org.sbml.jsbml.util.compilers

Class FormulaCompiler

java.lang.Object

org.sbml.jsbml.util.StringTools

org.sbml.jsbml.util.compilers.FormulaCompiler

All Implemented Interfaces:

ASTNodeCompiler

Direct Known Subclasses:

FormulaCompilerLibSBML, FormulaCompilerNoPiecewise, LibSBMLFormulaCompiler

public class FormulaCompiler
extends StringTools
implements ASTNodeCompiler

This class creates C-like infix formula Strings that represent the content of ASTNodes. These can be used to save equations in SBML with older than Level 2.

Since:

0.8

Version:

$Rev$

Author:

Alexander Dörr, Andreas Dräger

Field Summary

Fields

Modifier and Type	Field and Description
protected java.lang.String	EXPONENTIALE String used to represent the exponentiale constant
protected java.lang.String	FORMULA_ARGUMENT_SEPARATOR
protected java.lang.String	INVERSE_TRIGONOMETRIC_PREFIX All inverse trigonometric functions may be defined in the infix either using 'arc' as a prefix or simply 'a'

Fields inherited from class org.sbml.jsbml.util.StringTools

DECIMAL_FORMAT, REAL_FORMAT, SCIENTIFIC_FORMAT, underscore

Constructor Summary

Constructors

Constructor and Description
FormulaCompiler()

