Package psidev.psi.mi.jami.tab.extension

Class MitabOrganism

java.lang.Object

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

psidev.psi.mi.jami.tab.extension.MitabOrganism

All Implemented Interfaces:

FileSourceContext, Organism

public class MitabOrganism
extends DefaultOrganism
implements FileSourceContext

Mitab extension of Organism. It contains a FileSourceLocator

Since:

11/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
void	setSourceLocator(FileSourceLocator sourceLocator)	Sets the source locator
String	toString()

Methods inherited from class psidev.psi.mi.jami.model.impl.DefaultOrganism

equals, getAliases, getCellType, getCommonName, getCompartment, getScientificName, getTaxId, getTissue, hashCode, initialiseAliases, initialiseAliasesWith, setCellType, setCommonName, setCompartment, setScientificName, setTaxId, setTissue

Methods inherited from class java.lang.Object

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

Constructor Detail

MitabOrganism

public MitabOrganism(int taxId)

Constructor for MitabOrganism.

Parameters:

taxId - a int.

MitabOrganism

public MitabOrganism(int taxId,
                     String commonName)

Constructor for MitabOrganism.

Parameters:

taxId - a int.

commonName - a String object.

MitabOrganism

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

Constructor for MitabOrganism.

Parameters:

taxId - a int.

commonName - a String object.

scientificName - a String object.

MitabOrganism

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

Constructor for MitabOrganism.

Parameters:

taxId - a int.

cellType - a CvTerm object.

tissue - a CvTerm object.

compartment - a CvTerm object.

MitabOrganism

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

Constructor for MitabOrganism.

Parameters:

taxId - a int.

commonName - a String object.

cellType - a CvTerm object.

tissue - a CvTerm object.

compartment - a CvTerm object.

MitabOrganism

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

Constructor for MitabOrganism.

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

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

toString

public String toString()

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class DefaultOrganism

Returns:

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