Package org.biopax.paxtools.query.wrapperL3

Class GraphL3

java.lang.Object
org.biopax.paxtools.query.model.AbstractGraph
org.biopax.paxtools.query.wrapperL3.GraphL3
All Implemented Interfaces:
Graph
public class GraphL3 extends AbstractGraph
Wrapper for L3 Graphs.
Author:
Ozgun Babur

  • Field Details

    • model

      protected Model model
      The model to be wrapped.

    • filters

      protected List<Filter> filters

    • log

      protected final org.slf4j.Logger log
      Log for logging.

  • Constructor Details

    • GraphL3

      public GraphL3(Model model, Filter... filters)
      Constructor with the model and the IDs of the ubiquitous molecules. IDs can be null, meaning no labeling is desired.
      Parameters:
      model - Model to wrap
      filters - for filtering graph elements

  • Method Details

    • wrap

      public Node wrap(Object obj)
      This method creates a wrapper for every wrappable L3 element.
      Specified by:
      wrap in class AbstractGraph
      Parameters:
      obj - Object to wrap
      Returns:
      The wrapper

    • getKey

      public String getKey(Object wrapped)
      RDF IDs of elements is used as key in the object map.
      Specified by:
      getKey in class AbstractGraph
      Parameters:
      wrapped - Object to wrap
      Returns:
      Key

    • getWrapperSet

      public Set<Node> getWrapperSet(Set<?> objects)
      Gets wrappers of given elements
      Parameters:
      objects - Wrapped objects
      Returns:
      wrappers

    • getWrapperMap

      public Map<Object,Node> getWrapperMap(Set<?> objects)
      Gets an element-to-wrapper map for the given elements.
      Parameters:
      objects - Wrapped objects
      Returns:
      object-to-wrapper map

    • getWrappedSet

      public Set<Object> getWrappedSet(Set<? extends GraphObject> wrappers)
      Gets the wrapped objects of the given wrappers.
      Parameters:
      wrappers - Wrappers
      Returns:
      Wrapped objects

    • getModel

      public Model getModel()
      Returns:
      Wrapped model