libsbml version 2.3.4 XML API configuration file for use in Taverna workflows Sets the compartment of this CompartmentVolumeRule to a copy of sname. Creates a new CompartmentVolumeRule with its compartment, formula and (optionally) type attributes set. Creates a new CompartmentVolumeRule with its compartment, formula and (optionally) type attributes set. Creates a new CompartmentVolumeRule with its compartment, formula and (optionally) type attributes set. SBase 'objects' are abstract, i.e., they are not created. Rather, specific 'subclasses' are created (e.g., Model) and their SBASE_FIELDS are initialized with this function. The type of the specific 'subclass' is indicated by the given SBMLTypeCode. Creates a new ParseMessage by copying an existing ParseMessage. Creates a new ParseMessage by copying an existing ParseMessage. Creates a new ParseMessage by copying an existing ParseMessage. Creates a new ParseMessage by copying an existing ParseMessage. Creates a new ParseMessage by copying an existing ParseMessage. Creates a new ParseMessage by copying an existing ParseMessage. Creates a new FunctionDefinition, optionally with its id and math (via an infix formula string) attributes set. Sets the id of this FunctionDefinition to a copy of sid. Sets the name of this FunctionDefinition to a copy of string. Creates a new FunctionDefinition, optionally with its id and math (via an infix formula string) attributes set. Unsets the name of this FunctionDefinition. Creates a new FunctionDefinition, optionally with its id and math (via an infix formula string) attributes set. Creates a new FunctionDefinition, optionally with its id and math (via an infix formula string) attributes set. Sets the math of this FunctionDefinition to the given ASTNode. Creates a new Event with an id and trigger and (optionally) delay attributes set. Creates a new Event with an id and trigger and (optionally) delay attributes set. Appends the given EventAssignment to this Event. Sets the trigger of this Event to the given ASTNode. Unsets the name of this Event. Creates a new Event with an id and trigger and (optionally) delay attributes set. Unsets the timeUnits of this Event. Unsets the id of this Event. Sets the delay of this Event to the given ASTNode. Unsets the delay of this Event. Creates a new Event with an id and trigger and (optionally) delay attributes set. Sets the id of this Event to a copy of sid. Sets the name of this Event to a copy of string. Sets the timeUnits of this Event to a copy of sid. Creates a new Event with an id and trigger and (optionally) delay attributes set. Creates a new Event with an id and trigger and (optionally) delay attributes set. Creates a new Species, optionally with its id attribute set. Creates a new Species, optionally with its id attribute set. Sets the initialConcentration of this Species to value and marks the field as set. This method also unsets the initialAmount field. Unsets the charge of this Species. Sets the boundaryCondition of this Species to value. Unsets the spatialSizeUnits of this Species. Sets the constant field of this Species to value. Sets the units of this Species to a copy of sname (L1 only). Sets the charge of this Species to value and marks the field as set. Marks the initialAmount of this Species as unset. Moves the id field of this Species to its name field (iff name is not already set). This method is used for converting from L2 to L1. Sets the hasOnlySubstanceUnits field of this Species to value. Sets the initialAmount of this Species to value and marks the field as set. This method also unsets the initialConentration field. Sets the compartment of this Species to a copy of sid. Sets the spatialSizeUnits of this Species to a copy of sid. Sets the id of this Species to a copy of sid. Initializes the fields of this Species to their defaults: - boundaryCondition = false - constant = false (L2 only) Unsets the substanceUnits of this Species. Unsets the name of this Species. Moves the name field of this Species to its id field (iff id is not already set). This method is used for converting from L1 to L2. Unsets the units of this Species (L1 only). Sets the substanceUnits of this Species to a copy of sid. Sets the name of this Species to a copy of string (SName in L1). Unsets the initialConcentration of this Species. Sets the value of this ASTNode to the given real (double) in two parts: the mantissa and the exponent. The node type is set to AST_REAL_E. Attempts to convert this ASTNode to a canonical form and returns true if the conversion succeeded, false otherwise. Sets the value of this ASTNode to the given real (double) in two parts: the mantissa and the exponent. The