A B C D E F G H I J K L M N O P Q R S T U V W X

## 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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