Package org.biopax.paxtools.query.wrapperL3undirected

Class PhysicalEntityWrapper

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

  • Field Details

    • pe

      protected PhysicalEntity pe
      Wrapped PhysicalEntity.

    • upperEquivalentInited

      protected boolean upperEquivalentInited
      Flag to remember if parent equivalents initialized.

    • lowerEquivalentInited

      protected boolean lowerEquivalentInited
      Flag to remember if child equivalents initialized.

    • ubique

      protected boolean ubique
      Flag to say this is a ubiquitous molecule.

  • Constructor Details

    • PhysicalEntityWrapper

      public PhysicalEntityWrapper(PhysicalEntity pe, GraphL3Undirected graph)
      Constructor with the wrapped PhysicalEntity and the owner graph.
      Parameters:
      pe - PhysicalEntity to wrap
      graph - Owner graph

  • Method Details

    • isUbique

      public boolean isUbique()
      Description copied from interface: Node
      In biological graphs, some nodes are used ubiquitously like ATP, H2O, etc. While traversing a graph we do not want these molecules to link two reactions. So they should be labeled.
      Returns:
      Whether this is ubique

    • setUbique

      public void setUbique(boolean ubique)
      Set the ubique flag.
      Parameters:
      ubique - Whether this is a ubiquitous molecule

    • initUpstream

      public void initUpstream()
      Binds to upstream interactions.
      Overrides:
      initUpstream in class AbstractNode

    • initDownstream

      public void initDownstream()
      Binds to downstream interactions.
      Overrides:
      initDownstream in class AbstractNode

    • getUpperEquivalent

      public Collection<Node> getUpperEquivalent()
      Specified by:
      getUpperEquivalent in interface Node
      Overrides:
      getUpperEquivalent in class AbstractNode
      Returns:
      Parent equivalent objects

    • getLowerEquivalent

      public Collection<Node> getLowerEquivalent()
      Specified by:
      getLowerEquivalent in interface Node
      Overrides:
      getLowerEquivalent in class AbstractNode
      Returns:
      Child equivalent objects

    • initUpperEquivalent

      protected void initUpperEquivalent()
      Finds homology parent.

    • initLowerEquivalent

      protected void initLowerEquivalent()
      Finds member nodes if this is a homology node

    • isBreadthNode

      public boolean isBreadthNode()
      PhysicalEntity is a breadth node.
      Returns:
      True

    • getSign

      public int getSign()
      PhysicalEntity have positive sign.
      Returns:
      POSITIVE (1)

    • getKey

      public String getKey()
      RDF ID of the PhysicalEntity is used as key.
      Returns:
      Key

    • getPhysicalEntity

      public PhysicalEntity getPhysicalEntity()
      Returns:
      Wrapped PhysicalEntity

    • toString

      public String toString()
      Overrides:
      toString in class Object
      Returns:
      display name with ID added