info.bioinfweb.jphyloio

Interface ReadWriteConstants

All Known Implementing Classes:

AbstractCharLabelsReader, AbstractEventReader, AbstractIDLinkSetElementReader, AbstractNeXMLElementReader, AbstractNexusSetReader, AbstractPhylipEventReader, AbstractSetElementReader, AbstractTextEventReader, AbstractXMLEventReader, CharactersDataUnalignedBlockHandler, CharLabelsReader, CharSetReader, CharStateLabelsReader, DimensionsReader, ENewickNetworkReader, ENewickNetworksBlockHandler, FASTAEventReader, FormatReader, HotCommentDataReader, IDBasedSetsReader, MatrixReader, MEGAEventReader, NewickEventReader, NewickStringReader, NeXMLEventReader, NeXMLMetaEndElementReader, NeXMLMetaStartElementReader, NeXMLSetEndElementReader, NexusEventReader, NHXUtils, ObjectTranslatorFactory, PDEEventReader, PhylipEventReader, PhyloXMLEventReader, SequentialPhylipEventReader, TaxLabelsReader, TaxSetReader, TitleReader, TranslateReader, TreeReader, TreesBlockHandler, TreeSetReader, XTGEventReader

public interface ReadWriteConstants

Provides general constants for reading and writing phylogenetic file formats.

The DEFAULT_XXX_PREFIX constants are used by some reader implementations to generate event IDs. Their value may change any time without further notice. Such a change would not be considered as an API change and would not be reflected in a major version number increase. Application developers should never rely on expecting specific prefixes for event IDs.

Since:

0.0.0

Author:

Ben Stöver, Sarah Wiechers

Field Summary

Fields

Modifier and Type	Field and Description
static javax.xml.namespace.QName	ATTRIBUTE_STRING_KEY
static java.lang.String	ATTRIBUTES_NAMESPACE_FOLDER
static java.lang.String	DATA_TYPE_NAMESPACE_FOLDER
static javax.xml.namespace.QName	DATA_TYPE_SIMPLE_VALUE_LIST A custom data type defined in JPhyloIO that indicates that a list in the Newick/Nexus metadata notation as processed by ListTranslator is stored in an XML format.
static java.lang.String	DEFAULT_CHAR_SET_ID_PREFIX
static java.lang.String	DEFAULT_CHARACTER_DEFINITION_ID_PREFIX
static java.lang.String	DEFAULT_EDGE_ID_PREFIX
static java.lang.String	DEFAULT_GENERAL_ID_PREFIX
static java.lang.String	DEFAULT_MATRIX_ID_PREFIX
static int	DEFAULT_MAX_COMMENT_LENGTH
static int	DEFAULT_MAX_TOKENS_TO_READ
static java.lang.String	DEFAULT_META_ID_PREFIX
static java.lang.String	DEFAULT_NETWORK_ID_PREFIX
static java.lang.String	DEFAULT_NODE_EDGE_SET_ID_PREFIX
static java.lang.String	DEFAULT_NODE_ID_PREFIX
static java.lang.String	DEFAULT_OTU_ID_PREFIX
static java.lang.String	DEFAULT_OTU_LIST_ID_PREFIX
static java.lang.String	DEFAULT_OTU_SET_ID_PREFIX
static java.lang.String	DEFAULT_SEQUENCE_ID_PREFIX
static java.lang.String	DEFAULT_SEQUENCE_SET_ID_PREFIX
static java.lang.String	DEFAULT_TOKEN_DEFINITION_ID_PREFIX
static java.lang.String	DEFAULT_TOKEN_SET_ID_PREFIX
static java.lang.String	DEFAULT_TREE_ID_PREFIX
static java.lang.String	DEFAULT_TREE_NETWORK_GROUP_ID_PREFIX
static java.lang.String	DEFAULT_TREE_NETWORK_SET_ID_PREFIX
static java.lang.String	JPHYLOIO_ATTRIBUTES_NAMESPACE
static java.lang.String	JPHYLOIO_ATTRIBUTES_PREFIX
static java.lang.String	JPHYLOIO_DATA_TYPE_NAMESPACE The namespace for data types defined in JPhyloIO.
static java.lang.String	JPHYLOIO_DATA_TYPE_PREFIX The default namespace prefix for JPHYLOIO_DATA_TYPE_NAMESPACE.
static java.lang.String	JPHYLOIO_FORMATS_NAMESPACE_PREFIX
static java.lang.String	JPHYLOIO_GENERAL_NAMESPACE
static java.lang.String	JPHYLOIO_NAMESPACE_PREFIX
static java.lang.String	JPHYLOIO_PREDICATE_NAMESPACE
static java.lang.String	JPHYLOIO_PREDICATE_PREFIX
static javax.xml.namespace.QName	PREDICATE_CHARACTER_COUNT
static javax.xml.namespace.QName	PREDICATE_EDGE_LENGTH
static javax.xml.namespace.QName	PREDICATE_EDGE_SOURCE_NODE The following constants are currently only used in PhyloXML, but may be used by other formats in the future.
static javax.xml.namespace.QName	PREDICATE_EDGE_TARGET_NODE
static javax.xml.namespace.QName	PREDICATE_HAS_CUSTOM_XML
static javax.xml.namespace.QName	PREDICATE_HAS_LITERAL_METADATA
static javax.xml.namespace.QName	PREDICATE_HAS_RESOURCE_METADATA
static javax.xml.namespace.QName	PREDICATE_IS_CROSSLINK
static java.lang.String	PREDICATE_NAMESPACE_FOLDER
static java.lang.String	PREDICATE_PART_SEPERATOR
static javax.xml.namespace.QName	PREDICATE_SEQUENCE_COUNT
static java.lang.String	RESERVED_ID_PREFIX

