Package org.sbml.jsbml.math.compiler

Class LaTeXCompiler

java.lang.Object

org.sbml.jsbml.util.StringTools

org.sbml.jsbml.math.compiler.LaTeXCompiler

All Implemented Interfaces:

ASTNode2Compiler

public class LaTeXCompiler
extends StringTools
implements ASTNode2Compiler

Converts ASTNode2Value objects into a LaTeX String to be included into scientific writings or to be displayed in a GUI.

Since:

1.0

Author:

Andreas Dräger, Victor Kofia

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	bottomrule	Requires LaTeX package booktabs.
java.lang.String	CONSTANT_E
java.lang.String	CONSTANT_FALSE
static java.lang.String	CONSTANT_PI	The constant pi
java.lang.String	CONSTANT_TRUE
static java.lang.String	descriptionBegin	Surrounded by new line symbols.
static java.lang.String	descriptionEnd	Surrounded by new line symbols.
static java.lang.String	eqBegin	Surrounded by new line symbols.
static java.lang.String	eqEnd	End equation; cf. eqBegin.
static java.lang.String	leftBrace	Left parenthesis.
static java.lang.String	leftQuotationMark	An opening quotation mark.
static java.lang.String	lineBreak	This is a LaTeX line break.
static java.lang.String	midrule	Produces a fancy line in tables.
static java.lang.String	NEGATIVE_ININITY
static java.lang.String	or
static java.lang.String	POSITIVE_INFINITY
static java.lang.String	rightBrace
static java.lang.String	rightQuotationMark	An closing quotation mark.
static java.lang.String	toprule	Needed for the beginning of a table.
static java.lang.String	wedge
static java.lang.String	xor

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

DECIMAL_FORMAT, REAL_FORMAT, SCIENTIFIC_FORMAT, underscore

Constructor Summary

Constructors

Constructor	Description
LaTeXCompiler()
LaTeXCompiler(boolean namesInEquations)

