info.bioinfweb.jphyloio.events

Class NodeEvent

java.lang.Object

info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent

info.bioinfweb.jphyloio.events.LabeledEvent

info.bioinfweb.jphyloio.events.LabeledIDEvent

info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent

info.bioinfweb.jphyloio.events.NodeEvent

All Implemented Interfaces:

JPhyloIOEvent, LinkedIDEvent

public class NodeEvent
extends LinkedLabeledIDEvent

Event indicating a node in a tree or network.

This event is a start event, which is followed by an end event of the same content type. Comment and metainformation events maybe nested between this and its according end event. (See the description of JPhyloIOEventReader for the complete grammar definition of JPhyloIO event streams.)

Author:

Sarah Wiechers, Ben Stöver

Constructor Summary

Constructors

Constructor and Description
NodeEvent(java.lang.String id, java.lang.String label, java.lang.String linkedOTUID, boolean isRootNode)

Method Summary

Modifier and Type	Method and Description
boolean	isRootNode() Indicates whether this node is a root of its tree or network.

Methods inherited from class info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent

getLinkedID, hasLink

Methods inherited from class info.bioinfweb.jphyloio.events.LabeledIDEvent

checkID, getID

Methods inherited from class info.bioinfweb.jphyloio.events.LabeledEvent

getLabel, hasLabel

Methods inherited from class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent

asCharacterDefinitionEvent, asCharacterSetIntervalEvent, asCommentEvent, asEdgeEvent, asLabeledIDEvent, asLinkedLabeledIDEvent, asLiteralMetadataContentEvent, asLiteralMetadataEvent, asNodeEvent, asPartEndEvent, asResourceMetadataEvent, asSequenceTokensEvent, asSetElementEvent, asSingleSequenceTokenEvent, asSingleTokenDefinitionEvent, asTokenSetDefinitionEvent, asUnknownCommandEvent, createEndEvent, getType

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface info.bioinfweb.jphyloio.events.JPhyloIOEvent

asCharacterDefinitionEvent, asCharacterSetIntervalEvent, asCommentEvent, asEdgeEvent, asLabeledIDEvent, asLinkedLabeledIDEvent, asLiteralMetadataContentEvent, asLiteralMetadataEvent, asNodeEvent, asPartEndEvent, asResourceMetadataEvent, asSequenceTokensEvent, asSetElementEvent, asSingleSequenceTokenEvent, asSingleTokenDefinitionEvent, asTokenSetDefinitionEvent, asUnknownCommandEvent, getType

Constructor Detail

NodeEvent

public NodeEvent(java.lang.String id,
                 java.lang.String label,
                 java.lang.String linkedOTUID,
                 boolean isRootNode)

Method Detail

isRootNode

public boolean isRootNode()

Indicates whether this node is a root of its tree or network. One tree or network may contain alternative root nodes, but not all formats will support this.

Note that in case of trees this property indicates that this node can be one (alternative) root in a semantic sense. The topological representation of the tree is independent of this and only determined by how its nodes are linked by edge events. The presence of a root edge defining a length of a tree branch leading to the node that is topologically at the root of the tree is also fully independent of this property.

In NeXML root nodes are identified by having a root="true" attribute. In Newick and Nexus only the property of the topological root node is modeled by the [&R] or [&U] hot comments preceding a Newick string. The same applies for the rooted attribute of the phylogeny tag in PhyloXML.

Returns:

true if this node is a possible root or false otherwise