Package org.forester.phylogeny.data

Class BranchData

java.lang.Object
org.forester.phylogeny.data.BranchData
All Implemented Interfaces:
PhylogenyData
public class BranchData extends Object implements PhylogenyData

  • Constructor Details

    • BranchData

      public BranchData()

  • Method Details

    • addConfidence

      public void addConfidence(Confidence confidence)

    • asSimpleText

      public StringBuffer asSimpleText()
      Specified by:
      asSimpleText in interface PhylogenyData

    • asText

      public 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 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 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