## Uses of Class
info.bioinfweb.jphyloio.ReadWriteParameterMap

- Packages that use ReadWriteParameterMap
  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.factory | Contains interfaces and general implementations for creating JPhyloIO readers and writers related to `JPhyloIOReaderWriterFactory`.
  info.bioinfweb.jphyloio.formatinfo | Contains `JPhyloIOFormatInfo` and related classes that describe a format supported by JPhyloIO.
  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.nexml.receivers | Contains implementations for `JPhyloIOEventReceiver` necessary for writing NeXML.
  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.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.xtg | Contains classes for reading from and writing to streams/files in XTG format.
  info.bioinfweb.jphyloio.utils | Contains general tool classes of JPhyloIO.

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

    Methods in info.bioinfweb.jphyloio that return ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `protected ReadWriteParameterMap` | AbstractEventReader.`getParameters()`
    `ReadWriteParameterMap` | ReaderStreamDataProvider.`getParameters()` Returns the parameter map that was specified when the constructor of the associated reader was called.

    Methods in info.bioinfweb.jphyloio with parameters of type ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `static java.lang.String` | AbstractEventWriter.`createUniqueLabel(ReadWriteParameterMap parameters, AbstractEventWriter.UniqueLabelHandler handler, LabeledIDEvent event)`
    `static java.lang.String` | AbstractEventWriter.`createUniqueLabel(ReadWriteParameterMap parameters, AbstractEventWriter.UniqueLabelHandler handler, java.lang.String label1, java.lang.String id1, java.lang.String label2, java.lang.String id2)`
    `static java.lang.String` | AbstractEventWriter.`createUniqueLabel(ReadWriteParameterMap parameters, LabeledIDEvent event)`
    `static java.lang.String` | AbstractEventWriter.`createUniqueLinkedOTULabel(ReadWriteParameterMap parameters, AbstractEventWriter.UniqueLabelHandler handler, LinkedLabeledIDEvent event, OTUListDataAdapter otuList, boolean otuFirst)`
    `static long` | AbstractEventWriter.`determineMaxSequenceLength(MatrixDataAdapter matrix, ReadWriteParameterMap parameters)` Calculates the maximum sequence length in matrix with unequal lengths.
    `protected abstract void` | AbstractEventWriter.`doWriteDocument(DocumentDataAdapter document, java.io.Writer writer, ReadWriteParameterMap parameters)`
    `protected void` | AbstractSingleMatrixEventWriter.`doWriteDocument(DocumentDataAdapter document, java.io.Writer writer, ReadWriteParameterMap parameters)`
    `protected java.lang.String` | AbstractSingleMatrixEventWriter.`editSequenceOrNodeLabel(LinkedLabeledIDEvent event, ReadWriteParameterMap parameters, OTUListDataAdapter otuList)`
    `protected void` | AbstractEventWriter.`extendSequence(MatrixDataAdapter matrix, ReadWriteParameterMap parameters, java.lang.String sequenceID, long targetLength, java.lang.String extensionToken, JPhyloIOEventReceiver receiver)`
    `protected java.lang.String` | AbstractEventWriter.`getFileStartInfo(ReadWriteParameterMap parameters)`
    `static java.lang.String` | AbstractEventWriter.`getLinkedOTUNameOTUFirst(LinkedLabeledIDEvent linkedOTUEvent, OTUListDataAdapter otuList, ReadWriteParameterMap parameters)` Determines the name (label) to be used for the specified event when writing its data to a file.
    `static java.lang.String` | AbstractEventWriter.`getLinkedOTUNameOwnFirst(LinkedLabeledIDEvent linkedOTUEvent, OTUListDataAdapter otuList, ReadWriteParameterMap parameters)` Determines the name (label) to be used for the specified event when writing its data to a file.
    `static OTUListDataAdapter` | AbstractEventWriter.`getReferencedOTUList(DocumentDataAdapter document, ElementDataAdapter<LinkedLabeledIDEvent> source, ReadWriteParameterMap parameters)` Returns the OTU list found in `document` which is referenced by the specified event.
    `static void` | AbstractEventWriter.`logIngnoredOTULists(DocumentDataAdapter document, ApplicationLogger logger, ReadWriteParameterMap parameters, java.lang.String formatName, java.lang.String labeledElements)` Outputs a warning message, if the specified document data adapter provides one or more OTU lists.
    `void` | AbstractEventWriter.`writeDocument(DocumentDataAdapter document, java.io.File file, ReadWriteParameterMap parameters)`
    `void` | JPhyloIOEventWriter.`writeDocument(DocumentDataAdapter document, java.io.File file, ReadWriteParameterMap parameters)` Writes the data provided by the data adapter to a document in the according format of the implementing class.
    `void` | AbstractEventWriter.`writeDocument(DocumentDataAdapter document, java.io.OutputStream stream, ReadWriteParameterMap parameters)`
    `void` | JPhyloIOEventWriter.`writeDocument(DocumentDataAdapter document, java.io.OutputStream stream, ReadWriteParameterMap parameters)` Writes the data provided by the data adapter to a document in the according format of the implementing class.
    `void` | AbstractEventWriter.`writeDocument(DocumentDataAdapter document, java.io.Writer writer, ReadWriteParameterMap parameters)`
    `void` | JPhyloIOEventWriter.`writeDocument(DocumentDataAdapter document, java.io.Writer writer, ReadWriteParameterMap parameters)` Writes the data provided by the data adapter to a document in the according format of the implementing class.
    `static void` | AbstractEventWriter.`writeLineBreak(java.io.Writer writer, ReadWriteParameterMap parameters)` Writes the line separator, as it is specified in the parameter map or the line separator of the current operating system, if the map contains no according entry.
    `protected abstract void` | AbstractSingleMatrixEventWriter.`writeSingleMatrix(DocumentDataAdapter document, MatrixDataAdapter matrix, java.util.Iterator<java.lang.String> sequenceIDIterator, ReadWriteParameterMap parameters)` Implementations of this method should write a single matrix to their target format.