Method Summary

Modifier and Type	Method and Description
ASTNodeValue	abs(ASTNode node) The absolute value represented by the given ASTNode.
ASTNodeValue	and(java.util.List<ASTNode> nodes)
ASTNodeValue	arccos(ASTNode node)
ASTNodeValue	arccosh(ASTNode node)
ASTNodeValue	arccot(ASTNode node)
ASTNodeValue	arccoth(ASTNode node)
ASTNodeValue	arccsc(ASTNode node)
ASTNodeValue	arccsch(ASTNode node)
ASTNodeValue	arcsec(ASTNode node)
ASTNodeValue	arcsech(ASTNode node)
ASTNodeValue	arcsin(ASTNode node)
ASTNodeValue	arcsinh(ASTNode node)
ASTNodeValue	arctan(ASTNode node)
ASTNodeValue	arctanh(ASTNode node)
private static java.lang.StringBuffer	arith(char operator, java.lang.Object... elements) Basic method which links several elements with a mathematical operator.
static java.lang.StringBuffer	brackets(java.lang.Object sb)
ASTNodeValue	ceiling(ASTNode node)
protected java.lang.String	checkBrackets(ASTNode node) Creates brackets if needed.
protected java.lang.String	checkDenominatorBrackets(ASTNode node) Creates brackets if needed.
protected java.lang.String	checkRelationalArgumentBrackets(ASTNode node) Creates brackets if needed.
ASTNodeValue	compile(CallableSBase variable)
ASTNodeValue	compile(Compartment c)
ASTNodeValue	compile(double mantissa, int exponent, java.lang.String units) Creates an ASTNodeValue that represents a real number in scientific notation, i.e., mantissa * 10^exponent, and the given units.
ASTNodeValue	compile(double real, java.lang.String units)
ASTNodeValue	compile(int integer, java.lang.String units)
ASTNodeValue	compile(java.lang.String name) A compiler will also have to deal with a name.
private static boolean	containsArith(java.lang.Object something) Tests whether the String representation of the given object contains any arithmetic symbols and if the given object is already surrounded by brackets.
ASTNodeValue	cos(ASTNode node)
ASTNodeValue	cosh(ASTNode node)
ASTNodeValue	cot(ASTNode node)
ASTNodeValue	coth(ASTNode node)
ASTNodeValue	csc(ASTNode node)
ASTNodeValue	csch(ASTNode node)
ASTNodeValue	delay(java.lang.String delayName, ASTNode x, ASTNode y, java.lang.String timeUnits) Evaluates delay functions.
static java.lang.StringBuffer	diff(java.lang.Object... subtrahents) Returns the difference of the given elements as StringBuffer.
ASTNodeValue	eq(ASTNode left, ASTNode right) Equal.
ASTNodeValue	exp(ASTNode node)
ASTNodeValue	factorial(ASTNode node)
ASTNodeValue	floor(ASTNode node)
ASTNodeValue	frac(ASTNode numerator, ASTNode denominator) Fraction of two ASTNodes
ASTNodeValue	frac(int numerator, int denominator) A fraction of two int values.
static java.lang.StringBuffer	frac(java.lang.Object numerator, java.lang.Object denominator) Returns a fraction with the given elements as numerator and denominator.
ASTNodeValue	function(FunctionDefinition func, java.util.List<ASTNode> nodes)
protected ASTNodeValue	function(java.lang.String name, ASTNode... nodes)
ASTNodeValue	function(java.lang.String name, java.util.List<ASTNode> nodes)
ASTNodeValue	geq(ASTNode left, ASTNode right) Greater equal.
ASTNodeValue	getConstantAvogadro(java.lang.String name) Creates an ASTNodeValue that represent's Avogadro's number.
ASTNodeValue	getConstantE()
ASTNodeValue	getConstantFalse()
ASTNodeValue	getConstantPi()
ASTNodeValue	getConstantTrue()
ASTNodeValue	getNegativeInfinity()
ASTNodeValue	getPositiveInfinity()
ASTNodeValue	getRateOf(java.lang.String name)
protected static java.lang.StringBuffer	getSpecies(SpeciesReference ref) Returns the id of a PluginSpeciesReference object's belonging species as an object of type StringBuffer.
protected static double	getStoichiometry(SpeciesReference ref) Returns the value of a PluginSpeciesReference object's stoichiometry either as a double or, if the stoichiometry has an integer value, as an int object.
ASTNodeValue	gt(ASTNode left, ASTNode right) Greater than.
ASTNodeValue	implies(java.util.List<ASTNode> values) Returns the logical implies between two ASTNode.
ASTNodeValue	lambda(java.util.List<ASTNode> nodes) The body of a FunctionDefinition.
protected java.lang.String	lambdaBody(java.util.List<ASTNode> nodes) Creates the body of a lambda function, i.e., the argument list and the actual mathematical operation, all comma separated and surrounded in brackets.
ASTNodeValue	leq(ASTNode left, ASTNode right) Less equal.
ASTNodeValue	ln(ASTNode node) Natural logarithm.
ASTNodeValue	log(ASTNode node) Logarithm of the given value to base 10.
ASTNodeValue	log(ASTNode left, ASTNode right) Logarithm of the given value to the given base.
protected ASTNodeValue	logicalOperation(java.lang.String operator, java.util.List<ASTNode> nodes)
protected ASTNodeValue	logicalOperationFunction(java.lang.String operator, java.util.List<ASTNode> nodes)
ASTNodeValue	lt(ASTNode left, ASTNode right) Less than.
ASTNodeValue	max(java.util.List<ASTNode> values) Returns the maximum of the values.
ASTNodeValue	min(java.util.List<ASTNode> values) Returns the minimum of the values.
ASTNodeValue	minus(java.util.List<ASTNode> nodes) Subtraction.
ASTNodeValue	neq(ASTNode left, ASTNode right) Not equal.
ASTNodeValue	not(ASTNode node)
ASTNodeValue	or(java.util.List<ASTNode> nodes)
ASTNodeValue	piecewise(java.util.List<ASTNode> nodes)
ASTNodeValue	plus(java.util.List<ASTNode> nodes)
ASTNodeValue	pow(ASTNode left, ASTNode right)
static java.lang.StringBuffer	pow(java.lang.Object basis, java.lang.Object exponent) Returns the basis to the power of the exponent as StringBuffer.
ASTNodeValue	quotient(java.util.List<ASTNode> values) Returns the quotient of the division of the values.
protected java.lang.String	relation(ASTNode left, java.lang.String symbol, ASTNode right)
ASTNodeValue	rem(java.util.List<ASTNode> values) Returns the remainder of the division of the values.
ASTNodeValue	root(ASTNode rootExponent, ASTNode radiant)
ASTNodeValue	root(double rootExponent, ASTNode radiant)
static java.lang.StringBuffer	root(java.lang.Object exponent, java.lang.Object basis) Returns the exponent-th root of the basis as StringBuffer.
ASTNodeValue	sec(ASTNode node)
ASTNodeValue	sech(ASTNode node)
ASTNodeValue	selector(java.util.List<ASTNode> nodes)
protected static java.lang.StringBuffer	selector(java.lang.Object... elements) Returns the given selector as StringBuffer.
ASTNodeValue	sin(ASTNode node)
ASTNodeValue	sinh(ASTNode node)
ASTNodeValue	sqrt(ASTNode node) Square root.
static java.lang.StringBuffer	sqrt(java.lang.Object basis)
static java.lang.StringBuffer	sum(java.lang.Object... summands) Returns the sum of the given elements as StringBuffer.
ASTNodeValue	symbolTime(java.lang.String time) The simulation time.
ASTNodeValue	tan(ASTNode node)
ASTNodeValue	tanh(ASTNode node)
ASTNodeValue	times(java.util.List<ASTNode> nodes) Product of all given ASTNodes.
static java.lang.StringBuffer	times(java.lang.Object... factors) Returns the product of the given elements as StringBuffer.
ASTNodeValue	uMinus(ASTNode node) Unary minus, i.e., negation of the given ASTNode.
ASTNodeValue	unknownValue() Dealing with a malformed ASTNode.
ASTNodeValue	vector(java.util.List<ASTNode> nodes) Dealing with a vector.
protected static java.lang.StringBuffer	vector(java.lang.Object... elements) Returns the given vector as StringBuffer.
ASTNodeValue	xor(java.util.List<ASTNode> nodes) Exclusive or.

