Uses of Interface
info.bioinfweb.jphyloio.JPhyloIOEventReader

Packages that use JPhyloIOEventReader

Package	Description
info.bioinfweb.jphyloio	The main package of JPhyloIO.
info.bioinfweb.jphyloio.factory	Contains interfaces and general implementations for creating JPhyloIO readers and writers related to JPhyloIOReaderWriterFactory.
info.bioinfweb.jphyloio.formats.fasta	Contains classes for reading from and writing to streams/files in FASTA format.
info.bioinfweb.jphyloio.formats.mega	Contains classes for reading from and writing to streams/files in MEGA format.
info.bioinfweb.jphyloio.formats.newick	Contains classes for reading from and writing to streams/files in Newick tree format.
info.bioinfweb.jphyloio.formats.nexml	Contains classes for reading from and writing to streams/files in NeXML format.
info.bioinfweb.jphyloio.formats.nexus	Contains classes for reading from and writing to streams/files in Nexus format.
info.bioinfweb.jphyloio.formats.pde	Contains classes for reading from streams/files in PDE format.
info.bioinfweb.jphyloio.formats.phylip	Contains classes for reading from and writing to streams/files in Phylip format.
info.bioinfweb.jphyloio.formats.phyloxml	Contains classes for reading from and writing to streams/files in PhyloXML format.
info.bioinfweb.jphyloio.formats.text	Contains classes implementing shared functionality for reading from and writing to streams/files in text formats.
info.bioinfweb.jphyloio.formats.xml	Contains classes implementing shared functionality for reading from and writing to streams/files in XML formats.
info.bioinfweb.jphyloio.formats.xtg	Contains classes for reading from and writing to streams/files in XTG format.
info.bioinfweb.jphyloio.push	Contains classes that allow push-parsing.
info.bioinfweb.jphyloio.utils	Contains general tool classes of JPhyloIO.

Uses of JPhyloIOEventReader in info.bioinfweb.jphyloio

Classes in info.bioinfweb.jphyloio that implement JPhyloIOEventReader

Modifier and Type	Class and Description
class	AbstractEventReader<P extends ReaderStreamDataProvider<? extends AbstractEventReader<P>>> Basic implementation for event readers in PhyloIO.

Uses of JPhyloIOEventReader in info.bioinfweb.jphyloio.factory

Methods in info.bioinfweb.jphyloio.factory that return JPhyloIOEventReader

Modifier and Type	Method and Description
JPhyloIOEventReader	SingleReaderWriterFactory.getReader(java.io.InputStream stream, ReadWriteParameterMap parameters) Creates a new reader instance for the target format of this factory.
JPhyloIOEventReader	SingleReaderWriterFactory.getReader(java.io.Reader reader, ReadWriteParameterMap parameters) Creates a new reader instance for the target format of this factory.
JPhyloIOEventReader	JPhyloIOReaderWriterFactory.getReader(java.lang.String formatID, java.io.File file, ReadWriteParameterMap parameters)
JPhyloIOEventReader	JPhyloIOReaderWriterFactory.getReader(java.lang.String formatID, java.io.InputStream stream, ReadWriteParameterMap parameters)
JPhyloIOEventReader	JPhyloIOReaderWriterFactory.getReader(java.lang.String formatID, java.io.Reader reader, ReadWriteParameterMap parameters)
JPhyloIOEventReader	JPhyloIOReaderWriterFactory.guessReader(java.io.File file, ReadWriteParameterMap parameters) Tries to determine the format of the contents of the specified file as described in the documentation of JPhyloIOReaderWriterFactory.guessFormat(File) and than creates a reader for the according format from that stream.
JPhyloIOEventReader	JPhyloIOReaderWriterFactory.guessReader(java.io.InputStream stream, ReadWriteParameterMap parameters) Tries to determine the format of the contents of the specified input stream as described in the documentation of JPhyloIOReaderWriterFactory.guessFormat(InputStream), resets the input stream and than creates a reader for the according format from that stream.

Uses of JPhyloIOEventReader in info.bioinfweb.jphyloio.formats.fasta

Classes in info.bioinfweb.jphyloio.formats.fasta that implement JPhyloIOEventReader

Modifier and Type	Class and Description
class	FASTAEventReader Event based reader for FASTA alignment files.

Methods in info.bioinfweb.jphyloio.formats.fasta that return JPhyloIOEventReader

Modifier and Type	Method and Description
JPhyloIOEventReader	FASTAFactory.getReader(java.io.InputStream stream, ReadWriteParameterMap parameters)
JPhyloIOEventReader	FASTAFactory.getReader(java.io.Reader reader, ReadWriteParameterMap parameters)

Uses of JPhyloIOEventReader in info.bioinfweb.jphyloio.formats.mega

Classes in info.bioinfweb.jphyloio.formats.mega that implement JPhyloIOEventReader

Modifier and Type	Class and Description
class	MEGAEventReader Event based reader for MEGA alignment files.

