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

## A

AbstractCharLabelsReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters
  Implements shared functionality for Nexus command readers that process character (alignment column) definitions.
AbstractCharLabelsReader(String, NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.AbstractCharLabelsReader
AbstractEventReader<P extends ReaderStreamDataProvider<? extends AbstractEventReader<P>>> - Class in info.bioinfweb.jphyloio
  Basic implementation for event readers in PhyloIO.
AbstractEventReader(ReadWriteParameterMap, String) - Constructor for class info.bioinfweb.jphyloio.AbstractEventReader
AbstractEventWriter<P extends WriterStreamDataProvider<? extends AbstractEventWriter<P>>> - Class in info.bioinfweb.jphyloio
  Implements shared functionality for JPhyloIO event writers.
AbstractEventWriter() - Constructor for class info.bioinfweb.jphyloio.AbstractEventWriter
AbstractEventWriter.NoEditUniqueLabelHandler - Class in info.bioinfweb.jphyloio
AbstractEventWriter.UniqueLabelHandler - Interface in info.bioinfweb.jphyloio
AbstractIDLinkSetElementReader - Class in info.bioinfweb.jphyloio.formats.nexml.elementreader
  Element reader for NeXML sets that are represented as a sequence of `EventContentType.SET_ELEMENT` events.
AbstractIDLinkSetElementReader(EventContentType, EventContentType, QName...) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractIDLinkSetElementReader
  Creates a new instance of this class.
AbstractKeyValueCommandReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders
AbstractKeyValueCommandReader(String, String[], NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractKeyValueCommandReader
AbstractMetaXMLReader - Class in info.bioinfweb.jphyloio.formats.xml.stax
  Implements shared functionality for custom XML readers.
AbstractMetaXMLReader(XMLReaderStreamDataProvider<?>) - Constructor for class info.bioinfweb.jphyloio.formats.xml.stax.AbstractMetaXMLReader
AbstractMetaXMLWriter - Class in info.bioinfweb.jphyloio.formats.xml.stax
  Implements shared functionality for the StAX adapter writers of JPhyloIO.
AbstractMetaXMLWriter(JPhyloIOEventReceiver, XMLStreamWriter) - Constructor for class info.bioinfweb.jphyloio.formats.xml.stax.AbstractMetaXMLWriter
AbstractNeXMLDataReceiver - Class in info.bioinfweb.jphyloio.formats.nexml.receivers
  Implements basic functionality for event receivers writing NeXML.
AbstractNeXMLDataReceiver(NeXMLWriterStreamDataProvider, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.receivers.AbstractNeXMLDataReceiver
AbstractNeXMLDataReceiverMixin - Class in info.bioinfweb.jphyloio.formats.nexml.receivers
  Provides a set of static methods to be used as static imports when needed across multiple NeXML data receivers.
AbstractNeXMLDataReceiverMixin() - Constructor for class info.bioinfweb.jphyloio.formats.nexml.receivers.AbstractNeXMLDataReceiverMixin
AbstractNeXMLElementReader - Class in info.bioinfweb.jphyloio.formats.nexml.elementreader
  Processes a NeXML tag without any of its subelements.
AbstractNeXMLElementReader() - Constructor for class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractNeXMLElementReader
AbstractNeXMLElementReader.LabeledIDEventInformation - Class in info.bioinfweb.jphyloio.formats.nexml.elementreader
  Contains information about a `LabeledIDEvent`.
AbstractNeXMLElementReader.OTUorOTUsEventInformation - Class in info.bioinfweb.jphyloio.formats.nexml.elementreader
  Contains information about a `LinkedLabeledIDEvent`.
AbstractNexusBlockHandler - Class in info.bioinfweb.jphyloio.formats.nexus.blockhandlers
  Abstract implementation of `NexusBlockHandler` that stores a set of block names in an unmodifiable collection.
AbstractNexusBlockHandler(String[]) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.AbstractNexusBlockHandler
  Creates a new instance of this class.
AbstractNexusCommandEventReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders
  Implements shared functionality for classes implementing `NexusCommandEventReader`.
AbstractNexusCommandEventReader(String, String[], NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractNexusCommandEventReader
  Creates a new instance of this class.
AbstractNexusEventReceiver - Class in info.bioinfweb.jphyloio.formats.nexus.receivers
  Implements basic functionality for event receivers writing Nexus.
