Package org.biopax.paxtools.impl.level3

Class GeneticInteractionImpl

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

org.biopax.paxtools.impl.level3.GeneticInteractionImpl

All Implemented Interfaces:

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

public class GeneticInteractionImpl
extends InteractionImpl
implements GeneticInteraction

See Also:

• Serialized Form

Field Summary

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

Constructors

Constructor	Description
GeneticInteractionImpl()

Method Summary

Modifier and Type	Method	Description
void	addParticipant(Entity aParticipant)	The entities that participate in this interaction.
Score	getInteractionScore()
Class<? extends GeneticInteraction>	getModelInterface()	This method returns the actual model interface that a class implements.
PhenotypeVocabulary	getPhenotype()
void	setInteractionScore(Score interactionScore)
void	setPhenotype(PhenotypeVocabulary phenotype)

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

addInteractionType, getInteractionType, getParticipant, removeInteractionType, removeParticipant, setParticipant

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

getControlledOf, getPathwayComponentOf, getStepProcessOf

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

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

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

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

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, removeComment, setComment

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

equals, getAnnotations, getUri, 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.BioPAXElement

equivalenceCode, getAnnotations, getUri, isEquivalent

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.Interaction

addInteractionType, getInteractionType, getParticipant, removeInteractionType, removeParticipant

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

addComment, getComment, removeComment

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.Observable

addEvidence, getEvidence, removeEvidence

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

getControlledOf, getPathwayComponentOf, getStepProcessOf

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

addXref, getXref, removeXref

Constructor Details

GeneticInteractionImpl

public GeneticInteractionImpl()

Method Details

getModelInterface

public Class<? extends GeneticInteraction> getModelInterface()

Description copied from interface: BioPAXElement

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

Specified by:

getModelInterface in interface BioPAXElement

Overrides:

getModelInterface in class InteractionImpl

Returns:

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

getPhenotype

public PhenotypeVocabulary getPhenotype()

Specified by:

getPhenotype in interface GeneticInteraction

Returns:

The phenotype quality used to define this genetic interaction e.g. viability.

setPhenotype

public void setPhenotype(PhenotypeVocabulary phenotype)

Specified by:

setPhenotype in interface GeneticInteraction

Parameters:

phenotype - The phenotype quality used to define this genetic interaction e.g. viability.

getInteractionScore

public Score getInteractionScore()

Specified by:

getInteractionScore in interface GeneticInteraction

Returns:

The score of an interaction e.g. a genetic interaction score.

setInteractionScore

public void setInteractionScore(Score interactionScore)

Specified by:

setInteractionScore in interface GeneticInteraction

Parameters:

interactionScore - The score of an interaction e.g. a genetic interaction score.

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

Overrides:

addParticipant in class InteractionImpl

Parameters:

aParticipant - The entities that participate in this interaction.