    Constructors in info.bioinfweb.jphyloio with parameters of type ReadWriteParameterMap
    Constructor and Description
    `AbstractEventReader(ReadWriteParameterMap parameters, java.lang.String matchToken)`

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

    Methods in info.bioinfweb.jphyloio.dataadapters with parameters of type ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `boolean` | MatrixDataAdapter.`containsLongTokens(ReadWriteParameterMap parameters)` Returns whether tokens longer than one character are contained in the matrix modeled by this instance.
    `ObjectListDataAdapter<CharacterDefinitionEvent>` | MatrixDataAdapter.`getCharacterDefinitions(ReadWriteParameterMap parameters)` Returns a list of character definitions for the matrix modeled by this instance.
    `ObjectListDataAdapter<LinkedLabeledIDEvent>` | MatrixDataAdapter.`getCharacterSets(ReadWriteParameterMap parameters)` Returns a list of character sets defined for the matrix modeled by this instance.
    `long` | MatrixDataAdapter.`getColumnCount(ReadWriteParameterMap parameters)` Returns the number of columns the modeled matrix has, if it contains aligned data or -1 if it contains unaligned data and each sequence may have a different length.
    `long` | ObjectListDataAdapter.`getCount(ReadWriteParameterMap parameters)` Returns the number of objects to be returned by `ObjectListDataAdapter.getIDIterator(ReadWriteParameterMap)`.
    `ObjectListDataAdapter<EdgeEvent>` | TreeNetworkDataAdapter.`getEdges(ReadWriteParameterMap parameters)` Returns the set of edges contained in this tree or network.
    `java.util.Iterator<java.lang.String>` | ObjectListDataAdapter.`getIDIterator(ReadWriteParameterMap parameters)` Returns an iterator returning the IDs of all objects contained in the list modeled by this instance.
    `java.util.Iterator<MatrixDataAdapter>` | DocumentDataAdapter.`getMatrixIterator(ReadWriteParameterMap parameters)` Returns an iterator providing access to all matrices contained in the document to be written.
    `ObjectListDataAdapter<LinkedLabeledIDEvent>` | TreeNetworkDataAdapter.`getNodeEdgeSets(ReadWriteParameterMap parameters)` Returns a list of node-and-edge-sets defined for the tree modeled by this instance.
    `ObjectListDataAdapter<NodeEvent>` | TreeNetworkDataAdapter.`getNodes(ReadWriteParameterMap parameters)` Returns the set of nodes contained in this tree or network.
    `E` | ObjectListDataAdapter.`getObjectStartEvent(ReadWriteParameterMap parameters, java.lang.String id)` Returns the start event of an object determined by the specified object ID.
    `OTUListDataAdapter` | DocumentDataAdapter.`getOTUList(ReadWriteParameterMap parameters, java.lang.String id)` Returns the OTU list referenced by the specified ID.
    `long` | DocumentDataAdapter.`getOTUListCount(ReadWriteParameterMap parameters)` Returns the number of OTU lists provided by this document adapter.
    `java.util.Iterator<OTUListDataAdapter>` | DocumentDataAdapter.`getOTUListIterator(ReadWriteParameterMap parameters)` Returns an iterator providing access to all OTU lists contained in the document to be written.
    `ObjectListDataAdapter<LinkedLabeledIDEvent>` | OTUListDataAdapter.`getOTUSets(ReadWriteParameterMap parameters)` Returns a list of OTU sets defined for the OTU list modeled by this instance.
    `long` | MatrixDataAdapter.`getSequenceCount(ReadWriteParameterMap parameters)` Returns the number of sequences contained in this matrix.
    `java.util.Iterator<java.lang.String>` | MatrixDataAdapter.`getSequenceIDIterator(ReadWriteParameterMap parameters)` Returns an iterator returning the IDs of all sequences in the represented matrix.
    `long` | MatrixDataAdapter.`getSequenceLength(ReadWriteParameterMap parameters, java.lang.String sequenceID)` Returns the length for the specified sequence.
    `ObjectListDataAdapter<LinkedLabeledIDEvent>` | MatrixDataAdapter.`getSequenceSets(ReadWriteParameterMap parameters)` Returns a list of sequence sets defined for the matrix modeled by this instance.
    `LinkedLabeledIDEvent` | MatrixDataAdapter.`getSequenceStartEvent(ReadWriteParameterMap parameters, java.lang.String sequenceID)` Returns an event describing the sequence with the specified ID.
    `E` | ElementDataAdapter.`getStartEvent(ReadWriteParameterMap parameters)` Returns the start event of this data element.
    `ObjectListDataAdapter<TokenSetDefinitionEvent>` | MatrixDataAdapter.`getTokenSets(ReadWriteParameterMap parameters)` Returns a list of token sets defined for the matrix modeled by this instance.
    `java.util.Iterator<TreeNetworkGroupDataAdapter>` | DocumentDataAdapter.`getTreeNetworkGroupIterator(ReadWriteParameterMap parameters)` Returns an iterator providing access to all trees and network groups contained in the document to be written.
    `java.util.Iterator<TreeNetworkDataAdapter>` | TreeNetworkGroupDataAdapter.`getTreeNetworkIterator(ReadWriteParameterMap parameters)` Returns an iterator providing access to all trees and networks contained in the document to be written.
    `ObjectListDataAdapter<LinkedLabeledIDEvent>` | TreeNetworkGroupDataAdapter.`getTreeSets(ReadWriteParameterMap parameters)` Returns a list of tree sets defined for the tree-network-group modeled by this instance.
    `boolean` | TreeNetworkDataAdapter.`isTree(ReadWriteParameterMap parameters)` Determines whether this instance represents a phylogenetic tree or a phylogenetic network.
    `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 ReadWriteParameterMap in info.bioinfweb.jphyloio.dataadapters.implementations

