public class NodeData extends java.lang.Object implements PhylogenyData
Constructor and Description |
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NodeData() |
Modifier and Type | Method and Description |
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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.
|
public void addDistribution(Distribution distribution)
public void addReference(Reference reference)
public void addSequence(Sequence sequence)
public void addTaxonomy(Taxonomy taxonomy)
public java.lang.StringBuffer asSimpleText()
asSimpleText
in interface PhylogenyData
public java.lang.StringBuffer asText()
asText
in interface PhylogenyData
public PhylogenyData copy()
PhylogenyData
copy
in interface PhylogenyData
public BinaryCharacters getBinaryCharacters()
public Date getDate()
public Distribution getDistribution()
public Distribution getDistribution(int index)
public java.util.List<Distribution> getDistributions()
public Event getEvent()
public Identifier getNodeIdentifier()
public PropertiesMap getProperties()
public Reference getReference()
public Reference getReference(int index)
public java.util.List<Reference> getReferences()
public Sequence getSequence()
public Sequence getSequence(int index)
public java.util.List<Sequence> getSequences()
public java.util.List<Taxonomy> getTaxonomies()
public Taxonomy getTaxonomy()
public Taxonomy getTaxonomy(int index)
public boolean isEqual(PhylogenyData data)
PhylogenyData
isEqual
in interface PhylogenyData
public boolean isHasBinaryCharacters()
public boolean isHasDate()
public boolean isHasDistribution()
public boolean isHasEvent()
public boolean isHasNodeIdentifier()
public boolean isHasProperties()
public boolean isHasReference()
public boolean isHasSequence()
public boolean isHasTaxonomy()
public void setBinaryCharacters(BinaryCharacters binary_characters)
public void setDate(Date date)
public void setDistribution(Distribution distribution)
public void setDistribution(int index, Distribution distribution)
public void setEvent(Event event)
public void setNodeIdentifier(Identifier node_identifier)
public void setProperties(PropertiesMap custom_data)
public void setReference(int index, Reference reference)
public void setReference(Reference reference)
public void setSequence(int index, Sequence sequence)
public void setSequence(Sequence sequence)
public void setTaxonomy(int index, Taxonomy taxonomy)
public void setTaxonomy(Taxonomy taxonomy)
public java.lang.StringBuffer toNHX()
toNHX
in interface PhylogenyData
public void toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation) throws java.io.IOException
PhylogenyData
toPhyloXML
in interface PhylogenyData
java.io.IOException
public void setVector(java.util.List<java.lang.Double> vector)
public java.util.List<java.lang.Double> getVector()
public java.lang.String getNodeName()
public void setNodeName(java.lang.String node_name)
public void setNodeVisualizations(java.util.List<NodeVisualization> _node_visualizations)
public java.util.List<NodeVisualization> getNodeVisualizations()