Class List

Here are the classes, structs, unions and interfaces with brief descriptions:
DefaultErrorReportNxsReaderA subclass of NxsReader that is used preserves the same output style as version 2.0, but allows for more flexibility in the streams that are used for output
ExceptionRaisingNxsReaderA subclass of NxsReader that is used in much of NCL v2.1
Int2Type< v >
MultiFormatReaderA special class of PublicNexusReader, that can parse
NStrCaseInsensitiveEqualsFunction object (Unary Predicate functor) that stores one string
NStrCaseSensitiveEqualsFunction object (Unary Predicate functor) that stores one string
NxsAssumptionsBlockThis class handles reading and storage for the NxsReader block ASSUMPTIONS
NxsBlockThis is the base class from which all block classes are derived
NxsBlockFactoryThis abstract class defines the interface for a factory that can generate NxsBlocks
NxsCharactersBlockThis class handles reading and storage for the NEXUS block CHARACTERS
NxsCharactersBlockAPIIntended to specify the interface of a NxsCharactersBlock, but actually does not list all of the relevant functions
NxsCloneBlockFactoryA factory class that takes examplar that will be cloned to read each block
NxsCommentGeneral notes on NexusTokenizing
NxsConversionOutputRecordThis class is used internally to keep track of operations that may be needed to make taxon labels from different sources avoid clashing with each other
NxsDataBlockThis class handles reading and storage for the NEXUS block DATA
NxsDefaultPublicBlockFactoryA factory class that delegates calls to the other "default" public block parsers that NCL provides
NxsDiscreteDatatypeMapperThis class stores the information needed to map the internal storage for a cell of a matrix (a "state code") to the set of states that it corresponds to
NxsDiscreteDatumReference to a cell in a DiscreteMatrix
NxsDistanceDatumThis class stores pairwise distance values
NxsDistancesBlockThis class handles reading and storage for the NEXUS block DISTANCES
NxsExceptionException class that conveys a message specific to the problem encountered
NxsFullTreeDescriptionA class that encapsulates a newick string description of a tree and metadata about the tree
NxsIntStepMatrixInternal representation of a stepmatrix with cells composed of ints
NxsLabelToIndicesMapperThis is the base class for the block interfaces that correspond to blocks that hold ordered lists (TAXA, CHARACTERS, TREES)
NxsNCLAPIExceptionThrown when a programming error (a violation of one of the APIs used in NCL) is revealed
NxsReaderThis is the class that orchestrates the reading of a NEXUS data file, and so is the central class to NCL
NxsRealStepMatrixInternal representation of a stepmatrix with cells composed of doubles
NxsSetReaderA class for reading NEXUS set objects and storing them in a set of int values
NxsSimpleCommandStringsA structure for storing the name of a command and to maps of option names to value strings
NxsSimpleEdgeThe edge used by the NxsSimpleTree class
NxsSimpleNodeThe node used by the NxsSimpleTree class
NxsSimpleTreeA simple tree class
NxsStringA string class for use with the Nexus Class Library
NxsStringEqualBinary function class that performs case-Insensitive string compares
NxsTaxaBlockThe default implementation of the NxsTaxaBlockAPI that is used to parse TAXA blocks into a list of unique (case-insensitive) labels
NxsTaxaBlockAPIThis abstract class describes the interface that every block that wants to serve as a reader of NEXUS TAXA blocks should fulfill
NxsTaxaBlockSurrogateThis class is the base class for blocks that can (in a pinch) serve as a TAXA block reader(NxsCharactersBlock, NxsTreesBlock, NxsUnalignedBlock, and NxsDistancesBlock)
NxsTokenPosInfoStorage for a file position, line number and column number
NxsTransformationManagerNEXUS "types" (as in UserType and TypeSet commands) are assumptions about the costs of transformations of state (in parsimony
NxsTreesBlockThis class handles reading and storage for the NEXUS block TREES
NxsUnalignedBlockThis class handles reading and storage for the NEXUS block UNALIGNED
NxsUnimplementedExceptionThrown when an unimplemented method is called
ProcessedNxsTokenStorage for a single NEXUS token, and embedded comments, along with end-of-the-token file position information
PublicNexusReaderA NxsReader that uses clone factories to read public blocks
ScopedTwoDMatrix< T >Simple memory-management class for a 2-D array that is allocated using NewTwoDArray
Type2Type< T >
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