org.sbml.jsbml.util.compilers

Class LaTeXCompiler

java.lang.Object

org.sbml.jsbml.util.StringTools

org.sbml.jsbml.util.compilers.LaTeXCompiler

All Implemented Interfaces:

ASTNodeCompiler

public class LaTeXCompiler
extends StringTools
implements ASTNodeCompiler

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

Since:

0.8

Version:

$Rev$

Author:

Andreas Dräger

Field Summary

Fields

Modifier and Type	Field and 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.
static java.lang.String	implies
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
private boolean	printNameIfAvailable Important for LaTeX export to decide whether the name or the id of a NamedSBase should be printed.
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 and Description
LaTeXCompiler() Creates a new LaTeXCompiler instance.
LaTeXCompiler(boolean namesInEquations) Creates a new LaTeXCompiler instance.

Method Summary

Modifier and Type	Method and Description
ASTNodeValue	abs(ASTNode value) The absolute value represented by the given ASTNode.
ASTNodeValue	and(java.util.List<ASTNode> nodes)
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)
java.lang.StringBuilder	brackets(java.lang.Object formula) Encloses the given formula in brackets.
ASTNodeValue	ceiling(ASTNode value)
private java.lang.String	checkBrackets(ASTNode node) Creates brackets if needed.
java.lang.StringBuilder	colorbox(java.lang.String color, java.lang.Object what)
private static java.lang.StringBuilder	command(java.lang.String command, java.lang.Object what)
private static java.lang.StringBuilder	command(java.lang.String command, java.lang.Object first, java.lang.Object second)
ASTNodeValue	compile(CallableSBase variable)
ASTNodeValue	compile(Compartment c) This method returns the correct LaTeX expression for a function which returns the size of a compartment.
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 node)
ASTNodeValue	cosh(ASTNode node)
ASTNodeValue	cot(ASTNode node)
ASTNodeValue	coth(ASTNode node)
ASTNodeValue	csc(ASTNode node)
ASTNodeValue	csch(ASTNode node)
ASTNodeValue	delay(java.lang.String delayName, ASTNode x, ASTNode delay, java.lang.String timeUnits) Evaluates delay functions.
java.lang.StringBuffer	descriptionItem(java.lang.String item, java.lang.Object description) This method simplifies the process of creating descriptions.
ASTNodeValue	eq(ASTNode left, ASTNode right) Equal.
ASTNodeValue	exp(ASTNode node)
ASTNodeValue	factorial(ASTNode node)
ASTNodeValue	floor(ASTNode value)
java.lang.StringBuffer	format(double value) This method returns a StringBuffer representing a properly LaTeX formatted number.
ASTNodeValue	frac(ASTNode numerator, ASTNode denominator) Fraction of two ASTNodes
ASTNodeValue	frac(int numerator, int denominator) A fraction of two int values.
java.lang.StringBuilder	frac(java.lang.Object numerator, java.lang.Object denominator)
ASTNodeValue	function(FunctionDefinition fun, java.util.List<ASTNode> args)
private java.lang.StringBuilder	function(java.lang.String func, ASTNode value) Decides whether to produce brackets.
ASTNodeValue	function(java.lang.String functionDefinitionName, java.util.List<ASTNode> args)
private java.lang.StringBuilder	function(java.lang.String func, java.lang.Object value) Without brackets.
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()
private java.lang.StringBuilder	getNameOrID(NamedSBase sbase) If the field printNameIfAvailable is false this method returns a the id of the given SBase.
ASTNodeValue	getNegativeInfinity()
static java.lang.String	getNumbering(long number)
ASTNodeValue	getPositiveInfinity()
ASTNodeValue	getRateOf(java.lang.String name)
ASTNodeValue	gt(ASTNode left, ASTNode right) Greater than.
private static java.lang.StringBuffer	heading(java.lang.String kind, java.lang.String title, boolean numbering) Creates head lines.
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)
ASTNodeValue	implies(java.util.List<ASTNode> values) Returns the logical implies between two ASTNode.
boolean	isPrintNameIfAvailable()
java.lang.StringBuilder	label(java.lang.String id)
ASTNodeValue	lambda(java.util.List<ASTNode> nodes) The body of a FunctionDefinition.
ASTNodeValue	leq(ASTNode left, ASTNode right) Less equal.
ASTNodeValue	ln(ASTNode node) Natural logarithm.
ASTNodeValue	log(ASTNode node) Logarithm of the given value to base 10.
ASTNodeValue	log(ASTNode base, ASTNode value) Logarithm of the given value to the given base.
private ASTNodeValue	logicalOperation(java.lang.String symbol, java.util.List<ASTNode> values)
java.lang.StringBuffer	longtableHead(java.lang.String columnDef, java.lang.String caption, java.lang.String headLine) Creates a head for a longtable in LaTeX.
ASTNodeValue	lt(ASTNode left, ASTNode 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.
ASTNodeValue	max(java.util.List<ASTNode> values) Returns the maximum of the values.
java.lang.StringBuilder	mbox(java.lang.String s)
ASTNodeValue	min(java.util.List<ASTNode> values) Returns the minimum of the values.
ASTNodeValue	minus(java.util.List<ASTNode> nodes) Subtraction.
ASTNodeValue	neq(ASTNode left, ASTNode right) Not equal.
ASTNodeValue	not(ASTNode node)
ASTNodeValue	or(java.util.List<ASTNode> nodes)
ASTNodeValue	piecewise(java.util.List<ASTNode> nodes)
ASTNodeValue	plus(java.util.List<ASTNode> nodes)
ASTNodeValue	pow(ASTNode base, ASTNode exponent)
ASTNodeValue	quotient(java.util.List<ASTNode> values) Returns the quotient of the division of the values.
private java.lang.StringBuilder	relation(ASTNode left, java.lang.String relationSymbol, ASTNode right) Creates a relation between two ASTNodes.
ASTNodeValue	rem(java.util.List<ASTNode> values) Returns the remainder of the division of the values.
ASTNodeValue	root(ASTNode rootExponent, ASTNode value)
ASTNodeValue	root(double rootExponent, ASTNode radiant)
ASTNodeValue	sec(ASTNode node)
ASTNodeValue	sech(ASTNode node)
java.lang.StringBuffer	section(java.lang.String title, boolean numbering)
ASTNodeValue	selector(java.util.List<ASTNode> nodes)
void	setPrintNameIfAvailable(boolean printNameIfAvailable)
ASTNodeValue	sin(ASTNode node)
ASTNodeValue	sinh(ASTNode node)
ASTNodeValue	sqrt(ASTNode value) Square root.
java.lang.StringBuffer	subsection(java.lang.String title, boolean numbering)
java.lang.StringBuffer	subsubsection(java.lang.String title, boolean numbering)
ASTNodeValue	symbolTime(java.lang.String time) The simulation time.
ASTNodeValue	tan(ASTNode node)
ASTNodeValue	tanh(ASTNode 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)
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.
java.lang.StringBuffer	usepackage(java.lang.String latexPackage, java.lang.String... options) Creates a usepackage command for the given package with the optional options.
ASTNodeValue	vector(java.util.List<ASTNode> nodes) Dealing with a vector.
ASTNodeValue	xor(java.util.List<ASTNode> nodes) Exclusive or.