node type is set to AST_REAL_E. Creates a new ASTNode. Sets the value of this ASTNode to the given real (double) in two parts: the mantissa and the exponent. The node type is set to AST_REAL_E. Adds the given node as a child of this ASTNode. Child nodes are added in-order from 'left-to-right'. Adds the given node as a child of this ASTNode. This method adds child nodes from 'right-to-left'. Creates a new ASTNode. Sets the value of this ASTNode to the given character. Sets the type of this ASTNode to the given ASTNodeType. Sets the value of this ASTNode to the given name. Initializes the fields of this SpeciesReference to their defaults: - stoichiometry = 1 - denominator = 1 Sets the stoichiometryMath of this SpeciesReference to the given formula string. Sets the stoichiometry of this SpeciesReference to value. Creates a new SpeciesReference, optionally with its species, stoichiometry, and denominator attributes set. Creates a new SpeciesReference, optionally with its species, stoichiometry, and denominator attributes set. Creates a new SpeciesReference, optionally with its species, stoichiometry, and denominator attributes set. Sets the stoichiometryMath of this SpeciesReference to the given formula string. Sets the denominator of this SpeciesReference to value. Creates a new SpeciesReference, optionally with its species, stoichiometry, and denominator attributes set. Creates a new ModifierSpeciesReference, optionally with its species attribute set. Creates a new ModifierSpeciesReference, optionally with its species attribute set. Creates a new SpeciesConcentrationRule with its species, formula and (optionally) type attributes set. Creates a new SpeciesConcentrationRule with its species, formula and (optionally) type attributes set. Sets the species of this SpeciesConcentrationRule to a copy of sname. Creates a new SpeciesConcentrationRule with its species, formula and (optionally) type attributes set. Reads an SBML document from the given XML string. Writes the given SBML document to an in-memory string and returns a pointer to it. The string is owned by the caller and should be freed (with free()) when no longer needed. Writes the given MathML document to an in-memory string and returns a pointer to it. The string is owned by the caller and should be freed (with free()) when no longer needed. Writes the given SBML document to filename. Returns the name of the given RuleType. Parses the given SBML formula and returns a representation of it as an Abstract Syntax Tree (AST). Reads the MathML from the given XML string, constructs a corresponding abstract syntax tree and returns a pointer to the root of the tree. Writes the given MathML document to filename. Returns the RuleType with the given name (case-insensitive). Returns nonzero if string is the name of a valid unitKind. Returns the name of the given UnitKind. The caller does not own the returned string and is therefore not allowed to modify it. Returns the UnitKind with the given name (case-insensitive). Tests for logical equality between two UnitKinds. Sets the type of this Rule to the given RuleType. Creates a new AssignmentRule with its variable, math and (optionally) type attributes set. Creates a new AssignmentRule with its variable, math and (optionally) type attributes set. Creates a new AssignmentRule with its variable, math and (optionally) type attributes set. The function is kept for backward compatibility with the SBML L1 API. Creates a new AssignmentRule with its variable, math and (optionally) type attributes set. Sets the variable of this AssignmentRule to a copy of sid. Creates a new AssignmentRule with its variable, math and (optionally) type attributes set. Sets the fast status of this Reaction to value. Sets the name of this Reaction to a copy of string (SName in L1). Unsets the KineticLaw of this Reaction. Adds the given product (SpeciesReference) to this Reaction. Creates a new Reaction, optionally with its id, KineticLaw, and reversible attributes set. Sets the KineticLaw of this Reaction to the given KineticLaw. Creates a new Reaction, optionally with its id, KineticLaw, and reversible attributes set. Unsets the fast status of this Reation. Adds the given reactant (SpeciesReference) to this Reaction. Moves the name field of this Reaction to its id field (iff id is not already set). This method is used for converting from L1 to L2. Initializes the fields of this Reaction to their defaults, - reversible = true, - fast = false (L1 only) Creates a new Reaction, optionally with its id, KineticLaw, and reversible attributes set. Creates a new Reaction, optionally with its id, KineticLaw, and reversible attributes set. Moves the