## Uses of Interface
info.bioinfweb.jphyloio.dataadapters.JPhyloIOEventReceiver

- Packages that use JPhyloIOEventReceiver
  Package | Description
  --- | ---
  info.bioinfweb.jphyloio | The main package of JPhyloIO.
  info.bioinfweb.jphyloio.dataadapters | Contains adapter interfaces that should be implemented by adapters mediating between the business model of an application and implementations of `JPhyloIOEventWriter`.
  info.bioinfweb.jphyloio.dataadapters.implementations | Contains some basic (abstract) implementations of `JPhyloIOEventWriter`.
  info.bioinfweb.jphyloio.dataadapters.implementations.receivers | Contains some basic (abstract) implementations of `JPhyloIOEventReceiver` to be used by implementations of `JPhyloIOEventWriter`.
  info.bioinfweb.jphyloio.dataadapters.implementations.store | Contains implementations of data adapters that directly store their modeled data in mutable lists or maps instead of delegating to an application business model.
  info.bioinfweb.jphyloio.exception | Contains exceptions that are of general use in JPhyloIO.
  info.bioinfweb.jphyloio.formats.newick | Contains classes for reading from and writing to streams/files in Newick tree format.
  info.bioinfweb.jphyloio.formats.nexml.receivers | Contains implementations for `JPhyloIOEventReceiver` necessary for writing NeXML.
  info.bioinfweb.jphyloio.formats.nexus.receivers | Contains implementations of `JPhyloIOEventReceiver` used internally by `NexusEventReader`.
  info.bioinfweb.jphyloio.formats.phyloxml.receivers | Contains implementations for `JPhyloIOEventReceiver` necessary for writing PhyloXML.
  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.xml.receivers | Contains general (abstract) implementations for `JPhyloIOEventReceiver` necessary for writing XML formats.
  info.bioinfweb.jphyloio.formats.xml.stax | Contains implementations that allow StAX based reading and writing of XML metadata.
  info.bioinfweb.jphyloio.utils | Contains general tool classes of JPhyloIO.

- - ### Uses of JPhyloIOEventReceiver in info.bioinfweb.jphyloio

    Methods in info.bioinfweb.jphyloio with parameters of type JPhyloIOEventReceiver
    Modifier and Type | Method and Description
    --- | ---
    `protected void` | AbstractEventWriter.`extendSequence(MatrixDataAdapter matrix, ReadWriteParameterMap parameters, java.lang.String sequenceID, long targetLength, java.lang.String extensionToken, JPhyloIOEventReceiver receiver)`

  - ### Uses of JPhyloIOEventReceiver in info.bioinfweb.jphyloio.dataadapters

    Methods in info.bioinfweb.jphyloio.dataadapters with parameters of type JPhyloIOEventReceiver
    Modifier and Type | Method and Description
    --- | ---
    `void` | ObjectListDataAdapter.`writeContentData(ReadWriteParameterMap parameters, JPhyloIOEventReceiver receiver, java.lang.String id)` Writes the nested events in the specified object describing its contents.
    `void` | AnnotatedDataAdapter.`writeMetadata(ReadWriteParameterMap parameters, JPhyloIOEventReceiver receiver)` Writes events describing the metadata associated with the object represented by this instance.
    `void` | MatrixDataAdapter.`writeSequencePartContentData(ReadWriteParameterMap parameters, JPhyloIOEventReceiver receiver, java.lang.String sequenceID, long startColumn, long endColumn)` Implementing classes must write a sequence of events here, that describe the sequence tokens present in the specified column range.

  - ### Uses of JPhyloIOEventReceiver in info.bioinfweb.jphyloio.dataadapters.implementations

    Methods in info.bioinfweb.jphyloio.dataadapters.implementations with parameters of type JPhyloIOEventReceiver
    Modifier and Type | Method and Description
    --- | ---
    `void` | EmptyObjectListDataAdapter.`writeContentData(ReadWriteParameterMap parameters, JPhyloIOEventReceiver receiver, java.lang.String id)` Always throws an `IllegalArgumentException`, since this default implementation does not contain any objects.
    `void` | UndefinedOTUListDataAdapter.`writeContentData(ReadWriteParameterMap parameters, JPhyloIOEventReceiver receiver, java.lang.String id)`
    `void` | EmptyAnnotatedDataAdapter.`writeMetadata(ReadWriteParameterMap parameters, JPhyloIOEventReceiver receiver)` This default implementation does nothing and can be overwritten by inherited classes if necessary.
    `void` | UndefinedOTUListDataAdapter.`writeMetadata(ReadWriteParameterMap parameters, JPhyloIOEventReceiver receiver)`