Method Summary

Modifier and Type	Method	Description
<T> ASTNode2Value<java.lang.String>	abs(ASTNode2 value)	The absolute value represented by the given ASTNode2.
<T> ASTNode2Value<java.lang.String>	and(java.util.List<ASTNode2> nodes)
<T> ASTNode2Value<java.lang.String>	arccos(ASTNode2 value)
<T> ASTNode2Value<java.lang.String>	arccosh(ASTNode2 value)
<T> ASTNode2Value<java.lang.String>	arccot(ASTNode2 value)
<T> ASTNode2Value<java.lang.String>	arccoth(ASTNode2 value)
<T> ASTNode2Value<java.lang.String>	arccsc(ASTNode2 value)
<T> ASTNode2Value<java.lang.String>	arccsch(ASTNode2 value)
<T> ASTNode2Value<java.lang.String>	arcsec(ASTNode2 value)
<T> ASTNode2Value<java.lang.String>	arcsech(ASTNode2 value)
<T> ASTNode2Value<java.lang.String>	arcsin(ASTNode2 value)
<T> ASTNode2Value<java.lang.String>	arcsinh(ASTNode2 value)
<T> ASTNode2Value<java.lang.String>	arctan(ASTNode2 value)
<T> ASTNode2Value<java.lang.String>	arctanh(ASTNode2 value)
java.lang.StringBuilder	brackets(java.lang.Object formula)	Encloses the given formula in brackets.
<T> ASTNode2Value<java.lang.String>	ceiling(ASTNode2 value)
java.lang.StringBuilder	colorbox(java.lang.String color, java.lang.Object what)
<T> ASTNode2Value<java.lang.String>	compile(double mantissa, int exponent, java.lang.String units)	Creates an ASTNode2Value that represents a real number in scientific notation, i.e., mantissa * 10^exponent, and the given units.
<T> ASTNode2Value<java.lang.String>	compile(double real, java.lang.String units)
<T> ASTNode2Value<java.lang.Integer>	compile(int integer, java.lang.String units)
<T> ASTNode2Value<java.lang.String>	compile(java.lang.String name)	A compiler will also have to deal with a name.
<T> ASTNode2Value<java.lang.String>	compile(CallableSBase variable)
<T> ASTNode2Value<java.lang.String>	compile(Compartment c)	This method returns the correct LaTeX expression for a function which returns the size of a compartment.
<T> ASTNode2Value<java.lang.String>	cos(ASTNode2 node)
<T> ASTNode2Value<java.lang.String>	cosh(ASTNode2 node)
<T> ASTNode2Value<java.lang.String>	cot(ASTNode2 node)
<T> ASTNode2Value<java.lang.String>	coth(ASTNode2 node)
<T> ASTNode2Value<java.lang.String>	csc(ASTNode2 node)
<T> ASTNode2Value<java.lang.String>	csch(ASTNode2 node)
<T> ASTNode2Value<java.lang.String>	delay(java.lang.String delayName, ASTNode2 x, ASTNode2 delay)	Evaluates delay functions.
java.lang.StringBuffer	descriptionItem(java.lang.String item, java.lang.Object description)	This method simplifies the process of creating descriptions.
<T> ASTNode2Value<java.lang.String>	eq(ASTNode2 left, ASTNode2 right)	Equal.
<T> ASTNode2Value<java.lang.String>	exp(ASTNode2 node)
<T> ASTNode2Value<java.lang.String>	factorial(ASTNode2 node)
<T> ASTNode2Value<java.lang.String>	floor(ASTNode2 value)
java.lang.StringBuffer	format(double value)	This method returns a StringBuffer representing a properly LaTeX formatted number.
<T> ASTNode2Value<java.lang.String>	frac(int numerator, int denominator)	A fraction of two int values.
java.lang.StringBuilder	frac(java.lang.Object numerator, java.lang.Object denominator)
<T> ASTNode2Value<java.lang.String>	frac(ASTNode2 numerator, ASTNode2 denominator)	Fraction of two ASTNode2s
<T> ASTNode2Value<java.lang.String>	function(java.lang.String functionDefinitionName, java.util.List<ASTNode2> args)
<T> ASTNode2Value<java.lang.String>	function(FunctionDefinition fun, java.util.List<ASTNode2> args)
<T> ASTNode2Value<java.lang.String>	function(T functionDefinitionName, java.util.List<ASTNode2> args)
<T> ASTNode2Value<java.lang.String>	geq(ASTNode2 left, ASTNode2 right)	Greater equal.
<T> ASTNode2Value<java.lang.String>	getConstantAvogadro(java.lang.String name)	Creates an ASTNode2Value that represent's Avogadro's number.
<T> ASTNode2Value<java.lang.String>	getConstantE()
<T> ASTNode2Value<java.lang.String>	getConstantFalse()
<T> ASTNode2Value<java.lang.String>	getConstantPi()
<T> ASTNode2Value<java.lang.String>	getConstantTrue()
<T> ASTNode2Value<java.lang.String>	getNegativeInfinity()
static java.lang.String	getNumbering(long number)
<T> ASTNode2Value<java.lang.String>	getPositiveInfinity()
<T> ASTNode2Value<java.lang.String>	gt(ASTNode2 left, ASTNode2 right)	Greater than.
