org.sbml.jsbml.ext.arrays.compiler

Class VectorCompiler

java.lang.Object

org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

All Implemented Interfaces:

ASTNodeCompiler

public class VectorCompiler
extends java.lang.Object
implements ASTNodeCompiler

Since:

1.0

Version:

$Rev: 1963 $

Author:

Leandro Watanabe

Field Summary

Fields

Modifier and Type	Field and Description
private ASTNodeValue	dummy
private java.util.Map<java.lang.String,ASTNode>	idToVector
private boolean	isSetIdToVector
private Model	model
private ASTNode	node
private boolean	useId

Constructor Summary

Constructors

Constructor and Description
VectorCompiler(Model model)
VectorCompiler(Model model, boolean useId)
VectorCompiler(Model model, boolean useId, java.util.Map<java.lang.String,ASTNode> idToVector)

Method Summary

Methods

Modifier and Type	Method and Description
ASTNodeValue	abs(ASTNode value) The absolute value represented by the given ASTNode.
private void	absRecursive(ASTNode value) This function calculates the abs value of a vector element-wise.
ASTNodeValue	and(java.util.List<ASTNode> values)
private void	andRecursive(java.util.List<ASTNode> values, ASTNode node)
ASTNodeValue	arccos(ASTNode value)
ASTNodeValue	arccosh(ASTNode value)
private void	arccoshRecursive(ASTNode value)
private void	arccosRecursive(ASTNode value) This function calculates the arcccos value of a vector element-wise.
ASTNodeValue	arccot(ASTNode value)
ASTNodeValue	arccoth(ASTNode value)
private void	arccothRecursive(ASTNode value)
private void	arccotRecursive(ASTNode value)
ASTNodeValue	arccsc(ASTNode value)
ASTNodeValue	arccsch(ASTNode value)
private void	arccschRecursive(ASTNode value)
private void	arccscRecursive(ASTNode value)
ASTNodeValue	arcsec(ASTNode value)
ASTNodeValue	arcsech(ASTNode value)
private void	arcsechRecursive(ASTNode value)
private void	arcsecRecursive(ASTNode value)
ASTNodeValue	arcsin(ASTNode value)
ASTNodeValue	arcsinh(ASTNode value)
private void	arcsinhRecursive(ASTNode value)
private void	arcsinRecursive(ASTNode value)
ASTNodeValue	arctan(ASTNode value)
ASTNodeValue	arctanh(ASTNode value)
private void	arctanhRecursive(ASTNode value)
private void	arctanRecursive(ASTNode value)
ASTNodeValue	ceiling(ASTNode value)
private void	ceilingRecursive(ASTNode value)
void	clearIdToVector()
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 ASTNode	constructVector(ArraysSBasePlugin arraysPlugin, ASTNode node)
private ASTNode	constructVector(ArraysSBasePlugin arraysPlugin, NamedSBase sbase)
private ASTNode	constructVector(ArraysSBasePlugin arraysPlugin, Quantity quantity)
private ASTNode	constructVector(ArraysSBasePlugin arraysPlugin, SpeciesReference sbase)
ASTNodeValue	cos(ASTNode value)
ASTNodeValue	cosh(ASTNode value)
private void	coshRecursive(ASTNode value)
private void	cosRecursive(ASTNode value)
ASTNodeValue	cot(ASTNode value)
ASTNodeValue	coth(ASTNode value)
private void	cothRecursive(ASTNode value)
private void	cotRecursive(ASTNode value)
ASTNodeValue	csc(ASTNode value)
ASTNodeValue	csch(ASTNode value)
private void	cschRecursive(ASTNode value)
private void	cscRecursive(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.
private void	eqRecursive(ASTNode right, ASTNode left, ASTNode node)
ASTNodeValue	exp(ASTNode value)
private void	expRecursive(ASTNode value)
ASTNodeValue	factorial(ASTNode value)
private void	factorialRecursive(ASTNode value)
ASTNodeValue	floor(ASTNode value)
private void	floorRecursive(ASTNode value)
ASTNodeValue	frac(ASTNode numerator, ASTNode denominator) Fraction of two ASTNodes
ASTNodeValue	frac(int numerator, int denominator) A fraction of two int values.
private void	fracRecursive(ASTNode left, ASTNode right, ASTNode node)
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()
ASTNode	getNode()
ASTNodeValue	getPositiveInfinity()
private boolean	getScalarsAndVectors(java.util.List<ASTNode> values, java.util.List<ASTNode> vectors, java.util.List<ASTNode> scalars, java.util.List<ASTNode> ids)