    Methods in info.bioinfweb.jphyloio.dataadapters.implementations with parameters of type ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `ObjectListDataAdapter<CharacterDefinitionEvent>` | NoCharDefsNoSetsMatrixDataAdapter.`getCharacterDefinitions(ReadWriteParameterMap parameters)` Default implementation that always returns an empty object list adapter.
    `ObjectListDataAdapter<LinkedLabeledIDEvent>` | NoCharDefsNoSetsMatrixDataAdapter.`getCharacterSets(ReadWriteParameterMap parameters)` Default implementation that always returns an empty object list adapter
    `long` | EmptyObjectListDataAdapter.`getCount(ReadWriteParameterMap parameters)` This default implementation always returns 0.
    `long` | UndefinedOTUListDataAdapter.`getCount(ReadWriteParameterMap parameters)`
    `java.util.Iterator<java.lang.String>` | EmptyObjectListDataAdapter.`getIDIterator(ReadWriteParameterMap parameters)` This default implementation always returns an empty iterator.
    `java.util.Iterator<java.lang.String>` | UndefinedOTUListDataAdapter.`getIDIterator(ReadWriteParameterMap parameters)`
    `java.util.Iterator<MatrixDataAdapter>` | EmptyDocumentDataAdapter.`getMatrixIterator(ReadWriteParameterMap parameters)`
    `java.util.Iterator<MatrixDataAdapter>` | ListBasedDocumentDataAdapter.`getMatrixIterator(ReadWriteParameterMap parameters)`
    `ObjectListDataAdapter<LinkedLabeledIDEvent>` | NoSetsTreeNetworkDataAdapter.`getNodeEdgeSets(ReadWriteParameterMap parameters)` Default implementation that always returns an empty object list adapter.
    `E` | EmptyObjectListDataAdapter.`getObjectStartEvent(ReadWriteParameterMap parameters, java.lang.String id)`
    `LabeledIDEvent` | UndefinedOTUListDataAdapter.`getObjectStartEvent(ReadWriteParameterMap parameters, java.lang.String id)`
    `OTUListDataAdapter` | EmptyDocumentDataAdapter.`getOTUList(ReadWriteParameterMap parameters, java.lang.String id)`
    `OTUListDataAdapter` | ListBasedDocumentDataAdapter.`getOTUList(ReadWriteParameterMap parameters, java.lang.String id)`
    `long` | EmptyDocumentDataAdapter.`getOTUListCount(ReadWriteParameterMap parameters)`
    `long` | ListBasedDocumentDataAdapter.`getOTUListCount(ReadWriteParameterMap parameters)`
    `java.util.Iterator<OTUListDataAdapter>` | EmptyDocumentDataAdapter.`getOTUListIterator(ReadWriteParameterMap parameters)`
    `java.util.Iterator<OTUListDataAdapter>` | ListBasedDocumentDataAdapter.`getOTUListIterator(ReadWriteParameterMap parameters)`
    `ObjectListDataAdapter<LinkedLabeledIDEvent>` | UndefinedOTUListDataAdapter.`getOTUSets(ReadWriteParameterMap parameters)`
    `ObjectListDataAdapter<LinkedLabeledIDEvent>` | NoCharDefsNoSetsMatrixDataAdapter.`getSequenceSets(ReadWriteParameterMap parameters)` Default implementation that always returns an empty object list adapter.
    `LabeledIDEvent` | UndefinedOTUListDataAdapter.`getStartEvent(ReadWriteParameterMap parameters)`
    `ObjectListDataAdapter<TokenSetDefinitionEvent>` | NoCharDefsNoSetsMatrixDataAdapter.`getTokenSets(ReadWriteParameterMap parameters)` Default implementation that always returns an empty object list adapter.
    `java.util.Iterator<TreeNetworkGroupDataAdapter>` | EmptyDocumentDataAdapter.`getTreeNetworkGroupIterator(ReadWriteParameterMap parameters)`
    `java.util.Iterator<TreeNetworkGroupDataAdapter>` | ListBasedDocumentDataAdapter.`getTreeNetworkGroupIterator(ReadWriteParameterMap parameters)`
    `ObjectListDataAdapter<LinkedLabeledIDEvent>` | NoSetsTreeNetworkGroupDataAdapter.`getTreeSets(ReadWriteParameterMap parameters)` Default implementation that always returns an empty object list adapter.
    `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 ReadWriteParameterMap in info.bioinfweb.jphyloio.dataadapters.implementations.receivers

    Methods in info.bioinfweb.jphyloio.dataadapters.implementations.receivers that return ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `ReadWriteParameterMap` | BasicEventReceiver.`getParameterMap()`

    Constructors in info.bioinfweb.jphyloio.dataadapters.implementations.receivers with parameters of type ReadWriteParameterMap
    Constructor and Description
    `AbstractSequenceContentReceiver(P streamDataProvider, ReadWriteParameterMap parameterMap, boolean longTokens)`
    `BasicEventReceiver(P streamDataProvider, ReadWriteParameterMap parameterMap)` Creates a new instance of this class.

