Package org.biopax.paxtools.impl.level3

Class StoichiometryImpl

java.lang.Object
org.biopax.paxtools.impl.BioPAXElementImpl
org.biopax.paxtools.impl.level3.L3ElementImpl
org.biopax.paxtools.impl.level3.StoichiometryImpl
All Implemented Interfaces:
Serializable, Cloneable, BioPAXElement, Level3Element, Stoichiometry, UtilityClass
public class StoichiometryImpl extends L3ElementImpl implements Stoichiometry
See Also:

  • Constructor Details

    • StoichiometryImpl

      public StoichiometryImpl()

  • Method Details

    • getModelInterface

      public Class<? extends Stoichiometry> 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.

    • semanticallyEquivalent

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

    • 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 BioPAXElementImpl
      Returns:
      an integer that is same across all equivalent entities.

    • getPhysicalEntity

      public PhysicalEntity getPhysicalEntity()
      Specified by:
      getPhysicalEntity in interface Stoichiometry
      Returns:
      the physical entity to be annotated with stoichiometry.

    • setPhysicalEntity

      public void setPhysicalEntity(PhysicalEntity PhysicalEntity)
      Specified by:
      setPhysicalEntity in interface Stoichiometry
      Parameters:
      PhysicalEntity - entity to be annotated with stoichiometry.

    • getStoichiometricCoefficient

      public float getStoichiometricCoefficient()
      Description copied from interface: Stoichiometry
      Stoichiometric coefficient of the physicalEntity specified by Stoichiometry.getPhysicalEntity() in the context of the owner interaction or complex. This value can be any rational number. Generic values such as "n" or "n+1" should not be used - polymers are currently not covered.
      Specified by:
      getStoichiometricCoefficient in interface Stoichiometry
      Returns:
      Stoichiometric coefficient for one of the entities in an interaction or complex

    • setStoichiometricCoefficient

      public void setStoichiometricCoefficient(float newStoichiometricCoefficient)
      Description copied from interface: Stoichiometry
      Sets the stoichiometric coefficient of the physicalEntity specified by Stoichiometry.getPhysicalEntity() in the context of the owner interaction or complex. { can be any rational number. Generic values such as "n" or "n+1" should not be used - polymers are currently not covered.
      Specified by:
      setStoichiometricCoefficient in interface Stoichiometry
      Parameters:
      newStoichiometricCoefficient - of the physical entity