info.bioinfweb.jphyloio.events

Class CharacterSetIntervalEvent

java.lang.Object

info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent

info.bioinfweb.jphyloio.events.CharacterSetIntervalEvent

All Implemented Interfaces:

JPhyloIOEvent

public class CharacterSetIntervalEvent
extends ConcreteJPhyloIOEvent

Event that indicates that new information on a character set has been read.

This event defines an interval belonging to the current character set. All events of this type must be enclosed between a start and an end event with content type EventContentType.CHARACTER_SET. The start event will define the ID and the name of the set.

Note that in contrast to e.g. many alignment editors or the character set definitions in Nexus, column indices in JPhyloIO start with 0 and not with 1. The indices used by instances of this class must follow this convention and readers and writers will convert indices according to the conventions of their format.

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
CharacterSetIntervalEvent(long start, long end) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
long	getEnd() The first index after the new segment to be add to the character set with the specified name.
long	getStart() The first position of the new segment to be add to the character set with the specified name.

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

Constructor Detail

CharacterSetIntervalEvent

public CharacterSetIntervalEvent(long start,
                                 long end)

Creates a new instance of this class.

A segment ranges from getStart() to getEnd() - 1.

Parameters:

start - the index of the first position of the sequence segment to be add to the specified character set

end - the first index after the end of the sequence segment to be add to the specified character set

Throws:

java.lang.IndexOutOfBoundsException - if start or end are below 0

java.lang.IllegalArgumentException - if end is not greater than start (If a character set shall have no length, just omit nested interval event.)

Method Detail

getStart

public long getStart()

The first position of the new segment to be add to the character set with the specified name.

A segment ranges from getStart() to getEnd() - 1.

Returns:

the first position to be included in the character set

getEnd

public long getEnd()

The first index after the new segment to be add to the character set with the specified name.

A segment ranges from getStart() to getEnd() - 1.

Returns:

the first index after the segment to be add