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

    Methods in info.bioinfweb.jphyloio.dataadapters.implementations.store with parameters of type ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `boolean` | StoreMatrixDataAdapter.`containsLongTokens(ReadWriteParameterMap parameters)`
    `StoreObjectListDataAdapter<CharacterDefinitionEvent>` | StoreMatrixDataAdapter.`getCharacterDefinitions(ReadWriteParameterMap parameters)`
    `StoreObjectListDataAdapter<LinkedLabeledIDEvent>` | StoreMatrixDataAdapter.`getCharacterSets(ReadWriteParameterMap parameters)`
    `long` | StoreMatrixDataAdapter.`getColumnCount(ReadWriteParameterMap parameters)`
    `long` | StoreOTUListDataAdapter.`getCount(ReadWriteParameterMap parameters)`
    `long` | StoreObjectListDataAdapter.`getCount(ReadWriteParameterMap parameters)`
    `StoreObjectListDataAdapter<EdgeEvent>` | StoreTreeNetworkDataAdapter.`getEdges(ReadWriteParameterMap parameters)`
    `java.util.Iterator<java.lang.String>` | StoreOTUListDataAdapter.`getIDIterator(ReadWriteParameterMap parameters)`
    `java.util.Iterator<java.lang.String>` | StoreObjectListDataAdapter.`getIDIterator(ReadWriteParameterMap parameters)`
    `java.util.Iterator<MatrixDataAdapter>` | StoreDocumentDataAdapter.`getMatrixIterator(ReadWriteParameterMap parameters)`
    `ObjectListDataAdapter<LinkedLabeledIDEvent>` | StoreTreeNetworkDataAdapter.`getNodeEdgeSets(ReadWriteParameterMap parameters)`
    `StoreObjectListDataAdapter<NodeEvent>` | StoreTreeNetworkDataAdapter.`getNodes(ReadWriteParameterMap parameters)`
    `LabeledIDEvent` | StoreOTUListDataAdapter.`getObjectStartEvent(ReadWriteParameterMap parameters, java.lang.String id)`
    `E` | StoreObjectListDataAdapter.`getObjectStartEvent(ReadWriteParameterMap parameters, java.lang.String id)`
    `OTUListDataAdapter` | StoreDocumentDataAdapter.`getOTUList(ReadWriteParameterMap parameters, java.lang.String id)`
    `long` | StoreDocumentDataAdapter.`getOTUListCount(ReadWriteParameterMap parameters)`
    `java.util.Iterator<OTUListDataAdapter>` | StoreDocumentDataAdapter.`getOTUListIterator(ReadWriteParameterMap parameters)`
    `StoreObjectListDataAdapter<LinkedLabeledIDEvent>` | StoreOTUListDataAdapter.`getOTUSets(ReadWriteParameterMap parameters)`
    `long` | StoreMatrixDataAdapter.`getSequenceCount(ReadWriteParameterMap parameters)`
    `java.util.Iterator<java.lang.String>` | StoreMatrixDataAdapter.`getSequenceIDIterator(ReadWriteParameterMap parameters)`
    `long` | StoreMatrixDataAdapter.`getSequenceLength(ReadWriteParameterMap parameters, java.lang.String sequenceID)`
    `StoreObjectListDataAdapter<LinkedLabeledIDEvent>` | StoreMatrixDataAdapter.`getSequenceSets(ReadWriteParameterMap parameters)`
    `LinkedLabeledIDEvent` | StoreMatrixDataAdapter.`getSequenceStartEvent(ReadWriteParameterMap parameters, java.lang.String sequenceID)`
    `LinkedLabeledIDEvent` | StoreMatrixDataAdapter.`getStartEvent(ReadWriteParameterMap parameters)`
    `LabeledIDEvent` | StoreOTUListDataAdapter.`getStartEvent(ReadWriteParameterMap parameters)`
    `LabeledIDEvent` | StoreTreeNetworkDataAdapter.`getStartEvent(ReadWriteParameterMap parameters)`
    `LinkedLabeledIDEvent` | StoreTreeNetworkGroupDataAdapter.`getStartEvent(ReadWriteParameterMap parameters)`
    `StoreObjectListDataAdapter<TokenSetDefinitionEvent>` | StoreMatrixDataAdapter.`getTokenSets(ReadWriteParameterMap parameters)`
    `java.util.Iterator<TreeNetworkGroupDataAdapter>` | StoreDocumentDataAdapter.`getTreeNetworkGroupIterator(ReadWriteParameterMap parameters)`
    `java.util.Iterator<TreeNetworkDataAdapter>` | StoreTreeNetworkGroupDataAdapter.`getTreeNetworkIterator(ReadWriteParameterMap parameters)`
    `StoreObjectListDataAdapter<LinkedLabeledIDEvent>` | StoreTreeNetworkGroupDataAdapter.`getTreeSets(ReadWriteParameterMap parameters)`
    `boolean` | StoreTreeNetworkDataAdapter.`isTree(ReadWriteParameterMap parameters)`
    `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 ReadWriteParameterMap in info.bioinfweb.jphyloio.factory

