# Constant Field Values

## Contents

- info.bioinfweb.*

## info.bioinfweb.*

- info.bioinfweb.jphyloio.AbstractEventWriter<P extends WriterStreamDataProvider<? extends AbstractEventWriter<P>>>
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final java.lang.String` | `EDITED_LABEL_SEPARATOR` | `"_"`

- info.bioinfweb.jphyloio.ReadWriteConstants
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final java.lang.String` | `ATTRIBUTES_NAMESPACE_FOLDER` | `"Attributes"`
  `public static final java.lang.String` | `DATA_TYPE_NAMESPACE_FOLDER` | `"DataTypes"`
  `public static final java.lang.String` | `DEFAULT_CHAR_SET_ID_PREFIX` | `"charSet"`
  `public static final java.lang.String` | `DEFAULT_CHARACTER_DEFINITION_ID_PREFIX` | `"char"`
  `public static final java.lang.String` | `DEFAULT_EDGE_ID_PREFIX` | `"e"`
  `public static final java.lang.String` | `DEFAULT_GENERAL_ID_PREFIX` | `"id"`
  `public static final java.lang.String` | `DEFAULT_MATRIX_ID_PREFIX` | `"matrix"`
  `public static final int` | `DEFAULT_MAX_COMMENT_LENGTH` | `1048576`
  `public static final int` | `DEFAULT_MAX_TOKENS_TO_READ` | `2048`
  `public static final java.lang.String` | `DEFAULT_META_ID_PREFIX` | `"meta"`
  `public static final java.lang.String` | `DEFAULT_NETWORK_ID_PREFIX` | `"network"`
  `public static final java.lang.String` | `DEFAULT_NODE_EDGE_SET_ID_PREFIX` | `"nodeEdgeSet"`
  `public static final java.lang.String` | `DEFAULT_NODE_ID_PREFIX` | `"n"`
  `public static final java.lang.String` | `DEFAULT_OTU_ID_PREFIX` | `"otu"`
  `public static final java.lang.String` | `DEFAULT_OTU_LIST_ID_PREFIX` | `"otus"`
  `public static final java.lang.String` | `DEFAULT_OTU_SET_ID_PREFIX` | `"otuSet"`
  `public static final java.lang.String` | `DEFAULT_SEQUENCE_ID_PREFIX` | `"seq"`
  `public static final java.lang.String` | `DEFAULT_SEQUENCE_SET_ID_PREFIX` | `"sequenceSet"`
  `public static final java.lang.String` | `DEFAULT_TOKEN_DEFINITION_ID_PREFIX` | `"tokenDefinition"`
  `public static final java.lang.String` | `DEFAULT_TOKEN_SET_ID_PREFIX` | `"tokenSet"`
  `public static final java.lang.String` | `DEFAULT_TREE_ID_PREFIX` | `"tree"`
  `public static final java.lang.String` | `DEFAULT_TREE_NETWORK_GROUP_ID_PREFIX` | `"treesOrNetworks"`
  `public static final java.lang.String` | `DEFAULT_TREE_NETWORK_SET_ID_PREFIX` | `"treeNetworkSet"`
  `public static final java.lang.String` | `JPHYLOIO_ATTRIBUTES_NAMESPACE` | `"http://bioinfweb.info/xmlns/JPhyloIO/General/Attributes/"`
  `public static final java.lang.String` | `JPHYLOIO_ATTRIBUTES_PREFIX` | `"jpa"`
  `public static final java.lang.String` | `JPHYLOIO_DATA_TYPE_NAMESPACE` | `"http://bioinfweb.info/xmlns/JPhyloIO/General/DataTypes/"`
  `public static final java.lang.String` | `JPHYLOIO_DATA_TYPE_PREFIX` | `"jpd"`
  `public static final java.lang.String` | `JPHYLOIO_FORMATS_NAMESPACE_PREFIX` | `"http://bioinfweb.info/xmlns/JPhyloIO/Formats/"`
  `public static final java.lang.String` | `JPHYLOIO_GENERAL_NAMESPACE` | `"http://bioinfweb.info/xmlns/JPhyloIO/General/"`
  `public static final java.lang.String` | `JPHYLOIO_NAMESPACE_PREFIX` | `"http://bioinfweb.info/xmlns/JPhyloIO/"`
  `public static final java.lang.String` | `JPHYLOIO_PREDICATE_NAMESPACE` | `"http://bioinfweb.info/xmlns/JPhyloIO/General/Predicates/"`
  `public static final java.lang.String` | `JPHYLOIO_PREDICATE_PREFIX` | `"jpp"`
  `public static final java.lang.String` | `PREDICATE_NAMESPACE_FOLDER` | `"Predicates"`
  `public static final java.lang.String` | `PREDICATE_PART_SEPERATOR` | `"."`
  `public static final java.lang.String` | `RESERVED_ID_PREFIX` | `"info.bioinfweb.jphyloio.reservedIDs."`

