Package org.forester.phylogeny.data
Interface PhylogenyData
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- 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
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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.
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Method Detail
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asSimpleText
java.lang.StringBuffer asSimpleText()
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asText
java.lang.StringBuffer asText()
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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
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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
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toNHX
java.lang.StringBuffer toNHX()
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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
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