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