Uses of Interface
info.bioinfweb.jphyloio.events.JPhyloIOEvent

Packages that use JPhyloIOEvent

Package	Description
info.bioinfweb.jphyloio	The main package of JPhyloIO.
info.bioinfweb.jphyloio.dataadapters	Contains adapter interfaces that should be implemented by adapters mediating between the business model of an application and implementations of JPhyloIOEventWriter.
info.bioinfweb.jphyloio.dataadapters.implementations	Contains some basic (abstract) implementations of JPhyloIOEventWriter.
info.bioinfweb.jphyloio.dataadapters.implementations.receivers	Contains some basic (abstract) implementations of JPhyloIOEventReceiver to be used by implementations of JPhyloIOEventWriter.
info.bioinfweb.jphyloio.dataadapters.implementations.store	Contains implementations of data adapters that directly store their modeled data in mutable lists or maps instead of delegating to an application business model.
info.bioinfweb.jphyloio.events	Contains implementations of JPhyloIO events, triggered during event based parsing.
info.bioinfweb.jphyloio.events.meta	Contains event classes that model metadata, as well as related implementations.
info.bioinfweb.jphyloio.exception	Contains exceptions that are of general use in JPhyloIO.
info.bioinfweb.jphyloio.formats	The subpackages of this package contain implementations of JPhyloIO readers and writers for different formats.
info.bioinfweb.jphyloio.formats.newick	Contains classes for reading from and writing to streams/files in Newick tree format.
info.bioinfweb.jphyloio.formats.nexml	Contains classes for reading from and writing to streams/files in NeXML format.
info.bioinfweb.jphyloio.formats.nexml.receivers	Contains implementations for JPhyloIOEventReceiver necessary for writing NeXML.
info.bioinfweb.jphyloio.formats.nexus.commandreaders	Contains general classes for reading Nexus commands.
info.bioinfweb.jphyloio.formats.nexus.receivers	Contains implementations of JPhyloIOEventReceiver used internally by NexusEventReader.
info.bioinfweb.jphyloio.formats.phyloxml.receivers	Contains implementations for JPhyloIOEventReceiver necessary for writing PhyloXML.
info.bioinfweb.jphyloio.formats.text	Contains classes implementing shared functionality for reading from and writing to streams/files in text formats.
info.bioinfweb.jphyloio.formats.xml.stax	Contains implementations that allow StAX based reading and writing of XML metadata.
info.bioinfweb.jphyloio.push	Contains classes that allow push-parsing.
info.bioinfweb.jphyloio.utils	Contains general tool classes of JPhyloIO.

Uses of JPhyloIOEvent in info.bioinfweb.jphyloio

Methods in info.bioinfweb.jphyloio that return JPhyloIOEvent

Modifier and Type	Method and Description
JPhyloIOEvent	ParentEventInformation.getDirectParent()
JPhyloIOEvent	AbstractEventReader.getLastNonCommentEvent() Returns the last event that has been returned by previous calls of AbstractEventReader.readNextEvent() that was not a comment event.
JPhyloIOEvent	JPhyloIOEventReader.getLastNonCommentEvent() Returns the last event that has been returned by previous calls of #readNextEvent() that was not a comment event.
JPhyloIOEvent	ParentEventInformation.getParentFromBottom(int index)
JPhyloIOEvent	ParentEventInformation.getParentFromTop(int index)
JPhyloIOEvent	AbstractEventReader.getPreviousEvent() Returns the event that has been returned by the previous call of AbstractEventReader.readNextEvent().
JPhyloIOEvent	JPhyloIOEventReader.getPreviousEvent() Returns the event that was returned with the last call of JPhyloIOEventReader.next().
JPhyloIOEvent	AbstractEventReader.next()
JPhyloIOEvent	JPhyloIOEventReader.next() Returns the next event from the underlying document and moves one step forward.
JPhyloIOEvent	AbstractEventReader.nextOfType(java.util.Set<EventType> types)
JPhyloIOEvent	JPhyloIOEventReader.nextOfType(java.util.Set<EventType> types) Reads elements from the underlying stream until one of the specified is found or the end of the document is reached.
JPhyloIOEvent	AbstractEventReader.peek()
JPhyloIOEvent	JPhyloIOEventReader.peek() Returns the event from the underlying document that will be returned in the next call of JPhyloIOEventReader.next() without moving forward.

