org.sbml.jsbml.util.compilers

Class FindUnitsCompiler

java.lang.Object

org.sbml.jsbml.util.compilers.FindUnitsCompiler

All Implemented Interfaces:

ASTNodeCompiler

public class FindUnitsCompiler
extends java.lang.Object
implements ASTNodeCompiler

Finds if an ASTNode is using any units attribute. This ASTNodeCompiler is basically empty, only methods related to 'cn' elements are implemented

Since:

0.8

Version:

$Rev: 1757 $

Author:

Nicolas Rodriguez

Field Summary

Fields

Modifier and Type	Field and Description
private ASTNodeValue	dummyValue
private boolean	isUnitsDefined

Constructor Summary

Constructors

Constructor and Description
FindUnitsCompiler()

Method Summary

Methods

Modifier and Type	Method and Description
ASTNodeValue	abs(ASTNode value) The absolute value represented by the given ASTNode.
ASTNodeValue	and(java.util.List<ASTNode> values)
ASTNodeValue	arccos(ASTNode value)
ASTNodeValue	arccosh(ASTNode value)
ASTNodeValue	arccot(ASTNode value)
ASTNodeValue	arccoth(ASTNode value)
ASTNodeValue	arccsc(ASTNode value)
ASTNodeValue	arccsch(ASTNode value)
ASTNodeValue	arcsec(ASTNode value)
ASTNodeValue	arcsech(ASTNode value)
ASTNodeValue	arcsin(ASTNode value)
ASTNodeValue	arcsinh(ASTNode value)
ASTNodeValue	arctan(ASTNode value)
ASTNodeValue	arctanh(ASTNode value)
ASTNodeValue	ceiling(ASTNode value)
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.
ASTNodeValue	cos(ASTNode value)
ASTNodeValue	cosh(ASTNode value)
ASTNodeValue	cot(ASTNode value)
ASTNodeValue	coth(ASTNode value)
ASTNodeValue	csc(ASTNode value)
ASTNodeValue	csch(ASTNode value)
ASTNodeValue	delay(java.lang.String delayName, ASTNode x, ASTNode delay, java.lang.String timeUnits) Evaluates delay functions.
ASTNodeValue	eq(ASTNode left, ASTNode right) Equal.
ASTNodeValue	exp(ASTNode value)
ASTNodeValue	factorial(ASTNode value)
ASTNodeValue	floor(ASTNode value)
ASTNodeValue	frac(ASTNode numerator, ASTNode denominator) Fraction of two ASTNodes
ASTNodeValue	frac(int numerator, int denominator) A fraction of two int values.
ASTNodeValue	function(FunctionDefinition functionDefinition, java.util.List<ASTNode> args)
ASTNodeValue	function(java.lang.String functionDefinitionName, java.util.List<ASTNode> args)
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	gt(ASTNode left, ASTNode right) Greater than.
boolean	isUnitsDefined()
ASTNodeValue	lambda(java.util.List<ASTNode> values) The body of a FunctionDefinition.
ASTNodeValue	leq(ASTNode left, ASTNode right) Less equal.
ASTNodeValue	ln(ASTNode value) Natural logarithm.
ASTNodeValue	log(ASTNode value) Logarithm of the given value to base 10.
ASTNodeValue	log(ASTNode base, ASTNode value) Logarithm of the given value to the given base.
ASTNodeValue	lt(ASTNode left, ASTNode right) Less than.
ASTNodeValue	minus(java.util.List<ASTNode> values) Subtraction.
ASTNodeValue	neq(ASTNode left, ASTNode right) Not equal.
ASTNodeValue	not(ASTNode value)
ASTNodeValue	or(java.util.List<ASTNode> values)
ASTNodeValue	piecewise(java.util.List<ASTNode> values)
ASTNodeValue	plus(java.util.List<ASTNode> values)
ASTNodeValue	pow(ASTNode base, ASTNode exponent)
void	reset()
ASTNodeValue	root(ASTNode rootExponent, ASTNode radiant)
ASTNodeValue	root(double rootExponent, ASTNode radiant)
ASTNodeValue	sec(ASTNode value)
ASTNodeValue	sech(ASTNode value)
ASTNodeValue	selector(java.util.List<ASTNode> value)
ASTNodeValue	sin(ASTNode value)
ASTNodeValue	sinh(ASTNode value)
ASTNodeValue	sqrt(ASTNode radiant) Square root.
ASTNodeValue	symbolTime(java.lang.String time) The simulation time.
ASTNodeValue	tan(ASTNode value)
ASTNodeValue	tanh(ASTNode value)
ASTNodeValue	times(java.util.List<ASTNode> values) Product of all given ASTNodes.
ASTNodeValue	uMinus(ASTNode value) 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.
ASTNodeValue	xor(java.util.List<ASTNode> values) Exclusive or.

Methods inherited from class java.lang.Object

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

Field Detail

isUnitsDefined

private boolean isUnitsDefined

dummyValue

private final ASTNodeValue dummyValue

Constructor Detail

FindUnitsCompiler

public FindUnitsCompiler()

Method Detail

isUnitsDefined

public boolean isUnitsDefined()

reset

public void reset()

abs

public ASTNodeValue abs(ASTNode value)
                 throws SBMLException

Description copied from interface: ASTNodeCompiler

The absolute value represented by the given ASTNode.

Specified by:

abs in interface ASTNodeCompiler

Parameters:

value - Must be interpretable as a Number.