java.lang.StringBuilder	href(java.lang.String target, java.lang.Object text)	Creates a hyper link to the given target and the text to be visible in the document.
java.lang.StringBuilder	hyperref(java.lang.String target, java.lang.Object text)
boolean	isPrintNameIfAvailable()
java.lang.StringBuilder	label(java.lang.String id)
<T> ASTNode2Value<java.lang.String>	lambda(java.util.List<ASTNode2> nodes)	The body of a FunctionDefinition.
<T> ASTNode2Value<java.lang.String>	leq(ASTNode2 left, ASTNode2 right)	Less equal.
<T> ASTNode2Value<java.lang.String>	ln(ASTNode2 node)	Natural logarithm.
<T> ASTNode2Value<java.lang.String>	log(ASTNode2 node)	Logarithm of the given value to base 10.
<T> ASTNode2Value<java.lang.String>	log(ASTNode2 base, ASTNode2 value)	Logarithm of the given value to the given base.
java.lang.StringBuffer	longtableHead(java.lang.String columnDef, java.lang.String caption, java.lang.String headLine)	Creates a head for a longtable in LaTeX.
<T> ASTNode2Value<java.lang.String>	lt(ASTNode2 left, ASTNode2 right)	Less than.
static java.lang.String	maskSpecialChars(java.lang.String string)	Masks all special characters used by LaTeX with a backslash including hyphen symbols.
static java.lang.String	maskSpecialChars(java.lang.String string, boolean hyphen)
java.lang.StringBuffer	math(java.lang.Object formula)	Encloses the given formula in dollar symbols (inline math mode).
java.lang.StringBuilder	mathrm(char symbol)
java.lang.StringBuilder	mathrm(java.lang.String text)
java.lang.StringBuilder	mathtext(java.lang.String text)
java.lang.StringBuilder	mathtt(java.lang.String id)	Returns the LaTeX code to set the given String in type writer font within a math environment.
java.lang.StringBuilder	mbox(java.lang.String s)
<T> ASTNode2Value<java.lang.String>	minus(java.util.List<ASTNode2> nodes)	Subtraction.
<T> ASTNode2Value<java.lang.String>	neq(ASTNode2 left, ASTNode2 right)	Not equal.
<T> ASTNode2Value<java.lang.String>	not(ASTNode2 node)
<T> ASTNode2Value<java.lang.String>	or(java.util.List<ASTNode2> nodes)
<T> ASTNode2Value<java.lang.String>	piecewise(java.util.List<ASTNode2> nodes)
<T> ASTNode2Value<java.lang.String>	plus(java.util.List<ASTNode2> nodes)
<T> ASTNode2Value<java.lang.String>	pow(ASTNode2 base, ASTNode2 exponent)
<T> ASTNode2Value<java.lang.String>	root(double rootExponent, ASTNode2 radiant)
<T> ASTNode2Value<java.lang.String>	root(ASTNode2 rootExponent, ASTNode2 value)
<T> ASTNode2Value<java.lang.String>	sec(ASTNode2 node)
<T> ASTNode2Value<java.lang.String>	sech(ASTNode2 node)
java.lang.StringBuffer	section(java.lang.String title, boolean numbering)
<T> ASTNode2Value<java.lang.String>	selector(java.util.List<ASTNode2> nodes)
void	setPrintNameIfAvailable(boolean printNameIfAvailable)
<T> ASTNode2Value<java.lang.String>	sin(ASTNode2 node)
<T> ASTNode2Value<java.lang.String>	sinh(ASTNode2 node)
<T> ASTNode2Value<java.lang.String>	sqrt(ASTNode2 value)	Square root.
java.lang.StringBuffer	subsection(java.lang.String title, boolean numbering)
java.lang.StringBuffer	subsubsection(java.lang.String title, boolean numbering)
<T> ASTNode2Value<java.lang.String>	symbolTime(java.lang.String time)	The simulation time.
<T> ASTNode2Value<java.lang.String>	tan(ASTNode2 node)
<T> ASTNode2Value<java.lang.String>	tanh(ASTNode2 node)
java.lang.StringBuilder	textcolor(java.lang.String color, java.lang.Object text)
java.lang.StringBuilder	texttt(java.lang.String id)	Returns the LaTeX code to set the given String in type writer font.
java.lang.String	timeDerivative(java.lang.String variable)
<T> ASTNode2Value<java.lang.String>	times(java.util.List<ASTNode2> values)	Product of all given ASTNode2s.
<T> ASTNode2Value<java.lang.String>	uMinus(ASTNode2 value)	Unary minus, i.e., negation of the given ASTNode2.
<T> ASTNode2Value<java.lang.String>	unknownValue()	Dealing with a malformed ASTNode2.
java.lang.StringBuffer	usepackage(java.lang.String latexPackage, java.lang.String... options)	Creates a usepackage command for the given package with the optional options.
<T> ASTNode2Value<java.lang.String>	vector(java.util.List<ASTNode2> nodes)	Dealing with a vector.
<T> ASTNode2Value<java.lang.String>	xor(java.util.List<ASTNode2> nodes)	Exclusive or.