ASTNodeValue	gt(ASTNode left, ASTNode right) Greater than.
private void	gtRecursive(ASTNode left, ASTNode right, ASTNode node)
boolean	isSetIdToVector()
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.
private void	lnRecursive(ASTNode value)
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.
private void	logRecursive(ASTNode value)
ASTNodeValue	lt(ASTNode left, ASTNode right) Less than.
private void	ltRecursive(ASTNode left, ASTNode right, ASTNode node)
ASTNodeValue	minus(java.util.List<ASTNode> values) Subtraction.
ASTNodeValue	neq(ASTNode left, ASTNode right) Not equal.
private void	neqRecursive(ASTNode right, ASTNode left, ASTNode node)
ASTNodeValue	not(ASTNode value)
private void	notRecursive(ASTNode value)
ASTNodeValue	or(java.util.List<ASTNode> values)
private void	orRecursive(java.util.List<ASTNode> values, ASTNode node)
ASTNodeValue	piecewise(java.util.List<ASTNode> values)
private void	piecewiseRecursive(java.util.List<ASTNode> values, ASTNode vector)
ASTNodeValue	plus(java.util.List<ASTNode> values)
private void	plusRecursive(java.util.List<ASTNode> values, ASTNode node)
ASTNodeValue	pow(ASTNode base, ASTNode exponent)
private void	powRecursive(ASTNode left, ASTNode right, ASTNode node)
private void	recursiveReplaceDimensionId(ASTNode math, java.lang.String bvar, ASTNode value)
private ASTNode	replaceMath(ASTNode math, java.lang.String bvar, ASTNode value)
ASTNodeValue	root(ASTNode rootExponent, ASTNode radiant)
ASTNodeValue	root(double rootExponent, ASTNode radiant)
private void	scalarVectorAnd(ASTNode vector, ASTNode scalar)
private void	scalarVectorEq(ASTNode vector, ASTNode scalar)
private void	scalarVectorFrac(ASTNode scalar, ASTNode vector)
private void	scalarVectorGt(ASTNode scalarLHS, ASTNode vectorRHS)
private void	scalarVectorLt(ASTNode scalarLHS, ASTNode vectorRHS)
private void	scalarVectorNeq(ASTNode vector, ASTNode scalar)
private void	scalarVectorOr(ASTNode vector, ASTNode scalar)
private void	scalarVectorPlus(ASTNode vector, ASTNode scalar)
private void	scalarVectorPow(ASTNode scalarLHS, ASTNode vectorRHS)
private void	scalarVectorTimes(ASTNode vector, ASTNode scalar)
private void	scalarVectorXor(ASTNode vector, ASTNode scalar)
ASTNodeValue	sec(ASTNode value)
ASTNodeValue	sech(ASTNode value)
private void	sechRecursive(ASTNode value)
private void	secRecursive(ASTNode value)
ASTNodeValue	selector(java.util.List<ASTNode> nodes)
void	setIdToVector(java.util.Map<java.lang.String,ASTNode> idToVector)
void	setNode(ASTNode node)
ASTNodeValue	sin(ASTNode value)
ASTNodeValue	sinh(ASTNode value)
private void	sinhRecursive(ASTNode value)
private void	sinRecursive(ASTNode value)
ASTNodeValue	sqrt(ASTNode radiant) Square root.
private void	sqrtRecursive(ASTNode value)
ASTNodeValue	symbolTime(java.lang.String time) The simulation time.
ASTNodeValue	tan(ASTNode value)
ASTNodeValue	tanh(ASTNode value)
private void	tanhRecursive(ASTNode value)
private void	tanRecursive(ASTNode value)
ASTNodeValue	times(java.util.List<ASTNode> values) Product of all given ASTNodes.
private void	timesRecursive(java.util.List<ASTNode> values, ASTNode node)
private void	transformNamedSBase(SBase sbase)
private void	transformSBase(SBase sbase)
ASTNodeValue	uMinus(ASTNode value) Unary minus, i.e., negation of the given ASTNode.
private void	uMinusRecursive(ASTNode value)
ASTNodeValue	unknownValue() Dealing with a malformed ASTNode.
private void	updateASTNodeName(ASTNode node, int value)
private void	updateASTNodeName(ASTNode node, java.lang.String value)
ASTNodeValue	vector(java.util.List<ASTNode> nodes) Dealing with a vector.
private void	vectorScalarFrac(ASTNode vector, ASTNode scalar)
private void	vectorScalarGt(ASTNode vectorLHS, ASTNode scalarRHS)
private void	vectorScalarLt(ASTNode vectorLHS, ASTNode scalarRHS)
private void	vectorScalarPow(ASTNode vectorLHS, ASTNode scalarRHS)
ASTNodeValue	xor(java.util.List<ASTNode> values) Exclusive or.
private void	xorRecursive(java.util.List<ASTNode> values, ASTNode node)

