org.forester.phylogeny.data
Interface PhylogenyData

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

public interface PhylogenyData


Method Summary
 StringBuffer asSimpleText()
           
 StringBuffer asText()
           
 PhylogenyData copy()
          Creates a new PhylogenyData object with identical values as this PhylogenyData.
 boolean isEqual(PhylogenyData data)
          Compares this PhylogenyData to PhylogenyData data.
 StringBuffer toNHX()
           
 void toPhyloXML(Writer writer, int level, String indentation)
          Writes a phyloXML representation of this phylogeny data.
 

Method Detail

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