info.bioinfweb.jphyloio.formats.nexus

Interface NexusConstants

All Known Implementing Classes:

AbstractCharLabelsReader, AbstractKeyValueCommandReader, AbstractNexusEventReceiver, AbstractNexusSetReader, AbstractNexusSetsEventReceiver, AbstractNexusSetWriter, CharactersDataUnalignedBlockHandler, CharacterSetEventReceiver, CharLabelsReader, CharSetReader, CharStateLabelsReader, DefaultCommandReader, DimensionsReader, ENewickNetworkReader, ENewickNetworksBlockHandler, FormatReader, IDBasedSetsReader, LinkReader, MatrixReader, NexusEventReader, NexusEventWriter, NexusFactory, NexusNewickReaderNodeLabelProcessor, NexusReaderStreamDataProvider, ReferenceOnlySetReceiver, TaxaBlockHandler, TaxLabelsReader, TaxSetReader, TitleReader, TokenSetEventReceiver, TranslateReader, TreeReader, TreesBlockHandler, TreeSetReader

public interface NexusConstants

Defines constants necessary to read and write Nexus files.

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	ALTERNATIVE_END_COMMAND
static java.lang.String	BEGIN_COMMAND
static java.lang.String	BLOCK_NAME_CHARACTERS
static java.lang.String	BLOCK_NAME_DATA
static java.lang.String	BLOCK_NAME_NETWORKS This block name is not part of the initial Nexus standard and used by ENewickNetworksBlockHandler.
static java.lang.String	BLOCK_NAME_SETS
static java.lang.String	BLOCK_NAME_TAXA
static java.lang.String	BLOCK_NAME_TREES
static java.lang.String	BLOCK_NAME_UNALIGNED
static char	CHARACTER_NAME_STATES_SEPARATOR
static char	COMMAND_END
static java.lang.String	COMMAND_NAME_CHAR_LABELS
static java.lang.String	COMMAND_NAME_CHAR_SET
static java.lang.String	COMMAND_NAME_CHAR_STATE_LABELS
static java.lang.String	COMMAND_NAME_DIMENSIONS
static java.lang.String	COMMAND_NAME_FORMAT
static java.lang.String	COMMAND_NAME_LINK
static java.lang.String	COMMAND_NAME_MATRIX
static java.lang.String	COMMAND_NAME_NETWORK This command name is not part of the initial Nexus standard and used by ENewickNetworkReader.
static java.lang.String	COMMAND_NAME_TAX_LABELS
static java.lang.String	COMMAND_NAME_TAXON_SET
static java.lang.String	COMMAND_NAME_TITLE
static java.lang.String	COMMAND_NAME_TRANSLATE
static java.lang.String	COMMAND_NAME_TREE
static java.lang.String	COMMAND_NAME_TREE_SET
static char	COMMENT_END
static char	COMMENT_START
static java.lang.String	DIMENSIONS_SUBCOMMAND_NCHAR
static java.lang.String	DIMENSIONS_SUBCOMMAND_NEW_TAXA
static java.lang.String	DIMENSIONS_SUBCOMMAND_NTAX
static char	ELEMENT_SEPARATOR
static java.lang.String	END_COMMAND
static java.lang.String	FIRST_LINE
static java.lang.String	FORMAT_NAME_STANDARD
static java.lang.String	FORMAT_NAME_VECTOR
static java.lang.String	FORMAT_SUBCOMMAND_DATA_TYPE
static java.lang.String	FORMAT_SUBCOMMAND_GAP_CHAR
static java.lang.String	FORMAT_SUBCOMMAND_INTERLEAVE
static java.lang.String	FORMAT_SUBCOMMAND_MATCH_CHAR
static java.lang.String	FORMAT_SUBCOMMAND_MISSING_CHAR
static java.lang.String	FORMAT_SUBCOMMAND_NO_LABELS
static java.lang.String	FORMAT_SUBCOMMAND_NO_TOKENS
static java.lang.String	FORMAT_SUBCOMMAND_SYMBOLS
static java.lang.String	FORMAT_SUBCOMMAND_TOKENS
static java.lang.String	FORMAT_SUBCOMMAND_TRANSPOSE
static java.lang.String	FORMAT_VALUE_CONTINUOUS_DATA_TYPE
static java.lang.String	FORMAT_VALUE_DNA_DATA_TYPE
static java.lang.String	FORMAT_VALUE_MIXED_DATA_TYPE This is not part of the official Nexus definition, but is a MrBayes extension.
static java.lang.String	FORMAT_VALUE_NUCLEOTIDE_DATA_TYPE
static java.lang.String	FORMAT_VALUE_PROTEIN_DATA_TYPE
static java.lang.String	FORMAT_VALUE_RNA_DATA_TYPE
static java.lang.String	FORMAT_VALUE_STANDARD_DATA_TYPE
static char	KEY_VALUE_SEPARATOR
static char	MATRIX_POLYMORPHIC_TOKEN_END
static char	MATRIX_POLYMORPHIC_TOKEN_START
static char	MATRIX_UNCERTAINS_TOKEN_END
static char	MATRIX_UNCERTAINS_TOKEN_START
static java.lang.String	NEXUS_FORMAT_NAME
static java.lang.String	NEXUS_NAMESPACE_PREFIX
static java.lang.String	NEXUS_PREDICATE_NAMESPACE
static char	SET_END_INDEX_SYMBOL
static java.lang.String	SET_KEY_WORD_ALL
static java.lang.String	SET_KEY_WORD_REMAINING
static char	SET_REGULAR_INTERVAL_SYMBOL
static char	SET_TO_SYMBOL
static char	SET_VECTOR_CONTAINED
static char	SET_VECTOR_NOT_CONTAINED
static java.util.regex.Pattern	UNTIL_WHITESPACE_COMMENT_COMMAND_EQUAL_PATTERN
static java.util.regex.Pattern	UNTIL_WHITESPACE_COMMENT_COMMAND_PATTERN
static char	VALUE_DELIMITER
static char	WORD_DELIMITER

