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)