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

## R

RDF_DEFAULT_PRE - Static variable in class info.bioinfweb.jphyloio.formats.xml.XMLReadWriteUtils
reachElementEnd(JPhyloIOEventReader) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOReadingUtils
  Reads all events from the reader until one more end element than start elements is found.
read(String, TextReaderStreamDataProvider<?>, Collection<JPhyloIOEvent>, boolean) - Method in class info.bioinfweb.jphyloio.formats.newick.HotCommentDataReader
  Reads metadata from the specified hot comment and adds according events to the queue.
readAll(JPhyloIOEventReader) - Method in class info.bioinfweb.jphyloio.push.EventForwarder
  Consumes all available events from the specified listener and forwards them to the registered listeners.
readAttributes(P, StartElement, String, AttributeInfo...) - Method in class info.bioinfweb.jphyloio.formats.xml.elementreaders.AbstractXMLElementReader
readAttributes(P, StartElement, String, LinkedHashMap<QName, AttributeInfo>) - Method in class info.bioinfweb.jphyloio.formats.xml.elementreaders.AbstractXMLElementReader
readCharacters(String) - Method in class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
readCharacters(String, char, char) - Method in class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
  Reads characters from the stream and adds a respective sequence tokens event to the queue.
readComment() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventReader
  Calls `AbstractTextEventReader.readComment(char, char)` with according parameters and ensures visibility for `NexusReaderStreamDataProvider`.
readComment() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider
readComment(char, char) - Method in class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
  Reads a single comment from the reader.
readCurrentNode(JPhyloIOEventReader) - Method in class info.bioinfweb.jphyloio.push.EventForwarder
  Consumes all events between a start and its respective end event.
readDatatypeAttributeValue(String, StartElement) - Static method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLEventReader
ReadElement(String, Number, int) - Constructor for class info.bioinfweb.jphyloio.formats.newick.NewickUtils.ReadElement
ReaderStreamDataProvider<R extends AbstractEventReader<? extends ReaderStreamDataProvider<R>>> - Class in info.bioinfweb.jphyloio
  Stream data providers are objects used by helper classes of JPhyloIO event readers (e.g.
ReaderStreamDataProvider(R) - Constructor for class info.bioinfweb.jphyloio.ReaderStreamDataProvider
readEvent(NeXMLReaderStreamDataProvider, XMLEvent) - Method in class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractSetElementReader
readEvent(NeXMLReaderStreamDataProvider, XMLEvent) - Method in class info.bioinfweb.jphyloio.formats.nexml.elementreader.NeXMLMetaEndElementReader
readEvent(NeXMLReaderStreamDataProvider, XMLEvent) - Method in class info.bioinfweb.jphyloio.formats.nexml.elementreader.NeXMLMetaStartElementReader
readEvent(NeXMLReaderStreamDataProvider, XMLEvent) - Method in class info.bioinfweb.jphyloio.formats.nexml.elementreader.NeXMLSetEndElementReader
readEvent(NeXMLReaderStreamDataProvider, XMLEvent) - Method in class info.bioinfweb.jphyloio.formats.nexml.elementreader.NeXMLStartDocumentElementReader
readEvent(PhyloXMLReaderStreamDataProvider, XMLEvent) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.elementreader.PhyloXMLCharactersElementReader
readEvent(PhyloXMLReaderStreamDataProvider, XMLEvent) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.elementreader.PhyloXMLStartDocumentElementReader
readEvent(P, XMLEvent) - Method in class info.bioinfweb.jphyloio.formats.xml.elementreaders.CommentElementReader
readEvent(P, XMLEvent) - Method in class info.bioinfweb.jphyloio.formats.xml.elementreaders.StartDocumentElementReader
readEvent(P, XMLEvent) - Method in interface info.bioinfweb.jphyloio.formats.xml.elementreaders.XMLElementReader
readEvent(XMLReaderStreamDataProvider, XMLEvent) - Method in class info.bioinfweb.jphyloio.formats.xml.elementreaders.XMLEndElementReader
readEvent(XMLReaderStreamDataProvider, XMLEvent) - Method in class info.bioinfweb.jphyloio.formats.xml.elementreaders.XMLNoCharactersAllowedElementReader
readEvent(XMLReaderStreamDataProvider, XMLEvent) - Method in class info.bioinfweb.jphyloio.formats.xml.elementreaders.XMLStartElementReader
readEvent(XMLReaderStreamDataProvider, XMLEvent) - Method in class info.bioinfweb.jphyloio.formats.xtg.XTGFormattedTextElementReader
readKeyValueInformation(char, char, char, char) - Method in class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
readKeyValueMetaInformation() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventReader
readKeyValueMetaInformation() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider
readLiteralMetadataContentAsObject(JPhyloIOEventReader, Class<O>) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOReadingUtils
  Reads a subsequence from an JPhyloIO event stream modeling contents of a literal metadata element into an object of the specified class.