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

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

Methods inherited from class java.lang.Object

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

Field Detail

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

implies

public static final java.lang.String implies

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

printNameIfAvailable

private boolean printNameIfAvailable

Important for LaTeX export to decide whether the name or the id of a NamedSBase should be printed.

Constructor Detail

LaTeXCompiler

public LaTeXCompiler()

Creates a new LaTeXCompiler instance.

LaTeXCompiler

public LaTeXCompiler(boolean namesInEquations)

Creates a new LaTeXCompiler instance.

Parameters:

namesInEquations -

Method Detail

command

private static java.lang.StringBuilder command(java.lang.String command,
                                               java.lang.Object what)

Parameters:

command -

what -

Returns:

command

private static java.lang.StringBuilder command(java.lang.String command,
                                               java.lang.Object first,
                                               java.lang.Object second)

Parameters:

command -

first -

second -

Returns:

getNumbering

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

Parameters:

number -

Returns:

heading

private static java.lang.StringBuffer heading(java.lang.String kind,
                                              java.lang.String title,
                                              boolean numbering)

Creates head lines.

Parameters:

kind - E.g., section, subsection, subsubsection, paragraph etc.

title - The title of the heading.

numbering - If true a number will be placed in front of the title.

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 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> nodes)
                 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

brackets

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

Encloses the given formula in brackets.

Parameters:

formula -

Returns:

checkBrackets

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

Creates brackets if needed.

Parameters:

node -

Returns:

Throws:

SBMLException

ceiling

public ASTNodeValue ceiling(ASTNode value)
                     throws SBMLException

Specified by:

ceiling in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

colorbox

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

Parameters:

color -

what -

Returns:

compile

public ASTNodeValue 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 ASTNodeCompiler

Returns:

compile

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

Description copied from interface: ASTNodeCompiler

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

Specified by:

compile in interface ASTNodeCompiler

Parameters:

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

exponent - The exponent for the multiplier ten.

