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label - Variable in class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractNeXMLElementReader.LabeledIDEventInformation

LABEL_CHAR_SET_ID - Static variable in interface info.bioinfweb.jphyloio.formats.mega.MEGAConstants

LabeledEvent - Class in info.bioinfweb.jphyloio.events

LabeledEvent(EventContentType, String) - Constructor for class info.bioinfweb.jphyloio.events.LabeledEvent

LabeledIDEvent - Class in info.bioinfweb.jphyloio.events

Event that indicate data objects that carry an unique ID and a label.

LabeledIDEvent(EventContentType, String, String) - Constructor for class info.bioinfweb.jphyloio.events.LabeledIDEvent

Creates a new instance of this class.

LabeledIDEventInformation() - Constructor for class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractNeXMLElementReader.LabeledIDEventInformation

LabelEditingReporter - Class in info.bioinfweb.jphyloio.utils

Data storage class that allows instances of JPhyloIOEventWriter to give feedback to the application on how labels of different elements (e.g.

LabelEditingReporter() - Constructor for class info.bioinfweb.jphyloio.utils.LabelEditingReporter

LabelEditingReporter.LabelStatus - Enum in info.bioinfweb.jphyloio.utils

Enumerates the possible cases of how the label associated with a data element was treated by an instance of JPhyloIOEventWriter.

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

lineConsumed - Variable in class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader

LinkedIDEvent - Interface in info.bioinfweb.jphyloio.events

Interface to be implemented by event objects that can link previous events by their ID.

LinkedLabeledIDEvent - Class in info.bioinfweb.jphyloio.events

Instances of this class model data elements with an ID and an optional label, that link another data element in a phylogenetic document.

LinkedLabeledIDEvent(EventContentType, String, String, String) - Constructor for class info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent

Creates a new instance of this class.

LinkReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.all

Reads the LINK command of a Nexus block and stores the links in the shared information map of the stream data provider under the key NexusReaderStreamDataProvider.INFO_KEY_BLOCK_LINKS.

LinkReader(NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.all.LinkReader

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

Default implementation of DocumentDataAdapter.

ListBasedDocumentDataAdapter(ListOrderedMap<String, OTUListDataAdapter>, List<MatrixDataAdapter>, List<TreeNetworkGroupDataAdapter>) - Constructor for class info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter

Creates a new instance of this class using the specified lists.

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

Creates a new instance of this class with empty array lists for all properties.

listToString(Iterable<?>) - Static method in class info.bioinfweb.jphyloio.objecttranslation.implementations.ListTranslator

ListTranslator - Class in info.bioinfweb.jphyloio.objecttranslation.implementations

Reads and writes string representations of simple values as used in Newick or Nexus.

ListTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.ListTranslator

LiteralContentSequenceType - Enum in info.bioinfweb.jphyloio.events.meta

Enumerates the types of sequences of LiteralMetadataContentEvents that can be nested inside an LiteralMetadataEvent.

LiteralMetadataContentEvent - Class in info.bioinfweb.jphyloio.events.meta

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.

LiteralMetadataContentEvent(String, boolean) - Constructor for class info.bioinfweb.jphyloio.events.meta.LiteralMetadataContentEvent

Creates a new instance of this class.

LiteralMetadataContentEvent(Object, String) - Constructor for class info.bioinfweb.jphyloio.events.meta.LiteralMetadataContentEvent

Creates a new instance of this class.

LiteralMetadataContentEvent(XMLEvent, boolean) - Constructor for class info.bioinfweb.jphyloio.events.meta.LiteralMetadataContentEvent

Creates a new instance of this class wrapping an XMLEvent.

LiteralMetadataEvent - Class in info.bioinfweb.jphyloio.events.meta

Indicates that literal metadata is modeled at the current position of the document (event stream).

LiteralMetadataEvent(String, String, URIOrStringIdentifier, LiteralContentSequenceType) - Constructor for class info.bioinfweb.jphyloio.events.meta.LiteralMetadataEvent

LiteralMetadataEvent(String, String, URIOrStringIdentifier, URIOrStringIdentifier, LiteralContentSequenceType) - Constructor for class info.bioinfweb.jphyloio.events.meta.LiteralMetadataEvent

LiteralMetadataEvent(String, String, URIOrStringIdentifier, String, URIOrStringIdentifier, LiteralContentSequenceType) - Constructor for class info.bioinfweb.jphyloio.events.meta.LiteralMetadataEvent

logIngnoredOTULists(DocumentDataAdapter, ApplicationLogger, ReadWriteParameterMap, String, String) - Static method in class info.bioinfweb.jphyloio.AbstractEventWriter

Outputs a warning message, if the specified document data adapter provides one or more OTU lists.

LongTranslator - Class in info.bioinfweb.jphyloio.objecttranslation.implementations

An object translator from and to Long.

LongTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.LongTranslator

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