- FASTA_FORMAT_ID - Static variable in interface info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs
-
- 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
-
- FASTA_FORMAT_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.fasta.FASTAConstants
-
- FASTAConstants - Interface in info.bioinfweb.jphyloio.formats.fasta
-
- FASTAConstants - Interface in info.bioinfweb.jphyloio.formats.fasta
-
- FASTAEventReader - Class in info.bioinfweb.jphyloio.formats.fasta
-
Event based reader for FASTA alignment files.
- 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.
- 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 - Class in info.bioinfweb.jphyloio.formats.fasta
-
Event based writer for the FASTA format.
- FASTAEventWriter() - Constructor for class info.bioinfweb.jphyloio.formats.fasta.FASTAEventWriter
-
- 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 - 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
-
- FASTAFactory() - Constructor for class info.bioinfweb.jphyloio.formats.fasta.FASTAFactory
-
- FIELD_END_SYMBOL - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
-
- 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_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
-
- 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.nexml.NeXMLEventReader
-
- fillMap() - Method in class info.bioinfweb.jphyloio.formats.pde.PDEEventReader
-
- 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.phyloxml.PhyloXMLEventReader
-
- fillMap() - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
-
- fillMap() - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
-
- fillMap() - Method in class info.bioinfweb.jphyloio.formats.xtg.XTGEventReader
-
- fillMap() - Method in class info.bioinfweb.jphyloio.formats.xtg.XTGEventReader
-
- fireEvent(JPhyloIOEvent) - Method in class info.bioinfweb.jphyloio.AbstractEventReader
-
- fireEvent(JPhyloIOEvent) - Method in class info.bioinfweb.jphyloio.AbstractEventReader
-
- FIRST_CUSTOM_META_ID - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
-
- 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.mega.MEGAConstants
-
- FIRST_LINE - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
-
- 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 - Class in info.bioinfweb.jphyloio.objecttranslation.implementations
-
An object translator from and to
Float
.
- FloatTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.FloatTranslator
-
- 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.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.
- 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_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_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_NAME_VECTOR - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
-
- 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.mega.MEGAConstants
-
- FORMAT_SUBCOMMAND_DATA_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
-
- 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_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_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_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_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_MATCH_CHAR - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
-
- FORMAT_SUBCOMMAND_MISING - Static variable in interface info.bioinfweb.jphyloio.formats.mega.MEGAConstants
-
- FORMAT_SUBCOMMAND_MISING - 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_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_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_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_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_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_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_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_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_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.mega.MEGAConstants
-
- FORMAT_VALUE_DNA_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.nexus.NexusConstants
-
- 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_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.mega.MEGAConstants
-
- FORMAT_VALUE_NUCLEOTIDE_DATA_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
-
- 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.mega.MEGAConstants
-
- FORMAT_VALUE_PROTEIN_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.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.mega.MEGAConstants
-
- FORMAT_VALUE_RNA_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.nexus.NexusConstants
-
- FORMAT_VALUE_STANDARD_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 - 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
-
- 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, char) - Static method in class info.bioinfweb.jphyloio.formats.newick.NewickStringWriter
-
- formatToken(String) - Static method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter
-
- 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
-
- 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
-
- FULL_SCHEMA_LOCATION - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
-