Package org.biopax.paxtools.impl.level3

Class PathwayImpl

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.PathwayImpl
All Implemented Interfaces:
Serializable, Cloneable, BioPAXElement, Controller, Entity, Level3Element, Named, Observable, Pathway, Process, XReferrable
public class PathwayImpl extends ProcessImpl implements Pathway
See Also:

  • Constructor Details

    • PathwayImpl

      public PathwayImpl()

  • Method Details

    • getModelInterface

      public Class<? extends Pathway> 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.

    • getPathwayComponent

      public Set<Process> getPathwayComponent()
      Specified by:
      getPathwayComponent in interface Pathway

    • addPathwayComponent

      public void addPathwayComponent(Process component)
      Specified by:
      addPathwayComponent in interface Pathway

    • removePathwayComponent

      public void removePathwayComponent(Process component)
      Specified by:
      removePathwayComponent in interface Pathway

    • getPathwayOrder

      public Set<PathwayStep> getPathwayOrder()
      Specified by:
      getPathwayOrder in interface Pathway

    • addPathwayOrder

      public void addPathwayOrder(PathwayStep pathwayOrder)
      Specified by:
      addPathwayOrder in interface Pathway

    • removePathwayOrder

      public void removePathwayOrder(PathwayStep pathwayOrder)
      Specified by:
      removePathwayOrder in interface Pathway

    • getOrganism

      public BioSource getOrganism()
      Description copied from interface: Pathway
      An organism, e.g. 'Homo sapiens'. This is the organism that the entity is found in. Pathways may not have an organism associated with them, for instance, reference pathways from KEGG. Sequence-based entities (DNA, protein, RNA) may contain an xref to a sequence database that contains organism information, in which case the information should be consistent with the value for ORGANISM.
      Specified by:
      getOrganism in interface Pathway
      Returns:
      the organism for this gene.

    • setOrganism

      public void setOrganism(BioSource organism)
      Description copied from interface: Pathway
      An organism, e.g. 'Homo sapiens'. This is the organism that the entity is found in. Pathways may not have an organism associated with them, for instance, reference pathways from KEGG. Sequence-based entities (DNA, protein, RNA) may contain an xref to a sequence database that contains organism information, in which case the information should be consistent with the value for ORGANISM.
      Specified by:
      setOrganism in interface Pathway
      Parameters:
      organism - new organism for this gene

    • getControllerOf

      public Set<Control> getControllerOf()
      Description copied from interface: Controller
      This method returns the list of Control interactions that this entity controls. Reverse method of Control.getController(). Contents of this set is automatically maintained and should not be modified.
      Specified by:
      getControllerOf in interface Controller
      Returns:
      list of Control interactions that this entity controls.