org.forester.phylogeny.data

Class Annotation

java.lang.Object

org.forester.phylogeny.data.Annotation

All Implemented Interfaces:

java.lang.Comparable<Annotation>, MultipleUris, PhylogenyData

public class Annotation
extends java.lang.Object
implements PhylogenyData, MultipleUris, java.lang.Comparable<Annotation>

Constructor Summary

Constructors

Constructor and Description
Annotation(java.lang.String ref)

Method Summary

Methods

Modifier and Type	Method and Description
void	addUri(Uri uri)
java.lang.StringBuffer	asSimpleText()
java.lang.StringBuffer	asText()
int	compareTo(Annotation o)
PhylogenyData	copy() Creates a new PhylogenyData object with identical values as this PhylogenyData.
boolean	equals(java.lang.Object o)
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(int index)
java.util.List<Uri>	getUris()
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	setSource(java.lang.String source)
void	setType(java.lang.String type)
void	setUris(java.util.List<Uri> uris)
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, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Annotation

public Annotation(java.lang.String ref)

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()

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)

setSource

public void setSource(java.lang.String source)

setType

public void setType(java.lang.String type)

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

addUri

public void addUri(Uri uri)

Specified by:

addUri in interface MultipleUris

getUri

public Uri getUri(int index)

Specified by:

getUri in interface MultipleUris

getUris

public java.util.List<Uri> getUris()

Specified by:

getUris in interface MultipleUris

setUris

public void setUris(java.util.List<Uri> uris)

Specified by:

setUris in interface MultipleUris

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

compareTo

public int compareTo(Annotation o)

Specified by:

compareTo in interface java.lang.Comparable<Annotation>