Methods inherited from class org.sbml.jsbml.util.StringTools

append, append, concat, concatStringBuilder, encodeForHTML, fill, fill, firstLetterLowerCase, firstLetterUpperCase, getWordForNumber, leadingZeros, newLine, parseSBMLBoolean, parseSBMLDouble, parseSBMLInt, parseSBMLShort, toHTML, toHTML, toString, toString, toXMLAnnotationString, toXMLMessageString, toXMLNotesString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

FORMULA_ARGUMENT_SEPARATOR

protected java.lang.String FORMULA_ARGUMENT_SEPARATOR

INVERSE_TRIGONOMETRIC_PREFIX

protected java.lang.String INVERSE_TRIGONOMETRIC_PREFIX

All inverse trigonometric functions may be defined in the infix either using 'arc' as a prefix or simply 'a'

EXPONENTIALE

protected java.lang.String EXPONENTIALE

String used to represent the exponentiale constant

Constructor Detail

FormulaCompiler

public FormulaCompiler()

Method Detail

arith

private static final java.lang.StringBuffer arith(char operator,
                                                  java.lang.Object... elements)

Basic method which links several elements with a mathematical operator. All empty StringBuffer object are excluded.

Parameters:

operator -

elements -

Returns:

brackets

public static final java.lang.StringBuffer brackets(java.lang.Object sb)

Parameters:

sb -

Returns:

containsArith

private static boolean containsArith(java.lang.Object something)

Tests whether the String representation of the given object contains any arithmetic symbols and if the given object is already surrounded by brackets.

Parameters:

something -

Returns:

True if either brackets are set around the given object or the object does not contain any symbols such as +, -, *, /.

diff

public static final java.lang.StringBuffer diff(java.lang.Object... subtrahents)

Returns the difference of the given elements as StringBuffer.

Parameters:

subtrahents -

Returns:

frac

public static final java.lang.StringBuffer frac(java.lang.Object numerator,
                                                java.lang.Object denominator)

Returns a fraction with the given elements as numerator and denominator.

Parameters:

numerator -

denominator -

Returns:

getSpecies

protected static final java.lang.StringBuffer getSpecies(SpeciesReference ref)

Returns the id of a PluginSpeciesReference object's belonging species as an object of type StringBuffer.

Parameters:

ref -

Returns:

getStoichiometry

protected static final double getStoichiometry(SpeciesReference ref)

Returns the value of a PluginSpeciesReference object's stoichiometry either as a double or, if the stoichiometry has an integer value, as an int object.

Parameters:

ref -

Returns:

pow

public static final java.lang.StringBuffer pow(java.lang.Object basis,
                                               java.lang.Object exponent)

Returns the basis to the power of the exponent as StringBuffer. Several special cases are treated.

Parameters:

basis -

exponent -

Returns:

root

public static final java.lang.StringBuffer root(java.lang.Object exponent,
                                                java.lang.Object basis)
                                         throws java.lang.NumberFormatException

Returns the exponent-th root of the basis as StringBuffer.

Parameters:

exponent -

basis -

Returns:

Throws:

java.lang.NumberFormatException

java.util.IllegalFormatException - If the given exponent represents a zero.

selector

protected static final java.lang.StringBuffer selector(java.lang.Object... elements)

Returns the given selector as StringBuffer.