  - ### Uses of JPhyloIOEventReceiver in info.bioinfweb.jphyloio.dataadapters.implementations.receivers

    Classes in info.bioinfweb.jphyloio.dataadapters.implementations.receivers that implement JPhyloIOEventReceiver
    Modifier and Type | Class and Description
    --- | ---
    `class` | `AbstractSequenceContentReceiver<P extends WriterStreamDataProvider<? extends AbstractEventWriter<P>>>`
    `class` | `BasicEventReceiver<P extends WriterStreamDataProvider<? extends AbstractEventWriter<P>>>` Most event receivers will be inherited from this class.

  - ### Uses of JPhyloIOEventReceiver in info.bioinfweb.jphyloio.dataadapters.implementations.store

    Methods in info.bioinfweb.jphyloio.dataadapters.implementations.store with parameters of type JPhyloIOEventReceiver
    Modifier and Type | Method and Description
    --- | ---
    `void` | StoreOTUListDataAdapter.`writeContentData(ReadWriteParameterMap parameters, JPhyloIOEventReceiver receiver, java.lang.String id)`
    `void` | StoreObjectListDataAdapter.`writeContentData(ReadWriteParameterMap parameters, JPhyloIOEventReceiver receiver, java.lang.String id)`
    `void` | StoreAnnotatedDataAdapter.`writeMetadata(ReadWriteParameterMap parameters, JPhyloIOEventReceiver receiver)`
    `void` | StoreMatrixDataAdapter.`writeSequencePartContentData(ReadWriteParameterMap parameters, JPhyloIOEventReceiver receiver, java.lang.String sequenceID, long startColumn, long endColumn)`

  - ### Uses of JPhyloIOEventReceiver in info.bioinfweb.jphyloio.exception

    Methods in info.bioinfweb.jphyloio.exception that return JPhyloIOEventReceiver
    Modifier and Type | Method and Description
    --- | ---
    `JPhyloIOEventReceiver` | IllegalEventException.`getReceiver()`

    Methods in info.bioinfweb.jphyloio.exception with parameters of type JPhyloIOEventReceiver
    Modifier and Type | Method and Description
    --- | ---
    `static IllegalEventException` | IllegalEventException.`newInstance(JPhyloIOEventReceiver receiver, JPhyloIOEvent parentEvent, JPhyloIOEvent invalidEvent)` Tool method that creates a new instance of this class.

    Constructors in info.bioinfweb.jphyloio.exception with parameters of type JPhyloIOEventReceiver
    Constructor and Description
    `IllegalEventException(java.lang.String message, JPhyloIOEventReceiver receiver, JPhyloIOEvent parentEvent, JPhyloIOEvent invalidEvent)`

  - ### Uses of JPhyloIOEventReceiver in info.bioinfweb.jphyloio.formats.newick

    Classes in info.bioinfweb.jphyloio.formats.newick that implement JPhyloIOEventReceiver
    Modifier and Type | Class and Description
    --- | ---
    `class` | `NewickNodeEdgeEventReceiver<E extends JPhyloIOEvent>`

  - ### Uses of JPhyloIOEventReceiver in info.bioinfweb.jphyloio.formats.nexml.receivers

    Classes in info.bioinfweb.jphyloio.formats.nexml.receivers that implement JPhyloIOEventReceiver
    Modifier and Type | Class and Description
    --- | ---
    `class` | `AbstractNeXMLDataReceiver` Implements basic functionality for event receivers writing NeXML.
    `class` | `NeXMLAttributeMetadataReceiver` Receiver that is used to store the contents of metadata events with certain predicates in a map to be written as attribute/value pairs later on.
    `class` | `NeXMLCharacterSetEventReceiver` Receiver that ensures no other events than character set intervals are contained in a character set.
    `class` | `NeXMLCollectCharSetDataReceiver` Receiver that collects the IDs of character set elements.
    `class` | `NeXMLCollectNamespaceReceiver` Receiver that collects namespace definitions occurring in document metadata by calling the according methods of the `AbstractNeXMLDataReceiverMixin`.
    `class` | `NeXMLCollectSequenceDataReceiver` Receiver that collects information about the sequence tokens contained in a document.
    `class` | `NeXMLCollectSetMetadataReceiver` Receiver that collects information about sets contained in a document.
    `class` | `NeXMLCollectTokenSetDefinitionDataReceiver` Receiver that is used to check the contents of a token set.
    `class` | `NeXMLHandleSequenceDataReceiver` General implementation of a receiver that processes sequence tokens.
    `class` | `NeXMLIgnoreCertainMetadataReceiver` Receiver that is able to ignore metadata events with certain predicates, e.g.
    `class` | `NeXMLMetaDataReceiver` This receiver should be used if no other elements than meta are expected under an element.
    `class` | `NeXMLMolecularDataTokenDefinitionReceiver` Receiver that writes token definitions for molecular data, such as DNA, RNA or protein sequences.
    `class` | `NeXMLOnlyWriteMetaDataReceiver` Receiver that writes meta data but ignores other events that were processed previously.
    `class` | `NeXMLPredicateMetaReceiver` General implementation of a receiver that allows to process metadata events with certain predicates in a special way.
    `class` | `NeXMLSequenceTokensReceiver` Receiver that is used to write sequence tokens.
    `class` | `NeXMLTokenSetEventReceiver` Receiver that is used to write token sets.