- info.bioinfweb.jphyloio.ReadWriteParameterNames
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final java.lang.String` | `KEY_ALLOW_DEFAULT_NAMESPACE` | `"info.bioinfweb.jphyloio.allowDefaultNamespace"`
  `public static final java.lang.String` | `KEY_ALLOW_INTERLEAVED_PARSING` | `"info.bioinfweb.jphyloio.allowInterleavedParsing"`
  `public static final java.lang.String` | `KEY_ALWAYS_WRITE_NEXUS_NODE_LABELS` | `"info.bioinfweb.jphyloio.alwaysWriteNexusNodeLabels"`
  `public static final java.lang.String` | `KEY_APPLICATION_NAME` | `"info.bioinfweb.jphyloio.applicationName"`
  `public static final java.lang.String` | `KEY_APPLICATION_URL` | `"info.bioinfweb.jphyloio.applicationURL"`
  `public static final java.lang.String` | `KEY_APPLICATION_VERSION` | `"info.bioinfweb.jphyloio.applicationVersion"`
  `public static final java.lang.String` | `KEY_CREATE_UNKNOWN_COMMAND_EVENTS` | `"info.bioinfweb.jphyloio.createUnknownCommandEvents"`
  `public static final java.lang.String` | `KEY_CUSTOM_XML_NAMESPACE_HANDLING` | `"info.bioinfweb.jphyloio.customXMLNamespaceHandling"`
  `public static final java.lang.String` | `KEY_EXPECT_E_NEWICK` | `"info.bioinfweb.jphyloio.expectENewick"`
  `public static final java.lang.String` | `KEY_GENERATE_NEXUS_TRANSLATION_TABLE` | `"info.bioinfweb.jphyloio.generateTranslationTable"`
  `public static final java.lang.String` | `KEY_IGNORE_COMMENTS` | `"info.bioinfweb.jphyloio.ignoreComments"`
  `public static final java.lang.String` | `KEY_LABEL_EDITING_REPORTER` | `"info.bioinfweb.jphyloio.labelEditingReporter"`
  `public static final java.lang.String` | `KEY_LINE_LENGTH` | `"info.bioinfweb.jphyloio.lineLength"`
  `public static final java.lang.String` | `KEY_LINE_SEPARATOR` | `"info.bioinfweb.jphyloio.lineSeparator"`
  `public static final java.lang.String` | `KEY_LOGGER` | `"info.bioinfweb.jphyloio.logger"`
  `public static final java.lang.String` | `KEY_MATCH_TOKEN` | `"info.bioinfweb.jphyloio.matchToken"`
  `public static final java.lang.String` | `KEY_MAXIMUM_COMMENT_LENGTH` | `"info.bioinfweb.jphyloio.maxCommentLength"`
  `public static final java.lang.String` | `KEY_MAXIMUM_NAME_LENGTH` | `"info.bioinfweb.jphyloio.maximumNameLength"`
  `public static final java.lang.String` | `KEY_MAXIMUM_TOKENS_TO_READ` | `"info.bioinfweb.jphyloio.maxTokensToRead"`
  `public static final java.lang.String` | `KEY_NEXML_TOKEN_DEFINITION_LABEL` | `"info.bioinfweb.jphyloio.neXMLstandardDataLabel"`
  `public static final java.lang.String` | `KEY_NEXML_TOKEN_DEFINITION_LABEL_METADATA` | `"info.bioinfweb.jphyloio.neXMLstandardDataLabelMetadata"`
  `public static final java.lang.String` | `KEY_NEXML_TOKEN_TRANSLATION_STRATEGY` | `"info.bioinfweb.jphyloio.neXMLTokenTranslationStrategy"`
  `public static final java.lang.String` | `KEY_NEXUS_BLOCK_HANDLER_MAP` | `"info.bioinfweb.jphyloio.nexusBlockHandlerMap"`
  `public static final java.lang.String` | `KEY_NEXUS_COMMAND_READER_FACTORY` | `"info.bioinfweb.jphyloio.nexusCommandReaderFactory"`
  `public static final java.lang.String` | `KEY_OBJECT_TRANSLATOR_FACTORY` | `"info.bioinfweb.jphyloio.objectTranslatorFactory"`
  `public static final java.lang.String` | `KEY_PHYLOXML_CONSIDER_PHYLOGENY_AS_TREE` | `"info.bioinfweb.jphyloio.considerPhylogenyAsTree"`
  `public static final java.lang.String` | `KEY_PHYLOXML_EVENT_ID_TRANSLATION_MAP` | `"info.bioinfweb.jphyloio.phyloXMLEventIDTranslationMap"`
  `public static final java.lang.String` | `KEY_PHYLOXML_METADATA_TREATMENT` | `"info.bioinfweb.jphyloio.phyloXMLMetadataTreatment"`
  `public static final java.lang.String` | `KEY_PREFIX` | `"info.bioinfweb.jphyloio."`
  `public static final java.lang.String` | `KEY_RELAXED_PHYLIP` | `"info.bioinfweb.jphyloio.relaxedPhylip"`
  `public static final java.lang.String` | `KEY_REPLACE_MATCH_TOKENS` | `"info.bioinfweb.jphyloio.replaceMatchTokens"`
  `public static final java.lang.String` | `KEY_SEQUENCE_EXTENSION_TOKEN` | `"info.bioinfweb.jphyloio.sequenceExtensionToken"`
  `public static final java.lang.String` | `KEY_TRANSLATE_INTERNAL_NODE_NAMES` | `"info.bioinfweb.jphyloio.translateInternalNodeNames"`
  `public static final java.lang.String` | `KEY_USE_OTU_LABEL` | `"info.bioinfweb.jphyloio.useOTULabel"`
  `public static final java.lang.String` | `KEY_WRITER_INSTANCE` | `"info.bioinfweb.jphyloio.writerInstance"`

