Constructor Detail

• BranchData

  public BranchData()

Method Detail

• addConfidence

  public void addConfidence​(Confidence confidence)

• 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

• getBranchColor

  public BranchColor getBranchColor()

• getBranchWidth

  public BranchWidth getBranchWidth()

• getConfidence

  public Confidence getConfidence​(int index)

• getConfidences

  public java.util.List<Confidence> getConfidences()

• getNumberOfConfidences

  public int getNumberOfConfidences()

• 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

• isHasBranchColor

  public boolean isHasBranchColor()

• isHasBranchWidth

  public boolean isHasBranchWidth()

• isHasConfidences

  public boolean isHasConfidences()

• setBranchColor

  public void setBranchColor​(BranchColor branch_color)

• setBranchWidth

  public void setBranchWidth​(BranchWidth branch_width)

• 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