Methods inherited from class java.lang.Object

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

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

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

Field Detail

bottomrule

public static final java.lang.String bottomrule

Requires LaTeX package booktabs. Produces a fancy line at the bottom of a table. This variable also includes the end{longtable} command and a new line.

CONSTANT_PI

public static final java.lang.String CONSTANT_PI

The constant pi

See Also:

Constant Field Values

descriptionBegin

public static final java.lang.String descriptionBegin

Surrounded by new line symbols. The begin of a description environment in LaTeX.

descriptionEnd

public static final java.lang.String descriptionEnd

Surrounded by new line symbols. The end of a description environment.

eqBegin

public static final java.lang.String eqBegin

Surrounded by new line symbols. Begin equation. This type of equation requires the LaTeX package breqn. It will produce equations with automatic line breaks (LaTeX will compute the optimal place for line breaks). Unfortunately, this does not work for very long denominators.

eqEnd

public static final java.lang.String eqEnd

End equation; cf. eqBegin. Surrounded by new line symbols.

leftBrace

public static final java.lang.String leftBrace

Left parenthesis.

See Also:

Constant Field Values

leftQuotationMark

public static final java.lang.String leftQuotationMark

An opening quotation mark.

See Also:

Constant Field Values

lineBreak

public static final java.lang.String lineBreak

This is a LaTeX line break. The line break symbol double backslash followed by a new line symbol of the operating system.

midrule

public static final java.lang.String midrule

Produces a fancy line in tables. Requires LaTeX package booktabs. Starts and ends with a new line.

NEGATIVE_ININITY

public static final java.lang.String NEGATIVE_ININITY

See Also:

Constant Field Values

or

public static final java.lang.String or

See Also:

Constant Field Values

POSITIVE_INFINITY

public static final java.lang.String POSITIVE_INFINITY

See Also:

Constant Field Values

rightBrace

public static final java.lang.String rightBrace

See Also:

Constant Field Values

rightQuotationMark

public static final java.lang.String rightQuotationMark

An closing quotation mark.

See Also:

Constant Field Values

toprule

public static final java.lang.String toprule

Needed for the beginning of a table. Requires LaTeX package booktabs. Surrounded by new line symbols.

wedge

public static final java.lang.String wedge

See Also:

Constant Field Values

xor

public static final java.lang.String xor

See Also:

Constant Field Values

CONSTANT_E

public final java.lang.String CONSTANT_E

CONSTANT_FALSE

public final java.lang.String CONSTANT_FALSE

CONSTANT_TRUE

public final java.lang.String CONSTANT_TRUE

Constructor Detail

LaTeXCompiler

public LaTeXCompiler()

LaTeXCompiler

public LaTeXCompiler(boolean namesInEquations)

Parameters:

namesInEquations -

Method Detail

getNumbering

public static java.lang.String getNumbering(long number)

Parameters:

number -

Returns:

maskSpecialChars

public static java.lang.String maskSpecialChars(java.lang.String string)

Masks all special characters used by LaTeX with a backslash including hyphen symbols.

Parameters:

string -

Returns:

maskSpecialChars

public static java.lang.String maskSpecialChars(java.lang.String string,
                                                boolean hyphen)

Parameters:

string -

hyphen - if true a hyphen symbol is introduced at each position where a special character has to be masked anyway.

Returns:

abs

public <T> ASTNode2Value<java.lang.String> abs(ASTNode2 value)
                                        throws SBMLException

Description copied from interface: ASTNode2Compiler

The absolute value represented by the given ASTNode2.

Specified by:

abs in interface ASTNode2Compiler

Parameters:

value - Must be interpretable as a Number.

Returns:

Throws:

SBMLException

and

public <T> ASTNode2Value<java.lang.String> and(java.util.List<ASTNode2> nodes)
                                        throws SBMLException

Specified by:

and in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

arccos

public <T> ASTNode2Value<java.lang.String> arccos(ASTNode2 value)
                                           throws SBMLException

Specified by:

arccos in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

arccosh

public <T> ASTNode2Value<java.lang.String> arccosh(ASTNode2 value)
                                            throws SBMLException

Specified by:

arccosh in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

arccot

public <T> ASTNode2Value<java.lang.String> arccot(ASTNode2 value)
                                           throws SBMLException

Specified by:

arccot in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

arccoth

public <T> ASTNode2Value<java.lang.String> arccoth(ASTNode2 value)
                                            throws SBMLException

Specified by:

arccoth in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

arccsc

public <T> ASTNode2Value<java.lang.String> arccsc(ASTNode2 value)
                                           throws SBMLException

Specified by:

arccsc in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

arccsch

public <T> ASTNode2Value<java.lang.String> arccsch(ASTNode2 value)
                                            throws SBMLException

Specified by:

arccsch in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

arcsec

public <T> ASTNode2Value<java.lang.String> arcsec(ASTNode2 value)
                                           throws SBMLException

Specified by:

arcsec in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

arcsech

public <T> ASTNode2Value<java.lang.String> arcsech(ASTNode2 value)
                                            throws SBMLException

Specified by:

arcsech in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

arcsin

public <T> ASTNode2Value<java.lang.String> arcsin(ASTNode2 value)
                                           throws SBMLException

Specified by:

arcsin in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

arcsinh

public <T> ASTNode2Value<java.lang.String> arcsinh(ASTNode2 value)
                                            throws SBMLException

Specified by:

arcsinh in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

arctan

public <T> ASTNode2Value<java.lang.String> arctan(ASTNode2 value)
                                           throws SBMLException

Specified by:

arctan in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

arctanh

public <T> ASTNode2Value<java.lang.String> arctanh(ASTNode2 value)
                                            throws SBMLException

Specified by:

arctanh in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

brackets

public java.lang.StringBuilder brackets(java.lang.Object formula)

Encloses the given formula in brackets.

