Class Annotation

Method Details

• addUri

  public void addUri(Uri uri)

  Specified by:

  addUri in interface MultipleUris

• asSimpleText

  public StringBuffer asSimpleText()

  Specified by:

  asSimpleText in interface PhylogenyData

• asText

  public StringBuffer asText()

  Specified by:

  asText in interface PhylogenyData

• compareTo

  public int compareTo(Annotation o)

  Specified by:

  compareTo in interface 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(Object o)

  Overrides:

  equals in class Object

• getConfidence

  public Confidence getConfidence()

• getDesc

  public String getDesc()

• getEvidence

  public String getEvidence()

• getProperties

  public PropertiesMap getProperties()

• getRef

  public String getRef()

• getRefSource

  public final String getRefSource()

• getRefValue

  public final String getRefValue()

• getSource

  public String getSource()

• getType

  public String getType()

• getUri

  public Uri getUri(int index)

  Specified by:

  getUri in interface MultipleUris

• getUris

  public List<Uri> getUris()

  Specified by:

  getUris in interface MultipleUris

• 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(String desc)

• setEvidence

  public void setEvidence(String evidence)

• setProperties

  public void setProperties(PropertiesMap property)

• setSource

  public void setSource(String source)

• setType

  public void setType(String type)

• setUris

  public void setUris(List<Uri> uris)

  Specified by:

  setUris in interface MultipleUris

• toNHX

  public StringBuffer toNHX()

  Specified by:

  toNHX in interface PhylogenyData

• toPhyloXML

  public void toPhyloXML(Writer writer, int level, String indentation) throws IOException

  Description copied from interface: PhylogenyData

  Writes a phyloXML representation of this phylogeny data.

  Specified by:

  toPhyloXML in interface PhylogenyData

  Throws:

  IOException

• toString

  public String toString()

  Overrides:

  toString in class Object