Package org.forester.phylogeny.data

Class Taxonomy

java.lang.Object

org.forester.phylogeny.data.Taxonomy

All Implemented Interfaces:

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

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

Constructor Summary

Constructors

Constructor	Description
Taxonomy()

Method Summary

Modifier and Type	Method	Description
void	addUri(Uri uri)
java.lang.StringBuffer	asSimpleText()
java.lang.StringBuffer	asText()
int	compareTo(Taxonomy o)
PhylogenyData	copy()	Creates a new PhylogenyData object with identical values as this PhylogenyData.
boolean	equals(java.lang.Object o)
java.lang.String	getAuthority()
java.lang.String	getCommonName()
Identifier	getIdentifier()
java.util.List<java.lang.String>	getLineage()
java.lang.String	getRank()
java.lang.String	getScientificName()
java.util.List<java.lang.String>	getSynonyms()
java.lang.String	getTaxonomyCode()
Uri	getUri(int index)
java.util.List<Uri>	getUris()
int	hashCode()
void	init()
boolean	isEmpty()
boolean	isEqual(PhylogenyData data)	If this and taxonomy 'data' has an identifier, comparison will be based on that.
void	setAuthority(java.lang.String authority)
void	setCommonName(java.lang.String common_name)
void	setIdentifier(Identifier identifier)
void	setLineage(java.util.List<java.lang.String> lineage)
void	setRank(java.lang.String rank)
void	setScientificName(java.lang.String scientific_name)
void	setTaxonomyCode(java.lang.String taxonomy_code)
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, notify, notifyAll, wait, wait, wait

Constructor Detail

Taxonomy

public Taxonomy()

Method Detail

asSimpleText

public java.lang.StringBuffer asSimpleText()

Specified by:

asSimpleText in interface PhylogenyData

getUri

public Uri getUri(int index)

Specified by:

getUri in interface MultipleUris

addUri

public void addUri(Uri uri)

Specified by:

addUri in interface MultipleUris

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

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

getAuthority

public java.lang.String getAuthority()

getCommonName

public java.lang.String getCommonName()

getIdentifier

public Identifier getIdentifier()

getRank

public java.lang.String getRank()

getScientificName

public java.lang.String getScientificName()

getSynonyms

public java.util.List<java.lang.String> getSynonyms()

getTaxonomyCode

public java.lang.String getTaxonomyCode()

getUris

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

Specified by:

getUris in interface MultipleUris

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

init

public void init()

isEmpty

public boolean isEmpty()

isEqual

public boolean isEqual(PhylogenyData data)

If this and taxonomy 'data' has an identifier, comparison will be based on that. Otherwise, if this and taxonomy 'data' has a code, comparison will be based on that. Otherwise, if Taxonomy 'data' has a scientific name, comparison will be based on that (case insensitive!). Otherwise, if Taxonomy 'data' has a common name, comparison will be based on that (case insensitive!). (Note. This is important and should not be change without a very good reason.)

Specified by:

isEqual in interface PhylogenyData

Returns:

in general, true if and only if all fiels are exactly identical, false otherwise

setAuthority

public void setAuthority(java.lang.String authority)

setCommonName

public void setCommonName(java.lang.String common_name)

setIdentifier

public void setIdentifier(Identifier identifier)

setRank

public void setRank(java.lang.String rank)
             throws PhyloXmlDataFormatException

Throws:

PhyloXmlDataFormatException

setScientificName

public void setScientificName(java.lang.String scientific_name)

setTaxonomyCode

public void setTaxonomyCode(java.lang.String taxonomy_code)
                     throws PhyloXmlDataFormatException

Throws:

PhyloXmlDataFormatException

setUris

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

Specified by:

setUris in interface MultipleUris

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

compareTo

public int compareTo(Taxonomy o)

Specified by:

compareTo in interface java.lang.Comparable<Taxonomy>

setLineage

public void setLineage(java.util.List<java.lang.String> lineage)

getLineage

public java.util.List<java.lang.String> getLineage()