Methods in info.bioinfweb.jphyloio that return types with arguments of type JPhyloIOEvent

Modifier and Type	Method and Description
protected java.util.Collection<JPhyloIOEvent>	AbstractEventReader.getCurrentEventCollection() Returns the event collection that is currently used to take up new events.
java.util.Collection<JPhyloIOEvent>	ReaderStreamDataProvider.getCurrentEventCollection() Returns the event collection that is currently used to take up new events.
protected java.util.Queue<JPhyloIOEvent>	AbstractEventReader.getUpcomingEvents() Returns the queue to store events in, that shall be returned by upcoming calls of AbstractEventReader.next().
protected java.util.Collection<JPhyloIOEvent>	AbstractEventReader.resetCurrentEventCollection() Removes the event collection at the top of the eventCollections stack and returns it.
java.util.Collection<JPhyloIOEvent>	ReaderStreamDataProvider.resetCurrentEventCollection() Removes the event collection at the top of the eventCollections stack and returns it.
protected java.util.Collection<JPhyloIOEvent>	AbstractEventReader.setCurrentEventCollection(java.util.Collection<JPhyloIOEvent> newCollection) Adds a new current event collection to the stack.
java.util.Collection<JPhyloIOEvent>	ReaderStreamDataProvider.setCurrentEventCollection(java.util.Collection<JPhyloIOEvent> newCollection) Adds a new current event collection to the stack.

Methods in info.bioinfweb.jphyloio with parameters of type JPhyloIOEvent

Modifier and Type	Method and Description
protected void	ParentEventInformation.add(JPhyloIOEvent event)
protected void	AbstractEventReader.fireEvent(JPhyloIOEvent event)

Method parameters in info.bioinfweb.jphyloio with type arguments of type JPhyloIOEvent

Modifier and Type	Method and Description
protected java.util.Collection<JPhyloIOEvent>	AbstractEventReader.setCurrentEventCollection(java.util.Collection<JPhyloIOEvent> newCollection) Adds a new current event collection to the stack.
java.util.Collection<JPhyloIOEvent>	ReaderStreamDataProvider.setCurrentEventCollection(java.util.Collection<JPhyloIOEvent> newCollection) Adds a new current event collection to the stack.

Uses of JPhyloIOEvent in info.bioinfweb.jphyloio.dataadapters

Classes in info.bioinfweb.jphyloio.dataadapters with type parameters of type JPhyloIOEvent

Modifier and Type	Interface and Description
interface	ElementDataAdapter<E extends JPhyloIOEvent> Data adapters that model a data element identified by a certain start event should implement this interface.
interface	ObjectListDataAdapter<E extends JPhyloIOEvent> Allows to provide data for a list of phylogenetic objects.

Methods in info.bioinfweb.jphyloio.dataadapters with parameters of type JPhyloIOEvent

Modifier and Type	Method and Description
boolean	JPhyloIOEventReceiver.add(JPhyloIOEvent event) Adds a new event to the sequence written to this receiver.

Uses of JPhyloIOEvent in info.bioinfweb.jphyloio.dataadapters.implementations

Classes in info.bioinfweb.jphyloio.dataadapters.implementations with type parameters of type JPhyloIOEvent

Modifier and Type	Class and Description
class	EmptyAnnotatedDataAdapter<E extends JPhyloIOEvent> Default implementation of AnnotatedDataAdapter, which does not generate any metaevents.
class	EmptyObjectListDataAdapter<E extends JPhyloIOEvent> Empty implementation of ObjectListDataAdapter.