AbstractNexusEventReceiver(NexusWriterStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.receivers.AbstractNexusEventReceiver
AbstractNexusSetReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets
  General reader implementation to read the Nexus commands that define different kinds of sets.
AbstractNexusSetReader(EventContentType, String, String[], NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.AbstractNexusSetReader
AbstractNexusSetsEventReceiver - Class in info.bioinfweb.jphyloio.formats.nexus.receivers
  General implementation for event receivers writing Nexus set commands.
AbstractNexusSetsEventReceiver(NexusWriterStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.receivers.AbstractNexusSetsEventReceiver
  Creates a new instance of this class.
AbstractNexusSetWriter - Class in info.bioinfweb.jphyloio.formats.nexus
  Customizable implementation for writing different kinds of Nexus sets.
AbstractNexusSetWriter(NexusWriterStreamDataProvider, String, EventContentType, Iterator<? extends ElementDataAdapter<? extends LabeledIDEvent>>, AbstractNexusEventReceiver) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.AbstractNexusSetWriter
AbstractObjectTranslator<O> - Class in info.bioinfweb.jphyloio.objecttranslation.implementations
  Abstract base class for implementations of `ObjectTranslator` that implements `AbstractObjectTranslator.equals(Object)` and `AbstractObjectTranslator.hashCode()` based of the return values of `ObjectTranslator.getObjectClass()` and `ObjectTranslator.hasStringRepresentation()`.
AbstractObjectTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.AbstractObjectTranslator
AbstractPhylipEventReader<P extends TextReaderStreamDataProvider<? extends AbstractPhylipEventReader<P>>> - Class in info.bioinfweb.jphyloio.formats.phylip
  Implements shared functionality of Phylip event readers.
AbstractPhylipEventReader(PeekReader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader
AbstractPhylipEventReader(Reader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader
AbstractPhylipEventReader(InputStream, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader
AbstractPhylipEventReader(File, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader
AbstractPhylipFactory - Class in info.bioinfweb.jphyloio.formats.phylip
  Implements shared functionality for Phylip factories.
AbstractPhylipFactory() - Constructor for class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipFactory
AbstractSequenceContentReceiver<P extends WriterStreamDataProvider<? extends AbstractEventWriter<P>>> - Class in info.bioinfweb.jphyloio.dataadapters.implementations.receivers
AbstractSequenceContentReceiver(P, ReadWriteParameterMap, boolean) - Constructor for class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.AbstractSequenceContentReceiver
AbstractSetElementReader - Class in info.bioinfweb.jphyloio.formats.nexml.elementreader
  Abstract element reader that processes NeXML set tags that contain one or more attributes of the type `xs:IDREFS`.
AbstractSetElementReader(EventContentType, EventContentType, QName...) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractSetElementReader
AbstractSingleMatrixEventWriter<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>> - Class in info.bioinfweb.jphyloio
  Default implementation for writers that can only write a single matrix (multiple sequence alignment) to their target format, because that format does not support additional data.
AbstractSingleMatrixEventWriter(String) - Constructor for class info.bioinfweb.jphyloio.AbstractSingleMatrixEventWriter
  Creates a new instance of this class.
AbstractSingleReaderWriterFactory - Class in info.bioinfweb.jphyloio.factory
AbstractSingleReaderWriterFactory() - Constructor for class info.bioinfweb.jphyloio.factory.AbstractSingleReaderWriterFactory
AbstractStartStringSingleFactory - Class in info.bioinfweb.jphyloio.factory
  Abstract single format factory that implements the `checkFormat()` methods by testing of the read content start with a certain string, determined by `AbstractStartStringSingleFactory.getExpectedStart()`.
AbstractStartStringSingleFactory(String) - Constructor for class info.bioinfweb.jphyloio.factory.AbstractStartStringSingleFactory
  Creates a new instance of this class.
AbstractTextEventReader<P extends TextReaderStreamDataProvider<? extends AbstractTextEventReader<P>>> - Class in info.bioinfweb.jphyloio.formats.text
  Abstract base class for all readers that read their data from a file using a `PeekReader`.
AbstractTextEventReader(PeekReader, ReadWriteParameterMap, String) - Constructor for class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
  Creates a new instance of this class.
AbstractTextEventReader(Reader, ReadWriteParameterMap, String) - Constructor for class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
  Creates a new instance of this class.
AbstractTextEventReader(InputStream, ReadWriteParameterMap, String) - Constructor for class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
  Creates a new instance of this class.