    Methods in info.bioinfweb.jphyloio.factory with parameters of type ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `boolean` | AbstractSingleReaderWriterFactory.`checkFormat(java.io.InputStream stream, ReadWriteParameterMap parameters)`
    `boolean` | SingleReaderWriterFactory.`checkFormat(java.io.InputStream stream, ReadWriteParameterMap parameters)` Implementations should read the start of the stream here and determine whether the content could be valid according to the target format.
    `boolean` | AbstractStartStringSingleFactory.`checkFormat(java.io.Reader reader, ReadWriteParameterMap parameters)`
    `boolean` | SingleReaderWriterFactory.`checkFormat(java.io.Reader reader, ReadWriteParameterMap parameters)` Implementations should read the start of the characters returned by the reader here and determine whether the content could be valid according to the target format.
    `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)`
    `java.lang.String` | JPhyloIOReaderWriterFactory.`guessFormat(java.io.File file, ReadWriteParameterMap parameters)` Tries to determine the format of the contents of the specified file by examining at its beginning (e.g.
    `java.lang.String` | JPhyloIOReaderWriterFactory.`guessFormat(java.io.InputStream stream, ReadWriteParameterMap parameters)` Tries to determine the format of the contents of the specified input stream by examining at its beginning (e.g.
    `java.lang.String` | JPhyloIOReaderWriterFactory.`guessFormat(java.io.Reader reader, ReadWriteParameterMap parameters)` Tries to determine the format of the contents of the specified reader by examining at its beginning (e.g.
    `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.

    Constructors in info.bioinfweb.jphyloio.factory with parameters of type ReadWriteParameterMap
    Constructor and Description
    `JPhyloIOContentExtensionFileFilter(SingleReaderWriterFactory factory, ReadWriteParameterMap defaultParamaters, java.lang.String description, boolean addExtensionListToDescription, ContentExtensionFileFilter.TestStrategy testStrategy, boolean acceptFilesWithExceptions, java.lang.String... extensions)`

  - ### Uses of ReadWriteParameterMap in info.bioinfweb.jphyloio.formatinfo

    Constructors in info.bioinfweb.jphyloio.formatinfo with parameters of type ReadWriteParameterMap
    Constructor and Description
    `DefaultFormatInfo(SingleReaderWriterFactory factory, java.lang.String formatID, java.lang.String formatName, java.util.Set<EventContentType> supportedReaderContentTypes, java.util.Set<EventContentType> supportedWriterContentTypes, java.util.Map<EventContentType,MetadataModeling> supportedReaderMetadataModeling, java.util.Map<EventContentType,MetadataModeling> supportedWriterMetadataModeling, java.util.Set<java.lang.String> supportedReaderParameters, java.util.Set<java.lang.String> supportedWriterParameters, ReadWriteParameterMap filterParameters, java.lang.String filterDescription, java.lang.String... filterExtensions)` Creates a new instance of this class.

  - ### Uses of ReadWriteParameterMap in info.bioinfweb.jphyloio.formats.fasta

    Methods in info.bioinfweb.jphyloio.formats.fasta with parameters of type ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `JPhyloIOEventReader` | FASTAFactory.`getReader(java.io.InputStream stream, ReadWriteParameterMap parameters)`
    `JPhyloIOEventReader` | FASTAFactory.`getReader(java.io.Reader reader, ReadWriteParameterMap parameters)`
    `protected void` | FASTAEventWriter.`writeSingleMatrix(DocumentDataAdapter document, MatrixDataAdapter matrix, java.util.Iterator<java.lang.String> sequenceIDIterator, ReadWriteParameterMap parameters)`

    Constructors in info.bioinfweb.jphyloio.formats.fasta with parameters of type ReadWriteParameterMap
    Constructor and Description
    `FASTAEventReader(java.io.BufferedReader reader, ReadWriteParameterMap parameters)` Creates a new instance of this class.
    `FASTAEventReader(java.io.File file, ReadWriteParameterMap parameters)` Creates a new instance of this class.
    `FASTAEventReader(java.io.InputStream stream, ReadWriteParameterMap parameters)` Creates a new instance of this class.
    `FASTAEventReader(java.io.Reader reader, ReadWriteParameterMap parameters)` Creates a new instance of this class.

  - ### Uses of ReadWriteParameterMap in info.bioinfweb.jphyloio.formats.mega

    Methods in info.bioinfweb.jphyloio.formats.mega with parameters of type ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `JPhyloIOEventReader` | MEGAFactory.`getReader(java.io.InputStream stream, ReadWriteParameterMap parameters)`
    `JPhyloIOEventReader` | MEGAFactory.`getReader(java.io.Reader reader, ReadWriteParameterMap parameters)`

    Constructors in info.bioinfweb.jphyloio.formats.mega with parameters of type ReadWriteParameterMap
    Constructor and Description
    `MEGAEventReader(java.io.BufferedReader reader, ReadWriteParameterMap parameters)` Creates a new instance of this class.
    `MEGAEventReader(java.io.File file, ReadWriteParameterMap parameters)` Creates a new instance of this class.
    `MEGAEventReader(java.io.InputStream stream, ReadWriteParameterMap parameters)` Creates a new instance of this class.
    `MEGAEventReader(java.io.Reader reader, ReadWriteParameterMap parameters)` Creates a new instance of this class.

