de.bioforscher.singa.core.biology

Class Organism

java.lang.Object

de.bioforscher.singa.core.biology.Organism

All Implemented Interfaces:

Identifiable<NCBITaxonomyIdentifier>, Nameable

public class Organism
extends Object
implements Nameable, Identifiable<NCBITaxonomyIdentifier>

The organism class is used to store information about organisms, such as NCBITaxonomyIdentifier, names, and linage.

Author:

cl

Constructor Summary

Constructors

Constructor and Description
Organism(String scientificName) Creates a new organism with the given scientific name.

Method Summary

Modifier and Type	Method and Description
String	getCommonName() Returns a common name (such as "wild boar").
NCBITaxonomyIdentifier	getIdentifier() Returns the Identifier.
List<Taxon>	getLineage() Returns the linage as a list of Taxons.
String	getName() Returns the name, by which the object can be referenced.
String	getScientificName() Returns the scientific name (such as "Sus scrofa").
void	setCommonName(String commonName) Sets a common name (such as "wild boar").
void	setIdentifier(NCBITaxonomyIdentifier identifier) Sets the NCBITaxonomyIdentifier.
void	setLineage(List<Taxon> lineage) Sets the linage for this organism.
void	setScientificName(String scientificName) Sets the scientific name (such as "Sus scrofa").

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Organism

public Organism(String scientificName)

Creates a new organism with the given scientific name.

Parameters:

scientificName - A scientific name.

Method Detail

getScientificName

public String getScientificName()

Returns the scientific name (such as "Sus scrofa").

Returns:

The scientific name.

setScientificName

public void setScientificName(String scientificName)

Sets the scientific name (such as "Sus scrofa").

Parameters:

scientificName - The scientific name.

getCommonName

public String getCommonName()

Returns a common name (such as "wild boar").

Returns:

The common name.

setCommonName

public void setCommonName(String commonName)

Sets a common name (such as "wild boar").

Parameters:

commonName - The common name.

getName

public String getName()

Description copied from interface: Nameable

Returns the name, by which the object can be referenced.

Specified by:

getName in interface Nameable

Returns:

The name of the object.

getIdentifier

public NCBITaxonomyIdentifier getIdentifier()

Description copied from interface: Identifiable

Returns the Identifier.

Specified by:

getIdentifier in interface Identifiable<NCBITaxonomyIdentifier>

Returns:

The Identifier.

setIdentifier

public void setIdentifier(NCBITaxonomyIdentifier identifier)

Sets the NCBITaxonomyIdentifier.

Parameters:

identifier - The identifier.

getLineage

public List<Taxon> getLineage()

Returns the linage as a list of Taxons.

Returns:

The linage.

setLineage

public void setLineage(List<Taxon> lineage)

Sets the linage for this organism.

Parameters:

lineage - The linage.