Parameters:

formula -

Returns:

ceiling

public <T> ASTNode2Value<java.lang.String> ceiling(ASTNode2 value)
                                            throws SBMLException

Specified by:

ceiling in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

colorbox

public java.lang.StringBuilder colorbox(java.lang.String color,
                                        java.lang.Object what)

Parameters:

color -

what -

Returns:

compile

public <T> ASTNode2Value<java.lang.String> compile(CallableSBase variable)

Specified by:

compile in interface ASTNode2Compiler

Returns:

compile

public <T> ASTNode2Value<java.lang.String> compile(Compartment c)

This method returns the correct LaTeX expression for a function which returns the size of a compartment. This can be a volume, an area, a length or a point.

Specified by:

compile in interface ASTNode2Compiler

Returns:

compile

public <T> ASTNode2Value<java.lang.String> compile(double mantissa,
                                                   int exponent,
                                                   java.lang.String units)

Description copied from interface: ASTNode2Compiler

Creates an ASTNode2Value that represents a real number in scientific notation, i.e., mantissa * 10^exponent, and the given units.

Specified by:

compile in interface ASTNode2Compiler

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 <T> ASTNode2Value<java.lang.String> compile(double real,
                                                   java.lang.String units)

Specified by:

compile in interface ASTNode2Compiler

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 <T> ASTNode2Value<java.lang.Integer> compile(int integer,
                                                    java.lang.String units)

Specified by:

compile in interface ASTNode2Compiler

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 <T> ASTNode2Value<java.lang.String> compile(java.lang.String name)

Description copied from interface: ASTNode2Compiler

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 ASTNode2Value representing the current value of this Species.

Specified by:

compile in interface ASTNode2Compiler

Returns:

cos

public <T> ASTNode2Value<java.lang.String> cos(ASTNode2 node)
                                        throws SBMLException

Specified by:

cos in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

cosh

public <T> ASTNode2Value<java.lang.String> cosh(ASTNode2 node)
                                         throws SBMLException

Specified by:

cosh in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

cot

public <T> ASTNode2Value<java.lang.String> cot(ASTNode2 node)
                                        throws SBMLException

Specified by:

cot in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

coth

public <T> ASTNode2Value<java.lang.String> coth(ASTNode2 node)
                                         throws SBMLException

Specified by:

coth in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

csc

public <T> ASTNode2Value<java.lang.String> csc(ASTNode2 node)
                                        throws SBMLException

Specified by:

csc in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

csch

public <T> ASTNode2Value<java.lang.String> csch(ASTNode2 node)
                                         throws SBMLException

Specified by:

csch in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

delay

public <T> ASTNode2Value<java.lang.String> delay(java.lang.String delayName,
                                                 ASTNode2 x,
                                                 ASTNode2 delay)
                                          throws SBMLException

Description copied from interface: ASTNode2Compiler

Evaluates delay functions.

Specified by:

delay in interface ASTNode2Compiler

Parameters:

delayName - the name of this delay function.

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

Returns:

Throws:

SBMLException

descriptionItem

public java.lang.StringBuffer descriptionItem(java.lang.String item,
                                              java.lang.Object description)

This method simplifies the process of creating descriptions. There is an item entry together with a description. No new line or space is needed for separation.

Parameters:

item - e.g., "my item"

description - e.g., "my description"

Returns:

eq

public <T> ASTNode2Value<java.lang.String> eq(ASTNode2 left,
                                              ASTNode2 right)
                                       throws SBMLException

Description copied from interface: ASTNode2Compiler

Equal.

Specified by:

eq in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

exp

public <T> ASTNode2Value<java.lang.String> exp(ASTNode2 node)
                                        throws SBMLException

Specified by:

exp in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

factorial

public <T> ASTNode2Value<java.lang.String> factorial(ASTNode2 node)
                                              throws SBMLException

Specified by:

factorial in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

floor

public <T> ASTNode2Value<java.lang.String> floor(ASTNode2 value)
                                          throws SBMLException

Specified by:

floor in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

format

public java.lang.StringBuffer format(double value)

This method returns a StringBuffer representing a properly LaTeX formatted number.

