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, NodeVisualization, Point, Polygon, PropertiesMap, Property, ProteinDomain, Reference, RenderableDomainArchitecture, RenderableVector, Sequence, SequenceRelation, Taxonomy, Uri

public interface PhylogenyData

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.StringBuffer	asSimpleText()
java.lang.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.
java.lang.StringBuffer	toNHX()
void	toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation) Writes a phyloXML representation of this phylogeny data.

Method Detail

asSimpleText

java.lang.StringBuffer asSimpleText()

asText

java.lang.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

java.lang.StringBuffer toNHX()

toPhyloXML

void toPhyloXML(java.io.Writer writer,
              int level,
              java.lang.String indentation)
                throws java.io.IOException

Writes a phyloXML representation of this phylogeny data.

Parameters:

writer -

level -

indentation -

Throws:

java.io.IOException