id field of this Reaction to its name field (iff name is not already set). This method is used for converting from L2 to L1. Unsets the name of this Reaction. Adds the given modifier (ModifierSpeciesReference) to this Reaction. Sets the id of this Reaction to a copy of sid. Sets the reversible status of this Reaction to value. Creates a new Model, optionally with its id and name attributes set. Unsets the id of this Model. Creates a new Parameter (of a KineticLaw) inside this Model and returns a pointer to it. The Parameter is associated with the KineticLaw of the last Reaction created. Adds the given FunctionDefinition to this Model. Adds the given Compartment to this Model. Creates a new UnitDefinition inside this Model and returns it. Creates a new ParameterRule inside this Model and returns it. Creates a new RateRule inside this Model and returns it. Creates a new Compartment inside this Model and returns it. Creates a new KineticLaw inside this Model and returns a pointer to it. Creates a new Reaction inside this Model and returns. Creates a new AssignmentRule inside this Model and returns. Creates a new Modifer (i.e. ModifierSpeciesReference) inside this Model and returns a pointer to it. Creates a new Unit inside this Model and returns a pointer to it. Moves the id field to the name field for this Model and all of its contituent UnitDefinitions, Compartments, Species, Parameters, and Reactions. Moves the name field to the id field for this Model and all of its contituent UnitDefinitions, Compartments, Species, Parameters, and Reactions. Adds the given Species to this Model. Adds the given Event to this Model. Moves the name field of this Model to its id field (iff id is not already set). This method is used for converting from L1 to L2. Creates a new EventAssignment inside this Model and returns a pointer to it. Creates a new AlgebraicRule inside this Model and returns it. Sets the name of this Model to a copy of string (SName in L1). Creates a new Product (i.e. SpeciesReference) inside this Model and returns a pointer to it. Adds the given UnitDefinition to this Model. Creates a new CompartmentVolumeRule inside this Model and returns. Adds the given Rule to this Model. Creates a new Model, optionally with its id and name attributes set. Creates a new SpeciesConcentrationRule inside this Model and returns it. Creates a new Species inside this Model and returns. Moves the id field of this Model to its name field (iff name is not already set). This method is used for converting from L2 to L1. Creates a new Parameter inside this Model and returns. Creates a new Model, optionally with its id and name attributes set. Adds the given Reaction to this Model. Sets the id of this Model to a copy of sid. Creates a new FunctionDefinition inside this Model and returns it. Unsets the name of this Model. Adds the given Parameter to this Model. Creates a new Reactant (i.e. SpeciesReference) inside this Model and returns a pointer to it. Creates a new Event inside this Model and returns. Sets the formula of this Rule to a copy of string. This method is no longer necessary. LibSBML now keeps formula strings and math ASTs synchronized automatically. The method is kept around for backward compatibility (and is used internally). Sets the math of this Rule to the given ASTNode. This method is no longer necessary. LibSBML now keeps formula strings and math ASTs synchronized automatically. The method is kept around for backward compatibility (and is used internally). Creates a new Rule with its math attribute set. Creates a new Rule with its math attribute set. Creates a new Rule with its math attribute set. Creates a new SBMLDocument. The SBML level defaults to 2 and version defaults to 1. Creates a new Model (optionally with its Id attribute set) inside this SBMLDocument and returns it. Creates a new SBMLDocument. The SBML level defaults to 2 and version defaults to 1. Performs a set of semantic consistency checks on the document. Query the results by calling getWarning(), getNumError(),and getNumFatal(). Sets the level of this SBMLDocument to the given level number. Valid levels are currently 1 and 2. Sets the Model of this SBMLDocument to the given Model. Any previously defined model is unset and freed. Creates a new Model (optionally with its Id attribute set) inside this SBMLDocument and returns it. Sets the version of this SBMLDocument to the given version number. Valid versions are currently 1 and 2 for SBML L1 and 1 for SBML L2. Creates a new SBMLDocument. The SBML level defaults to 2 and version defaults to 1. Performs a set of semantic consistency checks on the document to establish whether it is compatible