Uses of JPhyloIOEvent in info.bioinfweb.jphyloio.dataadapters.implementations.receivers

Methods in info.bioinfweb.jphyloio.dataadapters.implementations.receivers that return JPhyloIOEvent

Modifier and Type	Method and Description
JPhyloIOEvent	BasicEventReceiver.getParentEvent()

Methods in info.bioinfweb.jphyloio.dataadapters.implementations.receivers that return types with arguments of type JPhyloIOEvent

Modifier and Type	Method and Description
java.util.Stack<JPhyloIOEvent>	BasicEventReceiver.getParentEvents()

Methods in info.bioinfweb.jphyloio.dataadapters.implementations.receivers with parameters of type JPhyloIOEvent

Modifier and Type	Method and Description
boolean	BasicEventReceiver.add(JPhyloIOEvent event)
protected boolean	AbstractSequenceContentReceiver.doAdd(JPhyloIOEvent event)
protected boolean	BasicEventReceiver.doAdd(JPhyloIOEvent event) This method is called internally by BasicEventReceiver.add(JPhyloIOEvent) to process events that do not model metadata or comments.
protected void	BasicEventReceiver.handleMetaEndEvent(JPhyloIOEvent event)

Uses of JPhyloIOEvent in info.bioinfweb.jphyloio.dataadapters.implementations.store

Classes in info.bioinfweb.jphyloio.dataadapters.implementations.store with type parameters of type JPhyloIOEvent

Modifier and Type	Class and Description
class	StoreAnnotatedDataAdapter<E extends JPhyloIOEvent>
class	StoreObjectData<E extends JPhyloIOEvent>

Methods in info.bioinfweb.jphyloio.dataadapters.implementations.store that return types with arguments of type JPhyloIOEvent

Modifier and Type	Method and Description
java.util.List<JPhyloIOEvent>	StoreAnnotatedDataAdapter.getAnnotations()
java.util.List<JPhyloIOEvent>	StoreObjectData.getObjectContent()
java.util.List<JPhyloIOEvent>	StoreObjectListDataAdapter.getObjectContent(java.lang.String id)

Constructor parameters in info.bioinfweb.jphyloio.dataadapters.implementations.store with type arguments of type JPhyloIOEvent

Constructor and Description
StoreAnnotatedDataAdapter(java.util.List<JPhyloIOEvent> annotations)
StoreDocumentDataAdapter(java.util.List<JPhyloIOEvent> annotations, org.apache.commons.collections4.OrderedMap<java.lang.String,OTUListDataAdapter> otusMap, java.util.List<MatrixDataAdapter> matrices, java.util.List<TreeNetworkGroupDataAdapter> treeNetworkGroups)
StoreMatrixDataAdapter(LinkedLabeledIDEvent alignmentStartEvent, boolean longTokens, java.util.List<JPhyloIOEvent> annotations)
StoreObjectData(E objectStartEvent, java.util.List<JPhyloIOEvent> objectContent)
StoreOTUListDataAdapter(LabeledIDEvent listStartEvent, java.util.List<JPhyloIOEvent> annotations)
StoreTreeNetworkDataAdapter(LabeledIDEvent startEvent, boolean isTree, java.util.List<JPhyloIOEvent> annotations)
StoreTreeNetworkGroupDataAdapter(LinkedLabeledIDEvent treeOrNetworkGroupStartEvent, java.util.List<JPhyloIOEvent> annotations)

Uses of JPhyloIOEvent in info.bioinfweb.jphyloio.events

Subinterfaces of JPhyloIOEvent in info.bioinfweb.jphyloio.events

Modifier and Type	Interface and Description
interface	LinkedIDEvent Interface to be implemented by event objects that can link previous events by their ID.

