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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