org.sbml.jsbml.util

Class ModelBuilder

java.lang.Object

org.sbml.jsbml.util.ModelBuilder

public class ModelBuilder
extends java.lang.Object

This class provides a collection of convenient methods to create SBML models and documents.

Since:

1.0

Version:

$Rev$

Author:

Andreas Dräger

Field Summary

Fields

Modifier and Type	Field and Description
private SBMLDocument	doc

Constructor Summary

Constructors

Constructor and Description
ModelBuilder(int level, int version)

Method Summary

Modifier and Type	Method and Description
Compartment	buildCompartment(java.lang.String id, boolean constant, java.lang.String name, double spatialDimensions, double size, java.lang.String sizeUnits)
Compartment	buildCompartment(java.lang.String id, boolean constant, java.lang.String name, double spatialDimensions, double size, Unit.Kind sizeUnits)
Compartment	buildCompartment(java.lang.String id, boolean constant, java.lang.String name, double spatialDimensions, double size, UnitDefinition sizeUnits)
static KineticLaw	buildKineticLaw(Reaction reaction, java.lang.String formula, Pair<java.lang.String,java.lang.Double>... localParameters)
Model	buildModel(java.lang.String id, java.lang.String name)
static void	buildModifiers(Reaction reaction, Pair<Species,java.lang.Integer>... modifiers) A convenient method to create multiple modifiers in one single step by passing the Species along with its role (SBO term) to this method.
Parameter	buildParameter(java.lang.String id, java.lang.String name, double value, boolean constant, java.lang.String units)
Parameter	buildParameter(java.lang.String id, java.lang.String name, double value, boolean constant, Unit.Kind units)
Parameter	buildParameter(java.lang.String id, java.lang.String name, double value, boolean constant, UnitDefinition units)
private static void	buildParticipants(ListOf<SpeciesReference> listOf, Pair<java.lang.Double,Species>... participants) This builds multiple reaction participants in one step and adds them to the given list of SpeciesReferences.
static void	buildProducts(Reaction reaction, Pair<java.lang.Double,Species>... products) Convenient method to build multiple products together with their stoichiometry in one step.
static void	buildReactants(Reaction reaction, Pair<java.lang.Double,Species>... reactants) Convenient method to build multiple reactants together with their stoichiometry in one step.
Reaction	buildReaction(java.lang.String id, java.lang.String name, Compartment compartment, boolean fast, boolean reversible)
Reaction	buildReaction(java.lang.String id, java.lang.String name, java.lang.String compartment, boolean fast, boolean reversible)
Species	buildSpecies(java.lang.String id, java.lang.String name, Compartment compartment, boolean hasOnlySubstanceUnits, boolean boundaryCondition, boolean constant, double initialConcentration, java.lang.String substanceUnits)
Species	buildSpecies(java.lang.String id, java.lang.String name, Compartment compartment, boolean hasOnlySubstanceUnits, boolean boundaryCondition, boolean constant, double initialConcentration, Unit.Kind substanceUnits)
Species	buildSpecies(java.lang.String id, java.lang.String name, Compartment compartment, boolean hasOnlySubstanceUnits, boolean boundaryCondition, boolean constant, double initialConcentration, UnitDefinition substanceUnits)
Species	buildSpecies(java.lang.String id, java.lang.String name, java.lang.String compartmentId, boolean hasOnlySubstanceUnits, boolean boundaryCondition, boolean constant, double initialConcentration, java.lang.String substanceUnits)
static Unit	buildUnit(UnitDefinition parent, double multiplier, int scale, Unit.Kind kind, double exponent)
UnitDefinition	buildUnitDefinition(java.lang.String id, java.lang.String name)
Model	getModel()
SBMLDocument	getSBMLDocument()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

doc

private SBMLDocument doc

Constructor Detail

ModelBuilder

public ModelBuilder(int level,
                    int version)

Parameters:

level -

version -

Method Detail

buildKineticLaw

public static KineticLaw buildKineticLaw(Reaction reaction,
                                         java.lang.String formula,
                                         Pair<java.lang.String,java.lang.Double>... localParameters)
                                  throws ParseException

Parameters:

reaction -

formula -

localParameters -

Returns:

Throws:

ParseException

buildModifiers

public static void buildModifiers(Reaction reaction,
                                  Pair<Species,java.lang.Integer>... modifiers)

A convenient method to create multiple modifiers in one single step by passing the Species along with its role (SBO term) to this method.

Parameters:

reaction - The Reaction for which modifiers are to be created.

modifiers - an array of Species along with an SBO term to be used to define the role of the modifier in this reaction.

buildParticipants

private static void buildParticipants(ListOf<SpeciesReference> listOf,
                                      Pair<java.lang.Double,Species>... participants)

This builds multiple reaction participants in one step and adds them to the given list of SpeciesReferences.

Parameters:

listOf - where to add new SpeciesReference

participants - the definition of stoichiometry and Species for which a reaction participant is to be created.

buildProducts

public static void buildProducts(Reaction reaction,
                                 Pair<java.lang.Double,Species>... products)

Convenient method to build multiple products together with their stoichiometry in one step. If the level is three or beyond, the constant attributes of the newly created products are set to true for convenience (as this is a required attribute).