Field Detail

NEXUS_FORMAT_NAME

static final java.lang.String NEXUS_FORMAT_NAME

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Constant Field Values

FIRST_LINE

static final java.lang.String FIRST_LINE

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Constant Field Values

BEGIN_COMMAND

static final java.lang.String BEGIN_COMMAND

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Constant Field Values

END_COMMAND

static final java.lang.String END_COMMAND

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Constant Field Values

ALTERNATIVE_END_COMMAND

static final java.lang.String ALTERNATIVE_END_COMMAND

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Constant Field Values

COMMAND_END

static final char COMMAND_END

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Constant Field Values

COMMENT_START

static final char COMMENT_START

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Constant Field Values

COMMENT_END

static final char COMMENT_END

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Constant Field Values

KEY_VALUE_SEPARATOR

static final char KEY_VALUE_SEPARATOR

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Constant Field Values

WORD_DELIMITER

static final char WORD_DELIMITER

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Constant Field Values

VALUE_DELIMITER

static final char VALUE_DELIMITER

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Constant Field Values

ELEMENT_SEPARATOR

static final char ELEMENT_SEPARATOR

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Constant Field Values

BLOCK_NAME_TAXA

static final java.lang.String BLOCK_NAME_TAXA

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Constant Field Values

BLOCK_NAME_CHARACTERS

static final java.lang.String BLOCK_NAME_CHARACTERS

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Constant Field Values

BLOCK_NAME_UNALIGNED

static final java.lang.String BLOCK_NAME_UNALIGNED

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Constant Field Values

BLOCK_NAME_DATA

static final java.lang.String BLOCK_NAME_DATA

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Constant Field Values

BLOCK_NAME_SETS

static final java.lang.String BLOCK_NAME_SETS

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Constant Field Values

BLOCK_NAME_TREES

static final java.lang.String BLOCK_NAME_TREES

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Constant Field Values

BLOCK_NAME_NETWORKS

static final java.lang.String BLOCK_NAME_NETWORKS

This block name is not part of the initial Nexus standard and used by ENewickNetworksBlockHandler.

