Package org.biojavax.bio.phylo.io.nexus

Classes to support the I/O of Nexus files.

Interface Summary

Interface	Description
CharactersBlockListener	Listens to events that represent Nexus characters blocks.
DataBlockListener	Listens to events that represent Nexus data blocks.
DistancesBlockListener	Listens to events that represent Nexus distances blocks.
NexusBlock	Represents a Nexus block.
NexusBlockBuilder	Builds a Nexus block from listening to events.
NexusBlockListener	Listens to events from NexusBlockParser objects to create objects.
NexusBlockParser	Parses Nexus blocks.
NexusFileListener	Listens to events fired by the Nexus parser.
NexusObject	Represents general info about nexus objects.
TaxaBlockListener	Listens to events that represent Nexus taxa blocks.
TreesBlockListener	Listens to events that represent Nexus trees blocks.

Class Summary

Class	Description
CharactersBlock	Represents Nexus characters blocks.
CharactersBlockBuilder	Builds Nexus characters blocks.
CharactersBlockParser	Parses Nexus characters blocks.
DataBlock	Represents Nexus data blocks.
DataBlockBuilder	Builds Nexus characters blocks.
DataBlockParser	Parses Nexus data blocks.
DistancesBlock	Represents Nexus distances blocks.
DistancesBlockBuilder	Builds Nexus distances blocks.
DistancesBlockParser	Parses Nexus distances blocks.
NexusBlock.Abstract
NexusBlockBuilder.Abstract	This abstract version knows how to build and add comments.
NexusBlockParser.Abstract	All block parsers should derive from this abstract parser.
NexusComment	Represents a Nexus comment, possibly nested.
NexusFile	Represents Nexus files.
NexusFileBuilder	Builds a Nexus file by listening to events.
NexusFileFormat	Reads/writes Nexus files and fires events at a NexusFileListener object.
NexusFileListener.Abstract	Example abstract implementation which all others should extend.
TaxaBlock	Represents Nexus taxa blocks.
TaxaBlockBuilder	Builds Nexus taxa blocks.
TaxaBlockParser	Parses Nexus taxa blocks.
TreesBlock	Represents Nexus trees blocks.
TreesBlock.NewickTreeString	A simple representation of a Newick tree as a single string.
TreesBlockBuilder	Builds Nexus taxa blocks.
TreesBlockParser	Parses Nexus taxa blocks.