Methods in info.bioinfweb.jphyloio.formats.mega that return JPhyloIOEventReader

Modifier and Type	Method and Description
JPhyloIOEventReader	MEGAFactory.getReader(java.io.InputStream stream, ReadWriteParameterMap parameters)
JPhyloIOEventReader	MEGAFactory.getReader(java.io.Reader reader, ReadWriteParameterMap parameters)

Uses of JPhyloIOEventReader in info.bioinfweb.jphyloio.formats.newick

Classes in info.bioinfweb.jphyloio.formats.newick that implement JPhyloIOEventReader

Modifier and Type	Class and Description
class	NewickEventReader Reads tree files in Newick format.

Methods in info.bioinfweb.jphyloio.formats.newick that return JPhyloIOEventReader

Modifier and Type	Method and Description
JPhyloIOEventReader	NewickFactory.getReader(java.io.InputStream stream, ReadWriteParameterMap parameters)
JPhyloIOEventReader	NewickFactory.getReader(java.io.Reader reader, ReadWriteParameterMap parameters)

Uses of JPhyloIOEventReader in info.bioinfweb.jphyloio.formats.nexml

Classes in info.bioinfweb.jphyloio.formats.nexml that implement JPhyloIOEventReader

Modifier and Type	Class and Description
class	NeXMLEventReader An event reader for the NeXML format.

Methods in info.bioinfweb.jphyloio.formats.nexml that return JPhyloIOEventReader

Modifier and Type	Method and Description
JPhyloIOEventReader	NeXMLFactory.getReader(java.io.InputStream stream, ReadWriteParameterMap parameters)
JPhyloIOEventReader	NeXMLFactory.getReader(java.io.Reader reader, ReadWriteParameterMap parameters)

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

Classes in info.bioinfweb.jphyloio.formats.nexus that implement JPhyloIOEventReader

Modifier and Type	Class and Description
class	NexusEventReader Event based reader for Nexus files.

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

Modifier and Type	Method and Description
JPhyloIOEventReader	NexusFactory.getReader(java.io.InputStream stream, ReadWriteParameterMap parameters)
JPhyloIOEventReader	NexusFactory.getReader(java.io.Reader reader, ReadWriteParameterMap parameters)

Uses of JPhyloIOEventReader in info.bioinfweb.jphyloio.formats.pde

Classes in info.bioinfweb.jphyloio.formats.pde that implement JPhyloIOEventReader

Modifier and Type	Class and Description
class	PDEEventReader Event reader for the PDE format used by the alignment editor PhyDE.

Methods in info.bioinfweb.jphyloio.formats.pde that return JPhyloIOEventReader

Modifier and Type	Method and Description
JPhyloIOEventReader	PDEFactory.getReader(java.io.InputStream stream, ReadWriteParameterMap parameters)
JPhyloIOEventReader	PDEFactory.getReader(java.io.Reader reader, ReadWriteParameterMap parameters)

Uses of JPhyloIOEventReader in info.bioinfweb.jphyloio.formats.phylip

Classes in info.bioinfweb.jphyloio.formats.phylip that implement JPhyloIOEventReader

Modifier and Type	Class and Description
class	AbstractPhylipEventReader<P extends TextReaderStreamDataProvider<? extends AbstractPhylipEventReader<P>>> Implements shared functionality of Phylip event readers.
class	PhylipEventReader Event based reader for Phylip alignment files.
class	SequentialPhylipEventReader Event based reader for sequential Phylip alignment files.

Methods in info.bioinfweb.jphyloio.formats.phylip that return JPhyloIOEventReader

Modifier and Type	Method and Description
JPhyloIOEventReader	PhylipFactory.getReader(java.io.InputStream stream, ReadWriteParameterMap parameters)
JPhyloIOEventReader	SequentialPhylipFactory.getReader(java.io.InputStream stream, ReadWriteParameterMap parameters)
JPhyloIOEventReader	PhylipFactory.getReader(java.io.Reader reader, ReadWriteParameterMap parameters)
JPhyloIOEventReader	SequentialPhylipFactory.getReader(java.io.Reader reader, ReadWriteParameterMap parameters)

Uses of JPhyloIOEventReader in info.bioinfweb.jphyloio.formats.phyloxml

Classes in info.bioinfweb.jphyloio.formats.phyloxml that implement JPhyloIOEventReader

Modifier and Type	Class and Description
class	PhyloXMLEventReader Event reader for the PhyloXML format.

Methods in info.bioinfweb.jphyloio.formats.phyloxml that return JPhyloIOEventReader

Modifier and Type	Method and Description
JPhyloIOEventReader	PhyloXMLFactory.getReader(java.io.InputStream stream, ReadWriteParameterMap parameters)
JPhyloIOEventReader	PhyloXMLFactory.getReader(java.io.Reader reader, ReadWriteParameterMap parameters)

Uses of JPhyloIOEventReader in info.bioinfweb.jphyloio.formats.text

Classes in info.bioinfweb.jphyloio.formats.text that implement JPhyloIOEventReader

Modifier and Type	Class and Description
class	AbstractTextEventReader<P extends TextReaderStreamDataProvider<? extends AbstractTextEventReader<P>>> Abstract base class for all readers that read their data from a file using a PeekReader.

