uk.ac.ebi.intact.model
Class Component

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

All Implemented Interfaces:

BasicObject, IntactObject, java.io.Serializable

public class Component

extends BasicObjectImpl

The specific instance of an interactor which participates in an interaction. The same interactor may participate more than once, for example to describe different roles of the Interactors. However, simple multimers should be expressed by the relativeQuantity attribute.

Version:

$Id: Component.java,v 1.10 2004/03/02 13:51:10 skerrien Exp $

Author:

hhe

See Also:

Serialized Form

Field Summary

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

ac, NEW_LINE

Constructor Summary

Component(Institution owner, Interaction interaction, Interactor interactor, CvComponentRole role)
Creates a valid Component instance.

Method Summary

void	addBindingDomain(Feature feature)
boolean	equals(java.lang.Object o) Equality for Components is currently based on object identity (i.e.
java.util.Collection	getBindingDomains()
CvComponentRole	getCvComponentRole()
java.lang.String	getCvComponentRoleAc()
BioSource	getExpressedIn()
java.lang.String	getExpressedInAc()
Interaction	getInteraction()
java.lang.String	getInteractionAc()
Interactor	getInteractor()
java.lang.String	getInteractorAc()
float	getStoichiometry()
int	hashCode() This class overwrites equals.
void	removeBindingDomain(Feature feature)
void	setBindingDomains(java.util.Collection someBindingDomain)
void	setCvComponentRole(CvComponentRole cvComponentRole)
void	setCvComponentRoleAc(java.lang.String ac)
void	setExpressedIn(BioSource expressedIn)
void	setExpressedInAc(java.lang.String ac)
void	setInteraction(Interaction interaction)
void	setInteractionAc(java.lang.String ac)
void	setInteractor(Interactor interactor) TODO document that non obvious method
void	setInteractorAc(java.lang.String ac)
void	setStoichiometry(float stoichiometry)

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

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

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.IntactObject

getAc, getCreated, getUpdated, setAc, setCreated, setUpdated

Constructor Detail

Component

public Component(Institution owner,
                 Interaction interaction,
                 Interactor interactor,
                 CvComponentRole role)

Creates a valid Component instance. To be valid, a Component must have at least:

• An onwer (Institution)
• a biological source that the interaaction was expressed in
• an Interaction that this instance is a Component of
• an Interactor which defines the entity (eg Protein) which takes part in the Interaction and is therefore the 'core' of this Component
• the biological role that this Component plays in the Interaction (eg bait/prey etc)

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 owner of this Component (non-null)

interaction - The Interaction this Component is a part of (non-null)

interactor - The 'wrapped active entity' (eg a Protein) that this Component represents in the Interaction (non-null)

role - The biological/experimental role played by this Component in the Interaction experiment (eg bait/prey). This is a controlled vocabulary term (non-null)

Throws:

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

Method Detail

getStoichiometry

public float getStoichiometry()

setStoichiometry

public void setStoichiometry(float stoichiometry)

getExpressedIn

public BioSource getExpressedIn()

setExpressedIn

public void setExpressedIn(BioSource expressedIn)

getInteractor

public Interactor getInteractor()

setInteractor

public void setInteractor(Interactor interactor)

TODO document that non obvious method

Parameters:

interactor -

getInteraction

public Interaction getInteraction()

setInteraction

public void setInteraction(Interaction interaction)

setBindingDomains

public void setBindingDomains(java.util.Collection someBindingDomain)

getBindingDomains

public java.util.Collection getBindingDomains()

addBindingDomain

public void addBindingDomain(Feature feature)

removeBindingDomain

public void removeBindingDomain(Feature feature)

getCvComponentRole

public CvComponentRole getCvComponentRole()

setCvComponentRole

public void setCvComponentRole(CvComponentRole cvComponentRole)

equals

public boolean equals(java.lang.Object o)

Equality for Components is currently based on object identity (i.e. the references point to the same objects) for Interactors, Interactions and CvComponentRoles.

Overrides:

equals in class java.lang.Object

Parameters:

o - The object to check

Returns:

true if the parameter equals this object, false otherwise

hashCode

public int hashCode()

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

Overrides:

hashCode in class java.lang.Object

Returns:

hash code of the object.

getInteractorAc

public java.lang.String getInteractorAc()

setInteractorAc

public void setInteractorAc(java.lang.String ac)

getInteractionAc

public java.lang.String getInteractionAc()

setInteractionAc

public void setInteractionAc(java.lang.String ac)

getCvComponentRoleAc

public java.lang.String getCvComponentRoleAc()

setCvComponentRoleAc

public void setCvComponentRoleAc(java.lang.String ac)

getExpressedInAc

public java.lang.String getExpressedInAc()

setExpressedInAc

public void setExpressedInAc(java.lang.String ac)