Methods inherited from class java.lang.Object

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

Field Detail

dummy

private final ASTNodeValue dummy

model

private final Model model

node

private ASTNode node

idToVector

private java.util.Map<java.lang.String,ASTNode> idToVector

isSetIdToVector

private boolean isSetIdToVector

useId

private final boolean useId

Constructor Detail

VectorCompiler

public VectorCompiler(Model model)

VectorCompiler

public VectorCompiler(Model model,
              boolean useId)

VectorCompiler

public VectorCompiler(Model model,
              boolean useId,
              java.util.Map<java.lang.String,ASTNode> idToVector)

Method Detail

getNode

public ASTNode getNode()

setNode

public void setNode(ASTNode node)

setIdToVector

public void setIdToVector(java.util.Map<java.lang.String,ASTNode> idToVector)

clearIdToVector

public void clearIdToVector()

isSetIdToVector

public boolean isSetIdToVector()

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

absRecursive

private void absRecursive(ASTNode value)
                   throws SBMLException

This function calculates the abs value of a vector element-wise.

Parameters:

value -

Throws:

SBMLException

and

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

Specified by:

and in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

andRecursive

private void andRecursive(java.util.List<ASTNode> values,
                ASTNode node)
                   throws java.lang.IndexOutOfBoundsException

Parameters:

values -

node -

Throws:

java.lang.IndexOutOfBoundsException

scalarVectorAnd

private void scalarVectorAnd(ASTNode vector,
                   ASTNode scalar)

Parameters:

values -

node -

arccos

public ASTNodeValue arccos(ASTNode value)
                    throws SBMLException

Specified by:

arccos in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arccosRecursive

private void arccosRecursive(ASTNode value)

This function calculates the arcccos value of a vector element-wise.

Parameters:

value -

Throws:

SBMLException

arccosh

public ASTNodeValue arccosh(ASTNode value)
                     throws SBMLException

Specified by:

arccosh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arccoshRecursive

private void arccoshRecursive(ASTNode value)
                       throws SBMLException

Throws:

SBMLException

arccot

public ASTNodeValue arccot(ASTNode value)
                    throws SBMLException

Specified by:

arccot in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arccotRecursive

private void arccotRecursive(ASTNode value)

arccoth

public ASTNodeValue arccoth(ASTNode value)
                     throws SBMLException

Specified by:

arccoth in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arccothRecursive

private void arccothRecursive(ASTNode value)

arccsc

public ASTNodeValue arccsc(ASTNode value)
                    throws SBMLException

Specified by:

arccsc in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arccscRecursive

private void arccscRecursive(ASTNode value)

arccsch

public ASTNodeValue arccsch(ASTNode value)
                     throws SBMLException

Specified by:

arccsch in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arccschRecursive

private void arccschRecursive(ASTNode value)

arcsec

public ASTNodeValue arcsec(ASTNode value)
                    throws SBMLException

Specified by:

arcsec in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arcsecRecursive

private void arcsecRecursive(ASTNode value)

arcsech

public ASTNodeValue arcsech(ASTNode value)
                     throws SBMLException

Specified by:

arcsech in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arcsechRecursive

private void arcsechRecursive(ASTNode value)

arcsin

public ASTNodeValue arcsin(ASTNode value)
                    throws SBMLException

Specified by:

arcsin in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arcsinRecursive

private void arcsinRecursive(ASTNode value)

arcsinh

public ASTNodeValue arcsinh(ASTNode value)
                     throws SBMLException

Specified by:

arcsinh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arcsinhRecursive

private void arcsinhRecursive(ASTNode value)

arctan

public ASTNodeValue arctan(ASTNode value)
                    throws SBMLException

Specified by:

arctan in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arctanRecursive

private void arctanRecursive(ASTNode value)

arctanh

public ASTNodeValue arctanh(ASTNode value)
                     throws SBMLException

Specified by:

arctanh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

arctanhRecursive

private void arctanhRecursive(ASTNode value)

ceiling

public ASTNodeValue ceiling(ASTNode value)
                     throws SBMLException