  - ### Uses of JPhyloIOEventReceiver in info.bioinfweb.jphyloio.formats.nexus.receivers

    Classes in info.bioinfweb.jphyloio.formats.nexus.receivers that implement JPhyloIOEventReceiver
    Modifier and Type | Class and Description
    --- | ---
    `class` | `AbstractNexusEventReceiver` Implements basic functionality for event receivers writing Nexus.
    `class` | `AbstractNexusSetsEventReceiver` General implementation for event receivers writing Nexus set commands.
    `class` | `CharacterSetEventReceiver`
    `class` | `ReferenceOnlySetReceiver`
    `class` | `TokenSetEventReceiver`

  - ### Uses of JPhyloIOEventReceiver in info.bioinfweb.jphyloio.formats.phyloxml.receivers

    Classes in info.bioinfweb.jphyloio.formats.phyloxml.receivers that implement JPhyloIOEventReceiver
    Modifier and Type | Class and Description
    --- | ---
    `class` | `PhyloXMLCollectMetadataDataReceiver` Receiver that is used to collect information from meta events (e.g.
    `class` | `PhyloXMLMetaDataReceiver` Receiver that implements a general strategy of writing metadata to a PhyloXML document.
    `class` | `PhyloXMLOnlyCustomXMLDataReceiver` Receiver, that writes only custom XML, e.g nested under `document`.
    `class` | `PhyloXMLPropertyMetadataReceiver` This receiver is used to write the contents of meta events to a document, if their predicates indicate that they contain information about a PhyloXML `property` tag.
    `class` | `PhyloXMLSpecificPredicatesDataReceiver` Receiver that is used to translate between meta events with certain predicates indicating they contain information about a PhyloXML tag and the actual tag.

  - ### Uses of JPhyloIOEventReceiver in info.bioinfweb.jphyloio.formats.text

    Classes in info.bioinfweb.jphyloio.formats.text that implement JPhyloIOEventReceiver
    Modifier and Type | Class and Description
    --- | ---
    `class` | `BasicTextCommentEventReceiver<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>>` Basic event receiver implementation that writes comments to text formats that are delimited by a start and an end string.
    `class` | `TextSequenceContentReceiver<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>>` Receiver that writes all encountered sequence tokens and comments to the current line and ignores all metadata.

  - ### Uses of JPhyloIOEventReceiver in info.bioinfweb.jphyloio.formats.xml

    Methods in info.bioinfweb.jphyloio.formats.xml with parameters of type JPhyloIOEventReceiver
    Modifier and Type | Method and Description
    --- | ---
    `javax.xml.stream.XMLEventWriter` | AbstractXMLEventWriter.`createMetaXMLEventWriter(JPhyloIOEventReceiver receiver)`
    `javax.xml.stream.XMLEventWriter` | JPhyloIOXMLEventWriter.`createMetaXMLEventWriter(JPhyloIOEventReceiver receiver)` Creates a new `XMLEventWriter` that allows to write events of XML content of literal metadata to this JPhyloIO event writer instance through that interface.
    `javax.xml.stream.XMLStreamWriter` | AbstractXMLEventWriter.`createMetaXMLStreamWriter(JPhyloIOEventReceiver receiver)`
    `javax.xml.stream.XMLStreamWriter` | JPhyloIOXMLEventWriter.`createMetaXMLStreamWriter(JPhyloIOEventReceiver receiver)` Creates a new `XMLStreamWriter` that allows to write events of XML content of literal metadata to this JPhyloIO event writer instance through that interface.

