A B C D E F G H I J K L M N O P Q R S T U V W X

## W

wasAtReceiverRootLevel() - Method in exception info.bioinfweb.jphyloio.exception.IllegalEventException
wasDelimited() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickToken
wasValueDelimited() - Method in class info.bioinfweb.jphyloio.formats.text.KeyValueInformation
  Determines whether the read value was delimited in the source stream.
WORD_DELIMITER - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
write() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickStringWriter
  Writes the tree data specified in the constructor to the specified stream.
write() - Method in class info.bioinfweb.jphyloio.formats.nexus.AbstractNexusSetWriter
writeAttribute(String, String, String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
writeAttribute(String, String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
writeAttribute(String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
writeBlockEnd() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter
writeBlockEnd() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusWriterStreamDataProvider
writeBlockStart(String) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter
writeBlockStart(String) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusWriterStreamDataProvider
writeCData(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
writeCharacters(char[], int, int) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
writeCharacters(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
writeCharSequencePartContent(JPhyloIOEventReceiver, long, long, CharSequence) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOWritingUtils
writeCommandEnd() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter
writeCommandEnd() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusWriterStreamDataProvider
writeComment(BasicEventReceiver<?>, CommentEvent, String, String) - Static method in class info.bioinfweb.jphyloio.formats.text.BasicTextCommentEventReceiver
writeComment(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
writeComments() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickNodeEdgeEventReceiver
writeContentData(ReadWriteParameterMap, JPhyloIOEventReceiver, String) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.EmptyObjectListDataAdapter
  Always throws an `IllegalArgumentException`, since this default implementation does not contain any objects.
writeContentData(ReadWriteParameterMap, JPhyloIOEventReceiver, String) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreObjectListDataAdapter
writeContentData(ReadWriteParameterMap, JPhyloIOEventReceiver, String) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreOTUListDataAdapter
writeContentData(ReadWriteParameterMap, JPhyloIOEventReceiver, String) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.UndefinedOTUListDataAdapter
writeContentData(ReadWriteParameterMap, JPhyloIOEventReceiver, String) - Method in interface info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter
  Writes the nested events in the specified object describing its contents.
writeCustomXML(XMLStreamWriter, ReadWriteParameterMap, XMLEvent) - Static method in class info.bioinfweb.jphyloio.formats.xml.XMLReadWriteUtils
writeCustomXMLTag(XMLEvent) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.receivers.PhyloXMLMetaDataReceiver
writeDefaultNamespace(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
writeDocument(DocumentDataAdapter, File, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.AbstractEventWriter
writeDocument(DocumentDataAdapter, OutputStream, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.AbstractEventWriter
writeDocument(DocumentDataAdapter, Writer, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.AbstractEventWriter
writeDocument(DocumentDataAdapter, OutputStream, ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.JPhyloIOEventWriter
  Writes the data provided by the data adapter to a document in the according format of the implementing class.
writeDocument(DocumentDataAdapter, File, ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.JPhyloIOEventWriter
  Writes the data provided by the data adapter to a document in the according format of the implementing class.
writeDocument(DocumentDataAdapter, Writer, ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.JPhyloIOEventWriter
  Writes the data provided by the data adapter to a document in the according format of the implementing class.
writeDTD(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
writeElementReference(SetElementEvent) - Method in class info.bioinfweb.jphyloio.formats.nexus.receivers.AbstractNexusSetsEventReceiver
writeEmptyElement(String, String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
  It depends on the implementation of XMLStreamWriter returned by `XMLOutputFactory.createXMLStreamWriter(java.io.Writer)` if a self-closing tag or a separate start and end tag is written by this method.
writeEmptyElement(String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
  It depends on the implementation of XMLStreamWriter returned by `XMLOutputFactory.createXMLStreamWriter(java.io.Writer)` if a self-closing tag or a separate start and end tag is written by this method.
writeEmptyElement(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
  It depends on the implementation of XMLStreamWriter returned by `XMLOutputFactory.createXMLStreamWriter(java.io.Writer)` if a self-closing tag or a separate start and end tag is written by this method.
writeEndDocument() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
writeEndElement() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
writeEntityRef(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
writeKeyValueExpression(Writer, String, String) - Static method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter
writeLabeledIDAttributes(LabeledIDEvent) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
writeLabeledIDAttributes(LabeledIDEvent, String) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
writeLineBreak(Writer, ReadWriteParameterMap) - Static method in class info.bioinfweb.jphyloio.AbstractEventWriter
  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.
writeLineStart(Writer, String) - Method in class info.bioinfweb.jphyloio.AbstractEventWriter
