCAppOptionsDlg
 CCAppPackagesDlg
 CCAppPopupClass CAppPopup allows applications to be launched based on standard registered types
 CCAppRegistryClass CAppRegistry defines the registry of application information for automated application link-outs
 CCAppTaskCAppTask - default implementation of IAppTask, use it as a base class for custom tasks
 CCAppTaskServiceCAppTaskService - Application Task Service
 CCAppTaskServiceEventCAppTaskServiceEvent
 CCAppTaskServiceExceptionCAppTaskServiceException
 CCAppTaskServiceGuiUpdateEvent
 CCArchiveCArchive - base class for file- or memory-based archives
 CCArchiveEntryInfoCArchiveEntryInfo class
 CCArchiveExceptionCArchiveException
 CCArchiveFileCArchiveFile – file-based archive
 CCArchiveMemoryCArchiveMemory – memory-based archive
 CCArchiveZipCArchiveZip – implementation of IArchive interface for ZIP-archives
 CCArg_Boolean
 CCArg_DataSize
 CCArg_DateTime
 CCArg_Dir
 CCArg_Double
 CCArg_ExcludedValue
 CCArg_Flag
 CCArg_InputFile
 CCArg_Int8
 CCArg_Integer
 CCArg_IOFile
 CCArg_Ios
 CCArg_NoValue
 CCArg_OutputFile
 CCArg_String
 CCArgAllowCArgAllow
 CCArgAllow_DoublesCArgAllow_Doubles
 CCArgAllow_Int8sCArgAllow_Int8s
 CCArgAllow_IntegersCArgAllow_Integers
 CCArgAllow_RegexpCArgAllow_Regexp
 CCArgAllow_StringCArgAllow_String
 CCArgAllow_StringsCArgAllow_Strings
 CCArgAllow_SymbolsCArgAllow_Symbols
 CCArgAllowGeneticCodeIntegerAuxiliary class to validate the genetic code input
 CCArgAllowIntegerSet
 CCArgAllowStringSet
 CCArgAllowValuesBetweenClass to constrain the values of an argument to those in between the values specified in the constructor
 CCArgAllowValuesGreaterThanOrEqualClass to constrain the values of an argument to those greater than or equal to the value specified in the constructor
 CCArgAllowValuesLessThanOrEqualClass to constrain the values of an argument to those less than or equal to the value specified in the constructor
 CCArgArray
 CCArgC
 CCArgDescCArgDesc
 CCArgDesc_agp_validate
 CCArgDesc_Alias
 CCArgDesc_Flag
 CCArgDesc_Key
 CCArgDesc_KeyDef
 CCArgDesc_KeyOpt
 CCArgDesc_NameOnly
 CCArgDesc_Opening
 CCArgDesc_Pos
 CCArgDesc_PosDef
 CCArgDesc_PosOpt
 CCArgDescDefault
 CCArgDescMandatory
 CCArgDescOptional
 CCArgDescriptionsCArgDescriptions
 CCArgDescSynopsis
 CCArgErrorHandlerCArgErrorHandler
 CCArgExceptionCArgException
 CCArgHelpExceptionCArgHelpException
 CCArgsCArgs
 CCArgumentsExceptionCArgumentsException
 CCArgValueCArgValue
 CCArrayHolderHelper class for holding and correct destruction of static array copy
 CCArrayStringFixed-buffer string type
 CCArticleIdCArticleId
 CCArticleId_BaseArticle Ids can be many ids for an article
 CCArticleIdSetCArticleIdSet
 CCArticleIdSet_BaseCArticleIdSet_Base
 CCAsapratio_contributionCAsapratio_contribution
 CCAsapratio_contribution_BaseCAsapratio_contribution_Base
 CCAsapratio_lc_heavypeakCAsapratio_lc_heavypeak
 CCAsapratio_lc_heavypeak_BaseCAsapratio_lc_heavypeak_Base
 CCAsapratio_lc_lightpeakCAsapratio_lc_lightpeak
 CCAsapratio_lc_lightpeak_BaseCAsapratio_lc_lightpeak_Base
 CCAsapratio_peptide_dataCAsapratio_peptide_data
 CCAsapratio_peptide_data_BaseCAsapratio_peptide_data_Base
 CCAsapratio_resultCAsapratio_result
 CCAsapratio_result_BaseASAPRatio quantitation results for search hit
 CCAsapratio_summaryCAsapratio_summary
 CCAsapratio_summary_BaseQuantitation
 CCAsapratio_timestampCAsapratio_timestamp
 CCAsapratio_timestamp_BaseCAsapratio_timestamp_Base
 CCAsBodyDiagFactory
 CCAscii85
 CCAsn2Asn
 CCAsn2AsnThread
 CCAsn2FastaApp
 CCAsn2FlatApp
 CCAsn2GffApp
 CCAsnBinTraits class for binary ASN.1
 CCAsnBinaryDefs
 CCAsnBinCompressedTraits class for compressed binary ASN.1 streams
 CCAsnBioContext
 CCAsnBioContextContainer
 CCAsnBlockEndItem
 CCAsnConverter
 CCAsnElementBlockCollapsed
 CCAsnElementBlockStart
 CCAsnElementItem
 CCAsnElementPrimitive
 CCAsnExporter
 CCAsnExporterFactory
 CCAsnExportJobCAsnExportJob
 CCAsnExportPage
 CCAsnExportParams
 CCASNFormatLoadManagerCASNFormatLoadManager
 CCAsnHeaderItem
 CCAsnHeaderPrimitive
 CCAsnObjectLoaderCAsnObjectLoader
 CCAsnOctetStringBlock
 CCAsnRetrieveJob
 CCAsnSizer
 CCAsnStyles
 CCAsnvalApp
 CCAsnViewContext
 CCAsnWriteNode
 CCAspNAsp-N, Nterm of D
 CCAspNDEEMSEnzymes_aspn_de Asp-N that cuts at D and E
 CCAssayCAssay
 CCAssay_BaseCAssay_Base
 CCAssemblyCAssembly
 CCAssembly_BaseA collection of genome sequence records (curated gene regions (NG's), contigs (NWNT's) and chromosomes (NC/AC's) produced by a genome sequence project
 CCAssemblyInfo
 CCAssemblyListPanel
 CCAssemblyLoadWizard
 CCAssemblyObjectLoaderCAssemblyObjectLoader
 CCAssemblyParserExceptionSeq-loc and seq-align mapper exceptions
 CCAssemblyProgramPanel
 CCAssemblySelPanel
 CCAssemblyTermCompleter
 CCAssemblyTrackFieldManager
 CCAssemblyTrackingListPanel
 CCAssemblyTrackingPanel
 CCAssignColumnValueDlg
 CCAssignFeatureId
 CCAsyncCallClass for GUI asyncronous execition
 CCAsyncCallDlg
 CCAsyncDiagHandler
 CCAsyncDiagThread
 CCAsyncMemberCall
 CCAsyncObjConvert
 CCAsyncObjConvert2
 CCAtomCAtom
 CCAtom_BaseAtoms in residue graphs are defined by elemental symbols and names
 CCAtom_idCAtom_id
 CCAtom_id_BaseCAtom_id_Base
 CCAtom_pntrCAtom_pntr
 CCAtom_pntr_BaseAtoms, residues and molecules within the current biostruc are referenced by hierarchical pointers
 CCAtom_pntr_setCAtom_pntr_set
 CCAtom_pntr_set_BaseCAtom_pntr_set_Base
 CCAtom_pntrsCAtom_pntrs
 CCAtom_pntrs_BaseCAtom_pntrs_Base
 CCAtomic_coordinatesCAtomic_coordinates
 CCAtomic_coordinates_BaseLiteral atomic coordinate values give location, occupancy and order parameters, and a pointer to a specific atom defined in the biostruc graph
 CCAtomic_occupanciesCAtomic_occupancies
 CCAtomic_occupancies_BaseCAtomic_occupancies_Base
 CCAtomic_temperature_factorsCAtomic_temperature_factors
 CCAtomic_temperature_factors_BaseCAtomic_temperature_factors_Base
 CCAtomicCounterCAtomicCounter
 CCAtomicCounter_WithAutoInitCAtomicCounter_WithAutoInit
 CCAttachAnnot_EditCommand
 CCAttachedHandles
 CCAttachEntry_EditCommand
 CCAttribFloatMenuItemClass CAttribFloatMenuItem
 CCAttribIntMenuItemClass CAttribIntMenuItem
 CCAttribMenuClass CAttribMenuItem
 CCAttribMenuInstanceSimple singleton class to allow multiple classes to share the same menu
 CCAttribMenuItemClass CAttribMenuItem
 CCAttribStringsMenuItemClass CAttribStringsMenuItem
 CCAttribTableColumnIdPanel
 CCAttribTableDelimitersPanel
 CCAttrListParser
 CCAttrRangeCollection
 CCAuth_list.hpp User-defined methods of the data storage class
 CCAuth_list_BaseAuthorship Group
 CCAuthor
 CCAuthor_BaseCAuthor_Base
 CCAuthor_fix_actionCAuthor_fix_action
 CCAuthor_fix_action_BaseCAuthor_fix_action_Base
 CCAuthorAffiliationPanel
 CCAuthorEditor
 CCAuthorizedAccessPanel
 CCAuthorNamesPanel
 CCAutoAddDesc
 CCAutoColValidatoraccession
 CCAutoColValidatorboolean
 CCAutoColValidatorcountry
 CCAutoColValidatordate
 CCAutoColValidatorgenome
 CCAutoColValidatorhaplotype
 CCAutoColValidatorisolation_source
 CCAutoColValidatorlineage
 CCAutoColValidatororgmod
 CCAutoColValidatororgname
 CCAutoColValidatororigin
 CCAutoColValidatorseqid
 CCAutoColValidatorserotype
 CCAutoColValidatorstrain
 CCAutoColValidatorsubsource
 CCAutoColValidatorsubtype
 CCAutoColValidatortaxid
 CCAutoCompleteComboCAutoCompleteComboBox
 CCAutoCompleteTextCtrlCAutoCompleteComboBox
 CCAutoDef
 CCAutodef_actionCAutodef_action
 CCAutodef_action_BaseCAutodef_action_Base
 CCAutoDefAvailableModifier
 CCAutoDefDemo
 CCAutodefDlg
 CCAutoDefExonListClause
 CCAutoDefFakePromoterClause
 CCAutodefFeatClausePanel
 CCAutoDefFeatureClause
 CCAutoDefFeatureClause_Base
 CCAutoDefGeneClusterClause
 CCAutoDefIntergenicSpacerClause
 CCAutodefJobCAutodefJob
 CCAutoDefMiscCommentClause
 CCAutoDefMobileElementClause
 CCAutoDefModifierCombo
 CCAutoDefNcRNAClause
 CCAutodefOptFeatPanel
 CCAutodefOrgPanel
 CCAutodefParamsPanel
 CCAutoDefParsedClause
 CCAutoDefParsedIntergenicSpacerClause
 CCAutoDefParsedRegionClause
 CCAutoDefParsedtRNAClause
 CCAutoDefPromoterClause
 CCAutoDefSatelliteClause
 CCAutoDefSourceDescription
 CCAutoDefSourceGroup
 CCAutoDefSourceModifierInfo
 CCAutodefToolManagerCAutodefToolManager
 CCAutoDefUnknownGeneList
 CCAutoDiscClass
 CCAutoEnvironmentVariableCAutoEnvironmentVariable
 CCAutofix_actionCAutofix_action
 CCAutofix_action_BaseCAutofix_action_Base
 CCAutogeneratedCleanupThis file was generated by application DATATOOL
 CCAutogeneratedExtendedCleanupThis file was generated by application DATATOOL
 CCAutoInitDescCSourceModParser