AbstractTextEventReader(File, ReadWriteParameterMap, String) - Constructor for class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
  Creates a new instance of this class.
AbstractTextEventWriter<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>> - Class in info.bioinfweb.jphyloio.formats.text
AbstractTextEventWriter() - Constructor for class info.bioinfweb.jphyloio.formats.text.AbstractTextEventWriter
AbstractXMLDataReceiver<P extends XMLWriterStreamDataProvider<? extends AbstractXMLEventWriter<P>>> - Class in info.bioinfweb.jphyloio.formats.xml.receivers
  Abstract implementation of a data receiver that can be used to write XML formats.
AbstractXMLDataReceiver(P, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.xml.receivers.AbstractXMLDataReceiver
AbstractXMLElementReader<P extends XMLReaderStreamDataProvider<? extends AbstractXMLEventReader<P>>> - Class in info.bioinfweb.jphyloio.formats.xml.elementreaders
  Abstract implementation of an element reader that is used to process parts of an XML document.
AbstractXMLElementReader() - Constructor for class info.bioinfweb.jphyloio.formats.xml.elementreaders.AbstractXMLElementReader
AbstractXMLEventReader<P extends XMLReaderStreamDataProvider<? extends AbstractXMLEventReader<P>>> - Class in info.bioinfweb.jphyloio.formats.xml
  Implements shared functionality for reading XML formats.
AbstractXMLEventReader(File, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
AbstractXMLEventReader(InputStream, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
AbstractXMLEventReader(XMLEventReader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
AbstractXMLEventReader(Reader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
AbstractXMLEventWriter<P extends XMLWriterStreamDataProvider<? extends AbstractXMLEventWriter<P>>> - Class in info.bioinfweb.jphyloio.formats.xml
  Implements shared functionality for writing XML formats.
AbstractXMLEventWriter() - Constructor for class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventWriter
AbstractXMLFactory - Class in info.bioinfweb.jphyloio.formats.xml
  Implements shared functionality for reader and writer factories of XML formats.
AbstractXMLFactory(QName) - Constructor for class info.bioinfweb.jphyloio.formats.xml.AbstractXMLFactory
  Creates a new instance of this class.
AbstractXMLObjectTranslator<O> - Class in info.bioinfweb.jphyloio.objecttranslation.implementations
  Abstract implementation for object translators that need XML tags to represent their object and do not support simple string representations.
AbstractXMLObjectTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.AbstractXMLObjectTranslator
acceptContent(FileInputStream) - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOContentExtensionFileFilter
add(JPhyloIOEvent) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
add(JPhyloIOEvent) - Method in interface info.bioinfweb.jphyloio.dataadapters.JPhyloIOEventReceiver
  Adds a new event to the sequence written to this receiver.
add(String, String) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.NexusTranslationTable
add(XMLEvent) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventWriter
add(XMLEventReader) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventWriter
add(JPhyloIOEvent) - Method in class info.bioinfweb.jphyloio.ParentEventInformation
addCharacterDefinition(String, long) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.AbstractCharLabelsReader
addEdit(EventContentType, String, String, boolean) - Method in class info.bioinfweb.jphyloio.utils.LabelEditingReporter
  Adds a new mapping from an element ID to the label used for it in the target document to this instance.
addEdit(LabeledIDEvent, String) - Method in class info.bioinfweb.jphyloio.utils.LabelEditingReporter
  Adds a new mapping from an element ID to the label used for it in the target document to this instance.
addENewickNetworksBlockSupport() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventReader
  Adds an instance of `ENewickNetworksBlockHandler` and `ENewickNetworkReader` to the maps of this instance in order to be able to read custom `NETWORK` blocks containing phylogenetic networks in the eNewick format.
addEventListener(JPhyloIOEventListener) - Method in class info.bioinfweb.jphyloio.AbstractEventReader
addEventListener(JPhyloIOEventListener) - Method in interface info.bioinfweb.jphyloio.JPhyloIOEventReader
  Adds a `JPhyloIOEventListener` to the reader that will be informed on all events generated by this reader (e.g.
addFactory(SingleReaderWriterFactory) - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
  Allows to add additional or replace existing single format factories to be used by this instance.
addHandler(NexusBlockHandler) - Method in class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.NexusBlockHandlerMap
  Adds a new handler to this map.
