Uses of Class
info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider

Packages that use NexusReaderStreamDataProvider

Package	Description
info.bioinfweb.jphyloio.formats.nexus	Contains classes for reading from and writing to streams/files in Nexus format.
info.bioinfweb.jphyloio.formats.nexus.blockhandlers	Contains implementations of NexusCommandEventReader for commands that are valid in all Nexus blocks.
info.bioinfweb.jphyloio.formats.nexus.commandreaders	Contains general classes for reading Nexus commands.
info.bioinfweb.jphyloio.formats.nexus.commandreaders.all	Contains implementations of NexusCommandEventReader for commands that are valid in all Nexus blocks.
info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters	Contains classes for reading Nexus commands in a CHARACTERS, UNALIGNED or DATA block.
info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets	Contains classes for reading Nexus commands in a SETS block.
info.bioinfweb.jphyloio.formats.nexus.commandreaders.taxa	Contains classes for reading Nexus commands in a TAXA block.
info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees	Contains classes for reading Nexus commands in a TREES block.

Uses of NexusReaderStreamDataProvider in info.bioinfweb.jphyloio.formats.nexus

Methods in info.bioinfweb.jphyloio.formats.nexus that return NexusReaderStreamDataProvider

Modifier and Type	Method and Description
protected NexusReaderStreamDataProvider	NexusEventReader.createStreamDataProvider()

Uses of NexusReaderStreamDataProvider in info.bioinfweb.jphyloio.formats.nexus.blockhandlers

Methods in info.bioinfweb.jphyloio.formats.nexus.blockhandlers with parameters of type NexusReaderStreamDataProvider

Modifier and Type	Method and Description
void	CharactersDataUnalignedBlockHandler.beforeCommand(NexusReaderStreamDataProvider streamDataProvider, java.lang.String commandName, NexusCommandEventReader commandReader)
void	NexusBlockHandler.beforeCommand(NexusReaderStreamDataProvider streamDataProvider, java.lang.String commandName, NexusCommandEventReader commandReader) This method is called before a command found in a block handled by this handler is processed, by calling the according command reader.
void	TaxaBlockHandler.beforeCommand(NexusReaderStreamDataProvider streamDataProvider, java.lang.String commandName, NexusCommandEventReader commandReader)
void	TreesBlockHandler.beforeCommand(NexusReaderStreamDataProvider streamDataProvider, java.lang.String commandName, NexusCommandEventReader commandReader)
void	CharactersDataUnalignedBlockHandler.handleBegin(NexusReaderStreamDataProvider streamDataProvider)
void	NexusBlockHandler.handleBegin(NexusReaderStreamDataProvider streamDataProvider) This method will be called by NexusEventReader each time a BEGIN command for a block listed in NexusBlockHandler.getBlockNames() is read.
void	TaxaBlockHandler.handleBegin(NexusReaderStreamDataProvider streamDataProvider)
void	TreesBlockHandler.handleBegin(NexusReaderStreamDataProvider streamDataProvider)
void	CharactersDataUnalignedBlockHandler.handleEnd(NexusReaderStreamDataProvider streamDataProvider)
void	NexusBlockHandler.handleEnd(NexusReaderStreamDataProvider streamDataProvider) This method will be called by NexusEventReader each time an END command for a block listed in NexusBlockHandler.getBlockNames() is read.
void	TaxaBlockHandler.handleEnd(NexusReaderStreamDataProvider streamDataProvider)
void	TreesBlockHandler.handleEnd(NexusReaderStreamDataProvider streamDataProvider)

Uses of NexusReaderStreamDataProvider in info.bioinfweb.jphyloio.formats.nexus.commandreaders

Methods in info.bioinfweb.jphyloio.formats.nexus.commandreaders that return NexusReaderStreamDataProvider

Modifier and Type	Method and Description
protected NexusReaderStreamDataProvider	AbstractNexusCommandEventReader.getStreamDataProvider()

Methods in info.bioinfweb.jphyloio.formats.nexus.commandreaders with parameters of type NexusReaderStreamDataProvider

Modifier and Type	Method and Description
NexusCommandEventReader	NexusCommandReaderFactory.createReader(java.lang.String blockName, java.lang.String commandName, NexusReaderStreamDataProvider streamDataProvider) Creates a new reader instance that is able to parse the specified command in the specified block, if an according class was registered in this factory instance.