Parameters:

value -

Returns:

frac

public <T> ASTNode2Value<java.lang.String> frac(ASTNode2 numerator,
                                                ASTNode2 denominator)
                                         throws SBMLException

Description copied from interface: ASTNode2Compiler

Fraction of two ASTNode2s

Specified by:

frac in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

frac

public <T> ASTNode2Value<java.lang.String> frac(int numerator,
                                                int denominator)

Description copied from interface: ASTNode2Compiler

A fraction of two int values.

Specified by:

frac in interface ASTNode2Compiler

Returns:

frac

public java.lang.StringBuilder frac(java.lang.Object numerator,
                                    java.lang.Object denominator)

Parameters:

numerator -

denominator -

Returns:

function

public <T> ASTNode2Value<java.lang.String> function(FunctionDefinition fun,
                                                    java.util.List<ASTNode2> args)
                                             throws SBMLException

Specified by:

function in interface ASTNode2Compiler

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

Returns:

Throws:

SBMLException

function

public <T> ASTNode2Value<java.lang.String> function(java.lang.String functionDefinitionName,
                                                    java.util.List<ASTNode2> args)
                                             throws SBMLException

Specified by:

function in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

function

public <T> ASTNode2Value<java.lang.String> function(T functionDefinitionName,
                                                    java.util.List<ASTNode2> args)
                                             throws SBMLException

Specified by:

function in interface ASTNode2Compiler

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

Returns:

Throws:

SBMLException

geq

public <T> ASTNode2Value<java.lang.String> geq(ASTNode2 left,
                                               ASTNode2 right)
                                        throws SBMLException

Description copied from interface: ASTNode2Compiler

Greater equal.

Specified by:

geq in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

getConstantAvogadro

public <T> ASTNode2Value<java.lang.String> getConstantAvogadro(java.lang.String name)

Description copied from interface: ASTNode2Compiler

Creates an ASTNode2Value that represent's Avogadro's number. Optionally, the compiler may associate the given name with this number.

Specified by:

getConstantAvogadro in interface ASTNode2Compiler

Parameters:

name - An optional name for Avogadro's number.

Returns:

getConstantE

public <T> ASTNode2Value<java.lang.String> getConstantE()

Specified by:

getConstantE in interface ASTNode2Compiler

Returns:

getConstantFalse

public <T> ASTNode2Value<java.lang.String> getConstantFalse()

Specified by:

getConstantFalse in interface ASTNode2Compiler

Returns:

getConstantPi

public <T> ASTNode2Value<java.lang.String> getConstantPi()

Specified by:

getConstantPi in interface ASTNode2Compiler

Returns:

getConstantTrue

public <T> ASTNode2Value<java.lang.String> getConstantTrue()

Specified by:

getConstantTrue in interface ASTNode2Compiler

Returns:

getNegativeInfinity

public <T> ASTNode2Value<java.lang.String> getNegativeInfinity()

Specified by:

getNegativeInfinity in interface ASTNode2Compiler

Returns:

getPositiveInfinity

public <T> ASTNode2Value<java.lang.String> getPositiveInfinity()

Specified by:

getPositiveInfinity in interface ASTNode2Compiler

Returns:

gt

public <T> ASTNode2Value<java.lang.String> gt(ASTNode2 left,
                                              ASTNode2 right)
                                       throws SBMLException

Description copied from interface: ASTNode2Compiler

Greater than.

Specified by:

gt in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

href

public java.lang.StringBuilder href(java.lang.String target,
                                    java.lang.Object text)

Creates a hyper link to the given target and the text to be visible in the document.

Parameters:

target - The target to which this link points to.

text - The text to be written in the link.

Returns:

hyperref

public java.lang.StringBuilder hyperref(java.lang.String target,
                                        java.lang.Object text)

Parameters:

target -

text -

Returns:

isPrintNameIfAvailable

public boolean isPrintNameIfAvailable()

Returns:

label

public java.lang.StringBuilder label(java.lang.String id)

Parameters:

id -

Returns:

lambda

public <T> ASTNode2Value<java.lang.String> lambda(java.util.List<ASTNode2> nodes)
                                           throws SBMLException

Description copied from interface: ASTNode2Compiler

The body of a FunctionDefinition.

Specified by:

lambda in interface ASTNode2Compiler

Parameters:

nodes - Place holders for arguments.

