org.forester.phylogeny.data

Class Taxonomy

java.lang.Object

org.forester.phylogeny.data.Taxonomy

All Implemented Interfaces:

PhylogenyData

public class Taxonomy
extends java.lang.Object
implements PhylogenyData

Constructor Summary

Constructors

Constructor and Description
Taxonomy()

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.
boolean	equals(java.lang.Object o)
java.lang.String	getAuthority()
java.lang.String	getCommonName()
Identifier	getIdentifier()
java.lang.String	getRank()
java.lang.String	getScientificName()
java.util.List<java.lang.String>	getSynonyms()
java.lang.String	getTaxonomyCode()
Uri	getUri()
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	setRank(java.lang.String rank)
void	setScientificName(java.lang.String scientific_name)
void	setTaxonomyCode(java.lang.String taxonomy_code)
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, 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

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()

getUri

public Uri getUri()

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)

setScientificName

public void setScientificName(java.lang.String scientific_name)

setTaxonomyCode

public void setTaxonomyCode(java.lang.String taxonomy_code)

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