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Base64BinaryTranslator - Class in info.bioinfweb.jphyloio.objecttranslation.implementations

An object translator between byte[] and xsd:base64Binary.

Base64BinaryTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.Base64BinaryTranslator

BasicEventReceiver<P extends WriterStreamDataProvider<? extends AbstractEventWriter<P>>> - Class in info.bioinfweb.jphyloio.dataadapters.implementations.receivers

Most event receivers will be inherited from this class.

BasicEventReceiver(P, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver

Creates a new instance of this class.

BasicTextCommentEventReceiver<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>> - Class in info.bioinfweb.jphyloio.formats.text

Basic event receiver implementation that writes comments to text formats that are delimited by a start and an end string.

BasicTextCommentEventReceiver(P, ReadWriteParameterMap, String, String) - Constructor for class info.bioinfweb.jphyloio.formats.text.BasicTextCommentEventReceiver

Creates a new instance of this class.

beforeCommand(NexusReaderStreamDataProvider, String, NexusCommandEventReader) - Method in class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.CharactersDataUnalignedBlockHandler

beforeCommand(NexusReaderStreamDataProvider, String, NexusCommandEventReader) - Method in interface info.bioinfweb.jphyloio.formats.nexus.blockhandlers.NexusBlockHandler

This method is called before a command found in a block handled by this handler is processed, by calling the according command reader.

beforeCommand(NexusReaderStreamDataProvider, String, NexusCommandEventReader) - Method in class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.TaxaBlockHandler

beforeCommand(NexusReaderStreamDataProvider, String, NexusCommandEventReader) - Method in class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.TreesBlockHandler

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

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

An object translator from and to BigDecimal.

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

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

An object translator from and to BigInteger.

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

BLOCK_COMMAND_CONNECTOR - Static variable in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.NexusCommandReaderFactory

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

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

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

This block name is not part of the initial Nexus standard and used by ENewickNetworksBlockHandler.

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

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

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

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

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

Used internally be NexusEventReader and related classes to map Nexus block titles to JPhyloIO IDs.

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

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

An object translator between {link Boolean} and xsd:boolean.

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

BRANCH_LENGTH_UNITS - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

BufferedEventInfo<E extends JPhyloIOEvent> - Class in info.bioinfweb.jphyloio.formats

Used to buffer information on an event and its nested events.

BufferedEventInfo(E) - Constructor for class info.bioinfweb.jphyloio.formats.BufferedEventInfo

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

An object translator from and to Byte.

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

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