Parameters:

elements -

Returns:

sqrt

public static final java.lang.StringBuffer sqrt(java.lang.Object basis)

Parameters:

basis -

Returns:

sum

public static final java.lang.StringBuffer sum(java.lang.Object... summands)

Returns the sum of the given elements as StringBuffer.

Parameters:

summands -

Returns:

times

public static final java.lang.StringBuffer times(java.lang.Object... factors)

Returns the product of the given elements as StringBuffer.

Parameters:

factors -

Returns:

vector

protected static final java.lang.StringBuffer vector(java.lang.Object... elements)

Returns the given vector as StringBuffer.

Parameters:

elements -

Returns:

abs

public ASTNodeValue abs(ASTNode node)
                 throws SBMLException

Description copied from interface: ASTNodeCompiler

The absolute value represented by the given ASTNode.

Specified by:

abs in interface ASTNodeCompiler

Parameters:

node - Must be interpretable as a Number.

Returns:

Throws:

SBMLException

and

public ASTNodeValue and(java.util.List<ASTNode> nodes)
                 throws SBMLException

Specified by:

and in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arccos

public ASTNodeValue arccos(ASTNode node)
                    throws SBMLException

Specified by:

arccos in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arccosh

public ASTNodeValue arccosh(ASTNode node)
                     throws SBMLException

Specified by:

arccosh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arccot

public ASTNodeValue arccot(ASTNode node)
                    throws SBMLException

Specified by:

arccot in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arccoth

public ASTNodeValue arccoth(ASTNode node)
                     throws SBMLException

Specified by:

arccoth in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arccsc

public ASTNodeValue arccsc(ASTNode node)
                    throws SBMLException

Specified by:

arccsc in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arccsch

public ASTNodeValue arccsch(ASTNode node)
                     throws SBMLException

Specified by:

arccsch in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arcsec

public ASTNodeValue arcsec(ASTNode node)
                    throws SBMLException

Specified by:

arcsec in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arcsech

public ASTNodeValue arcsech(ASTNode node)
                     throws SBMLException

Specified by:

arcsech in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arcsin

public ASTNodeValue arcsin(ASTNode node)
                    throws SBMLException

Specified by:

arcsin in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arcsinh

public ASTNodeValue arcsinh(ASTNode node)
                     throws SBMLException

Specified by:

arcsinh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arctan

public ASTNodeValue arctan(ASTNode node)
                    throws SBMLException

Specified by:

arctan in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arctanh

public ASTNodeValue arctanh(ASTNode node)
                     throws SBMLException

Specified by:

arctanh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

ceiling

public ASTNodeValue ceiling(ASTNode node)
                     throws SBMLException

Specified by:

ceiling in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

checkBrackets

protected java.lang.String checkBrackets(ASTNode node)
                                  throws SBMLException

Creates brackets if needed.

Parameters:

node -

Returns:

Throws:

SBMLException

checkDenominatorBrackets

protected java.lang.String checkDenominatorBrackets(ASTNode node)
                                             throws SBMLException

Creates brackets if needed.

Parameters:

node -

Returns:

Throws:

SBMLException

checkRelationalArgumentBrackets

protected java.lang.String checkRelationalArgumentBrackets(ASTNode node)
                                                    throws SBMLException

Creates brackets if needed.

Parameters:

node -

Returns:

Throws:

SBMLException

compile

public ASTNodeValue compile(Compartment c)

Specified by:

compile in interface ASTNodeCompiler

Returns:

compile

public ASTNodeValue compile(double mantissa,
                            int exponent,
                            java.lang.String units)

Description copied from interface: ASTNodeCompiler

Creates an ASTNodeValue that represents a real number in scientific notation, i.e., mantissa * 10^exponent, and the given units.

Specified by:

compile in interface ASTNodeCompiler

Parameters:

mantissa - The number to be multiplied with ten to the power of the given exponent.

exponent - The exponent for the multiplier ten.

units - The identifier of the units object associated with the number represented by this element. Can be null if no units have been defined.

Returns:

compile

public ASTNodeValue compile(double real,
                            java.lang.String units)

Specified by:

compile in interface ASTNodeCompiler

units - A String representing the Unit of the given number. This can be the identifier of a UnitDefinition in the model or a literal in Kind. Can be null if no units have been defined.

Returns:

compile

public ASTNodeValue compile(int integer,
                            java.lang.String units)

Specified by:

compile in interface ASTNodeCompiler

units - A String representing the Unit of the given number. This can be the identifier of a UnitDefinition in the model or a literal in Kind. Can be null if no units have been defined.

