org.forester.phylogeny.data
Class Annotation

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

public class Annotation
extends Object
implements PhylogenyData


Constructor Summary
Annotation()
           
 
Method Summary
 StringBuffer asSimpleText()
           
 StringBuffer asText()
           
 PhylogenyData copy()
          Creates a new PhylogenyData object with identical values as this PhylogenyData.
 Confidence getConfidence()
           
 String getDesc()
           
 String getEvidence()
           
 PropertiesMap getProperties()
           
 String getRef()
           
 String getSource()
           
 String getType()
           
 Uri getUri()
           
 boolean isEqual(PhylogenyData data)
          Compares this PhylogenyData to PhylogenyData data.
 void setConfidence(Confidence confidence)
           
 void setDesc(String desc)
           
 void setEvidence(String evidence)
           
 void setProperties(PropertiesMap property)
           
 void setRef(String ref)
           
 void setSource(String source)
           
 void setType(String type)
           
 void setUri(Uri uri)
           
 StringBuffer toNHX()
           
 void toPhyloXML(Writer writer, int level, String indentation)
          Writes a phyloXML representation of this phylogeny data.
 String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

Annotation

public Annotation()
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

getConfidence

public Confidence getConfidence()

getDesc

public String getDesc()

getEvidence

public String getEvidence()

getProperties

public PropertiesMap getProperties()

getRef

public String getRef()

getSource

public String getSource()

getType

public String getType()

getUri

public Uri getUri()

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

setConfidence

public void setConfidence(Confidence confidence)

setDesc

public void setDesc(String desc)

setEvidence

public void setEvidence(String evidence)

setProperties

public void setProperties(PropertiesMap property)

setRef

public void setRef(String ref)

setSource

public void setSource(String source)

setType

public void setType(String type)

setUri

public void setUri(Uri uri)

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

toString

public String toString()
Overrides:
toString in class Object