Field Detail

DEFAULT_MAX_TOKENS_TO_READ

static final int DEFAULT_MAX_TOKENS_TO_READ

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Constant Field Values

DEFAULT_MAX_COMMENT_LENGTH

static final int DEFAULT_MAX_COMMENT_LENGTH

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Constant Field Values

PREDICATE_PART_SEPERATOR

static final java.lang.String PREDICATE_PART_SEPERATOR

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Constant Field Values

ATTRIBUTES_NAMESPACE_FOLDER

static final java.lang.String ATTRIBUTES_NAMESPACE_FOLDER

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Constant Field Values

PREDICATE_NAMESPACE_FOLDER

static final java.lang.String PREDICATE_NAMESPACE_FOLDER

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Constant Field Values

DATA_TYPE_NAMESPACE_FOLDER

static final java.lang.String DATA_TYPE_NAMESPACE_FOLDER

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Constant Field Values

JPHYLOIO_NAMESPACE_PREFIX

static final java.lang.String JPHYLOIO_NAMESPACE_PREFIX

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Constant Field Values

JPHYLOIO_GENERAL_NAMESPACE

static final java.lang.String JPHYLOIO_GENERAL_NAMESPACE

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Constant Field Values

JPHYLOIO_ATTRIBUTES_NAMESPACE

static final java.lang.String JPHYLOIO_ATTRIBUTES_NAMESPACE

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Constant Field Values

JPHYLOIO_ATTRIBUTES_PREFIX

static final java.lang.String JPHYLOIO_ATTRIBUTES_PREFIX

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Constant Field Values

ATTRIBUTE_STRING_KEY

static final javax.xml.namespace.QName ATTRIBUTE_STRING_KEY

JPHYLOIO_PREDICATE_NAMESPACE

static final java.lang.String JPHYLOIO_PREDICATE_NAMESPACE

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Constant Field Values

JPHYLOIO_PREDICATE_PREFIX

static final java.lang.String JPHYLOIO_PREDICATE_PREFIX

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Constant Field Values

JPHYLOIO_FORMATS_NAMESPACE_PREFIX

static final java.lang.String JPHYLOIO_FORMATS_NAMESPACE_PREFIX

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Constant Field Values

PREDICATE_HAS_LITERAL_METADATA

static final javax.xml.namespace.QName PREDICATE_HAS_LITERAL_METADATA

PREDICATE_HAS_RESOURCE_METADATA

static final javax.xml.namespace.QName PREDICATE_HAS_RESOURCE_METADATA

PREDICATE_HAS_CUSTOM_XML

static final javax.xml.namespace.QName PREDICATE_HAS_CUSTOM_XML

PREDICATE_SEQUENCE_COUNT

static final javax.xml.namespace.QName PREDICATE_SEQUENCE_COUNT

PREDICATE_CHARACTER_COUNT

static final javax.xml.namespace.QName PREDICATE_CHARACTER_COUNT

PREDICATE_EDGE_SOURCE_NODE

static final javax.xml.namespace.QName PREDICATE_EDGE_SOURCE_NODE

The following constants are currently only used in PhyloXML, but may be used by other formats in the future.

