org.forester.phylogeny.data

Class NodeData

java.lang.Object

org.forester.phylogeny.data.NodeData

All Implemented Interfaces:

PhylogenyData

public class NodeData
extends java.lang.Object
implements PhylogenyData

Constructor Summary

Constructors

Constructor and Description
NodeData()

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.StringBuffer	asSimpleText()
java.lang.StringBuffer	asText()
PhylogenyData	copy() Creates a new PhylogenyData object with identical values as this PhylogenyData.
BinaryCharacters	getBinaryCharacters()
Date	getDate()
Distribution	getDistribution()
Event	getEvent()
Identifier	getNodeIdentifier()
PropertiesMap	getProperties()
Reference	getReference()
Sequence	getSequence()
Taxonomy	getTaxonomy()
boolean	isEqual(PhylogenyData data) Compares this PhylogenyData to PhylogenyData data.
boolean	isHasBinaryCharacters()
boolean	isHasDate()
boolean	isHasDistribution()
boolean	isHasEvent()
boolean	isHasNodeIdentifier()
boolean	isHasProperties()
boolean	isHasReference()
boolean	isHasSequence()
boolean	isHasTaxonomy()
void	setBinaryCharacters(BinaryCharacters binary_characters)
void	setDate(Date date)
void	setDistribution(Distribution distribution)
void	setEvent(Event event)
void	setNodeIdentifier(Identifier node_identifier)
void	setProperties(PropertiesMap custom_data)
void	setReference(Reference reference)
void	setSequence(Sequence sequence)
void	setTaxonomy(Taxonomy taxonomy)
java.lang.StringBuffer	toNHX()
void	toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation) Writes a phyloXML representation of this phylogeny data.

Methods inherited from class java.lang.Object

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

Constructor Detail

NodeData

public NodeData()

Method Detail

asSimpleText

public java.lang.StringBuffer asSimpleText()

Specified by:

asSimpleText in interface PhylogenyData

asText

public java.lang.StringBuffer asText()

Specified by:

asText in interface PhylogenyData

copy

public PhylogenyData copy()

Description copied from interface: PhylogenyData

Creates a new PhylogenyData object with identical values as this PhylogenyData. This ~should~ return a deep copy, but not there yet.

Specified by:

copy in interface PhylogenyData

Returns:

a ~deep~ copy of this PhylogenyData

getBinaryCharacters

public BinaryCharacters getBinaryCharacters()

getDate

public Date getDate()

getDistribution

public Distribution getDistribution()

getEvent

public Event getEvent()

getNodeIdentifier

public Identifier getNodeIdentifier()

getProperties

public PropertiesMap getProperties()

getReference

public Reference getReference()

getSequence

public Sequence getSequence()

getTaxonomy

public Taxonomy getTaxonomy()

isEqual

public boolean isEqual(PhylogenyData data)

Description copied from interface: PhylogenyData

Compares this PhylogenyData to PhylogenyData data. In general, this should return true if and only if all fiels are exactly identical.

Specified by:

isEqual in interface PhylogenyData

Returns:

in general, true if and only if all fiels are exactly identical, false otherwise

isHasBinaryCharacters

public boolean isHasBinaryCharacters()

isHasDate

public boolean isHasDate()

isHasDistribution

public boolean isHasDistribution()

isHasEvent

public boolean isHasEvent()

isHasNodeIdentifier

public boolean isHasNodeIdentifier()

isHasProperties

public boolean isHasProperties()

isHasReference

public boolean isHasReference()

isHasSequence

public boolean isHasSequence()

isHasTaxonomy

public boolean isHasTaxonomy()

setBinaryCharacters

public void setBinaryCharacters(BinaryCharacters binary_characters)

setDate

public void setDate(Date date)

setDistribution

public void setDistribution(Distribution distribution)

setEvent

public void setEvent(Event event)

setNodeIdentifier

public void setNodeIdentifier(Identifier node_identifier)

setProperties

public void setProperties(PropertiesMap custom_data)

setReference

public void setReference(Reference reference)

setSequence

public void setSequence(Sequence sequence)

setTaxonomy

public void setTaxonomy(Taxonomy taxonomy)

toNHX

public java.lang.StringBuffer toNHX()

Specified by:

toNHX in interface PhylogenyData

toPhyloXML

public void toPhyloXML(java.io.Writer writer,
              int level,
              java.lang.String indentation)
                throws java.io.IOException

Description copied from interface: PhylogenyData

Writes a phyloXML representation of this phylogeny data.

Specified by:

toPhyloXML in interface PhylogenyData

Throws:

java.io.IOException