 CCAutoInitPtrCAutoInitPtr<>::
 CCAutoInitPtr_BaseCAutoInitPtr_Base::
 CCAutoInitRefCAutoInitRef<>::
 CCAutomaticGenCodeSingletonInitializes and uninitializes the genetic code singleton as if it was an automatic variable (to facilitate use in our unit tests and in the CBlastOptions object)
 CCAutomationException
 CCAutomationObject
 CCAutomationProc
 CCAutoNcbiConfigFileAuxiliary class to write temporary NCBI configuration files in the local directory for the purpose of testing the CBlastScopeSource configuration class via this file (and override any other installed NCBI configuration files)
 CCAutoOutputFileResetAuxiliary class to store the name of an output file, which is reset every time its GetStream method is invoked
 CCAutoPointerTypeInfo
 CCAutoPtrTypeInfo
 CCAutoRegistrarAuxiliary class to register the BLAST database data loader of choice (information provided in the constructor) and deactivate it on object destruction
 CCAutoSaverEventCWorkspaceAutoSaver
 CCAutoTrans
 CCAuxiliaryManagedWrapperGeneratorToolDummyImpl
 CCAVApp
 CCAxisAreaClass CAxisArea
 CCAxisRendererClass CAxisRenderer
 CCBackgroundHost
 CCBadResiduesException
 CCBam2GraphApp
 CCBam2Seq_graphCBam2Seq_graph
 CCBAM_DataLoaderCF
 CCBamAlignIterator
 CCBAMBlobId
 CCBamCoverageGraphPanel
 CCBAMDataLoader
 CCBAMDataLoader_Impl
 CCBamDb
 CCBamDSEvtHandlerCBamDSEvtHandler - wxEvtHandler-derived adapter for Bam data source
 CCBamException
 CCBamFileAlign
 CCBamFileInfo
 CCBamIndexingPanel
 CCBamLoadingJobCBamLoadingJob
 CCBamLoadOptionPanelCBamLoadOptionPanel
 CCBamMgr
 CCBamRcFormatter
 CCBamRef
 CCBamRefSeqChunkInfo
 CCBamRefSeqInfo
 CCBamRefSeqIterator
 CCBamRefSequencesPanel
 CCBamRefTraits
 CCBamRefTraits< AlignAccessAlignmentEnumerator >
 CCBamRefTraits< AlignAccessRefSeqEnumerator >
 CCBamRefTraits< const AlignAccessDB >
 CCBamRefTraits< const AlignAccessMgr >
 CCBamRefTraits< const BAMAlignment >
 CCBamRefTraits< const BAMFile >
 CCBamString
 CCBamUIDataSourceCBamUIDataSource
 CCBamUIDataSourceTypeCBamUIDataSourceType
 CCBamUILoadManager
 CCBandAligner
 CCBase64BinaryDataType
 CCBaseAddressCBaseAddress
 CCBaseAddress_Base======================== PROPERTIES ===================================== Possible Types include StringPropertyType (text with no subelements), GenericPropertyType (any content), or something more specific
 CCBaseClusterer
 CCBaseCountItem
 CCBaseNRCriteria
 CCBaseTextOStream
 CCBaseURLCBaseURL
 CCBaseURL_BaseURL value from dbSNP_main.BaseURL links table
 CCBasicFastaWrapperConcrete implementations of the CFastaIOWrapper virtual class
 CCBasicRelation
 CCBatchFeatJobCBatchFeatJob: a job class for loading annotated features from a given a set of sequences within the corresponding visible ranges
 CCBatchJobResultCBatchJobResult – the data structure holding the seqgraphic job results for a batch job processing
 CCBatchSizeMixerClass to mix batch size for BLAST runs
 CCBatchSubmitAttrParser
 CCBBox
 CCBDB_BLobDemo1BLob Demo application
 CCBDB_BlobDeMuxVolume split BLOB demultiplexer
 CCBDB_BlobDeMux_RoundRobinBLOB demultiplexer implements round-robin volume rotation
 CCBDB_BlobDeMuxPersistentSplit demux which can save and load state into a file Stateful (persistent) class
 CCBDB_BlobDeMuxSplitBase class for page-split demultiplexers
 CCBDB_BlobDictionaryTemplatized candidate for dictionaries This template defines the basic interface that must be supported by all dictionaries
 CCBDB_BlobDictionary< Int4 >
 CCBDB_BlobDictionary< Uint4 >Pass-through for Uint4 key types
 CCBDB_BlobDictStore
 CCBDB_BLobFileBerkeley DB BLOB File class
 CCBDB_BlobMetaContainerContainer of BLOB attributes Encapsulates: BLOB maps of several BLOBs (offsets there point in super BLOB) Super BLOB location table (offsets and sizes in external file)
 CCBDB_BlobReaderWriterStream style BDB BLOB reader
 CCBDB_BlobSplitStoreBLOB storage based on single unsigned integer key Supports BLOB volumes and different base page size files in the volume to guarantee the best fit
 CCBDB_BlobStoreDictPersistent storage for demux information
 CCBDB_BLobStreamBerkeley DB BLOB File stream
 CCBDB_BufferManagerBDB Data Field Buffer manager class
 CCBDB_BvPropertyStore
 CCBDB_BvSplitDictStore
 CCBDB_BvStoreBasic template class for bitvector storage
 CCBDB_CacheBDB cache implementation
 CCBDB_CacheHolderClass container for BDB cache objects
 CCBDB_CacheIReader
 CCBDB_CacheIWriter
 CCBDB_CacheReaderCFClass factory for BDB implementation of ICache
 CCBDB_CacheVerifyAppBDB cache verify application
 CCBDB_CheckPointThreadTransaction checkpoint / memptrickle thread
 CCBDB_ConditionHandleFile cursor condition handle
 CCBDB_ConfigStructureParser
 CCBDB_CursorGuardBDB Cursor guard
 CCBDB_DumpScannerQuery scanner
 CCBDB_EnvBDB environment object a collection including support for some or all of caching, locking, logging and transaction subsystems
 CCBDB_ErrnoExceptionBDB errno exception class
 CCBDB_ExceptionBase BDB exception class
 CCBDB_ExtBlobMapBLOB map, encapsulates collection of BLOB ids and BLOB locations
 CCBDB_ExtBlobStoreExternal BLOB store
 CCBDB_FC_ConditionInternal class used by CBDB_FileCursor to represent search condition criteries
 CCBDB_FieldBase class for constructing BDB fields
 CCBDB_FieldChar
 CCBDB_FieldDoubleDouble precision floating point field type
 CCBDB_FieldFactoryClass factory for BDB field types
 CCBDB_FieldFixedByteStringFixed length bytestring
 CCBDB_FieldFloatFloat field type
 CCBDB_FieldInt1Int1 field type
 CCBDB_FieldInt2Int2 field type
 CCBDB_FieldInt4Int4 field type
 CCBDB_FieldInt8Int8 field type
 CCBDB_FieldInterfacesInterface definition class for field construction
 CCBDB_FieldLStringLength prefised string field type
 CCBDB_FieldSimpleTemplate class for building simple scalar data fields
 CCBDB_FieldSimpleFloatTemplate class for building simple scalar floating point compatible fields
 CCBDB_FieldSimpleIntTemplate class for building simple scalar integer compatible data fields
 CCBDB_FieldStringString field type designed to work with C-strings (ASCIIZ)
 CCBDB_FieldStringBaseString field type
 CCBDB_FieldStringCaseCase-insensitive (but case preserving) string field type
 CCBDB_FieldUCharChar field type
 CCBDB_FieldUint1Uint1 field type
 CCBDB_FieldUint2Uint2 field type
 CCBDB_FieldUint4Uint4 field type
 CCBDB_FieldUint8Uint8 field type
 CCBDB_FileBerkeley DB file class
 CCBDB_FileCursorBerkeley DB file cursor class
 CCBDB_FileDumperUtility class to convert DBD files into text files
 CCBDB_FileDumperAppBDB file dumper application
 CCBDB_FileScannerScans the BDB file, searches the matching records
 CCBDB_IdBlobFileVariant of BLOB storage for integer key database
 CCBDB_IdFileBerkeley DB file class optimized to work with tables having int as the primary key
 CCBDB_LibExceptionBDB library exception
 CCBDB_LobFileBerkeley DB Large Object File class
 CCBDB_MatrixBvStoreMatrix BV store
 CCBDB_MergeBlobWalkerGeneric iterator to traverse any CBDB_BLobFile for volume merge BF - any CBDB_BLobFile derived class
 CCBDB_MergeBlobWalkerAsyncGeneric iterator to traverse any CBDB_BLobFile for volume merge BF - any CBDB_BLobFile derived class This implementation supports asyncronous processing
 CCBDB_MergeStoreMerge store saves result to BLOB store
 CCBDB_MergeStoreAsyncMerge store saves result to BLOB store
 CCBDB_MergeTest
 CCBDB_MultiRowBufferMultirow buffer for reading many rows in one call
 CCBDB_PersistentSplitStore
 CCBDB_PhoneBookDemo1
 CCBDB_PhoneBookDemo2
 CCBDB_PhoneBookDemo3
 CCBDB_PropertyDictionary
 CCBDB_QueryQuery class incapsulates query tree (query clause) and implements set of utility methods to construct query trees
 CCBDB_QueryNodeQuery node class
 CCBDB_QueryParserEnvironmentClass passed to Lex/Bison (yylex/yyparse) functions
 CCBDB_RangeMapRange map class, stores unsigned integer range mappings like 10 to 15 maps into 100 to 115
 CCBDB_RawFileRaw file class wraps up basic Berkeley DB operations
 CCBDB_SplitCursor
 CCBDB_SplitTest
 CCBDB_StrErrAdaptAuxiliary exception class to wrap up Berkeley DB strerror function
 CCBDB_TransactionBDB transaction object
 CCBDB_TypeMapperInternal template used for compiler based type mapping (C++ templates specialization emplyed here)
 CCBDB_TypeMapper< int >
 CCBDB_TypeMapper< string >
 CCBDB_VolumesVolumes management
 CCBDB_VolumesExceptionExceptions specific to volumes management
 CCBDB_VolumesTransactionTransaction class for volumes management
