Class Taxonomy

    • Constructor Detail

      • Taxonomy

        public Taxonomy()
    • Method Detail

      • 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
      • equals

        public boolean equals​(java.lang.Object o)
        Overrides:
        equals in class java.lang.Object
      • getAuthority

        public java.lang.String getAuthority()
      • getCommonName

        public java.lang.String getCommonName()
      • getIdentifier

        public Identifier getIdentifier()
      • getRank

        public java.lang.String getRank()
      • getScientificName

        public java.lang.String getScientificName()
      • getSynonyms

        public java.util.List<java.lang.String> getSynonyms()
      • getTaxonomyCode

        public java.lang.String getTaxonomyCode()
      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class java.lang.Object
      • init

        public void init()
      • isEmpty

        public boolean isEmpty()
      • isEqual

        public boolean isEqual​(PhylogenyData data)
        If this and taxonomy 'data' has an identifier, comparison will be based on that. Otherwise, if this and taxonomy 'data' has a code, comparison will be based on that. Otherwise, if Taxonomy 'data' has a scientific name, comparison will be based on that (case insensitive!). Otherwise, if Taxonomy 'data' has a common name, comparison will be based on that (case insensitive!). (Note. This is important and should not be change without a very good reason.)
        Specified by:
        isEqual in interface PhylogenyData
        Returns:
        in general, true if and only if all fiels are exactly identical, false otherwise
      • setAuthority

        public void setAuthority​(java.lang.String authority)
      • setCommonName

        public void setCommonName​(java.lang.String common_name)
      • setIdentifier

        public void setIdentifier​(Identifier identifier)
      • setScientificName

        public void setScientificName​(java.lang.String scientific_name)
      • setUris

        public void setUris​(java.util.List<Uri> uris)
        Specified by:
        setUris in interface MultipleUris
      • 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
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • compareTo

        public int compareTo​(Taxonomy o)
        Specified by:
        compareTo in interface java.lang.Comparable<Taxonomy>
      • setLineage

        public void setLineage​(java.util.List<java.lang.String> lineage)
      • getLineage

        public java.util.List<java.lang.String> getLineage()