Classes in info.bioinfweb.jphyloio.events that implement JPhyloIOEvent

Modifier and Type	Class and Description
class	CharacterDefinitionEvent Event that indicates a defined character (alignment column).
class	CharacterSetIntervalEvent Event that indicates that new information on a character set has been read.
class	CommentEvent Event that indicates that a comment has been parsed at the current position or within the data the last non-comment event has been parsed from.
class	ConcreteJPhyloIOEvent Implements basic functionality for JPhyloIOEvents.
class	ContinuedEvent Base class for events that have a content that may be split across separate subsequent events, if it is large.
class	EdgeEvent Event indicating an edge in a tree or network.
class	LabeledEvent
class	LabeledIDEvent Event that indicate data objects that carry an unique ID and a label.
class	LinkedLabeledIDEvent Instances of this class model data elements with an ID and an optional label, that link another data element in a phylogenetic document.
class	NodeEvent Event indicating a node in a tree or network.
class	PartEndEvent Indicates the end of a part of a sequence or character set definition.
class	SequenceTokensEvent Indicates that one or more sequence tokens have been read from an alignment.
class	SetElementEvent Event object that models an ID-based link to an object that is contained in set.
class	SingleSequenceTokenEvent
class	SingleTokenDefinitionEvent Event that indicates the definition of a single new valid token that could be contained in a sequence of the current alignment.
class	TokenSetDefinitionEvent Event that indicates that a (predefined) definition of a character state set was found in the parsed file.
class	UnknownCommandEvent Event to be fired, if an unknown command was found (e.g.

Uses of JPhyloIOEvent in info.bioinfweb.jphyloio.events.meta

Classes in info.bioinfweb.jphyloio.events.meta that implement JPhyloIOEvent

Modifier and Type	Class and Description
class	LiteralMetadataContentEvent This event represents a value of a literal metadata and is therefore always nested inside start and end events of the type EventContentType.LITERAL_META.
class	LiteralMetadataEvent Indicates that literal metadata is modeled at the current position of the document (event stream).
class	ResourceMetadataEvent Indicates that metadata linking a RDF resource has been encountered at the current position of the document.

Uses of JPhyloIOEvent in info.bioinfweb.jphyloio.exception

Methods in info.bioinfweb.jphyloio.exception that return JPhyloIOEvent

Modifier and Type	Method and Description
JPhyloIOEvent	IllegalEventException.getInvalidEvent()
JPhyloIOEvent	IllegalEventException.getParentEvent()

Methods in info.bioinfweb.jphyloio.exception with parameters of type JPhyloIOEvent

Modifier and Type	Method and Description
static IllegalEventException	IllegalEventException.newInstance(JPhyloIOEventReceiver receiver, JPhyloIOEvent parentEvent, JPhyloIOEvent invalidEvent) Tool method that creates a new instance of this class.

Constructors in info.bioinfweb.jphyloio.exception with parameters of type JPhyloIOEvent

Constructor and Description
IllegalEventException(java.lang.String message, JPhyloIOEventReceiver receiver, JPhyloIOEvent parentEvent, JPhyloIOEvent invalidEvent)

Uses of JPhyloIOEvent in info.bioinfweb.jphyloio.formats

Classes in info.bioinfweb.jphyloio.formats with type parameters of type JPhyloIOEvent

Modifier and Type	Class and Description
class	BufferedEventInfo<E extends JPhyloIOEvent> Used to buffer information on an event and its nested events.

Methods in info.bioinfweb.jphyloio.formats that return types with arguments of type JPhyloIOEvent

Modifier and Type	Method and Description
java.util.Collection<JPhyloIOEvent>	NodeEdgeInfo.getNestedEdgeEvents()
java.util.List<JPhyloIOEvent>	BufferedEventInfo.getNestedEvents()
java.util.Collection<JPhyloIOEvent>	NodeEdgeInfo.getNestedNodeEvents()

Constructor parameters in info.bioinfweb.jphyloio.formats with type arguments of type JPhyloIOEvent

