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E

E_NEWICK_EDGE_TYPE_HYBRIDIZATION - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants

E_NEWICK_EDGE_TYPE_LATERAL_GENE_TRANSFER - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants

E_NEWICK_EDGE_TYPE_RECOMBINATION - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants

E_NEWICK_NAMESPACE_PREFIX - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants

E_NEWICK_NETWORK_DATA_SEPARATOR - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants

EdgeEvent - Class in info.bioinfweb.jphyloio.events

Event indicating an edge in a tree or network.

EdgeEvent(String, String, String, String, double) - Constructor for class info.bioinfweb.jphyloio.events.EdgeEvent

Creates a new instance of this class that represents an internal edge or a root edge.

EdgeEvent(String, String, String, double) - Constructor for class info.bioinfweb.jphyloio.events.EdgeEvent

Creates a new instance of this class that represents a root edge.

EDITED_LABEL_SEPARATOR - Static variable in class info.bioinfweb.jphyloio.AbstractEventWriter

editLabel(String) - Method in class info.bioinfweb.jphyloio.AbstractEventWriter.NoEditUniqueLabelHandler

editLabel(String) - Method in interface info.bioinfweb.jphyloio.AbstractEventWriter.UniqueLabelHandler

editSequenceOrNodeLabel(LinkedLabeledIDEvent, ReadWriteParameterMap, OTUListDataAdapter) - Method in class info.bioinfweb.jphyloio.AbstractSingleMatrixEventWriter

ELEMENT_SEPARATOR - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants

ELEMENT_SEPERATOR - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants

ElementDataAdapter<E extends JPhyloIOEvent> - Interface in info.bioinfweb.jphyloio.dataadapters

Data adapters that model a data element identified by a certain start event should implement this interface.

elementIndexByName(String) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.AbstractNexusSetReader

Converts the Nexus name of a set element to its index.

elementIndexByName(String) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.CharSetReader

elementIndexByName(String) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.IDBasedSetsReader

EmptyAnnotatedDataAdapter<E extends JPhyloIOEvent> - Class in info.bioinfweb.jphyloio.dataadapters.implementations

Default implementation of AnnotatedDataAdapter, which does not generate any metaevents.

EmptyAnnotatedDataAdapter() - Constructor for class info.bioinfweb.jphyloio.dataadapters.implementations.EmptyAnnotatedDataAdapter

EmptyDocumentDataAdapter - Class in info.bioinfweb.jphyloio.dataadapters.implementations

An implementation of DocumentDataAdapter that models an empty document.

EmptyDocumentDataAdapter() - Constructor for class info.bioinfweb.jphyloio.dataadapters.implementations.EmptyDocumentDataAdapter

EmptyObjectListDataAdapter<E extends JPhyloIOEvent> - Class in info.bioinfweb.jphyloio.dataadapters.implementations

Empty implementation of ObjectListDataAdapter.

EmptyObjectListDataAdapter() - Constructor for class info.bioinfweb.jphyloio.dataadapters.implementations.EmptyObjectListDataAdapter

END_COMMAND - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants

ENewickNetworkReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees

Nexus command reader for the custom NETWORK command.

ENewickNetworkReader(NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.ENewickNetworkReader

ENewickNetworksBlockHandler - Class in info.bioinfweb.jphyloio.formats.nexus.blockhandlers

A Nexus block handler to read phylogenetic networks from a NETWORK block containing network definitions in the eNewick format.

ENewickNetworksBlockHandler() - Constructor for class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.ENewickNetworksBlockHandler

EnumTranslator<E extends java.lang.Enum<E>> - Class in info.bioinfweb.jphyloio.objecttranslation.implementations

EnumTranslator(Class<E>) - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.EnumTranslator

Creates a new instance of this class.

equals(Object) - Method in class info.bioinfweb.jphyloio.events.meta.URIOrStringIdentifier

equals(Object) - Method in class info.bioinfweb.jphyloio.events.type.EventType

equals(Object) - Method in class info.bioinfweb.jphyloio.formats.xml.elementreaders.XMLElementReaderKey

equals(Object) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.AbstractObjectTranslator

equalsStringOrURI(URIOrStringIdentifier) - Method in class info.bioinfweb.jphyloio.events.meta.URIOrStringIdentifier

Tests whether this and the other object have an equal string representation or an equal URI or both.

EventContentType - Enum in info.bioinfweb.jphyloio.events.type

Enumerates the content types of a JPhyloIOEvent.

EventForwarder - Class in info.bioinfweb.jphyloio.push

Tool class that consumes all events provided by an implementation of JPhyloIOEventReader and forwards them to one or more JPhyloIOEventListeners.

EventForwarder() - Constructor for class info.bioinfweb.jphyloio.push.EventForwarder

eventsUpcoming() - Method in class info.bioinfweb.jphyloio.ReaderStreamDataProvider

Checks whether events are waiting the event queue of the associated event reader.

EventTopologyType - Enum in info.bioinfweb.jphyloio.events.type

Allows to determine between events that start and a end a data model structure (e.g.

EventType - Class in info.bioinfweb.jphyloio.events.type

Event type object that combines the content and topology type of an event.

EventType(EventContentType, EventTopologyType) - Constructor for class info.bioinfweb.jphyloio.events.type.EventType

Creates a new instance of this class.

extendSequence(MatrixDataAdapter, ReadWriteParameterMap, String, long, String, JPhyloIOEventReceiver) - Method in class info.bioinfweb.jphyloio.AbstractEventWriter

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