A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

T

tan(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

tan(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

tan(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

tan(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

tan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

tan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

tan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

tan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

tan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

tan(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

tan(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

tan(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

tan(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

tan(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

tanh(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

tanh(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

tanh(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

tanh(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

tanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

tanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

tanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

tanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

tanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

tanh(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

tanh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

tanh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

tanh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

tanh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

tensor - org.sbml.jsbml.ext.spatial.DiffusionKind

Tensor

Term - Class in org.sbml.jsbml.ontology

This is a convenient wrapper class for the corresponding implementation of Term in BioJava as it provides specialized methods to obtain the information from the SBO OBO file directly and under the same name as the keys are given in that file.

Term(Term) - Constructor for class org.sbml.jsbml.ontology.Term

Creates a new Term instance.

TESLA - org.sbml.jsbml.Unit.Kind

The tesla unit.

text - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants

text - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

text - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent

Text - Class in org.sbml.jsbml.ext.render

Text() - Constructor for class org.sbml.jsbml.ext.render.Text

Text(int, int) - Constructor for class org.sbml.jsbml.ext.render.Text

Text(Text) - Constructor for class org.sbml.jsbml.ext.render.Text

textAnchor - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

textcolor(String, Object) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

textcolor(String, Object) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

TextConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the Text class.

TextConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.TextConstraints

textGlyph - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants

TextGlyph - Class in org.sbml.jsbml.ext.layout

The TextGlyph class describes the position and dimension of text labels.

TextGlyph() - Constructor for class org.sbml.jsbml.ext.layout.TextGlyph

TextGlyph(int, int) - Constructor for class org.sbml.jsbml.ext.layout.TextGlyph

TextGlyph(String) - Constructor for class org.sbml.jsbml.ext.layout.TextGlyph

TextGlyph(String, int, int) - Constructor for class org.sbml.jsbml.ext.layout.TextGlyph

TextGlyph(TextGlyph) - Constructor for class org.sbml.jsbml.ext.layout.TextGlyph

TEXTGLYPH - org.sbml.jsbml.ext.render.Style.Type

TextGlyphConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the TextGlyph class.

TextGlyphConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.TextGlyphConstraints

textGlyphIsIndependent(TextGlyph) - Static method in class org.sbml.jsbml.ext.render.director.LayoutDirector

Check whether a text glyph represents an independent text (i.e. it is not associated with any other graphical object or species.

texttt(String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

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

texttt(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

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

thresholdLevel - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

TidySBMLWriter - Class in org.sbml.jsbml

Provides methods for writing SBML to files, text strings or streams.

TidySBMLWriter() - Constructor for class org.sbml.jsbml.TidySBMLWriter

Creates a new TidySBMLWriter.

TidySBMLWriter(char, short) - Constructor for class org.sbml.jsbml.TidySBMLWriter

Creates a new TidySBMLWriter that uses the given character for indentation of the XML representation of SBML data structures (with the given number of such symbols).

TidySBMLWriter(String, String) - Constructor for class org.sbml.jsbml.TidySBMLWriter

Creates a new SBMLWriter for the program with the given name and version.

TidySBMLWriter(String, String, char, short) - Constructor for class org.sbml.jsbml.TidySBMLWriter

Creates a new SBMLWriter for the program with the given name and version that uses the given character for indentation of the XML representation of SBML data structures (with the given number of such symbols).

TidySBMLWriter(TidySBMLWriter) - Constructor for class org.sbml.jsbml.TidySBMLWriter

Clone constructor.

time(int, int) - Static method in class org.sbml.jsbml.UnitDefinition

Returns the predefined unit for time.

TIME - Static variable in class org.sbml.jsbml.UnitDefinition

Identifier of the (for the SBML Levels 1 and 2) predefined UnitDefinition time.

timeConversionFactor - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

timeDerivative(String) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

timeDerivative(String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

times(Object...) - Static method in class org.sbml.jsbml.math.compiler.HTMLFormula

Returns the product of the given elements as StringBuffer.

times(Object...) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler

Returns the product of the given elements as StringBuffer.

times(Object...) - Static method in class org.sbml.jsbml.util.compilers.HTMLFormula

Returns the product of the given elements as StringBuffer.

times(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

times(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

times(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

times(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler

Product of all given ASTNodes.

times(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler

times(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler

times(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler

times(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

times(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler

times(List<ASTNode2>) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler

Product of all given ASTNode2s.