Returns:

Throws:

SBMLException

leq

public <T> ASTNode2Value<java.lang.String> leq(ASTNode2 left,
                                               ASTNode2 right)
                                        throws SBMLException

Description copied from interface: ASTNode2Compiler

Less equal.

Specified by:

leq in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

ln

public <T> ASTNode2Value<java.lang.String> ln(ASTNode2 node)
                                       throws SBMLException

Description copied from interface: ASTNode2Compiler

Natural logarithm.

Specified by:

ln in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

log

public <T> ASTNode2Value<java.lang.String> log(ASTNode2 node)
                                        throws SBMLException

Description copied from interface: ASTNode2Compiler

Logarithm of the given value to base 10.

Specified by:

log in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

log

public <T> ASTNode2Value<java.lang.String> log(ASTNode2 base,
                                               ASTNode2 value)
                                        throws SBMLException

Description copied from interface: ASTNode2Compiler

Logarithm of the given value to the given base.

Specified by:

log in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

longtableHead

public java.lang.StringBuffer longtableHead(java.lang.String columnDef,
                                            java.lang.String caption,
                                            java.lang.String headLine)

Creates a head for a longtable in LaTeX.

Parameters:

columnDef - without leading and ending brackets, e.g., "lrrc",

caption - caption of this table without leading and ending brackets

headLine - table head without leading and ending brackets and without double backslashes at the end

Returns:

lt

public <T> ASTNode2Value<java.lang.String> lt(ASTNode2 left,
                                              ASTNode2 right)
                                       throws SBMLException

Description copied from interface: ASTNode2Compiler

Less than.

Specified by:

lt in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

math

public java.lang.StringBuffer math(java.lang.Object formula)

Encloses the given formula in dollar symbols (inline math mode).

Parameters:

formula -

Returns:

mathrm

public java.lang.StringBuilder mathrm(char symbol)

Parameters:

symbol -

Returns:

mathrm

public java.lang.StringBuilder mathrm(java.lang.String text)

Parameters:

text -

Returns:

mathtext

public java.lang.StringBuilder mathtext(java.lang.String text)

Parameters:

text -

Returns:

mathtt

public java.lang.StringBuilder mathtt(java.lang.String id)

Returns the LaTeX code to set the given String in type writer font within a math environment.

Parameters:

id -

Returns:

mbox

public java.lang.StringBuilder mbox(java.lang.String s)

Parameters:

s -

Returns:

minus

public <T> ASTNode2Value<java.lang.String> minus(java.util.List<ASTNode2> nodes)
                                          throws SBMLException

Description copied from interface: ASTNode2Compiler

Subtraction.

Specified by:

minus in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

neq

public <T> ASTNode2Value<java.lang.String> neq(ASTNode2 left,
                                               ASTNode2 right)
                                        throws SBMLException

Description copied from interface: ASTNode2Compiler

Not equal.

Specified by:

neq in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

not

public <T> ASTNode2Value<java.lang.String> not(ASTNode2 node)
                                        throws SBMLException

Specified by:

not in interface ASTNode2Compiler

Parameters:

node - This value must be interpretable as a Boolean.

Returns:

Throws:

SBMLException

or

public <T> ASTNode2Value<java.lang.String> or(java.util.List<ASTNode2> nodes)
                                       throws SBMLException

Specified by:

or in interface ASTNode2Compiler

Parameters:

nodes - These values must be interpretable as a Boolean.

Returns:

Throws:

SBMLException

piecewise

public <T> ASTNode2Value<java.lang.String> piecewise(java.util.List<ASTNode2> nodes)
                                              throws SBMLException

Specified by:

piecewise in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

plus

public <T> ASTNode2Value<java.lang.String> plus(java.util.List<ASTNode2> nodes)
                                         throws SBMLException

Specified by:

plus in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

pow

public <T> ASTNode2Value<java.lang.String> pow(ASTNode2 base,
                                               ASTNode2 exponent)
                                        throws SBMLException

Specified by:

pow in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

root

public <T> ASTNode2Value<java.lang.String> root(ASTNode2 rootExponent,
                                                ASTNode2 value)
                                         throws SBMLException

Specified by:

root in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

root

public <T> ASTNode2Value<java.lang.String> root(double rootExponent,
                                                ASTNode2 radiant)
                                         throws SBMLException

Specified by:

root in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

sec

public <T> ASTNode2Value<java.lang.String> sec(ASTNode2 node)
                                        throws SBMLException

