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 Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	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