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

Returns:

compile

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

Specified by:

compile in interface ASTNodeCompiler

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

Returns:

compile

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

Specified by:

compile in interface ASTNodeCompiler

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

Returns:

compile

public ASTNodeValue compile(CallableSBase variable)

Specified by:

compile in interface ASTNodeCompiler

Returns:

compile

public ASTNodeValue compile(java.lang.String name)

Description copied from interface: ASTNodeCompiler

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

Specified by:

compile in interface ASTNodeCompiler

Returns:

cos

public ASTNodeValue cos(ASTNode node)
                 throws SBMLException

Specified by:

cos in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

cosh

public ASTNodeValue cosh(ASTNode node)
                  throws SBMLException

Specified by:

cosh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

cot

public ASTNodeValue cot(ASTNode node)
                 throws SBMLException

Specified by:

cot in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

coth

public ASTNodeValue coth(ASTNode node)
                  throws SBMLException

Specified by:

coth in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

csc

public ASTNodeValue csc(ASTNode node)
                 throws SBMLException

Specified by:

csc in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

csch

public ASTNodeValue csch(ASTNode node)
                  throws SBMLException

Specified by:

csch in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

delay

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

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 ASTNodeValue eq(ASTNode left,
                       ASTNode right)
                throws SBMLException

Description copied from interface: ASTNodeCompiler

Equal.

Specified by:

eq in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

exp

public ASTNodeValue exp(ASTNode node)
                 throws SBMLException

Specified by:

exp in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

factorial

public ASTNodeValue factorial(ASTNode node)
                       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

format

public java.lang.StringBuffer format(double value)

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

Parameters:

value -

Returns:

frac

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

Description copied from interface: ASTNodeCompiler

Fraction of two ASTNodes

Specified by:

frac in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

frac

public ASTNodeValue frac(int numerator,
                         int denominator)

Description copied from interface: ASTNodeCompiler

A fraction of two int values.

Specified by:

frac in interface ASTNodeCompiler

Returns:

frac

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

Parameters:

numerator -

denominator -

Returns:

function

public ASTNodeValue function(FunctionDefinition fun,
                             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

function

private java.lang.StringBuilder function(java.lang.String func,
                                         ASTNode value)
                                  throws SBMLException

Decides whether to produce brackets.

Parameters:

func -

value -

Returns:

Throws:

SBMLException

function

private java.lang.StringBuilder function(java.lang.String func,
                                         java.lang.Object value)

Without brackets.

Parameters:

func -

value -

Returns:

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:

getNameOrID

private java.lang.StringBuilder getNameOrID(NamedSBase sbase)

If the field printNameIfAvailable is false this method returns a the id of the given SBase. If printNameIfAvailable is true this method looks for the name of the given SBase and will return it.

Parameters:

sbase - the SBase, whose name or id is to be returned.

Returns:

The name or the ID of the SBase (according to the field printNameIfAvailable), whose LaTeX special symbols are masked and which is type set in typewriter font if it is an id. The mathmode argument decides if mathtt or mathrm has to be used.

getNegativeInfinity

public ASTNodeValue getNegativeInfinity()

Specified by:

getNegativeInfinity in interface ASTNodeCompiler

Returns:

getPositiveInfinity

public ASTNodeValue getPositiveInfinity()

Specified by:

getPositiveInfinity in interface ASTNodeCompiler

Returns:

gt

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

Description copied from interface: ASTNodeCompiler

Greater than.

Specified by:

gt in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

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

Description copied from interface: ASTNodeCompiler

The body of a FunctionDefinition.

Specified by:

lambda in interface ASTNodeCompiler

Parameters:

nodes - Place holders for arguments.

Returns:

Throws:

SBMLException

leq

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

Description copied from interface: ASTNodeCompiler

Less equal.

Specified by:

leq in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

ln

public ASTNodeValue ln(ASTNode node)
                throws SBMLException

Description copied from interface: ASTNodeCompiler

Natural logarithm.

Specified by:

ln in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

log

public ASTNodeValue log(ASTNode node)
                 throws SBMLException

Description copied from interface: ASTNodeCompiler

Logarithm of the given value to base 10.