times(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler

times(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler

times(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler

times(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler

times(ASTNode...) - Static method in class org.sbml.jsbml.ASTNode

Creates an ASTNode of type times and adds the given nodes as children.

times(ASTNode2, double) - Static method in class org.sbml.jsbml.math.ASTFactory

Adds a real number to ASTNode2

times(ASTNode2, int) - Static method in class org.sbml.jsbml.math.ASTFactory

Adds an integer to ASTNode2

times(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory

Creates a new ASTTimesNode with exactly two children

times(MathContainer, CallableSBase...) - Static method in class org.sbml.jsbml.ASTNode

Multiplies several CallableSBase objects.

times(T...) - Static method in class org.sbml.jsbml.math.compiler.FormulaCompiler

Returns the product of the given elements as StringBuffer.

TIMES - org.sbml.jsbml.ASTNode.Type

TIMES - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants

RegularExpression Id.

TIMES - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants

RegularExpression Id.

TIMES - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants

RegularExpression Id.

TIMES - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants

RegularExpression Id.

TIMES - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants

RegularExpression Id.

TIMES - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants

RegularExpression Id.

TIMES - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants

RegularExpression Id.

TIMES - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants

RegularExpression Id.

TIMES - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants

RegularExpression Id.

timeUnits - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent

TimeUnitsAllowedInKL - org.sbml.jsbml.SBMLException.Code

Disallowed value for attribute timeUnits

TimeUnitsEvent - org.sbml.jsbml.SBMLException.Code

Units of timeUnits are not time units

TimeUnitsNoLongerValid - org.sbml.jsbml.SBMLException.Code

timeUnits not supported in this Level+Version of SBML

TimeUnitsRemoved - org.sbml.jsbml.SBMLException.Code

The timeUnits attribute is invalid in this Level+Version of SBML

toArray() - Method in class org.sbml.jsbml.ListOf

toArray(T[]) - Method in class org.sbml.jsbml.ListOf

toASTNode(ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory

Converts a ASTNode2 to a ASTNode.

toASTNode2() - Method in class org.sbml.jsbml.ASTNode

Return the ASTNode2 corresponding to the current ASTNode

toASTNode2(ASTNode) - Static method in class org.sbml.jsbml.math.ASTFactory

toBoolean() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value

Analog to the toDouble() method but this method tries to evaluate the value contained in this object to a boolean value.

toBoolean() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue

Analog to the toDouble() method but this method tries to evaluate the value contained in this object to a boolean value.

toCallableSBase() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value

toCallableSBase() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue

toClass() - Method in enum org.sbml.jsbml.ListOf.Type

Gives the corresponding Class object for this ListOf.Type.

toDouble() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value

toDouble() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue

toFloat() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value

toFloat() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue

toFontFamily(String) - Static method in enum org.sbml.jsbml.ext.render.FontFamily

Checks if a given String value matches one of the FontFamily hints.

toFormula() - Method in class org.sbml.jsbml.ASTNode

Converts this ASTNode to a text string using a specific syntax for mathematical formulas.

toFormula() - Method in class org.sbml.jsbml.EventAssignment

Creates a formula String representation of this assignment.

toFormula() - Method in class org.sbml.jsbml.math.AbstractASTNode

toFormula() - Method in class org.sbml.jsbml.math.ASTArithmeticOperatorNode

toFormula() - Method in class org.sbml.jsbml.math.ASTBoolean

toFormula() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode

toFormula() - Method in class org.sbml.jsbml.math.ASTCiNumberNode

toFormula() - Method in class org.sbml.jsbml.math.ASTCnExponentialNode

toFormula() - Method in class org.sbml.jsbml.math.ASTCnIntegerNode

toFormula() - Method in class org.sbml.jsbml.math.ASTCnRationalNode

toFormula() - Method in class org.sbml.jsbml.math.ASTCnRealNode

toFormula() - Method in class org.sbml.jsbml.math.ASTConstantNumber

toFormula() - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode

toFormula() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode

toFormula() - Method in class org.sbml.jsbml.math.ASTDivideNode

toFormula() - Method in class org.sbml.jsbml.math.ASTHyperbolicNode

toFormula() - Method in class org.sbml.jsbml.math.ASTLambdaFunctionNode

toFormula() - Method in class org.sbml.jsbml.math.ASTLogarithmNode

toFormula() - Method in class org.sbml.jsbml.math.ASTLogicalOperatorNode

toFormula() - Method in class org.sbml.jsbml.math.ASTMinusNode

toFormula() - Method in interface org.sbml.jsbml.math.ASTNode2

Converts this ASTNode2 to a text string using a specific syntax for mathematical formulas.

