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

- Packages that use DocumentDataAdapter
  Package | Description
  --- | ---
  info.bioinfweb.jphyloio | The main package of JPhyloIO.
  info.bioinfweb.jphyloio.dataadapters.implementations | Contains some basic (abstract) 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.formats.fasta | Contains classes for reading from and writing to streams/files in FASTA format.
  info.bioinfweb.jphyloio.formats.newick | Contains classes for reading from and writing to streams/files in Newick tree format.
  info.bioinfweb.jphyloio.formats.nexus | Contains classes for reading from and writing to streams/files in Nexus format.
  info.bioinfweb.jphyloio.formats.phylip | Contains classes for reading from and writing to streams/files in Phylip 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.

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

    Methods in info.bioinfweb.jphyloio with parameters of type DocumentDataAdapter
    Modifier and Type | Method and Description
    --- | ---
    `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)`
    `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.
    `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.

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

    Classes in info.bioinfweb.jphyloio.dataadapters.implementations that implement DocumentDataAdapter
    Modifier and Type | Class and Description
    --- | ---
    `class` | `EmptyDocumentDataAdapter` An implementation of `DocumentDataAdapter` that models an empty document.
    `class` | `ListBasedDocumentDataAdapter` Default implementation of `DocumentDataAdapter`.

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

    Classes in info.bioinfweb.jphyloio.dataadapters.implementations.store that implement DocumentDataAdapter
    Modifier and Type | Class and Description
    --- | ---
    `class` | `StoreDocumentDataAdapter`

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

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

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

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

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

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

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

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

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

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

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

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

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