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)