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Constant Field Values

COMMAND_NAME_TITLE

static final java.lang.String COMMAND_NAME_TITLE

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Constant Field Values

COMMAND_NAME_LINK

static final java.lang.String COMMAND_NAME_LINK

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Constant Field Values

COMMAND_NAME_TAX_LABELS

static final java.lang.String COMMAND_NAME_TAX_LABELS

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Constant Field Values

COMMAND_NAME_DIMENSIONS

static final java.lang.String COMMAND_NAME_DIMENSIONS

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Constant Field Values

COMMAND_NAME_FORMAT

static final java.lang.String COMMAND_NAME_FORMAT

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Constant Field Values

COMMAND_NAME_CHAR_LABELS

static final java.lang.String COMMAND_NAME_CHAR_LABELS

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Constant Field Values

COMMAND_NAME_CHAR_STATE_LABELS

static final java.lang.String COMMAND_NAME_CHAR_STATE_LABELS

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Constant Field Values

COMMAND_NAME_MATRIX

static final java.lang.String COMMAND_NAME_MATRIX

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Constant Field Values

COMMAND_NAME_TRANSLATE

static final java.lang.String COMMAND_NAME_TRANSLATE

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Constant Field Values

COMMAND_NAME_TREE

static final java.lang.String COMMAND_NAME_TREE

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Constant Field Values

COMMAND_NAME_CHAR_SET

static final java.lang.String COMMAND_NAME_CHAR_SET

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Constant Field Values

COMMAND_NAME_TAXON_SET

static final java.lang.String COMMAND_NAME_TAXON_SET

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Constant Field Values

COMMAND_NAME_TREE_SET

static final java.lang.String COMMAND_NAME_TREE_SET

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Constant Field Values

COMMAND_NAME_NETWORK

static final java.lang.String COMMAND_NAME_NETWORK

This command name is not part of the initial Nexus standard and used by ENewickNetworkReader.