- info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final int` | `DEFAULT_READ_AHEAD_LIMIT` | `8192`

- info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final java.lang.String` | `FASTA_FORMAT_ID` | `"info.bioinfweb.jphyloio.fasta"`
  `public static final java.lang.String` | `FORMAT_ID_PREFIX` | `"info.bioinfweb.jphyloio."`
  `public static final java.lang.String` | `MEGA_FORMAT_ID` | `"info.bioinfweb.jphyloio.mega"`
  `public static final java.lang.String` | `NEWICK_FORMAT_ID` | `"info.bioinfweb.jphyloio.newick"`
  `public static final java.lang.String` | `NEXML_FORMAT_ID` | `"info.bioinfweb.jphyloio.nexml"`
  `public static final java.lang.String` | `NEXUS_FORMAT_ID` | `"info.bioinfweb.jphyloio.nexus"`
  `public static final java.lang.String` | `PDE_FORMAT_ID` | `"info.bioinfweb.jphyloio.pde"`
  `public static final java.lang.String` | `PHYLIP_FORMAT_ID` | `"info.bioinfweb.jphyloio.phylip"`
  `public static final java.lang.String` | `PHYLOXML_FORMAT_ID` | `"info.bioinfweb.jphyloio.phyloxml"`
  `public static final java.lang.String` | `SEQUENTIAL_PHYLIP_FORMAT_ID` | `"info.bioinfweb.jphyloio.sequentialphylip"`
  `public static final java.lang.String` | `XTG_FORMAT_ID` | `"info.bioinfweb.jphyloio.xtg"`

- info.bioinfweb.jphyloio.formats.fasta.FASTAConstants
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final char` | `COMMENT_START_CHAR` | `59`
  `public static final int` | `DEFAULT_LINE_LENGTH` | `80`
  `public static final java.lang.String` | `FASTA_FORMAT_NAME` | `"FASTA"`
  `public static final char` | `NAME_START_CHAR` | `62`

- info.bioinfweb.jphyloio.formats.mega.MEGAConstants
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final char` | `COMMAND_END` | `59`
  `public static final java.lang.String` | `COMMAND_NAME_DESCRIPTION` | `"DESCRIPTION"`
  `public static final java.lang.String` | `COMMAND_NAME_DOMAIN` | `"DOMAIN"`
  `public static final java.lang.String` | `COMMAND_NAME_FORMAT` | `"FORMAT"`
  `public static final java.lang.String` | `COMMAND_NAME_GENE` | `"GENE"`
  `public static final java.lang.String` | `COMMAND_NAME_LABEL` | `"LABEL"`
  `public static final java.lang.String` | `COMMAND_NAME_TITLE` | `"TITLE"`
  `public static final char` | `COMMAND_START` | `33`
  `public static final char` | `COMMENT_END` | `93`
  `public static final char` | `COMMENT_START` | `91`
  `public static final char` | `DEFAULT_LABEL_CHAR` | `95`
  `public static final java.lang.String` | `FIRST_LINE` | `"#MEGA"`
  `public static final java.lang.String` | `FORMAT_SUBCOMMAND_DATA_FORMAT` | `"DATAFORMAT"`
  `public static final java.lang.String` | `FORMAT_SUBCOMMAND_DATA_TYPE` | `"DATATYPE"`
  `public static final java.lang.String` | `FORMAT_SUBCOMMAND_IDENTICAL` | `"IDENTICAL"`
  `public static final java.lang.String` | `FORMAT_SUBCOMMAND_INDEL` | `"INDEL"`
  `public static final java.lang.String` | `FORMAT_SUBCOMMAND_MISSING` | `"MISSING"`
  `public static final java.lang.String` | `FORMAT_SUBCOMMAND_NSITES` | `"NSITES"`
  `public static final java.lang.String` | `FORMAT_SUBCOMMAND_NTAXA` | `"NTAXA"`
  `public static final java.lang.String` | `FORMAT_VALUE_DNA_DATA_TYPE` | `"DNA"`
  `public static final java.lang.String` | `FORMAT_VALUE_INTERLEAVED_DATA_FORMAT` | `"INTERLEAVED"`
  `public static final java.lang.String` | `FORMAT_VALUE_NUCLEOTIDE_DATA_TYPE` | `"NUCLEOTIDE"`
  `public static final java.lang.String` | `FORMAT_VALUE_PROTEIN_DATA_TYPE` | `"PROTEIN"`
  `public static final java.lang.String` | `FORMAT_VALUE_RNA_DATA_TYPE` | `"RNA"`
  `public static final java.lang.String` | `LABEL_CHAR_SET_ID` | `"MEGALabelCharacterSet"`
  `public static final java.lang.String` | `MEGA_FORMAT_NAME` | `"MEGA"`
  `public static final java.lang.String` | `MEGA_NAMESPACE_PREFIX` | `"http://bioinfweb.info/xmlns/JPhyloIO/Formats/MEGA/"`
  `public static final java.lang.String` | `MEGA_PREDICATE_NAMESPACE` | `"http://bioinfweb.info/xmlns/JPhyloIO/Formats/MEGA/Predicates/"`
  `public static final char` | `SEUQUENCE_START` | `35`