Specified by:

log in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

log

public ASTNodeValue log(ASTNode 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

logicalOperation

private ASTNodeValue logicalOperation(java.lang.String symbol,
                                      java.util.List<ASTNode> values)
                               throws SBMLException

Parameters:

symbol -

values -

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 ASTNodeValue lt(ASTNode left,
                       ASTNode right)
                throws SBMLException

Description copied from interface: ASTNodeCompiler

Less than.

Specified by:

lt in interface ASTNodeCompiler

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

Description copied from interface: ASTNodeCompiler

Subtraction.

Specified by:

minus in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

neq

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

Description copied from interface: ASTNodeCompiler

Not equal.

Specified by:

neq in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

not

public ASTNodeValue not(ASTNode node)
                 throws SBMLException

Specified by:

not in interface ASTNodeCompiler

Parameters:

node - This value must be interpretable as a Boolean.

Returns:

Throws:

SBMLException

or

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

Specified by:

or in interface ASTNodeCompiler

Parameters:

nodes - These values must be interpretable as a Boolean.

Returns:

Throws:

SBMLException

piecewise

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

Specified by:

piecewise in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

plus

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

Specified by:

plus in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

pow

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

Specified by:

pow in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

relation

private java.lang.StringBuilder relation(ASTNode left,
                                         java.lang.String relationSymbol,
                                         ASTNode right)
                                  throws SBMLException

Creates a relation between two ASTNodes.

Parameters:

left -

relationSymbol -

right -

Returns:

Throws:

SBMLException

root

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

Specified by:

root in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

root

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

Specified by:

root in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

sec

public ASTNodeValue sec(ASTNode node)
                 throws SBMLException

Specified by:

sec in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

sech

public ASTNodeValue sech(ASTNode node)
                  throws SBMLException

Specified by:

sech in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

section

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

Parameters:

title -

numbering -

Returns:

setPrintNameIfAvailable

public void setPrintNameIfAvailable(boolean printNameIfAvailable)

Parameters:

printNameIfAvailable -

sin

public ASTNodeValue sin(ASTNode node)
                 throws SBMLException

Specified by:

sin in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

sinh

public ASTNodeValue sinh(ASTNode node)
                  throws SBMLException

Specified by:

sinh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

sqrt

public ASTNodeValue sqrt(ASTNode value)
                  throws SBMLException

Description copied from interface: ASTNodeCompiler

Square root.

Specified by:

sqrt in interface ASTNodeCompiler

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 ASTNodeValue symbolTime(java.lang.String time)

Description copied from interface: ASTNodeCompiler

The simulation time.

Specified by:

symbolTime in interface ASTNodeCompiler

Parameters:

time - The name of the time symbol.

Returns:

An ASTNodeValue that represents the current time.

tan

public ASTNodeValue tan(ASTNode node)
                 throws SBMLException

Specified by:

tan in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

tanh

public ASTNodeValue tanh(ASTNode node)
                  throws SBMLException

Specified by:

tanh in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

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 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()

Description copied from interface: ASTNodeCompiler

Dealing with a malformed ASTNode.

Specified by:

unknownValue in interface ASTNodeCompiler

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.

xor

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

Description copied from interface: ASTNodeCompiler

Exclusive or.

Specified by:

xor in interface ASTNodeCompiler

Parameters:

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

Returns:

Throws:

SBMLException

selector

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

Specified by:

selector in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

vector

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

Description copied from interface: ASTNodeCompiler

Dealing with a vector.

Specified by:

vector in interface ASTNodeCompiler

Returns:

Throws:

SBMLException

max

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

Description copied from interface: ASTNodeCompiler

Returns the maximum of the values.

Specified by:

max in interface ASTNodeCompiler

Returns:

the maximum of the values.

min

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

Description copied from interface: ASTNodeCompiler

Returns the minimum of the values.

Specified by:

min in interface ASTNodeCompiler

Returns:

the minimum of the values.

quotient

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

Description copied from interface: ASTNodeCompiler

Returns the quotient of the division of the values.

Specified by:

quotient in interface ASTNodeCompiler

Returns:

the quotient of the values.

rem

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

Description copied from interface: ASTNodeCompiler

Returns the remainder of the division of the values.

Specified by:

rem in interface ASTNodeCompiler

Returns:

the remainder of the division of the values.

implies

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

Description copied from interface: ASTNodeCompiler

Returns the logical implies between two ASTNode.

Truth table:

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

Specified by:

implies in interface ASTNodeCompiler

Returns:

the logical implies between two ASTNode.

getRateOf

public ASTNodeValue getRateOf(java.lang.String name)

Specified by:

getRateOf in interface ASTNodeCompiler

Returns: