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