org.forester.phylogeny.data
Class Annotation
java.lang.Object
org.forester.phylogeny.data.Annotation
- All Implemented Interfaces:
- PhylogenyData
public class Annotation
- extends Object
- implements PhylogenyData
Annotation
public Annotation()
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