Package org.biopax.paxtools.model.level3

Interface Pathway

All Superinterfaces:
BioPAXElement, Cloneable, Controller, Entity, Level3Element, Named, Observable, Process, Serializable, XReferrable
All Known Implementing Classes:
PathwayImpl
public interface Pathway extends Process, Controller

  • Method Details

    • getPathwayComponent

      Set<Process> getPathwayComponent()

    • addPathwayComponent

      void addPathwayComponent(Process components)

    • removePathwayComponent

      void removePathwayComponent(Process components)

    • getPathwayOrder

      Set<PathwayStep> getPathwayOrder()

    • addPathwayOrder

      void addPathwayOrder(PathwayStep order)

    • removePathwayOrder

      void removePathwayOrder(PathwayStep order)

    • getOrganism

      BioSource getOrganism()
      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.
      Returns:
      the organism for this gene.

    • setOrganism

      void setOrganism(BioSource source)
      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.
      Parameters:
      source - new organism for this gene