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

    Methods in info.bioinfweb.jphyloio.formats.newick that return ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `ReadWriteParameterMap` | DefaultNewickWriterNodeLabelProcessor.`getParameters()`

    Methods in info.bioinfweb.jphyloio.formats.newick with parameters of type ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `boolean` | NewickFactory.`checkFormat(java.io.Reader reader, ReadWriteParameterMap parameters)` Since there is no real characteristic starting string for any Newick file, it is just checked whether at least five events (if available) can be created from the input without an exception.
    `protected void` | NewickEventWriter.`doWriteDocument(DocumentDataAdapter document, java.io.Writer writer, ReadWriteParameterMap parameters)`
    `JPhyloIOEventReader` | NewickFactory.`getReader(java.io.InputStream stream, ReadWriteParameterMap parameters)`
    `JPhyloIOEventReader` | NewickFactory.`getReader(java.io.Reader reader, ReadWriteParameterMap parameters)`

    Constructors in info.bioinfweb.jphyloio.formats.newick with parameters of type ReadWriteParameterMap
    Constructor and Description
    `DefaultNewickWriterNodeLabelProcessor(OTUListDataAdapter otuList, ReadWriteParameterMap parameters)`
    `NewickEventReader(java.io.BufferedReader reader, ReadWriteParameterMap parameters)` Creates a new instance of this class.
    `NewickEventReader(java.io.File file, ReadWriteParameterMap parameters)` Creates a new instance of this class.
    `NewickEventReader(java.io.InputStream stream, ReadWriteParameterMap parameters)` Creates a new instance of this class.
    `NewickEventReader(java.io.Reader reader, ReadWriteParameterMap parameters)` Creates a new instance of this class.
    `NewickNodeEdgeEventReceiver(TextWriterStreamDataProvider<?> streamDataProvider, ReadWriteParameterMap parameterMap)`
    `NewickStringWriter(TextWriterStreamDataProvider<?> streamDataProvider, TreeNetworkDataAdapter tree, NewickWriterNodeLabelProcessor nodeLabelProcessor, ReadWriteParameterMap parameters)` Creates a new instance of this class.

  - ### Uses of ReadWriteParameterMap in info.bioinfweb.jphyloio.formats.nexml

    Methods in info.bioinfweb.jphyloio.formats.nexml with parameters of type ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `JPhyloIOEventReader` | NeXMLFactory.`getReader(java.io.InputStream stream, ReadWriteParameterMap parameters)`
    `JPhyloIOEventReader` | NeXMLFactory.`getReader(java.io.Reader reader, ReadWriteParameterMap parameters)`

    Constructors in info.bioinfweb.jphyloio.formats.nexml with parameters of type ReadWriteParameterMap
    Constructor and Description
    `NeXMLEventReader(java.io.File file, ReadWriteParameterMap parameters)`
    `NeXMLEventReader(java.io.InputStream stream, ReadWriteParameterMap parameters)`
    `NeXMLEventReader(java.io.Reader reader, ReadWriteParameterMap parameters)`
    `NeXMLEventReader(javax.xml.stream.XMLEventReader xmlReader, ReadWriteParameterMap parameters)`

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

    Methods in info.bioinfweb.jphyloio.formats.nexml.receivers with parameters of type ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `static void` | AbstractNeXMLDataReceiverMixin.`checkLiteralContentMeta(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameters, LiteralMetadataContentEvent event)`
    `static void` | AbstractNeXMLDataReceiverMixin.`handleLiteralContentMeta(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameters, LiteralMetadataContentEvent event)`

    Constructors in info.bioinfweb.jphyloio.formats.nexml.receivers with parameters of type ReadWriteParameterMap
    Constructor and Description
    `AbstractNeXMLDataReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap)`
    `NeXMLAttributeMetadataReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, javax.xml.namespace.QName... predicates)`
    `NeXMLCharacterSetEventReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap)`
    `NeXMLCollectCharSetDataReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, java.lang.String charSetID)`
    `NeXMLCollectNamespaceReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap)`
    `NeXMLCollectSequenceDataReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, boolean longTokens)`
    `NeXMLCollectSetMetadataReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, java.lang.String setID, boolean ignoreMetadata)`
    `NeXMLCollectTokenSetDefinitionDataReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, java.lang.String tokenSetDefinitionID)`
    `NeXMLHandleSequenceDataReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, boolean longTokens)`
    `NeXMLIgnoreCertainMetadataReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, boolean writePredicateMetadata, javax.xml.namespace.QName... predicates)` Creates a new instance of this class.
    `NeXMLMetaDataReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap)`
    `NeXMLMolecularDataTokenDefinitionReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, java.lang.String tokenSetID)`
    `NeXMLOnlyWriteMetaDataReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap)`
    `NeXMLPredicateMetaReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, javax.xml.namespace.QName... predicates)` Creates a new instance of this class.
    `NeXMLSequenceTokensReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, boolean longTokens)`
    `NeXMLTokenSetEventReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, java.lang.String tokenSetID)`

  - ### Uses of ReadWriteParameterMap in info.bioinfweb.jphyloio.formats.nexus

    Methods in info.bioinfweb.jphyloio.formats.nexus that return ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `protected ReadWriteParameterMap` | NexusEventWriter.`getParameters()`
    `ReadWriteParameterMap` | NexusWriterStreamDataProvider.`getParameters()`