with L1 and can be converted. Query the results by calling getWarning(), getNumError(),and getNumFatal(). Sets the timeUnits of this KineticLaw to a copy of sname. Sets the substanceUnits of this KineticLaw to a copy of sname. Sets the formula of this KineticLaw to a copy of string. Adds the given Parameter to this KineticLaw. Creates a new KineticLaw, optionally with its formula, timeUnits and/or substanceUnits set. Creates a new KineticLaw, optionally with its formula, timeUnits and/or substanceUnits set. Creates a new KineticLaw, optionally with its formula, timeUnits and/or substanceUnits set. Sets the math of this KineticLaw to the given ASTNode. Unsets the timeUnits of this KineticLaw. This method is no longer necessary. LibSBML now keeps formula strings and math ASTs synchronized automatically. The method is kept around for backward compatibility (and is used internally). This method is no longer necessary. LibSBML now keeps formula strings and math ASTs synchronized automatically. The method is kept around for backward compatibility (and is used internally). Unsets the substanceUnits of this KineticLaw. Creates a new KineticLaw, optionally with its formula, timeUnits and/or substanceUnits set. Sets the units of this Compartment to a copy of sid. Sets the outside of this Compartment to a copy of sid. Moves the id field of this Compartment to its name field (iff name is not already set). This method is used for converting from L2 to L1. Unsets the size (volume in L1) of this Compartment. Creates a new Compartment, optionally with its id attribute set. Moves the name field of this Compartment to its id field (iff id is not already set). This method is used for converting from L1 to L2. Unsets the units of this Compartment. Initializes the fields of this Compartment to their defaults. Creates a new Compartment, optionally with its id attribute set. Sets the spatialDimensions of this Compartment to value. If value is not one of [0, 1, 2, 3] the function will have no effect (i.e. spatialDimensions will not be set). Sets the id of this Compartment to a copy of sid. Sets the volume (size in L2) of this Compartment to value. Unsets the outside of this Compartment. Unsets the name of this Compartment. Sets the size (volume in L1) of this Compartment to value. Unsets the volume (size in L2) of this Compartment. Sets the constant field of this Compartment to value. Sets the name of this Compartment to a copy of string (SName in L1). Sets the constant field of this Parameter to value. Creates a new Parameter, with its id and value attributes set and optionally its units and constant attributes. Sets the id of this Parameter to a copy of sid. Unsets the units of this Parameter. Sets the name of this Parameter to a copy of string (SName in L1). Unsets the value of this Parameter. Creates a new Parameter, with its id and value attributes set and optionally its units and constant attributes. Creates a new Parameter, with its id and value attributes set and optionally its units and constant attributes. Sets the units of this Parameter to a copy of sid. Moves the name field of this Parameter to its id field (iff id is not already set). This method is used for converting from L1 to L2. Initializes the fields of this Parameter to their defaults. Unsets the name of this Parameter. Creates a new Parameter, with its id and value attributes set and optionally its units and constant attributes. Moves the id field of this Parameter to its name field (iff name is not already set). This method is used for converting from L2 to L1. Sets the initialAmount of this Parameter to value and marks the field as set. Creates a new Parameter, with its id and value attributes set and optionally its units and constant attributes. Creates a new EventAssignment with its variable and math attributes set. Creates a new EventAssignment with its variable and math attributes set. Creates a new EventAssignment with its variable and math attributes set. Sets the variable of this EventAssignment to a copy of sid. Creates a new EventAssignment with its variable and math attributes set. Sets the math of this EventAssignment to the given ASTNode. Creates a new AlgebraicRule with its math attribute set. Creates a new AlgebraicRule with its math attribute set. Creates a new AlgebraicRule with its math attribute set. Sets the species of this SimpleSpeciesReference to a copy of sid. Creates a new SimpleSpeciesReference, optionally with its species attribute set. Creates a new SimpleSpeciesReference, optionally with its species attribute set. Adds (prefix, URI) to this list of XML namespaces. Adds (prefix, URI) to this list of XML namespaces. If prefix