uk.ac.ebi.intact.model
Class InteractionImpl

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

All Implemented Interfaces:

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

public class InteractionImpl

extends InteractorImpl

implements Editable, Interaction

Represents an interaction. Interaction is derived from Interactor, therefore a given interaction can participate in new interactions. This allows to build up hierachical assemblies. An Interaction may also have other Interactions as products. This allows to model decomposition of complexes into subcomplexes.

Version:

$Id: InteractionImpl.java,v 1.1 2004/01/31 11:31:41 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

InteractionImpl(java.util.Collection experiments, java.util.Collection components, CvInteractionType type, java.lang.String shortLabel, Institution owner)
Creates a valid Interaction instance.

Method Summary

void	addComponent(Component component)
void	addExperiment(Experiment experiment)
void	addReleased(Product product)
boolean	equals(java.lang.Object o) Equality for Interactions is currently based on equality for Interactors, CvInteractionType, kD and Components.
Component	getBait() Returns the first components marked as bait.
java.util.Collection	getComponents()
CvInteractionType	getCvInteractionType()
java.lang.String	getCvInteractionTypeAc()
java.util.Collection	getExperiments()
java.lang.Float	getKD()
java.util.Collection	getReleased()
int	hashCode() This class overwrites equals.
void	removeComponent(Component component)
void	removeExperiment(Experiment experiment)
void	removeReleased(Product product)
void	setComponents(java.util.Collection someComponent)
void	setCvInteractionType(CvInteractionType cvInteractionType)
void	setCvInteractionTypeAc(java.lang.String ac)
void	setExperiments(java.util.Collection someExperiment)
void	setKD(java.lang.Float kD)
void	setReleased(java.util.Collection someReleased)
java.lang.String	toString()

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

addActiveInstance, addProduct, getActiveInstances, getBioSource, getBioSourceAc, getProducts, removeActiveInstance, removeProduct, setActiveInstances, setBioSource, setBioSourceAc, setProducts

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.Interactor

addActiveInstance, addProduct, getActiveInstances, getBioSource, getBioSourceAc, getProducts, removeActiveInstance, removeProduct, setActiveInstances, setBioSource, setBioSourceAc, setProducts

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

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 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

InteractionImpl

public InteractionImpl(java.util.Collection experiments,
                       java.util.Collection components,
                       CvInteractionType type,
                       java.lang.String shortLabel,
                       Institution owner)

Creates a valid Interaction instance. This requires at least the following:

• At least one valid Experiment
• at least two Components
• an Interaction type (eg covalent binding)
• a dissociation constant (ie kD), as a Float object
• a short label to refer to this instance

A side-effect of this constructor is to set the created and updated fields of the instance to the current time. NOTE: the BioSource value is required for this class as it is not set via Interactor - this will be taken from the (first) Experiment in the Collection parameter. It is tehrefore assumed that the Experiment will be a valid one.

Parameters:

experiments - A Collection of Experiments which observed this Interaction (non-empty) NB The BioSource for this Interaction will be taken from the first element of this Collection.

components - A Collection of Interaction components (eg Proteins). This cannot be null but may be empty to allow creation of an Interaction for later population with Components

type - The type of Interaction observed - may be null if initially unkown

shortLabel - The short label to refer to this instance (non-null)

Throws:

java.lang.NullPointerException - thrown if any of the specified paraneters are null OR the Experiment does not contain a BioSource.

java.lang.IllegalArgumentException - thrown if either of the experiments or components Collections are empty, or if there are less than two components specified

Method Detail

getKD

public java.lang.Float getKD()

Specified by:

getKD in interface Interaction

setKD

public void setKD(java.lang.Float kD)

Specified by:

setKD in interface Interaction

setComponents

public void setComponents(java.util.Collection someComponent)

Specified by:

setComponents in interface Interaction

getComponents

public java.util.Collection getComponents()

Specified by:

getComponents in interface Interaction

addComponent

public void addComponent(Component component)

Specified by:

addComponent in interface Interaction

removeComponent

public void removeComponent(Component component)

Specified by:

removeComponent in interface Interaction

setReleased

public void setReleased(java.util.Collection someReleased)

Specified by:

setReleased in interface Interaction

getReleased

public java.util.Collection getReleased()

Specified by:

getReleased in interface Interaction

addReleased

public void addReleased(Product product)

Specified by:

addReleased in interface Interaction

removeReleased

public void removeReleased(Product product)

Specified by:

removeReleased in interface Interaction

setExperiments

public void setExperiments(java.util.Collection someExperiment)

Specified by:

setExperiments in interface Interaction

getExperiments

public java.util.Collection getExperiments()

Specified by:

getExperiments in interface Interaction

addExperiment

public void addExperiment(Experiment experiment)

Specified by:

addExperiment in interface Interaction

removeExperiment

public void removeExperiment(Experiment experiment)

Specified by:

removeExperiment in interface Interaction

getCvInteractionType

public CvInteractionType getCvInteractionType()

Specified by:

getCvInteractionType in interface Interaction

setCvInteractionType

public void setCvInteractionType(CvInteractionType cvInteractionType)

Specified by:

setCvInteractionType in interface Interaction

getCvInteractionTypeAc

public java.lang.String getCvInteractionTypeAc()

Specified by:

getCvInteractionTypeAc in interface Interaction

setCvInteractionTypeAc

public void setCvInteractionTypeAc(java.lang.String ac)

Specified by:

setCvInteractionTypeAc in interface Interaction

getBait

public Component getBait()

Returns the first components marked as bait. If no such components is found, return null.

Specified by:

getBait in interface Interaction

Returns:

The first components marked as bait, otherwise null.

equals

public boolean equals(java.lang.Object o)

Equality for Interactions is currently based on equality for Interactors, CvInteractionType, kD and Components.

Specified by:

equals in interface Interaction

Overrides:

equals in class InteractorImpl

Parameters:

o - The object to check

Returns:

true if the parameter equals this object, false otherwise

See Also:

InteractorImpl, Component, CvInteractionType

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 Interaction

Overrides:

hashCode in class InteractorImpl

Returns:

hash code of the object.

toString

public java.lang.String toString()

Specified by:

toString in interface Interaction

Overrides:

toString in class InteractorImpl