 CCBDBEnvKeeperApp
 CCBDBEnvKeeperConnectionFactory
 CCBDBEnvKeeperConnectionHandlerActual event (command) responder (session state machine)
 CCBDBEnvKeeperServerMain server class
 CCBedFeatureRecordEncapsulation of the BED feature record
 CCBedLoadManagerCBedLoadManager
 CCBedLoadParams
 CCBedObjectLoaderCBedObjectLoader
 CCBedParamsPanel
 CCBedReaderCReaderBase implementation that reads BED data files, either a single object or all objects found
 CCBedTrackRecordEncapsulation of a track line in the BED file format
 CCBedWriterCWriterBase implementation that will render given Genbank objects in the BED file format (http://http://genome.ucsc.edu/FAQ/FAQformat#format1)
 CCBeginDragOutsideEvent
 CCBeginInfoClass holding information about root of non-modifiable object hierarchy Do not use it directly
 CCBestChoiceTrackerTracks the best score (lowest value)
 CCBestFeatFinder
 CCBestI
 CCBestIntron
 CCBigIntDataType
 CCBigIntEnumDataType
 CCBinaryKmerCountsK-mer counts implemented as bit vectors
 CCBinaryListBuilderBinary GI or TI List Builder
 CCBinomialOrgNameCBinomialOrgName
 CCBinomialOrgName_BaseCBinomialOrgName_Base
 CCBinsDS
 CCBinsDSType
 CCBinsGlyph
 CCBinsJobCBinsJob
 CCBinsTrack
 CCBinsTrackFactory
 CCBiomol_descrCBiomol_descr
 CCBiomol_descr_BaseA biomolecule description refers to the chemical structure of a molecule or component substructures
 CCBioObjectId
 CCBiosampleChkApp
 CCBiosampleFieldDiff
 CCBioseq
 CCBioseq_ADJACENT_PSEUDOGENES
 CCBioseq_BAD_LOCUS_TAG_FORMAT
 CCBioseq_Base*** Sequence ******************************** *
 CCBioseq_Base_Info
 CCBioseq_CDS_TRNA_OVERLAP
 CCBioseq_CICBioseq_CI
 CCBioseq_CONTAINED_CDS
 CCBioseq_COUNT_PROTEINS
 CCBioseq_COUNT_RRNAS
 CCBioseq_COUNT_TRNAS
 CCBioseq_DISC_10_PERCENTN
 CCBioseq_DISC_BACTERIA_SHOULD_NOT_HAVE_MRNA
 CCBioseq_DISC_BACTERIAL_PARTIAL_NONEXTENDABLE_EXCEPTION
 CCBioseq_DISC_BACTERIAL_PARTIAL_NONEXTENDABLE_PROBLEMS
 CCBioseq_DISC_BAD_BACTERIAL_GENE_NAME
 CCBioseq_DISC_BAD_BGPIPE_QUALS
 CCBioseq_DISC_BAD_GENE_STRAND
 CCBioseq_DISC_CDS_HAS_NEW_EXCEPTION
 CCBioseq_DISC_CDS_PRODUCT_FIND
 CCBioseq_DISC_CDS_WITHOUT_MRNA
 CCBioseq_DISC_CHECK_RNA_PRODUCTS_AND_COMMENTS
 CCBioseq_DISC_COUNT_NUCLEOTIDES
 CCBioseq_DISC_DUP_DEFLINE
 CCBioseq_DISC_DUP_GENPRODSET_TRANSCRIPT_ID
 CCBioseq_DISC_EXON_INTRON_CONFLICT
 CCBioseq_DISC_FEAT_OVERLAP_SRCFEAT
 CCBioseq_DISC_FEATURE_COUNT
 CCBioseq_DISC_FEATURE_COUNT_oncaller
 CCBioseq_DISC_FEATURE_LIST
 CCBioseq_DISC_FEATURE_MOLTYPE_MISMATCH
 CCBioseq_DISC_GAPS
 CCBioseq_DISC_GENE_PARTIAL_CONFLICT
 CCBioseq_DISC_INCONSISTENT_MOLINFO_TECH
 CCBioseq_DISC_INTERNAL_TRANSCRIBED_SPACER_RRNA
 CCBioseq_DISC_LONG_NO_ANNOTATION
 CCBioseq_DISC_MICROSATELLITE_REPEAT_TYPE
 CCBioseq_DISC_MISSING_DEFLINES
 CCBioseq_DISC_MITOCHONDRION_REQUIRED
 CCBioseq_DISC_mRNA_ON_WRONG_SEQUENCE_TYPE
 CCBioseq_DISC_PARTIAL_PROBLEMS
 CCBioseq_DISC_PERCENT_N
 CCBioseq_DISC_POSSIBLE_LINKER
 CCBioseq_DISC_PROTEIN_NAMES
 CCBioseq_DISC_PROTEIN_NAMES_global
 CCBioseq_DISC_QUALITY_SCORES
 CCBioseq_DISC_RBS_WITHOUT_GENE
 CCBioseq_DISC_RETROVIRIDAE_DNA
 CCBioseq_DISC_SHORT_INTRON
 CCBioseq_DISC_SHORT_RRNA
 CCBioseq_DISC_SUSPECT_MISC_FEATURES
 CCBioseq_DISC_SUSPECT_RRNA_PRODUCTS
 CCBioseq_DISC_SUSPICIOUS_NOTE_TEXT
 CCBioseq_DUP_GENPRODSET_PROTEIN
 CCBioseq_DUPLICATE_GENE_LOCUS
 CCBioseq_DUPLICATE_LOCUS_TAGS
 CCBioseq_DUPLICATE_LOCUS_TAGS_global
 CCBioseq_EC_NUMBER_NOTE
 CCBioseq_EC_NUMBER_ON_UNKNOWN_PROTEIN
 CCBioseq_EditHandleCBioseq_EditHandle
 CCBioseq_EUKARYOTE_SHOULD_HAVE_MRNA
 CCBioseq_EXTRA_GENES
 CCBioseq_FEATURE_LOCATION_CONFLICT
 CCBioseq_FIND_BADLEN_TRNAS
 CCBioseq_FIND_DUP_RRNAS
 CCBioseq_FIND_DUP_TRNAS
 CCBioseq_FIND_OVERLAPPED_GENES
 CCBioseq_FIND_STRAND_TRNAS
 CCBioseq_GENE_PRODUCT_CONFLICT
 CCBioseq_HandleCBioseq_Handle
 CCBioseq_INCONSISTENT_LOCUS_TAG_PREFIX
 CCBioseq_INCONSISTENT_PROTEIN_ID
 CCBioseq_INCONSISTENT_SOURCE_DEFLINE
 CCBioseq_Info
 CCBioseq_JOINED_FEATURES
 CCBioseq_MISSING_GENES
 CCBioseq_missing_genes_oncaller
 CCBioseq_missing_genes_regular
 CCBioseq_MISSING_GENPRODSET_PROTEIN
 CCBioseq_MISSING_GENPRODSET_TRANSCRIPT_ID
 CCBioseq_MISSING_LOCUS_TAGS
 CCBioseq_MISSING_PROTEIN_ID
 CCBioseq_MOLTYPE_NOT_MRNA
 CCBioseq_MRNA_SHOULD_HAVE_PROTEIN_TRANSCRIPT_IDS
 CCBioseq_MULTIPLE_CDS_ON_MRNA
 CCBioseq_N_RUNS
 CCBioseq_N_RUNS_14
 CCBioseq_NO_ANNOTATION
 CCBioseq_NO_PRODUCT_STRING
 CCBioseq_NON_GENE_LOCUS_TAG
 CCBioseq_NON_RETROVIRIDAE_PROVIRAL
 CCBioseq_NOTE_NO_TRANSL
 CCBioseq_on_Aa
 CCBioseq_on_bad_gene_name
 CCBioseq_on_base
 CCBioseq_on_cd_feat
 CCBioseq_on_feat_cnt
 CCBioseq_on_locus_tags
 CCBioseq_on_mRNA
 CCBioseq_on_mrna
 CCBioseq_on_SUSPECT_RULE
 CCBioseq_on_tax_def
 CCBioseq_ONCALLER_GENE_MISSING
 CCBioseq_ONCALLER_HAS_STANDARD_NAME
 CCBioseq_ONCALLER_HIV_RNA_INCONSISTENT
 CCBioseq_ONCALLER_ORDERED_LOCATION
 CCBioseq_ONCALLER_SUPERFLUOUS_GENE
 CCBioseq_OVERLAPPING_CDS
 CCBioseq_OVERLAPPING_GENES
 CCBioseq_PARTIAL_CDS_COMPLETE_SEQUENCE
 CCBioseq_PSEUDO_MISMATCH
 CCBioseq_RNA_CDS_OVERLAP
 CCBioseq_RNA_NO_PRODUCT
 CCBioseq_RNA_PROVIRAL
 CCBioseq_RRNA_NAME_CONFLICTS
 CCBioseq_ScopeInfo
 CCBioseq_SEQ_ID_PHRASES
 CCBioseq_set
 CCBioseq_set_Base*** Sequence Collections ******************************** * just a collection
 CCBioseq_set_EditHandleCBioseq_set_EditHandle
 CCBioseq_set_HandleCBioseq_set_Handle
 CCBioseq_set_Info
 CCBioseq_set_ScopeInfo
 CCBioseq_setHandler
 CCBioseq_SHORT_CONTIG
 CCBioseq_SHORT_PROT_SEQUENCES
 CCBioseq_SHORT_SEQUENCES
 CCBioseq_SHORT_SEQUENCES_200
 CCBioseq_SHOW_HYPOTHETICAL_CDS_HAVING_GENE_NAME
 CCBioseq_SHOW_TRANSL_EXCEPT
 CCBioseq_SplitInfo
 CCBioseq_SUSPECT_PHRASES
 CCBioseq_TECHNIQUE_NOT_TSA
 CCBioseq_TEST_BAD_GENE_NAME
 CCBioseq_TEST_BAD_MRNA_QUAL
 CCBioseq_TEST_CDS_HAS_CDD_XREF
 CCBioseq_TEST_COUNT_UNVERIFIED
 CCBioseq_TEST_DUP_GENES_OPPOSITE_STRANDS
 CCBioseq_TEST_EXON_ON_MRNA
 CCBioseq_TEST_LOW_QUALITY_REGION
 CCBioseq_TEST_MRNA_OVERLAPPING_PSEUDO_GENE
 CCBioseq_TEST_MRNA_SEQUENCE_MINUS_STRAND_FEATURES
 CCBioseq_test_on_all_annot
 CCBioseq_test_on_bac_partial
 CCBioseq_test_on_cd_4_transl
 CCBioseq_test_on_genprod_set
 CCBioseq_test_on_missing_genes
 CCBioseq_test_on_molinfo
 CCBioseq_test_on_prot
 CCBioseq_test_on_protfeat
 CCBioseq_test_on_rna
 CCBioseq_test_on_rrna
 CCBioseq_test_on_suspect_phrase
 CCBioseq_TEST_ORGANELLE_NOT_GENOMIC
 CCBioseq_TEST_ORGANELLE_PRODUCTS
 CCBioseq_TEST_OVERLAPPING_RRNAS
 CCBioseq_TEST_SHORT_LNCRNA
 CCBioseq_TEST_TAXNAME_NOT_IN_DEFLINE
 CCBioseq_TEST_TERMINAL_NS
 CCBioseq_TEST_UNNECESSARY_VIRUS_GENE
 CCBioseq_TEST_UNUSUAL_MISC_RNA
 CCBioseq_TEST_UNUSUAL_NT
 CCBioseq_TEST_UNWANTED_SPACER
 CCBioseq_TRANSL_NO_NOTE
 CCBioseq_TRANSL_TOO_LONG
 CCBioseq_ZERO_BASECOUNT
 CCBioseqContext
 CCBioseqEditor
 CCBioseqEditorFactory
 CCBioseqGaps_CIThis iterates over the runs of Ns of each sequence
 CCBioseqHandler
 CCBioseqSeqInfoSrcImplementation of the IBlastSeqInfoSrc interface to encapsulate retrieval of sequence identifiers and lengths from a CBioseq/CBioseq_set object
 CCBioseqSet_DISC_NONWGS_SETS_PRESENT
 CCBioseqSet_DISC_SEGSETS_PRESENT
 CCBioseqSet_on_class
 CCBioseqSet_TEST_SMALL_GENOME_SET_PROBLEM
 CCBioseqSet_TEST_UNWANTED_SET_WRAPPER
 CCBioseqSetTestAndRepData
 CCBioseqTestAndRepData
 CCBioseqUpdater
 CCBioSource
 CCBioSource_Base********************************************************************
 CCBioSourceAutoComplete
 CCBioSourceKind
 CCBioSourcePanel
 CCBiostruc
 CCBiostruc_alignCBiostruc_align
 CCBiostruc_align_BaseCBiostruc_align_Base
 CCBiostruc_align_seqCBiostruc_align_seq
 CCBiostruc_align_seq_BaseDisplay seq structure align only
 CCBiostruc_annot_setCBiostruc_annot_set
 CCBiostruc_annot_set_BaseA biostruc annotation set is a means to collect ASN.1 data for biostruc features into one file
 CCBiostruc_BaseA structure report or "biostruc" describes the components of a biomolecular assembly in terms of their names and descriptions, and a chemical graph giving atomic formula, connectivity and chirality
 CCBiostruc_descrCBiostruc_descr
 CCBiostruc_descr_BaseThe description of a biostruc refers to both the reported chemical and spatial structure of a biomolecular assembly
 CCBiostruc_featureCBiostruc_feature
 CCBiostruc_feature_BaseAn explicitly specified type in Biostruc-feature allows for efficient extraction and indexing of feature sets of a specific type
 CCBiostruc_feature_idCBiostruc_feature_id
 CCBiostruc_feature_id_BaseCBiostruc_feature_id_Base
 CCBiostruc_feature_setCBiostruc_feature_set
