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(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

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

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(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

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

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.

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

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

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

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

TextAnchor - Enum in org.sbml.jsbml.ext.render

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

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

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

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

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

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

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

Predefined unit for 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(ASTNode...) - Static method in class org.sbml.jsbml.ASTNode

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

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

Multiplies several CallableSBase objects.

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

Creates a new ASTTimesNode with exactly two 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(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(Object...) - Static method in class org.sbml.jsbml.math.compiler.FormulaCompiler

Returns the product of the given elements as StringBuffer.

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

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

Returns the product of the given elements as StringBuffer.

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 - 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.

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

Returns the product of the given elements as StringBuffer.

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

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.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

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

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

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

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

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

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

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

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

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

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

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

Creates an HTML string representation of this UnitDefinition.

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

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

Creates an HTML string representation of this UnitDefinition.

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.

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

Describes the input token stream.

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

Constructs a new token for the specified Image and Kind.

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.text.parser

Describes the input token stream.

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

No-argument constructor

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

No arg constructor.

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

Constructor with message and reason.

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

Full Constructor.

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

Token Manager Error.

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

No arg constructor.

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

Constructor with message and reason.

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

Full Constructor.

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

Writes an ASTNode2 the mathML.

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

Deprecated.

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

Writes an ASTNode the mathML.

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

Deprecated.

Write output as String.

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

Deprecated.

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.

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

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.AbstractMathContainer

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

Returns the name of the component, if it is available.

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

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

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

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

Returns the information about the Creator as a String.

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

Returns a String containing the qualifier and all the resource URIs of this CVTerm.

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

toString() - Method in class org.sbml.jsbml.ext.arrays.Dimension

toString() - Method in class org.sbml.jsbml.ext.arrays.Index

toString() - Method in class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef

Returns the name of the component, if it is available.

toString() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

toString() - Method in class org.sbml.jsbml.ext.comp.Port

toString() - Method in class org.sbml.jsbml.ext.comp.ReplacedBy

toString() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

toString() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

toString() - Method in class org.sbml.jsbml.ext.distrib.DistribInput

toString() - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

toString() - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

toString() - Method in class org.sbml.jsbml.ext.dyn.DynElement

toString() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

toString() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

toString() - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent

toString() - Method in class org.sbml.jsbml.ext.fbc.FBCReactionPlugin

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

Deprecated.

toString() - Method in class org.sbml.jsbml.ext.fbc.GeneProduct

toString() - Method in class org.sbml.jsbml.ext.fbc.GeneProductRef

toString() - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator

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

toString() - Method in class org.sbml.jsbml.ext.groups.Group

toString() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

toString() - Method in class org.sbml.jsbml.ext.groups.Member

toString() - Method in class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph

toString() - Method in class org.sbml.jsbml.ext.layout.BoundingBox

toString() - Method in class org.sbml.jsbml.ext.layout.CubicBezier

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

toString() - Method in class org.sbml.jsbml.ext.layout.Dimensions

toString() - Method in class org.sbml.jsbml.ext.layout.Layout

toString() - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin

toString() - Method in class org.sbml.jsbml.ext.layout.LineSegment

toString() - Method in class org.sbml.jsbml.ext.layout.Point

toString() - Method in class org.sbml.jsbml.ext.layout.TextGlyph

toString() - Method in class org.sbml.jsbml.ext.multi.DenotedSpeciesTypeComponentIndex

toString() - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

toString() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

toString() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

toString() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

toString() - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite

toString() - Method in class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue

toString() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

toString() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

toString() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

toString() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureValue

toString() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

toString() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

toString() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

toString() - Method in class org.sbml.jsbml.ext.qual.FunctionTerm

toString() - Method in class org.sbml.jsbml.ext.qual.Input

toString() - Method in class org.sbml.jsbml.ext.qual.Output

toString() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

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

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

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

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

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

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

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

toString() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

toString() - Method in class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

toString() - Method in class org.sbml.jsbml.ext.spatial.AdjacentDomains

toString() - Method in class org.sbml.jsbml.ext.spatial.AnalyticVolume

toString() - Method in class org.sbml.jsbml.ext.spatial.Boundary

toString() - Method in class org.sbml.jsbml.ext.spatial.CompartmentMapping

toString() - Method in class org.sbml.jsbml.ext.spatial.CoordinateComponent

toString() - Method in class org.sbml.jsbml.ext.spatial.CSGeometry

toString() - Method in class org.sbml.jsbml.ext.spatial.CSGHomogeneousTransformation

toString() - Method in class org.sbml.jsbml.ext.spatial.CSGObject

toString() - Method in class org.sbml.jsbml.ext.spatial.CSGPrimitive

toString() - Method in class org.sbml.jsbml.ext.spatial.CSGPseudoPrimitive

toString() - Method in class org.sbml.jsbml.ext.spatial.CSGRotation

toString() - Method in class org.sbml.jsbml.ext.spatial.CSGScale

toString() - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator

toString() - Method in class org.sbml.jsbml.ext.spatial.CSGTranslation

toString() - Method in class org.sbml.jsbml.ext.spatial.Domain

toString() - Method in class org.sbml.jsbml.ext.spatial.DomainType

toString() - Method in class org.sbml.jsbml.ext.spatial.Geometry

toString() - Method in class org.sbml.jsbml.ext.spatial.GeometryDefinition

toString() - Method in class org.sbml.jsbml.ext.spatial.InteriorPoint

toString() - Method in class org.sbml.jsbml.ext.spatial.OrdinalMapping

toString() - Method in class org.sbml.jsbml.ext.spatial.ParameterType

toString() - Method in class org.sbml.jsbml.ext.spatial.ParametricObject

toString() - Method in class org.sbml.jsbml.ext.spatial.PolygonObject

Deprecated.

toString() - Method in class org.sbml.jsbml.ext.spatial.SampledField

toString() - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry

toString() - Method in class org.sbml.jsbml.ext.spatial.SampledVolume

toString() - Method in class org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin

toString() - Method in class org.sbml.jsbml.ext.spatial.SpatialModelPlugin

toString() - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints

toString() - Method in class org.sbml.jsbml.ext.spatial.SpatialReactionPlugin

toString() - Method in class org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin

toString() - Method in class org.sbml.jsbml.ext.spatial.TransformationComponent

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.SimpleSpeciesReference

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

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

Returns the image.

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

Produces a text formula representation of this unit.

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

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

Allows for Locale-dependent number formatting.

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.XMLNode

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

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

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.

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

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

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

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

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

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

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

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

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

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.

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.

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.

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.

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.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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