Class NodeData

    • 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)
      • 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
      • 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()
      • 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)