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

A

add(String) - Method in class jigcell.sbml2.Annotations

add(String) - Method in class jigcell.sbml2.Notes

add_escapes(String) - Method in exception jigcell.sbml2.jep.ParseException

Used to convert raw characters to their escaped version when these raw version cannot be used as part of an ASCII string literal.

addAttribute(String, String) - Method in class jigcell.sbml2.XMLPrinter

addBaseUnit(String) - Static method in class jigcell.sbml2.Unit

addChild(Node) - Method in class jigcell.sbml2.math.Node

addChild(SBMLNode) - Method in class jigcell.sbml2.math.SBMLNode

addCompartment(Compartment) - Method in class jigcell.sbml2.Model

addCustomElement(XMLElement, String, String) - Method in class jigcell.sbml2.XMLPrinter

addElement(XMLElement) - Method in class jigcell.sbml2.XMLPrinter

addElementList(XMLElement, String, Collection) - Method in class jigcell.sbml2.XMLPrinter

addEscapes(String) - Static method in error jigcell.sbml2.jep.TokenMgrError

Replaces unprintable characters by their espaced (or unicode escaped) equivalents in the given string

addEvent(Event) - Method in class jigcell.sbml2.Model

addEventAssignment(EventAssignment) - Method in class jigcell.sbml2.Event

addFromObject(FromObjectReference) - Method in class jigcell.sbml2.Link

From object methods

addFunction(String, PostfixMathCommandI) - Method in class jigcell.sbml2.jep.JEP

Adds a new function to the parser.

addFunctionDefinition(FunctionDefinition) - Method in class jigcell.sbml2.Model

addInstance(Instance) - Method in class jigcell.sbml2.Model

AdditiveExpression() - Method in class jigcell.sbml2.jep.Parser

addLink(Link) - Method in class jigcell.sbml2.Model

addModel(Model) - Method in class jigcell.sbml2.Model

addModifier(Species) - Method in class jigcell.sbml2.Reaction

addModifier(ModifierSpeciesReference) - Method in class jigcell.sbml2.Reaction

addParameter(Parameter) - Method in class jigcell.sbml2.KineticLaw

addParameter(Parameter) - Method in class jigcell.sbml2.Model

addProduct(Species) - Method in class jigcell.sbml2.Reaction

addProduct(SpeciesReference) - Method in class jigcell.sbml2.Reaction

addReactant(Species) - Method in class jigcell.sbml2.Reaction

addReactant(SpeciesReference) - Method in class jigcell.sbml2.Reaction

addReaction(Reaction) - Method in class jigcell.sbml2.Model

addRule(Rule) - Method in class jigcell.sbml2.Model

addSpecies(Species) - Method in class jigcell.sbml2.Model

addSpeciesStoichiometry(Model, List, int, SpeciesReference, boolean) - Method in class jigcell.sbml2.ConservationRelationFinder

addStandardFunctions() - Method in class jigcell.sbml2.jep.JEP

Adds the standard functions to the parser.

addSymbol(String) - Method in class jigcell.sbml2.math.SymbolTable

Add id to the symbol table.

addSymbol(String, String) - Method in class jigcell.sbml2.math.SymbolTable

Add a symbol with name and id.

addText(String) - Method in class jigcell.sbml2.XMLPrinter

addToErrorList(String) - Method in class jigcell.sbml2.jep.EvaluatorVisitor

Adds an error message to the list of errors

addToErrorList(String) - Method in class jigcell.sbml2.jep.Parser

addToObject(ToObjectReference) - Method in class jigcell.sbml2.Link

To object methods

addUnit(Unit) - Method in class jigcell.sbml2.UnitDefinition

addUnitDefinition(UnitDefinition) - Method in class jigcell.sbml2.Model

adjustBeginLineColumn(int, int) - Method in class jigcell.sbml2.jep.JavaCharStream

Method to adjust line and column numbers for the start of a token.

AdjustBuffSize() - Method in class jigcell.sbml2.jep.JavaCharStream

AlgebraicModelTests - Class in jigcell.sbml2.tests

A collection of tests to exercise the reference model for algebraic rules.

AlgebraicModelTests(String) - Constructor for class jigcell.sbml2.tests.AlgebraicModelTests

Creates a new test for the reference model for algebraic rules.

AlgebraicModelTests2 - Class in jigcell.sbml2.tests

A collection of tests to exercise the reference model for algebraic rules.

AlgebraicModelTests2(String) - Constructor for class jigcell.sbml2.tests.AlgebraicModelTests2

Creates a new test for the reference model for algebraic rules.

AlgebraicRule - Class in jigcell.sbml2

A rule 0=f(W) where f is an arbitrary function and a suitable W must be found.

AlgebraicRule() - Constructor for class jigcell.sbml2.AlgebraicRule

AlgebraicRule(AlgebraicRule) - Constructor for class jigcell.sbml2.AlgebraicRule

Creates a copy of this existing object.