  - ### Uses of JPhyloIOEventReceiver in info.bioinfweb.jphyloio.formats.xml.receivers

    Classes in info.bioinfweb.jphyloio.formats.xml.receivers that implement JPhyloIOEventReceiver
    Modifier and Type | Class and Description
    --- | ---
    `class` | `AbstractXMLDataReceiver<P extends XMLWriterStreamDataProvider<? extends AbstractXMLEventWriter<P>>>` Abstract implementation of a data receiver that can be used to write XML formats.

  - ### Uses of JPhyloIOEventReceiver in info.bioinfweb.jphyloio.formats.xml.stax

    Methods in info.bioinfweb.jphyloio.formats.xml.stax that return JPhyloIOEventReceiver
    Modifier and Type | Method and Description
    --- | ---
    `protected JPhyloIOEventReceiver` | AbstractMetaXMLWriter.`getReceiver()`

    Constructors in info.bioinfweb.jphyloio.formats.xml.stax with parameters of type JPhyloIOEventReceiver
    Constructor and Description
    `AbstractMetaXMLWriter(JPhyloIOEventReceiver receiver, javax.xml.stream.XMLStreamWriter underlyingXMLWriter)`
    `MetaXMLEventWriter(JPhyloIOEventReceiver receiver, javax.xml.stream.XMLStreamWriter underlyingXMLWriter)` Creates a new instance of this class.
    `MetaXMLStreamWriter(JPhyloIOEventReceiver receiver, javax.xml.stream.XMLStreamWriter underlyingXMLWriter)` Creates a new instance of this class.

  - ### Uses of JPhyloIOEventReceiver in info.bioinfweb.jphyloio.utils

    Methods in info.bioinfweb.jphyloio.utils with parameters of type JPhyloIOEventReceiver
    Modifier and Type | Method and Description
    --- | ---
    `static void` | JPhyloIOWritingUtils.`writeCharSequencePartContent(JPhyloIOEventReceiver receiver, long startColumn, long endColumn, java.lang.CharSequence source)`
    `static void` | JPhyloIOWritingUtils.`writeListSequencePartContent(JPhyloIOEventReceiver receiver, long startColumn, long endColumn, java.util.List<?> source)`
    `static void` | JPhyloIOWritingUtils.`writeSimpleLiteralMetadata(JPhyloIOEventReceiver receiver, java.lang.String id, java.lang.String label, javax.xml.namespace.QName predicate, javax.xml.namespace.QName originalType, java.lang.Object objectValue)` Writes an event subsequence modeling a literal metadata annotation with a simple value.
    `static void` | JPhyloIOWritingUtils.`writeSimpleLiteralMetadata(JPhyloIOEventReceiver receiver, java.lang.String id, java.lang.String label, javax.xml.namespace.QName predicate, javax.xml.namespace.QName originalType, java.lang.Object objectValue, java.lang.String stringRepresentation)` Writes an event subsequence modeling a literal metadata annotation with a simple value.
    `static void` | JPhyloIOWritingUtils.`writeSimpleLiteralMetadata(JPhyloIOEventReceiver receiver, java.lang.String id, java.lang.String label, URIOrStringIdentifier predicate, URIOrStringIdentifier originalType, java.lang.Object objectValue, java.lang.String stringRepresentation)` Writes an event subsequence modeling a literal metadata annotation with a simple value.
    `static void` | JPhyloIOWritingUtils.`writeTerminalResourceMetadata(JPhyloIOEventReceiver receiver, java.lang.String id, java.lang.String label, javax.xml.namespace.QName rel, java.net.URI hRef)` Writes a `ResourceMetadataEvent` and its respective end event to the specified receiver.
    `static void` | JPhyloIOWritingUtils.`writeTerminalResourceMetadata(JPhyloIOEventReceiver receiver, java.lang.String id, java.lang.String label, javax.xml.namespace.QName rel, java.net.URI hRef, java.lang.String about)` Writes a `ResourceMetadataEvent` and its respective end event to the specified receiver.
    `static void` | JPhyloIOWritingUtils.`writeTerminalResourceMetadata(JPhyloIOEventReceiver receiver, java.lang.String id, java.lang.String label, URIOrStringIdentifier rel, java.net.URI hRef)` Writes a `ResourceMetadataEvent` and its respective end event to the specified receiver.
    `static void` | JPhyloIOWritingUtils.`writeTerminalResourceMetadata(JPhyloIOEventReceiver receiver, java.lang.String id, java.lang.String label, URIOrStringIdentifier rel, java.net.URI hRef, java.lang.String about)` Writes a `ResourceMetadataEvent` and its respective end event to the specified receiver.