org.forester.phylogeny.data

Class Annotation

java.lang.Object

org.forester.phylogeny.data.Annotation

All Implemented Interfaces:

PhylogenyData

public class Annotation
extends java.lang.Object
implements PhylogenyData

Constructor Summary

Constructors

Constructor and Description
Annotation()

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.StringBuffer	asSimpleText()
java.lang.StringBuffer	asText()
PhylogenyData	copy() Creates a new PhylogenyData object with identical values as this PhylogenyData.
Confidence	getConfidence()
java.lang.String	getDesc()
java.lang.String	getEvidence()
PropertiesMap	getProperties()
java.lang.String	getRef()
java.lang.String	getSource()
java.lang.String	getType()
Uri	getUri()
boolean	isEqual(PhylogenyData data) Compares this PhylogenyData to PhylogenyData data.
void	setConfidence(Confidence confidence)
void	setDesc(java.lang.String desc)
void	setEvidence(java.lang.String evidence)
void	setProperties(PropertiesMap property)
void	setRef(java.lang.String ref)
void	setSource(java.lang.String source)
void	setType(java.lang.String type)
void	setUri(Uri uri)
java.lang.StringBuffer	toNHX()
void	toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation) Writes a phyloXML representation of this phylogeny data.
java.lang.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 java.lang.StringBuffer asSimpleText()

Specified by:

asSimpleText in interface PhylogenyData

asText

public java.lang.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 java.lang.String getDesc()

getEvidence

public java.lang.String getEvidence()

getProperties

public PropertiesMap getProperties()

getRef

public java.lang.String getRef()

getSource

public java.lang.String getSource()

getType

public java.lang.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(java.lang.String desc)

setEvidence

public void setEvidence(java.lang.String evidence)

setProperties

public void setProperties(PropertiesMap property)

setRef

public void setRef(java.lang.String ref)

setSource

public void setSource(java.lang.String source)

setType

public void setType(java.lang.String type)

setUri

public void setUri(Uri uri)

toNHX

public java.lang.StringBuffer toNHX()

Specified by:

toNHX in interface PhylogenyData

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 interface PhylogenyData

Throws:

java.io.IOException

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object