Returns:

compile

public ASTNodeValue compile(CallableSBase variable)

Specified by:

compile in interface ASTNodeCompiler

Returns:

compile

public ASTNodeValue compile(java.lang.String name)

Description copied from interface: ASTNodeCompiler

A compiler will also have to deal with a name. The meaning of this can be various. For instance, the name may refer to a Species in the system. In case of numerical computation, the ASTNodeCompiler must create an ASTNodeValue representing the current value of this Species.

Specified by:

compile in interface ASTNodeCompiler

Returns:

cos

public ASTNodeValue cos(ASTNode node)
                 throws SBMLException

Specified by:

cos in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

cosh

public ASTNodeValue cosh(ASTNode node)
                  throws SBMLException

Specified by:

cosh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

cot

public ASTNodeValue cot(ASTNode node)
                 throws SBMLException

Specified by:

cot in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

coth

public ASTNodeValue coth(ASTNode node)
                  throws SBMLException

Specified by:

coth in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

csc

public ASTNodeValue csc(ASTNode node)
                 throws SBMLException

Specified by:

csc in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

csch

public ASTNodeValue csch(ASTNode node)
                  throws SBMLException

Specified by:

csch in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

delay

public ASTNodeValue delay(java.lang.String delayName,
                          ASTNode x,
                          ASTNode y,
                          java.lang.String timeUnits)
                   throws SBMLException

Description copied from interface: ASTNodeCompiler

Evaluates delay functions.

Specified by:

delay in interface ASTNodeCompiler

Parameters:

delayName - the name of this delay function.

y - an expression of a positive duration time (the amoutn of delay)

timeUnits - the units for the delay.

Returns:

Throws:

SBMLException

eq

public ASTNodeValue eq(ASTNode left,
                       ASTNode right)
                throws SBMLException

Description copied from interface: ASTNodeCompiler

Equal.

Specified by:

eq in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

exp

public ASTNodeValue exp(ASTNode node)
                 throws SBMLException

Specified by:

exp in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

factorial

public ASTNodeValue factorial(ASTNode node)

Specified by:

factorial in interface ASTNodeCompiler

Returns:

floor

public ASTNodeValue floor(ASTNode node)
                   throws SBMLException

Specified by:

floor in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

frac

public ASTNodeValue frac(ASTNode numerator,
                         ASTNode denominator)
                  throws SBMLException

Description copied from interface: ASTNodeCompiler

Fraction of two ASTNodes

Specified by:

frac in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

frac

public ASTNodeValue frac(int numerator,
                         int denominator)

Description copied from interface: ASTNodeCompiler

A fraction of two int values.

Specified by:

frac in interface ASTNodeCompiler

Returns:

function

public ASTNodeValue function(FunctionDefinition func,
                             java.util.List<ASTNode> nodes)
                      throws SBMLException

Specified by:

function in interface ASTNodeCompiler

nodes - Values to be inserted into the parameter list of the function.

Returns:

Throws:

SBMLException

function

protected ASTNodeValue function(java.lang.String name,
                                ASTNode... nodes)
                         throws SBMLException

Parameters:

name -

nodes -

Returns:

Throws:

SBMLException

function

public ASTNodeValue function(java.lang.String name,
                             java.util.List<ASTNode> nodes)
                      throws SBMLException

Specified by:

function in interface ASTNodeCompiler

Parameters:

name -

nodes -

Returns:

Throws:

SBMLException

geq

public ASTNodeValue geq(ASTNode left,
                        ASTNode right)
                 throws SBMLException

Description copied from interface: ASTNodeCompiler

Greater equal.

Specified by:

geq in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

getConstantAvogadro

public ASTNodeValue getConstantAvogadro(java.lang.String name)

Description copied from interface: ASTNodeCompiler

Creates an ASTNodeValue that represent's Avogadro's number. Optionally, the compiler may associate the given name with this number.

Specified by:

getConstantAvogadro in interface ASTNodeCompiler

Parameters:

name - An optional name for Avogadro's number.

