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()

• 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()

• isEmpty

  public boolean isEmpty()

• isHasDate

  public boolean isHasDate()

• isHasDistribution

  public boolean isHasDistribution()

• isHasEvent

  public boolean isHasEvent()

• 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)

• 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)

• setNodeVisualData

  public void setNodeVisualData​(NodeVisualData node_visual_data)

• getNodeVisualData

  public NodeVisualData getNodeVisualData()