Class SBMLReader

java.lang.Object
org.episteme.core.io.AbstractResourceReader<SBMLModel>
org.episteme.natural.biology.loaders.sbml.SBMLReader
All Implemented Interfaces:
ResourceIO<SBMLModel>, ResourceReader<SBMLModel>
public class SBMLReader extends AbstractResourceReader<SBMLModel>
Systems Biology Markup Language (SBML) Reader.

Parses SBML files using the JSBML library, supporting SBML Level 3 Core and common extensions like FBC (Flux Balance Constraints).

Supported Features:

  • Model metadata (name, ID, notes)
  • Compartments with sizes and units
  • Species (metabolites) with concentrations
  • Reactions with kinetic laws and stoichiometry
  • Parameters (global and local)
  • FBC extension for flux balance analysis

Example Usage: 

SBMLReader reader = new SBMLReader();
SBMLModel model = reader.read(new File("ecoli_core.xml"));

System.out.println("Model: " + model.getName());
System.out.println("Species: " + model.getSpeciesCount());
System.out.println("Reactions: " + model.getReactionCount());

// Get stoichiometry matrix for FBA
RealDoubleMatrix stoichiometry = model.getStoichiometryMatrix();

* @see SBML.org
Since:
1.0
Author:
Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

  • Constructor Details

    • SBMLReader

      public SBMLReader()
      Creates a new SBMLReader.

  • Method Details

    • getResourcePath

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

    • getResourceType

      public Class<SBMLModel> 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 SBMLModel loadFromSource(String resourceId) throws Exception
      Specified by:
      loadFromSource in class AbstractResourceReader<SBMLModel>
      Throws:
      Exception

    • loadFromInputStream

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

    • read

      public SBMLModel read(File file) throws SBMLException
      Reads an SBML model from a file.
      Parameters:
      file - the SBML file
      Returns:
      an SBMLModel containing the parsed data
      Throws:
      SBMLException - if parsing fails

    • read

      public SBMLModel read(InputStream input) throws SBMLException
      Reads an SBML model from an input stream.
      Parameters:
      input - the input stream containing SBML data
      Returns:
      an SBMLModel containing the parsed data
      Throws:
      SBMLException - if parsing fails