    Methods in info.bioinfweb.jphyloio.formats.nexus with parameters of type ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `protected void` | NexusEventWriter.`doWriteDocument(DocumentDataAdapter document, java.io.Writer writer, ReadWriteParameterMap parameters)`
    `JPhyloIOEventReader` | NexusFactory.`getReader(java.io.InputStream stream, ReadWriteParameterMap parameters)`
    `JPhyloIOEventReader` | NexusFactory.`getReader(java.io.Reader reader, ReadWriteParameterMap parameters)`

    Constructors in info.bioinfweb.jphyloio.formats.nexus with parameters of type ReadWriteParameterMap
    Constructor and Description
    `NexusEventReader(java.io.File file, ReadWriteParameterMap parameters)` Creates a new instance of this class with a default block handler map and command reader factory.
    `NexusEventReader(java.io.InputStream stream, ReadWriteParameterMap parameters)` Creates a new instance of this class.
    `NexusEventReader(PeekReader reader, ReadWriteParameterMap parameters)` Creates a new instance of this class with a default block handler map and command reader factory.
    `NexusEventReader(java.io.Reader reader, ReadWriteParameterMap parameters)` Creates a new instance of this class with a default block handler map and command reader factory.
    `NexusNewickWriterNodeLabelProcessor(OTUListDataAdapter otuList, java.util.Map<java.lang.String,java.lang.Long> indexMap, ReadWriteParameterMap parameters)`

  - ### Uses of ReadWriteParameterMap in info.bioinfweb.jphyloio.formats.pde

    Methods in info.bioinfweb.jphyloio.formats.pde with parameters of type ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `JPhyloIOEventReader` | PDEFactory.`getReader(java.io.InputStream stream, ReadWriteParameterMap parameters)`
    `JPhyloIOEventReader` | PDEFactory.`getReader(java.io.Reader reader, ReadWriteParameterMap parameters)`

    Constructors in info.bioinfweb.jphyloio.formats.pde with parameters of type ReadWriteParameterMap
    Constructor and Description
    `PDEEventReader(java.io.File file, ReadWriteParameterMap parameters)`
    `PDEEventReader(java.io.InputStream stream, ReadWriteParameterMap parameters)`
    `PDEEventReader(java.io.Reader reader, ReadWriteParameterMap parameters)`
    `PDEEventReader(javax.xml.stream.XMLEventReader xmlReader, ReadWriteParameterMap parameters)`

  - ### Uses of ReadWriteParameterMap in info.bioinfweb.jphyloio.formats.phylip

    Methods in info.bioinfweb.jphyloio.formats.phylip with parameters of type ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `boolean` | AbstractPhylipFactory.`checkFormat(java.io.Reader reader, ReadWriteParameterMap parameters)`
    `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)`
    `protected void` | PhylipEventWriter.`writeSingleMatrix(DocumentDataAdapter document, MatrixDataAdapter matrix, java.util.Iterator<java.lang.String> sequenceIDIterator, ReadWriteParameterMap parameters)`

    Constructors in info.bioinfweb.jphyloio.formats.phylip with parameters of type ReadWriteParameterMap
    Constructor and Description
    `AbstractPhylipEventReader(java.io.File file, ReadWriteParameterMap parameters)`
    `AbstractPhylipEventReader(java.io.InputStream stream, ReadWriteParameterMap parameters)`
    `AbstractPhylipEventReader(PeekReader reader, ReadWriteParameterMap parameters)`
    `AbstractPhylipEventReader(java.io.Reader reader, ReadWriteParameterMap parameters)`
    `PhylipEventReader(java.io.BufferedReader reader, ReadWriteParameterMap parameters)` Creates a new instance of this class.
    `PhylipEventReader(java.io.File file, ReadWriteParameterMap parameters)` Creates a new instance of this class.
    `PhylipEventReader(java.io.InputStream stream, ReadWriteParameterMap parameters)` Creates a new instance of this class.
    `PhylipEventReader(java.io.Reader reader, ReadWriteParameterMap parameters)` Creates a new instance of this class.
    `SequentialPhylipEventReader(java.io.BufferedReader reader, ReadWriteParameterMap parameters)` Creates a new instance of this class.
    `SequentialPhylipEventReader(java.io.File file, ReadWriteParameterMap parameters)` Creates a new instance of this class.
    `SequentialPhylipEventReader(java.io.InputStream stream, ReadWriteParameterMap parameters)` Creates a new instance of this class.
    `SequentialPhylipEventReader(java.io.Reader reader, ReadWriteParameterMap parameters)` Creates a new instance of this class.

  - ### Uses of ReadWriteParameterMap in info.bioinfweb.jphyloio.formats.phyloxml

    Methods in info.bioinfweb.jphyloio.formats.phyloxml with parameters of type ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `JPhyloIOEventReader` | PhyloXMLFactory.`getReader(java.io.InputStream stream, ReadWriteParameterMap parameters)`
    `JPhyloIOEventReader` | PhyloXMLFactory.`getReader(java.io.Reader reader, ReadWriteParameterMap parameters)`

    Constructors in info.bioinfweb.jphyloio.formats.phyloxml with parameters of type ReadWriteParameterMap
    Constructor and Description
    `PhyloXMLEventReader(java.io.File file, ReadWriteParameterMap parameters)`
    `PhyloXMLEventReader(java.io.InputStream stream, ReadWriteParameterMap parameters)`
    `PhyloXMLEventReader(java.io.Reader reader, ReadWriteParameterMap parameters)`
    `PhyloXMLEventReader(javax.xml.stream.XMLEventReader xmlReader, ReadWriteParameterMap parameters)`