- info.bioinfweb.jphyloio.formats.newick.NewickConstants
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final char` | `ALLOCATION_SEPARATOR_SYMBOL` | `44`
  `public static final char` | `ALLOCATION_SYMBOL` | `61`
  `public static final char` | `ALTERNATIVE_NAME_DELIMITER` | `34`
  `public static final char` | `COMMENT_END` | `93`
  `public static final char` | `COMMENT_START` | `91`
  `public static final java.lang.String` | `E_NEWICK_EDGE_TYPE_HYBRIDIZATION` | `"H"`
  `public static final java.lang.String` | `E_NEWICK_EDGE_TYPE_LATERAL_GENE_TRANSFER` | `"LRT"`
  `public static final java.lang.String` | `E_NEWICK_EDGE_TYPE_RECOMBINATION` | `"R"`
  `public static final java.lang.String` | `E_NEWICK_NAMESPACE_PREFIX` | `"http://bioinfweb.info/xmlns/JPhyloIO/Formats/ENewick/"`
  `public static final java.lang.String` | `E_NEWICK_NETWORK_DATA_SEPARATOR` | `"#"`
  `public static final char` | `ELEMENT_SEPERATOR` | `44`
  `public static final char` | `FIELD_END_SYMBOL` | `125`
  `public static final char` | `FIELD_START_SYMBOL` | `123`
  `public static final char` | `FIELD_VALUE_SEPARATOR_SYMBOL` | `44`
  `public static final char` | `FREE_NAME_BLANK` | `95`
  `public static final char` | `HOT_COMMENT_START_SYMBOL` | `38`
  `public static final char` | `INDEX_END_SYMBOL` | `93`
  `public static final char` | `INDEX_START_SYMBOL` | `91`
  `public static final char` | `LENGTH_SEPERATOR` | `58`
  `public static final char` | `NAME_DELIMITER` | `39`
  `public static final java.lang.String` | `NEWICK_DATA_TYPE_NAMESPACE` | `"http://bioinfweb.info/xmlns/JPhyloIO/Formats/Newick/DataTypes/"`
  `public static final java.lang.String` | `NEWICK_FORMAT_NAME` | `"Newick"`
  `public static final java.lang.String` | `NEWICK_NAMESPACE_PREFIX` | `"http://bioinfweb.info/xmlns/JPhyloIO/Formats/Newick/"`
  `public static final java.lang.String` | `NHX_KEY_CONFIDENCE` | `"B"`
  `public static final java.lang.String` | `NHX_KEY_EVENT` | `"D"`
  `public static final java.lang.String` | `NHX_KEY_GENE_NAME` | `"GN"`
  `public static final java.lang.String` | `NHX_KEY_PREFIX` | `"NHX:"`
  `public static final java.lang.String` | `NHX_KEY_SCIENTIFIC_NAME` | `"S"`
  `public static final java.lang.String` | `NHX_KEY_SEQUENCE_ACCESSION` | `"AC"`
  `public static final java.lang.String` | `NHX_KEY_TAXONOMY_ID` | `"T"`
  `public static final java.lang.String` | `NHX_START` | `"&&NHX:"`
  `public static final char` | `NHX_VALUE_SEPARATOR_SYMBOL` | `58`
  `public static final java.lang.String` | `ROOTED_HOT_COMMENT` | `"&r"`
  `public static final char` | `SUBTREE_END` | `41`
  `public static final char` | `SUBTREE_START` | `40`
  `public static final char` | `TERMINAL_SYMBOL` | `59`
  `public static final java.lang.String` | `UNROOTED_HOT_COMMENT` | `"&u"`

- info.bioinfweb.jphyloio.formats.newick.NewickNodeEdgeEventReceiver<E extends JPhyloIOEvent>
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final char` | `STRING_DELEMITER_REPLACEMENT` | `39`