Constructor and Description
NodeEdgeInfo(java.lang.String id, double length, java.util.Collection<JPhyloIOEvent> nestedNodeEvents, java.util.Collection<JPhyloIOEvent> nestedEdgeEvents)
NodeEdgeInfo(java.lang.String id, double length, java.util.Collection<JPhyloIOEvent> nestedNodeEvents, java.util.Collection<JPhyloIOEvent> nestedEdgeEvents)

Uses of JPhyloIOEvent in info.bioinfweb.jphyloio.formats.newick

Classes in info.bioinfweb.jphyloio.formats.newick with type parameters of type JPhyloIOEvent

Modifier and Type	Class and Description
class	NewickNodeEdgeEventReceiver<E extends JPhyloIOEvent>

Methods in info.bioinfweb.jphyloio.formats.newick with parameters of type JPhyloIOEvent

Modifier and Type	Method and Description
protected void	NewickNodeEdgeEventReceiver.handleMetaEndEvent(JPhyloIOEvent event)

Method parameters in info.bioinfweb.jphyloio.formats.newick with type arguments of type JPhyloIOEvent

Modifier and Type	Method and Description
void	HotCommentDataReader.read(java.lang.String comment, TextReaderStreamDataProvider<?> streamDataProvider, java.util.Collection<JPhyloIOEvent> eventQueue, boolean isOnNode) Reads metadata from the specified hot comment and adds according events to the queue.

Uses of JPhyloIOEvent in info.bioinfweb.jphyloio.formats.nexml

Methods in info.bioinfweb.jphyloio.formats.nexml that return types with arguments of type JPhyloIOEvent

Modifier and Type	Method and Description
protected java.util.Collection<JPhyloIOEvent>	NeXMLReaderTokenSetInformation.getNestedEvents()

Uses of JPhyloIOEvent in info.bioinfweb.jphyloio.formats.nexml.receivers

Methods in info.bioinfweb.jphyloio.formats.nexml.receivers with parameters of type JPhyloIOEvent

Modifier and Type	Method and Description
protected boolean	NeXMLCharacterSetEventReceiver.doAdd(JPhyloIOEvent event)
protected boolean	NeXMLCollectCharSetDataReceiver.doAdd(JPhyloIOEvent event)
protected boolean	NeXMLCollectSetMetadataReceiver.doAdd(JPhyloIOEvent event)
protected boolean	NeXMLCollectTokenSetDefinitionDataReceiver.doAdd(JPhyloIOEvent event)
protected boolean	NeXMLHandleSequenceDataReceiver.doAdd(JPhyloIOEvent event)
protected boolean	NeXMLMolecularDataTokenDefinitionReceiver.doAdd(JPhyloIOEvent event)
protected boolean	NeXMLOnlyWriteMetaDataReceiver.doAdd(JPhyloIOEvent event)
protected boolean	NeXMLTokenSetEventReceiver.doAdd(JPhyloIOEvent event)
protected void	NeXMLAttributeMetadataReceiver.handleMetaEndEvent(JPhyloIOEvent event)
protected void	NeXMLCollectNamespaceReceiver.handleMetaEndEvent(JPhyloIOEvent event)
protected void	NeXMLCollectSetMetadataReceiver.handleMetaEndEvent(JPhyloIOEvent event)
protected void	NeXMLIgnoreCertainMetadataReceiver.handleMetaEndEvent(JPhyloIOEvent event)
protected void	NeXMLMetaDataReceiver.handleMetaEndEvent(JPhyloIOEvent event)
protected void	NeXMLMolecularDataTokenDefinitionReceiver.handleMetaEndEvent(JPhyloIOEvent event)
protected void	NeXMLSequenceTokensReceiver.handleMetaEndEvent(JPhyloIOEvent event)
static void	AbstractNeXMLDataReceiverMixin.handleMetaEndEvent(NeXMLWriterStreamDataProvider streamDataProvider, JPhyloIOEvent event)

