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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 `JPhyloIOEventListener`s.
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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