 CCBiostruc_feature_set_BaseNamed model features refer to sets of residues or atoms, or a region in the model space
 CCBiostruc_feature_set_descrCBiostruc_feature_set_descr
 CCBiostruc_feature_set_descr_BaseCBiostruc_feature_set_descr_Base
 CCBiostruc_feature_set_idCBiostruc_feature_set_id
 CCBiostruc_feature_set_id_BaseCBiostruc_feature_set_id_Base
 CCBiostruc_graphCBiostruc_graph
 CCBiostruc_graph_BaseA biostruc graph contains the complete chemical graph of the biomolecular assembly
 CCBiostruc_graph_pntrCBiostruc_graph_pntr
 CCBiostruc_graph_pntr_BaseCBiostruc_graph_pntr_Base
 CCBiostruc_historyCBiostruc_history
 CCBiostruc_history_BaseThe history of a biostruc indicates it's origin and it's update history within MMDB, the NCBI-maintained molecular structure database
 CCBiostruc_idCBiostruc_id
 CCBiostruc_id_BaseA Biostruc-id is a collection identifiers for the molecular assembly
 CCBiostruc_modelCBiostruc_model
 CCBiostruc_model_BaseA structural model maps chemical components into a measured three- dimensional space
 CCBiostruc_molecule_pntrCBiostruc_molecule_pntr
 CCBiostruc_molecule_pntr_BaseAtom, residue or molecule motifs describe a substructure defined by a set of nodes from the chemical graph
 CCBiostruc_replaceCBiostruc_replace
 CCBiostruc_replace_BaseCBiostruc_replace_Base
 CCBiostruc_residue_graph_setCBiostruc_residue_graph_set
 CCBiostruc_residue_graph_set_BaseA biostruc residue graph set is a collection of residue graphs
 CCBiostruc_residue_graph_set_pntrCBiostruc_residue_graph_set_pntr
 CCBiostruc_residue_graph_set_pntr_BaseCBiostruc_residue_graph_set_pntr_Base
 CCBiostruc_scriptCBiostruc_script
 CCBiostruc_script_BaseWhen a Biostruc-Feature with a Biostruc-script is initiated, it should play the specified steps one at a time, setting the feature-do list as the active display
 CCBiostruc_script_stepCBiostruc_script_step
 CCBiostruc_script_step_BaseCBiostruc_script_step_Base
 CCBiostruc_seqCBiostruc_seq
 CCBiostruc_seq_BaseDisplay structure seq added by yanli
 CCBiostruc_seqsCBiostruc_seqs
 CCBiostruc_seqs_aligns_cddCBiostruc_seqs_aligns_cdd
 CCBiostruc_seqs_aligns_cdd_BaseCBiostruc_seqs_aligns_cdd_Base
 CCBiostruc_seqs_BaseDisplay blast alignment along with neighbor's structure added by yanli
 CCBiostruc_setCBiostruc_set
 CCBiostruc_set_BaseA biostruc set is a means to collect ASN.1 data for many biostrucs in one file, as convenient for application programs
 CCBiostruc_sourceCBiostruc_source
 CCBiostruc_source_BaseThe origin of a biostruc is a reference to another database
 CCBioTreeBasic tree structure for biological applications
 CCBioTreeAttrReaderParser-reader for BKBTA - biotree attributes format
 CCBioTreeContainer
 CCBioTreeContainer_BaseCBioTreeContainer_Base
 CCBioTreeContainerHandler******************************************************************* Moved from plugins/algo/init *******************************************************************
 CCBioTreeConvert2ContainerFuncVisitor functor to convert dynamic tree nodes to ASN.1 BioTree container
 CCBioTreeEmptyNodeDataBasic node data structure used by BioTreeBaseNode
 CCBioTreeFeatureDictionaryFeature dictionary
 CCBioTreeFeatureListFeatures storage for the bio tree node
 CCBioTreeFeaturePairTree node feature pair (id to string)
 CCBioTreeForestSet of BioTree objects managed as a single forest
 CCBioTreeSelection
 CCBitStringDataType
 CCBitStringDataValue
 CCBitStringFunctions
 CCBitStringTypeStrings
 CCBl2SeqRuns the BLAST algorithm between 2 sequences
 CCBlast4_alignments_for_queryCBlast4_alignments_for_query
 CCBlast4_alignments_for_query_BaseAlignments for one query, compiled from the raw SeqAlign results
 CCBlast4_archiveCBlast4_archive
 CCBlast4_archive_BaseAn archive format for results
 CCBlast4_common_optionsCBlast4_common_options
 CCBlast4_common_options_BaseCBlast4_common_options_Base
 CCBlast4_common_options_db_restrictionCBlast4_common_options_db_restriction
 CCBlast4_common_options_db_restriction_BaseCBlast4_common_options_db_restriction_Base
 CCBlast4_common_options_db_restriction_by_organismCBlast4_common_options_db_restriction_by_organism
 CCBlast4_common_options_db_restriction_by_organism_BaseData types to be used in BLAST4 "Lite"
 CCBlast4_common_options_discontiguous_megablastCBlast4_common_options_discontiguous_megablast
 CCBlast4_common_options_discontiguous_megablast_BaseCBlast4_common_options_discontiguous_megablast_Base
 CCBlast4_common_options_nucleotide_queryCBlast4_common_options_nucleotide_query
 CCBlast4_common_options_nucleotide_query_BaseCBlast4_common_options_nucleotide_query_Base
 CCBlast4_common_options_query_filteringCBlast4_common_options_query_filtering
 CCBlast4_common_options_query_filtering_BaseCBlast4_common_options_query_filtering_Base
 CCBlast4_common_options_repeats_filteringCBlast4_common_options_repeats_filtering
 CCBlast4_common_options_repeats_filtering_BaseCBlast4_common_options_repeats_filtering_Base
 CCBlast4_common_options_scoringCBlast4_common_options_scoring
 CCBlast4_common_options_scoring_BaseCBlast4_common_options_scoring_Base
 CCBlast4_cutoffCBlast4_cutoff
 CCBlast4_cutoff_BaseOther types in alphabetical order
 CCBlast4_database
 CCBlast4_database_BaseCBlast4_database_Base
 CCBlast4_database_infoCBlast4_database_info
 CCBlast4_database_info_BaseCBlast4_database_info_Base
 CCBlast4_errorCBlast4_error
 CCBlast4_error_BaseErrors
 CCBlast4_finish_params_replyCBlast4_finish_params_reply
 CCBlast4_finish_params_reply_BaseCBlast4_finish_params_reply_Base
 CCBlast4_finish_params_requestCBlast4_finish_params_request
 CCBlast4_finish_params_request_BaseEND ADD EXT INFO
 CCBlast4_get_databases_ex_replyCBlast4_get_databases_ex_reply
 CCBlast4_get_databases_ex_reply_BaseCBlast4_get_databases_ex_reply_Base
 CCBlast4_get_databases_ex_requestCBlast4_get_databases_ex_request
 CCBlast4_get_databases_ex_request_BaseCBlast4_get_databases_ex_request_Base
 CCBlast4_get_databases_replyCBlast4_get_databases_reply
 CCBlast4_get_databases_reply_BaseCBlast4_get_databases_reply_Base
 CCBlast4_get_matrices_replyCBlast4_get_matrices_reply
 CCBlast4_get_matrices_reply_BaseCBlast4_get_matrices_reply_Base
 CCBlast4_get_parameters_replyCBlast4_get_parameters_reply
 CCBlast4_get_parameters_reply_BaseCBlast4_get_parameters_reply_Base
 CCBlast4_get_paramsets_replyCBlast4_get_paramsets_reply
 CCBlast4_get_paramsets_reply_BaseNote: Paramsets and tasks represent the same concept: a human readable description that represents a set of parameters with specific values to accomplish a given task
 CCBlast4_get_programs_replyCBlast4_get_programs_reply
 CCBlast4_get_programs_reply_BaseCBlast4_get_programs_reply_Base
 CCBlast4_get_protocol_info_replyCBlast4_get_protocol_info_reply
 CCBlast4_get_protocol_info_reply_BaseCBlast4_get_protocol_info_reply_Base
 CCBlast4_get_protocol_info_requestCBlast4_get_protocol_info_request
 CCBlast4_get_protocol_info_request_BaseSupport for version and checking availability of methods
 CCBlast4_get_queries_replyCBlast4_get_queries_reply
 CCBlast4_get_queries_reply_BaseCBlast4_get_queries_reply_Base
 CCBlast4_get_request_info_replyCBlast4_get_request_info_reply
 CCBlast4_get_request_info_reply_BaseCBlast4_get_request_info_reply_Base
 CCBlast4_get_request_info_requestCBlast4_get_request_info_request
 CCBlast4_get_request_info_request_BaseFetch information about the search request
 CCBlast4_get_search_info_replyCBlast4_get_search_info_reply
 CCBlast4_get_search_info_reply_BaseCBlast4_get_search_info_reply_Base
 CCBlast4_get_search_info_requestCBlast4_get_search_info_request
 CCBlast4_get_search_info_request_BaseVariose search information
 CCBlast4_get_search_results_replyCBlast4_get_search_results_reply
 CCBlast4_get_search_results_reply_BaseCBlast4_get_search_results_reply_Base
 CCBlast4_get_search_results_requestCBlast4_get_search_results_request
 CCBlast4_get_search_results_request_BaseCBlast4_get_search_results_request_Base
 CCBlast4_get_search_status_replyCBlast4_get_search_status_reply
 CCBlast4_get_search_status_reply_BaseReply to retrieve the status of a given search
 CCBlast4_get_search_status_requestCBlast4_get_search_status_request
 CCBlast4_get_search_status_request_BaseRequest to retrieve the status of a given search
 CCBlast4_get_search_strategy_replyCBlast4_get_search_strategy_reply
 CCBlast4_get_search_strategy_reply_BaseReturn the search strategy (i.e
 CCBlast4_get_search_strategy_requestCBlast4_get_search_strategy_request
 CCBlast4_get_search_strategy_request_BaseFetch the search strategy (i.e
