info.bioinfweb.jphyloio.events.type

Enum EventContentType

java.lang.Object

java.lang.Enum<EventContentType>

info.bioinfweb.jphyloio.events.type.EventContentType

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<EventContentType>

public enum EventContentType
extends java.lang.Enum<EventContentType>

Enumerates the content types of a JPhyloIOEvent. Elements of each content type can either occur in one version in combination with EventTopologyType.SOLE or in two versions in combination with EventTopologyType.START or EventTopologyType.END.

The documentation of the single types includes information on which event classes are used with each type and whether it is separated into a start and end event or not. In addition, the documentation of JPhyloIOEventReader contains a full grammar of JPhyloIO event streams.

Author:

Ben Stöver, Sarah Wiechers

See Also:

JPhyloIOEventReader, EventTopologyType, EventType

Enum Constant Summary

Enum Constants

Enum Constant and Description
ALIGNMENT Indicates the start or the end of the contents of a matrix.
CHARACTER_DEFINITION Indicates a defined character (alignment column).
CHARACTER_SET Indicates the start or end of a sequence of CHARACTER_SET_INTERVAL events.
CHARACTER_SET_INTERVAL Indicates a single interval of a character set.
COMMENT Indicates a comment found in the underlying data source.
DOCUMENT Indicates the start or the end of the read document.
EDGE Indicates an edge in a phylogenetic tree or network.
LITERAL_META Indicates the start or the end of a literal meta information.
LITERAL_META_CONTENT Indicates literal metadata content was found in the underlying data source.
NETWORK Indicates the start or the end of the contents of a phylogenetic network.
NODE Indicates a node in a phylogenetic tree or network.
NODE_EDGE_SET Indicates the start or end of a sequence of SET_ELEMENT events that define a set of node and edges (including root edges).
OTU Indicates the start or the end of an OTU/taxon definition.
OTU_LIST Indicates the start or the end of a list of OTU/taxon definitions.
OTU_SET Indicates the start or end of a sequence of SET_ELEMENT events that define a set of OTUs.
RESOURCE_META Indicates the start or the end of a resource meta information.
ROOT_EDGE Indicates a root edge in a phylogenetic tree.
SEQUENCE Indicates the start or the end of the contents of a sequence in a matrix.
SEQUENCE_SET Indicates the start or end of a sequence of SET_ELEMENT events that define a set of sequences.
SEQUENCE_TOKENS Indicates a number of sequence tokens.
SET_ELEMENT Indicates a member of a set that is linked by its ID.
SINGLE_SEQUENCE_TOKEN Indicates a number a single sequence token.
SINGLE_TOKEN_DEFINITION Indicates the definition of a single sequence token symbol.
TOKEN_SET_DEFINITION Indicates the start or end of a token set definition.
TREE Indicates the start or the end of the contents of a phylogenetic tree.
TREE_NETWORK_GROUP Indicates the start or the end of a sequence of phylogenetic trees and network.
TREE_NETWORK_SET Indicates the start or end of a sequence of SET_ELEMENT events that define a set of trees and networks.
UNKNOWN_COMMAND Events of this type are used by some readers to provide the application with contents of unknown commands in a format.

Method Summary

Modifier and Type	Method and Description
static EventContentType	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static EventContentType[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

DOCUMENT

public static final EventContentType DOCUMENT

Indicates the start or the end of the read document.

Both start and end events of this type are instances of ConcreteJPhyloIOEvent.

This content type will never be combined with EventTopologyType.SOLE.

RESOURCE_META

public static final EventContentType RESOURCE_META

Indicates the start or the end of a resource meta information.

Start events of this type are instances of ResourceMetadataEvent, end events are instances of ConcreteJPhyloIOEvent.

This content type will never be combined with EventTopologyType.SOLE.

LITERAL_META

public static final EventContentType LITERAL_META

Indicates the start or the end of a literal meta information.

Start events of this type are instances of LiteralMetadataEvent, end events are instances of ConcreteJPhyloIOEvent.

This content type will never be combined with EventTopologyType.SOLE.

LITERAL_META_CONTENT

public static final EventContentType LITERAL_META_CONTENT

Indicates literal metadata content was found in the underlying data source.

Events of this type are instances of LiteralMetadataContentEvent and always have the topology type EventTopologyType.SOLE and therefore no nested events.

