org.forester.phylogeny.data
Class NodeData

java.lang.Object
  extended by org.forester.phylogeny.data.NodeData
All Implemented Interfaces:
PhylogenyData

public class NodeData
extends Object
implements PhylogenyData


Constructor Summary
NodeData()
           
 
Method Summary
 StringBuffer asSimpleText()
           
 StringBuffer asText()
           
 PhylogenyData copy()
          Creates a new PhylogenyData object with identical values as this PhylogenyData.
 BinaryCharacters getBinaryCharacters()
           
 Date getDate()
           
 Distribution getDistribution()
           
 Event getEvent()
           
 Identifier getNodeIdentifier()
           
 PropertiesMap getProperties()
           
 Reference getReference()
           
 Sequence getSequence()
           
 Taxonomy getTaxonomy()
           
 boolean isEqual(PhylogenyData data)
          Compares this PhylogenyData to PhylogenyData data.
 boolean isHasBinaryCharacters()
           
 boolean isHasDate()
           
 boolean isHasDistribution()
           
 boolean isHasEvent()
           
 boolean isHasNodeIdentifier()
           
 boolean isHasProperties()
           
 boolean isHasReference()
           
 boolean isHasSequence()
           
 boolean isHasTaxonomy()
           
 void setBinaryCharacters(BinaryCharacters binary_characters)
           
 void setDate(Date date)
           
 void setDistribution(Distribution distribution)
           
 void setEvent(Event event)
           
 void setNodeIdentifier(Identifier node_identifier)
           
 void setProperties(PropertiesMap custom_data)
           
 void setReference(Reference reference)
           
 void setSequence(Sequence sequence)
           
 void setTaxonomy(Taxonomy taxonomy)
           
 StringBuffer toNHX()
           
 void toPhyloXML(Writer writer, int level, String indentation)
          Writes a phyloXML representation of this phylogeny data.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

NodeData

public NodeData()
Method Detail

asSimpleText

public StringBuffer asSimpleText()
Specified by:
asSimpleText in interface PhylogenyData

asText

public StringBuffer asText()
Specified by:
asText in interface PhylogenyData

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 interface PhylogenyData
Returns:
a ~deep~ copy of this PhylogenyData

getBinaryCharacters

public BinaryCharacters getBinaryCharacters()

getDate

public Date getDate()

getDistribution

public Distribution getDistribution()

getEvent

public Event getEvent()

getNodeIdentifier

public Identifier getNodeIdentifier()

getProperties

public PropertiesMap getProperties()

getReference

public Reference getReference()

getSequence

public Sequence getSequence()

getTaxonomy

public Taxonomy getTaxonomy()

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 interface PhylogenyData
Returns:
in general, true if and only if all fiels are exactly identical, false otherwise

isHasBinaryCharacters

public boolean isHasBinaryCharacters()

isHasDate

public boolean isHasDate()

isHasDistribution

public boolean isHasDistribution()

isHasEvent

public boolean isHasEvent()

isHasNodeIdentifier

public boolean isHasNodeIdentifier()

isHasProperties

public boolean isHasProperties()

isHasReference

public boolean isHasReference()

isHasSequence

public boolean isHasSequence()

isHasTaxonomy

public boolean isHasTaxonomy()

setBinaryCharacters

public void setBinaryCharacters(BinaryCharacters binary_characters)

setDate

public void setDate(Date date)

setDistribution

public void setDistribution(Distribution distribution)

setEvent

public void setEvent(Event event)

setNodeIdentifier

public void setNodeIdentifier(Identifier node_identifier)

setProperties

public void setProperties(PropertiesMap custom_data)

setReference

public void setReference(Reference reference)

setSequence

public void setSequence(Sequence sequence)

setTaxonomy

public void setTaxonomy(Taxonomy taxonomy)

toNHX

public StringBuffer toNHX()
Specified by:
toNHX in interface PhylogenyData

toPhyloXML

public void toPhyloXML(Writer writer,
                       int level,
                       String indentation)
                throws IOException
Description copied from interface: PhylogenyData
Writes a phyloXML representation of this phylogeny data.

Specified by:
toPhyloXML in interface PhylogenyData
Throws:
IOException