Package org.biopax.paxtools.io

Interface BioPAXIOHandler

All Known Implementing Classes:
BioPAXIOHandlerAdapter, SimpleIOHandler
public interface BioPAXIOHandler
This interface defines IO related operations that can be performed on BioPAX models.

  • Method Details

    • fixReusedPEPs

      void fixReusedPEPs(boolean fixReusedPEPs)
      This option is only applicable two level 2 models. When enabled it will replicate illegally reused pysicalEntityParticipants in Level2 files.
      Parameters:
      fixReusedPEPs - true or false

    • convertFromOWL

      Model convertFromOWL(InputStream in)
      This method will read the OWL document given by the input stream and will convert it into an in memory BioPAX model.
      Parameters:
      in - a BioPAX data input stream (RDF/XML format)
      Returns:
      new BioPAX object Model

    • convertToOWL

      void convertToOWL(Model model, OutputStream outputStream)
      This method will write the model to the output stream. Default encoding is RDF/XML.
      Parameters:
      model - a BioPAX model
      outputStream - output stream

    • isFixReusedPEPs

      boolean isFixReusedPEPs()
      This option is only applicable two level 2 models. When enabled it will replicate illegally reused pysicalEntityParticipants in Level2 files.
      Returns:
      true if this option is enabled.

    • getFactory

      BioPAXFactory getFactory()
      Returns:
      the factory that is used to create new BioPAX POJOs during a BioPAXIOHandler operation.

    • setFactory

      void setFactory(BioPAXFactory factory)
      Parameters:
      factory - used for creating objects

    • getEditorMap

      EditorMap getEditorMap()
      Returns:
      EditorMap used for this handler.

    • setEditorMap

      void setEditorMap(EditorMap editorMap)
      Parameters:
      editorMap - used for this handler.

    • getLevel

      BioPAXLevel getLevel()
      Returns:
      The level of the model that is being read.

    • convertToOWL

      void convertToOWL(Model model, OutputStream outputStream, String... ids)
      This method will "excise" a new model from the given model that contains the objects with given ids and their dependents.
      Parameters:
      model - BioPAX object model to be exported to the output stream as RDF/XML
      outputStream - the stream
      ids - optional list of absolute URIs of BioPAX objects - roots/seeds for extracting a sub-model to be exported