Constructors in info.bioinfweb.jphyloio.formats.nexus.commandreaders with parameters of type NexusReaderStreamDataProvider

Constructor and Description
AbstractKeyValueCommandReader(java.lang.String commandName, java.lang.String[] validBlocks, NexusReaderStreamDataProvider nexusDocument)
AbstractNexusCommandEventReader(java.lang.String commandName, java.lang.String[] validBlocks, NexusReaderStreamDataProvider streamDataProvider) Creates a new instance of this class.
DefaultCommandReader(java.lang.String commandName, NexusReaderStreamDataProvider streamDataProvider) Creates a new instance of this class.

Uses of NexusReaderStreamDataProvider in info.bioinfweb.jphyloio.formats.nexus.commandreaders.all

Constructors in info.bioinfweb.jphyloio.formats.nexus.commandreaders.all with parameters of type NexusReaderStreamDataProvider

Constructor and Description
LinkReader(NexusReaderStreamDataProvider nexusDocument)
TitleReader(NexusReaderStreamDataProvider nexusDocument)

Uses of NexusReaderStreamDataProvider in info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters

Constructors in info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters with parameters of type NexusReaderStreamDataProvider

Constructor and Description
AbstractCharLabelsReader(java.lang.String commandName, NexusReaderStreamDataProvider streamDataProvider)
CharLabelsReader(NexusReaderStreamDataProvider streamDataProvider)
CharStateLabelsReader(NexusReaderStreamDataProvider streamDataProvider)
DimensionsReader(NexusReaderStreamDataProvider nexusDocument)
FormatReader(NexusReaderStreamDataProvider nexusDocument)
MatrixReader(NexusReaderStreamDataProvider nexusDocument)

Uses of NexusReaderStreamDataProvider in info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets

Constructors in info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets with parameters of type NexusReaderStreamDataProvider

Constructor and Description
AbstractNexusSetReader(EventContentType setType, java.lang.String commandName, java.lang.String[] validBlocks, NexusReaderStreamDataProvider nexusDocument)
CharSetReader(NexusReaderStreamDataProvider streamDataProvider)
IDBasedSetsReader(EventContentType setType, java.lang.String commandName, java.lang.String linkedBlockTypeName, EventContentType elementType, NexusReaderStreamDataProvider streamDataProvider)
TaxSetReader(NexusReaderStreamDataProvider streamDataProvider)
TreeSetReader(NexusReaderStreamDataProvider streamDataProvider)

Uses of NexusReaderStreamDataProvider in info.bioinfweb.jphyloio.formats.nexus.commandreaders.taxa

Constructors in info.bioinfweb.jphyloio.formats.nexus.commandreaders.taxa with parameters of type NexusReaderStreamDataProvider

Constructor and Description
TaxLabelsReader(NexusReaderStreamDataProvider nexusDocument)

Uses of NexusReaderStreamDataProvider in info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees

Constructors in info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees with parameters of type NexusReaderStreamDataProvider

Constructor and Description
ENewickNetworkReader(NexusReaderStreamDataProvider nexusDocument)
NexusNewickReaderNodeLabelProcessor(NexusReaderStreamDataProvider streamDataProvider)
TranslateReader(NexusReaderStreamDataProvider nexusDocument)
TreeReader(NexusReaderStreamDataProvider nexusDocument)
TreeReader(java.lang.String commandName, java.lang.String[] validBlocks, NexusReaderStreamDataProvider streamDataProvider)