Specified by:

ceiling in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

ceilingRecursive

private void ceilingRecursive(ASTNode value)

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:

transformNamedSBase

private void transformNamedSBase(SBase sbase)

constructVector

private ASTNode constructVector(ArraysSBasePlugin arraysPlugin,
                      NamedSBase sbase)

constructVector

private ASTNode constructVector(ArraysSBasePlugin arraysPlugin,
                      Quantity quantity)

constructVector

private ASTNode constructVector(ArraysSBasePlugin arraysPlugin,
                      ASTNode node)

cos

public ASTNodeValue cos(ASTNode value)
                 throws SBMLException

Specified by:

cos in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

cosRecursive

private void cosRecursive(ASTNode value)

cosh

public ASTNodeValue cosh(ASTNode value)
                  throws SBMLException

Specified by:

cosh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

coshRecursive

private void coshRecursive(ASTNode value)

cot

public ASTNodeValue cot(ASTNode value)
                 throws SBMLException

Specified by:

cot in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

cotRecursive

private void cotRecursive(ASTNode value)

coth

public ASTNodeValue coth(ASTNode value)
                  throws SBMLException

Specified by:

coth in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

cothRecursive

private void cothRecursive(ASTNode value)

csc

public ASTNodeValue csc(ASTNode value)
                 throws SBMLException

Specified by:

csc in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

cscRecursive

private void cscRecursive(ASTNode value)

csch

public ASTNodeValue csch(ASTNode value)
                  throws SBMLException

Specified by:

csch in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

cschRecursive

private void cschRecursive(ASTNode value)

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

eqRecursive

private void eqRecursive(ASTNode right,
               ASTNode left,
               ASTNode node)
                  throws java.lang.IndexOutOfBoundsException,
                         SBMLException

Parameters:

values -

node -

Throws:

java.lang.IndexOutOfBoundsException

SBMLException

scalarVectorEq

private void scalarVectorEq(ASTNode vector,
                  ASTNode scalar)

Parameters:

values -

node -

exp

public ASTNodeValue exp(ASTNode value)
                 throws SBMLException

Specified by:

exp in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

expRecursive

private void expRecursive(ASTNode value)

factorial

public ASTNodeValue factorial(ASTNode value)
                       throws SBMLException

Specified by:

factorial in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

factorialRecursive

private void factorialRecursive(ASTNode value)

floor

public ASTNodeValue floor(ASTNode value)
                   throws SBMLException

Specified by:

floor in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

floorRecursive

private void floorRecursive(ASTNode value)

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

fracRecursive

private void fracRecursive(ASTNode left,
                 ASTNode right,
                 ASTNode node)
                    throws java.lang.IndexOutOfBoundsException

Parameters:

values -

node -

Throws:

java.lang.IndexOutOfBoundsException

vectorScalarFrac

private void vectorScalarFrac(ASTNode vector,
                    ASTNode scalar)

scalarVectorFrac

private void scalarVectorFrac(ASTNode scalar,
                    ASTNode vector)

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:

getScalarsAndVectors

private boolean getScalarsAndVectors(java.util.List<ASTNode> values,
                           java.util.List<ASTNode> vectors,
                           java.util.List<ASTNode> scalars,
                           java.util.List<ASTNode> ids)

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

gtRecursive

private void gtRecursive(ASTNode left,
               ASTNode right,
               ASTNode node)
                  throws java.lang.IndexOutOfBoundsException

Parameters:

values -

node -

Throws:

java.lang.IndexOutOfBoundsException

vectorScalarGt

private void vectorScalarGt(ASTNode vectorLHS,
                  ASTNode scalarRHS)

Parameters:

values -

node -

scalarVectorGt

private void scalarVectorGt(ASTNode scalarLHS,
                  ASTNode vectorRHS)

Parameters:

values -

node -

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

lnRecursive

private void lnRecursive(ASTNode value)

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

logRecursive

private void logRecursive(ASTNode value)

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

ltRecursive

private void ltRecursive(ASTNode left,
               ASTNode right,
               ASTNode node)
                  throws java.lang.IndexOutOfBoundsException

Parameters:

values -

node -

Throws:

java.lang.IndexOutOfBoundsException

vectorScalarLt

private void vectorScalarLt(ASTNode vectorLHS,
                  ASTNode scalarRHS)

Parameters:

values -

node -

scalarVectorLt

private void scalarVectorLt(ASTNode scalarLHS,
                  ASTNode vectorRHS)