addIgnoredComments(long) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
addIgnoredLiteralMetadata(long) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
addIgnoredResourceMetadata(long) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
addIgnoreLogMessage(ApplicationLogger, String, String) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
addJPhyloIOHandlers() - Method in class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.NexusBlockHandlerMap
  Adds all handlers that are available in JPhyloIO to this instance.
addJPhyloIOReaders() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.NexusCommandReaderFactory
  Adds all Nexus command readers available in JPhyloIO to this instance.
addJPhyloIOTranslators(boolean) - Method in class info.bioinfweb.jphyloio.objecttranslation.ObjectTranslatorFactory
  Adds all translators for custom types defined in JPhyloIO.
addNextEvents() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickStringReader
  Creates the next JPhyloIO event(s) from the Newick string provided by the underlying reader.
addReaderClass(Class<? extends NexusCommandEventReader>) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.NexusCommandReaderFactory
  Adds a new type of reader to this factory instance.
addRemainingEvents(CharacterStateSetType) - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLMolecularDataTokenDefinitionReceiver
  Determines the type of alignment to which additional token definitions need to be add.
addStoredEvents() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractKeyValueCommandReader
  Implementations that need to store events, until all generated events are known should add such events to the queue, when this method is called.
addStoredEvents() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.all.LinkReader
addStoredEvents() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.DimensionsReader
addStoredEvents() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.FormatReader
  Adds the stored token set event with nested single token definition events to the queue, if present.
addToDocumentIDs(String) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
addTranslator(ObjectTranslator<?>, boolean, QName, QName...) - Method in class info.bioinfweb.jphyloio.objecttranslation.ObjectTranslatorFactory
  Registers a new translator in this factory for one or more data types.
addXSDTranslators(boolean) - Method in class info.bioinfweb.jphyloio.objecttranslation.ObjectTranslatorFactory
  Adds all translators for XSD types available in JPhyloIO.
ALIGN_LEFT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ALIGN_RIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ALIGN_TREE_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ALL_BLOCKS_IDENTIFIER - Static variable in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.NexusCommandReaderFactory
ALLOCATION_SEPARATOR_SYMBOL - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
ALLOCATION_SYMBOL - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
ALTERNATIVE_END_COMMAND - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
ALTERNATIVE_NAME_DELIMITER - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
AMINO_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
AnnotatedDataAdapter - Interface in info.bioinfweb.jphyloio.dataadapters
  Superinterface for all data adapters providing metadata to the object they model.
anyLabelEdited(EventContentType) - Method in class info.bioinfweb.jphyloio.utils.LabelEditingReporter
  Determines whether any label of data elements of the specified content type was edited.
APPLIES_TO_ANNOTATION - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
APPLIES_TO_CLADE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
APPLIES_TO_NODE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
APPLIES_TO_OTHER - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
APPLIES_TO_PARENT_BRANCH - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
APPLIES_TO_PHYLOGENY - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
asCharacterDefinitionEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
asCharacterDefinitionEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
  Casts this event to a character definition event.
asCharacterSetIntervalEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
asCharacterSetIntervalEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
  Casts this event to a character set event.
asCommentEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
asCommentEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
  Casts this event to a comment event.
asEdgeEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
asEdgeEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
  Casts this event to a tree or graph edge event.
asLabeledIDEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
asLabeledIDEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
  Casts this event to a labeled ID event.
asLinkedLabeledIDEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
asLinkedLabeledIDEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
  Casts this event to a basic OTU event.
asLiteralMetadataContentEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
asLiteralMetadataContentEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
  Casts this event to a literal content metadata event.
asLiteralMetadataEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
asLiteralMetadataEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
  Casts this event to a literal metadata event.
asNodeEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
asNodeEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
  Casts this event to a tree or graph node event.
asPartEndEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
asPartEndEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
  Casts this event to a part end event.
asResourceMetadataEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
asResourceMetadataEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
  Casts this event to a resource metadata event.
asSequenceTokensEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
asSequenceTokensEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
  Casts this event to a tokens event.
asSetElementEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
asSetElementEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
  Casts this event to a set element event.
asSingleSequenceTokenEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
asSingleSequenceTokenEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
  Casts this event to a single token event.
asSingleTokenDefinitionEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
asSingleTokenDefinitionEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
  Casts this event to a single character state symbol definition event.
asTokenSetDefinitionEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
asTokenSetDefinitionEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
  Casts this event to a character state set definition event.
asUnknownCommandEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
asUnknownCommandEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
  Casts this event to an unknown command event.
