This the XML API description file for libsbml-2.3.4. Note that this API description is for a hacked version of the Java binding to libsbml-2.3.4 where methods parameters have been modified to use Java classes as opposed to the primitive types. Creates a new ListOf. Adds item to the beginning of this ListOf. Removes the nth item from this List and returns a pointer to it. If n > ListOf.getNumItems() returns 0. Adds item to the end of this List. Initializes the fields of this Parameter to their defaults: - constant = true (L2 only) Creates a new Parameter, with its id and value attributes set and optionally its units and constant attributes. Sets the name of this Parameter to a copy of string (SName in L1). 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. 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. Unsets the value of this Parameter. <p/> In SBML L1v1, a Parameter value is required and therefore <b>should always be set</b>. In L1v2 and beyond, a value is optional and as such may or may not be set. Sets the initialAmount of this Parameter to value and marks the field as set. 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. Sets the units of this Parameter to a copy of sid. Unsets the units of this Parameter. 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 name of this Parameter. <p/> In SBML L1, a Parameter name is required and therefore <b>should always be set</b>. In L2, name is optional and as such may or may not be set. Creates a new SpeciesConcentrationRule with its species, formula and type attributes set. Creates a new SpeciesConcentrationRule with its species, formula and type attributes set. Sets the species of this SpeciesConcentrationRule to a copy of sname. Creates a new SpeciesConcentrationRule with its species, formula and type attributes set. Creates a new ParameterRule with its name, formula and type attributes set. Sets the units for this ParameterRule to a copy of sname. Sets the (Parameter) name for this ParameterRule to a copy of sname. Creates a new ParameterRule with its name, formula and type attributes set. Unsets the units for this ParameterRule. Creates a new ParameterRule with its name, formula and type attributes set. Creates a new SimpleSpeciesReference, optionally with its species attribute set. Sets the species of this SimpleSpeciesReference to a copy of sid. Creates a new SimpleSpeciesReference, optionally with its species attribute set. Writes the given MathML document to the output stream. Creates a new MathMLWriter. Writes the given MathML document to an in-memory string and returns a pointer to it. 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. Sets the compartment of this CompartmentVolumeRule to a copy of sname. Creates a new CompartmentVolumeRule with its compartment, formula and (optionally) type attributes set. Sets the fast status of this Reaction to value. Sets the reversible status of this Reaction to value. Unsets the name of this Reaction. Initializes the fields of this Reaction to their defaults: <p/> - reversible = true - fast = false (L1 only) 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. 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. Adds the given product (SpeciesReference) to this Reaction. Unsets the fast status of this Reation. Creates a new Reaction, optionally with its id, KineticLaw, and reversible attributes set. Sets the name of this Reaction to a copy of string (SName in L1). Unsets the KineticLaw of this Reaction. Sets the id of this Reaction to a copy of sid. Adds the given modifier (ModifierSpeciesReference) to this Reaction. Creates a new Reaction, optionally with its id, KineticLaw, and reversible attributes set. Adds the given reactant (SpeciesReference) to this Reaction. Sets the KineticLaw of this Reaction to the given KineticLaw. 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. 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. Creates a new RateRule with its variable and math attributes set. Creates a new ASTNode. Sets the value of this ASTNode to the given character. If character is one of '+', '-', '*', '/' or '\^', the node type will be set accordingly. For all other characters, the node type will be set to AST_UNKNOWN. Sets the type of this ASTNode to the given ASTNodeType. 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'. 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 name. 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. This method adds child nodes from 'right-to-left'. Unsets the id of this Event. Unsets the name of this Event. Appends the given EventAssignment to this Event. Creates a new Event with an id and trigger and delay attributes set. Creates a new Event with an id and trigger and delay attributes set. Sets the id of this Event to a copy of sid. Sets the timeUnits of this Event to a copy of sid. Sets the trigger of this Event to the given ASTNode. Sets the name of this Event to a copy of string. Creates a new Event with an id and trigger and delay attributes set. Creates a new Event with an id and trigger and delay attributes set. Creates a new Event with an id and trigger and delay attributes set. Sets the delay of this Event to the given ASTNode. Creates a new Event with an id and trigger and delay attributes set. Unsets the delay of this Event. Unsets the timeUnits of this Event. Sets the variable of this EventAssignment to a copy of sid. Creates a new EventAssignment, optionally with its variable and math attributes set. Creates a new EventAssignment, optionally with its variable and math attributes set. Sets the math of this EventAssignment to the given ASTNode. Creates a new EventAssignment, optionally with its variable and math attributes set. Creates a new EventAssignment, optionally with its variable and math attributes set. Marks the initialAmount of this Species as unset. Sets the initialAmount of this Species to value and marks the field as set. This method also unsets the initialConentration field. 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 initialConcentration of this Species to value and marks the field as set. This method also unsets the initialAmount field. Unsets the units of this Species (L1 only). 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). Unsets the name of this Species. Sets the compartment of this Species to a copy of sid. Unsets the initialConcentration of this Species. Sets the spatialSizeUnits of this Species to a copy of sid. Initializes the fields of this Species to their defaults: <p/> - boundaryCondition = false - constant = false (L2 only) Creates a new Species, optionally with its id attribute set. Unsets the charge of this Species. Sets the id of this Species to a copy of sid. Unsets the substanceUnits of this Species. Creates a new Species, optionally with its id attribute set. Sets the name of this Species to a copy of string (SName in L1). 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. Sets the boundaryCondition of this Species to value. Sets the substanceUnits of this Species to a copy of sid. Sets the hasOnlySubstanceUnits field of this Species to value. Sets the charge of this Species to value and marks the field as set. Creates a new SBMLWriter. 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. Sets the name of this program, i.e. the one about to write out the SBMLDocument. 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. <p/> In SBML L1, a UnitDefinition name is required and therefore <b>should always be set</b>. In L2, name is optional and as such may or may not be set. 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. Adds the given Unit to 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. Creates a new Unit, optionally with its kind (via string), exponent, scale, multiplier, and offset attributes set. Sets the exponent of this Unit to the given value. Sets the kind of this Unit to the given UnitKind. 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. 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 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. Sets the scale of this Unit to the given value. Initializes the fields of this Unit to their defaults: exponent = 1, scale = 0, multiplier = 1.0, offset = 0.0 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 schema validation level used by this SBMLReader. Sets the schema filename used by this SBMLReader to validate SBML Level 1 version 2 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. Reads an SBML document from the given XML string. Sets the schema filename used by this SBMLReader to validate SBML Level 1 version 1 documents. Sets the schema validation level used by this SBMLReader. Sets the stoichiometry of this SpeciesReference to value. Sets the stoichiometryMath of this SpeciesReference to the given formula string. Creates a new SpeciesReference, optionally with its species, stoichiometry, and denominator attributes set. Initializes the fields of this SpeciesReference to their defaults: stoichiometry = 1, denominator = 1 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 SpeciesReference, optionally with its species, stoichiometry, and denominator attributes set. Sets the math of this MathMLDocument to the given ASTNode. Creates a new MathMLDocument. 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 formula of this Rule to a copy of string. Creates a new Rule with its math attribute set. 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. Sets the math of this Rule to the given ASTNode. Creates a new Rule with its math attribute set. 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 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 version of this SBMLDocument to the given version number. Valid versions are currently 1 and 2 for SBML L1 and 1 for SBML L2. Sets the Model of this SBMLDocument to the given Model. Any previously defined model is unset and freed. Sets the level of this SBMLDocument to the given level number. Valid levels are currently 1 and 2. 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. Creates a new Model (optionally with its Id attribute set) inside this SBMLDocument and returns it. 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(). Creates a new XMLNamespace with prefix and URI. Unsets the id of this Model. Creates a new Event inside this Model and returns. Adds the given Reaction to this Model. Creates a new Model, optionally with its id and name attributes set. Creates a new ParameterRule inside this Model and returns it. Creates a new Reaction inside this Model and returns it. Creates a new EventAssignment inside this Model and returns a pointer to it. The EventAssignment is added to the the last Event created. Adds the given Species to this Model. Creates a new KineticLaw inside this Model and returns a pointer to it. The KineticLaw is associated with the last Reaction created. Sets the id of this Model to a copy of sid. Creates a new Compartment inside this Model and returns it. Creates a new Model, optionally with its id and name attributes set. Creates a new RateRule inside this Model and returns it. Creates a new Modifer (i.e. ModifierSpeciesReference) inside this Model and returns a pointer to it. Creates a new Parameter (of a KineticLaw) inside this Model and returns a pointer to it. Creates a new Parameter inside this Model and returns. Creates a new AlgebraicRule inside this Model and returns it. Moves the id field of this Model to its name field (if name is not already set). This method is used for converting from L2 to L1. Unsets the name of this Model. Sets the name of this Model to a copy of string (SName in L1). Creates a new Model, optionally with its id and name attributes set. Creates a new Unit inside this Model and returns a pointer to it. The Unit is added to the last UnitDefinition created. Creates a new AssignmentRule inside this Model and returns it. Creates a new CompartmentVolumeRule inside this Model and returns it. Moves the id field to the name field for this Model and all of its contituent UnitDefinitions, Compartments, Species, Parameters, and Reactions. This method is used for converting from L2 to L1. Adds the given UnitDefinition to this Model. Moves the name field of this Model to its id field (if id is not already set). This method is used for converting from L1 to L2. Adds the given Event to this Model. Creates a new Product (i.e. SpeciesReference) inside this Model and returns a pointer to it. Adds the given Rule to this Model. Creates a new UnitDefinition inside this Model and returns it. Creates a new Reactant (i.e. SpeciesReference) inside this Model and returns a pointer to it. Adds the given Parameter to this Model. Creates a new Species inside this Model and returns it. Creates a new SpeciesConcentrationRule inside this Model and returns it. Moves the name field to the id field for this Model and all of its contituent UnitDefinitions, Compartments, Species, Parameters, and Reactions. This method is used for converting from L1 to L2. Creates a new FunctionDefinition inside this Model and returns it. Adds the given FunctionDefinition to this Model. Adds the given Compartment to this Model. Sets the math of this FunctionDefinition to the given ASTNode. Creates a new FunctionDefinition, optionally with its id and math attributes set. Creates a new FunctionDefinition, optionally with its id and math attributes set. Sets the name of this FunctionDefinition to a copy of string. Sets the id of this FunctionDefinition to a copy of sid. Creates a new FunctionDefinition, optionally with its id and math attributes set. Creates a new FunctionDefinition, optionally with its id and math attributes set. Unsets the name of this FunctionDefinition. Creates a new ModifierSpeciesReference, optionally with its species attribute set. Creates a new ModifierSpeciesReference, optionally with its species attribute set. Creates a new KineticLaw, optionally with its formula, timeUnits and/or substanceUnits set. Sets the math of this KineticLaw to the given ASTNode. 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. 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 substanceUnits of this KineticLaw to a copy of sname. Unsets the substanceUnits of this KineticLaw. 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). Sets the timeUnits of this KineticLaw to a copy of sname. Creates a new KineticLaw, optionally with its formula, timeUnits and/or substanceUnits set. Returns the name of the given UnitKind. The caller does not own the returned string and is therefore not allowed to modify it. Reads an SBML document from the given XML string. Reads the MathML from the given XML string, constructs a corresponding abstract syntax tree and returns a pointer to the root of the tree. Parses the given SBML formula and returns a representation of it as an Abstract Syntax Tree (AST). The root node of the AST is returned. Returns nonzero if string is the name of a valid unitKind. 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 filename. Tests for logical equality between two UnitKinds. Returns the UnitKind with the given name (case-insensitive). Writes the given MathML document to an in-memory string and returns a pointer to it. Returns the name of the given RuleType. The caller does not own the returned string and is therefore not allowed to modify it. Returns the RuleType with the given name (case-insensitive). Writes the given SBML document to filename. Sets the id of this Compartment to a copy of sid. Unsets the units of this Compartment. Sets the spatialDimensions of this Compartment to value. Creates a new Compartment, optionally with its id attribute set. Unsets the name of this Compartment. Sets the volume (size in L2) of this Compartment to value. 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. Sets the outside of this Compartment to a copy of sid. Unsets the outside of this Compartment. Unsets the volume (size in L2) of this Compartment. Sets the name of this Compartment to a copy of string (SName in L1). Sets the size (volume in L1) of this Compartment to value. Unsets the size (volume in L1) of this Compartment. Sets the units of this Compartment to a copy of sid. Initializes the fields of this Compartment to their defaults. 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. Sets the constant field of this Compartment to value. Creates a new AssignmentRule with its variable, math and type attributes set. Creates a new AssignmentRule with its variable, math and type attributes set. The function is kept for backward compatibility with the SBML L1 API. Creates a new AssignmentRule with its variable, math and type attributes set. Sets the type of this Rule to the given RuleType. Creates a new AssignmentRule with its variable, math and type attributes set. Creates a new AssignmentRule with its variable, math and type attributes set. Sets the variable of this AssignmentRule to a copy of sid. 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. Adds (prefix, URI) to this list of XML namespaces. Adds (prefix, URI) to this list of XML namespaces.