AND - Static variable in interface jigcell.sbml2.jep.ParserConstants

Annotations - Class in jigcell.sbml2

Stores the annotation metadata for an SBML node.

Annotations() - Constructor for class jigcell.sbml2.Annotations

annotations - Variable in class jigcell.sbml2.Annotations

annotations - Variable in class jigcell.sbml2.SBase

ANNOTATIONS - Static variable in class jigcell.sbml2.SBMLLevel2Reader

AnyConstant() - Method in class jigcell.sbml2.jep.Parser

appendToValue(String) - Method in class jigcell.sbml2.math.Node

arg - Variable in class jigcell.sbml2.jep.Parser.JJCalls

ArgumentList(int, String) - Method in class jigcell.sbml2.jep.Parser

argumentNum - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

AssignmentModelTests - Class in jigcell.sbml2.tests

A collection of tests to exercise the reference model for assignment rules.

AssignmentModelTests(String) - Constructor for class jigcell.sbml2.tests.AssignmentModelTests

Creates a new test for the reference model for assignment rules.

AssignmentModelTests2 - Class in jigcell.sbml2.tests

A collection of tests to exercise the reference model for assignment rules.

AssignmentModelTests2(String) - Constructor for class jigcell.sbml2.tests.AssignmentModelTests2

Creates a new test for the reference model for assignment rules.

AssignmentRule - Class in jigcell.sbml2

A rule x=f(W) where x is a variable and f is an arbitrary function not dependent on x.

AssignmentRule() - Constructor for class jigcell.sbml2.AssignmentRule

AssignmentRule(AssignmentRule) - Constructor for class jigcell.sbml2.AssignmentRule

Creates a copy of this existing object.

assignmentsElement - Variable in class jigcell.sbml2.Event

associative - Static variable in class jigcell.sbml2.math.InfixExpression

associative - Variable in class jigcell.sbml2.math.MathMLConvertor

ASTConstant - Class in jigcell.sbml2.jep

Constant Node

ASTConstant(int) - Constructor for class jigcell.sbml2.jep.ASTConstant

ASTConstant(Parser, int) - Constructor for class jigcell.sbml2.jep.ASTConstant

ASTElse - Class in jigcell.sbml2.jep

ASTElse(int) - Constructor for class jigcell.sbml2.jep.ASTElse

ASTElse(Parser, int) - Constructor for class jigcell.sbml2.jep.ASTElse

ASTElseIfThen - Class in jigcell.sbml2.jep

ASTElseIfThen(int) - Constructor for class jigcell.sbml2.jep.ASTElseIfThen

ASTElseIfThen(Parser, int) - Constructor for class jigcell.sbml2.jep.ASTElseIfThen

ASTFunNode - Class in jigcell.sbml2.jep

Function Node

ASTFunNode(int) - Constructor for class jigcell.sbml2.jep.ASTFunNode

Creates a new ASTFunNode

ASTFunNode(Parser, int) - Constructor for class jigcell.sbml2.jep.ASTFunNode

Creates a new ASTFunNode

ASTIfThen - Class in jigcell.sbml2.jep

ASTIfThen(int) - Constructor for class jigcell.sbml2.jep.ASTIfThen

ASTIfThen(Parser, int) - Constructor for class jigcell.sbml2.jep.ASTIfThen

ASTPiecewise - Class in jigcell.sbml2.jep

ASTPiecewise(int) - Constructor for class jigcell.sbml2.jep.ASTPiecewise

ASTPiecewise(Parser, int) - Constructor for class jigcell.sbml2.jep.ASTPiecewise

ASTStart - Class in jigcell.sbml2.jep

Start Node

ASTStart(int) - Constructor for class jigcell.sbml2.jep.ASTStart

ASTStart(Parser, int) - Constructor for class jigcell.sbml2.jep.ASTStart

ASTVarNode - Class in jigcell.sbml2.jep

Variable Node

ASTVarNode(int) - Constructor for class jigcell.sbml2.jep.ASTVarNode

ASTVarNode(Parser, int) - Constructor for class jigcell.sbml2.jep.ASTVarNode

attributes - Variable in class jigcell.sbml2.math.Node

attributes - Variable in class jigcell.sbml2.XMLPrinter

available - Variable in class jigcell.sbml2.jep.JavaCharStream

B

backup(int) - Method in class jigcell.sbml2.jep.JavaCharStream

baseUnits - Static variable in class jigcell.sbml2.Unit

beginColumn - Variable in class jigcell.sbml2.jep.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

beginLine - Variable in class jigcell.sbml2.jep.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

BeginToken() - Method in class jigcell.sbml2.jep.JavaCharStream

boundaryCondition - Variable in class jigcell.sbml2.Species

BoundaryModelTests - Class in jigcell.sbml2.tests

A collection of tests to exercise the reference model for boundary conditions.

BoundaryModelTests(String) - Constructor for class jigcell.sbml2.tests.BoundaryModelTests

Creates a new test for the reference model for boundary conditions.

BoundaryModelTests2 - Class in jigcell.sbml2.tests

A collection of tests to exercise the reference model for boundary conditions.

BoundaryModelTests2(String) - Constructor for class jigcell.sbml2.tests.BoundaryModelTests2

Creates a new test for the reference model for boundary conditions.

BranchModelTests - Class in jigcell.sbml2.tests

A collection of tests to exercise the reference model for branching models.

BranchModelTests(String) - Constructor for class jigcell.sbml2.tests.BranchModelTests

Creates a new test for the reference model for branching models.

BranchModelTests2 - Class in jigcell.sbml2.tests

A collection of tests to exercise the reference model for branching models.

BranchModelTests2(String) - Constructor for class jigcell.sbml2.tests.BranchModelTests2

Creates a new test for the reference model for branching models.

bufcolumn - Variable in class jigcell.sbml2.jep.JavaCharStream

buffer - Variable in class jigcell.sbml2.jep.JavaCharStream

bufline - Variable in class jigcell.sbml2.jep.JavaCharStream

bufpos - Variable in class jigcell.sbml2.jep.JavaCharStream

bufsize - Variable in class jigcell.sbml2.jep.JavaCharStream

BVARMODE - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

C

characters(char[], int, int) - Method in class jigcell.sbml2.math.MathMLConvertorSAX

characters(char[], int, int) - Method in class jigcell.sbml2.math.MathMLExpression.MathMLHandler

characters(char[], int, int) - Method in class jigcell.sbml2.XMLReader

charge - Variable in class jigcell.sbml2.Species

checkNoteFormat - Static variable in class jigcell.sbml2.Notes

checkStack(Stack) - Method in class jigcell.sbml2.jep.function.PostfixMathCommand

Check whether the stack is not null, throw an Exception if it is.

children - Variable in class jigcell.sbml2.jep.SimpleNode

children - Variable in class jigcell.sbml2.math.Node

children - Variable in class jigcell.sbml2.math.SBMLNode

childrenAccept(ParserVisitor, Object) - Method in class jigcell.sbml2.jep.SimpleNode

Accept the visitor.

childrenAcceptReverse(ParserVisitor, Object) - Method in class jigcell.sbml2.jep.SimpleNode

Accept the visitor in Reverse.

CIMODE - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

clear() - Method in class jigcell.sbml2.Annotations

clear() - Method in class jigcell.sbml2.Notes

clearNodeScope(Node) - Method in class jigcell.sbml2.jep.JJTParserState

closeNodeScope(Node, int) - Method in class jigcell.sbml2.jep.JJTParserState

closeNodeScope(Node, boolean) - Method in class jigcell.sbml2.jep.JJTParserState

CNMODE - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

column - Variable in class jigcell.sbml2.jep.JavaCharStream

Compartment - Class in jigcell.sbml2

A bounded space in which species are located.

Compartment() - Constructor for class jigcell.sbml2.Compartment

Compartment(Compartment) - Constructor for class jigcell.sbml2.Compartment

Creates a copy of this existing object.

Compartment(String, String) - Constructor for class jigcell.sbml2.Compartment

COMPARTMENT - Static variable in class jigcell.sbml2.Model

compartment - Variable in class jigcell.sbml2.Species

CompartmentModelTests - Class in jigcell.sbml2.tests

A collection of tests to exercise the reference model for compartments.

CompartmentModelTests(String) - Constructor for class jigcell.sbml2.tests.CompartmentModelTests

Creates a new test for the reference model for compartments.

CompartmentModelTests2 - Class in jigcell.sbml2.tests

A collection of tests to exercise the reference model for compartments.

CompartmentModelTests2(String) - Constructor for class jigcell.sbml2.tests.CompartmentModelTests2

Creates a new test for the reference model for compartments.

compartments - Variable in class jigcell.sbml2.Model

compartmentsElement - Variable in class jigcell.sbml2.Model

Condition() - Method in class jigcell.sbml2.jep.Parser

ConnectiveCondition() - Method in class jigcell.sbml2.jep.Parser

conservationRelation - Variable in class jigcell.sbml2.ConservationRelationFinder.ConservationRelation

conservationRelationCount - Variable in class jigcell.sbml2.ConservationRelationFinder

ConservationRelationFinder - Class in jigcell.sbml2

Detects, enumerates, and validates the conservation relations in a model.

ConservationRelationFinder(Model) - Constructor for class jigcell.sbml2.ConservationRelationFinder

Computes the conservation relations for a model.

