uk.ac.ebi.intact.model
Class Experiment

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.Experiment

All Implemented Interfaces:

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

public class Experiment

extends AnnotatedObjectImpl

implements Editable

Represents one experiment. Describes the conditions in which the experiment has been performed. The information should allow to classify experiments and make them comparable. The Experiment object does not aim to contain enough information to redo the experiment, it refers to the original publication for this purpose.

Version:

$Id: Experiment.java,v 1.13 2004/03/02 13:51:42 skerrien Exp $

Author:

hhe

See Also:

Serialized Form

Field Summary

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

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

Method Summary

void	addInteraction(Interaction interaction)
boolean	equals(java.lang.Object o) Equality for Experiments is currently based on equality for AnnotatedObjects and BioSources only.
BioSource	getBioSource()
java.lang.String	getBioSourceAc()
CvIdentification	getCvIdentification()
java.lang.String	getCvIdentificationAc()
CvInteraction	getCvInteraction()
java.lang.String	getCvInteractionAc()
java.util.Collection	getInteractions()
Experiment	getRelatedExperiment()
java.lang.String	getRelatedExperimentAc()
static Experiment	getShallowCopy(Experiment experiment) Builds a SHALLOW copy of the Experiment parameter.
int	hashCode() This class overwrites equals.
void	removeInteraction(Interaction interaction)
void	setBioSource(BioSource bioSource)
void	setBioSourceAc(java.lang.String ac)
void	setCvIdentification(CvIdentification cvIdentification)
void	setCvIdentificationAc(java.lang.String ac)
void	setCvInteraction(CvInteraction cvInteraction)
void	setCvInteractionAc(java.lang.String ac)
void	setInteractions(java.util.Collection someInteraction)
void	setRelatedExperiment(Experiment experiment)
void	setRelatedExperimentAc(java.lang.String ac)
java.lang.String	toString()

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, 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

Constructor Detail

Experiment

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

Creates a valid Experiment instance. A valid Experiment must contain at least a shortLabel that refers to it, an owner of the Experiment and also the biological source of the experiment data (ie organism). A side-effect of this constructor is to set the created and updated fields of the instance to the current time.

Parameters:

owner - The Institution which owns this Experiment (non-null)

shortLabel - A String which can be used to refer to the Experiment (non-null)

source - The biological source of the experimental data (non-null)

Throws:

java.lang.NullPointerException - thrown if any of the parameters are not set

Method Detail

getShallowCopy

public static Experiment getShallowCopy(Experiment experiment)

Builds a SHALLOW copy of the Experiment parameter. This means that a new Experiment instance is returned, but you should be aware that the object references it contains point to the objects referenced in the original object .

Parameters:

experiment - The Experiment you want a shallow copy of

Returns:

Experiment a new Experiment instance containing new references to the parameter object's attributes.

Throws:

java.lang.NullPointerException - thrown if required items are not present in the parameter Experiment instance.

setInteractions

public void setInteractions(java.util.Collection someInteraction)

getInteractions

public java.util.Collection getInteractions()

addInteraction

public void addInteraction(Interaction interaction)

removeInteraction

public void removeInteraction(Interaction interaction)

getRelatedExperiment

public Experiment getRelatedExperiment()

setRelatedExperiment

public void setRelatedExperiment(Experiment experiment)

getCvIdentification

public CvIdentification getCvIdentification()

setCvIdentification

public void setCvIdentification(CvIdentification cvIdentification)

getCvInteraction

public CvInteraction getCvInteraction()

setCvInteraction

public void setCvInteraction(CvInteraction cvInteraction)

getBioSource

public BioSource getBioSource()

setBioSource

public void setBioSource(BioSource bioSource)

getRelatedExperimentAc

public java.lang.String getRelatedExperimentAc()

setRelatedExperimentAc

public void setRelatedExperimentAc(java.lang.String ac)

getCvIdentificationAc

public java.lang.String getCvIdentificationAc()

setCvIdentificationAc

public void setCvIdentificationAc(java.lang.String ac)

getCvInteractionAc

public java.lang.String getCvInteractionAc()

setCvInteractionAc

public void setCvInteractionAc(java.lang.String ac)

getBioSourceAc

public java.lang.String getBioSourceAc()

setBioSourceAc

public void setBioSourceAc(java.lang.String ac)

equals

public boolean equals(java.lang.Object o)

Equality for Experiments is currently based on equality for AnnotatedObjects and BioSources only.

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:

AnnotatedObject

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.

toString

public java.lang.String toString()

Specified by:

toString in interface AnnotatedObject

Overrides:

toString in class AnnotatedObjectImpl