- info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final java.lang.String` | `DEFAULT_TOKEN_DEFINITION_SET_ID_PREFIX` | `"tokenSetDEFAULT"`
  `public static final java.lang.String` | `NEXML_DEFAULT_NAMESPACE_PREFIX` | `"nex"`
  `public static final java.lang.String` | `NEXML_FORMAT_NAME` | `"NeXML"`
  `public static final java.lang.String` | `NEXML_NAMESPACE` | `"http://www.nexml.org/2009"`
  `public static final java.lang.String` | `NEXML_NAMESPACE_PREFIX` | `"http://bioinfweb.info/xmlns/JPhyloIO/Formats/NeXML/"`
  `public static final java.lang.String` | `NEXML_PREDICATE_NAMESPACE` | `"http://bioinfweb.info/xmlns/JPhyloIO/Formats/NeXML/Predicates/"`
  `public static final java.lang.String` | `NEXML_VERSION` | `"0.9"`
  `public static final java.lang.String` | `TYPE_CONTIN_CELLS` | `"ContinuousCells"`
  `public static final java.lang.String` | `TYPE_CONTIN_SEQ` | `"ContinuousSeqs"`
  `public static final java.lang.String` | `TYPE_DNA_CELLS` | `"DnaCells"`
  `public static final java.lang.String` | `TYPE_DNA_SEQS` | `"DnaSeqs"`
  `public static final java.lang.String` | `TYPE_FLOAT_NETWORK` | `"FloatNetwork"`
  `public static final java.lang.String` | `TYPE_FLOAT_TREE` | `"FloatTree"`
  `public static final java.lang.String` | `TYPE_INT_NETWORK` | `"IntNetwork"`
  `public static final java.lang.String` | `TYPE_INT_TREE` | `"IntTree"`
  `public static final java.lang.String` | `TYPE_LITERAL_META` | `"LiteralMeta"`
  `public static final java.lang.String` | `TYPE_PROTEIN_CELLS` | `"ProteinCells"`
  `public static final java.lang.String` | `TYPE_PROTEIN_SEQS` | `"ProteinSeqs"`
  `public static final java.lang.String` | `TYPE_RESOURCE_META` | `"ResourceMeta"`
  `public static final java.lang.String` | `TYPE_RESTRICTION_CELLS` | `"RestrictionCells"`
  `public static final java.lang.String` | `TYPE_RESTRICTION_SEQS` | `"RestrictionSeqs"`
  `public static final java.lang.String` | `TYPE_RNA_CELLS` | `"RnaCells"`
  `public static final java.lang.String` | `TYPE_RNA_SEQS` | `"RnaSeqs"`
  `public static final java.lang.String` | `TYPE_STANDARD_CELLS` | `"StandardCells"`
  `public static final java.lang.String` | `TYPE_STANDARD_SEQ` | `"StandardSeqs"`
  `public static final java.lang.String` | `UNDEFINED_OTU_ID_PREFIX` | `"undefinedOTU"`
  `public static final java.lang.String` | `UNDEFINED_OTU_LABEL` | `"UNDEFINED OTU generated by JPhyloIO"`
  `public static final java.lang.String` | `UNDEFINED_OTUS_ID_PREFIX` | `"undefinedOTUs"`
  `public static final java.lang.String` | `UNDEFINED_OTUS_LABEL` | `"UNDEFINED OTU list generated by JPhyloIO"`