 CCBlast4_get_seq_parts_replyCBlast4_get_seq_parts_reply
 CCBlast4_get_seq_parts_reply_BaseCBlast4_get_seq_parts_reply_Base
 CCBlast4_get_seq_parts_requestCBlast4_get_seq_parts_request
 CCBlast4_get_seq_parts_request_BaseFetch parts of sequences from a BLAST database
 CCBlast4_get_sequences_replyCBlast4_get_sequences_reply
 CCBlast4_get_sequences_reply_BaseCBlast4_get_sequences_reply_Base
 CCBlast4_get_sequences_requestCBlast4_get_sequences_request
 CCBlast4_get_sequences_request_BaseFetch sequence data from a BLAST database
 CCBlast4_get_windowmasked_taxids_replyCBlast4_get_windowmasked_taxids_reply
 CCBlast4_get_windowmasked_taxids_reply_BaseCBlast4_get_windowmasked_taxids_reply_Base
 CCBlast4_ka_blockCBlast4_ka_block
 CCBlast4_ka_block_BaseCBlast4_ka_block_Base
 CCBlast4_maskCBlast4_mask
 CCBlast4_mask_BaseMasking locations for a query's frame
 CCBlast4_matrix_idCBlast4_matrix_id
 CCBlast4_matrix_id_BaseCBlast4_matrix_id_Base
 CCBlast4_options_liteCBlast4_options_lite
 CCBlast4_options_lite_BaseCBlast4_options_lite_Base
 CCBlast4_parameterCBlast4_parameter
 CCBlast4_parameter_BaseCBlast4_parameter_Base
 CCBlast4_parameter_infoCBlast4_parameter_info
 CCBlast4_parameter_info_BaseCBlast4_parameter_info_Base
 CCBlast4_parameters
 CCBlast4_parameters_BaseCBlast4_parameters_Base
 CCBlast4_phi_alignmentsCBlast4_phi_alignments
 CCBlast4_phi_alignments_BaseCBlast4_phi_alignments_Base
 CCBlast4_program_infoCBlast4_program_info
 CCBlast4_program_info_BaseCBlast4_program_info_Base
 CCBlast4_queries
 CCBlast4_queries_BaseIf a PSSM is used (ie
 CCBlast4_queue_search_replyCBlast4_queue_search_reply
 CCBlast4_queue_search_reply_BaseCBlast4_queue_search_reply_Base
 CCBlast4_queue_search_requestCBlast4_queue_search_request
 CCBlast4_queue_search_request_BaseOptions have been broken down into three groups as part of the BLAST API work
 CCBlast4_queue_search_request_liteCBlast4_queue_search_request_lite
 CCBlast4_queue_search_request_lite_BaseSimplified search submission structure
 CCBlast4_range
 CCBlast4_range_BaseRange on a sequence - zero offset
 CCBlast4_replyCBlast4_reply
 CCBlast4_reply_BaseReplies
 CCBlast4_reply_bodyCBlast4_reply_body
 CCBlast4_reply_body_BaseCBlast4_reply_body_Base
 CCBlast4_requestCBlast4_request
 CCBlast4_request_BaseRequests
 CCBlast4_request_bodyCBlast4_request_body
 CCBlast4_request_body_BaseCBlast4_request_body_Base
 CCBlast4_seq_part_dataCBlast4_seq_part_data
 CCBlast4_seq_part_data_BaseBundles Seq-ids and sequence data to fulfill requests of type Blast4-get-seq-parts-request
 CCBlast4_simple_alignmentCBlast4_simple_alignment
 CCBlast4_simple_alignment_BaseA single alignment
 CCBlast4_simple_resultsCBlast4_simple_results
 CCBlast4_simple_results_BaseComplete set of simple Blast results
 CCBlast4_subjectCBlast4_subject
 CCBlast4_subject_BaseCBlast4_subject_Base
 CCBlast4_task_infoCBlast4_task_info
 CCBlast4_task_info_BaseSelf documenting task structure
 CCBlast4_valueCBlast4_value
 CCBlast4_value_BaseCBlast4_value_Base
 CCBlast4ClientCBlast4Client
 CCBlast4Client_BaseCBlast4Client_Base
 CCBlast4FieldField properties for options in a Blast4 parameter list
 CCBLAST_DB_DialogCBLAST_DB_Dialog
 CCBlast_db_mask_infoCBlast_db_mask_info
 CCBlast_db_mask_info_BaseDefines the masking information for a set of sequences
 CCBlast_def_line
 CCBlast_def_line_BaseCBlast_def_line_Base
 CCBlast_def_line_set
 CCBlast_def_line_set_BaseAll deflines for an entry
 CCBLAST_Dlg_Item
 CCBlast_ExtendWordWrapper class for Blast_ExtendWord
 CCBlast_mask_listCBlast_mask_list
 CCBlast_mask_list_BaseCBlast_mask_list_Base
 CCBlast_MessageWrapper class for Blast_Message
 CCBLAST_SequenceBlkWrapper class for BLAST_SequenceBlk
 CCBlastAdvancedProteinOptionsHandleHandle to the Advanced BLASTP options
 CCBlastAligner
 CCBlastAncillaryDataClass used to return ancillary data from a blast search, i.e
 CCBlastAppArgsBase command line argument class for a generic BLAST command line binary
 CCBlastArgs
 CCBlastBioseqMakerAuxiliary class for creating Bioseqs given SeqIds
 CCBlastDatabaseArgsArgument class to collect database/subject arguments
 CCBlastDatabaseOptionsWrapper class for BlastDatabaseOptions
 CCBLASTDatabases
 CCBlastDb_DataLoaderCFData Loader Factory for BlastDbDataLoader
 CCBlastDBAliasAppThe main application class
 CCBlastDbBioseqSource
 CCBlastDbBlob`Blob' Class for SeqDB (and WriteDB)
 CCBlastDbCheckApplicationCBlastDbCheckApplication: the main application class
 CCBlastDbCheckLog
 CCBlastDBCmdAppThe application class
 CCBlastDbDataLoader
 CCBlastDBExtractorClass to extract data from a BLAST database given an identifier
 CCBlastDbFinderFunctor class for FindFilesInDir
 CCBlastDbFormatterCustomizable BLAST DB information formatter interface
 CCBlastDbMetadataProxy class for retrieving meta data from a BLAST DB
 CCBlastDBSeqIdEncapsulates identifier to retrieve data from a BLAST database
 CCBlastDbSet
 CCBlastDemoApplication
 CCBLASTDlgItemData
 CCBlastEffectiveLengthsOptionsWrapper class for BlastEffectiveLengthsOptions
 CCBlastEffectiveLengthsParametersWrapper class for BlastEffectiveLengthsParameters
 CCBlastExceptionDefines BLAST error codes (user errors included)
 CCBlastExtendTestFixture
 CCBlastExtensionOptionsWrapper class for BlastExtensionOptions
 CCBlastExtensionParametersWrapper class for BlastExtensionParameters
 CCBlastFastaInputSourceClass representing a text file containing sequences in fasta format
 CCBlastFilterTest
 CCBlastFormatThis class formats the BLAST results for command line applications
 CCBlastFormatterAppThe application class
 CCBlastFormattingMatrix256x256 matrix used for calculating positives etc
 CCBlastFormatUtilSetting up scope
 CCBlastGapAlignStructWrapper class for BlastGapAlignStruct
 CCBlastHitMatrixThis class displays the image of the hitmatrix view for blast 2 seq results
 CCBlastHitMatrixCGIApplicationCBlastHitMatrixCGIApplication This CGI loads an accession from GenBank, extract a Seq-annot from the sequence and renders a pairwise alignment between the first two Seq-id in the alignment
 CCBlastHitMatrixCGIException
 CCBlastHitSavingOptionsWrapper class for BlastHitSavingOptions
 CCBlastHitSavingParametersWrapper class for BlastHitSavingParameters
 CCBlastHSPListQueueDataData structure for the queue implementation of BlastHSPStream
 CCBlastHSPResultsWrapper class for BlastHSPResults
 CCBlastInitialWordOptionsWrapper class for BlastInitialWordOptions
 CCBlastInitialWordParametersWrapper class for BlastInitialWordParameters
 CCBlastInputGeneralized converter from an abstract source of biological sequence data to collections of blast input
 CCBlastInputDemoApplication
 CCBlastInputReaderClass to read non-FASTA sequence input to BLAST programs using the various data loaders configured in CBlastScopeSource objects
 CCBlastInputSourceBase class representing a source of biological sequences
 CCBlastInputSourceConfigClass that centralizes the configuration data for sequences to be converted
 CCBlastMaskLocWrapper class for BlastMaskLoc
 CCBlastnApp
 CCBlastnAppArgsHandles command line arguments for blastn binary
 CCBlastNucleotideOptionsHandleHandle to the nucleotide-nucleotide options to the BLAST algorithm
 CCBlastOptionsEncapsulates ALL the BLAST algorithm's options
 CCBlastOptionsBuilderClass to build CBlastOptionsHandle from blast4 ASN objects
 CCBlastOptionsFactoryCreates BlastOptionsHandle objects with default values for the programs/tasks requested
 CCBlastOptionsHandleHandle to the options to the BLAST algorithm
 CCBlastOptionsLocalEncapsulates all blast input parameters
 CCBlastOptionsMementoClass that allows the transfer of data structures from the CBlastOptionsLocal class to either the BLAST preliminary or traceback search classes
 CCBlastOptionsRemoteEncapsulates all blast input parameters
 CCBlastOutputCBlastOutput
 CCBlastOutput2CBlastOutput2
 CCBlastOutput2_BaseCBlastOutput2_Base
 CCBlastOutput_BaseCBlastOutput_Base
 CCBlastpApp
 CCBlastpAppArgsHandles command line arguments for blastp binary
 CCBLASTParamsCBLASTParams - save user-specified parameters and preferences
 CCBlastPrelimSearchSearch class to perform the preliminary stage of the BLAST search
 CCBlastProteinOptionsHandleHandle to the protein-protein options to the BLAST algorithm
 CCBlastQueryFilteredFramesCollection of BlastSeqLoc lists for filtering processing
 CCBlastQueryInfoWrapper class for BlastQueryInfo
