libSBML Perl API
libSBML 5.8.0 Perl API
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A helper class for controlling the behavior of the text-string formula parser.
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 , along with its variants
and , are the interfaces to a parser for mathematical formulas expressed as text strings. The parser converts the text-string formulas into Abstract Syntax Trees (ASTs), represented in libSBML using ASTNode objects. Compared to the parser implemented by the function , which was designed primarily for converting the mathematical formula strings in SBML Level 1, the "L3" variant of the parser accepts an extended formula syntax. It also has a number of configurable behaviors. This class (L3ParserSettings) is an object used to communicate the configuration settings with callers.
The following aspects of the parser are configurable:
log
with a single argument ("log(x)
") can be parsed as log10(x)
, ln(x)
, or treated as an error, as desired. - -3
") can be removed from the input entirely and single unary minuses can be incorporated into the number node, or all minuses can be preserved in the AST node structure. avogadro
can be parsed as a MathML csymbol or as an identifier. SId
) from that model are used in preference to pre-defined MathML 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/>
. 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/>
. To obtain the default configuration values, callers can use the functionTo change the configuration, callers can create an L3ParserSettings object, set the desired characteristics using the methods provided, and pass that object to
Public Member Functions | |
const Model * | getModel () const |
Returns the Model object referenced by this L3ParserSettings object. More... | |
bool | getParseAvogadroCsymbol () const |
Returns true if the current settings are oriented towards handling avogadro for SBML Level 3. More... | |
bool | getParseCollapseMinus () const |
Returns a flag indicating the current behavior set for handling multiple unary minuses in formulas. More... | |
ParseLogType_t | getParseLog () const |
Returns the current setting indicating what to do with formulas containing the function log with one argument. More... | |
bool | getParseUnits () const |
Returns if the current settings allow units in text-string mathematical formulas. More... | |
L3ParserSettings () | |
Creates a new L3ParserSettings object with default values. More... | |
L3ParserSettings (Model *model, ParseLogType_t parselog, bool collapseminus, bool parseunits, bool avocsymbol) | |
Creates a new L3ParserSettings object with specific values for all possible settings. 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 string avogadro in mathematical formulas. More... | |
void | setParseCollapseMinus (bool collapseminus) |
Sets the behavior for handling unary minuses appearing in mathematical formulas. More... | |
void | setParseLog (ParseLogType_t type) |
Sets the behavior for handling log in mathematical formulas. More... | |
void | setParseUnits (bool units) |
Sets the parser's behavior in handling units associated with numbers in a mathematical formula. More... | |
void | unsetModel () |
Sets the Model reference in this L3ParserSettings object to NULL . More... | |
~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 Model to NULL
and other settings to L3P_PARSE_LOG_AS_LOG10
, L3P_EXPAND_UNARY_MINUS
, L3P_PARSE_UNITS
, and L3P_AVOGADRO_IS_CSYMBOL
.
L3ParserSettings::L3ParserSettings | ( | Model * | model, |
ParseLogType_t | parselog, | ||
bool | collapseminus, | ||
bool | parseunits, | ||
bool | avocsymbol | ||
) |
Creates a new L3ParserSettings object with specific values for all possible settings.
model | a Model object to be used for disambiguating identifiers |
parselog | a flag that controls how the parser will handle the symbol log in formulas |
collapseminus | a flag that controls how the parser will handle minus signs |
parseunits | a flag that controls how the parser will handle apparent references to units of measurement associated with raw numbers in a formula |
avocsymbol | a flag that controls how the parser will handle the appearance of the symbol avogadro in a formula |
L3ParserSettings::~L3ParserSettings | ( | ) |
Destroys this L3ParserSettings object.
const Model * L3ParserSettings::getModel | ( | ) | const |
Returns the Model object referenced by this L3ParserSettings object.
bool L3ParserSettings::getParseAvogadroCsymbol | ( | ) | const |
Returns true
if the current settings are oriented towards handling avogadro
for SBML Level 3.
SBML Level 3 defines a symbol for representing the value of Avogadro's constant, but it is not defined in SBML Level 2. As a result, the text-string formula parser must behave differently depending on which SBML Level is being targeted.
true
): tells the parser to translate the string avogadro
(in any capitalization) into an AST node of type AST_NAME_AVOGADRO. false
): tells the parser to translate the string avogadro
into an AST of type AST_NAME.bool L3ParserSettings::getParseCollapseMinus | ( | ) | const |
Returns a flag indicating the current behavior set for handling multiple unary minuses in formulas.
This setting affects two behaviors. First, pairs of multiple unary minuses in a row (e.g., "- -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_REAL with a value of -4.1
, or it can be turned into a node of type AST_MINUS having a child node of type AST_REAL. 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:
true
): collapse unary minuses where possible. false
): do not collapse unary minuses, and instead translate each one into an AST node of type AST_MINUS.ParseLogType_t L3ParserSettings::getParseLog | ( | ) | const |
Returns the current setting indicating what to do with formulas containing 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.
bool L3ParserSettings::getParseUnits | ( | ) | const |
Returns if
the current settings allow units in text-string mathematical formulas.
In SBML Level 2, there is no means of associating a unit of measurement with a pure number in a formula, while SBML Level 3 does define a syntax for this. In Level 3, MathML <cn>
elements can have an attribute named units
placed in the SBML namespace, which can be used to indicate the units to be associated with the number. The text-string infix formula parser allows units to be placed after raw numbers; they are interpreted as unit identifiers for units defined by the SBML specification or in the containing Model object. Some examples include: "4 mL
", "2.01 Hz
", "3.1e-6 M
", and "(5/8) inches
". To produce a valid SBML model, there must either exist a UnitDefinition corresponding to the identifier of the unit, or the unit must be defined in Table 2 of the SBML specification.
Since SBML Level 2 does not have the ability to associate units with pure numbers, the value should be set to false
when parsing text-string formulas intended for use in SBML Level 2 documents.
true
): parse units in the text-string formula. false
): treat units in the text-string formula as errors.void L3ParserSettings::setModel | ( | const Model * | model | ) |
Sets the model reference in this L3ParserSettings object.
When a Model object is provided, identifiers (values of type SId
) from that model are used in preference to pre-defined MathML 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 string avogadro
in mathematical formulas.
SBML Level 3 defines a symbol for representing the value of Avogadro's constant, but it is not defined in SBML Level 2. As a result, the text-string formula parser must behave differently depending on which SBML Level is being targeted. The argument to this method can be one of two values:
true
): tells the parser to translate the string avogadro
(in any capitalization) into an AST node of type AST_NAME_AVOGADRO. false
): tells the parser to translate the string avogadro
into an AST of type AST_NAME.Since SBML Level 2 does not define a symbol for Avogadro's constant, the value should be set to false
when parsing text-string formulas intended for use in SBML Level 2 documents.
l2only | a boolean value (one of the constants L3P_AVOGADRO_IS_CSYMBOL or L3P_AVOGADRO_IS_NAME) indicating how the string avogadro should be treated when encountered in a formula. |
void L3ParserSettings::setParseCollapseMinus | ( | bool | collapseminus | ) |
Sets the behavior for handling unary minuses appearing in mathematical formulas.
This setting affects two behaviors. First, pairs of multiple unary minuses in a row (e.g., "- -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_REAL with a value of -4.1
, or it can be turned into a node of type AST_MINUS having a child node of type AST_REAL. 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:
true
): collapse unary minuses where possible. false
): do not collapse unary minuses, and instead translate each one into an AST node of type AST_MINUS.collapseminus | a boolean value (one of the constants L3P_COLLAPSE_UNARY_MINUS or L3P_EXPAND_UNARY_MINUS) indicating how unary minus signs in the input should be handled. |
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, as desired.
type | a constant, one of following three possibilities: |
void L3ParserSettings::setParseUnits | ( | bool | units | ) |
Sets the parser's behavior in handling units associated with numbers in a mathematical formula.
In SBML Level 2, there is no means of associating a unit of measurement with a pure number in a formula, while SBML Level 3 does define a syntax for this. In Level 3, MathML <cn>
elements can have an attribute named units
placed in the SBML namespace, which can be used to indicate the units to be associated with the number. The text-string infix formula parser allows units to be placed after raw numbers; they are interpreted as unit identifiers for units defined by the SBML specification or in the containing Model object. Some examples include: "4 mL
", "2.01 Hz
", "3.1e-6 M
", and "(5/8) inches
". To produce a valid SBML model, there must either exist a UnitDefinition corresponding to the identifier of the unit, or the unit must be defined in Table 2 of the SBML specification.
units | A boolean indicating whether to parse units:
|
void L3ParserSettings::unsetModel | ( | ) |
Sets the Model reference in this L3ParserSettings object to NULL
.