Constructor Detail

• Reference

  public Reference(java.lang.String desc)

• Reference

  public Reference(java.lang.String desc,
                   java.lang.String doi)

Method Detail

• asSimpleText

  public java.lang.StringBuffer asSimpleText()

  Specified by:

  asSimpleText in interface PhylogenyData

• 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

• getDoi

  public java.lang.String getDoi()

• getDescription

  public java.lang.String getDescription()

• 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

• setDoi

  public void setDoi(java.lang.String doi)
              throws PhyloXmlDataFormatException

  Throws:

  PhyloXmlDataFormatException

• setValue

  public void setValue(java.lang.String value)

• 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