starts with 'xmlns:' (case-insensitive), it will be removed. Creates a new UnitDefinition, optionally with its id and name attributes set. Creates a new UnitDefinition, optionally with its id and name attributes set. Unsets the name of this UnitDefinition. Sets the name of this UnitDefinition to a copy of string (SName in L1). Sets the id of this UnitDefinition to a copy of sid. Moves the id field of this UnitDefinition to its name field (iff name is not already set). This method is used for converting from L2 to L1. Adds the given Unit to this UnitDefinition. Creates a new UnitDefinition, optionally with its id and name attributes set. Moves the name field of this UnitDefinition to its id field (iff id is not already set). This method is used for converting from L1 to L2. Creates a new RateRule with its variable and math attributes set. Creates a new RateRule with its variable and math attributes set. Creates a new RateRule with its variable and math attributes set. Sets the variable of this RateRule to a copy of sid. Creates a new RateRule with its variable and math attributes set. Sets the schema filename used by this SBMLReader to validate SBML Level 1 version 1 documents. Creates a new SBMLReader and returns it. Creates a new SBMLReader and returns it. Sets the schema filename used by this SBMLReader to validate SBML Level 2 version 1 documents. Sets the schema filename used by this SBMLReader to validate SBML Level 1 version 2 documents. Sets the schema validation level used by this SBMLReader. Sets the schema validation level used by this SBMLReader. Reads an SBML document from the given XML string. Creates a new XMLNamespace with prefix and URI. If prefix starts with 'xmlns:' (case-insensitive), it will be removed. Creates a new ParameterRule with its name, formula and (optionally) type attributes set. Sets the (Parameter) name for this ParameterRule to a copy of sname. Creates a new ParameterRule with its name, formula and (optionally) type attributes set. Creates a new ParameterRule with its name, formula and (optionally) type attributes set. Unsets the units for this ParameterRule. Sets the units for this ParameterRule to a copy of sname. Sets the math of this MathMLDocument to the given ASTNode. Creates a new MathMLDocument. Adds item to the beginning of this ListOf. Adds item to the end of this List. Creates a new ListOf. Removes the nth item from this List and returns a pointer to it. Sets the version of this program, i.e. the one about to write out the SBMLDocument. Writes the given SBML document to the output stream. Writes the given SBML document to an in-memory string and returns a pointer to it. The string is owned by the caller and should be freed (with free()) when no longer needed. Creates a new SBMLWriter. Sets the name of this program, i.e. the one about to write out the SBMLDocument. Creates a new MathMLWriter. Writes the given MathML document to an in-memory string and returns a pointer to it. The string is owned by the caller and should be freed (with free()) when no longer needed. Writes the given MathML document to the output stream. Initializes the fields of this Unit to their defaults. Creates a new Unit, optionally with its kind (via string), exponent, scale, multiplier, and offset attributes set. Creates a new Unit, optionally with its kind (via string), exponent, scale, multiplier, and offset attributes set. Creates a new Unit, optionally with its kind (via string), exponent, scale, multiplier, and offset attributes set. Creates a new Unit, optionally with its kind (via string), exponent, scale, multiplier, and offset attributes set. Creates a new Unit, optionally with its kind (via string), exponent, scale, multiplier, and offset attributes set. Creates a new Unit, optionally with its kind (via string), exponent, scale, multiplier, and offset attributes set. Sets the kind of this Unit to the given UnitKind. Sets the exponent of this Unit to the given value. Sets the scale of this Unit to the given value. Creates a new Unit, optionally with its kind (via string), exponent, scale, multiplier, and offset attributes set. Creates a new Unit, optionally with its kind (via string), exponent, scale, multiplier, and offset attributes set. Creates a new Unit, optionally with its kind (via string), exponent, scale, multiplier, and offset attributes set. Creates a new Unit, optionally with its kind (via string), exponent, scale, multiplier, and offset attributes set. Sets the offset of this Unit to the given value. Sets the multiplier of this Unit to the given value. Creates a new Unit, optionally with its kind (via string), exponent, scale, multiplier, and offset attributes set.