PREDICATE_EDGE_TARGET_NODE

static final javax.xml.namespace.QName PREDICATE_EDGE_TARGET_NODE

PREDICATE_EDGE_LENGTH

static final javax.xml.namespace.QName PREDICATE_EDGE_LENGTH

PREDICATE_IS_CROSSLINK

static final javax.xml.namespace.QName PREDICATE_IS_CROSSLINK

JPHYLOIO_DATA_TYPE_NAMESPACE

static final java.lang.String JPHYLOIO_DATA_TYPE_NAMESPACE

The namespace for data types defined in JPhyloIO.

Since:

0.3.0

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Constant Field Values

JPHYLOIO_DATA_TYPE_PREFIX

static final java.lang.String JPHYLOIO_DATA_TYPE_PREFIX

The default namespace prefix for JPHYLOIO_DATA_TYPE_NAMESPACE.

Since:

0.3.0

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Constant Field Values

DATA_TYPE_SIMPLE_VALUE_LIST

static final javax.xml.namespace.QName DATA_TYPE_SIMPLE_VALUE_LIST

A custom data type defined in JPhyloIO that indicates that a list in the Newick/Nexus metadata notation as processed by ListTranslator is stored in an XML format.

Since:

0.3.0

RESERVED_ID_PREFIX

static final java.lang.String RESERVED_ID_PREFIX

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Constant Field Values

DEFAULT_GENERAL_ID_PREFIX

static final java.lang.String DEFAULT_GENERAL_ID_PREFIX

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Constant Field Values

DEFAULT_META_ID_PREFIX

static final java.lang.String DEFAULT_META_ID_PREFIX

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Constant Field Values

DEFAULT_OTU_LIST_ID_PREFIX

static final java.lang.String DEFAULT_OTU_LIST_ID_PREFIX

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Constant Field Values

DEFAULT_OTU_ID_PREFIX

static final java.lang.String DEFAULT_OTU_ID_PREFIX

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Constant Field Values

DEFAULT_OTU_SET_ID_PREFIX

static final java.lang.String DEFAULT_OTU_SET_ID_PREFIX

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Constant Field Values

DEFAULT_MATRIX_ID_PREFIX

static final java.lang.String DEFAULT_MATRIX_ID_PREFIX

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Constant Field Values

DEFAULT_SEQUENCE_ID_PREFIX

static final java.lang.String DEFAULT_SEQUENCE_ID_PREFIX

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Constant Field Values

DEFAULT_SEQUENCE_SET_ID_PREFIX

static final java.lang.String DEFAULT_SEQUENCE_SET_ID_PREFIX

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Constant Field Values

DEFAULT_CHARACTER_DEFINITION_ID_PREFIX

static final java.lang.String DEFAULT_CHARACTER_DEFINITION_ID_PREFIX

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Constant Field Values

DEFAULT_CHAR_SET_ID_PREFIX

static final java.lang.String DEFAULT_CHAR_SET_ID_PREFIX

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Constant Field Values

DEFAULT_TOKEN_SET_ID_PREFIX

static final java.lang.String DEFAULT_TOKEN_SET_ID_PREFIX

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Constant Field Values

DEFAULT_TOKEN_DEFINITION_ID_PREFIX

static final java.lang.String DEFAULT_TOKEN_DEFINITION_ID_PREFIX

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Constant Field Values

DEFAULT_TREE_ID_PREFIX

static final java.lang.String DEFAULT_TREE_ID_PREFIX

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Constant Field Values

DEFAULT_NETWORK_ID_PREFIX

static final java.lang.String DEFAULT_NETWORK_ID_PREFIX

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Constant Field Values

DEFAULT_TREE_NETWORK_GROUP_ID_PREFIX

static final java.lang.String DEFAULT_TREE_NETWORK_GROUP_ID_PREFIX

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Constant Field Values

DEFAULT_TREE_NETWORK_SET_ID_PREFIX

static final java.lang.String DEFAULT_TREE_NETWORK_SET_ID_PREFIX

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Constant Field Values

DEFAULT_NODE_ID_PREFIX

static final java.lang.String DEFAULT_NODE_ID_PREFIX

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Constant Field Values

DEFAULT_EDGE_ID_PREFIX

static final java.lang.String DEFAULT_EDGE_ID_PREFIX

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Constant Field Values

DEFAULT_NODE_EDGE_SET_ID_PREFIX

static final java.lang.String DEFAULT_NODE_EDGE_SET_ID_PREFIX

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Constant Field Values