Package org.forester.phylogeny.data

Class NodeData

java.lang.Object
org.forester.phylogeny.data.NodeData
All Implemented Interfaces:
PhylogenyData
public class NodeData extends Object implements PhylogenyData

  • Constructor Details

    • NodeData

      public NodeData()

  • Method Details

    • 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 StringBuffer asSimpleText()
      Specified by:
      asSimpleText in interface PhylogenyData

    • asText

      public 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 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 List<Reference> getReferences()

    • getSequence

      public Sequence getSequence()
      Convenience method -- always returns the first Sequence.
      Returns:
      Sequence

    • getSequence

      public Sequence getSequence(int index)

    • getSequences

      public List<Sequence> getSequences()

    • getTaxonomies

      public 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 StringBuffer toNHX()
      Specified by:
      toNHX in interface PhylogenyData

    • toPhyloXML

      public void toPhyloXML(Writer writer, int level, String indentation) throws IOException
      Description copied from interface: PhylogenyData
      Writes a phyloXML representation of this phylogeny data.
      Specified by:
      toPhyloXML in interface PhylogenyData
      Throws:
      IOException

    • setVector

      public void setVector(List<Double> vector)

    • getVector

      public List<Double> getVector()

    • getNodeName

      public String getNodeName()

    • setNodeName

      public void setNodeName(String node_name)

    • setNodeVisualData

      public void setNodeVisualData(NodeVisualData node_visual_data)

    • getNodeVisualData

      public NodeVisualData getNodeVisualData()