Parameters:

reaction - the Reaction for which products are to be created.

products - the definition of stoichiometry and Species for which a product is to be created.

buildReactants

public static void buildReactants(Reaction reaction,
                                  Pair<java.lang.Double,Species>... reactants)

Convenient method to build multiple reactants together with their stoichiometry in one step. If the level is three or beyond, the constant attributes of the newly created reactants are set to true for convenience (as this is a required attribute).

Parameters:

reaction - the Reaction for which reactants are to be created.

reactants - the definition of stoichiometry and Species for which a reactant is to be created.

buildUnit

public static Unit buildUnit(UnitDefinition parent,
                             double multiplier,
                             int scale,
                             Unit.Kind kind,
                             double exponent)

Parameters:

parent -

multiplier -

scale -

kind -

exponent -

Returns:

buildCompartment

public Compartment buildCompartment(java.lang.String id,
                                    boolean constant,
                                    java.lang.String name,
                                    double spatialDimensions,
                                    double size,
                                    java.lang.String sizeUnits)

Parameters:

id -

constant -

name -

spatialDimensions -

size -

sizeUnits -

Returns:

buildCompartment

public Compartment buildCompartment(java.lang.String id,
                                    boolean constant,
                                    java.lang.String name,
                                    double spatialDimensions,
                                    double size,
                                    Unit.Kind sizeUnits)

Parameters:

id -

constant -

name -

spatialDimensions -

size -

sizeUnits -

Returns:

buildCompartment

public Compartment buildCompartment(java.lang.String id,
                                    boolean constant,
                                    java.lang.String name,
                                    double spatialDimensions,
                                    double size,
                                    UnitDefinition sizeUnits)

Parameters:

id -

constant -

name -

spatialDimensions -

size -

sizeUnits -

Returns:

buildModel

public Model buildModel(java.lang.String id,
                        java.lang.String name)

Parameters:

id -

name -

Returns:

buildParameter

public Parameter buildParameter(java.lang.String id,
                                java.lang.String name,
                                double value,
                                boolean constant,
                                java.lang.String units)

Parameters:

id -

name -

value -

constant -

units -

Returns:

buildParameter

public Parameter buildParameter(java.lang.String id,
                                java.lang.String name,
                                double value,
                                boolean constant,
                                Unit.Kind units)

Parameters:

id -

name -

value -

constant -

units -

Returns:

buildParameter

public Parameter buildParameter(java.lang.String id,
                                java.lang.String name,
                                double value,
                                boolean constant,
                                UnitDefinition units)

Parameters:

id -

name -

value -

constant -

units -

Returns:

buildReaction

public Reaction buildReaction(java.lang.String id,
                              java.lang.String name,
                              Compartment compartment,
                              boolean fast,
                              boolean reversible)

Parameters:

id -

name -

compartment -

fast -

reversible -

Returns:

buildReaction

public Reaction buildReaction(java.lang.String id,
                              java.lang.String name,
                              java.lang.String compartment,
                              boolean fast,
                              boolean reversible)

Parameters:

id -

name -

compartment -

fast -

reversible -

Returns:

buildSpecies

public Species buildSpecies(java.lang.String id,
                            java.lang.String name,
                            Compartment compartment,
                            boolean hasOnlySubstanceUnits,
                            boolean boundaryCondition,
                            boolean constant,
                            double initialConcentration,
                            java.lang.String substanceUnits)

Parameters:

id -

name -

compartment -

hasOnlySubstanceUnits -

boundaryCondition -

constant -

initialConcentration -

substanceUnits -

Returns:

buildSpecies

public Species buildSpecies(java.lang.String id,
                            java.lang.String name,
                            Compartment compartment,
                            boolean hasOnlySubstanceUnits,
                            boolean boundaryCondition,
                            boolean constant,
                            double initialConcentration,
                            Unit.Kind substanceUnits)

Parameters:

id -

name -

compartment -

hasOnlySubstanceUnits -

boundaryCondition -

constant -

initialConcentration -

substanceUnits -

Returns:

buildSpecies

public Species buildSpecies(java.lang.String id,
                            java.lang.String name,
                            Compartment compartment,
                            boolean hasOnlySubstanceUnits,
                            boolean boundaryCondition,
                            boolean constant,
                            double initialConcentration,
                            UnitDefinition substanceUnits)

Parameters:

id -

name -

compartment -

hasOnlySubstanceUnits -

boundaryCondition -

constant -

initialConcentration -

substanceUnits -

Returns:

buildSpecies

public Species buildSpecies(java.lang.String id,
                            java.lang.String name,
                            java.lang.String compartmentId,
                            boolean hasOnlySubstanceUnits,
                            boolean boundaryCondition,
                            boolean constant,
                            double initialConcentration,
                            java.lang.String substanceUnits)

Parameters:

id -

name -

compartmentId -

hasOnlySubstanceUnits -

boundaryCondition -

constant -

initialConcentration -

substanceUnits -

Returns:

buildUnitDefinition

public UnitDefinition buildUnitDefinition(java.lang.String id,
                                          java.lang.String name)

Parameters:

id -

name -

Returns:

getModel

public Model getModel()

Returns:

getSBMLDocument

public SBMLDocument getSBMLDocument()

Returns:

the doc