Package org.forester.phylogeny.data

Interface PhylogenyData

All Known Subinterfaces:
GoTerm, RenderablePhylogenyData
All Known Implementing Classes:
Accession, Annotation, BasicGoTerm, BinaryCharacters, BranchColor, BranchData, BranchWidth, Confidence, Date, Distribution, DomainArchitecture, Event, Identifier, NodeData, NodeVisualData, Point, Polygon, PropertiesMap, Property, ProteinDomain, Reference, RenderableDomainArchitecture, RenderableMsaSequence, RenderableVector, Sequence, SequenceRelation, Taxonomy, Uri
public interface PhylogenyData

  • Method Details

    • asSimpleText

      StringBuffer asSimpleText()

    • asText

      StringBuffer asText()

    • copy

      PhylogenyData copy()
      Creates a new PhylogenyData object with identical values as this PhylogenyData. This ~should~ return a deep copy, but not there yet.
      Returns:
      a ~deep~ copy of this PhylogenyData

    • isEqual

      boolean isEqual(PhylogenyData data)
      Compares this PhylogenyData to PhylogenyData data. In general, this should return true if and only if all fiels are exactly identical.
      Parameters:
      PhylogenyData - the PhylogenyData to compare to
      Returns:
      in general, true if and only if all fiels are exactly identical, false otherwise

    • toNHX

      StringBuffer toNHX()

    • toPhyloXML

      void toPhyloXML(Writer writer, int level, String indentation) throws IOException
      Writes a phyloXML representation of this phylogeny data.
      Parameters:
      writer -
      level -
      indentation -
      Throws:
      IOException