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Constant Field Values

DIMENSIONS_SUBCOMMAND_NEW_TAXA

static final java.lang.String DIMENSIONS_SUBCOMMAND_NEW_TAXA

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Constant Field Values

DIMENSIONS_SUBCOMMAND_NTAX

static final java.lang.String DIMENSIONS_SUBCOMMAND_NTAX

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Constant Field Values

DIMENSIONS_SUBCOMMAND_NCHAR

static final java.lang.String DIMENSIONS_SUBCOMMAND_NCHAR

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Constant Field Values

FORMAT_NAME_STANDARD

static final java.lang.String FORMAT_NAME_STANDARD

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Constant Field Values

FORMAT_NAME_VECTOR

static final java.lang.String FORMAT_NAME_VECTOR

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Constant Field Values

FORMAT_SUBCOMMAND_DATA_TYPE

static final java.lang.String FORMAT_SUBCOMMAND_DATA_TYPE

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Constant Field Values

FORMAT_SUBCOMMAND_TOKENS

static final java.lang.String FORMAT_SUBCOMMAND_TOKENS

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Constant Field Values

FORMAT_SUBCOMMAND_NO_TOKENS

static final java.lang.String FORMAT_SUBCOMMAND_NO_TOKENS

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Constant Field Values

FORMAT_SUBCOMMAND_INTERLEAVE

static final java.lang.String FORMAT_SUBCOMMAND_INTERLEAVE

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Constant Field Values

FORMAT_SUBCOMMAND_TRANSPOSE

static final java.lang.String FORMAT_SUBCOMMAND_TRANSPOSE

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Constant Field Values

FORMAT_SUBCOMMAND_NO_LABELS

static final java.lang.String FORMAT_SUBCOMMAND_NO_LABELS

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Constant Field Values

FORMAT_SUBCOMMAND_MATCH_CHAR

static final java.lang.String FORMAT_SUBCOMMAND_MATCH_CHAR

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Constant Field Values

FORMAT_SUBCOMMAND_MISSING_CHAR

static final java.lang.String FORMAT_SUBCOMMAND_MISSING_CHAR

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Constant Field Values

FORMAT_SUBCOMMAND_GAP_CHAR

static final java.lang.String FORMAT_SUBCOMMAND_GAP_CHAR

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Constant Field Values

FORMAT_SUBCOMMAND_SYMBOLS

static final java.lang.String FORMAT_SUBCOMMAND_SYMBOLS

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Constant Field Values

FORMAT_VALUE_STANDARD_DATA_TYPE

static final java.lang.String FORMAT_VALUE_STANDARD_DATA_TYPE

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Constant Field Values

FORMAT_VALUE_NUCLEOTIDE_DATA_TYPE

static final java.lang.String FORMAT_VALUE_NUCLEOTIDE_DATA_TYPE

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Constant Field Values

FORMAT_VALUE_DNA_DATA_TYPE

static final java.lang.String FORMAT_VALUE_DNA_DATA_TYPE

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Constant Field Values

FORMAT_VALUE_RNA_DATA_TYPE

static final java.lang.String FORMAT_VALUE_RNA_DATA_TYPE

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Constant Field Values

FORMAT_VALUE_PROTEIN_DATA_TYPE

static final java.lang.String FORMAT_VALUE_PROTEIN_DATA_TYPE

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Constant Field Values

FORMAT_VALUE_CONTINUOUS_DATA_TYPE

static final java.lang.String FORMAT_VALUE_CONTINUOUS_DATA_TYPE

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Constant Field Values

FORMAT_VALUE_MIXED_DATA_TYPE

static final java.lang.String FORMAT_VALUE_MIXED_DATA_TYPE

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

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Constant Field Values

CHARACTER_NAME_STATES_SEPARATOR

static final char CHARACTER_NAME_STATES_SEPARATOR

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Constant Field Values

MATRIX_POLYMORPHIC_TOKEN_START

static final char MATRIX_POLYMORPHIC_TOKEN_START

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Constant Field Values

MATRIX_POLYMORPHIC_TOKEN_END

static final char MATRIX_POLYMORPHIC_TOKEN_END

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Constant Field Values

MATRIX_UNCERTAINS_TOKEN_START

static final char MATRIX_UNCERTAINS_TOKEN_START

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Constant Field Values

MATRIX_UNCERTAINS_TOKEN_END

static final char MATRIX_UNCERTAINS_TOKEN_END

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Constant Field Values

SET_TO_SYMBOL

static final char SET_TO_SYMBOL

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Constant Field Values

SET_END_INDEX_SYMBOL

static final char SET_END_INDEX_SYMBOL

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Constant Field Values

SET_REGULAR_INTERVAL_SYMBOL

static final char SET_REGULAR_INTERVAL_SYMBOL

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Constant Field Values

SET_KEY_WORD_ALL

static final java.lang.String SET_KEY_WORD_ALL

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Constant Field Values

SET_KEY_WORD_REMAINING

static final java.lang.String SET_KEY_WORD_REMAINING

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Constant Field Values

SET_VECTOR_NOT_CONTAINED

static final char SET_VECTOR_NOT_CONTAINED

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Constant Field Values

SET_VECTOR_CONTAINED

static final char SET_VECTOR_CONTAINED

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Constant Field Values

NEXUS_NAMESPACE_PREFIX

static final java.lang.String NEXUS_NAMESPACE_PREFIX

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Constant Field Values

NEXUS_PREDICATE_NAMESPACE

static final java.lang.String NEXUS_PREDICATE_NAMESPACE

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Constant Field Values

UNTIL_WHITESPACE_COMMENT_COMMAND_PATTERN

static final java.util.regex.Pattern UNTIL_WHITESPACE_COMMENT_COMMAND_PATTERN

UNTIL_WHITESPACE_COMMENT_COMMAND_EQUAL_PATTERN

static final java.util.regex.Pattern UNTIL_WHITESPACE_COMMENT_COMMAND_EQUAL_PATTERN