Package org.forester.phylogeny.data
Class NodeData
- java.lang.Object
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- org.forester.phylogeny.data.NodeData
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- All Implemented Interfaces:
PhylogenyData
public class NodeData extends java.lang.Object implements PhylogenyData
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Constructor Summary
Constructors Constructor Description NodeData()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addDistribution(Distribution distribution)
void
addReference(Reference reference)
void
addSequence(Sequence sequence)
void
addTaxonomy(Taxonomy taxonomy)
java.lang.StringBuffer
asSimpleText()
java.lang.StringBuffer
asText()
PhylogenyData
copy()
Creates a new PhylogenyData object with identical values as this PhylogenyData.BinaryCharacters
getBinaryCharacters()
Date
getDate()
Distribution
getDistribution()
Convenience method -- always returns the first Distribution.Distribution
getDistribution(int index)
java.util.List<Distribution>
getDistributions()
Event
getEvent()
java.lang.String
getNodeName()
NodeVisualData
getNodeVisualData()
PropertiesMap
getProperties()
Reference
getReference()
Convenience method -- always returns the first Reference.Reference
getReference(int index)
java.util.List<Reference>
getReferences()
Sequence
getSequence()
Convenience method -- always returns the first Sequence.Sequence
getSequence(int index)
java.util.List<Sequence>
getSequences()
java.util.List<Taxonomy>
getTaxonomies()
Taxonomy
getTaxonomy()
Convenience method -- always returns the first Taxonomy.Taxonomy
getTaxonomy(int index)
java.util.List<java.lang.Double>
getVector()
boolean
isEmpty()
boolean
isEqual(PhylogenyData data)
Compares this PhylogenyData to PhylogenyData data.boolean
isHasBinaryCharacters()
boolean
isHasDate()
boolean
isHasDistribution()
boolean
isHasEvent()
boolean
isHasProperties()
boolean
isHasReference()
boolean
isHasSequence()
boolean
isHasTaxonomy()
void
setBinaryCharacters(BinaryCharacters binary_characters)
void
setDate(Date date)
void
setDistribution(int index, Distribution distribution)
void
setDistribution(Distribution distribution)
Convenience method -- always sets the first Distribution.void
setEvent(Event event)
void
setNodeName(java.lang.String node_name)
void
setNodeVisualData(NodeVisualData node_visual_data)
void
setProperties(PropertiesMap custom_data)
void
setReference(int index, Reference reference)
void
setReference(Reference reference)
Convenience method -- always sets the first Reference.void
setSequence(int index, Sequence sequence)
void
setSequence(Sequence sequence)
Convenience method -- always sets the first Sequence.void
setTaxonomy(int index, Taxonomy taxonomy)
void
setTaxonomy(Taxonomy taxonomy)
Convenience method -- always sets the first Taxonomy.void
setVector(java.util.List<java.lang.Double> vector)
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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addDistribution
public void addDistribution(Distribution distribution)
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addReference
public void addReference(Reference reference)
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addSequence
public void addSequence(Sequence sequence)
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addTaxonomy
public void addTaxonomy(Taxonomy taxonomy)
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asSimpleText
public java.lang.StringBuffer asSimpleText()
- Specified by:
asSimpleText
in interfacePhylogenyData
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asText
public java.lang.StringBuffer asText()
- Specified by:
asText
in interfacePhylogenyData
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copy
public PhylogenyData copy()
Description copied from interface:PhylogenyData
Creates a new PhylogenyData object with identical values as this PhylogenyData. This ~should~ return a deep copy, but not there yet.- Specified by:
copy
in interfacePhylogenyData
- Returns:
- a ~deep~ copy of this PhylogenyData
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getBinaryCharacters
public BinaryCharacters getBinaryCharacters()
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getDate
public Date getDate()
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getDistribution
public Distribution getDistribution()
Convenience method -- always returns the first Distribution.- Returns:
- Distribution
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getDistribution
public Distribution getDistribution(int index)
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getDistributions
public java.util.List<Distribution> getDistributions()
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getEvent
public Event getEvent()
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getProperties
public PropertiesMap getProperties()
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getReference
public Reference getReference()
Convenience method -- always returns the first Reference.- Returns:
- Reference
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getReference
public Reference getReference(int index)
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getReferences
public java.util.List<Reference> getReferences()
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getSequence
public Sequence getSequence()
Convenience method -- always returns the first Sequence.- Returns:
- Sequence
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getSequence
public Sequence getSequence(int index)
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getSequences
public java.util.List<Sequence> getSequences()
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getTaxonomies
public java.util.List<Taxonomy> getTaxonomies()
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getTaxonomy
public Taxonomy getTaxonomy()
Convenience method -- always returns the first Taxonomy.- Returns:
- Taxonomy
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getTaxonomy
public Taxonomy getTaxonomy(int index)
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isEqual
public boolean isEqual(PhylogenyData data)
Description copied from interface:PhylogenyData
Compares this PhylogenyData to PhylogenyData data. In general, this should return true if and only if all fiels are exactly identical.- Specified by:
isEqual
in interfacePhylogenyData
- Returns:
- in general, true if and only if all fiels are exactly identical, false otherwise
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isHasBinaryCharacters
public boolean isHasBinaryCharacters()
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isEmpty
public boolean isEmpty()
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isHasDate
public boolean isHasDate()
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isHasDistribution
public boolean isHasDistribution()
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isHasEvent
public boolean isHasEvent()
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isHasProperties
public boolean isHasProperties()
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isHasReference
public boolean isHasReference()
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isHasSequence
public boolean isHasSequence()
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isHasTaxonomy
public boolean isHasTaxonomy()
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setBinaryCharacters
public void setBinaryCharacters(BinaryCharacters binary_characters)
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setDate
public void setDate(Date date)
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setDistribution
public void setDistribution(Distribution distribution)
Convenience method -- always sets the first Distribution.
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setDistribution
public void setDistribution(int index, Distribution distribution)
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setEvent
public void setEvent(Event event)
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setProperties
public void setProperties(PropertiesMap custom_data)
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setReference
public void setReference(int index, Reference reference)
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setReference
public void setReference(Reference reference)
Convenience method -- always sets the first Reference.
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setSequence
public void setSequence(int index, Sequence sequence)
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setSequence
public void setSequence(Sequence sequence)
Convenience method -- always sets the first Sequence.
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setTaxonomy
public void setTaxonomy(int index, Taxonomy taxonomy)
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setTaxonomy
public void setTaxonomy(Taxonomy taxonomy)
Convenience method -- always sets the first Taxonomy.
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toNHX
public java.lang.StringBuffer toNHX()
- Specified by:
toNHX
in interfacePhylogenyData
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toPhyloXML
public void toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation) throws java.io.IOException
Description copied from interface:PhylogenyData
Writes a phyloXML representation of this phylogeny data.- Specified by:
toPhyloXML
in interfacePhylogenyData
- Throws:
java.io.IOException
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setVector
public void setVector(java.util.List<java.lang.Double> vector)
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getVector
public java.util.List<java.lang.Double> getVector()
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getNodeName
public java.lang.String getNodeName()
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setNodeName
public void setNodeName(java.lang.String node_name)
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setNodeVisualData
public void setNodeVisualData(NodeVisualData node_visual_data)
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getNodeVisualData
public NodeVisualData getNodeVisualData()
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