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

NodeData()

Method Summary

void	addDistribution(Distribution distribution)
void	addReference(Reference reference)
void	addSequence(Sequence sequence)
void	addTaxonomy(Taxonomy taxonomy)
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() Convenience method -- always returns the first Distribution.
Distribution	getDistribution(int index)
java.util.List<Distribution>	getDistributions()
Event	getEvent()
Identifier	getNodeIdentifier()
java.lang.String	getNodeName()
java.util.List<NodeVisualization>	getNodeVisualizations()
PropertiesMap	getProperties()
Reference	getReference() Convenience method -- always returns the first Reference.
Reference	getReference(int index)
java.util.List<Reference>	getReferences()
Sequence	getSequence() Convenience method -- always returns the first Sequence.
Sequence	getSequence(int index)
java.util.List<Sequence>	getSequences()
java.util.List<Taxonomy>	getTaxonomies()
Taxonomy	getTaxonomy() Convenience method -- always returns the first Taxonomy.
Taxonomy	getTaxonomy(int index)
java.util.List<java.lang.Double>	getVector()
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) Convenience method -- always sets the first Distribution.
void	setDistribution(int index, Distribution distribution)
void	setEvent(Event event)
void	setNodeIdentifier(Identifier node_identifier)
void	setNodeName(java.lang.String node_name)
void	setNodeVisualizations(java.util.List<NodeVisualization> _node_visualizations)
void	setProperties(PropertiesMap custom_data)
void	setReference(int index, Reference reference)
void	setReference(Reference reference) Convenience method -- always sets the first Reference.
void	setSequence(int index, Sequence sequence)
void	setSequence(Sequence sequence) Convenience method -- always sets the first Sequence.
void	setTaxonomy(int index, Taxonomy taxonomy)
void	setTaxonomy(Taxonomy taxonomy) Convenience method -- always sets the first Taxonomy.
void	setVector(java.util.List<java.lang.Double> vector)
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

addDistribution

public void addDistribution(Distribution distribution)

addReference

public void addReference(Reference reference)

addSequence

public void addSequence(Sequence sequence)

addTaxonomy

public void addTaxonomy(Taxonomy taxonomy)

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()

Convenience method -- always returns the first Distribution.

Returns:

Distribution

getDistribution

public Distribution getDistribution(int index)

getDistributions

public java.util.List<Distribution> getDistributions()

getEvent

public Event getEvent()

getNodeIdentifier

public Identifier getNodeIdentifier()

getProperties

public PropertiesMap getProperties()

getReference

public Reference getReference()

Convenience method -- always returns the first Reference.

Returns:

Reference

getReference

public Reference getReference(int index)

getReferences

public java.util.List<Reference> getReferences()

getSequence

public Sequence getSequence()

Convenience method -- always returns the first Sequence.

Returns:

Sequence

getSequence

public Sequence getSequence(int index)

getSequences

public java.util.List<Sequence> getSequences()

getTaxonomies

public java.util.List<Taxonomy> getTaxonomies()

getTaxonomy

public Taxonomy getTaxonomy()

Convenience method -- always returns the first Taxonomy.

Returns:

Taxonomy

getTaxonomy

public Taxonomy getTaxonomy(int index)

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)

Convenience method -- always sets the first Distribution.

setDistribution

public void setDistribution(int index,
                            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(int index,
                         Reference reference)

setReference

public void setReference(Reference reference)

Convenience method -- always sets the first Reference.

setSequence

public void setSequence(int index,
                        Sequence sequence)

setSequence

public void setSequence(Sequence sequence)

Convenience method -- always sets the first Sequence.

setTaxonomy

public void setTaxonomy(int index,
                        Taxonomy taxonomy)

setTaxonomy

public void setTaxonomy(Taxonomy taxonomy)

Convenience method -- always sets the first 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

setVector

public void setVector(java.util.List<java.lang.Double> vector)

getVector

public java.util.List<java.lang.Double> getVector()

getNodeName

public java.lang.String getNodeName()

setNodeName

public void setNodeName(java.lang.String node_name)

setNodeVisualizations

public void setNodeVisualizations(java.util.List<NodeVisualization> _node_visualizations)

getNodeVisualizations

public java.util.List<NodeVisualization> getNodeVisualizations()