Package org.biopax.paxtools.query.wrapperL3undirected

Class ControlWrapper

java.lang.Object
org.biopax.paxtools.query.model.AbstractNode
org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper
All Implemented Interfaces:
GraphObject, Node
public class ControlWrapper extends AbstractNode
Wrapper for the Control class.
Author:
Ozgun Babur

  • Field Details

    • ctrl

      protected Control ctrl
      Wrapped control.

    • sign

      protected int sign
      Sign of the control.

    • transcription

      protected boolean transcription
      Flag to indicate if this control is related to a transcription.

  • Constructor Details

    • ControlWrapper

      protected ControlWrapper(Control ctrl, Graph graph)
      Constructor with the Control and the owner graph.
      Parameters:
      ctrl - Control to be wrapped
      graph - Owner graph

  • Method Details

    • isBreadthNode

      public boolean isBreadthNode()
      Control is not a breadth node.
      Returns:
      False

    • getSign

      public int getSign()
      Description copied from interface: Node
      Some nodes can have a sign (typically non-breadth nodes).
      Returns:
      Sign of the Control

    • isUbique

      public boolean isUbique()
      Controls are not ubiquitous molecules.
      Returns:
      False

    • getKey

      public String getKey()
      RDF ID of the Control is its key.
      Returns:
      Key

    • init

      public void init()
      Extracts the sign and the type of the Control.
      Specified by:
      init in interface Node
      Overrides:
      init in class AbstractNode

    • initUpstream

      public void initUpstream()
      Binds the controller and other Controls that controls this control.
      Overrides:
      initUpstream in class AbstractNode

    • initDownstream

      public void initDownstream()
      Binds the controlled objects.
      Overrides:
      initDownstream in class AbstractNode

    • getControl

      public Control getControl()
      Gets the wrapped Control.
      Returns:
      The Control

    • getUpperEquivalent

      public Collection<Node> getUpperEquivalent()
      Control cannot have an equivalent.
      Specified by:
      getUpperEquivalent in interface Node
      Overrides:
      getUpperEquivalent in class AbstractNode
      Returns:
      Empty set

    • getLowerEquivalent

      public Collection<Node> getLowerEquivalent()
      Control cannot have an equivalent.
      Specified by:
      getLowerEquivalent in interface Node
      Overrides:
      getLowerEquivalent in class AbstractNode
      Returns:
      Empty set

    • isTranscription

      public boolean isTranscription()
      Description copied from class: AbstractNode
      Nodes are not transcription by default.
      Specified by:
      isTranscription in interface Node
      Overrides:
      isTranscription in class AbstractNode
      Returns:
      whether this Control is related to a transcription event

    • setTranscription

      public void setTranscription(boolean transcription)
      Make or not make this control related to a transcription.
      Parameters:
      transcription - whether this Control is related to a transcription