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F

FASTA_FORMAT_ID - Static variable in interface info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs

FASTA_FORMAT_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.fasta.FASTAConstants

FASTAConstants - Interface in info.bioinfweb.jphyloio.formats.fasta

Contains format specific constants used by FASTAEventReader and FASTAEventWriter.

FASTAEventReader - Class in info.bioinfweb.jphyloio.formats.fasta

Event based reader for FASTA alignment files.

FASTAEventReader(BufferedReader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.fasta.FASTAEventReader

Creates a new instance of this class.

FASTAEventReader(File, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.fasta.FASTAEventReader

Creates a new instance of this class.

FASTAEventReader(InputStream, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.fasta.FASTAEventReader

Creates a new instance of this class.

FASTAEventReader(Reader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.fasta.FASTAEventReader

Creates a new instance of this class.

FASTAEventWriter - Class in info.bioinfweb.jphyloio.formats.fasta

Event based writer for the FASTA format.

FASTAEventWriter() - Constructor for class info.bioinfweb.jphyloio.formats.fasta.FASTAEventWriter

FASTAFactory - Class in info.bioinfweb.jphyloio.formats.fasta

Reader and writer factory for the FASTA format.

FASTAFactory() - Constructor for class info.bioinfweb.jphyloio.formats.fasta.FASTAFactory

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

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

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

fillMap() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLEventReader

fillMap() - Method in class info.bioinfweb.jphyloio.formats.pde.PDEEventReader

fillMap() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLEventReader

fillMap() - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader

fillMap() - Method in class info.bioinfweb.jphyloio.formats.xtg.XTGEventReader

fireEvent(JPhyloIOEvent) - Method in class info.bioinfweb.jphyloio.AbstractEventReader

FIRST_CUSTOM_META_ID - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants

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

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

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

An object translator from and to Float.

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

flush() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventWriter

This method has no effect in this writer, since the underlying JPhyloIOEventWriter does not implement a flush() method.

flush() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter

This method has no effect in this writer, since the underlying JPhyloIOEventWriter does not implement a flush() method.

FORMAT_ID_PREFIX - Static variable in interface info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs

The prefix of all format IDs defined in JPhyloIO.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

This is not part of the official Nexus definition, but is a MrBayes extension.

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

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

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

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

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

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

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

FormatReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters

Parser for the Format command in a Characters, Unaligned or Data block.

FormatReader(NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.FormatReader

formatToken(String, char) - Static method in class info.bioinfweb.jphyloio.formats.newick.NewickStringWriter

formatToken(String) - Static method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter

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

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

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