toFormula() - Method in class org.sbml.jsbml.math.ASTPiecewiseFunctionNode

toFormula() - Method in class org.sbml.jsbml.math.ASTPlusNode

toFormula() - Method in class org.sbml.jsbml.math.ASTPowerNode

toFormula() - Method in class org.sbml.jsbml.math.ASTQualifierNode

toFormula() - Method in class org.sbml.jsbml.math.ASTRelationalOperatorNode

toFormula() - Method in class org.sbml.jsbml.math.ASTRootNode

toFormula() - Method in class org.sbml.jsbml.math.ASTTimesNode

toFormula() - Method in class org.sbml.jsbml.math.ASTTrigonometricNode

toFormula() - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode

toFormula() - Method in class org.sbml.jsbml.math.ASTUnknown

toFormula(FormulaCompiler) - Method in class org.sbml.jsbml.ASTNode

Converts this ASTNode to a text string using a specific FormulaCompiler.

toGeneralPath(Curve) - Static method in class org.sbml.jsbml.ext.render.director.Geometry

toHTML(String) - Static method in class org.sbml.jsbml.util.StringTools

Returns a HTML formated String, in which each line is at most lineBreak symbols long.

toHTML(String, int) - Static method in class org.sbml.jsbml.util.StringTools

Returns a HTML formated String, in which each line is at most lineBreak symbols long.

toHTML(Unit) - Static method in class org.sbml.jsbml.math.compiler.HTMLFormula

toHTML(Unit) - Static method in class org.sbml.jsbml.util.compilers.HTMLFormula

toHTML(UnitDefinition) - Static method in class org.sbml.jsbml.math.compiler.HTMLFormula

Creates an HTML string representation of this UnitDefinition.

toHTML(UnitDefinition) - Static method in class org.sbml.jsbml.util.compilers.HTMLFormula

Creates an HTML string representation of this UnitDefinition.

toInteger() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value

This method is analog to the toDouble method but tries to convert this value into an integer.

toInteger() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue

This method is analog to the toDouble method but tries to convert this value into an integer.

token - Variable in class org.sbml.jsbml.math.parser.FormulaParser

Current token.

token - Variable in class org.sbml.jsbml.math.parser.FormulaParserASTNode2

Current token.

token - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3

Current token.

token - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2

Current token.

token - Variable in class org.sbml.jsbml.text.parser.CobraFormulaParser

Current token.

token - Variable in class org.sbml.jsbml.text.parser.FormulaParser

Current token.

token - Variable in class org.sbml.jsbml.text.parser.FormulaParserASTNode2

Current token.

token - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3

Current token.

token - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2

Current token.

Token - Class in org.sbml.jsbml.math.parser

Describes the input token stream.

Token - Class in org.sbml.jsbml.text.parser

Describes the input token stream.

Token() - Constructor for class org.sbml.jsbml.math.parser.Token

No-argument constructor

Token() - Constructor for class org.sbml.jsbml.text.parser.Token

No-argument constructor

Token(int) - Constructor for class org.sbml.jsbml.math.parser.Token

Constructs a new token for the specified Image.

Token(int) - Constructor for class org.sbml.jsbml.text.parser.Token

Constructs a new token for the specified Image.

Token(int, String) - Constructor for class org.sbml.jsbml.math.parser.Token

Constructs a new token for the specified Image and Kind.

Token(int, String) - Constructor for class org.sbml.jsbml.text.parser.Token

Constructs a new token for the specified Image and Kind.

token_source - Variable in class org.sbml.jsbml.math.parser.FormulaParser

Generated Token Manager.

token_source - Variable in class org.sbml.jsbml.math.parser.FormulaParserASTNode2

Generated Token Manager.

token_source - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3

Generated Token Manager.

token_source - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2

Generated Token Manager.

token_source - Variable in class org.sbml.jsbml.text.parser.CobraFormulaParser

Generated Token Manager.

token_source - Variable in class org.sbml.jsbml.text.parser.FormulaParser

Generated Token Manager.

token_source - Variable in class org.sbml.jsbml.text.parser.FormulaParserASTNode2

Generated Token Manager.

token_source - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3

Generated Token Manager.

token_source - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2

Generated Token Manager.

tokenImage - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants

Literal token values.

tokenImage - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants

Literal token values.

tokenImage - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants

Literal token values.

tokenImage - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants

Literal token values.

tokenImage - Variable in exception org.sbml.jsbml.math.parser.ParseException

This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred.

tokenImage - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants

Literal token values.

tokenImage - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants

Literal token values.

tokenImage - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants

Literal token values.

tokenImage - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants

Literal token values.

tokenImage - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants

Literal token values.

tokenImage - Variable in exception org.sbml.jsbml.text.parser.ParseException

This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred.