- info.bioinfweb.jphyloio.formats.nexus.NexusConstants
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final java.lang.String` | `ALTERNATIVE_END_COMMAND` | `"ENDBLOCK"`
  `public static final java.lang.String` | `BEGIN_COMMAND` | `"BEGIN"`
  `public static final java.lang.String` | `BLOCK_NAME_CHARACTERS` | `"CHARACTERS"`
  `public static final java.lang.String` | `BLOCK_NAME_DATA` | `"DATA"`
  `public static final java.lang.String` | `BLOCK_NAME_NETWORKS` | `"NETWORKS"`
  `public static final java.lang.String` | `BLOCK_NAME_SETS` | `"SETS"`
  `public static final java.lang.String` | `BLOCK_NAME_TAXA` | `"TAXA"`
  `public static final java.lang.String` | `BLOCK_NAME_TREES` | `"TREES"`
  `public static final java.lang.String` | `BLOCK_NAME_UNALIGNED` | `"UNALIGNED"`
  `public static final char` | `CHARACTER_NAME_STATES_SEPARATOR` | `47`
  `public static final char` | `COMMAND_END` | `59`
  `public static final java.lang.String` | `COMMAND_NAME_CHAR_LABELS` | `"CHARLABELS"`
  `public static final java.lang.String` | `COMMAND_NAME_CHAR_SET` | `"CHARSET"`
  `public static final java.lang.String` | `COMMAND_NAME_CHAR_STATE_LABELS` | `"CHARSTATELABELS"`
  `public static final java.lang.String` | `COMMAND_NAME_DIMENSIONS` | `"DIMENSIONS"`
  `public static final java.lang.String` | `COMMAND_NAME_FORMAT` | `"FORMAT"`
  `public static final java.lang.String` | `COMMAND_NAME_LINK` | `"LINK"`
  `public static final java.lang.String` | `COMMAND_NAME_MATRIX` | `"MATRIX"`
  `public static final java.lang.String` | `COMMAND_NAME_NETWORK` | `"NETWORK"`
  `public static final java.lang.String` | `COMMAND_NAME_TAX_LABELS` | `"TAXLABELS"`
  `public static final java.lang.String` | `COMMAND_NAME_TAXON_SET` | `"TAXSET"`
  `public static final java.lang.String` | `COMMAND_NAME_TITLE` | `"TITLE"`
  `public static final java.lang.String` | `COMMAND_NAME_TRANSLATE` | `"TRANSLATE"`
  `public static final java.lang.String` | `COMMAND_NAME_TREE` | `"TREE"`
  `public static final java.lang.String` | `COMMAND_NAME_TREE_SET` | `"TREESET"`
  `public static final char` | `COMMENT_END` | `93`
  `public static final char` | `COMMENT_START` | `91`
  `public static final java.lang.String` | `DIMENSIONS_SUBCOMMAND_NCHAR` | `"NCHAR"`
  `public static final java.lang.String` | `DIMENSIONS_SUBCOMMAND_NEW_TAXA` | `"NEWTAXA"`
  `public static final java.lang.String` | `DIMENSIONS_SUBCOMMAND_NTAX` | `"NTAX"`
  `public static final char` | `ELEMENT_SEPARATOR` | `44`
  `public static final java.lang.String` | `END_COMMAND` | `"END"`
  `public static final java.lang.String` | `FIRST_LINE` | `"#NEXUS"`
  `public static final java.lang.String` | `FORMAT_NAME_STANDARD` | `"STANDARD"`
  `public static final java.lang.String` | `FORMAT_NAME_VECTOR` | `"VECTOR"`
  `public static final java.lang.String` | `FORMAT_SUBCOMMAND_DATA_TYPE` | `"DATATYPE"`
  `public static final java.lang.String` | `FORMAT_SUBCOMMAND_GAP_CHAR` | `"GAP"`
  `public static final java.lang.String` | `FORMAT_SUBCOMMAND_INTERLEAVE` | `"INTERLEAVE"`
  `public static final java.lang.String` | `FORMAT_SUBCOMMAND_MATCH_CHAR` | `"MATCHCHAR"`
  `public static final java.lang.String` | `FORMAT_SUBCOMMAND_MISSING_CHAR` | `"MISSING"`
  `public static final java.lang.String` | `FORMAT_SUBCOMMAND_NO_LABELS` | `"NOLABELS"`
  `public static final java.lang.String` | `FORMAT_SUBCOMMAND_NO_TOKENS` | `"NOTOKENS"`
  `public static final java.lang.String` | `FORMAT_SUBCOMMAND_SYMBOLS` | `"SYMBOLS"`
  `public static final java.lang.String` | `FORMAT_SUBCOMMAND_TOKENS` | `"TOKENS"`
  `public static final java.lang.String` | `FORMAT_SUBCOMMAND_TRANSPOSE` | `"TRANSPOSE"`
  `public static final java.lang.String` | `FORMAT_VALUE_CONTINUOUS_DATA_TYPE` | `"CONTINUOUS"`
  `public static final java.lang.String` | `FORMAT_VALUE_DNA_DATA_TYPE` | `"DNA"`
  `public static final java.lang.String` | `FORMAT_VALUE_MIXED_DATA_TYPE` | `"MIXED"`
  `public static final java.lang.String` | `FORMAT_VALUE_NUCLEOTIDE_DATA_TYPE` | `"NUCLEOTIDE"`
  `public static final java.lang.String` | `FORMAT_VALUE_PROTEIN_DATA_TYPE` | `"PROTEIN"`
  `public static final java.lang.String` | `FORMAT_VALUE_RNA_DATA_TYPE` | `"RNA"`
  `public static final java.lang.String` | `FORMAT_VALUE_STANDARD_DATA_TYPE` | `"STANDARD"`
  `public static final char` | `KEY_VALUE_SEPARATOR` | `61`
  `public static final char` | `MATRIX_POLYMORPHIC_TOKEN_END` | `41`
  `public static final char` | `MATRIX_POLYMORPHIC_TOKEN_START` | `40`
  `public static final char` | `MATRIX_UNCERTAINS_TOKEN_END` | `125`
  `public static final char` | `MATRIX_UNCERTAINS_TOKEN_START` | `123`
  `public static final java.lang.String` | `NEXUS_FORMAT_NAME` | `"Nexus"`
  `public static final java.lang.String` | `NEXUS_NAMESPACE_PREFIX` | `"http://bioinfweb.info/xmlns/JPhyloIO/Formats/Nexus/"`
  `public static final java.lang.String` | `NEXUS_PREDICATE_NAMESPACE` | `"http://bioinfweb.info/xmlns/JPhyloIO/Formats/Nexus/Predicates/"`
  `public static final char` | `SET_END_INDEX_SYMBOL` | `46`
  `public static final java.lang.String` | `SET_KEY_WORD_ALL` | `"ALL"`
  `public static final java.lang.String` | `SET_KEY_WORD_REMAINING` | `"REMAINING"`
  `public static final char` | `SET_REGULAR_INTERVAL_SYMBOL` | `92`
  `public static final char` | `SET_TO_SYMBOL` | `45`
  `public static final char` | `SET_VECTOR_CONTAINED` | `49`
  `public static final char` | `SET_VECTOR_NOT_CONTAINED` | `48`
  `public static final char` | `VALUE_DELIMITER` | `34`
  `public static final char` | `WORD_DELIMITER` | `39`

