Class SBMLModel

java.lang.Object
org.episteme.natural.biology.loaders.sbml.SBMLModel
All Implemented Interfaces:
UniversalDataModel
public class SBMLModel extends Object implements UniversalDataModel
Represents an SBML model for systems biology.

Contains compartments, species (metabolites), reactions, and parameters from an SBML file. Provides methods to construct stoichiometry matrices for flux balance analysis.

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

  • Constructor Details

    • SBMLModel

      public SBMLModel()

  • Method Details

    • getId

      public String getId()

    • setId

      public void setId(String id)

    • getName

      public String getName()

    • setName

      public void setName(String name)

    • getLevel

      public int getLevel()

    • setLevel

      public void setLevel(int level)

    • getVersion

      public int getVersion()

    • setVersion

      public void setVersion(int version)

    • getNotes

      public String getNotes()

    • setNotes

      public void setNotes(String notes)

    • getCompartments

      public List<SBMLCompartment> getCompartments()

    • addCompartment

      public void addCompartment(SBMLCompartment compartment)

    • getSpecies

      public List<SBMLSpecies> getSpecies()

    • addSpecies

      public void addSpecies(SBMLSpecies sp)

    • getSpeciesById

      public SBMLSpecies getSpeciesById(String id)

    • getSpeciesCount

      public int getSpeciesCount()

    • getReactions

      public List<SBMLReaction> getReactions()

    • addReaction

      public void addReaction(SBMLReaction reaction)

    • getReactionById

      public SBMLReaction getReactionById(String id)

    • getReactionCount

      public int getReactionCount()

    • getParameters

      public List<SBMLParameter> getParameters()

    • addParameter

      public void addParameter(SBMLParameter parameter)

    • getGeneProducts

      public List<SBMLGeneProduct> getGeneProducts()

    • addGeneProduct

      public void addGeneProduct(SBMLGeneProduct geneProduct)

    • getInternalMetabolites

      public List<SBMLSpecies> getInternalMetabolites()
      Returns the list of internal metabolites (non-boundary species).

    • getBoundaryMetabolites

      public List<SBMLSpecies> getBoundaryMetabolites()
      Returns the list of boundary metabolites.

    • getStoichiometryMatrix

      public RealDoubleMatrix getStoichiometryMatrix()
      Constructs the stoichiometry matrix S where S[i][j] is the stoichiometric coefficient of species i in reaction j.

      Reactants have negative coefficients, products have positive. Only internal (non-boundary) species are included.

      Returns:
      the stoichiometry matrix as a RealDoubleMatrix

    • getMetaboliteOrder

      public List<String> getMetaboliteOrder()
      Returns species IDs in the order used by the stoichiometry matrix.

    • getReactionOrder

      public List<String> getReactionOrder()
      Returns reaction IDs in the order used by the stoichiometry matrix.

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • getModelType

      public String getModelType()
      Description copied from interface: UniversalDataModel
      Returns a unique identifier for the type of data model. Examples: "SPATIAL_GEOMETRY", "ECONOMIC_PORTFOLIO", "ARCHITECTURAL_PLAN".
      Specified by:
      getModelType in interface UniversalDataModel

    • getMetadata

      public Map<String,Object> getMetadata()
      Description copied from interface: UniversalDataModel
      Returns a map of metadata for this model (e.g., creation date, source).
      Specified by:
      getMetadata in interface UniversalDataModel

    • getQuantities

      public Map<String, Quantity<?>> getQuantities()
      Description copied from interface: UniversalDataModel
      Returns the primary physical values associated with this model. This allows generic tools to extract and convert measurements.
      Specified by:
      getQuantities in interface UniversalDataModel