UNKNOWN_COMMAND

public static final EventContentType UNKNOWN_COMMAND

Events of this type are used by some readers to provide the application with contents of unknown commands in a format.

Events of this type are instances of UnknownCommandEvent and always have the topology type EventTopologyType.SOLE.

COMMENT

public static final EventContentType COMMENT

Indicates a comment found in the underlying data source.

Events of this type are instances of CommentEvent and always have the topology type EventTopologyType.SOLE and therefore no nested events.

OTU_LIST

public static final EventContentType OTU_LIST

Indicates the start or the end of a list of OTU/taxon definitions.

Start events of this type are instances of LabeledIDEvent, end events are instances of ConcreteJPhyloIOEvent.

This content type will never be combined with EventTopologyType.SOLE.

OTU

public static final EventContentType OTU

Indicates the start or the end of an OTU/taxon definition.

Start events of this type are instances of LabeledIDEvent, end events are instances of ConcreteJPhyloIOEvent.

This content type will never be combined with EventTopologyType.SOLE.

ALIGNMENT

public static final EventContentType ALIGNMENT

Indicates the start or the end of the contents of a matrix.

Start events of this type are instances of LinkedLabeledIDEvent, end events are instances of ConcreteJPhyloIOEvent. Start events optionally link an OTU list.

This content type will never be combined with EventTopologyType.SOLE.

CHARACTER_DEFINITION

public static final EventContentType CHARACTER_DEFINITION

Indicates a defined character (alignment column). Events of this type may have nested elements. Events of this type are optional and most readers will create them only if a character label or associated metadata is present or if an ID has explicitly been defined in the document that is read.

Start events of this type are instances of CharacterDefinitionEvent, end events are instances of ConcreteJPhyloIOEvent.

This content type will never be combined with EventTopologyType.SOLE.

SEQUENCE

public static final EventContentType SEQUENCE

Indicates the start or the end of the contents of a sequence in a matrix.

Start events of this type are instances of LinkedLabeledIDEvent, end events are instances of PartEndEvent. Start events optionally link a single OTU.

This content type will never be combined with EventTopologyType.SOLE.

SEQUENCE_TOKENS

public static final EventContentType SEQUENCE_TOKENS

Indicates a number of sequence tokens. Events of this type never have nested elements.

Events of this type are instances of SequenceTokensEvent and always have the topology type EventTopologyType.SOLE.

SINGLE_SEQUENCE_TOKEN

public static final EventContentType SINGLE_SEQUENCE_TOKEN

Indicates a number a single sequence token. Events of this type may have nested elements.

Start events of this type are instances of SingleSequenceTokenEvent, end events are instances of ConcreteJPhyloIOEvent.

This content type will never be combined with EventTopologyType.SOLE.

TREE_NETWORK_GROUP

public static final EventContentType TREE_NETWORK_GROUP

Indicates the start or the end of a sequence of phylogenetic trees and network. (Such group corresponds e.g. to the contents of a TREES block in Nexus or a trees tag in NeXML.)

Start events of this type are instances of LinkedLabeledIDEvent, end events are instances of ConcreteJPhyloIOEvent. Start events optionally link an OTU list that is valid for all contained trees and networks.

This content type will never be combined with EventTopologyType.SOLE.

NETWORK

public static final EventContentType NETWORK

Indicates the start or the end of the contents of a phylogenetic network.

Start events of this type are instances of LabeledIDEvent, end events are instances of ConcreteJPhyloIOEvent.

This content type will never be combined with EventTopologyType.SOLE.

TREE

public static final EventContentType TREE

Indicates the start or the end of the contents of a phylogenetic tree.

Start events of this type are instances of LabeledIDEvent, end events are instances of ConcreteJPhyloIOEvent.

This content type will never be combined with EventTopologyType.SOLE.

In some formats metaevents indicating whether the tree shall be displayed rooted or unrooted may follow the start event of this type.

NODE

public static final EventContentType NODE

Indicates a node in a phylogenetic tree or network.

Start events of this type are instances of NodeEvent, end events are instances of ConcreteJPhyloIOEvent. Start events optionally link a single OTU.

This content type will never be combined with EventTopologyType.SOLE.

