| DefaultErrorReportNxsReader | A 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 |
| ExceptionRaisingNxsReader | A subclass of NxsReader that is used in much of NCL v2.1 |
| Int2Type< v > | |
| MultiFormatReader | A special class of PublicNexusReader, that can parse |
| NStrCaseInsensitiveEquals | Function object (Unary Predicate functor) that stores one string |
| NStrCaseSensitiveEquals | Function object (Unary Predicate functor) that stores one string |
| NxsAssumptionsBlock | This class handles reading and storage for the NxsReader block ASSUMPTIONS |
| NxsBlock | This is the base class from which all block classes are derived |
| NxsBlockFactory | This abstract class defines the interface for a factory that can generate NxsBlocks |
| NxsCharactersBlock | This class handles reading and storage for the NEXUS block CHARACTERS |
| NxsCharactersBlockAPI | Intended to specify the interface of a NxsCharactersBlock, but actually does not list all of the relevant functions |
| NxsCloneBlockFactory | A factory class that takes examplar that will be cloned to read each block |
| NxsComment | General notes on NexusTokenizing |
| NxsConversionOutputRecord | This 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 |
| NxsCXXDiscreteMatrix | |
| NxsDataBlock | This class handles reading and storage for the NEXUS block DATA |
| NxsDefaultPublicBlockFactory | A factory class that delegates calls to the other "default" public block parsers that NCL provides |
| NxsDiscreteDatatypeMapper | This 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 |
| NxsDiscreteDatum | Reference to a cell in a DiscreteMatrix |
| NxsDistanceDatum | This class stores pairwise distance values |
| NxsDistancesBlock | This class handles reading and storage for the NEXUS block DISTANCES |
| NxsException | Exception class that conveys a message specific to the problem encountered |
| NxsFullTreeDescription | A class that encapsulates a newick string description of a tree and metadata about the tree |
| NxsIntStepMatrix | Internal representation of a stepmatrix with cells composed of ints |
| NxsLabelToIndicesMapper | This is the base class for the block interfaces that correspond to blocks that hold ordered lists (TAXA, CHARACTERS, TREES) |
| NxsNCLAPIException | Thrown when a programming error (a violation of one of the APIs used in NCL) is revealed |
| NxsReader | This is the class that orchestrates the reading of a NEXUS data file, and so is the central class to NCL |
| NxsRealStepMatrix | Internal representation of a stepmatrix with cells composed of doubles |
| NxsSetReader | A class for reading NEXUS set objects and storing them in a set of int values |
| NxsSimpleCommandStrings | A structure for storing the name of a command and to maps of option names to value strings |
| NxsSimpleEdge | The edge used by the NxsSimpleTree class |
| NxsSimpleNode | The node used by the NxsSimpleTree class |
| NxsSimpleTree | A simple tree class |
| NxsString | A string class for use with the Nexus Class Library |
| NxsStringEqual | Binary function class that performs case-Insensitive string compares |
| NxsTaxaBlock | The default implementation of the NxsTaxaBlockAPI that is used to parse TAXA blocks into a list of unique (case-insensitive) labels |
| NxsTaxaBlockAPI | This abstract class describes the interface that every block that wants to serve as a reader of NEXUS TAXA blocks should fulfill |
| NxsTaxaBlockSurrogate | This class is the base class for blocks that can (in a pinch) serve as a TAXA block reader(NxsCharactersBlock, NxsTreesBlock, NxsUnalignedBlock, and NxsDistancesBlock) |
| NxsToken | |
| NxsTokenPosInfo | Storage for a file position, line number and column number |
| NxsTransformationManager | NEXUS "types" (as in UserType and TypeSet commands) are assumptions about the costs of transformations of state (in parsimony |
| NxsTreesBlock | This class handles reading and storage for the NEXUS block TREES |
| NxsUnalignedBlock | This class handles reading and storage for the NEXUS block UNALIGNED |
| NxsUnimplementedException | Thrown when an unimplemented method is called |
| ProcessedNxsToken | Storage for a single NEXUS token, and embedded comments, along with end-of-the-token file position information |
| PublicNexusReader | A 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 > | |
1.6.3
