## 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.