Uses of JPhyloIOEvent in info.bioinfweb.jphyloio.formats.nexus.commandreaders

Method parameters in info.bioinfweb.jphyloio.formats.nexus.commandreaders with type arguments of type JPhyloIOEvent

Modifier and Type	Method and Description
protected void	AbstractNexusCommandEventReader.consumeWhiteSpaceAndCommentsToBuffer(java.util.Collection<JPhyloIOEvent> buffer)

Uses of JPhyloIOEvent in info.bioinfweb.jphyloio.formats.nexus.receivers

Methods in info.bioinfweb.jphyloio.formats.nexus.receivers with parameters of type JPhyloIOEvent

Modifier and Type	Method and Description
protected boolean	AbstractNexusSetsEventReceiver.doAdd(JPhyloIOEvent event)
protected boolean	TokenSetEventReceiver.doAdd(JPhyloIOEvent event)

Uses of JPhyloIOEvent in info.bioinfweb.jphyloio.formats.phyloxml.receivers

Methods in info.bioinfweb.jphyloio.formats.phyloxml.receivers with parameters of type JPhyloIOEvent

Modifier and Type	Method and Description
protected void	PhyloXMLCollectMetadataDataReceiver.handleMetaEndEvent(JPhyloIOEvent event)
protected void	PhyloXMLMetaDataReceiver.handleMetaEndEvent(JPhyloIOEvent event)
protected void	PhyloXMLOnlyCustomXMLDataReceiver.handleMetaEndEvent(JPhyloIOEvent event)
protected void	PhyloXMLPropertyMetadataReceiver.handleMetaEndEvent(JPhyloIOEvent event)
protected void	PhyloXMLSpecificPredicatesDataReceiver.handleMetaEndEvent(JPhyloIOEvent event)

Uses of JPhyloIOEvent in info.bioinfweb.jphyloio.formats.text

Methods in info.bioinfweb.jphyloio.formats.text that return JPhyloIOEvent

Modifier and Type	Method and Description
protected JPhyloIOEvent	AbstractTextEventReader.readCharacters(java.lang.String currentSequenceName)
protected JPhyloIOEvent	AbstractTextEventReader.readCharacters(java.lang.String currentSequenceName, char commentStart, char commentEnd) Reads characters from the stream and adds a respective sequence tokens event to the queue.

Uses of JPhyloIOEvent in info.bioinfweb.jphyloio.formats.xml.stax

Methods in info.bioinfweb.jphyloio.formats.xml.stax with parameters of type JPhyloIOEvent

Modifier and Type	Method and Description
protected javax.xml.stream.events.XMLEvent	AbstractMetaXMLReader.obtainXMLContentEvent(JPhyloIOEvent jPhyloIOEvent)

Uses of JPhyloIOEvent in info.bioinfweb.jphyloio.push

Methods in info.bioinfweb.jphyloio.push with parameters of type JPhyloIOEvent

Modifier and Type	Method and Description
void	JPhyloIOEventListener.processEvent(JPhyloIOEventReader source, JPhyloIOEvent event) Called after an event was received from a reader instance.

Uses of JPhyloIOEvent in info.bioinfweb.jphyloio.utils

Methods in info.bioinfweb.jphyloio.utils with type parameters of type JPhyloIOEvent

Modifier and Type	Method and Description
static <E extends JPhyloIOEvent> java.util.List<E>	JPhyloIOReadingUtils.collectEvents(JPhyloIOEventReader reader, java.util.Set<EventType> types, java.lang.Class<E> instanceClass) Reads all (remaining) events from the specified reader and adds events that implement the specified class and have a type that is contained in the specified set to the returned list.

Methods in info.bioinfweb.jphyloio.utils that return types with arguments of type JPhyloIOEvent

Modifier and Type	Method and Description
static java.util.List<JPhyloIOEvent>	JPhyloIOReadingUtils.collectEvents(JPhyloIOEventReader reader, java.util.Set<EventType> types) Reads all (remaining) events from the specified reader and adds events that have a type that is contained in the # specified set to the returned list.