libSBML C++ API
libSBML 5.19.0 C++ API
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@sbmlpackage{core}
This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.
The function SBML_parseL3FormulaWithSettings()
Public Member Functions | |
bool | getComparisonCaseSensitivity () const |
Returns true if the parser is configured to match built-in symbols in a case-insensitive way. More... | |
const Model * | getModel () const |
Returns the Model object referenced by this L3ParserSettings object. More... | |
bool | getParseAvogadroCsymbol () const |
Indicates the current behavior set for handling avogadro for SBML Level 3. More... | |
bool | getParseCollapseMinus () const |
Indicates the current behavior set for handling multiple unary minuses in formulas. More... | |
bool | getParseL3v2Functions () const |
Indicates the current behavior set for handling whether to parse the functions added in L3v2 as that MathML or not. More... | |
ParseLogType_t | getParseLog () const |
Indicates the current behavior set for handling the function log with one argument. More... | |
bool | getParseModuloL3v2 () const |
Indicates the current behavior set for handling the % symbol in mathematical formulas. More... | |
bool | getParsePackageMath (ExtendedMathType_t package) const |
Indicates the current behavior set for handling whether to parse the functions added in the given package as that MathML or not. More... | |
bool | getParseUnits () const |
Indicates the current behavior set for handling units in text-string mathematical formulas. More... | |
L3ParserSettings () | |
Creates a new L3ParserSettings object with default values. More... | |
L3ParserSettings (const L3ParserSettings &source) | |
Copy constructor. More... | |
L3ParserSettings (Model *model, ParseLogType_t parselog, bool collapseminus, bool parseunits, bool avocsymbol, bool caseSensitive=false, SBMLNamespaces *sbmlns=NULL, bool moduloL3v2=false, bool l3v2functions=false) | |
Creates a new L3ParserSettings object with specific values for all possible settings. More... | |
L3ParserSettings & | operator= (const L3ParserSettings &source) |
Assignment operator. More... | |
void | setComparisonCaseSensitivity (bool strcmp) |
Sets the parser's behavior with respect to case sensitivity for recognizing predefined symbols. More... | |
void | setModel (const Model *model) |
Sets the model reference in this L3ParserSettings object. More... | |
void | setParseAvogadroCsymbol (bool l2only) |
Sets the parser's behavior in handling the symbol avogadro in mathematical formulas. More... | |
void | setParseCollapseMinus (bool collapseminus) |
Sets the behavior for handling unary minuses appearing in mathematical formulas. More... | |
void | setParseL3v2Functions (bool l3v2functions) |
Sets the behavior for handling functions added in SBML L3v2. More... | |
void | setParseLog (ParseLogType_t type) |
Sets the behavior for handling log in mathematical formulas. More... | |
void | setParseModuloL3v2 (bool modulol3v2) |
Sets the behavior for handling the % symbol in mathematical formulas. More... | |
void | setParsePackageMath (ExtendedMathType_t package, bool parsepackage) |
Sets the behavior for handling functions added in SBML packages. More... | |
void | setParseUnits (bool units) |
Sets the parser's behavior in handling units associated with numbers in a mathematical formula. More... | |
void | unsetModel () |
Unsets the Model reference in this L3ParserSettings object. More... | |
virtual | ~L3ParserSettings () |
Destroys this L3ParserSettings object. More... | |
L3ParserSettings::L3ParserSettings | ( | ) |
Creates a new L3ParserSettings object with default values.
This is the default constructor for the L3ParserSettings object. It sets the stored Model object to NULL
and sets the following field values in the L3ParserSettings object:
L3ParserSettings::L3ParserSettings | ( | Model * | model, |
ParseLogType_t | parselog, | ||
bool | collapseminus, | ||
bool | parseunits, | ||
bool | avocsymbol, | ||
bool | caseSensitive = false , |
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SBMLNamespaces * | sbmlns = NULL , |
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bool | moduloL3v2 = false , |
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bool | l3v2functions = false |
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) |
Creates a new L3ParserSettings object with specific values for all possible settings.
model | a Model object to be used for disambiguating identifiers encountered by SBML_parseL3FormulaWithSettings() |
L3ParserSettings::L3ParserSettings | ( | const L3ParserSettings & | source | ) |
Copy constructor.
source | the instance to copy. |
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virtual |
Destroys this L3ParserSettings object.
bool L3ParserSettings::getComparisonCaseSensitivity | ( | ) | const |
Returns true
if the parser is configured to match built-in symbols in a case-insensitive way.
true
if matches are done in a case-sensitive manner, and false
if the parser will recognize built-in functions and constants regardless of case,.const Model * L3ParserSettings::getModel | ( | ) | const |
Returns the Model object referenced by this L3ParserSettings object.
SId
) from that model are used in preference to pre-defined MathML symbol definitions. More precisely, the Model entities whose identifiers will shadow identical symbols in the mathematical formula are: Species, Compartment, Parameter, Reaction, and SpeciesReference. For instance, if the parser is given a Model containing a Species with the identifier "pi
", and the formula to be parsed is "3*pi
", the MathML produced will contain the construct <ci> pi </ci>
instead of the construct <pi/>
. Similarly, when a Model object is provided, SId
values of user-defined functions present in the Model will be used preferentially over pre-defined MathML functions. For example, if the passed-in Model contains a FunctionDefinition with the identifier "sin
", that function will be used instead of the predefined MathML function <sin/>
.bool L3ParserSettings::getParseAvogadroCsymbol | ( | ) | const |
Indicates the current behavior set for handling avogadro
for SBML Level 3.
This method returns the current setting of the avogadro
-handling behavior in this L3ParserSettings object. The possible values are as follows:
bool L3ParserSettings::getParseCollapseMinus | ( | ) | const |
Indicates the current behavior set for handling multiple unary minuses in formulas.
- -3
") can be collapsed and ignored in the input, or the multiple minuses can be preserved in the AST node tree that is generated by the parser. Second, minus signs in front of numbers can be collapsed into the number node itself; for example, a "- 4.1
" can be turned into a single ASTNode of type AST_REALendif A boolean indicating the behavior currently set. The possible values are as follows: setParseCollapseMinus() bool L3ParserSettings::getParseL3v2Functions | ( | ) | const |
Indicates the current behavior set for handling whether to parse the functions added in L3v2 as that MathML or not.
ParseLogType_t L3ParserSettings::getParseLog | ( | ) | const |
Indicates the current behavior set for handling the function log
with one argument.
The function log
with a single argument ("log(x)
") can be parsed as log10(x)
, ln(x)
, or treated as an error, as desired. These three possible behaviors are indicated, respectively, by the values L3P_PARSE_LOG_AS_LOG10endif
bool L3ParserSettings::getParseModuloL3v2 | ( | ) | const |
Indicates the current behavior set for handling the % symbol in mathematical formulas.
bool L3ParserSettings::getParsePackageMath | ( | ExtendedMathType_t | package | ) | const |
Indicates the current behavior set for handling whether to parse the functions added in the given package as that MathML or not.
package | an ExtendedMathType_t indicating the extended math package to be set. |
bool L3ParserSettings::getParseUnits | ( | ) | const |
Indicates the current behavior set for handling units in text-string mathematical formulas.
Since SBML Level 2 does not have the ability to associate units with pure numbers, the value should be expected to be false
(L3P_NO_UNITSendif
L3ParserSettings & L3ParserSettings::operator= | ( | const L3ParserSettings & | source | ) |
Assignment operator.
void L3ParserSettings::setComparisonCaseSensitivity | ( | bool | strcmp | ) |
Sets the parser's behavior with respect to case sensitivity for recognizing predefined symbols.
strcmp | a boolean indicating whether to be case sensitive (if true ) or be case insensitive (if false ). |
void L3ParserSettings::setModel | ( | const Model * | model | ) |
Sets the model reference in this L3ParserSettings object.
SId
) from that model are used in preference to pre-defined MathML symbol definitions. More precisely, the Model entities whose identifiers will shadow identical symbols in the mathematical formula are: Species, Compartment, Parameter, Reaction, and SpeciesReference. For instance, if the parser is given a Model containing a Species with the identifier "pi
", and the formula to be parsed is "3*pi
", the MathML produced will contain the construct <ci> pi </ci>
instead of the construct <pi/>
. Similarly, when a Model object is provided, SId
values of user-defined functions present in the Model will be used preferentially over pre-defined MathML functions. For example, if the passed-in Model contains a FunctionDefinition with the identifier "sin
", that function will be used instead of the predefined MathML function <sin/>
.model | a Model object to be used for disambiguating identifiers. |
void L3ParserSettings::setParseAvogadroCsymbol | ( | bool | l2only | ) |
Sets the parser's behavior in handling the symbol avogadro
in mathematical formulas.
This method allows callers to set the avogadro
-handling behavior in this L3ParserSettings object. The possible values of l2only
are as follows:
Since SBML Level 2 does not define a symbol for Avogadro's constant, the value should be set to L3P_AVOGADRO_IS_NAMEendif
void L3ParserSettings::setParseCollapseMinus | ( | bool | collapseminus | ) |
Sets the behavior for handling unary minuses appearing in mathematical formulas.
- -3
") can be collapsed and ignored in the input, or the multiple minuses can be preserved in the AST node tree that is generated by the parser. Second, minus signs in front of numbers can be collapsed into the number node itself; for example, a "- 4.1
" can be turned into a single ASTNode of type AST_REALendif This method lets you tell the parser which behavior to use—either collapse minuses or always preserve them. The two possibilities are represented using the following constants: collapseminus a boolean value (one of the constants #L3P_COLLAPSE_UNARY_MINUS L3P_COLLAPSE_UNARY_MINUSendif void L3ParserSettings::setParseL3v2Functions | ( | bool | l3v2functions | ) |
Sets the behavior for handling functions added in SBML L3v2.
This method lets you tell the parser which behavior to use—either to parse the functions added in L3v2 as their built-in counterparts, or as generic functions with that name (to be defined by SBML as function definitions). The two possibilities are represented using the following constants:
l3v2functions | a boolean value (one of the constants L3P_PARSE_L3V2_FUNCTIONS_DIRECTLYendif |
void L3ParserSettings::setParseLog | ( | ParseLogType_t | type | ) |
Sets the behavior for handling log
in mathematical formulas.
The function log
with a single argument ("log(x)
") can be parsed as log10(x)
, ln(x)
, or treated as an error. These three behaviors are set, respectively, by using the value L3P_PARSE_LOG_AS_LOG10endif
void L3ParserSettings::setParseModuloL3v2 | ( | bool | modulol3v2 | ) |
Sets the behavior for handling the % symbol in mathematical formulas.
This method lets you tell the parser which behavior to use—either parse % as the 'rem' function or as a piecewise function with the same interpretation. The two possibilities are represented using the following constants:
modulol3v2 | a boolean value (one of the constants L3P_MODULO_IS_PIECEWISEendif |
void L3ParserSettings::setParsePackageMath | ( | ExtendedMathType_t | package, |
bool | parsepackage | ||
) |
Sets the behavior for handling functions added in SBML packages.
This method lets you tell the parser which behavior to use—either to parse the functions added in a given package as their built-in counterparts, or as generic functions with that name (to be defined by SBML as function definitions). The two possibilities are represented using the following constants:
package | an ExtendedMathType_t indicating the extended math package to be queried. |
parsepackage | a boolean value (one of the constants L3P_PARSE_L3V2_FUNCTIONS_DIRECTLYendif |
void L3ParserSettings::setParseUnits | ( | bool | units | ) |
Sets the parser's behavior in handling units associated with numbers in a mathematical formula.
This method sets the formula parser's behavior with respect to units.
units | a boolean indicating whether to parse units. The possible values are as follows: |
void L3ParserSettings::unsetModel | ( | ) |
Unsets the Model reference in this L3ParserSettings object.
The effect of calling this method is to set the stored model value to NULL
.