TokenMgrError - Error in org.sbml.jsbml.math.parser

Token Manager Error.

TokenMgrError - Error in org.sbml.jsbml.text.parser

Token Manager Error.

TokenMgrError() - Constructor for error org.sbml.jsbml.math.parser.TokenMgrError

No arg constructor.

TokenMgrError() - Constructor for error org.sbml.jsbml.text.parser.TokenMgrError

No arg constructor.

TokenMgrError(boolean, int, int, int, String, char, int) - Constructor for error org.sbml.jsbml.math.parser.TokenMgrError

Full Constructor.

TokenMgrError(boolean, int, int, int, String, char, int) - Constructor for error org.sbml.jsbml.text.parser.TokenMgrError

Full Constructor.

TokenMgrError(String, int) - Constructor for error org.sbml.jsbml.math.parser.TokenMgrError

Constructor with message and reason.

TokenMgrError(String, int) - Constructor for error org.sbml.jsbml.text.parser.TokenMgrError

Constructor with message and reason.

ToL3Converter - Class in org.sbml.jsbml.util.converters

ToL3Converter(ValuePair<Integer, Integer>) - Constructor for class org.sbml.jsbml.util.converters.ToL3Converter

ToL3Converter(ValuePair<Integer, Integer>, ValuePair<Integer, Integer>) - Constructor for class org.sbml.jsbml.util.converters.ToL3Converter

ToL3V2Converter - Class in org.sbml.jsbml.util.converters

ToL3V2Converter() - Constructor for class org.sbml.jsbml.util.converters.ToL3V2Converter

toLaTeX() - Method in class org.sbml.jsbml.ASTNode

Converts this node recursively into a LaTeX formatted String.

toLaTeX() - Method in class org.sbml.jsbml.math.AbstractASTNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTArithmeticOperatorNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTBoolean

toLaTeX() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTCiNumberNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTCnExponentialNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTCnIntegerNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTCnRationalNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTCnRealNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTConstantNumber

toLaTeX() - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTDivideNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTHyperbolicNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTLambdaFunctionNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTLogarithmNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTLogicalOperatorNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTMinusNode

toLaTeX() - Method in interface org.sbml.jsbml.math.ASTNode2

Converts this node recursively into a LaTeX formatted String.

toLaTeX() - Method in class org.sbml.jsbml.math.ASTPiecewiseFunctionNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTPlusNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTPowerNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTQualifierNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTRelationalOperatorNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTRootNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTTimesNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTTrigonometricNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode

toLaTeX() - Method in class org.sbml.jsbml.math.ASTUnknown

toLong() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value

toLong() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue

toMathML() - Method in class org.sbml.jsbml.ASTNode

Converts this node recursively into a MathML string that corresponds to the subset of MathML defined in the SBML specification.