Specified by:

sec in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

sech

public <T> ASTNode2Value<java.lang.String> sech(ASTNode2 node)
                                         throws SBMLException

Specified by:

sech in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

section

public java.lang.StringBuffer section(java.lang.String title,
                                      boolean numbering)

Parameters:

title -

numbering -

Returns:

selector

public <T> ASTNode2Value<java.lang.String> selector(java.util.List<ASTNode2> nodes)
                                             throws SBMLException

Specified by:

selector in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

setPrintNameIfAvailable

public void setPrintNameIfAvailable(boolean printNameIfAvailable)

Parameters:

printNameIfAvailable -

sin

public <T> ASTNode2Value<java.lang.String> sin(ASTNode2 node)
                                        throws SBMLException

Specified by:

sin in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

sinh

public <T> ASTNode2Value<java.lang.String> sinh(ASTNode2 node)
                                         throws SBMLException

Specified by:

sinh in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

sqrt

public <T> ASTNode2Value<java.lang.String> sqrt(ASTNode2 value)
                                         throws SBMLException

Description copied from interface: ASTNode2Compiler

Square root.

Specified by:

sqrt in interface ASTNode2Compiler

Parameters:

value - This value must be interpretable as a Number.

Returns:

Throws:

SBMLException

subsection

public java.lang.StringBuffer subsection(java.lang.String title,
                                         boolean numbering)

Parameters:

title -

numbering -

Returns:

subsubsection

public java.lang.StringBuffer subsubsection(java.lang.String title,
                                            boolean numbering)

Parameters:

title -

numbering -

Returns:

symbolTime

public <T> ASTNode2Value<java.lang.String> symbolTime(java.lang.String time)

Description copied from interface: ASTNode2Compiler

The simulation time.

Specified by:

symbolTime in interface ASTNode2Compiler

Parameters:

time - The name of the time symbol.

Returns:

An ASTNode2Value that represents the current time.

tan

public <T> ASTNode2Value<java.lang.String> tan(ASTNode2 node)
                                        throws SBMLException

Specified by:

tan in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

tanh

public <T> ASTNode2Value<java.lang.String> tanh(ASTNode2 node)
                                         throws SBMLException

Specified by:

tanh in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

textcolor

public java.lang.StringBuilder textcolor(java.lang.String color,
                                         java.lang.Object text)

Parameters:

color -

text -

Returns:

texttt

public java.lang.StringBuilder texttt(java.lang.String id)

Returns the LaTeX code to set the given String in type writer font.

Parameters:

id -

Returns:

timeDerivative

public java.lang.String timeDerivative(java.lang.String variable)

Parameters:

variable -

Returns:

times

public <T> ASTNode2Value<java.lang.String> times(java.util.List<ASTNode2> values)
                                          throws SBMLException

Description copied from interface: ASTNode2Compiler

Product of all given ASTNode2s.

Specified by:

times in interface ASTNode2Compiler

Parameters:

values - These values must be interpretable to Number.

Returns:

Throws:

SBMLException

uMinus

public <T> ASTNode2Value<java.lang.String> uMinus(ASTNode2 value)
                                           throws SBMLException

Description copied from interface: ASTNode2Compiler

Unary minus, i.e., negation of the given ASTNode2.

Specified by:

uMinus in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

unknownValue

public <T> ASTNode2Value<java.lang.String> unknownValue()

Description copied from interface: ASTNode2Compiler

Dealing with a malformed ASTNode2.

Specified by:

unknownValue in interface ASTNode2Compiler

Returns:

usepackage

public java.lang.StringBuffer usepackage(java.lang.String latexPackage,
                                         java.lang.String... options)

Creates a usepackage command for the given package with the optional options.

Parameters:

latexPackage - the name of the latex package

options - options without commas

Returns:

usepackage command including system-dependent new line character.

vector

public <T> ASTNode2Value<java.lang.String> vector(java.util.List<ASTNode2> nodes)
                                           throws SBMLException

Description copied from interface: ASTNode2Compiler

Dealing with a vector.

Specified by:

vector in interface ASTNode2Compiler

Returns:

Throws:

SBMLException

xor

public <T> ASTNode2Value<java.lang.String> xor(java.util.List<ASTNode2> nodes)
                                        throws SBMLException

Description copied from interface: ASTNode2Compiler

Exclusive or.

Specified by:

xor in interface ASTNode2Compiler

Parameters:

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

Returns:

Throws:

SBMLException