libSBML Perl API
5.20.4
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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 written as text strings. The inverse function is and its variants such as The parsers and the formula writers convert between a text-string representation of mathematical formulas and Abstract Syntax Trees (ASTs), represented in libSBML using ASTNode objects. Compared to the parser and writer implemented by the functions and , which were designed primarily for converting the mathematical formula strings in SBML Level 1, the SBML Level 3 or "L3" variants of the parser and writer use an extended formula syntax. They also have 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 using L3ParserSettings objects. (For the formula writer, only a subset of these settings is relevant; please see the documentation for for more information about which ones).
SId
) from the model in preference to pre-defined MathML symbols 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 by the parser will contain the construct <ci> pi </ci>
instead of the construct <pi/>
. Another 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/>
. log
with a single argument ("log(x)
") can be parsed as log10(x)
, ln(x)
, or treated as an error, as desired. - -3
") from the input and incorporate single unary minuses into the number node, or (2) preserve all minuses in the AST node structure, turning them into ASTNode objects of type number id
" can be interpreted as a numerical value number
followed by units of measurement indicated by id
, or it can be treated as a syntax error. (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.) avogadro
can be parsed either as a MathML csymbol or as a identifier. More specifically, "avogadro
" can be treated as an ASTNode of type or of type To obtain the default configuration values, callers can use the function . To 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 | |
bool | getComparisonCaseSensitivity () const |
Returns true if the parser is configured to match built-in symbols in a case-insensitive way. | |
const Model * | getModel () const |
Returns the Model object referenced by this L3ParserSettings object. | |
bool | getParseAvogadroCsymbol () const |
Indicates the current behavior set for handling avogadro for SBML Level 3. | |
bool | getParseCollapseMinus () const |
Indicates the current behavior set for handling multiple unary minuses in formulas. | |
bool | getParseL3v2Functions () const |
Indicates the current behavior set for handling whether to parse the functions added in L3v2 as that MathML or not. | |
ParseLogType_t | getParseLog () const |
Indicates the current behavior set for handling the function log with one argument. | |
bool | getParseModuloL3v2 () const |
Indicates the current behavior set for handling the % symbol in mathematical formulas. | |
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. | |
bool | getParseUnits () const |
Indicates the current behavior set for handling units in text-string mathematical formulas. | |
L3ParserSettings () | |
Creates a new L3ParserSettings object with default values. | |
L3ParserSettings (const L3ParserSettings &source) | |
Copy constructor. | |
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. | |
L3ParserSettings & | operator= (const L3ParserSettings &source) |
Assignment operator. | |
void | setComparisonCaseSensitivity (bool strcmp) |
Sets the parser's behavior with respect to case sensitivity for recognizing predefined symbols. | |
void | setModel (const Model *model) |
Sets the model reference in this L3ParserSettings object. | |
void | setParseAvogadroCsymbol (bool l2only) |
Sets the parser's behavior in handling the symbol avogadro in mathematical formulas. | |
void | setParseCollapseMinus (bool collapseminus) |
Sets the behavior for handling unary minuses appearing in mathematical formulas. | |
void | setParseL3v2Functions (bool l3v2functions) |
Sets the behavior for handling functions added in SBML L3v2. | |
void | setParseLog (ParseLogType_t type) |
Sets the behavior for handling log in mathematical formulas. | |
void | setParseModuloL3v2 (bool modulol3v2) |
Sets the behavior for handling the % symbol in mathematical formulas. | |
void | setParsePackageMath (ExtendedMathType_t package, bool parsepackage) |
Sets the behavior for handling functions added in SBML packages. | |
void | setParseUnits (bool units) |
Sets the parser's behavior in handling units associated with numbers in a mathematical formula. | |
void | unsetModel () |
Unsets the Model reference in this L3ParserSettings object. | |
virtual | ~L3ParserSettings () |
Destroys this L3ParserSettings object. | |
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:
NULL
(which indicates that no syntax extensions due to SBML Level 3 packages will be assumed—the formula parser will only understand the core syntax described in the documentation for ). L3ParserSettings::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.
model | a Model object to be used for disambiguating identifiers encountered by in mathematical formulas. |
parselog | ("parse log") a flag that controls how the parser will handle the symbol 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, by using the parameter values , , or , respectively. |
collapseminus | ("collapse minus") a flag that controls how the parser will handle minus signs in formulas. Unary minus signs can be collapsed or preserved; that is, sequential pairs of unary minuses (e.g., "- -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. The possible values of this field are (to collapse unary minuses) and (to expand unary minuses). |
parseunits | ("parse units") a flag that controls how the parser will handle apparent references to units of measurement associated with raw numbers in a formula. If set to the value , units are parsed; if set to the value , units are not parsed. |
avocsymbol | ("Avogadro csymbol") a flag that controls how the parser will handle the appearance of the symbol avogadro in a formula. If set to the value , the symbol is interpreted as the SBML/MathML csymbol avogadro ; if set to the value , the symbol is interpreted as a plain symbol name. |
caseSensitive | ("case sensitive") a flag that controls how the cases of alphabetical characters are treated when symbols are compared. If the flag is set to the value , symbols are compared in a case-insensitive manner, which means that mathematical functions such as "sin" will be matched no matter what their case is: "Sin" , "SIN" , etc. If the flag is set to the value , symbols are interpreted in a case-sensitive manner. |
sbmlns | ("SBML namespaces") an SBML namespaces object. The namespaces identify the SBML Level 3 packages that can extend the syntax understood by the formula parser. When non-NULL , the parser will interpret additional syntax defined by the packages; for example, it may understand vector/array extensions introduced by the SBML Level 3 Arrays package. |
moduloL3v2 | ("modulo L3v2") a flag that controls how the parser will handle the % ('modulo') symbol in formulas. By default, the parser will convert 'a % b' to a piecewise function that properly calculates the remainder of a with respect to be, but the parser can also be set to produce the MathML rem function, should the target of the produced ASTNode be an SBML Level 3 Version 2 document, where the rem function is legal. The possible values of this field are (to parse % as a piecewise function) and (to parse % as rem ). |
l3v2functions | ("parse L3v2 functions directly") is a Boolean flag that controls how to translate certain mathematical functions added in SBML Level 3 Version 2 Core. The parser can either turn them into specific AST node types, or turn them all into with the name set to the function name in question. |
L3ParserSettings::L3ParserSettings | ( | const L3ParserSettings & | source | ) |
Copy constructor.
