Class Confidence

    • Field Detail

      • CONFIDENCE_DEFAULT_VALUE

        public static final int CONFIDENCE_DEFAULT_VALUE
        See Also:
        Constant Field Values
      • FORMATTER

        public static final java.text.NumberFormat FORMATTER
    • Constructor Detail

      • Confidence

        public Confidence()
      • Confidence

        public Confidence​(double value,
                          java.lang.String type)
      • Confidence

        public Confidence​(double value,
                          java.lang.String type,
                          double sd)
    • Method Detail

      • asText

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

        public int compareTo​(Confidence confidence)
        Specified by:
        compareTo in interface java.lang.Comparable<Confidence>
      • 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
      • getType

        public java.lang.String getType()
      • getValue

        public double getValue()
      • getStandardDeviation

        public double getStandardDeviation()
      • init

        public void init()
      • isEqual

        public boolean isEqual​(PhylogenyData confidence)
        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
      • setType

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

        public void setValue​(double value)
      • setStandardDeviation

        public void setStandardDeviation​(double sd)
      • 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