Module omix.api
Package omix.lang.model

Interface MetabolicNetwork

All Superinterfaces:
Item, Network
@OVLExtensible
@Deprecated(since="Omix 2.0")
@ReplacedBy("omix.lang.model.Model")
public interface MetabolicNetwork
extends Network
Deprecated.
Represents the metabolic network diagram. This Java interface represents MetabolicNetwork in OVL. It contain all methods available in OVL.
Author:
Dr. Peter Droste, Omix Visualization

  • Method Details

    • metabolites

      List<? extends Metabolite> metabolites()
      Deprecated.
      Returns an unchangeable List of all metabolite nodes.
      Returns:
      list of metabolites

    • reactions

      List<? extends Reaction> reactions()
      Deprecated.
      Returns an unchangeable List of all reaction nodes.
      Returns:
      list of reactions

    • pathways

      List<? extends Pathway> pathways()
      Deprecated.
      Returns an unchangeable List of all pathway items.
      Returns:
      list of pathways

    • compartments

      List<? extends Compartment> compartments()
      Deprecated.
      Returns an unchangeable List of all compartment items.
      Returns:
      list of compartments

    • graphicsNodes

      List<? extends GraphicsNode> graphicsNodes()
      Deprecated.
      Returns an unchangeable List of all graphics node items.
      Returns:
      list of node items
      Since:
      Omix 1.8.0

    • graphicsEdges

      List<? extends GraphicsEdge> graphicsEdges()
      Deprecated.
      Returns an unchangeable List of all graphics edges (connection edges).
      Returns:
      list of graphics edges
      Since:
      Omix 1.8.0

    • fluxEdges

      List<? extends FluxEdge> fluxEdges()
      Deprecated.
      Returns an unchangeable List of all flux edges.
      Returns:
      list of flux edges

    • effectorEdges

      List<? extends EffectorEdge> effectorEdges()
      Deprecated.
      Returns an unchangeable List of all effector edges.
      Returns:
      list of effector edges

    • comments

      @Deprecated default List<? extends Comment> comments()
      Deprecated.
      Returns an unchangeable List of all top level comment items.
      Returns:
      list of comments

    • graphicsItems

      List<? extends GraphicsItem> graphicsItems()
      Deprecated.
      Returns an unchangeable List of all graphical items.
      Returns:
      list of graphical items

    • getMetabolite

      Metabolite getMetabolite​(String name)
      Deprecated.
      Returns the (compartment free) metabolite node of the given name if available, otherwise null. In order to get access to metabolites contained in a compartment call Compartment.getMetabolite(String).
      Parameters:
      name - of metabolite
      Returns:
      found metabolite

    • getReaction

      Reaction getReaction​(String name)
      Deprecated.
      Returns the reaction nodes of the given name if available, otherwise null.
      Parameters:
      name - of the reaction
      Returns:
      found reaction

    • getPathway

      Pathway getPathway​(String name)
      Deprecated.
      Returns the pathway of the given name if available, otherwise null.
      Parameters:
      name - of the pathway
      Returns:
      found pathway

    • getCompartment

      Compartment getCompartment​(String name)
      Deprecated.
      Returns a toplevel compartment of the given name if available, otherwise null. In order to get access to a sub compartment call Compartment.getSubCompartment(String).
      Parameters:
      name - of the compartment
      Returns:
      found compartment

    • getGraphicsNode

      GraphicsNode getGraphicsNode​(String identifier)
      Deprecated.
      Returns the graphics node item with the given identifier if available, otherwise null.
      Parameters:
      identifier - of the graphics node
      Returns:
      found graphics node

    • getGraphicsItem

      GraphicsItem getGraphicsItem​(String identifier)
      Deprecated.
      Returns the graphics item with the given identifier if available, otherwise null.
      Parameters:
      identifier - of the graphics item
      Returns:
      found graphics item
      Since:
      Omix 1.8.0

    • getComment

      @Deprecated default Comment getComment​(String identifier)
      Deprecated.
      Returns the top level comment item with the given identifier if available, otherwise null.
      Parameters:
      identifier - of the comment item
      Returns:
      found comment item