Returns:

getConstantE

public ASTNodeValue getConstantE()

Specified by:

getConstantE in interface ASTNodeCompiler

Returns:

getConstantFalse

public ASTNodeValue getConstantFalse()

Specified by:

getConstantFalse in interface ASTNodeCompiler

Returns:

getConstantPi

public ASTNodeValue getConstantPi()

Specified by:

getConstantPi in interface ASTNodeCompiler

Returns:

getConstantTrue

public ASTNodeValue getConstantTrue()

Specified by:

getConstantTrue in interface ASTNodeCompiler

Returns:

getNegativeInfinity

public ASTNodeValue getNegativeInfinity()

Specified by:

getNegativeInfinity in interface ASTNodeCompiler

Returns:

getPositiveInfinity

public ASTNodeValue getPositiveInfinity()

Specified by:

getPositiveInfinity in interface ASTNodeCompiler

Returns:

gt

public ASTNodeValue gt(ASTNode left,
                       ASTNode right)
                throws SBMLException

Description copied from interface: ASTNodeCompiler

Greater than.

Specified by:

gt in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

lambda

public ASTNodeValue lambda(java.util.List<ASTNode> nodes)
                    throws SBMLException

Description copied from interface: ASTNodeCompiler

The body of a FunctionDefinition.

Specified by:

lambda in interface ASTNodeCompiler

Parameters:

nodes - Place holders for arguments.

Returns:

Throws:

SBMLException

lambdaBody

protected java.lang.String lambdaBody(java.util.List<ASTNode> nodes)
                               throws SBMLException

Creates the body of a lambda function, i.e., the argument list and the actual mathematical operation, all comma separated and surrounded in brackets.

Parameters:

nodes -

Returns:

Throws:

SBMLException

leq

public ASTNodeValue leq(ASTNode left,
                        ASTNode right)
                 throws SBMLException

Description copied from interface: ASTNodeCompiler

Less equal.

Specified by:

leq in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

ln

public ASTNodeValue ln(ASTNode node)
                throws SBMLException

Description copied from interface: ASTNodeCompiler

Natural logarithm.

Specified by:

ln in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

log

public ASTNodeValue log(ASTNode node)
                 throws SBMLException

Description copied from interface: ASTNodeCompiler

Logarithm of the given value to base 10.

Specified by:

log in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

log

public ASTNodeValue log(ASTNode left,
                        ASTNode right)
                 throws SBMLException

Description copied from interface: ASTNodeCompiler

Logarithm of the given value to the given base.

Specified by:

log in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

logicalOperation

protected ASTNodeValue logicalOperation(java.lang.String operator,
                                        java.util.List<ASTNode> nodes)
                                 throws SBMLException

Parameters:

operator -

nodes -

Returns:

Throws:

SBMLException

logicalOperationFunction

protected ASTNodeValue logicalOperationFunction(java.lang.String operator,
                                                java.util.List<ASTNode> nodes)

lt

public ASTNodeValue lt(ASTNode left,
                       ASTNode right)
                throws SBMLException

Description copied from interface: ASTNodeCompiler

Less than.

Specified by:

lt in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

minus

public ASTNodeValue minus(java.util.List<ASTNode> nodes)
                   throws SBMLException

Description copied from interface: ASTNodeCompiler

Subtraction.

Specified by:

minus in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

neq

public ASTNodeValue neq(ASTNode left,
                        ASTNode right)
                 throws SBMLException

Description copied from interface: ASTNodeCompiler

Not equal.

Specified by:

neq in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

not

public ASTNodeValue not(ASTNode node)
                 throws SBMLException

Specified by:

not in interface ASTNodeCompiler

Parameters:

node - This value must be interpretable as a Boolean.

Returns:

Throws:

SBMLException

or

public ASTNodeValue or(java.util.List<ASTNode> nodes)
                throws SBMLException

Specified by:

or in interface ASTNodeCompiler

Parameters:

nodes - These values must be interpretable as a Boolean.

Returns:

Throws:

SBMLException

piecewise

public ASTNodeValue piecewise(java.util.List<ASTNode> nodes)
                       throws SBMLException

Specified by:

piecewise in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

plus

public ASTNodeValue plus(java.util.List<ASTNode> nodes)
                  throws SBMLException

Specified by:

plus in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

pow

public ASTNodeValue pow(ASTNode left,
                        ASTNode right)
                 throws SBMLException

Specified by:

pow in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

relation

protected java.lang.String relation(ASTNode left,
                                    java.lang.String symbol,
                                    ASTNode right)
                             throws SBMLException

Parameters:

left -

symbol -

right -

Returns:

Throws:

SBMLException

root

public ASTNodeValue root(ASTNode rootExponent,
                         ASTNode radiant)
                  throws SBMLException

