org.biopax.paxtools.impl.level3

Class InteractionImpl

java.lang.Object

org.biopax.paxtools.impl.BioPAXElementImpl

org.biopax.paxtools.impl.level3.L3ElementImpl

org.biopax.paxtools.impl.level3.XReferrableImpl

org.biopax.paxtools.impl.level3.NamedImpl

org.biopax.paxtools.impl.level3.EntityImpl

org.biopax.paxtools.impl.level3.ProcessImpl

org.biopax.paxtools.impl.level3.InteractionImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, Entity, Interaction, Level3Element, Named, Observable, Process, XReferrable

Direct Known Subclasses:

ControlImpl, ConversionImpl, GeneticInteractionImpl, MolecularInteractionImpl, TemplateReactionImpl

@Entity
 @Indexed
 @Boost(value=1.5f)
public class InteractionImpl
extends ProcessImpl
implements Interaction

See Also:

Serialized Form

Field Summary

Fields inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

FIELD_AVAILABILITY, FIELD_COMMENT, FIELD_DATASOURCE, FIELD_ECNUMBER, FIELD_KEYWORD, FIELD_NAME, FIELD_ORGANISM, FIELD_PATHWAY, FIELD_SEQUENCE, FIELD_TERM, FIELD_XREFDB, FIELD_XREFID, FILTER_BY_DATASOURCE, FILTER_BY_ORGANISM

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

Constructors

Constructor and Description
InteractionImpl()

Method Summary

Modifier and Type	Method and Description
void	addInteractionType(InteractionVocabulary newinteractionType) Controlled vocabulary term annotating the interaction type for example, "phosphorylation reaction".
void	addParticipant(Entity aParticipant) The entities that participate in this interaction.
Set<InteractionVocabulary>	getInteractionType() Controlled vocabulary term annotating the interaction type for example, "phosphorylation reaction".
Class<? extends Interaction>	getModelInterface() This method returns the actual model interface that a class implements.
Set<Entity>	getParticipant() The entities that participate in this interaction.
void	removeInteractionType(InteractionVocabulary oldinteractionType) Controlled vocabulary term annotating the interaction type for example, "phosphorylation reaction".
void	removeParticipant(Entity aParticipant) The entities that participate in this interaction.
void	setInteractionType(Set<InteractionVocabulary> interactionType)
protected void	setParticipant(Set<Entity> participant)

Methods inherited from class org.biopax.paxtools.impl.level3.ProcessImpl

getControlledOf, getPathwayComponentOf, getStepProcessOf, setControlledOf, setPathwayComponentOf, setStepProcessOf

Methods inherited from class org.biopax.paxtools.impl.level3.EntityImpl

addAvailability, addDataSource, addEvidence, getAvailability, getDataSource, getEvidence, getParticipantOf, removeAvailability, removeDataSource, removeEvidence, semanticallyEquivalent, setAvailability, setDataSource, setEvidence, setParticipantOf

Methods inherited from class org.biopax.paxtools.impl.level3.NamedImpl

addName, getDisplayName, getDisplayNameX, getName, getStandardName, getStandardNameX, removeName, setDisplayName, setDisplayNameX, setName, setStandardName, setStandardNameX

Methods inherited from class org.biopax.paxtools.impl.level3.XReferrableImpl

addXref, equivalenceCode, getXref, removeXref, setXref

Methods inherited from class org.biopax.paxtools.impl.level3.L3ElementImpl

addComment, getComment, getDatasources, getKeywords, getOrganisms, getParentPathways, removeComment, setComment

Methods inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

equals, getAnnotations, getPk, getRDFId, hashCode, isEquivalent, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biopax.paxtools.model.level3.Process

getControlledOf, getPathwayComponentOf, getStepProcessOf

Methods inherited from interface org.biopax.paxtools.model.level3.Entity

addAvailability, addDataSource, getAvailability, getDataSource, getParticipantOf, removeAvailability, removeDataSource

Methods inherited from interface org.biopax.paxtools.model.level3.Observable

addEvidence, getEvidence, removeEvidence

Methods inherited from interface org.biopax.paxtools.model.level3.Named

addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setName, setStandardName

Methods inherited from interface org.biopax.paxtools.model.level3.XReferrable

addXref, getXref, removeXref

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement

equivalenceCode, getAnnotations, getRDFId, isEquivalent

Constructor Detail

InteractionImpl

public InteractionImpl()

Method Detail

getModelInterface

public Class<? extends Interaction> getModelInterface()

Description copied from interface: BioPAXElement

This method returns the actual model interface that a class implements.