 CCBlastQuerySourceBioseqSetImplements the IBlastQuerySource interface using a CBioseq_set as data source
 CCBlastQuerySourceOMImplements the object manager dependant version of the IBlastQuerySource
 CCBlastQueryVectorQuery Vector
 CCBlastRPSAuxInfoWrapper class to manage the BlastRPSAuxInfo structure, as currently there aren't any allocation or deallocation functions for this structure in the CORE of BLAST
 CCBlastRPSInfoWrapper class to manage the BlastRPSInfo structure, as currently there aren't any allocation or deallocation functions for this structure in the CORE of BLAST
 CCBlastRPSOptionsHandleHandle to the rpsblast options to the BLAST algorithm
 CCBlastSampleApplication
 CCBlastScopeSourceClass whose purpose is to create CScope objects which have data loaders added with different priorities, so that the BLAST database data loader is used first, then the Genbank data loader
 CCBlastScopeSourceWrapperRAII class for the CBlastScopeSource
 CCBlastScoreBlkWrapper class for BlastScoreBlk
 CCBlastScorer
 CCBlastScoringOptionsWrapper class for BlastScoringOptions
 CCBlastScoringParametersWrapper class for BlastScoringParameters
 CCBLASTSearchOptionsPanel
 CCBLASTSearchParamsPanel
 CCBlastSearchQuerySearch Query
 CCBlastSearchTaskTODO
 CCBLASTSearchToolManagerCBLASTSearchToolManager
 CCBlastSeqLocWrapper class for BlastSeqLoc
 CCBlastSeqLocWrapWrapper for BlastSeqLoc structure
 CCBlastSeqSrcWrapper class for BlastSeqSrc
 CCBlastSeqSrcIteratorWrapper class for BlastSeqSrcIterator
 CCBLASTSeqToolJobCBLASTSeqToolJob
 CCBLASTSeqToolManagerCBLASTSeqToolManager
 CCBlastSequenceSource
 CCBlastSeqVectorFromCSeq_dataImplementation of the IBlastSeqVector interface which obtains data from a CSeq_data object
 CCBlastSeqVectorOMImplementation of the IBlastSeqVector interface which obtains data from a CSeq_loc and a CScope relying on the CSeqVector class
 CCBlastServicesAPI for Remote Blast Services
 CCBlastServicesExceptionRemoteServicesException
 CCBlastSetupTestFixture
 CCBlastSystemExceptionDefines system exceptions occurred while running BLAST
 CCBlastTabular
 CCBlastTabularInfoClass containing information needed for tabular formatting of BLAST results
 CCBLASTToolManagerBaseCBLASTToolManagerBase
 CCBlastTracebackSearch
 CCBlastVersionKeeps track of the version of the BLAST engine in the NCBI C++ toolkit
 CCBlastxApp
 CCBlastxAppArgsHandles command line arguments for blastx binary
 CCBlastxOptionsHandleHandle to the translated nucleotide-protein options to the BLAST algorithm
 CCBlob_Annot_Info
 CCBlob_id
 CCBlob_Info
 CCBlobBookmarkObject used to store bookmarks to blobs to be changed later
 CCBlobBookmarkImpl
 CCBlobCacher
 CCBlobId
 CCBlobIdFor
 CCBlobIdKey
 CCBlobIStream
 CCBlobLoader
 CCBlobMetaDBDictionary file, storing references on external BLOB file (super BLOB structure)
 CCBlobOStream
 CCBlobReader
 CCBlobRetriever
 CCBlobSplitter
 CCBlobSplitterImpl
 CCBlobStateExceptionBlob state exceptions, used by GenBank loader
 CCBlobStorage_NetCacheCBlobStorage_NetCache – NetCache-based implementation of IBlobStorage
 CCBlobStorage_NullAn Empty implementation of Blob Storage Interface
 CCBlobStorageExceptionBlob Storage Exception
 CCBlobStorageFactoryBlob Storage Factory interface
 CCBlobStorageFactory_NullBlob Storage Factory interface
 CCBlobStorageNetCacheCF
 CCBlobStoreBase
 CCBlobStoreDynamic
 CCBlobStoreStatic
 CCBlobStreamHelper
 CCBlobWriter
 CCBlockDataValue
 CCBlockedAlignmentEditor
 CCBlockingQueueCBlockingQueue<> – queue of requests, with efficiently blocking Get()
 CCBlockingQueue_ForServer
 CCBlockingQueueException
 CCBlockPropertyCBlockProperty
 CCBlockProperty_BaseRudimentary block/core-model, to be used with block-based alignment routines and threading
 CCBMARefinerBlockEditPhase
 CCBMARefinerCycle
 CCBMARefinerEngine
 CCBMARefinerLOOPhase
 CCBMARefinerPhase
 CCBMARefinerTrial
 CCBMode
 CCBondList
 CCBondPanel
 CCBookChapterPanel
 CCBookmarkClass CBookmark defines the data stored in an individual sequence-based bookmark
 CCBookmarkManagerClass CBookmarkManager manages a set of bookmarks, complete with hooks for serialization and efficient retrieval of bookmarks for a given seq-id
 CCBookmarksHandlerClass CBookmarksHandler represents in GUI a bookmarks on a sequence bar
 CCBookPanel
 CCBoolDataType
 CCBoolGuard
 CCBoundaryParamsIBoundaryParams
 CCBoundaryParmsCBoundaryParms
 CCBoundaryPointsCBoundaryPoints
 CCBoundaryShapeRectCBoundaryShapeRect
 CCBoundaryShapeRectBaseCBoundaryShapeRectBase
 CCBoundaryShapeRoundedRectCBoundaryShapeRoundedRect
 CCBoundaryShapeTriCBoundaryShapeTri
 CCBoyerMooreMatcherThis implemetation uses the Boyer-Moore alg
 CCBrickCBrick
 CCBrick_BaseA brick is defined by the coordinates of eight corners
 CCBroadcastDialog
 CCBroadcastVRChangeDialog
 CCBrowserData
 CCBrowserUtils
 CCBssInfoApp
 CCBucketPoolBucket of resourse pools
 CCBufferedLineReaderImplementation of ILineReader for IReader
 CCBufferWriter
 CCBufferWriterStream
 CCBuildAlnVecJobCBuildAlnVecJob
 CCBuildAlnVecResultCBuildAlnVecResult
 CCBuildDatabaseBuild BlastDB format databases from various data sources
 CCBuildOptionsDlgCwxBuildOptionsDlg
 CCBuildSparseAlnJobCBuildSparseAlnJob
 CCBuildSparseAlnResultCBuildAlnVecResult
 CCBuildTypeUtility class for distinguish between static and dll builds
 CCBulkCDS
 CCBulkCDSAddPanel
 CCBulkCmdDlg
 CCBulkCmdPanel
 CCBulkEditFeatDlg
 CCBulkFeatureAddDlg
 CCBulkGene
 CCBulkInsertObject used to perform bulk-inserting operations to database
 CCBulkInsertImpl
 CCBulkLocationPanel
 CCBulkMolinfoEditDlg
 CCBulkOtherAddPanel
 CCBulkRna
 CCBulkRNAAddPanel
 CCBundle_seqs_alignsCBundle_seqs_aligns
 CCBundle_seqs_aligns_BaseGeneric bundle of sequence and alignment info
 CCButtonList
 CCButtonPanel
 CCBV_PoolBlockAllocThread-safe pool block allocator for NCBI bitsets
 CCBVector_data
 CCBVector_data_BaseClass for serializing bm::bvector<> see include/util/bitset/bm.h Since bvector<> serialization doesn't keep size we have to add it explicitly
 CCBvGapFactoryBit-vector factory
 CCBVResourcePoolResource pool for bit-vectors Bit-vector creation-destruction can be expensive, use pool to recycle used objects
 CCByte_graphCByte_graph
 CCByte_graph_BaseInteger from 0-255
 CCByteOrderMarkByte Order Mark helper class to use in serialization
 CCByteSource
 CCByteSourceReader
 CCByteStreamBuf
 CCByteSwapCByteSwap
 CCBZip2CompressionCBZip2Compression
 CCBZip2CompressionFileCBZip2CompressionFile class –
 CCBZip2CompressorCBZip2Compressor – bzip2 based compressor
 CCBZip2DecompressorCBZip2Decompressor – bzip2 based decompressor
 CCBZip2StreamCompressorCBZip2StreamCompressor – bzip2 based compression stream processor
 CCBZip2StreamDecompressorCBZip2StreamDecompressor – bzip2 based decompression stream processor
 CCCacheCache template
 CCCacheBlobStream
 CCCacheBufferResizeStrategyBuffer resize strategy, to balance memory reallocs and heap consumption
 CCCacheCleanerThreadThread class, peridically calls ICache::Purge to remove obsolete elements
 CCCachedDictionaryClass CCachedDictionary provides an internalized mechanism for caching the alternates returned by SuggestAlternates()
 CCCacheDemoApp
 CCCachedSeqDataForRemoteThis class defines a "bundle" of elements to cache which are then returned by CRemoteBlastDbAdapter
 CCCachedSequenceManages a TSE and its subordinate chunks for all implementations of the IBlastDbAdapter interface
 CCCachedTaxon3
 CCCachedTaxon3_impl
 CCCachedTipHandle
 CCCacheElement_HandlerDefault (NOP) element handler
 CCCacheElement_LessCompare cache elements by weight/order
 CCCacheExceptionException thrown by CCache
 CCCacheHashedContentHashed content cache
 CCCacheHolder
 CCCacheReader
 CCCacheReaderCF
 CCCacheWriter
 CCCacheWriterCFClass factory for Cache writer
 CCCalcBoundary
 CCCalcCaretPosOStream
 CCCalcCharsOStream
 CCCalcCircularTree
 CCCalcDataPosOStream
 CCCalcNBPosOStream
 CCCalcRadialTree
 CCCalcRectangularTree
 CCCalcSizeCache
 CCCalcSizeOStream
 CCCalcSizeStream
 CCCalcSlantedTree
 CCCalcTextPosOStream
 CCCallableStatement
 CCCameraCCamera
 CCCamera_BaseThe camera is a position relative to the world coordinates of the structure referred to by a location
 CCCanceledImpl
 CCCancelGuard
 CCCancelRequestException
 CCCapChangePanel
 CCCategoryCCategory
 CCCategory_BaseCCategory_Base
 CCCategoryConfigData structure holding configuration for a track
 CCCDataMiningEvent
 CCCdCore
 CCCdd
 CCCdd_BaseCdd is the basic ASN.1 object storing an annotated and curated set of alignments (formulated as a set of pairwise master-slave alignments)
