Class Annotation

    • Constructor Detail

      • Annotation

        public Annotation()
      • Annotation

        public Annotation​(java.lang.String ref)
      • Annotation

        public Annotation​(java.lang.String ref_source,
                          java.lang.String ref_value)
    • Method Detail

      • asText

        public java.lang.StringBuffer asText()
        Specified by:
        asText in interface PhylogenyData
      • compareTo

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

        public Confidence getConfidence()
      • getDesc

        public java.lang.String getDesc()
      • getEvidence

        public java.lang.String getEvidence()
      • getRef

        public java.lang.String getRef()
      • getRefSource

        public final java.lang.String getRefSource()
      • getRefValue

        public final java.lang.String getRefValue()
      • getSource

        public java.lang.String getSource()
      • getType

        public java.lang.String getType()
      • 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
      • setConfidence

        public void setConfidence​(Confidence confidence)
      • setDesc

        public void setDesc​(java.lang.String desc)
      • setEvidence

        public void setEvidence​(java.lang.String evidence)
      • setProperties

        public void setProperties​(PropertiesMap property)
      • setSource

        public void setSource​(java.lang.String source)
      • setType

        public void setType​(java.lang.String type)
      • 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