readLiteralMetadataContentAsString(JPhyloIOEventReader) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOReadingUtils
  This convenience method calls `JPhyloIOReadingUtils.readLiteralMetadataContentAsStringBuilder(JPhyloIOEventReader)` internally and converts its content to a `String` if the builder is not `null`.
readLiteralMetadataContentAsStringBuilder(JPhyloIOEventReader) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOReadingUtils
  Reads a subsequence from an JPhyloIO event stream modeling contents of a literal metadata element into a string builder.
readMatrixDimensions() - Method in class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader
readNextElement(String, int, int) - Static method in class info.bioinfweb.jphyloio.formats.newick.NewickUtils
readNextEvent() - Method in class info.bioinfweb.jphyloio.AbstractEventReader
  Method to be implemented be inherited classes that adds at least one additional event (determined from the underlying data source) to the event queue.
readNextEvent() - Method in class info.bioinfweb.jphyloio.formats.fasta.FASTAEventReader
readNextEvent() - Method in class info.bioinfweb.jphyloio.formats.mega.MEGAEventReader
readNextEvent() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickEventReader
readNextEvent() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractNexusCommandEventReader
readNextEvent() - Method in interface info.bioinfweb.jphyloio.formats.nexus.commandreaders.NexusCommandEventReader
  Adds at least one additional event (generated from the current Nexus command) to the event queue.
readNextEvent() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventReader
readNextEvent() - Method in class info.bioinfweb.jphyloio.formats.phylip.PhylipEventReader
readNextEvent() - Method in class info.bioinfweb.jphyloio.formats.phylip.SequentialPhylipEventReader
readNextEvent() - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
readNexusWord() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventReader
readNexusWord() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider
readPositiveInteger(long) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventReader
  Tries to read a positive integer from the current position of the underlying stream-
readPositiveInteger(long) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider
  Tries to read a positive integer from the current position of the underlying stream-
readSequence(NeXMLReaderStreamDataProvider, String, TokenTranslationStrategy) - Method in class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractNeXMLElementReader
  Parses a sequence string to a list of single tokens by using the provided `TokenTranslationStrategy`.
readSequenceName() - Method in class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader
readToken(char, char, char, char) - Method in class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
readUntil(JPhyloIOEventReader, EventContentType) - Method in class info.bioinfweb.jphyloio.push.EventForwarder
  Consumes all available events from the specified listener and forwards them to the registered listeners until an event of the specified type is reached.
readUntil(JPhyloIOEventReader, Set<EventContentType>) - Method in class info.bioinfweb.jphyloio.push.EventForwarder
  Consumes all available events from the specified listener and forwards them to the registered listeners until any event of one of the specified types is reached.
ReadWriteConstants - Interface in info.bioinfweb.jphyloio
  Provides general constants for reading and writing phylogenetic file formats.
ReadWriteParameterMap - Class in info.bioinfweb.jphyloio
  Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.