 CCCdd_book_refCCdd_book_ref
 CCCdd_book_ref_BaseRecord a link to Entrez Books
 CCCdd_DataLoaderCF
 CCCdd_descrCCdd_descr
 CCCdd_descr_BaseThe description of CDD's refers to the specific set of aligned sequences, the region that is being aligned and the information contained in the alignment
 CCCdd_descr_setCCdd_descr_set
 CCCdd_descr_set_BaseCCdd_descr_set_Base
 CCCdd_idCCdd_id
 CCCdd_id_BaseCCdd_id_Base
 CCCdd_id_setCCdd_id_set
 CCCdd_id_set_BaseCCdd_id_set_Base
 CCCdd_org_refCCdd_org_ref
 CCCdd_org_ref_BaseDealing with lists of preferred tax-nodes
 CCCdd_org_ref_setCCdd_org_ref_set
 CCCdd_org_ref_set_BaseCCdd_org_ref_set_Base
 CCCdd_pref_node_descrCCdd_pref_node_descr
 CCCdd_pref_node_descr_BaseCCdd_pref_node_descr_Base
 CCCdd_pref_node_descr_setCCdd_pref_node_descr_set
 CCCdd_pref_node_descr_set_BaseCCdd_pref_node_descr_set_Base
 CCCdd_pref_nodesCCdd_pref_nodes
 CCCdd_pref_nodes_BaseCCdd_pref_nodes_Base
 CCCdd_ProjectCCdd_Project
 CCCdd_Project_BaseCd colors are as: 0000FF for red, 00FF00 for green, FF0000 for blue
 CCCdd_repeatCCdd_repeat
 CCCdd_repeat_BaseRecord whether the CD contains repeated sequence/structure motifs
 CCCdd_ScriptCCdd_Script
 CCCdd_Script_BaseCCdd_Script_Base
 CCCdd_setCCdd_set
 CCCdd_set_BaseCCdd_set_Base
 CCCdd_treeCCdd_tree
 CCCdd_tree_BaseCdd-tree stores the hierarchy of CDDs
 CCCdd_tree_setCCdd_tree_set
 CCCdd_tree_set_BaseCCdd_tree_set_Base
 CCCdd_ViewerCCdd_Viewer
 CCCdd_Viewer_BaseCCdd_Viewer_Base
 CCCdd_Viewer_RectCCdd_Viewer_Rect
 CCCdd_Viewer_Rect_BaseCdd projects store a set of CDs, typically related to each other relationships would be specified using the ancestors fields in the individual CD objects
 CCCdDbPriority
 CCCddDataLoader
 CCCddDeltaHeadersTest
 CCCddHeadersTest
 CCCddInputDataStrategy for pre-processing RPS-BLAST matches for PSSM computation
 CCCdFromFasta
 CCCdregionCCdregion
 CCCdregion_Base*** CdRegion *********************************************** * * Instructions to translate from a nucleic acid to a peptide * conflict means it's supposed to translate but doesn't *
 CCCdregion_translatePublic interface for coding region translation function Uses CTrans_table in <objects/seqfeat/Genetic_code_table.hpp> for rapid translation from a given genetic code, allowing all of the iupac nucleotide ambiguity characters
 CCCdsConfig
 CCCDSExceptionPanel
 CCCdsForMrnaPlugin
 CCCdsFromGeneMrnaExon
 CCCDSGeneProt_constraint_fieldCCDSGeneProt_constraint_field
 CCCDSGeneProt_constraint_field_BaseCCDSGeneProt_constraint_field_Base
 CCCDSGeneProt_field_pairCCDSGeneProt_field_pair
 CCCDSGeneProt_field_pair_BaseCCDSGeneProt_field_pair_Base
 CCCDSGeneProt_pseudo_constraintCCDSGeneProt_pseudo_constraint
 CCCDSGeneProt_pseudo_constraint_BaseCCDSGeneProt_pseudo_constraint_Base
 CCCDSGeneProt_qual_constraintCCDSGeneProt_qual_constraint
 CCCDSGeneProt_qual_constraint_BaseCCDSGeneProt_qual_constraint_Base
 CCCDSGeneProtFieldNamePanel
 CCCdsGlyph
 CCCDSInfo
 CCCDSProductPanel
 CCCDSProteinPanel
 CCCdsToMatPeptide
 CCCDStomRNALinkBuilder
 CCCDSTranslationPanel
 CCCellHyperlinks
 CCCgi2RCgiApp
 CCCgiApplication
 CCCgiApplicationCached
 CCCgiContext
 CCCgiCookieCCgiCookie::
 CCCgiCookieExceptionCCgiCookieException
 CCCgiCookiesCCgiCookies::
 CCCgiEntries_Parser
 CCCgiEntry
 CCCgiEntryReader
 CCCgiEntryReaderContext
 CCCgiEnvHolder
 CCCgiErrnoExceptionCCgiErrnoException
 CCCgiException
 CCCgiFontTestApp
 CCCgiHeadExceptionCCgiHeadException
 CCCgiIbuffer
 CCCgiObuffer
 CCCgiParseExceptionCCgiParseException
 CCCgiRedirectApplicationCCgiRedirectApplication
 CCCgiRequestCCgiRequest::
 CCCgiRequestExceptionCCgiRequestException
 CCCgiResponse
 CCCgiResponseExceptionCCgiResponseException
 CCCgiSampleApplication
 CCCgiServerContext
 CCCgiSessionCCgiSession
 CCCgiSession_NetCache
 CCCgiSessionExceptionCCgiSessionException
 CCCgiSessionParameters
 CCCgiSessionSampleApplication
 CCCgiStatistics
 CCCGIStreamReader
 CCCgiStreamWrapper
 CCCgiStreamWrapperWriter
 CCCGIStreamWriter
 CCCgiTunnel2Grid
 CCCgiUserAgentCCgiUserAgent
 CCCgiVersionInfo
 CCCgiWorkerNodeJob
 CCCgiWorkerNodeJobFactory
 CCCGPSetData
 CCChain
 CCChainer
 CCChainerArgUtil
 CCChainMembers
 CCChangeCaseSubpanel
 CCChangePhyloPropertyCmd
 CCChangePhyloTreeCommand
 CCChangeSeqdescTitleCommand
 CCChangeStructuredCommentKeyword
 CCChangeUnindexedObjectCommand
 CCCharacterSetCCharacterSet
 CCCharacterSet_BaseNcbi: removed BootstrapperComponentsLocation ncbi: removed BootstrapperComponentsUrl ncbi: removed BootstrapperEnabled
 CCCharHistogramCCharHistogram
 CCCharInSet
 CCCharPtrFunctions
 CCChartElem
 CCCharVectorFunctions
 CCCharVectorFunctionsBase
 CCCharVectorTypeInfo
 CCCheckBoxCCheckBox
 CCCheckBox_BaseCCheckBox_Base
 CCCheckingClass
 CCCheckMeWrapper around an object of type TValue, that makes it mandatory to check object value somehow after each assignment
 CCChecksumCChecksum – Checksum calculator
 CCChecksumExceptionCChecksumException
 CCChecksumStreamWriterCChecksumStreamWriter
 CCChem_graph_alignmentCChem_graph_alignment
 CCChem_graph_alignment_BaseA biostruc alignment establishes an equivalence of nodes in the chemical graphs of two or more biostrucs
 CCChem_graph_interactionCChem_graph_interaction
 CCChem_graph_interaction_BaseCChem_graph_interaction_Base
 CCChem_graph_pntrsCChem_graph_pntrs
 CCChem_graph_pntrs_BaseCChem_graph_pntrs_Base
 CCChimeraCommentDescriptorTableCommandConverter
 CCChimeraPanel
 CCChiral_centerCChiral_center
 CCChiral_center_BaseChiral centers are atoms with tetrahedral geometry
 CCChoiceCChoice
 CCChoice_BaseCChoice_Base
 CCChoiceDataType
 CCChoiceItemCChoiceItem
 CCChoiceItem_BaseCChoiceItem_Base
 CCChoicePointerTypeInfo
 CCChoicePtrRefTypeStrings
 CCChoicePtrTypeStrings
 CCChoiceRefTypeStrings
 CCChoiceTypeInfo
 CCChoiceTypeInfoFunctions
 CCChoiceTypeStrings
 CCChooseSetClassDlg
 CCChymoPEMSEnzymes_chymotrypsin_p chymotrypsin without proline rule
 CCChymotrypsin
 CCCigar
 CCCIGAR_FormatterThe base class for alignment formatters which use CIGAR format
 CCCit_art
 CCCit_art_BaseCitation Types article in journal or book
 CCCit_book
 CCCit_book_BaseBook citation
 CCCit_gen
 CCCit_gen_BaseNOT from ANSI, this is a catchall
 CCCit_jour
 CCCit_jour_BaseJournal citation
 CCCit_let
 CCCit_let_BaseLetter, thesis, or manuscript
 CCCit_pat
 CCCit_pat_BasePatent number and date-issue were made optional in 1997 to support patent applications being issued from the USPTO Semantically a Cit-pat must have either a patent number or an application number (or both) to be valid patent citation
 CCCit_proc
 CCCit_proc_BaseMeeting proceedings
 CCCit_sub
 CCCit_sub_BaseNOTE: this is just to cite a direct data submission, see NCBI-Submit for the form of a sequence submission citation for a direct submission
 CCCitationColumn
 CCCitationsPanel
 CCCitRetractCCitRetract
 CCCitRetract_BaseCCitRetract_Base
 CCCitSubPanel
 CCCLCCL
 CCCL_BaseNcbi: removed ReadLinesFromFile ncbi: removed RegisterAssembly ncbi: removed RemoveDir ncbi: removed RemoveDuplicates ncbi: removed RequiresFramework35SP1Assembly ncbi: removed ResolveAssemblyReference ncbi: removed ResolveComReference ncbi: removed ResolveKeySource ncbi: removed ResolveManifestFiles ncbi: removed ResolveNativeReference ncbi: removed ResolveNonMSBuildProjectOutput ncbi: removed SGen ncbi: removed SignFile ncbi: removed TlbImp ncbi: removed Touch ncbi: removed UnregisterAssembly ncbi: removed UpdateManifest ncbi: removed Vbc ncbi: removed VCBuild ncbi: removed Warning ncbi: removed WriteCodeFragment ncbi: removed WriteLinesToFile ncbi: removed XslTransformation ncbi: removed CodeAnalysis ==================== NATIVE CL/LINK TASKS ==========================
 CCClassCode
 CCClassContext
 CCClassInfoHelper
 CCClassInfoHelperBase
 CCClassPrePostReadWrite
 CCClassRefTypeStrings
 CCClassTypeInfo
 CCClassTypeInfoBase
 CCClassTypeStrings
 CCClCompileCClCompile
 CCClCompile_BaseNcbi: removed COMFileReference ncbi: removed Xdcmake ncbi: removed Bscmake
 CCCleanup
 CCCleanupAlignmentsJobCCleanupAlignmentsJob
 CCCleanupAlignmentsParamsPanel
 CCCleanupAlignmentsToolManagerCCleanupAlignmentsToolManager
 CCCleanupApp
 CCCleanupChangeAll the changes made during cleanup
 CCCleanupJobCCleanupJob
 CCCleanupPanel
 CCCleanupParams
 CCCleanupProcess
 CCCleanupToolCCleanupTool
 CCClearFeatureId
 CCClearKeywords
 CCCleave
 CCCleaveFactoryFactory to return back object for enzyme
 CCClickableItem
 CCClickableItemListPanel
