Class BioPAXReader

java.lang.Object
org.episteme.core.io.AbstractResourceReader<BioPAXModel>
org.episteme.natural.biology.loaders.biopax.BioPAXReader
All Implemented Interfaces:
ResourceIO<BioPAXModel>, ResourceReader<BioPAXModel>
public class BioPAXReader extends AbstractResourceReader<BioPAXModel>
BioPAX Reader for biological pathways and networks.

BioPAX (Biological Pathway Exchange) is an RDF/OWL-based format for exchanging pathway, metabolic, and signaling data.

Since:
1.0
Author:
Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

  • Constructor Details

    • BioPAXReader

      public BioPAXReader()

  • Method Details

    • getResourcePath

      public String getResourcePath()
      Description copied from interface: ResourceIO
      Returns the base path where this resource is located.

    • getResourceType

      public Class<BioPAXModel> getResourceType()
      Description copied from interface: ResourceIO
      Returns the type of resource.

    • getName

      public String getName()
      Description copied from interface: ResourceIO
      Returns the display name of this resource handler. MUST be implemented with I18N support.
      Returns:
      the display name

    • getDescription

      public String getDescription()
      Description copied from interface: ResourceIO
      Returns a short description of this resource handler. MUST be implemented with I18N support.
      Returns:
      the description

    • getLongDescription

      public String getLongDescription()
      Description copied from interface: ResourceIO
      Returns a long description of this resource handler. MUST be implemented with I18N support.
      Returns:
      the long description

    • getCategory

      public String getCategory()
      Description copied from interface: ResourceIO
      Returns the category for grouping. MUST be implemented with I18N support.
      Returns:
      the category name

    • getSupportedVersions

      public String[] getSupportedVersions()
      Description copied from interface: ResourceIO
      Returns the supported versions of the format this reader/writer handles.

      Each implementation MUST override this method to declare which versions of the underlying format are supported. The returned array should contain version strings in the format's standard notation (e.g., "3.0", "2.1", "Level 3 Version 2").

      Examples:

      • MathML: {"3.0", "2.0"}
      • SBML: {"Level 3 Version 2", "Level 3 Version 1", "Level 2 Version 5"}
      • PhyloXML: {"1.10", "1.00"}

      Returns:
      array of supported version strings, never null (empty array if version-agnostic)

    • loadFromSource

      protected BioPAXModel loadFromSource(String resourceId) throws Exception
      Specified by:
      loadFromSource in class AbstractResourceReader<BioPAXModel>
      Throws:
      Exception

    • loadFromInputStream

      protected BioPAXModel loadFromInputStream(InputStream is, String id) throws Exception
      Overrides:
      loadFromInputStream in class AbstractResourceReader<BioPAXModel>
      Throws:
      Exception

    • read

      public BioPAXModel read(InputStream input) throws BioPAXException
      Throws:
      BioPAXException

    • read

      public BioPAXModel read(File file) throws BioPAXException
      Throws:
      BioPAXException