ATTR_ABOUT - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_ABSENT_COUNT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_ADAPTER_ID - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_ADAPTER_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_ADAPTER_PURPOSE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_ALIGN_TO_SUBTREE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_ALIGNMENT_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
ATTR_ALT_UNIT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_ANCHOR_0 - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_ANCHOR_1 - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_APPLIES_TO - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_BG_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_BOTTOM - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_BRANCH_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_BRANCH_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_BRANCH_LENGTH_SCALE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_BRANCH_LENGTH_UNIT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_CAPTION_LINK_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_CAPTION_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_CELL_SET_LINKED_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_CHAR_SET_LINKED_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_CHARSET_LABEL - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
ATTR_CODON_POSITION - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_COLLAPSE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
ATTR_COMMENT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_CONFIDENCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_CONSTANT_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_CONTENT - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_DATATYPE - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_DATATYPE - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
ATTR_DATATYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_DECIMAL_FORMAT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_DESC - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_DISTANCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_DOI - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_EDGE_RADIUS - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_EVIDENCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_FONT_FAMILY - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_FROM - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_GAINED_COUNT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_GENERATOR - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_GEO_DATUM - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_HEIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_HREF - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_ICON - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_ICON_FILLED - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_ICON_HEIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_ICON_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_ID - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_ID - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
ATTR_ID - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_ID - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_ID_PROVIDER - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_ID_REF - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_ID_REF_0 - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_ID_REF_1 - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_ID_SOURCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_IS_ALIGNED - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_LABEL - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_LABEL_ABOVE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_LABEL_HEIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_LABEL_SPACING - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_LABEL_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_LEFT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_LEGEND_POS - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_LEGEND_SPACING - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_LEGEND_STYLE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_LINE_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_LINE_NO - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_LINE_POS - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_LINE_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_LOCALE_COUNTRY - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_LOCALE_LANG - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_LOCALE_VARIANT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_LOST_COUNT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_MIN_BRANCH_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_MIN_SPACE_ABOVE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_MIN_SPACE_BELOW - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_MIN_TREE_DISTANCE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_NODE_EDGE_SET_LINKED_EDGE_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_NODE_EDGE_SET_LINKED_NODE_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_NODE_EDGE_SET_LINKED_ROOTEDGE_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_OTU_SET_LINKED_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_OTUS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_PIE_CAPTION - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_PIE_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_POSITION_LABELS_TO_LEFT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_PRESENT_COUNT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_PROPERTY - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_REF - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_REL - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_REROOTABLE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_RIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_ROOT - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_ROOTED - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_SCALE_BAR_ALIGN - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_SCALE_BAR_DISTANCE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_SCALE_BAR_HEIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_SCALE_BAR_INCREASE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_SCALE_BAR_LONG_INTERVAL - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_SCALE_BAR_SMALL_INTERVAL - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_SCALE_BAR_START - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_SCALE_BAR_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_SEQUENCE_COUNT - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
ATTR_SEQUENCE_INDEX - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
ATTR_SEQUENCE_SET_LINKED_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_SHOW_INTERNAL_LINES - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_SHOW_NULL_LINES - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_SHOW_ROOTED - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_SHOW_SCALE_BAR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_SHOW_TITLE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_SINGLE_CHAR_LINK - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_SINGLE_OTU_LINK - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_SINGLE_STATE_LINK - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_SOURCE - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_SOURCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_STANDARD_DEVIATION - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_STATE_SET_LINKED_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_STATES - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_SYMBOL - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_TARGET - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_TEXT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_TEXT_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_TEXT_HEIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_TEXT_IS_DECIMAL - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_TEXT_ORIENTATION - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_TEXT_STYLE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_TO - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_TOKENS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_TOP - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_TREE_SET_LINKED_NETWORK_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_TREE_SET_LINKED_TREE_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_UNIQUE_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_UNIT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
ATTR_VERSION - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTR_VERSION - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
ATTR_VISIBILITY - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
ATTR_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
ATTR_XSI_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
ATTRIBUTE_STRING_KEY - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
AttributeInfo - Class in info.bioinfweb.jphyloio.formats.xml
  This class models an XML attribute.
AttributeInfo(QName, QName, QName) - Constructor for class info.bioinfweb.jphyloio.formats.xml.AttributeInfo
ATTRIBUTES_NAMESPACE_FOLDER - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants

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