 CCClickableItemPanel
 CCClickablePairPanel
 CCClickableText
 CCClientPseudoDataType
 CCClientPseudoTypeStrings
 CCClIncludeCClInclude
 CCClInclude_BaseCClInclude_Base
 CCClipboard
 CCClippedScorer
 CCClockPanelWMClientCClockPanelWMClient
 CCClockViewCClockView
 CCClockViewFactoryCClockViewFactory
 CCClone_refCClone_ref
 CCClone_ref_Base*** Clone-ref *********************************************** * * Specification of clone features *
 CCClone_seqCClone_seq
 CCClone_seq_BaseCClone_seq_Base
 CCClone_seq_setCClone_seq_set
 CCClone_seq_set_BaseCClone_seq_set_Base
 CCCloneConcordancySorterCCloneConcordancySorter is a feature sorter used to sort clone features based on clone concordancy
 CCClonePlacementGlyphCClonePlacementGlyph is similar to CFeatureGlyph, but with different rendering style and settings
 CCClonePlacementParamsCClonePlacementParams:
 CCCLRSupportCCLRSupport
 CCCLRSupport_BaseNcbi: removed CheckForOverflowUnderflow
 CCClustalwToolCClustalwTool
 CCClustalwToolJobCClustalwToolJob
 CCClustalwToolPanel
 CCClustalwToolParams
 CCClustererInterface for CClusterer class used for clustering any type of data based on distance matrix
 CCClustererApplication
 CCClustererExceptionExceptions for CClusterer class
 CCCmdAddCDS
 CCCmdAddSeqEntry
 CCCmdChangeAlign
 CCCmdChangeBioseqInst
 CCCmdChangeBioseqSet
 CCCmdChangeGraph
 CCCmdChangeSeq_feat
 CCCmdChangeSeqEntry
 CCCmdChangeSetClass
 CCCmdComposite
 CCCmdCreateAlign
 CCCmdCreateDesc
 CCCmdCreateFeat
 CCCmdCreateSeq_annot
 CCCmdDelBioseqInst
 CCCmdDelBioseqSet
 CCCmdDelDesc
 CCCmdDelSeq_align
 CCCmdDelSeq_annot
 CCCmdDelSeq_feat
 CCCmdDelSeq_graph
 CCCmdFactory
 CCCmdInsertBioseqSet
 CCCmdLineArgList
 CCCmdLineBlastXML2ReportDataStrategy class to gather the data for generating BLAST XML output
 CCCmdLineBlastXMLReportDataStrategy class to gather the data for generating BLAST XML output
 CCCmdPromoteCDS
 CCCmdPropagateFeat
 CCCmdPropagateFeatSeqUpd
 CCCmdTableAssignColumn
 CCCmdTableChangeCell
 CCCmdTableCopyColumn
 CCCn3d_backbone_label_styleCCn3d_backbone_label_style
 CCCn3d_backbone_label_style_BaseStyle blob for backbone labels
 CCCn3d_backbone_styleCCn3d_backbone_style
 CCCn3d_backbone_style_BaseStyle blob for backbones only
 CCCn3d_colorCCn3d_color
 CCCn3d_color_BaseRGB triplet, interpreted (after division by the scale-factor) as floating point values which should range from [0..1]
 CCCn3d_general_styleCCn3d_general_style
 CCCn3d_general_style_BaseStyle blob for other objects
 CCCn3d_GL_matrixCCn3d_GL_matrix
 CCCn3d_GL_matrix_BaseGL-ordered transformation matrix
 CCCn3d_molecule_locationCCn3d_molecule_location
 CCCn3d_molecule_location_BaseSet of locations on a particular chain
 CCCn3d_object_locationCCn3d_object_location
 CCCn3d_object_location_BaseSet of locations on a particular structure object (e.g., a PDB/MMDB structure), which may include multiple ranges of residues each on multiple chains
 CCCn3d_residue_rangeCCn3d_residue_range
 CCCn3d_residue_range_BaseRange of residues in a chain, identified by MMDB residue-id (e.g., numbered from 1)
 CCCn3d_style_dictionaryCCn3d_style_dictionary
 CCCn3d_style_dictionary_BaseGlobal settings, and a lookup table of styles for user annotations
 CCCn3d_style_settingsCCn3d_style_settings
 CCCn3d_style_settings_BaseRendering settings for Cn3D (mirrors StyleSettings class)
 CCCn3d_style_settings_setCCn3d_style_settings_set
 CCCn3d_style_settings_set_BaseCCn3d_style_settings_set_Base
 CCCn3d_style_table_idCCn3d_style_table_id
 CCCn3d_style_table_id_BaseCCn3d_style_table_id_Base
 CCCn3d_style_table_itemCCn3d_style_table_item
 CCCn3d_style_table_item_BaseCCn3d_style_table_item_Base
 CCCn3d_user_annotationCCn3d_user_annotation
 CCCn3d_user_annotation_BaseInformation for an individual user annotation
 CCCn3d_user_annotationsCCn3d_user_annotations
 CCCn3d_user_annotations_BaseThe list of annotations for a given CDD/mime
 CCCn3d_vectorCCn3d_vector
 CCCn3d_vector_BaseFloating point 3d vector
 CCCn3d_view_settingsCCn3d_view_settings
 CCCn3d_view_settings_BaseParameters used to set up the camera in Cn3D
 CCCNBr
 CCCObjectClassInfo
 CCCode_breakCCode_break
 CCCode_break_BaseSpecific codon exceptions NCBIstdaa code
 CCCodeBreakCompare
 CCCodeBreakEqual
 CCCodeGenerator
 CCCodingPropensity
 CCCodingRegion
 CCCodonsRecColumn
 CCCodonsStringListValidator
 CCCodonStartColumn
 CCCoiledCoil
 CCCollisionGrid2DClass CCollisionHash2D
 CCColor_propCColor_prop
 CCColor_prop_BaseCColor_prop_Base
 CCColorPanel
 CCColorPickerValidator
 CCColorTableMethodCColorTableMethod
 CCColorTableScoringPanelCColorTableScoringPanel - Properties Panel for CColorTableMethod
 CCColumnLayoutCColumnLayout is for creating layout by sorting glyphs into 'columns'
 CCColumnScoringMethodCColumnScoringMethod
 CCColumnScoringPanelCColumnScoringPanel
 CCColumnValidator
 CCColumnValidatorRegistry
 CCCombinatorCall
 CCComboChartClass CComboChart
 CCComboChartDataSourceClass CComboChartDataSource
 CCCommandArgDescriptionsCCommandArgDescriptions
 CCCommandLineOrderPolicy
 CCCommandLineParser
 CCCommandProcessor
 CCCommandToFocusHandler
 CCCommentCComment
 CCComment_BaseCComment_Base
 CCComment_rule
 CCComment_rule_BaseCComment_rule_Base
 CCComment_set
 CCComment_set_BaseCComment_set_Base
 CCCommentColumn
 CCCommentConfigCCommentConfig – help config class for holding a set of settings for a comment glyph
 CCCommentDescField
 CCCommentDescriptorTableCommandConverter
 CCCommentDiagFactory
 CCCommentDiagHandler
 CCCommentGlyphCCommentGlyph – utility class for having comments in graphical glyphs
 CCCommentItem
 CCCommentPanel
 CCComments
 CCCommonBytes_tableCCommonBytes_table
 CCCommonBytes_table_BaseCCommonBytes_table_Base
 CCCommonComponentScorer
 CCCommonString_tableCCommonString_table
 CCCommonString_table_BaseCCommonString_table_Base
 CCCommonTaxTreeToolCCommonTaxTreeTool
 CCCompactLayoutCCompactLayout is amed to generate more compact 2D layout policy than layered layout for glyphs with non-uniform height
 CCCompareByLeafCount
 CCCompareCRefUserCall
 CCCompareFeatsCCompareFeats represens a result of comparison of two features
 CCCompareSeq_locsCCompareSeq_locs is used for comparing locations of two features on the same coordinate system It is agnostic to what type of feature it is and only compares the internal structure of the locs
 CCCompareSeqRegionsCompare multiple feature annotations on the specified seq_locs
 CCCompartApp
 CCCompartApplication
 CCCompartmentAccessor
 CCCompartmentFinder
 CCCompartOptions
 CCCompatDiagHandler
 CCCompatStreamDiagHandler
 CCCompileCCompile
 CCCompile_BaseSource files for compiler
 CCCompilerToolImplCCompilerToolImpl
 CCComplexRelation
 CCComponentCComponent
 CCComponent_BaseCComponent_Base
 CCComponentIDToolApp
 CCComponentSearchForm
 CCComponentSearchJobCComponentSearchJob
 CCComponentSearchQueryCComponentSearchTool
 CCComponentSearchToolCComponentSearchTool
 CCComponentTrackCComponentTrack
 CCComponentTrackFactoryCComponentTrackFactory
 CCComponentVersionInfo
 CCCompositeAppTaskCCompositeAppTask - an application task that consists of subtasks
 CCCompositeTextItem
 CCCompositionBasedStatsArgsArgument class for collecting composition based statistics options
 CCCompoundIDBase64-encoded ID string that contains extractable typed fields
 CCCompoundIDDumpParser
 CCCompoundIDExceptionException class for use by CCompoundIDPool, CCompoundID, and CCompoundIDField
 CCCompoundIDFieldCompound ID field – an element of the compound ID that has a type and a value
 CCCompoundIDPoolPool of recycled CCompoundID objects
 CCCompoundRegistryCCompoundRegistry
 CCCompoundRWRegistryCCompoundRWRegistry
 CCCompressedFile
 CCCompression
 CCCompressionException
 CCCompressionFile
 CCCompressionIOStream
 CCCompressionIStream
 CCCompressionOStream
 CCCompressionProcessor
 CCCompressionStream
 CCCompressionStreambuf
 CCCompressionStreamProcessor
 CCCompressionUtil
 CCCompressIStreamCCompressIStream
 CCCompressOStreamCCompressOStream
 CCCompressStreamCCompressStream
 CCCompSpans
 CCCompVal
 CCCOMReferenceCCOMReference
 CCCOMReference_BaseReference to a COM component
 CCConcurrentMap
 CCConditionVariable
 CCConditionVariableExceptionCConditionVariableException
 CCConeCCone
 CCCone_BaseCCone_Base
 CCConfig
 CCConfigExceptionCConfigException
 CCConfigurationCConfiguration
 CCConfiguration_BaseCConfiguration_Base
 CCConfigurationImplCConfigurationImpl
 CCConfigurationsCConfigurations
 CCConfigurations_BaseCConfigurations_Base