Parameters:

values -

node -

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

neqRecursive

private void neqRecursive(ASTNode right,
                ASTNode left,
                ASTNode node)
                   throws java.lang.IndexOutOfBoundsException

Parameters:

values -

node -

Throws:

java.lang.IndexOutOfBoundsException

scalarVectorNeq

private void scalarVectorNeq(ASTNode vector,
                   ASTNode scalar)

Parameters:

values -

node -

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

notRecursive

private void notRecursive(ASTNode value)

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

orRecursive

private void orRecursive(java.util.List<ASTNode> values,
               ASTNode node)
                  throws java.lang.IndexOutOfBoundsException

Parameters:

values -

node -

Throws:

java.lang.IndexOutOfBoundsException

scalarVectorOr

private void scalarVectorOr(ASTNode vector,
                  ASTNode scalar)

Parameters:

values -

node -

piecewise

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

Specified by:

piecewise in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

piecewiseRecursive

private void piecewiseRecursive(java.util.List<ASTNode> values,
                      ASTNode vector)
                         throws SBMLException

Throws:

SBMLException

plus

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

Specified by:

plus in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

plusRecursive

private void plusRecursive(java.util.List<ASTNode> values,
                 ASTNode node)
                    throws java.lang.IndexOutOfBoundsException,
                           SBMLException

Parameters:

values -

node -

Throws:

java.lang.IndexOutOfBoundsException

SBMLException

scalarVectorPlus

private void scalarVectorPlus(ASTNode vector,
                    ASTNode scalar)

Parameters:

values -

node -

pow

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

Specified by:

pow in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

powRecursive

private void powRecursive(ASTNode left,
                ASTNode right,
                ASTNode node)
                   throws java.lang.IndexOutOfBoundsException

Parameters:

values -

node -

Throws:

java.lang.IndexOutOfBoundsException

vectorScalarPow

private void vectorScalarPow(ASTNode vectorLHS,
                   ASTNode scalarRHS)

Parameters:

values -

node -

scalarVectorPow

private void scalarVectorPow(ASTNode scalarLHS,
                   ASTNode vectorRHS)

Parameters:

values -

node -

replaceMath

private ASTNode replaceMath(ASTNode math,
                  java.lang.String bvar,
                  ASTNode value)

recursiveReplaceDimensionId

private void recursiveReplaceDimensionId(ASTNode math,
                               java.lang.String bvar,
                               ASTNode value)

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

secRecursive

private void secRecursive(ASTNode value)

sech

public ASTNodeValue sech(ASTNode value)
                  throws SBMLException

Specified by:

sech in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

sechRecursive

private void sechRecursive(ASTNode value)

selector

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

Specified by:

selector in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

sin

public ASTNodeValue sin(ASTNode value)
                 throws SBMLException

Specified by:

sin in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

sinRecursive

private void sinRecursive(ASTNode value)

sinh

public ASTNodeValue sinh(ASTNode value)
                  throws SBMLException

Specified by:

sinh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

sinhRecursive

private void sinhRecursive(ASTNode value)

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

sqrtRecursive

private void sqrtRecursive(ASTNode value)

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

tanRecursive

private void tanRecursive(ASTNode value)

tanh

public ASTNodeValue tanh(ASTNode value)
                  throws SBMLException

Specified by:

tanh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

tanhRecursive

private void tanhRecursive(ASTNode value)

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

timesRecursive

private void timesRecursive(java.util.List<ASTNode> values,
                  ASTNode node)
                     throws java.lang.IndexOutOfBoundsException

Parameters:

values -

node -

Throws:

java.lang.IndexOutOfBoundsException

scalarVectorTimes

private void scalarVectorTimes(ASTNode vector,
                     ASTNode scalar)

Parameters:

values -

node -

transformSBase

private void transformSBase(SBase sbase)

constructVector

private ASTNode constructVector(ArraysSBasePlugin arraysPlugin,
                      SpeciesReference sbase)

updateASTNodeName

private void updateASTNodeName(ASTNode node,
                     int value)

updateASTNodeName

private void updateASTNodeName(ASTNode node,
                     java.lang.String value)

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

uMinusRecursive

private void uMinusRecursive(ASTNode value)

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

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

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

xorRecursive

private void xorRecursive(java.util.List<ASTNode> values,
                ASTNode node)
                   throws java.lang.IndexOutOfBoundsException

Parameters:

values -

node -

Throws:

java.lang.IndexOutOfBoundsException

scalarVectorXor

private void scalarVectorXor(ASTNode vector,
                   ASTNode scalar)

Parameters:

values -

node -