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

    Constructors in info.bioinfweb.jphyloio.formats.phyloxml.receivers with parameters of type ReadWriteParameterMap
    Constructor and Description
    `PhyloXMLCollectMetadataDataReceiver(PhyloXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap)`
    `PhyloXMLMetaDataReceiver(PhyloXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, PropertyOwner propertyOwner)`
    `PhyloXMLOnlyCustomXMLDataReceiver(PhyloXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, PropertyOwner propertyOwner)`
    `PhyloXMLPropertyMetadataReceiver(PhyloXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, PropertyOwner propertyOwner)`
    `PhyloXMLSpecificPredicatesDataReceiver(PhyloXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, PropertyOwner propertyOwner, javax.xml.namespace.QName parentPredicate)`

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

    Methods in info.bioinfweb.jphyloio.formats.text with parameters of type ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `protected void` | AbstractTextEventWriter.`doWriteDocument(DocumentDataAdapter document, java.io.Writer writer, ReadWriteParameterMap parameters)`

    Constructors in info.bioinfweb.jphyloio.formats.text with parameters of type ReadWriteParameterMap
    Constructor and Description
    `AbstractTextEventReader(java.io.File file, ReadWriteParameterMap parameters, java.lang.String matchToken)` Creates a new instance of this class.
    `AbstractTextEventReader(java.io.InputStream stream, ReadWriteParameterMap parameters, java.lang.String matchToken)` Creates a new instance of this class.
    `AbstractTextEventReader(PeekReader reader, ReadWriteParameterMap parameters, java.lang.String matchToken)` Creates a new instance of this class.
    `AbstractTextEventReader(java.io.Reader reader, ReadWriteParameterMap parameters, java.lang.String matchToken)` Creates a new instance of this class.
    `BasicTextCommentEventReceiver(P streamDataProvider, ReadWriteParameterMap parameterMap, java.lang.String commentStart, java.lang.String commentEnd)` Creates a new instance of this class.
    `TextSequenceContentReceiver(P streamDataProvider, ReadWriteParameterMap parameterMap, boolean longTokens, java.lang.String commentStart, java.lang.String commentEnd)`

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

    Methods in info.bioinfweb.jphyloio.formats.xml that return ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `protected ReadWriteParameterMap` | AbstractXMLEventWriter.`getParameters()`

    Methods in info.bioinfweb.jphyloio.formats.xml with parameters of type ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `boolean` | AbstractXMLFactory.`checkFormat(java.io.Reader reader, ReadWriteParameterMap parameters)` Tests whether the specified reader provides an XML document and whether the local part of the start tag of it equals to the local part of `AbstractXMLFactory.getRootTag()`.
    `protected void` | AbstractXMLEventWriter.`doWriteDocument(DocumentDataAdapter document, java.io.Writer writer, ReadWriteParameterMap parameters)`
    `static void` | XMLReadWriteUtils.`manageLiteralContentMetaNamespaces(XMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameters, LiteralMetadataContentEvent event)` This method manages namespaces used or declared in any custom XML events depending on the parameter `ReadWriteParameterNames.KEY_CUSTOM_XML_NAMESPACE_HANDLING`.
    `static void` | XMLReadWriteUtils.`writeCustomXML(javax.xml.stream.XMLStreamWriter writer, ReadWriteParameterMap parameters, javax.xml.stream.events.XMLEvent event)`

    Constructors in info.bioinfweb.jphyloio.formats.xml with parameters of type ReadWriteParameterMap
    Constructor and Description
    `AbstractXMLEventReader(java.io.File file, ReadWriteParameterMap parameters)`
    `AbstractXMLEventReader(java.io.InputStream stream, ReadWriteParameterMap parameters)`
    `AbstractXMLEventReader(java.io.Reader reader, ReadWriteParameterMap parameters)`
    `AbstractXMLEventReader(javax.xml.stream.XMLEventReader xmlReader, ReadWriteParameterMap parameters)`

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

    Constructors in info.bioinfweb.jphyloio.formats.xml.receivers with parameters of type ReadWriteParameterMap
    Constructor and Description
    `AbstractXMLDataReceiver(P streamDataProvider, ReadWriteParameterMap parameterMap)`

  - ### Uses of ReadWriteParameterMap in info.bioinfweb.jphyloio.formats.xtg

    Methods in info.bioinfweb.jphyloio.formats.xtg with parameters of type ReadWriteParameterMap
    Modifier and Type | Method and Description
    --- | ---
    `JPhyloIOEventReader` | XTGFactory.`getReader(java.io.InputStream stream, ReadWriteParameterMap parameters)`
    `JPhyloIOEventReader` | XTGFactory.`getReader(java.io.Reader reader, ReadWriteParameterMap parameters)`

    Constructors in info.bioinfweb.jphyloio.formats.xtg with parameters of type ReadWriteParameterMap
    Constructor and Description
    `XTGEventReader(java.io.File file, ReadWriteParameterMap parameters)`
    `XTGEventReader(java.io.InputStream stream, ReadWriteParameterMap parameters)`
    `XTGEventReader(java.io.Reader reader, ReadWriteParameterMap parameters)`
    `XTGEventReader(javax.xml.stream.XMLEventReader xmlReader, ReadWriteParameterMap parameters)`

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

    Constructors in info.bioinfweb.jphyloio.utils with parameters of type ReadWriteParameterMap
    Constructor and Description
    `TreeTopologyExtractor(TreeNetworkDataAdapter adapter, ReadWriteParameterMap parameters)`