Specified by:

root in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

root

public ASTNodeValue root(double rootExponent,
                         ASTNode radiant)
                  throws SBMLException

Specified by:

root in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

sec

public ASTNodeValue sec(ASTNode node)
                 throws SBMLException

Specified by:

sec in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

sech

public ASTNodeValue sech(ASTNode node)
                  throws SBMLException

Specified by:

sech in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

sin

public ASTNodeValue sin(ASTNode node)
                 throws SBMLException

Specified by:

sin in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

sinh

public ASTNodeValue sinh(ASTNode node)
                  throws SBMLException

Specified by:

sinh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

sqrt

public ASTNodeValue sqrt(ASTNode node)
                  throws SBMLException

Description copied from interface: ASTNodeCompiler

Square root.

Specified by:

sqrt in interface ASTNodeCompiler

Parameters:

node - This value must be interpretable as a Number.

Returns:

Throws:

SBMLException

symbolTime

public ASTNodeValue symbolTime(java.lang.String time)

Description copied from interface: ASTNodeCompiler

The simulation time.

Specified by:

symbolTime in interface ASTNodeCompiler

Parameters:

time - The name of the time symbol.

Returns:

An ASTNodeValue that represents the current time.

tan

public ASTNodeValue tan(ASTNode node)
                 throws SBMLException

Specified by:

tan in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

tanh

public ASTNodeValue tanh(ASTNode node)
                  throws SBMLException

Specified by:

tanh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

times

public ASTNodeValue times(java.util.List<ASTNode> nodes)
                   throws SBMLException

Description copied from interface: ASTNodeCompiler

Product of all given ASTNodes.

Specified by:

times in interface ASTNodeCompiler

Parameters:

nodes - These values must be interpretable to Number.

Returns:

Throws:

SBMLException

uMinus

public ASTNodeValue uMinus(ASTNode node)
                    throws SBMLException

Description copied from interface: ASTNodeCompiler

Unary minus, i.e., negation of the given ASTNode.

Specified by:

uMinus in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

unknownValue

public ASTNodeValue unknownValue()
                          throws SBMLException

Description copied from interface: ASTNodeCompiler

Dealing with a malformed ASTNode.

Specified by:

unknownValue in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

xor

public ASTNodeValue xor(java.util.List<ASTNode> nodes)
                 throws SBMLException

Description copied from interface: ASTNodeCompiler

Exclusive or.

Specified by:

xor in interface ASTNodeCompiler

Parameters:

nodes - It must be possible to evaluate the given values to Boolean.

Returns:

Throws:

SBMLException

selector

public ASTNodeValue selector(java.util.List<ASTNode> nodes)
                      throws SBMLException

Specified by:

selector in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

vector

public ASTNodeValue vector(java.util.List<ASTNode> nodes)
                    throws SBMLException

Description copied from interface: ASTNodeCompiler

Dealing with a vector.

Specified by:

vector in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

max

public ASTNodeValue max(java.util.List<ASTNode> values)

Description copied from interface: ASTNodeCompiler

Returns the maximum of the values.

Specified by:

max in interface ASTNodeCompiler

Returns:

the maximum of the values.

min

public ASTNodeValue min(java.util.List<ASTNode> values)

Description copied from interface: ASTNodeCompiler

Returns the minimum of the values.

Specified by:

min in interface ASTNodeCompiler

Returns:

the minimum of the values.

quotient

public ASTNodeValue quotient(java.util.List<ASTNode> values)

Description copied from interface: ASTNodeCompiler

Returns the quotient of the division of the values.

Specified by:

quotient in interface ASTNodeCompiler

Returns:

the quotient of the values.

rem

public ASTNodeValue rem(java.util.List<ASTNode> values)

Description copied from interface: ASTNodeCompiler

Returns the remainder of the division of the values.

Specified by:

rem in interface ASTNodeCompiler

Returns:

the remainder of the division of the values.

implies

public ASTNodeValue implies(java.util.List<ASTNode> values)

Description copied from interface: ASTNodeCompiler

Returns the logical implies between two ASTNode.

Truth table:

 p   q  p→q
 
 T   T   T
 T   F   F
 F   T   T
 F   F   T

Specified by:

implies in interface ASTNodeCompiler

Returns:

the logical implies between two ASTNode.

getRateOf

public ASTNodeValue getRateOf(java.lang.String name)

Specified by:

getRateOf in interface ASTNodeCompiler

Returns: