info.bioinfweb.jphyloio.formats.nexml

Interface NeXMLConstants

All Known Implementing Classes:

AbstractIDLinkSetElementReader, AbstractNeXMLDataReceiver, AbstractNeXMLDataReceiverMixin, AbstractNeXMLElementReader, AbstractSetElementReader, NeXMLAttributeMetadataReceiver, NeXMLCharacterSetEventReceiver, NeXMLCollectCharSetDataReceiver, NeXMLCollectNamespaceReceiver, NeXMLCollectSequenceDataReceiver, NeXMLCollectSetMetadataReceiver, NeXMLCollectTokenSetDefinitionDataReceiver, NeXMLEventReader, NeXMLEventWriter, NeXMLFactory, NeXMLHandleSequenceDataReceiver, NeXMLIgnoreCertainMetadataReceiver, NeXMLMetaDataReceiver, NeXMLMetaEndElementReader, NeXMLMetaStartElementReader, NeXMLMolecularDataTokenDefinitionReceiver, NeXMLOnlyWriteMetaDataReceiver, NeXMLPredicateMetaReceiver, NeXMLSequenceTokensReceiver, NeXMLSetEndElementReader, NeXMLTokenSetEventReceiver, NeXMLWriterAlignmentInformation, NeXMLWriterStreamDataProvider, UndefinedOTUListDataAdapter

public interface NeXMLConstants

Defines constants necessary to read and write NeXML files.

Author:

Sarah Wiechers

Field Summary

Fields

Modifier and Type	Field and Description
static javax.xml.namespace.QName	ATTR_ABOUT
static javax.xml.namespace.QName	ATTR_CELL_SET_LINKED_IDS
static javax.xml.namespace.QName	ATTR_CHAR_SET_LINKED_IDS
static javax.xml.namespace.QName	ATTR_CODON_POSITION
static javax.xml.namespace.QName	ATTR_CONTENT
static javax.xml.namespace.QName	ATTR_DATATYPE
static javax.xml.namespace.QName	ATTR_GENERATOR
static javax.xml.namespace.QName	ATTR_HREF
static javax.xml.namespace.QName	ATTR_ID
static javax.xml.namespace.QName	ATTR_LABEL
static javax.xml.namespace.QName	ATTR_LENGTH
static javax.xml.namespace.QName	ATTR_NODE_EDGE_SET_LINKED_EDGE_IDS
static javax.xml.namespace.QName	ATTR_NODE_EDGE_SET_LINKED_NODE_IDS
static javax.xml.namespace.QName	ATTR_NODE_EDGE_SET_LINKED_ROOTEDGE_IDS
static javax.xml.namespace.QName	ATTR_OTU_SET_LINKED_IDS
static javax.xml.namespace.QName	ATTR_OTUS
static javax.xml.namespace.QName	ATTR_PROPERTY
static javax.xml.namespace.QName	ATTR_REL
static javax.xml.namespace.QName	ATTR_ROOT
static javax.xml.namespace.QName	ATTR_SEQUENCE_SET_LINKED_IDS
static javax.xml.namespace.QName	ATTR_SINGLE_CHAR_LINK
static javax.xml.namespace.QName	ATTR_SINGLE_OTU_LINK
static javax.xml.namespace.QName	ATTR_SINGLE_STATE_LINK
static javax.xml.namespace.QName	ATTR_SOURCE
static javax.xml.namespace.QName	ATTR_STATE_SET_LINKED_IDS
static javax.xml.namespace.QName	ATTR_STATES
static javax.xml.namespace.QName	ATTR_SYMBOL
static javax.xml.namespace.QName	ATTR_TARGET
static javax.xml.namespace.QName	ATTR_TOKENS
static javax.xml.namespace.QName	ATTR_TREE_SET_LINKED_NETWORK_IDS
static javax.xml.namespace.QName	ATTR_TREE_SET_LINKED_TREE_IDS
static javax.xml.namespace.QName	ATTR_VERSION
static javax.xml.namespace.QName	ATTR_XSI_TYPE
static java.lang.String	DEFAULT_TOKEN_DEFINITION_SET_ID_PREFIX
static java.lang.String	NEXML_DEFAULT_NAMESPACE_PREFIX
static java.lang.String	NEXML_FORMAT_NAME
static java.lang.String	NEXML_NAMESPACE
static java.lang.String	NEXML_NAMESPACE_PREFIX
static java.lang.String	NEXML_PREDICATE_NAMESPACE
static java.lang.String	NEXML_VERSION
static javax.xml.namespace.QName	PREDICATE_CHAR_ATTR_CODON_POSITION
static javax.xml.namespace.QName	PREDICATE_CHAR_ATTR_TOKENS
static javax.xml.namespace.QName	PREDICATE_FORMAT
static javax.xml.namespace.QName	PREDICATE_MATRIX
static javax.xml.namespace.QName	PREDICATE_ORIGINAL_LABEL
static javax.xml.namespace.QName	PREDICATE_ORIGINAL_TOKEN_NAME
static javax.xml.namespace.QName	TAG_CELL
static javax.xml.namespace.QName	TAG_CHAR
static javax.xml.namespace.QName	TAG_CHARACTERS
static javax.xml.namespace.QName	TAG_EDGE
static javax.xml.namespace.QName	TAG_FORMAT
static javax.xml.namespace.QName	TAG_MATRIX
static javax.xml.namespace.QName	TAG_MEMBER
static javax.xml.namespace.QName	TAG_META
static javax.xml.namespace.QName	TAG_NETWORK
static javax.xml.namespace.QName	TAG_NODE
static javax.xml.namespace.QName	TAG_OTU
static javax.xml.namespace.QName	TAG_OTUS
static javax.xml.namespace.QName	TAG_POLYMORPHIC
static javax.xml.namespace.QName	TAG_ROOT
static javax.xml.namespace.QName	TAG_ROOTEDGE
static javax.xml.namespace.QName	TAG_ROW
static javax.xml.namespace.QName	TAG_SEQ
static javax.xml.namespace.QName	TAG_SET
static javax.xml.namespace.QName	TAG_STATE
static javax.xml.namespace.QName	TAG_STATES
static javax.xml.namespace.QName	TAG_TREE
static javax.xml.namespace.QName	TAG_TREES
static javax.xml.namespace.QName	TAG_UNCERTAIN
static java.lang.String	TYPE_CONTIN_CELLS
static java.lang.String	TYPE_CONTIN_SEQ
static java.lang.String	TYPE_DNA_CELLS
static java.lang.String	TYPE_DNA_SEQS
static java.lang.String	TYPE_FLOAT_NETWORK
static java.lang.String	TYPE_FLOAT_TREE
static java.lang.String	TYPE_INT_NETWORK
static java.lang.String	TYPE_INT_TREE
static java.lang.String	TYPE_LITERAL_META
static java.lang.String	TYPE_PROTEIN_CELLS
static java.lang.String	TYPE_PROTEIN_SEQS
static java.lang.String	TYPE_RESOURCE_META
static java.lang.String	TYPE_RESTRICTION_CELLS
static java.lang.String	TYPE_RESTRICTION_SEQS
static java.lang.String	TYPE_RNA_CELLS
static java.lang.String	TYPE_RNA_SEQS
static java.lang.String	TYPE_STANDARD_CELLS
static java.lang.String	TYPE_STANDARD_SEQ
static java.lang.String	UNDEFINED_OTU_ID_PREFIX
static java.lang.String	UNDEFINED_OTU_LABEL
static java.lang.String	UNDEFINED_OTUS_ID_PREFIX
static java.lang.String	UNDEFINED_OTUS_LABEL

Field Detail

NEXML_FORMAT_NAME

static final java.lang.String NEXML_FORMAT_NAME

See Also:

Constant Field Values

NEXML_VERSION

static final java.lang.String NEXML_VERSION

See Also:

Constant Field Values

NEXML_DEFAULT_NAMESPACE_PREFIX

static final java.lang.String NEXML_DEFAULT_NAMESPACE_PREFIX

See Also:

Constant Field Values

NEXML_NAMESPACE

static final java.lang.String NEXML_NAMESPACE

See Also:

Constant Field Values

TAG_ROOT

static final javax.xml.namespace.QName TAG_ROOT

TAG_META

static final javax.xml.namespace.QName TAG_META

TAG_SET

static final javax.xml.namespace.QName TAG_SET

TAG_OTUS

static final javax.xml.namespace.QName TAG_OTUS

TAG_OTU

static final javax.xml.namespace.QName TAG_OTU

TAG_CHARACTERS

static final javax.xml.namespace.QName TAG_CHARACTERS

TAG_FORMAT

static final javax.xml.namespace.QName TAG_FORMAT

TAG_STATES

static final javax.xml.namespace.QName TAG_STATES

TAG_STATE

static final javax.xml.namespace.QName TAG_STATE

TAG_POLYMORPHIC

static final javax.xml.namespace.QName TAG_POLYMORPHIC

TAG_UNCERTAIN

static final javax.xml.namespace.QName TAG_UNCERTAIN

TAG_MEMBER

static final javax.xml.namespace.QName TAG_MEMBER

TAG_CHAR

static final javax.xml.namespace.QName TAG_CHAR

TAG_MATRIX

static final javax.xml.namespace.QName TAG_MATRIX

TAG_ROW

static final javax.xml.namespace.QName TAG_ROW

TAG_CELL

static final javax.xml.namespace.QName TAG_CELL

TAG_SEQ

static final javax.xml.namespace.QName TAG_SEQ

TAG_TREES

static final javax.xml.namespace.QName TAG_TREES

TAG_TREE

static final javax.xml.namespace.QName TAG_TREE

TAG_NETWORK

static final javax.xml.namespace.QName TAG_NETWORK

TAG_NODE

static final javax.xml.namespace.QName TAG_NODE

TAG_EDGE

static final javax.xml.namespace.QName TAG_EDGE

TAG_ROOTEDGE

static final javax.xml.namespace.QName TAG_ROOTEDGE

ATTR_VERSION

static final javax.xml.namespace.QName ATTR_VERSION

ATTR_GENERATOR

static final javax.xml.namespace.QName ATTR_GENERATOR

ATTR_ID

static final javax.xml.namespace.QName ATTR_ID

ATTR_LABEL

static final javax.xml.namespace.QName ATTR_LABEL

ATTR_ABOUT

static final javax.xml.namespace.QName ATTR_ABOUT

ATTR_SINGLE_OTU_LINK

static final javax.xml.namespace.QName ATTR_SINGLE_OTU_LINK

ATTR_OTUS

static final javax.xml.namespace.QName ATTR_OTUS

ATTR_SYMBOL

static final javax.xml.namespace.QName ATTR_SYMBOL

ATTR_SINGLE_STATE_LINK

static final javax.xml.namespace.QName ATTR_SINGLE_STATE_LINK

ATTR_STATES

static final javax.xml.namespace.QName ATTR_STATES

ATTR_SINGLE_CHAR_LINK

static final javax.xml.namespace.QName ATTR_SINGLE_CHAR_LINK

ATTR_ROOT

static final javax.xml.namespace.QName ATTR_ROOT

ATTR_TOKENS

static final javax.xml.namespace.QName ATTR_TOKENS

ATTR_CODON_POSITION

static final javax.xml.namespace.QName ATTR_CODON_POSITION

ATTR_SOURCE

static final javax.xml.namespace.QName ATTR_SOURCE

ATTR_TARGET

static final javax.xml.namespace.QName ATTR_TARGET

ATTR_LENGTH

static final javax.xml.namespace.QName ATTR_LENGTH

ATTR_XSI_TYPE

static final javax.xml.namespace.QName ATTR_XSI_TYPE

ATTR_DATATYPE

static final javax.xml.namespace.QName ATTR_DATATYPE

ATTR_HREF

static final javax.xml.namespace.QName ATTR_HREF

ATTR_REL

static final javax.xml.namespace.QName ATTR_REL

ATTR_CONTENT

static final javax.xml.namespace.QName ATTR_CONTENT

ATTR_PROPERTY

static final javax.xml.namespace.QName ATTR_PROPERTY

ATTR_OTU_SET_LINKED_IDS

static final javax.xml.namespace.QName ATTR_OTU_SET_LINKED_IDS

ATTR_STATE_SET_LINKED_IDS

static final javax.xml.namespace.QName ATTR_STATE_SET_LINKED_IDS

ATTR_CHAR_SET_LINKED_IDS

static final javax.xml.namespace.QName ATTR_CHAR_SET_LINKED_IDS

ATTR_CELL_SET_LINKED_IDS

static final javax.xml.namespace.QName ATTR_CELL_SET_LINKED_IDS

ATTR_SEQUENCE_SET_LINKED_IDS

static final javax.xml.namespace.QName ATTR_SEQUENCE_SET_LINKED_IDS

ATTR_NODE_EDGE_SET_LINKED_NODE_IDS

static final javax.xml.namespace.QName ATTR_NODE_EDGE_SET_LINKED_NODE_IDS

ATTR_NODE_EDGE_SET_LINKED_EDGE_IDS

static final javax.xml.namespace.QName ATTR_NODE_EDGE_SET_LINKED_EDGE_IDS

ATTR_NODE_EDGE_SET_LINKED_ROOTEDGE_IDS

static final javax.xml.namespace.QName ATTR_NODE_EDGE_SET_LINKED_ROOTEDGE_IDS

ATTR_TREE_SET_LINKED_TREE_IDS

static final javax.xml.namespace.QName ATTR_TREE_SET_LINKED_TREE_IDS

ATTR_TREE_SET_LINKED_NETWORK_IDS

static final javax.xml.namespace.QName ATTR_TREE_SET_LINKED_NETWORK_IDS

TYPE_DNA_SEQS

static final java.lang.String TYPE_DNA_SEQS

See Also:

Constant Field Values

TYPE_DNA_CELLS

static final java.lang.String TYPE_DNA_CELLS

See Also:

Constant Field Values

TYPE_RNA_SEQS

static final java.lang.String TYPE_RNA_SEQS

See Also:

Constant Field Values

TYPE_RNA_CELLS

static final java.lang.String TYPE_RNA_CELLS

See Also:

Constant Field Values

TYPE_PROTEIN_SEQS

static final java.lang.String TYPE_PROTEIN_SEQS

See Also:

Constant Field Values

TYPE_PROTEIN_CELLS

static final java.lang.String TYPE_PROTEIN_CELLS

See Also:

Constant Field Values

TYPE_RESTRICTION_SEQS

static final java.lang.String TYPE_RESTRICTION_SEQS

See Also:

Constant Field Values

TYPE_RESTRICTION_CELLS

static final java.lang.String TYPE_RESTRICTION_CELLS

See Also:

Constant Field Values

TYPE_CONTIN_SEQ

static final java.lang.String TYPE_CONTIN_SEQ

See Also:

Constant Field Values

TYPE_CONTIN_CELLS

static final java.lang.String TYPE_CONTIN_CELLS

See Also:

Constant Field Values

TYPE_STANDARD_SEQ

static final java.lang.String TYPE_STANDARD_SEQ

See Also:

Constant Field Values

TYPE_STANDARD_CELLS

static final java.lang.String TYPE_STANDARD_CELLS

See Also:

Constant Field Values

TYPE_FLOAT_TREE

static final java.lang.String TYPE_FLOAT_TREE

See Also:

Constant Field Values

TYPE_INT_TREE

static final java.lang.String TYPE_INT_TREE

See Also:

Constant Field Values

TYPE_FLOAT_NETWORK

static final java.lang.String TYPE_FLOAT_NETWORK

See Also:

Constant Field Values

TYPE_INT_NETWORK

static final java.lang.String TYPE_INT_NETWORK

See Also:

Constant Field Values

TYPE_LITERAL_META

static final java.lang.String TYPE_LITERAL_META

See Also:

Constant Field Values

TYPE_RESOURCE_META

static final java.lang.String TYPE_RESOURCE_META

See Also:

Constant Field Values

UNDEFINED_OTUS_ID_PREFIX

static final java.lang.String UNDEFINED_OTUS_ID_PREFIX

See Also:

Constant Field Values

UNDEFINED_OTUS_LABEL

static final java.lang.String UNDEFINED_OTUS_LABEL

See Also:

Constant Field Values

UNDEFINED_OTU_ID_PREFIX

static final java.lang.String UNDEFINED_OTU_ID_PREFIX

See Also:

Constant Field Values

UNDEFINED_OTU_LABEL

static final java.lang.String UNDEFINED_OTU_LABEL

See Also:

Constant Field Values

DEFAULT_TOKEN_DEFINITION_SET_ID_PREFIX

static final java.lang.String DEFAULT_TOKEN_DEFINITION_SET_ID_PREFIX

See Also:

Constant Field Values

NEXML_NAMESPACE_PREFIX

static final java.lang.String NEXML_NAMESPACE_PREFIX

See Also:

Constant Field Values

NEXML_PREDICATE_NAMESPACE

static final java.lang.String NEXML_PREDICATE_NAMESPACE

See Also:

Constant Field Values

PREDICATE_CHAR_ATTR_TOKENS

static final javax.xml.namespace.QName PREDICATE_CHAR_ATTR_TOKENS

PREDICATE_CHAR_ATTR_CODON_POSITION

static final javax.xml.namespace.QName PREDICATE_CHAR_ATTR_CODON_POSITION

PREDICATE_FORMAT

static final javax.xml.namespace.QName PREDICATE_FORMAT

PREDICATE_MATRIX

static final javax.xml.namespace.QName PREDICATE_MATRIX

PREDICATE_ORIGINAL_LABEL

static final javax.xml.namespace.QName PREDICATE_ORIGINAL_LABEL

PREDICATE_ORIGINAL_TOKEN_NAME

static final javax.xml.namespace.QName PREDICATE_ORIGINAL_TOKEN_NAME