toMathML() - Method in class org.sbml.jsbml.math.AbstractASTNode

toMathML() - Method in class org.sbml.jsbml.math.ASTArithmeticOperatorNode

toMathML() - Method in class org.sbml.jsbml.math.ASTBoolean

toMathML() - Method in class org.sbml.jsbml.math.ASTCiFunctionNode

toMathML() - Method in class org.sbml.jsbml.math.ASTCiNumberNode

toMathML() - Method in class org.sbml.jsbml.math.ASTCnExponentialNode

toMathML() - Method in class org.sbml.jsbml.math.ASTCnIntegerNode

toMathML() - Method in class org.sbml.jsbml.math.ASTCnRationalNode

toMathML() - Method in class org.sbml.jsbml.math.ASTCnRealNode

toMathML() - Method in class org.sbml.jsbml.math.ASTConstantNumber

toMathML() - Method in class org.sbml.jsbml.math.ASTCSymbolDelayNode

toMathML() - Method in class org.sbml.jsbml.math.ASTCSymbolTimeNode

toMathML() - Method in class org.sbml.jsbml.math.ASTDivideNode

toMathML() - Method in class org.sbml.jsbml.math.ASTHyperbolicNode

toMathML() - Method in class org.sbml.jsbml.math.ASTLambdaFunctionNode

toMathML() - Method in class org.sbml.jsbml.math.ASTLogarithmNode

toMathML() - Method in class org.sbml.jsbml.math.ASTLogicalOperatorNode

toMathML() - Method in class org.sbml.jsbml.math.ASTMinusNode

toMathML() - Method in interface org.sbml.jsbml.math.ASTNode2

Converts this node recursively into a MathML string that corresponds to the subset of MathML defined in the SBML specification.

toMathML() - Method in class org.sbml.jsbml.math.ASTPiecewiseFunctionNode

toMathML() - Method in class org.sbml.jsbml.math.ASTPlusNode

toMathML() - Method in class org.sbml.jsbml.math.ASTPowerNode

toMathML() - Method in class org.sbml.jsbml.math.ASTRelationalOperatorNode

toMathML() - Method in class org.sbml.jsbml.math.ASTRootNode

toMathML() - Method in class org.sbml.jsbml.math.ASTTimesNode

toMathML() - Method in class org.sbml.jsbml.math.ASTTrigonometricNode

toMathML() - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode

toMathML() - Method in class org.sbml.jsbml.math.ASTUnknown

toMathML(boolean, boolean, int) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler

Deprecated.

toMathML(Writer, Document, boolean, boolean, int) - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser

Deprecated.

toMathML(ASTNode) - Static method in class org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler

Writes an ASTNode the mathML.

toMathML(ASTNode2) - Static method in class org.sbml.jsbml.math.compiler.MathMLXMLStreamCompiler

Writes an ASTNode2 the mathML.

toMathML(Document, boolean, boolean, int) - Static method in class org.sbml.jsbml.xml.parsers.MathMLParser

Deprecated.

Write output as String.

toNode() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value

toNode() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue

toNumber() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value

Tries to convert the value contained in this object into a double number.

toNumber() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue

Tries to convert the value contained in this object into a double number.

TOP - org.sbml.jsbml.ext.render.VTextAnchor

toprule - Static variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler

Needed for the beginning of a table.

toprule - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler

Needed for the beginning of a table.

toSBOterm() - Method in enum org.sbml.jsbml.ext.layout.SpeciesReferenceRole

toSId(String) - Static method in class org.sbml.jsbml.util.SBMLtools

toSimpleString() - Method in class org.sbml.jsbml.ASTNode

Returns a simple String representing the content of the ASTNode.

toString() - Method in class org.sbml.jsbml.AbstractSBase

Returns a String representing this SBase with all the attributes that are defined.

toString() - Method in class org.sbml.jsbml.AbstractTreeNode

toString() - Method in class org.sbml.jsbml.ASTNode

toString() - Method in enum org.sbml.jsbml.ext.fbc.FluxBound.Operation

Deprecated.

toString() - Method in enum org.sbml.jsbml.ext.fbc.Objective.Type

toString() - Method in enum org.sbml.jsbml.ext.layout.CurveSegment.Type

toString() - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector

toString() - Method in enum org.sbml.jsbml.ext.render.FontFamily

toString() - Method in class org.sbml.jsbml.ext.render.RelAbsVector

Produces a string for debugging etc.

toString() - Method in enum org.sbml.jsbml.ext.render.RenderCurveSegment.Type

toString() - Method in class org.sbml.jsbml.ext.render.RenderGroup

toString() - Method in class org.sbml.jsbml.ext.render.Text

toString() - Method in class org.sbml.jsbml.History

Formats this history as string: the Creation-Date, as well as the number of contributors and the number of modification-dates will be given.

toString() - Method in exception org.sbml.jsbml.LevelVersionError

toString() - Method in interface org.sbml.jsbml.math.ASTNode2

toString() - Method in class org.sbml.jsbml.math.ASTUnknown

toString() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value

toString() - Method in class org.sbml.jsbml.math.parser.Token

Returns the image.