- info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final java.lang.String` | `INFO_CHARACTER_NAME_TO_INDEX_MAP` | `"info.bioinfweb.jphyloio.nexus.characters.characterNameToIndexMap"`
  `public static final java.lang.String` | `INFO_KEY_BLOCK_ID_MAP` | `"info.bioinfweb.jphyloio.nexus.taxa.blockTitleToIDMap"`
  `public static final java.lang.String` | `INFO_KEY_BLOCK_LINKS` | `"info.bioinfweb.jphyloio.nexus.blockLinks"`
  `public static final java.lang.String` | `INFO_KEY_BLOCK_START_EVENT_FIRED` | `"info.bioinfweb.jphyloio.nexus.blockStartEventFired"`
  `public static final java.lang.String` | `INFO_KEY_BLOCK_TITLE` | `"info.bioinfweb.jphyloio.nexus.blockTitle"`
  `public static final java.lang.String` | `INFO_KEY_CURRENT_BLOCK_ID` | `"info.bioinfweb.jphyloio.nexus.currentBlockID"`
  `public static final java.lang.String` | `INFO_KEY_ELEMENT_LIST` | `"info.bioinfweb.jphyloio.nexus.elementlist"`
  `public static final java.lang.String` | `INFO_KEY_MATRIX_WIDTHS_MAP` | `"info.bioinfweb.jphyloio.nexus.matrixWidths"`
  `public static final java.lang.String` | `INFO_KEY_NEXUS_NAME_TO_ID_MAP` | `"info.bioinfweb.jphyloio.nexus.nameToIDMap"`
  `public static final java.lang.String` | `INFO_KEY_TREES_TRANSLATION` | `"info.bioinfweb.jphyloio.nexus.trees.translate"`

- info.bioinfweb.jphyloio.formats.nexus.commandreaders.NexusCommandReaderFactory
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final java.lang.String` | `ALL_BLOCKS_IDENTIFIER` | `"ALL BLOCKS"`
  `public static final char` | `BLOCK_COMMAND_CONNECTOR` | `46`

- info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.DimensionsReader
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final java.lang.String` | `INFO_KEY_CHAR` | `"info.bioinfweb.jphyloio.nexus.ntax"`
  `public static final java.lang.String` | `INFO_KEY_NTAX` | `"info.bioinfweb.jphyloio.nexus.ntax"`

- info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.FormatReader
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final java.lang.String` | `INFO_KEY_INTERLEAVE` | `"info.bioinfweb.jphyloio.nexus.interleave"`
  `public static final java.lang.String` | `INFO_KEY_LABELS` | `"info.bioinfweb.jphyloio.nexus.labels"`
  `public static final java.lang.String` | `INFO_KEY_TOKENS_FORMAT` | `"info.bioinfweb.jphyloio.nexus.tokens"`
  `public static final java.lang.String` | `INFO_KEY_TRANSPOSE` | `"info.bioinfweb.jphyloio.nexus.transpose"`

- info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.NexusNewickReaderNodeLabelProcessor
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final boolean` | `DEFAULT_TRANSLATE_INTERNAL_NODE_NAMES` | `false`

- info.bioinfweb.jphyloio.formats.pde.PDEConstants
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final java.lang.String` | `AMINO_TYPE` | `"amino"`
  `public static final java.lang.String` | `DNA_TYPE` | `"dna"`
  `public static final int` | `FIRST_CUSTOM_META_ID` | `32`
  `public static final int` | `META_ID_ACCESS_NUMBER` | `3`
  `public static final int` | `META_ID_COMMENT` | `4`
  `public static final int` | `META_ID_LINKED_FILE` | `2`
  `public static final int` | `META_ID_SEQUENCE_LABEL` | `1`
  `public static final java.lang.String` | `META_TYPE_FILE` | `"FILE"`
  `public static final java.lang.String` | `META_TYPE_NUMBER` | `"NUMBER"`
  `public static final java.lang.String` | `META_TYPE_STRING` | `"STRING"`
  `public static final java.lang.String` | `PDE_FORMAT_NAME` | `"PDE (PhyDE)"`
  `public static final java.lang.String` | `PDE_NAMESPACE_PREFIX` | `"http://bioinfweb.info/xmlns/JPhyloIO/Formats/PDE/"`
  `public static final java.lang.String` | `PDE_PREDICATE_NAMESPACE` | `"http://bioinfweb.info/xmlns/JPhyloIO/Formats/PDE/Predicates/"`
  `public static final java.lang.String` | `SEQUENCE_END` | `"/FF"`
  `public static final java.lang.String` | `UNKNOWN_CHARS` | `"/FE"`

- info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipFactory
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final int` | `MAXIMUM_EXPECTED_DIGITS_OR_WHITESPACE` | `128`

- info.bioinfweb.jphyloio.formats.phylip.PhylipConstants
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final int` | `DEFAULT_NAME_LENGTH` | `10`
  `public static final java.lang.String` | `PHYLIP_FORMAT_NAME` | `"Phylip"`
  `public static final java.lang.String` | `PREMATURE_NAME_END_CHARACTER` | `"\t"`
  `public static final java.lang.String` | `SEQUENTIAL_PHYLIP_FORMAT_NAME` | `"Sequential Phylip"`

