Package 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
public class InteractionImpl extends ProcessImpl implements Interaction
See Also:

  • Constructor Details

    • InteractionImpl

      public InteractionImpl()

  • Method Details

    • 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.

    • 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.