toString() - Method in class org.sbml.jsbml.ontology.Term

toString() - Method in class org.sbml.jsbml.ontology.Triple

toString() - Method in exception org.sbml.jsbml.PropertyException

toString() - Method in class org.sbml.jsbml.SBMLDocument

toString() - Method in exception org.sbml.jsbml.SBMLError

toString() - Method in class org.sbml.jsbml.SBMLReader

toString() - Method in class org.sbml.jsbml.SBMLWriter

toString() - Method in class org.sbml.jsbml.text.parser.Token

Returns the image.

toString() - Method in class org.sbml.jsbml.UnitDefinition

toString() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue

toString() - Method in class org.sbml.jsbml.util.Message

toString() - Method in class org.sbml.jsbml.util.Option

toString() - Method in class org.sbml.jsbml.util.Pair

toString() - Method in class org.sbml.jsbml.util.TreeNodeAdapter

toString() - Method in class org.sbml.jsbml.util.TreeNodeRemovedEvent

toString() - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML

toString() - Method in class org.sbml.jsbml.xml.XMLAttributes

toString() - Method in class org.sbml.jsbml.xml.XMLNamespaces

toString() - Method in class org.sbml.jsbml.xml.XMLNode

toString() - Method in class org.sbml.jsbml.xml.XMLTriple

toString(double) - Static method in class org.sbml.jsbml.util.StringTools

Returns a String from the given value that does not contain a point zero at the end if the given value represents an integer number.

toString(PropertyChangeEvent) - Method in class org.sbml.jsbml.util.SimpleTreeNodeChangeListener

toString(Locale, double) - Static method in class org.sbml.jsbml.util.StringTools

Allows for Locale-dependent number formatting.

toXML() - Method in class org.sbml.jsbml.CVTerm

toXML(String, StringBuffer) - Method in class org.sbml.jsbml.CVTerm

Writes all the MIRIAM annotations of the CVTerm in 'buffer'

toXML(XMLNode) - Static method in class org.sbml.jsbml.util.SBMLtools

toXML(XMLNode) - Static method in class org.sbml.jsbml.xml.parsers.XMLNodeWriter

toXMLAnnotationString(String) - Static method in class org.sbml.jsbml.util.StringTools

Checks whether a given String fits into the definition of the XML annotation String in SBML.

toXMLMessageString(String) - Static method in class org.sbml.jsbml.util.StringTools

Checks whether a given String fits into the definition of the XML message String in SBML.

toXMLNode() - Method in class org.sbml.jsbml.CVTerm

toXMLNotesString(String) - Static method in class org.sbml.jsbml.util.StringTools

Checks whether a given String fits into the definition of the XML notes String in SBML.

toXMLString() - Method in class org.sbml.jsbml.xml.XMLNode

Returns a string representation of this XMLNode.

transfer(SBMLDocument, String[]) - Method in class org.sbml.jsbml.ext.fbc.converters.NotesToAnnotation

Transfers information from the Cobra style notes of species and reactions to the annotations (see example below).

transform - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

Transformation - Class in org.sbml.jsbml.ext.render

Transformation() - Constructor for class org.sbml.jsbml.ext.render.Transformation

Creates an Transformation instance

Transformation(int, int) - Constructor for class org.sbml.jsbml.ext.render.Transformation

Creates an Transformation instance

Transformation(Transformation) - Constructor for class org.sbml.jsbml.ext.render.Transformation

Clone constructor

Transformation2D - Class in org.sbml.jsbml.ext.render

Transformation2D() - Constructor for class org.sbml.jsbml.ext.render.Transformation2D

Creates an Transformation2D instance

Transformation2D(int, int) - Constructor for class org.sbml.jsbml.ext.render.Transformation2D

Transformation2D(Transformation2D) - Constructor for class org.sbml.jsbml.ext.render.Transformation2D

Clone constructor

Transformation2DConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the Transformation2D class.

Transformation2DConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.Transformation2DConstraints

transformationComponent - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

TransformationComponent - Class in org.sbml.jsbml.ext.spatial

TransformationComponent() - Constructor for class org.sbml.jsbml.ext.spatial.TransformationComponent

TransformationComponent(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.TransformationComponent

TransformationComponent(TransformationComponent) - Constructor for class org.sbml.jsbml.ext.spatial.TransformationComponent

TransformationComponentConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the TransformationComponent class.

TransformationComponentConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.TransformationComponentConstraints

TransformationConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the Transformation class.

TransformationConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.TransformationConstraints

Transition - Class in org.sbml.jsbml.ext.qual

A Transition defines the changes in level associated with the QualitativeSpecies that occur when a Transition is enabled.

