Package psidev.psi.mi.jami.xml.model.extension.xml253

Class XmlOrganism

java.lang.Object

psidev.psi.mi.jami.xml.model.extension.xml253.XmlOrganism

All Implemented Interfaces:

com.sun.xml.bind.Locatable, FileSourceContext, Organism

Direct Known Subclasses:

HostOrganism

public class XmlOrganism
extends Object
implements Organism, FileSourceContext, com.sun.xml.bind.Locatable

Xml implementation of an organism

Since:

22/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object o)
Collection<Alias>	getAliases()	getAliases.
CvTerm	getCellType()	Getter for the field cellType.
String	getCommonName()	getCommonName.
CvTerm	getCompartment()	Getter for the field compartment.
String	getScientificName()	getScientificName.
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
int	getTaxId()	Getter for the field taxId.
CvTerm	getTissue()	Getter for the field tissue.
int	hashCode()
void	setCellType(CvTerm cellType)	Sets the cell type
void	setCommonName(String name)	Set the common name
void	setCompartment(CvTerm compartment)	Sets the compartment.
void	setJAXBCellType(XmlOpenCvTerm cellType)	setJAXBCellType.
void	setJAXBCompartment(XmlOpenCvTerm compartment)	setJAXBCompartment.
void	setJAXBNames(NamesContainer value)	Sets the value of the names property.
void	setJAXBTaxId(int id)	setJAXBTaxId.
void	setJAXBTissue(XmlOpenCvTerm tissue)	setJAXBTissue.
void	setScientificName(String name)	Set the scientific name
void	setSourceLocator(FileSourceLocator sourceLocator)	Sets the source locator
void	setTaxId(int id)	Sets the taxonomy identifier of the organism.
void	setTissue(CvTerm tissue)	Sets the tissue
Locator	sourceLocation()
String	toString()	toString

Methods inherited from class java.lang.Object

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

Constructor Detail

XmlOrganism

public XmlOrganism()

Constructor for XmlOrganism.

XmlOrganism

public XmlOrganism(int taxId)

Constructor for XmlOrganism.

Parameters:

taxId - a int.

XmlOrganism

public XmlOrganism(int taxId,
                   String commonName)

Constructor for XmlOrganism.

Parameters:

taxId - a int.

commonName - a String object.

XmlOrganism

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

Constructor for XmlOrganism.

Parameters:

taxId - a int.

commonName - a String object.

scientificName - a String object.

XmlOrganism

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

Constructor for XmlOrganism.

Parameters:

taxId - a int.

cellType - a CvTerm object.

tissue - a CvTerm object.

compartment - a CvTerm object.

XmlOrganism

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

Constructor for XmlOrganism.

Parameters:

taxId - a int.

commonName - a String object.

cellType - a CvTerm object.

tissue - a CvTerm object.

compartment - a CvTerm object.

XmlOrganism

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

Constructor for XmlOrganism.

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

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

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.

getCommonName

public String getCommonName()

getCommonName.

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()

getScientificName.

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

getAliases

public Collection<Alias> getAliases()

getAliases.

Specified by:

getAliases in interface Organism

Returns:

a Collection object.

setJAXBNames

public void setJAXBNames(NamesContainer value)

Sets the value of the names property.

Parameters:

value - allowed object is NamesContainer

setJAXBCellType

public void setJAXBCellType(XmlOpenCvTerm cellType)

setJAXBCellType.

Parameters:

cellType - a XmlOpenCvTerm object.

setJAXBCompartment

public void setJAXBCompartment(XmlOpenCvTerm compartment)

setJAXBCompartment.

Parameters:

compartment - a XmlOpenCvTerm object.

setJAXBTissue

public void setJAXBTissue(XmlOpenCvTerm tissue)

setJAXBTissue.

Parameters:

tissue - a XmlOpenCvTerm object.

setJAXBTaxId

public void setJAXBTaxId(int id)

setJAXBTaxId.

Parameters:

id - a int.

sourceLocation

public Locator sourceLocation()

Specified by:

sourceLocation in interface com.sun.xml.bind.Locatable

getSourceLocator

public FileSourceLocator getSourceLocator()

Getter for the field sourceLocator.

Specified by:

getSourceLocator in interface FileSourceContext

Returns:

a FileSourceLocator object.

setSourceLocator

public void setSourceLocator(FileSourceLocator sourceLocator)

Sets the source locator

Specified by:

setSourceLocator in interface FileSourceContext

Parameters:

sourceLocator - : the file locator

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

toString

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class Object

Returns:

the file source context as a String. If the source locator is not null, it should give the source locator properties