writeLineStart(Writer, String) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter
writeLineStart(String) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusWriterStreamDataProvider
writeLinkCommand(String, String, EventContentType) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter
writeLinkCommand(String, String, EventContentType) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusWriterStreamDataProvider
writeLinkedLabeledIDAttributes(LinkedLabeledIDEvent, QName, boolean) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
writeListSequencePartContent(JPhyloIOEventReceiver, long, long, List<?>) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOWritingUtils
writeMetadata(ReadWriteParameterMap, JPhyloIOEventReceiver) - Method in interface info.bioinfweb.jphyloio.dataadapters.AnnotatedDataAdapter
  Writes events describing the metadata associated with the object represented by this instance.
writeMetadata(ReadWriteParameterMap, JPhyloIOEventReceiver) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.EmptyAnnotatedDataAdapter
  This default implementation does nothing and can be overwritten by inherited classes if necessary.
writeMetadata(ReadWriteParameterMap, JPhyloIOEventReceiver) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreAnnotatedDataAdapter
writeMetadata(ReadWriteParameterMap, JPhyloIOEventReceiver) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.UndefinedOTUListDataAdapter
writeMetadata() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickNodeEdgeEventReceiver
  Write the metadata stored in this receiver into a Newick/Nexus hot comment.
writeNamespace(String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
writeProcessingInstruction(String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
writeProcessingInstruction(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
writePropertyTag(URIOrStringIdentifier, URIOrStringIdentifier, String, boolean) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.receivers.PhyloXMLMetaDataReceiver
writeRemainingStandardTokenDefinitions() - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLTokenSetEventReceiver
WriterStreamDataProvider<R extends AbstractEventWriter<? extends WriterStreamDataProvider<R>>> - Class in info.bioinfweb.jphyloio
WriterStreamDataProvider(R) - Constructor for class info.bioinfweb.jphyloio.WriterStreamDataProvider
writeSequencePartContentData(ReadWriteParameterMap, JPhyloIOEventReceiver, String, long, long) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreMatrixDataAdapter
writeSequencePartContentData(ReadWriteParameterMap, JPhyloIOEventReceiver, String, long, long) - Method in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
  Implementing classes must write a sequence of events here, that describe the sequence tokens present in the specified column range.
writeSimpleLiteralMetadata(JPhyloIOEventReceiver, String, String, URIOrStringIdentifier, URIOrStringIdentifier, Object, String) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOWritingUtils
  Writes an event subsequence modeling a literal metadata annotation with a simple value.
writeSimpleLiteralMetadata(JPhyloIOEventReceiver, String, String, QName, QName, Object, String) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOWritingUtils
  Writes an event subsequence modeling a literal metadata annotation with a simple value.
writeSimpleLiteralMetadata(JPhyloIOEventReceiver, String, String, QName, QName, Object) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOWritingUtils
  Writes an event subsequence modeling a literal metadata annotation with a simple value.
writeSingleMatrix(DocumentDataAdapter, MatrixDataAdapter, Iterator<String>, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.AbstractSingleMatrixEventWriter
  Implementations of this method should write a single matrix to their target format.
writeSingleMatrix(DocumentDataAdapter, MatrixDataAdapter, Iterator<String>, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.fasta.FASTAEventWriter
writeSingleMatrix(DocumentDataAdapter, MatrixDataAdapter, Iterator<String>, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.phylip.PhylipEventWriter
writeStartDocument() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
writeStartDocument(String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
writeStartDocument(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
writeStartElement(String, String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
writeStartElement(String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
writeStartElement(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
writeTerminalResourceMetadata(JPhyloIOEventReceiver, String, String, URIOrStringIdentifier, URI, String) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOWritingUtils
  Writes a `ResourceMetadataEvent` and its respective end event to the specified receiver.
writeTerminalResourceMetadata(JPhyloIOEventReceiver, String, String, URIOrStringIdentifier, URI) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOWritingUtils
  Writes a `ResourceMetadataEvent` and its respective end event to the specified receiver.
writeTerminalResourceMetadata(JPhyloIOEventReceiver, String, String, QName, URI, String) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOWritingUtils
  Writes a `ResourceMetadataEvent` and its respective end event to the specified receiver.
writeTerminalResourceMetadata(JPhyloIOEventReceiver, String, String, QName, URI) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOWritingUtils
  Writes a `ResourceMetadataEvent` and its respective end event to the specified receiver.
writeXMLRepresentation(XMLStreamWriter, Object, WriterStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLColorTranslator
writeXMLRepresentation(XMLStreamWriter, Object, WriterStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.SimpleValueTranslator
  Writes the string representation of the specified object to an XML stream.
writeXMLRepresentation(XMLStreamWriter, Object, WriterStreamDataProvider<?>) - Method in interface info.bioinfweb.jphyloio.objecttranslation.ObjectTranslator
  Writes the XML representation of the specified object into the specified XML writer.

A B C D E F G H I J K L M N O P Q R S T U V W X