Returns:

Throws:

SBMLException

and

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

Specified by:

and in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arccos

public ASTNodeValue arccos(ASTNode value)
                    throws SBMLException

Specified by:

arccos in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arccosh

public ASTNodeValue arccosh(ASTNode value)
                     throws SBMLException

Specified by:

arccosh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arccot

public ASTNodeValue arccot(ASTNode value)
                    throws SBMLException

Specified by:

arccot in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arccoth

public ASTNodeValue arccoth(ASTNode value)
                     throws SBMLException

Specified by:

arccoth in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arccsc

public ASTNodeValue arccsc(ASTNode value)
                    throws SBMLException

Specified by:

arccsc in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arccsch

public ASTNodeValue arccsch(ASTNode value)
                     throws SBMLException

Specified by:

arccsch in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arcsec

public ASTNodeValue arcsec(ASTNode value)
                    throws SBMLException

Specified by:

arcsec in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arcsech

public ASTNodeValue arcsech(ASTNode value)
                     throws SBMLException

Specified by:

arcsech in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arcsin

public ASTNodeValue arcsin(ASTNode value)
                    throws SBMLException

Specified by:

arcsin in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arcsinh

public ASTNodeValue arcsinh(ASTNode value)
                     throws SBMLException

Specified by:

arcsinh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arctan

public ASTNodeValue arctan(ASTNode value)
                    throws SBMLException

Specified by:

arctan in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arctanh

public ASTNodeValue arctanh(ASTNode value)
                     throws SBMLException

Specified by:

arctanh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

ceiling

public ASTNodeValue ceiling(ASTNode value)
                     throws SBMLException

Specified by:

ceiling in interface ASTNodeCompiler

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 Unit.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 Unit.Kind. Can be null if no units have been defined.

Returns:

compile

public ASTNodeValue compile(CallableSBase variable)
                     throws SBMLException

Specified by:

compile in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

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 value)
                 throws SBMLException

Specified by:

cos in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

cosh

public ASTNodeValue cosh(ASTNode value)
                  throws SBMLException

Specified by:

cosh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

cot

public ASTNodeValue cot(ASTNode value)
                 throws SBMLException

Specified by:

cot in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

coth

public ASTNodeValue coth(ASTNode value)
                  throws SBMLException

Specified by:

coth in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

csc

public ASTNodeValue csc(ASTNode value)
                 throws SBMLException

Specified by:

csc in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

csch

public ASTNodeValue csch(ASTNode value)
                  throws SBMLException

Specified by:

csch in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

delay

public ASTNodeValue delay(java.lang.String delayName,
                 ASTNode x,
                 ASTNode delay,
                 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.

delay - 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 value)
                 throws SBMLException

Specified by:

exp in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

factorial

public ASTNodeValue factorial(ASTNode value)
                       throws SBMLException

Specified by:

factorial in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

floor

public ASTNodeValue floor(ASTNode value)
                   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)
                  throws SBMLException

Description copied from interface: ASTNodeCompiler

A fraction of two int values.

Specified by:

frac in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

function

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

Specified by:

function in interface ASTNodeCompiler

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

Returns:

Throws:

SBMLException

function

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

Specified by:

function in interface ASTNodeCompiler

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

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()
                                 throws SBMLException

Specified by:

getNegativeInfinity in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

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> values)
                    throws SBMLException

Description copied from interface: ASTNodeCompiler

The body of a FunctionDefinition.

Specified by:

lambda in interface ASTNodeCompiler

Parameters:

values - Place holders for arguments.

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 value)
                throws SBMLException

Description copied from interface: ASTNodeCompiler

Natural logarithm.

Specified by:

ln in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

log

public ASTNodeValue log(ASTNode value)
                 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 base,
               ASTNode value)
                 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

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> values)
                   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 value)
                 throws SBMLException

Specified by:

not in interface ASTNodeCompiler

Parameters:

value - This value must be interpretable as a Boolean.

Returns:

Throws:

SBMLException

or

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

Specified by:

or in interface ASTNodeCompiler

Parameters:

values - These values must be interpretable as a Boolean.

Returns:

Throws:

SBMLException

piecewise

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

Specified by:

piecewise in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

plus

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

Specified by:

plus in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

pow

public ASTNodeValue pow(ASTNode base,
               ASTNode exponent)
                 throws SBMLException

Specified by:

pow in interface ASTNodeCompiler

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 value)
                 throws SBMLException

Specified by:

sec in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

sech

public ASTNodeValue sech(ASTNode value)
                  throws SBMLException

Specified by:

sech in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

sin

public ASTNodeValue sin(ASTNode value)
                 throws SBMLException

Specified by:

sin in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

sinh

public ASTNodeValue sinh(ASTNode value)
                  throws SBMLException

Specified by:

sinh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

sqrt

public ASTNodeValue sqrt(ASTNode radiant)
                  throws SBMLException

Description copied from interface: ASTNodeCompiler

Square root.

Specified by:

sqrt in interface ASTNodeCompiler

Parameters:

radiant - 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 value)
                 throws SBMLException

Specified by:

tan in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

tanh

public ASTNodeValue tanh(ASTNode value)
                  throws SBMLException

Specified by:

tanh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

times

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

Description copied from interface: ASTNodeCompiler

Product of all given ASTNodes.

Specified by:

times in interface ASTNodeCompiler

Parameters:

values - These values must be interpretable to Number.

Returns:

Throws:

SBMLException

uMinus

public ASTNodeValue uMinus(ASTNode value)
                    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> values)
                 throws SBMLException

Description copied from interface: ASTNodeCompiler

Exclusive or.

Specified by:

xor in interface ASTNodeCompiler

Parameters:

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

Returns:

Throws:

SBMLException

selector

public ASTNodeValue selector(java.util.List<ASTNode> value)
                      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