source | the instance to copy. |
|
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.
"sin"
and "piecewise"
, and for constants such as "true"
and "avogadro"
. Setting this option to causes the parser to become case sensitive. In that mode, for example, the symbols "sin"
and "true"
will match the built-in values, but the symbols "SIN"
, "Sin"
, "True"
, "TRUE"
, and so on, will not. 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.
avogadro
in the input as a reference to the MathML csymbol for Avogadro's constant defined in the SBML Level 3 specification. For Level 2, it must treat avogadro
as just another plain symbol. This method returns the current setting of the avogadro
-handling behavior in this L3ParserSettings object. The possible values are as follows:
true
): tells the parser to translate the string avogadro
(in any capitalization) into an AST node of type false
): tells the parser to translate the string avogadro
into an AST of type or
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 with a value of -4.1
, or it can be turned into a node of type having a child node of type . true
): collapse unary minuses where possible. false
): do not collapse unary minuses, and instead translate each one into an AST node of type bool L3ParserSettings::getParseL3v2Functions | ( | ) | const |
Indicates the current behavior set for handling whether to parse the functions added in L3v2 as that MathML or not.
true
): parse the strings rateOf
, implies
, max
, min
, quotient
, and rem
as , , , , , and , respectively. false
): parse the strings rateOf
, implies
, max
, min
, quotient
, and rem
all as with the appropriate name set. 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 , , and
bool L3ParserSettings::getParseModuloL3v2 | ( | ) | const |
Indicates the current behavior set for handling the % symbol in mathematical formulas.
true
): use the 'rem' MathML function ( ). false
): use a piecewise function ( ) to encode the modulo rule explicitly. 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. |
true
): parse any string defined in a given SBML L3 package as its corresponding ASTType_t. (value = false
): parse any string that would have been defined in the given SBML L3 package as or
with the appropriate name set.
bool L3ParserSettings::getParseUnits | ( | ) | const |
Indicates the current behavior set for handling units in text-string mathematical formulas.
<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 Level 3 specification. Since SBML Level 2 does not have the ability to associate units with pure numbers, the value should be expected to be 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. 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.
"sin"
and "piecewise"
, and for constants such as "true"
and "avogadro"
. Setting this option to causes the parser to become case sensitive. In that mode, for example, the symbols "sin"
and "true"
will match the built-in values, but the symbols "SIN"
, "Sin"
, "True"
, "TRUE"
, and so on, will not. 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.
avogadro
in the input as a reference to the MathML csymbol for Avogadro's constant defined in the SBML Level 3 specification. For Level 2, it must treat avogadro
as just another plain symbol. This method allows callers to set the avogadro
-handling behavior in this L3ParserSettings object. The possible values of l2only
are as follows:
true
): tells the parser to translate the string avogadro
(in any capitalization) into an AST node of type false
): tells the parser to translate the string avogadro
into an AST of type Since SBML Level 2 does not define a symbol for Avogadro's constant, the value should be set to when parsing text-string formulas intended for use in SBML Level 2 documents.
l2only | a boolean value indicating how the string avogadro should be treated when encountered in a formula. This will be one of the values or |
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 with a value of -4.1
, or it can be turned into a node of type having a child node of type . 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 collapseminus | a boolean value (one of the constants or ) indicating how unary minus signs in the input should be handled. |
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:
true
): parse the strings rateOf
, implies
, max
, min
, quotient
, and rem
as , , , , , and , respectively. false
): parse the strings rateOf
, implies
, max
, min
, quotient
, and rem
all as with the appropriate name set. l3v2functions | a boolean value (one of the constants or ) indicating how to interpret those function names. |
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 , , or
for the type
parameter.
type | a constant, one of following three possibilities: |
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:
true
): use the 'rem' MathML function ( ). false
): use a piecewise function ( ) to encode the modulo rule explicitly. modulol3v2 | a boolean value (one of the constants or ) indicating how the % symbol in the input should be handled. |
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:
true
): parse any string defined in a given SBML L3 package as its corresponding ASTType_t. (value = false
): parse any string that would have been defined in the given SBML L3 package as or
with the appropriate name set.
package | an ExtendedMathType_t indicating the extended math package to be queried. |
parsepackage | a boolean value (one of the constants or ) indicating how to interpret those function names. |
void L3ParserSettings::setParseUnits | ( | bool | units | ) |
Sets the parser's behavior in handling units associated with numbers in a mathematical formula.
<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 Level 3 specification. 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: |
true
): parse units in the text-string formula. false
): treat units in the text-string formula as errors. 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
.