- info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final java.lang.String` | `APPLIES_TO_ANNOTATION` | `"annotation"`
  `public static final java.lang.String` | `APPLIES_TO_CLADE` | `"clade"`
  `public static final java.lang.String` | `APPLIES_TO_NODE` | `"node"`
  `public static final java.lang.String` | `APPLIES_TO_OTHER` | `"other"`
  `public static final java.lang.String` | `APPLIES_TO_PARENT_BRANCH` | `"parent_branch"`
  `public static final java.lang.String` | `APPLIES_TO_PHYLOGENY` | `"phylogeny"`
  `public static final java.lang.String` | `JPHYLOIO_PHYLOXML_NAMESPACE` | `"http://bioinfweb.info/xmlns/JPhyloIO/PhyloXML/"`
  `public static final java.lang.String` | `PHYLOXML_DATA_TYPE_NAMESPACE` | `"http://bioinfweb.info/xmlns/JPhyloIO/PhyloXML/DataTypes/"`
  `public static final java.lang.String` | `PHYLOXML_DEFAULT_PRE` | `"phy"`
  `public static final java.lang.String` | `PHYLOXML_FORMAT_NAME` | `"PhyloXML"`
  `public static final java.lang.String` | `PHYLOXML_NAMESPACE` | `"http://www.phyloxml.org"`
  `public static final java.lang.String` | `PHYLOXML_PREDICATE_NAMESPACE` | `"http://bioinfweb.info/xmlns/JPhyloIO/PhyloXML/Predicates/"`
  `public static final java.lang.String` | `PHYLOXML_SCHEMA_LOCATION_URI` | `"http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd"`
  `public static final java.lang.String` | `TYPE_NETWORK_EDGE` | `"network_edge"`

- info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader<P extends XMLReaderStreamDataProvider<? extends AbstractXMLEventReader<P>>>
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final java.lang.String` | `INTERNAL_USE_NAMESPACE` | `"http://bioinfweb.info/xmlns/JPhyloIO/internalUse"`

- info.bioinfweb.jphyloio.formats.xml.XMLReadWriteUtils
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final java.lang.String` | `DEFAULT_NAMESPACE_PREFIX` | `"p"`
  `public static final java.lang.String` | `NAMESPACE_RDF` | `"http://www.w3.org/1999/02/22-rdf-syntax-ns"`
  `public static final java.lang.String` | `RDF_DEFAULT_PRE` | `"rdf"`
  `public static final java.lang.String` | `SCHEMA_LOCATION` | `"schemaLocation"`
  `public static final java.lang.String` | `XSD_DEFAULT_PRE` | `"xsd"`
  `public static final java.lang.String` | `XSI_DEFAULT_PRE` | `"xsi"`

- info.bioinfweb.jphyloio.formats.xtg.XTGConstants
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final java.lang.String` | `ALIGN_LEFT` | `"left"`
  `public static final java.lang.String` | `ALIGN_RIGHT` | `"right"`
  `public static final java.lang.String` | `ALIGN_TREE_WIDTH` | `"treeWidth"`
  `public static final java.lang.String` | `BRANCH_LENGTH_UNITS` | `"u"`
  `public static final java.lang.String` | `DEPRECATED_VALUE_LEAVES_ADAPTER` | `"info.bioinfweb.treegraph.defaultLeafsAdapter"`
  `public static final java.lang.String` | `FULL_SCHEMA_LOCATION` | `"http://bioinfweb.info/xmlns/xtg http://bioinfweb.info/xmlns/xtg/1.4.xsd"`
  `public static final java.lang.String` | `MILLIMETERS` | `"mm"`
  `public static final java.lang.String` | `NAMESPACE_URI` | `"http://bioinfweb.info/xmlns/xtg"`
  `public static final java.lang.String` | `ORIENT_DOWN` | `"down"`
  `public static final java.lang.String` | `ORIENT_HORIZONTAL` | `"horizontal"`
  `public static final java.lang.String` | `ORIENT_UP` | `"up"`
  `public static final java.lang.String` | `PRE_LEGEND_ANCHOR` | `"Anchor"`
  `public static final java.lang.String` | `STYLE_BOLD` | `"b"`
  `public static final java.lang.String` | `STYLE_BRACE` | `"brace"`
  `public static final java.lang.String` | `STYLE_BRACKET` | `"bracket"`
  `public static final java.lang.String` | `STYLE_ITALIC` | `"i"`
  `public static final java.lang.String` | `STYLE_UNDERLINE` | `"u"`
  `public static final java.lang.String` | `VALUE_ADAPTER_PURPOSE_PREFIX` | `"info.bioinfweb.treegraph."`
  `public static final java.lang.String` | `VALUE_LEAVES_ADAPTER` | `"info.bioinfweb.treegraph.defaultLeavesAdapter"`
  `public static final java.lang.String` | `VALUE_SUPPORT_VALUES_ADAPTER` | `"info.bioinfweb.treegraph.defaultSupportAdapter"`
  `public static final java.lang.String` | `VERSION` | `"1.4"`
  `public static final java.lang.String` | `XTG` | `"xtg"`
  `public static final java.lang.String` | `XTG_DATA_TYPE_NAMESPACE` | `"http://bioinfweb.info/xmlns/JPhyloIO/Formats/XTG/DataTypes/"`
  `public static final java.lang.String` | `XTG_FORMAT_NAME` | `"Extensible TreeGraph 2 format"`
  `public static final java.lang.String` | `XTG_NAMESPACE_PREFIX` | `"http://bioinfweb.info/xmlns/JPhyloIO/Formats/XTG/"`
  `public static final java.lang.String` | `XTG_PREDICATE_NAMESPACE` | `"http://bioinfweb.info/xmlns/JPhyloIO/Formats/XTG/Predicates/"`

- info.bioinfweb.jphyloio.objecttranslation.implementations.SimpleValueTranslator<O>
  Modifier and Type | Constant Field | Value
  --- | --- | ---
  `public static final int` | `MAX_STRING_REPRESENTATION_LENGTH` | `16384`