uk.ac.ebi.intact.model
Class BioSource

java.lang.Object
  |
  +--uk.ac.ebi.intact.model.IntactObjectImpl
        |
        +--uk.ac.ebi.intact.model.BasicObjectImpl
              |
              +--uk.ac.ebi.intact.model.AnnotatedObjectImpl
                    |
                    +--uk.ac.ebi.intact.model.BioSource

All Implemented Interfaces:

AnnotatedObject, BasicObject, Editable, IntactObject, java.io.Serializable

public class BioSource

extends AnnotatedObjectImpl

implements Editable

Represents a biological source. TODO write a proper comment

Version:

$id$

Author:

hhe

See Also:

Serialized Form

Field Summary

java.lang.String	cvCellCycleAc
java.lang.String	cvCellTypeAc
java.lang.String	cvCompartmentAc
java.lang.String	cvDevelopmentalStageAc
java.lang.String	cvTissueAc

Fields inherited from class uk.ac.ebi.intact.model.AnnotatedObjectImpl

annotations, curator, curatorAc, fullName, references, shortLabel, xrefs

Fields inherited from class uk.ac.ebi.intact.model.IntactObjectImpl

ac, NEW_LINE

Constructor Summary

BioSource(Institution owner, java.lang.String shortLabel, java.lang.String taxId)
Creates a valid BioSource (ie a source organism) instance.

Method Summary

boolean	equals(java.lang.Object o) Equality for BioSources is currently based on equality for AnnotatedObjects and taxIds (String representation of an integer).
CvCellCycle	getCvCellCycle()
java.lang.String	getCvCellCycleAc()
CvCellType	getCvCellType()
java.lang.String	getCvCellTypeAc()
CvCompartment	getCvCompartment()
java.lang.String	getCvCompartmentAc()
CvDevelopmentalStage	getCvDevelopmentalStage()
java.lang.String	getCvDevelopmentalStageAc()
CvTissue	getCvTissue()
java.lang.String	getCvTissueAc()
java.lang.String	getTaxId()
int	hashCode() This class overwrites equals.
void	setCvCellCycle(CvCellCycle cvCellCycle)
void	setCvCellCycleAc(java.lang.String ac)
void	setCvCellType(CvCellType cvCellType)
void	setCvCellTypeAc(java.lang.String ac)
void	setCvCompartment(CvCompartment cvCompartment)
void	setCvCompartmentAc(java.lang.String ac)
void	setCvDevelopmentalStage(CvDevelopmentalStage cvDevelopmentalStage)
void	setCvDevelopmentalStageAc(java.lang.String ac)
void	setCvTissue(CvTissue cvTissue)
void	setCvTissueAc(java.lang.String ac)
void	setTaxId(java.lang.String taxId)

Methods inherited from class uk.ac.ebi.intact.model.AnnotatedObjectImpl

addAlias, addAnnotation, addReference, addXref, getAliases, getAnnotations, getCurator, getCuratorAc, getFullName, getReferences, getShortLabel, getXrefs, removeAlias, removeAnnotation, removeReference, removeXref, setAliases, setAnnotation, setCurator, setCuratorAc, setFullName, setReferences, setShortLabel, setXrefs, toString, update, updateUniqueAnnotation

Methods inherited from class uk.ac.ebi.intact.model.BasicObjectImpl

addEvidence, getEvidences, getOwner, getOwnerAc, removeEvidence, setEvidences, setOwner, setOwnerAc

Methods inherited from class uk.ac.ebi.intact.model.IntactObjectImpl

getAc, getCreated, getUpdated, setAc, setCreated, setUpdated

Methods inherited from class java.lang.Object

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

Methods inherited from interface uk.ac.ebi.intact.model.BasicObject

addEvidence, getEvidences, getOwner, getOwnerAc, removeEvidence, setEvidences, setOwner, setOwnerAc

Methods inherited from interface uk.ac.ebi.intact.model.IntactObject

getAc, getCreated, getUpdated, setAc, setCreated, setUpdated

Field Detail

cvCellCycleAc

public java.lang.String cvCellCycleAc

cvDevelopmentalStageAc

public java.lang.String cvDevelopmentalStageAc

cvTissueAc

public java.lang.String cvTissueAc

cvCellTypeAc

public java.lang.String cvCellTypeAc

cvCompartmentAc

public java.lang.String cvCompartmentAc

Constructor Detail

BioSource

public BioSource(Institution owner,
                 java.lang.String shortLabel,
                 java.lang.String taxId)

Creates a valid BioSource (ie a source organism) instance. A valid instance must have at least a non-null shortLabel specified. A side-effect of this constructor is to set the created and updated fields of the instance to the current time.

Parameters:

shortLabel - The label used to identify this instance

taxId - the NCBI taxId, which must be unique if defined (may be null)

owner - The Institution which 'owns' this BioSource

Throws:

java.lang.NullPointerException - thrown if either no shortLabel or Institution specified.

Method Detail

getTaxId

public java.lang.String getTaxId()

setTaxId

public void setTaxId(java.lang.String taxId)

getCvCellCycle

public CvCellCycle getCvCellCycle()

setCvCellCycle

public void setCvCellCycle(CvCellCycle cvCellCycle)

getCvDevelopmentalStage

public CvDevelopmentalStage getCvDevelopmentalStage()

setCvDevelopmentalStage

public void setCvDevelopmentalStage(CvDevelopmentalStage cvDevelopmentalStage)

getCvTissue

public CvTissue getCvTissue()

setCvTissue

public void setCvTissue(CvTissue cvTissue)

getCvCellType

public CvCellType getCvCellType()

setCvCellType

public void setCvCellType(CvCellType cvCellType)

getCvCompartment

public CvCompartment getCvCompartment()

setCvCompartment

public void setCvCompartment(CvCompartment cvCompartment)

getCvCompartmentAc

public java.lang.String getCvCompartmentAc()

setCvCompartmentAc

public void setCvCompartmentAc(java.lang.String ac)

getCvCellCycleAc

public java.lang.String getCvCellCycleAc()

setCvCellCycleAc

public void setCvCellCycleAc(java.lang.String ac)

getCvCellTypeAc

public java.lang.String getCvCellTypeAc()

setCvCellTypeAc

public void setCvCellTypeAc(java.lang.String ac)

getCvTissueAc

public java.lang.String getCvTissueAc()

setCvTissueAc

public void setCvTissueAc(java.lang.String ac)

getCvDevelopmentalStageAc

public java.lang.String getCvDevelopmentalStageAc()

setCvDevelopmentalStageAc

public void setCvDevelopmentalStageAc(java.lang.String ac)

equals

public boolean equals(java.lang.Object o)

Equality for BioSources is currently based on equality for AnnotatedObjects and taxIds (String representation of an integer).

Specified by:

equals in interface AnnotatedObject

Overrides:

equals in class AnnotatedObjectImpl

Parameters:

o - The object to check

Returns:

true if the parameter equals this object, false otherwise

See Also:

AnnotatedObjectImpl

hashCode

public int hashCode()

Description copied from class: AnnotatedObjectImpl

This class overwrites equals. To ensure proper functioning of HashTable, hashCode must be overwritten, too.

Specified by:

hashCode in interface AnnotatedObject

Overrides:

hashCode in class AnnotatedObjectImpl

Returns:

hash code of the object.