Uses of JPhyloIOEventReader in info.bioinfweb.jphyloio.formats.xml

Subinterfaces of JPhyloIOEventReader in info.bioinfweb.jphyloio.formats.xml

Modifier and Type	Interface and Description
interface	JPhyloIOXMLEventReader Interface providing basic functionality for all JPhyloIO readers of XML formats.

Classes in info.bioinfweb.jphyloio.formats.xml that implement JPhyloIOEventReader

Modifier and Type	Class and Description
class	AbstractXMLEventReader<P extends XMLReaderStreamDataProvider<? extends AbstractXMLEventReader<P>>> Implements shared functionality for reading XML formats.

Uses of JPhyloIOEventReader in info.bioinfweb.jphyloio.formats.xtg

Classes in info.bioinfweb.jphyloio.formats.xtg that implement JPhyloIOEventReader

Modifier and Type	Class and Description
class	XTGEventReader Event reader for the extensible TreeGraph 2 format (XTG) used by the phylogenetic tree editor TreeGraph 2.

Methods in info.bioinfweb.jphyloio.formats.xtg that return JPhyloIOEventReader

Modifier and Type	Method and Description
JPhyloIOEventReader	XTGFactory.getReader(java.io.InputStream stream, ReadWriteParameterMap parameters)
JPhyloIOEventReader	XTGFactory.getReader(java.io.Reader reader, ReadWriteParameterMap parameters)

Uses of JPhyloIOEventReader in info.bioinfweb.jphyloio.push

Methods in info.bioinfweb.jphyloio.push with parameters of type JPhyloIOEventReader

Modifier and Type	Method and Description
void	JPhyloIOEventListener.processEvent(JPhyloIOEventReader source, JPhyloIOEvent event) Called after an event was received from a reader instance.
void	EventForwarder.readAll(JPhyloIOEventReader reader) Consumes all available events from the specified listener and forwards them to the registered listeners.
void	EventForwarder.readCurrentNode(JPhyloIOEventReader reader) Consumes all events between a start and its respective end event.
void	EventForwarder.readUntil(JPhyloIOEventReader reader, EventContentType type) Consumes all available events from the specified listener and forwards them to the registered listeners until an event of the specified type is reached.
void	EventForwarder.readUntil(JPhyloIOEventReader reader, java.util.Set<EventContentType> types) Consumes all available events from the specified listener and forwards them to the registered listeners until any event of one of the specified types is reached.

Uses of JPhyloIOEventReader in info.bioinfweb.jphyloio.utils

Methods in info.bioinfweb.jphyloio.utils that return JPhyloIOEventReader

Modifier and Type	Method and Description
JPhyloIOEventReader	SequenceTokensEventManager.getOwner() Returns the reader instance using this object.

Methods in info.bioinfweb.jphyloio.utils with parameters of type JPhyloIOEventReader

Modifier and Type	Method and Description
static java.util.List<JPhyloIOEvent>	JPhyloIOReadingUtils.collectEvents(JPhyloIOEventReader reader, java.util.Set<EventType> types) Reads all (remaining) events from the specified reader and adds events that have a type that is contained in the # specified set to the returned list.
static <E extends JPhyloIOEvent> java.util.List<E>	JPhyloIOReadingUtils.collectEvents(JPhyloIOEventReader reader, java.util.Set<EventType> types, java.lang.Class<E> instanceClass) Reads all (remaining) events from the specified reader and adds events that implement the specified class and have a type that is contained in the specified set to the returned list.
static void	JPhyloIOReadingUtils.reachElementEnd(JPhyloIOEventReader reader) Reads all events from the reader until one more end element than start elements is found.
static <O> O	JPhyloIOReadingUtils.readLiteralMetadataContentAsObject(JPhyloIOEventReader reader, java.lang.Class<O> objectClass) Reads a subsequence from an JPhyloIO event stream modeling contents of a literal metadata element into an object of the specified class.
static java.lang.String	JPhyloIOReadingUtils.readLiteralMetadataContentAsString(JPhyloIOEventReader reader) This convenience method calls JPhyloIOReadingUtils.readLiteralMetadataContentAsStringBuilder(JPhyloIOEventReader) internally and converts its content to a String if the builder is not null.
static java.lang.StringBuilder	JPhyloIOReadingUtils.readLiteralMetadataContentAsStringBuilder(JPhyloIOEventReader reader) Reads a subsequence from an JPhyloIO event stream modeling contents of a literal metadata element into a string builder.

Constructors in info.bioinfweb.jphyloio.utils with parameters of type JPhyloIOEventReader

Constructor and Description
SequenceTokensEventManager(JPhyloIOEventReader owner, java.lang.String matchToken) Creates a new instance of this class.