EDGE

public static final EventContentType EDGE

Indicates an edge in a phylogenetic tree or network.

Start events of this type are instances of EdgeEvent, end events are instances of ConcreteJPhyloIOEvent.

This content type will never be combined with EventTopologyType.SOLE.

ROOT_EDGE

public static final EventContentType ROOT_EDGE

Indicates a root edge in a phylogenetic tree. Events of this type are not allowed to be nested under networks and at most one may be nested under a tree.

Start events of this type are instances of EdgeEvent, end events are instances of ConcreteJPhyloIOEvent.

This content type will never be combined with EventTopologyType.SOLE.

TOKEN_SET_DEFINITION

public static final EventContentType TOKEN_SET_DEFINITION

Indicates the start or end of a token set definition.

Start events of this type are instances of TokenSetDefinitionEvent, end events are instances of ConcreteJPhyloIOEvent.

This content type will never be combined with EventTopologyType.SOLE.

SINGLE_TOKEN_DEFINITION

public static final EventContentType SINGLE_TOKEN_DEFINITION

Indicates the definition of a single sequence token symbol. Such events are nested in TOKEN_SET_DEFINITION.

Start events of this type are instances of SingleTokenDefinitionEvent, end events are instances of ConcreteJPhyloIOEvent.

This content type will never be combined with EventTopologyType.SOLE.

CHARACTER_SET

public static final EventContentType CHARACTER_SET

Indicates the start or end of a sequence of CHARACTER_SET_INTERVAL events.

Start events of this type are instances of LinkedLabeledIDEvent, end events are instances of PartEndEvent. The start events link a matrix by their ID using LinkedLabeledIDEvent.getLinkedID().

This content type will never be combined with EventTopologyType.SOLE.

CHARACTER_SET_INTERVAL

public static final EventContentType CHARACTER_SET_INTERVAL

Indicates a single interval of a character set. Such events are nested in CHARACTER_SET and TOKEN_SET_DEFINITION.

Events of this type are instances of CharacterSetIntervalEvent and always have the topology type EventTopologyType.SOLE.

SET_ELEMENT

public static final EventContentType SET_ELEMENT

Indicates a member of a set that is linked by its ID. Such events are nested e.g. in OTU_SET and TREE_NETWORK_SET. (Note that character and token sets represent their members in a different way).

Events of this type are instances of SetElementEvent and always have the topology type EventTopologyType.SOLE.

OTU_SET

public static final EventContentType OTU_SET

Indicates the start or end of a sequence of SET_ELEMENT events that define a set of OTUs.

Start events of this type are instances of LinkedLabeledIDEvent, end events are instances of PartEndEvent. The start events link an OTU list by their ID using LinkedLabeledIDEvent.getLinkedID().

This content type will never be combined with EventTopologyType.SOLE.

SEQUENCE_SET

public static final EventContentType SEQUENCE_SET

Indicates the start or end of a sequence of SET_ELEMENT events that define a set of sequences.

Start events of this type are instances of LinkedLabeledIDEvent, end events are instances of PartEndEvent. The start events link an alignment by their ID using LinkedLabeledIDEvent.getLinkedID().

This content type will never be combined with EventTopologyType.SOLE.

TREE_NETWORK_SET

public static final EventContentType TREE_NETWORK_SET

Indicates the start or end of a sequence of SET_ELEMENT events that define a set of trees and networks.

Start events of this type are instances of LinkedLabeledIDEvent, end events are instances of PartEndEvent. The start events link a tree/network group by their ID using LinkedLabeledIDEvent.getLinkedID().

This content type will never be combined with EventTopologyType.SOLE.

NODE_EDGE_SET

public static final EventContentType NODE_EDGE_SET

Indicates the start or end of a sequence of SET_ELEMENT events that define a set of node and edges (including root edges).

Start events of this type are instances of LinkedLabeledIDEvent, end events are instances of PartEndEvent. The start events link a tree or network by their ID using LinkedLabeledIDEvent.getLinkedID().

This content type will never be combined with EventTopologyType.SOLE.

Method Detail

values

public static EventContentType[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (EventContentType c : EventContentType.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static EventContentType valueOf(java.lang.String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

java.lang.IllegalArgumentException - if this enum type has no constant with the specified name

java.lang.NullPointerException - if the argument is null