ReadWriteParameterMap() - Constructor for class info.bioinfweb.jphyloio.ReadWriteParameterMap
ReadWriteParameterNames - Interface in info.bioinfweb.jphyloio
  Provides the names of parameters supported by one or more readers or writers included in JPhyloIO.
readXMLRepresentation(XMLEventReader, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLColorTranslator
readXMLRepresentation(XMLEventReader, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.SimpleValueTranslator
  Reads an object from the character data available at the current position of the XML reader.
readXMLRepresentation(XMLEventReader, ReaderStreamDataProvider<?>) - Method in interface info.bioinfweb.jphyloio.objecttranslation.ObjectTranslator
  Tries to create a new instance of the handled object type from the data provided by the specified XML reader.
ReferenceOnlySetReceiver - Class in info.bioinfweb.jphyloio.formats.nexus.receivers
ReferenceOnlySetReceiver(NexusWriterStreamDataProvider, Set<EventContentType>, Set<EventContentType>) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.receivers.ReferenceOnlySetReceiver
ReferenceOnlySetReceiver(NexusWriterStreamDataProvider, Set<EventContentType>) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.receivers.ReferenceOnlySetReceiver
RELAXED_PHYLIP_NAME_PATTERN - Static variable in interface info.bioinfweb.jphyloio.formats.phylip.PhylipConstants
remove() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventReader
removeAllFactories() - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
  Removes all single format factories from the internal map of this instance.
removeEventListener(JPhyloIOEventListener) - Method in class info.bioinfweb.jphyloio.AbstractEventReader
removeEventListener(JPhyloIOEventListener) - Method in interface info.bioinfweb.jphyloio.JPhyloIOEventReader
  Removes a `JPhyloIOEventListener` from the reader.
representationToJava(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLColorTranslator
representationToJava(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.AbstractXMLObjectTranslator
representationToJava(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.IllegalArgumentExceptionSimpleValueTranslator
representationToJava(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.ListTranslator
  Reads a string representation of a simple value list into an implementation of `List`.
representationToJava(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.NumericValueTranslator
representationToJava(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.StringTranslator
representationToJava(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.URITranslator
representationToJava(String, ReaderStreamDataProvider<?>) - Method in interface info.bioinfweb.jphyloio.objecttranslation.ObjectTranslator
  Converts the specified string representation to a new instance of the according Java object.
require(int, String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
RESERVED_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
resetCurrentEventCollection() - Method in class info.bioinfweb.jphyloio.AbstractEventReader
  Removes the event collection at the top of the eventCollections stack and returns it.
resetCurrentEventCollection() - Method in class info.bioinfweb.jphyloio.ReaderStreamDataProvider
  Removes the event collection at the top of the eventCollections stack and returns it.
resetHasMetadata() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.receivers.PhyloXMLCollectMetadataDataReceiver
ResourceMetadataEvent - Class in info.bioinfweb.jphyloio.events.meta
  Indicates that metadata linking a RDF resource has been encountered at the current position of the document.
ResourceMetadataEvent(String, String, URIOrStringIdentifier, URI, String) - Constructor for class info.bioinfweb.jphyloio.events.meta.ResourceMetadataEvent
  Creates a new instance of this class.
ResourceMetadataEvent(String, String, QName, URI, String) - Constructor for class info.bioinfweb.jphyloio.events.meta.ResourceMetadataEvent
  Creates a new instance of this class.
ResourceMetadataEvent(String, String, QName) - Constructor for class info.bioinfweb.jphyloio.events.meta.ResourceMetadataEvent
  Creates a new instance of this class with no `hRef` and no `about` values.
ResourceMetadataEvent(String, String, URIOrStringIdentifier) - Constructor for class info.bioinfweb.jphyloio.events.meta.ResourceMetadataEvent
  Creates a new instance of this class with no `hRef` and no `about` values.
ROOTED_HOT_COMMENT - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants

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