Package psidev.psi.mi.jami.model.impl

Class DefaultOrganism

java.lang.Object

psidev.psi.mi.jami.model.impl.DefaultOrganism

All Implemented Interfaces:

Organism

Direct Known Subclasses:

MitabOrganism

public class DefaultOrganism
extends Object
implements Organism

Default implementation for organism Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousOrganismComparator

Since:

22/01/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
DefaultOrganism(int taxId)	Constructor for DefaultOrganism.
DefaultOrganism(int taxId, String commonName)	Constructor for DefaultOrganism.
DefaultOrganism(int taxId, String commonName, String scientificName)	Constructor for DefaultOrganism.
DefaultOrganism(int taxId, String commonName, String scientificName, CvTerm cellType, CvTerm tissue, CvTerm compartment)	Constructor for DefaultOrganism.
DefaultOrganism(int taxId, String commonName, CvTerm cellType, CvTerm tissue, CvTerm compartment)	Constructor for DefaultOrganism.
DefaultOrganism(int taxId, CvTerm cellType, CvTerm tissue, CvTerm compartment)	Constructor for DefaultOrganism.

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object o)
Collection<Alias>	getAliases()	Getter for the field aliases.
CvTerm	getCellType()	Getter for the field cellType.
String	getCommonName()	Getter for the field commonName.
CvTerm	getCompartment()	Getter for the field compartment.
String	getScientificName()	Getter for the field scientificName.
int	getTaxId()	Getter for the field taxId.
CvTerm	getTissue()	Getter for the field tissue.
int	hashCode()
protected void	initialiseAliases()	initialiseAliases
protected void	initialiseAliasesWith(Collection<Alias> aliases)	initialiseAliasesWith
void	setCellType(CvTerm cellType)	Sets the cell type
void	setCommonName(String name)	Set the common name
void	setCompartment(CvTerm compartment)	Sets the compartment.
void	setScientificName(String name)	Set the scientific name
void	setTaxId(int id)	Sets the taxonomy identifier of the organism.
void	setTissue(CvTerm tissue)	Sets the tissue
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

DefaultOrganism

public DefaultOrganism(int taxId)

Constructor for DefaultOrganism.

Parameters:

taxId - a int.

DefaultOrganism

public DefaultOrganism(int taxId,
                       String commonName)

Constructor for DefaultOrganism.

Parameters:

taxId - a int.

commonName - a String object.

DefaultOrganism

public DefaultOrganism(int taxId,
                       String commonName,
                       String scientificName)

Constructor for DefaultOrganism.

Parameters:

taxId - a int.

commonName - a String object.

scientificName - a String object.

DefaultOrganism

public DefaultOrganism(int taxId,
                       CvTerm cellType,
                       CvTerm tissue,
                       CvTerm compartment)

Constructor for DefaultOrganism.

Parameters:

taxId - a int.

cellType - a CvTerm object.

tissue - a CvTerm object.

compartment - a CvTerm object.

DefaultOrganism

public DefaultOrganism(int taxId,
                       String commonName,
                       CvTerm cellType,
                       CvTerm tissue,
                       CvTerm compartment)

Constructor for DefaultOrganism.

Parameters:

taxId - a int.

commonName - a String object.

cellType - a CvTerm object.

tissue - a CvTerm object.

compartment - a CvTerm object.

DefaultOrganism

public DefaultOrganism(int taxId,
                       String commonName,
                       String scientificName,
                       CvTerm cellType,
                       CvTerm tissue,
                       CvTerm compartment)

Constructor for DefaultOrganism.

Parameters:

taxId - a int.

commonName - a String object.

scientificName - a String object.

cellType - a CvTerm object.

tissue - a CvTerm object.

compartment - a CvTerm object.

Method Detail

initialiseAliases

protected void initialiseAliases()

initialiseAliases

initialiseAliasesWith

protected void initialiseAliasesWith(Collection<Alias> aliases)

initialiseAliasesWith

Parameters:

aliases - a Collection object.

getCommonName

public String getCommonName()

Getter for the field commonName.

Specified by:

getCommonName in interface Organism

Returns:

a String object.

setCommonName

public void setCommonName(String name)

Set the common name

Specified by:

setCommonName in interface Organism

Parameters:

name - : common name or mnemonic (or scientific name if no common names/mnemonic)

getScientificName

public String getScientificName()

Getter for the field scientificName.

Specified by:

getScientificName in interface Organism

Returns:

a String object.

setScientificName

public void setScientificName(String name)

Set the scientific name

Specified by:

setScientificName in interface Organism

Parameters:

name - : scientific name

getTaxId

public int getTaxId()

Getter for the field taxId.

Specified by:

getTaxId in interface Organism

Returns:

a int.

setTaxId

public void setTaxId(int id)

Sets the taxonomy identifier of the organism. It should be : - '-1' for 'in vitro' - '-2' for 'chemical synthesis' - '-3' for unknown - '-4' for in vivo - valid NCBI taxonomy identifier (Ex: 9606 for human)

Specified by:

setTaxId in interface Organism

Parameters:

id - a int.

getAliases

public Collection<Alias> getAliases()

Getter for the field aliases.

Specified by:

getAliases in interface Organism

Returns:

a Collection object.

getCellType

public CvTerm getCellType()

Getter for the field cellType.

Specified by:

getCellType in interface Organism

Returns:

a CvTerm object.

setCellType

public void setCellType(CvTerm cellType)

Sets the cell type

Specified by:

setCellType in interface Organism

Parameters:

cellType - : cell type

getCompartment

public CvTerm getCompartment()

Getter for the field compartment.

Specified by:

getCompartment in interface Organism

Returns:

a CvTerm object.

setCompartment

public void setCompartment(CvTerm compartment)

Sets the compartment.

Specified by:

setCompartment in interface Organism

Parameters:

compartment - : the compartment

getTissue

public CvTerm getTissue()

Getter for the field tissue.

Specified by:

getTissue in interface Organism

Returns:

a CvTerm object.

setTissue

public void setTissue(CvTerm tissue)

Sets the tissue

Specified by:

setTissue in interface Organism

Parameters:

tissue - : tissue

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object