Constructor Detail

• PropertiesMap

  public PropertiesMap​()

Method Detail

• size

  public int size​()

• addProperty

  public void addProperty​(Property property)
                   throws java.lang.IllegalArgumentException

  Throws:

  java.lang.IllegalArgumentException

• 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

• getProperties

  public java.util.SortedMap<java.lang.String,Property> getProperties​()

• getPropertiesArray

  public Property[] getPropertiesArray​()

• getPropertiesWithGivenReferencePrefix

  public java.util.List<Property> getPropertiesWithGivenReferencePrefix​(java.lang.String ref_prefix)
                                                                 throws java.lang.IllegalArgumentException

  Throws:

  java.lang.IllegalArgumentException

• getProperty

  public Property getProperty​(java.lang.String ref)
                       throws java.lang.IllegalArgumentException

  Throws:

  java.lang.IllegalArgumentException

• getPropertyRefs

  public java.lang.String[] getPropertyRefs​()

  Returns all property refs of this PhylogenyNode as String array.

• 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

• refExists

  public boolean refExists​(java.lang.String ref)

• removeProperty

  public Property removeProperty​(java.lang.String ref)
                          throws java.lang.IllegalArgumentException

  Throws:

  java.lang.IllegalArgumentException

• removePropertiesWithGivenReferencePrefix

  public java.util.List<java.lang.String> removePropertiesWithGivenReferencePrefix​(java.lang.String ref_prefix)
                                                                            throws java.lang.IllegalArgumentException

  Throws:

  java.lang.IllegalArgumentException

• 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