info.bioinfweb.jphyloio.events

Class EdgeEvent

java.lang.Object

info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent

info.bioinfweb.jphyloio.events.LabeledEvent

info.bioinfweb.jphyloio.events.LabeledIDEvent

info.bioinfweb.jphyloio.events.EdgeEvent

All Implemented Interfaces:

JPhyloIOEvent

public class EdgeEvent
extends LabeledIDEvent

Event indicating an edge in a tree or network. Edges are directed and connect a source node with a target node, which are references by their IDs. If an edge represents a root of a tree or network, its source node ID reference is null. All referenced nodes must have been defined in the event stream before this event is fired.

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:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
EdgeEvent(java.lang.String id, java.lang.String label, java.lang.String targetID, double length) Creates a new instance of this class that represents a root edge.
EdgeEvent(java.lang.String id, java.lang.String label, java.lang.String sourceID, java.lang.String targetID, double length) Creates a new instance of this class that represents an internal edge or a root edge.

Method Summary

Modifier and Type	Method and Description
double	getLength() Returns the length of this edge.
java.lang.String	getSourceID() Returns the ID of the source node linked by this edge.
java.lang.String	getTargetID() Returns the ID of the target node linked by this edge.
boolean	hasLength() Indicates whether this edge has a defined length.
boolean	hasSource() Indicates whether this edge has a source node and can therefore be considered a root edge.
java.lang.String	toString()

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, wait, wait, wait

Constructor Detail

EdgeEvent

public EdgeEvent(java.lang.String id,
                 java.lang.String label,
                 java.lang.String sourceID,
                 java.lang.String targetID,
                 double length)

Creates a new instance of this class that represents an internal edge or a root edge. If sourceID is null the content type will be EventContentType.ROOT_EDGE and otherwise it will be EventContentType.EDGE.

Parameters:

id - the unique ID associated with the represented edge (Must be a valid NCName.)

label - an optional label associated with this edge (Maybe null.)

sourceID - the ID of the source node of this edge (Maybe null if a root edge shall be created.)

targetID - the ID of the target node of this edge

length - an optional lengths of this edge (Maybe Double.NaN if no length is given.)

Throws:

java.lang.NullPointerException - if id, sourceID or targetID are null

java.lang.IllegalArgumentException - if id, sourceID or targetID are not a valid NCNames

EdgeEvent

public EdgeEvent(java.lang.String id,
                 java.lang.String label,
                 java.lang.String targetID,
                 double length)

Creates a new instance of this class that represents a root edge.

Parameters:

id - the unique ID associated with the represented edge (Must be a valid NCName.)

label - an optional label associated with this edge (Maybe null.)

targetID - the ID of the target node of this edge

length - an optional lengths of this edge (Maybe Double.NaN if no length is given.)

Throws:

java.lang.NullPointerException - if id or targetID are null

java.lang.IllegalArgumentException - if id or targetID are not a valid NCNames

Method Detail

getSourceID

public java.lang.String getSourceID()

Returns the ID of the source node linked by this edge.

Returns:

the ID of the source node or null if this event represents a root edge

See Also:

hasSource()

hasSource

public boolean hasSource()

Indicates whether this edge has a source node and can therefore be considered a root edge.

If this method returns true, getSourceID() will return null.

Returns:

true if this edge has a source node or false otherwise

getTargetID

public java.lang.String getTargetID()

Returns the ID of the target node linked by this edge.

Returns:

the ID of the target node (never null)

getLength

public double getLength()

Returns the length of this edge.

Additional information (e.g. on length confidence intervals) maybe given in upcoming nested metaevents.

Returns:

the length of this edge or Double.NaN if this edge does not have a defined length

hasLength

public boolean hasLength()

Indicates whether this edge has a defined length.

If this method returns false, getLength() will return Double#NaN.

Returns:

true if this edge has a defined length or false otherwise

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object