Package org.biopax.paxtools.impl.level3

Class ConversionImpl

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.ConversionImpl
All Implemented Interfaces:
Serializable, Cloneable, BioPAXElement, Conversion, Entity, Interaction, Level3Element, Named, Observable, Process, XReferrable
Direct Known Subclasses:
BiochemicalReactionImpl, ComplexAssemblyImpl, DegradationImpl, TransportImpl
public class ConversionImpl extends InteractionImpl implements Conversion
See Also:

  • Constructor Details

    • ConversionImpl

      public ConversionImpl()

  • Method Details

    • getModelInterface

      public Class<? extends Conversion> 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.

    • getRight

      public Set<PhysicalEntity> getRight()
      Description copied from interface: Conversion
      The participants on the right side of the conversion interaction. Since conversion interactions may proceed in either the right-to-right or right-to-right direction, occupants of the right property may be either reactants or products. right is a sub-property of participants.
      Specified by:
      getRight in interface Conversion
      Returns:
      The participants on the right side of the conversion interaction.

    • addRight

      public void addRight(PhysicalEntity right)
      Description copied from interface: Conversion
      Adds a participant to the right side of the conversion interaction. Since conversion interactions may proceed in either the right-to-right or right-to-right direction, occupants of the right property may be either reactants or products. right is a sub-property of participants.
      Specified by:
      addRight in interface Conversion
      Parameters:
      right - participants to be added to the right side of the conversion interaction.

    • removeRight

      public void removeRight(PhysicalEntity right)
      Description copied from interface: Conversion
      Removes a participant from the right side of the conversion interaction. Since conversion interactions may proceed in either the right-to-right or right-to-right direction, occupants of the right property may be either reactants or products. right is a sub-property of participants.
      Specified by:
      removeRight in interface Conversion
      Parameters:
      right - participants to be removed from the right side of the conversion interaction.

    • getLeft

      public Set<PhysicalEntity> getLeft()
      Description copied from interface: Conversion
      The participants on the left side of the conversion interaction. Since conversion interactions may proceed in either the left-to-right or right-to-left direction, occupants of the left property may be either reactants or products. left is a sub-property of participants.
      Specified by:
      getLeft in interface Conversion
      Returns:
      The participants on the left side of the conversion interaction.

    • addLeft

      public void addLeft(PhysicalEntity left)
      Description copied from interface: Conversion
      Adds a participant to the left side of the conversion interaction. Since conversion interactions may proceed in either the left-to-right or right-to-left direction, occupants of the left property may be either reactants or products. left is a sub-property of participants.
      Specified by:
      addLeft in interface Conversion
      Parameters:
      left - participants to be added to the left side of the conversion interaction.

    • removeLeft

      public void removeLeft(PhysicalEntity left)
      Description copied from interface: Conversion
      Removes a participant from the left side of the conversion interaction. Since conversion interactions may proceed in either the left-to-right or right-to-left direction, occupants of the left property may be either reactants or products. left is a sub-property of participants.
      Specified by:
      removeLeft in interface Conversion
      Parameters:
      left - participants to be removed from the left side of the conversion interaction.

    • getSpontaneous

      public Boolean getSpontaneous()
      Description copied from interface: Conversion
      Specifies whether a conversion occurs spontaneously or not. If the spontaneity is not known,this property should not be specified.
      Specified by:
      getSpontaneous in interface Conversion
      Returns:
      whether if this conversion is spontaneous.

    • setSpontaneous

      public void setSpontaneous(Boolean spontaneous)
      Description copied from interface: Conversion
      Specifies whether a conversion occurs spontaneously or not. If the spontaneity is not known,this property should not be specified.
      Specified by:
      setSpontaneous in interface Conversion
      Parameters:
      spontaneous - Whether if this conversion is spontaneous.

    • getParticipantStoichiometry

      public Set<Stoichiometry> getParticipantStoichiometry()
      Description copied from interface: Conversion
      Stoichiometry of the left (Conversion.getLeft()) and right(Conversion.getRight()) participants. Note: This is a "bridge" workaround for the n-ary relationship problem. There is no default stoichiometry ( e.g. 1). Leaving this out will create reactions with unknown stoichiometry. It is a best practice to define the stoichiometry of each participant. It is invalid to define more than one stoichiometry per participant. It is invalid to reuse stoichiometry instances across conversions.
      Specified by:
      getParticipantStoichiometry in interface Conversion
      Returns:
      Stoichiometry of the left (Conversion.getLeft()) and right(Conversion.getRight()) participants.

    • addParticipantStoichiometry

      public void addParticipantStoichiometry(Stoichiometry participantStoichiometry)
      Description copied from interface: Conversion
      This method adds a stoichiometry for one of the participants of this conversion.
      Specified by:
      addParticipantStoichiometry in interface Conversion
      Parameters:
      participantStoichiometry - to be added

    • removeParticipantStoichiometry

      public void removeParticipantStoichiometry(Stoichiometry participantStoichiometry)
      Description copied from interface: Conversion
      This method removes a stoichiometry for one of the participants of this conversion.
      Specified by:
      removeParticipantStoichiometry in interface Conversion
      Parameters:
      participantStoichiometry - to be removed

    • getConversionDirection

      public ConversionDirectionType getConversionDirection()
      Description copied from interface: Conversion
      This property represents the direction of the reaction. If a reaction will run in a single direction under all biological contexts then it is considered irreversible and has a direction. Otherwise it is reversible.
      Specified by:
      getConversionDirection in interface Conversion
      Returns:
      One of REVERSIBLE, LEFT-TO-RIGHT or RIGHT-TO-LEFT

    • setConversionDirection

      public void setConversionDirection(ConversionDirectionType spontanousType)
      Description copied from interface: Conversion
      This property represents the direction of the reaction. If a reaction will run in a single direction under all biological contexts then it is considered irreversible and has a direction. Otherwise it is reversible.
      Specified by:
      setConversionDirection in interface Conversion
      Parameters:
      spontanousType - One of REVERSIBLE, LEFT-TO-RIGHT or RIGHT-TO-LEFT -- null for unknown.

    • semanticallyEquivalent

      protected boolean semanticallyEquivalent(BioPAXElement element)
      Overrides:
      semanticallyEquivalent in class EntityImpl

    • equivalenceCode

      public int equivalenceCode()
      Description copied from interface: BioPAXElement
      If two elements are equivalent, then their equivalence code should be the same.
      Specified by:
      equivalenceCode in interface BioPAXElement
      Overrides:
      equivalenceCode in class XReferrableImpl
      Returns:
      an integer that is same across all equivalent entities.