Specified by:

getModelInterface in interface BioPAXElement

Returns:

an interface from org.biopax.paxtools.model package corresponding to a BioPAX class.

getInteractionType

public Set<InteractionVocabulary> getInteractionType()

Description copied from interface: Interaction

Controlled vocabulary term annotating the interaction type for example, "phosphorylation reaction". This annotation is meant to be human readable and may not be suitable for computing tasks, like reasoning, that require formal vocabulary systems. For instance, this information would be useful for display on a web page or for querying a database. The PSI-MI interaction type controlled vocabulary should be used. This is browsable at: OLS: PSI-MI Contents of this set should not be modified. Use add/remove instead.

Specified by:

getInteractionType in interface Interaction

Returns:

Controlled vocabulary term annotating the interaction type.

addInteractionType

public void addInteractionType(InteractionVocabulary newinteractionType)

Description copied from interface: Interaction

Controlled vocabulary term annotating the interaction type for example, "phosphorylation reaction". This annotation is meant to be human readable and may not be suitable for computing tasks, like reasoning, that require formal vocabulary systems. For instance, this information would be useful for display on a web page or for querying a database. The PSI-MI interaction type controlled vocabulary should be used. This is browsable at: OLS: PSI-MI Contents of this set should not be modified. Use add/remove instead.

Specified by:

addInteractionType in interface Interaction

Parameters:

newinteractionType - Controlled vocabulary term annotating the interaction type.

removeInteractionType

public void removeInteractionType(InteractionVocabulary oldinteractionType)

Description copied from interface: Interaction

Controlled vocabulary term annotating the interaction type for example, "phosphorylation reaction". This annotation is meant to be human readable and may not be suitable for computing tasks, like reasoning, that require formal vocabulary systems. For instance, this information would be useful for display on a web page or for querying a database. The PSI-MI interaction type controlled vocabulary should be used. This is browsable at: OLS: PSI-MI Contents of this set should not be modified. Use add/remove instead.

Specified by:

removeInteractionType in interface Interaction

Parameters:

oldinteractionType - Controlled vocabulary term annotating the interaction type.

setInteractionType

public void setInteractionType(Set<InteractionVocabulary> interactionType)

getParticipant

public Set<Entity> getParticipant()

Description copied from interface: Interaction

The entities that participate in this interaction. For example, in a biochemical reaction, the participants are the union of the reactants and the products of the reaction. Multiple sub-properties of participant are defined, such as left and right used in the BiochemicalReaction class and controller and controlled, used in the Control class. Any value of the sub-properties is automatically values of the participant property. Contents of this set should not be modified. Use add/remove instead.

Specified by:

getParticipant in interface Interaction

Returns:

The entities that participate in this interaction.

setParticipant

protected void setParticipant(Set<Entity> participant)

addParticipant

public void addParticipant(Entity aParticipant)

Description copied from interface: Interaction

The entities that participate in this interaction. For example, in a biochemical reaction, the participants are the union of the reactants and the products of the reaction. Multiple sub-properties of participant are defined, such as left and right used in the BiochemicalReaction class and controller and controlled, used in the Control class. Any value of the sub-properties is automatically values of the participant property. Contents of this set should not be modified. Use add/remove instead.

Specified by:

addParticipant in interface Interaction

Parameters:

aParticipant - The entities that participate in this interaction.

removeParticipant

public void removeParticipant(Entity aParticipant)

Description copied from interface: Interaction

The entities that participate in this interaction. For example, in a biochemical reaction, the participants are the union of the reactants and the products of the reaction. Multiple sub-properties of participant are defined, such as left and right used in the BiochemicalReaction class and controller and controlled, used in the Control class. Any value of the sub-properties is automatically values of the participant property. Contents of this set should not be modified. Use add/remove instead.

Specified by:

removeParticipant in interface Interaction

Parameters:

aParticipant - The entities that participate in this interaction.