Package psidev.psi.mi.jami.model

Interface ModelledInteraction

All Superinterfaces:

Interaction<ModelledParticipant>

All Known Subinterfaces:

Complex, ExtendedPsiXmlModelledInteraction, ExtendedPsiXmlModelledInteraction, ModelledBinaryInteraction

All Known Implementing Classes:

AbstractComplexRef, AbstractComplexRef, AbstractComplexRef, AbstractXmlComplex, AbstractXmlComplex, AbstractXmlComplex, AbstractXmlModelledInteraction, AbstractXmlModelledInteraction, AbstractXmlModelledInteraction, DefaultComplex, DefaultModelledBinaryInteraction, DefaultModelledInteraction, DefaultNamedModelledBinaryInteraction, DefaultNamedModelledInteraction, DefaultXmlComplex, DefaultXmlComplex, DefaultXmlComplex, DefaultXmlModelledInteraction, DefaultXmlModelledInteraction, DefaultXmlModelledInteraction, MitabComplex, MitabModelledBinaryInteraction, MitabModelledInteraction, ModelledBinaryInteractionWrapper, XmlBasicInteractionComplexWrapper, XmlBasicInteractionComplexWrapper, XmlBasicInteractionComplexWrapper, XmlComplex, XmlComplex, XmlComplex, XmlInteractionEvidenceComplexWrapper, XmlInteractionEvidenceComplexWrapper, XmlInteractionEvidenceComplexWrapper, XmlModelledBinaryInteraction, XmlModelledBinaryInteraction, XmlModelledBinaryInteractionWrapper, XmlModelledBinaryInteractionWrapper, XmlModelledInteraction, XmlModelledInteraction, XmlModelledInteraction, XmlModelledInteractionComplexWrapper, XmlModelledInteractionComplexWrapper, XmlModelledInteractionComplexWrapper

public interface ModelledInteraction
extends Interaction<ModelledParticipant>

An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...

Since:

11/12/12

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields

Modifier and Type	Field	Description
static String	ECO	Constant ECO="evidence ontology"
static String	ECO_MI	Constant ECO_MI="MI:1331"

Method Summary

Modifier and Type	Method	Description
<C extends CooperativeEffect> Collection<C>	getCooperativeEffects()	The collection of cooperative effects associated with this modelledInteraction.
CvTerm	getEvidenceType()	The evidence type for this modelled interactions.
<I extends InteractionEvidence> Collection<I>	getInteractionEvidences()	Interaction evidences supporting this modelled interaction.
<C extends ModelledConfidence> Collection<C>	getModelledConfidences()	The confidences in this interaction.
<P extends ModelledParameter> Collection<P>	getModelledParameters()	Collection of numerical parameters for this interaction.
Source	getSource()	The source which reported this modelled interaction.
void	setEvidenceType(CvTerm eco)	Sets the evidence type
void	setSource(Source source)	Sets the source reporting the interaction.

Methods inherited from interface psidev.psi.mi.jami.model.Interaction

addAllParticipants, addParticipant, getAnnotations, getChecksums, getCreatedDate, getIdentifiers, getInteractionType, getParticipants, getRigid, getShortName, getUpdatedDate, getXrefs, removeAllParticipants, removeParticipant, setCreatedDate, setInteractionType, setRigid, setShortName, setUpdatedDate

Field Detail

ECO

static final String ECO

Constant ECO="evidence ontology"

See Also:

Constant Field Values

ECO_MI

static final String ECO_MI

Constant ECO_MI="MI:1331"

See Also:

Constant Field Values

Method Detail

getInteractionEvidences

<I extends InteractionEvidence> Collection<I> getInteractionEvidences()

Interaction evidences supporting this modelled interaction. The collection cannot be null. If the modelled interaction does not have experimental interactions attached to it, the method should return an empty set

Type Parameters:

I - an I object

Returns:

the collection of experimental evidences

getSource

Source getSource()

The source which reported this modelled interaction. It can be an organization, institute, ... It can be null if the source is unknown or not relevant. Ex: IntAct, MINT, DIP, ...

Returns:

the source

setSource

void setSource(Source source)

Sets the source reporting the interaction.

Parameters:

source - : source for this interaction

getModelledConfidences

<C extends ModelledConfidence> Collection<C> getModelledConfidences()

The confidences in this interaction. The Collection cannot be null. If the interaction does not have any confidences, the method should return an empty Collection. Ex: author based scores, statistical confidences, ...

Type Parameters:

C - a C object

Returns:

the confidences

getModelledParameters

<P extends ModelledParameter> Collection<P> getModelledParameters()

Collection of numerical parameters for this interaction. The set cannot be null. If the interaction does not have any parameters, the method should return an empty Collection. Ex: IC50, ...

Type Parameters:

P - a P object

Returns:

the parameters

getCooperativeEffects

<C extends CooperativeEffect> Collection<C> getCooperativeEffects()

The collection of cooperative effects associated with this modelledInteraction. The collection cannot be null. If the ModelledInteraction does not have any cooperative effects, this method should return an empty collection.

Type Parameters:

C - a C object

Returns:

the collection of cooperative effects for this modelled interaction

getEvidenceType

CvTerm getEvidenceType()

The evidence type for this modelled interactions. Usually this Cv term is ECO (evidence code ontology) code. It can be null. Ex: ECO:0000021, physical interaction evidence

Returns:

the evidence type

setEvidenceType

void setEvidenceType(CvTerm eco)

Sets the evidence type

Parameters:

eco - : the evidence type