Transition() - Constructor for class org.sbml.jsbml.ext.qual.Transition

Creates a new Transition instance.

Transition(int, int) - Constructor for class org.sbml.jsbml.ext.qual.Transition

Creates a new Transition instance.

Transition(String) - Constructor for class org.sbml.jsbml.ext.qual.Transition

Creates a new Transition instance.

Transition(String, int, int) - Constructor for class org.sbml.jsbml.ext.qual.Transition

Creates a new Transition instance.

Transition(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.qual.Transition

Creates a new Transition instance.

Transition(Transition) - Constructor for class org.sbml.jsbml.ext.qual.Transition

Creates a new Transition instance.

TransitionConstraints - Class in org.sbml.jsbml.validator.offline.constraints

TransitionConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.TransitionConstraints

transitionEffect - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

translateX - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

translateY - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

translateZ - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

TreeNodeAdapter - Class in org.sbml.jsbml.util

This class is a wrapper element for any Object that should be linked into a tree data structure as represented by AbstractTreeNode, but that might by itself not be an instance of TreeNode, i.e., not compatible with the remaining tree data structure.

TreeNodeAdapter(Object, TreeNode) - Constructor for class org.sbml.jsbml.util.TreeNodeAdapter

Creates a new TreeNode wrapper for the given TreeNodeAdapter.userObject that will be linked to the given AbstractTreeNode.parent within an exisiting tree.

TreeNodeAdapter(TreeNodeAdapter) - Constructor for class org.sbml.jsbml.util.TreeNodeAdapter

Copy constructor for the given node.

TreeNodeChangeEvent - Class in org.sbml.jsbml.util

This event tells an TreeNodeChangeListener which values have been changed in an SBase and also provides the old and the new value.

TreeNodeChangeEvent(TreeNode, String, Object, Object) - Constructor for class org.sbml.jsbml.util.TreeNodeChangeEvent

TreeNodeChangeEvent(TreeNodeChangeEvent) - Constructor for class org.sbml.jsbml.util.TreeNodeChangeEvent

TreeNodeChangeListener - Interface in org.sbml.jsbml.util

A listener interface that allows applications to get notified if the state of any TreeNode object changes.

TreeNodeConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Class used to always add a ValidationFunction that is used to recursively validate the jsbml tree structure.

TreeNodeConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.TreeNodeConstraints

TreeNodeRemovedEvent - Class in org.sbml.jsbml.util

A special EventObject to notify a TreeNodeChangeListener about a removed node and its previous position within the tree.

TreeNodeRemovedEvent(TreeNode, TreeNode) - Constructor for class org.sbml.jsbml.util.TreeNodeRemovedEvent

Creates a new TreeNodeRemovedEvent that contains information about an element that has just been removed from a tree together with its previous parent node.

TreeNodeRemovedEvent(TreeNodeRemovedEvent) - Constructor for class org.sbml.jsbml.util.TreeNodeRemovedEvent

Clone constructor.

TreeNodeWithChangeSupport - Interface in org.sbml.jsbml.util

This interface extends the regular recursively defined TreeNode by adding methods to keep track of changes within the tree, such as adding/removing, or exchanging of child nodes or the change of any other attributes.

triangle - org.sbml.jsbml.ext.spatial.PolygonKind

Trigger - Class in org.sbml.jsbml

Represents the trigger XML element of a SBML file.

Trigger() - Constructor for class org.sbml.jsbml.Trigger

Creates a Trigger instance.

Trigger(int, int) - Constructor for class org.sbml.jsbml.Trigger

Creates a Trigger instance from a level and version.

Trigger(Trigger) - Constructor for class org.sbml.jsbml.Trigger

Creates a Trigger instance from a given Trigger.

TriggerConstraints - Class in org.sbml.jsbml.validator.offline.constraints

TriggerConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.TriggerConstraints

TriggerMathNotBoolean - org.sbml.jsbml.SBMLException.Code

Non-boolean math expression in trigger definition

Triple - Class in org.sbml.jsbml.ontology

This is a wrapper class for the corresponding BioJava class Triple, to allow for simplified access to the properties of a subject-predicate-object triple in this ontology.

Triple(Triple) - Constructor for class org.sbml.jsbml.ontology.Triple

Creates a new Triple from a given corresponding object from BioJava.

truncationLowerBound - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

truncationUpperBound - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

type - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

type - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants

type - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants

type - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

type - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants

type - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent

typeList - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

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