ConservationRelationFinder.ConservationRelation - Class in jigcell.sbml2

Represents a single conservation relation.

ConservationRelationFinder.ConservationRelation(Map, String) - Constructor for class jigcell.sbml2.ConservationRelationFinder.ConservationRelation

Creates a new conservation relation.

constant - Variable in class jigcell.sbml2.Compartment

constant - Variable in class jigcell.sbml2.Parameter

constant - Variable in class jigcell.sbml2.Species

countDependentRows(double[][], int, int) - Static method in class jigcell.sbml2.ConservationRelationFinder

createAttributesText(Attributes, Map) - Static method in class jigcell.sbml2.XMLReader

createNumber(double) - Method in class jigcell.sbml2.jep.type.DoubleNumberFactory

Creates a Double object initialized to the value of the parameter.

createNumber(double) - Method in interface jigcell.sbml2.jep.type.NumberFactory

Creates a number object and initializes its value.

CSYMBOLMODE - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

curChar - Variable in class jigcell.sbml2.jep.ParserTokenManager

curLexState - Variable in class jigcell.sbml2.jep.ParserTokenManager

curNumberOfParameters - Variable in class jigcell.sbml2.jep.function.PostfixMathCommand

Number of parameters to be used for the next run() invocation.

current - Variable in class jigcell.sbml2.math.MathMLExpression.MathMLHandler

currentNode - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

currentToken - Variable in exception jigcell.sbml2.jep.ParseException

This is the last token that has been consumed successfully.

cycle - Variable in class jigcell.sbml2.tests.SBMLModelTests

D

debug - Static variable in class jigcell.sbml2.jep.EvaluatorVisitor

Debug flag

debug - Static variable in class jigcell.sbml2.jep.JEP

Debug flag for extra command line output

debugStream - Variable in class jigcell.sbml2.jep.ParserTokenManager

DECIMAL_LITERAL - Static variable in interface jigcell.sbml2.jep.ParserConstants

DEFAULT - Static variable in interface jigcell.sbml2.jep.ParserConstants

defaultLexState - Variable in class jigcell.sbml2.jep.ParserTokenManager

delay - Variable in class jigcell.sbml2.Event

delayElement - Variable in class jigcell.sbml2.Event

DELAYMODE - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

DelayModelTests - Class in jigcell.sbml2.tests

A collection of tests to exercise the reference model for delay equations.

DelayModelTests(String) - Constructor for class jigcell.sbml2.tests.DelayModelTests

Creates a new test for the reference model for delay equations.

DelayModelTests2 - Class in jigcell.sbml2.tests

A collection of tests to exercise the reference model for delay equations.

DelayModelTests2(String) - Constructor for class jigcell.sbml2.tests.DelayModelTests2

Creates a new test for the reference model for delay equations.

dependentSpeciesId - Variable in class jigcell.sbml2.ConservationRelationFinder.ConservationRelation

DIGIT - Static variable in interface jigcell.sbml2.jep.ParserConstants

disable_tracing() - Method in class jigcell.sbml2.jep.Parser

DIV - Static variable in interface jigcell.sbml2.jep.ParserConstants

document - Variable in class jigcell.sbml2.SBMLLevel2Reader

Done() - Method in class jigcell.sbml2.jep.JavaCharStream

DONT_LOOKUP_SYMBOLS - Static variable in class jigcell.sbml2.math.InfixExpression

doubleEquals(double, double) - Method in class jigcell.sbml2.tests.SBMLModelTests

DoubleNumberFactory - Class in jigcell.sbml2.jep.type

Default class for creating number objects.

DoubleNumberFactory() - Constructor for class jigcell.sbml2.jep.type.DoubleNumberFactory

dump(String) - Method in class jigcell.sbml2.jep.SimpleNode

dumpSymbolTable(PrintWriter) - Method in class jigcell.sbml2.math.SymbolTable

Write the symbol table to out.

dumpSymbolTable() - Method in class jigcell.sbml2.math.SymbolTable

E

element - Variable in class jigcell.sbml2.math.SBMLNode

elementNameToClass - Static variable in class jigcell.sbml2.SBMLLevel2Reader

elements - Variable in class jigcell.sbml2.XMLPrinter

ELSE - Static variable in interface jigcell.sbml2.jep.ParserConstants

ELSEIF - Static variable in interface jigcell.sbml2.jep.ParserConstants

emptySymbolTable() - Method in class jigcell.sbml2.math.SymbolTable

enable_tracing() - Method in class jigcell.sbml2.jep.Parser

endColumn - Variable in class jigcell.sbml2.jep.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

endDocument() - Method in class jigcell.sbml2.math.MathMLConvertorSAX

endDocument() - Method in class jigcell.sbml2.math.MathMLExpression.MathMLHandler

endElement(String, String, String) - Method in class jigcell.sbml2.math.MathMLConvertorSAX

endElement(String, String, String) - Method in class jigcell.sbml2.math.MathMLExpression.MathMLHandler

endElement(String, String, String) - Method in class jigcell.sbml2.SBMLLevel2Reader

endLine - Variable in class jigcell.sbml2.jep.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

endLocalTextElement() - Method in class jigcell.sbml2.XMLReader

endSBMLElement(String) - Method in class jigcell.sbml2.SBMLLevel2Reader

ENOTATION - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

ENOTATIONSEP - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

EOF - Static variable in interface jigcell.sbml2.jep.ParserConstants

eol - Variable in exception jigcell.sbml2.jep.ParseException

The end of line string for this machine.

EQ - Static variable in interface jigcell.sbml2.jep.ParserConstants

equals(Object) - Method in class jigcell.sbml2.Unit

error(SAXParseException) - Method in class jigcell.sbml2.math.MathMLConvertorSAX.MyErrorHandler

errorCode - Variable in error jigcell.sbml2.jep.TokenMgrError

Indicates the reason why the exception is thrown.

errorFlag - Variable in class jigcell.sbml2.jep.EvaluatorVisitor

Flag for errors during evaluation

errorList - Variable in class jigcell.sbml2.jep.EvaluatorVisitor

The current error list

errorList - Variable in class jigcell.sbml2.jep.JEP

Error List

errorStream - Variable in class jigcell.sbml2.XMLReader

ESC - Static variable in interface jigcell.sbml2.jep.ParserConstants

ESCAP - Static variable in interface jigcell.sbml2.jep.ParserConstants

ev - Variable in class jigcell.sbml2.jep.JEP

Evaluator

EvaluatorVisitor - Class in jigcell.sbml2.jep

This class is used for the evaluation of an expression.

EvaluatorVisitor() - Constructor for class jigcell.sbml2.jep.EvaluatorVisitor

Constructor.

Event - Class in jigcell.sbml2

Instantaneous discontinuous state changes to the model that are applied when a criterion is met.

Event() - Constructor for class jigcell.sbml2.Event

Event(Event) - Constructor for class jigcell.sbml2.Event

Creates a copy of this existing object.

Event(String, String) - Constructor for class jigcell.sbml2.Event

EVENT - Static variable in class jigcell.sbml2.Model

eventAssignment - Variable in class jigcell.sbml2.Event

EventAssignment - Class in jigcell.sbml2

A variable assignment that takes place when an event is executed.

EventAssignment() - Constructor for class jigcell.sbml2.EventAssignment

EventAssignment(EventAssignment) - Constructor for class jigcell.sbml2.EventAssignment

Creates a copy of this existing object.

EventModelTests - Class in jigcell.sbml2.tests

A collection of tests to exercise the reference model for events.

EventModelTests(String) - Constructor for class jigcell.sbml2.tests.EventModelTests

Creates a new test for the reference model for events.

EventModelTests2 - Class in jigcell.sbml2.tests

A collection of tests to exercise the reference model for events.

EventModelTests2(String) - Constructor for class jigcell.sbml2.tests.EventModelTests2

Creates a new test for the reference model for events.

events - Variable in class jigcell.sbml2.Model

eventsElement - Variable in class jigcell.sbml2.Model

ExpandBuff(boolean) - Method in class jigcell.sbml2.jep.JavaCharStream

expectedTokenSequences - Variable in exception jigcell.sbml2.jep.ParseException

Each entry in this array is an array of integers.

EXPONENT - Static variable in interface jigcell.sbml2.jep.ParserConstants

exponent - Variable in class jigcell.sbml2.Unit

Expression() - Method in class jigcell.sbml2.jep.Parser

expression - Variable in class jigcell.sbml2.math.InfixExpression

F

FALSE - Static variable in interface jigcell.sbml2.jep.ParserConstants

fast - Variable in class jigcell.sbml2.Reaction

fatalError(SAXParseException) - Method in class jigcell.sbml2.math.MathMLConvertorSAX.MyErrorHandler

FillBuff() - Method in class jigcell.sbml2.jep.JavaCharStream

fillStoichiometryMatrix(Model, List, List, int, int, int) - Method in class jigcell.sbml2.ConservationRelationFinder

findAFortranName(String) - Method in class jigcell.sbml2.math.SymbolTable

Takes a valid Fortran identifier name or string and finds a similar identifier name that is not already used in fortranNameCol.

findBaseUnit(String) - Static method in class jigcell.sbml2.Unit

findElementWithId(String, int) - Method in class jigcell.sbml2.Model

Searches the model for an sbml element with the given id.

findElementWithName(String, int) - Method in class jigcell.sbml2.Model

findParameterWithId(String) - Method in class jigcell.sbml2.KineticLaw

first - Variable in class jigcell.sbml2.jep.Parser.JJCalls

firstPiece - Static variable in class jigcell.sbml2.math.MathMLConvertor

FLOATING_POINT_LITERAL - Static variable in interface jigcell.sbml2.jep.ParserConstants

forbiddenSymbols - Static variable in class jigcell.sbml2.math.SymbolTable

FORTRAN_CHARACTER_STRING - Static variable in class jigcell.sbml2.math.SymbolTable.Mode

The mode for Fortran character strings.

FORTRAN_IDENTIFIER - Static variable in class jigcell.sbml2.math.SymbolTable.Mode

fortranNameCol - Variable in class jigcell.sbml2.math.SymbolTable

fortranNameColRev - Variable in class jigcell.sbml2.math.SymbolTable

fromObjectElement - Variable in class jigcell.sbml2.Link

FromObjectReference - Class in jigcell.sbml2

A reference to a object contained in the model.

FromObjectReference() - Constructor for class jigcell.sbml2.FromObjectReference

FromObjectReference(FromObjectReference) - Constructor for class jigcell.sbml2.FromObjectReference

Creates a copy of this existing object.

FromObjectReference(SimpleObjectReference) - Constructor for class jigcell.sbml2.FromObjectReference

FromObjectReference(String) - Constructor for class jigcell.sbml2.FromObjectReference

fromObjectReference - Variable in class jigcell.sbml2.Link

Function() - Method in class jigcell.sbml2.jep.Parser

functionArgs - Variable in class jigcell.sbml2.math.MathMLExpression

FunctionDefinition - Class in jigcell.sbml2

Associates an identifier with a function definition.

FunctionDefinition() - Constructor for class jigcell.sbml2.FunctionDefinition

FunctionDefinition(FunctionDefinition) - Constructor for class jigcell.sbml2.FunctionDefinition

Creates a copy of this existing object.

FunctionDefinition(String, String) - Constructor for class jigcell.sbml2.FunctionDefinition

FUNCTIONDEFINITION - Static variable in class jigcell.sbml2.Model

functionDefinitions - Variable in class jigcell.sbml2.Model

functionDefinitionsElement - Variable in class jigcell.sbml2.Model

FunctionModelTests - Class in jigcell.sbml2.tests

A collection of tests to exercise the reference model for function definitions.

FunctionModelTests(String) - Constructor for class jigcell.sbml2.tests.FunctionModelTests

Creates a new test for the reference model for function definitions.

FunctionModelTests2 - Class in jigcell.sbml2.tests

A collection of tests to exercise the reference model for function definitions.

FunctionModelTests2(String) - Constructor for class jigcell.sbml2.tests.FunctionModelTests2

Creates a new test for the reference model for function definitions.

functions - Static variable in class jigcell.sbml2.math.MathMLConvertorSAX

FunctionTable - Class in jigcell.sbml2.jep

FunctionTable() - Constructor for class jigcell.sbml2.jep.FunctionTable

funTab - Variable in class jigcell.sbml2.jep.JEP

Function Table

G

GE - Static variable in interface jigcell.sbml2.jep.ParserConstants

gen - Variable in class jigcell.sbml2.jep.Parser.JJCalls

generate1(int) - Static method in class jigcell.sbml2.tests.ModelGenerator

Generates a model with equal numbers of species and reactions.

generate2(int) - Static method in class jigcell.sbml2.tests.ModelGenerator

Generates a model with many more species than reactions.

generate3(int) - Static method in class jigcell.sbml2.tests.ModelGenerator

Generates a model with many more reactions than species.

generateMathML(Node) - Method in class jigcell.sbml2.math.MathMLExpression

generateParseException() - Method in class jigcell.sbml2.jep.Parser

genExpression(Node) - Method in class jigcell.sbml2.math.InfixExpression

Convert a parse tree into Fortran 90 code.

genSimpleTree(Node) - Method in class jigcell.sbml2.math.MathMLExpression

Create a simple mathematical parse tree (roughly a binary tree).

get(int) - Method in class jigcell.sbml2.Annotations

get(int) - Method in class jigcell.sbml2.Notes

getAnnotations() - Method in class jigcell.sbml2.SBase

getAssignmentsElement() - Method in class jigcell.sbml2.Event

getAttributes() - Method in class jigcell.sbml2.math.Node

getBaseUnits() - Static method in class jigcell.sbml2.Unit

Set[Unit] of the SBML base units.

getBeginColumn() - Method in class jigcell.sbml2.jep.JavaCharStream

getBeginLine() - Method in class jigcell.sbml2.jep.JavaCharStream

getCharge() - Method in class jigcell.sbml2.Species

getChild(int) - Method in class jigcell.sbml2.math.Node

getChildren() - Method in class jigcell.sbml2.math.Node

getColumn() - Method in class jigcell.sbml2.jep.JavaCharStream

Deprecated.

getColumn() - Method in exception jigcell.sbml2.jep.ParseException

Returns the column number of the token in which the error occured

getCompartment() - Method in class jigcell.sbml2.Species

getCompartment(Model) - Method in class jigcell.sbml2.Species

getCompartments() - Method in class jigcell.sbml2.Model

getCompartmentsElement() - Method in class jigcell.sbml2.Model

getConservationRelation() - Method in class jigcell.sbml2.ConservationRelationFinder.ConservationRelation

getConservationRelations() - Method in class jigcell.sbml2.ConservationRelationFinder

Computes the List[ConservationRelation] of conservation relations in the model.

getDefaultUnits() - Method in class jigcell.sbml2.Compartment

getDelay() - Method in class jigcell.sbml2.Event

getDelayElement() - Method in class jigcell.sbml2.Event

getDependentSpeciesId() - Method in class jigcell.sbml2.ConservationRelationFinder.ConservationRelation

getElement() - Method in class jigcell.sbml2.math.SBMLNode

Getter for property element.

getEndColumn() - Method in class jigcell.sbml2.jep.JavaCharStream

getEndLine() - Method in class jigcell.sbml2.jep.JavaCharStream

getErrorInfo() - Method in class jigcell.sbml2.jep.JEP

Reports information on the errors that occured during the most recent action.

getErrorInfo() - Method in exception jigcell.sbml2.jep.ParseException

getErrorInfo() was added to the parser generated code to provide clean output instead of the standard format of Exception.toString().

getEventAssignment() - Method in class jigcell.sbml2.Event

getEvents() - Method in class jigcell.sbml2.Model

getEventsElement() - Method in class jigcell.sbml2.Model

getExponent() - Method in class jigcell.sbml2.Unit

getExpression() - Method in class jigcell.sbml2.math.InfixExpression

getExpression(String, int) - Method in class jigcell.sbml2.math.InfixExpression

getExpression(String, int, String) - Method in class jigcell.sbml2.math.InfixExpression

getExpression() - Method in class jigcell.sbml2.math.MathMLExpression

Converts the MathML parse tree into a traditional math parse tree and returns the result.

getFromObjectElement() - Method in class jigcell.sbml2.Link

getFromObjectReference() - Method in class jigcell.sbml2.Link

getFunctionArguments() - Method in class jigcell.sbml2.math.MathMLExpression

Return an array of strings of the function arguments.

getFunctionDefinitions() - Method in class jigcell.sbml2.Model

getFunctionDefinitionsElement() - Method in class jigcell.sbml2.Model

getFunctions() - Method in class jigcell.sbml2.math.MathMLConvertorSAX

getHasOnlySubstanceUnits() - Method in class jigcell.sbml2.Species

getHref() - Method in class jigcell.sbml2.Instance

getId() - Method in class jigcell.sbml2.jep.SimpleNode

Returns the id of the node (for simpler identification).

getId() - Method in class jigcell.sbml2.SBaseId

getIdentifiers(Node) - Static method in class jigcell.sbml2.math.MathMLExpression

Gets all identifiers in the parse tree cur and returns them.

getIdentifiers_(Node) - Static method in class jigcell.sbml2.math.MathMLExpression

GetImage() - Method in class jigcell.sbml2.jep.JavaCharStream

getInitialAmount() - Method in class jigcell.sbml2.Species

getInitialConcentration() - Method in class jigcell.sbml2.Species

getInstances() - Method in class jigcell.sbml2.Model

getInstancesElement() - Method in class jigcell.sbml2.Model

getKind() - Method in class jigcell.sbml2.Unit

getKindName() - Method in class jigcell.sbml2.Unit

getKineticLaw() - Method in class jigcell.sbml2.Reaction

getLevel() - Method in class jigcell.sbml2.SBMLLevel2Document

getLine() - Method in class jigcell.sbml2.jep.JavaCharStream

Deprecated.

getLine() - Method in exception jigcell.sbml2.jep.ParseException

Returns the line number of the token in which the error occured

getLinks() - Method in class jigcell.sbml2.Model

getLinksElement() - Method in class jigcell.sbml2.Model

getListOfChildren() - Method in class jigcell.sbml2.math.Node

getLocalName() - Method in class jigcell.sbml2.math.Node

getMath() - Method in class jigcell.sbml2.EventAssignment

getMath() - Method in class jigcell.sbml2.FunctionDefinition

getMath() - Method in class jigcell.sbml2.KineticLaw

getMath() - Method in interface jigcell.sbml2.MathElement

getMath() - Method in class jigcell.sbml2.Rule

getMath() - Method in class jigcell.sbml2.StoichiometryMath

getMathMLParseTree() - Method in class jigcell.sbml2.math.MathMLExpression

getMessage() - Method in exception jigcell.sbml2.jep.ParseException

This method has the standard behavior when this object has been created using the standard constructors.

getMessage() - Method in error jigcell.sbml2.jep.TokenMgrError

You can also modify the body of this method to customize your error messages.

getMetaid() - Method in class jigcell.sbml2.SBase

getModel() - Method in class jigcell.sbml2.SBMLLevel2Document

getModels() - Method in class jigcell.sbml2.Model

getModelsElement() - Method in class jigcell.sbml2.Model

getModifier() - Method in class jigcell.sbml2.Reaction

getModifiersElement() - Method in class jigcell.sbml2.Reaction

getMultiplier() - Method in class jigcell.sbml2.Unit

getName() - Method in class jigcell.sbml2.jep.ASTFunNode

Returns the name of the node (operator symbol or function name).

getName() - Method in class jigcell.sbml2.jep.ASTVarNode

Returns the name of the variable.

getName() - Method in class jigcell.sbml2.SBaseId

getNextToken() - Method in class jigcell.sbml2.jep.Parser

getNextToken() - Method in class jigcell.sbml2.jep.ParserTokenManager

getNotes - Static variable in class jigcell.sbml2.Notes

getNotes() - Method in class jigcell.sbml2.SBase

getNumberFactory() - Method in class jigcell.sbml2.jep.JEP

Returns the number factory.

getNumberOfParameters() - Method in class jigcell.sbml2.jep.function.PostfixMathCommand

Return the required number of parameters.

getNumberOfParameters() - Method in interface jigcell.sbml2.jep.function.PostfixMathCommandI

Returns the number of required parameters, or -1 if any number of parameters is allowed.

getNumChildren() - Method in class jigcell.sbml2.math.Node

getObject() - Method in class jigcell.sbml2.SimpleObjectReference

getOffset() - Method in class jigcell.sbml2.Unit

getOrder(Node) - Method in class jigcell.sbml2.math.InfixExpression

getOutside() - Method in class jigcell.sbml2.Compartment

getOutside(Model) - Method in class jigcell.sbml2.Compartment

getParameter() - Method in class jigcell.sbml2.KineticLaw

getParameterElement() - Method in class jigcell.sbml2.KineticLaw

getParameters() - Method in class jigcell.sbml2.Model

getParametersElement() - Method in class jigcell.sbml2.Model

getParent() - Method in class jigcell.sbml2.math.Node

getParent() - Method in class jigcell.sbml2.math.SBMLNode

getParseExceptionInfo(SAXParseException) - Method in class jigcell.sbml2.math.MathMLConvertorSAX.MyErrorHandler

Returns a string describing parse exception details

getPFMC() - Method in class jigcell.sbml2.jep.ASTFunNode

Returns the math command class associated with this node.

getProduct() - Method in class jigcell.sbml2.Reaction

getProductsElement() - Method in class jigcell.sbml2.Reaction

getQName() - Method in class jigcell.sbml2.math.Node

getRDF() - Method in class jigcell.sbml2.SBase

getReactant() - Method in class jigcell.sbml2.Reaction

getReactantsElement() - Method in class jigcell.sbml2.Reaction

getReactions() - Method in class jigcell.sbml2.Model

getReactionsElement() - Method in class jigcell.sbml2.Model

getRoot() - Method in class jigcell.sbml2.math.MathMLConvertorSAX

Getter for property root.

getRules() - Method in class jigcell.sbml2.Model

getRulesElement() - Method in class jigcell.sbml2.Model

getSBMLString(String) - Method in class jigcell.sbml2.jep.JEP

getSBMLString() - Method in class jigcell.sbml2.jep.ParserDumpVisitor

getScale() - Method in class jigcell.sbml2.Unit

getSimpleName() - Method in class jigcell.sbml2.math.Node

getSize() - Method in class jigcell.sbml2.Compartment

getSpatialDimensions() - Method in class jigcell.sbml2.Compartment

getSpatialSizeUnits() - Method in class jigcell.sbml2.Species

getSpatialSizeUnits(Model) - Method in class jigcell.sbml2.Species

getSpecies() - Method in class jigcell.sbml2.Model

getSpecies() - Method in class jigcell.sbml2.SimpleSpeciesReference

getSpecies(Model) - Method in class jigcell.sbml2.SimpleSpeciesReference

getSpeciesElement() - Method in class jigcell.sbml2.Model

getStoichiometry() - Method in class jigcell.sbml2.SpeciesReference

getStoichiometryMath() - Method in class jigcell.sbml2.SpeciesReference

getSubObjectElement() - Method in class jigcell.sbml2.FromObjectReference

getSubObjectElement() - Method in class jigcell.sbml2.ToObjectReference

getSubObjectReference() - Method in class jigcell.sbml2.FromObjectReference

getSubObjectReference() - Method in class jigcell.sbml2.ToObjectReference

getSubstanceUnits() - Method in class jigcell.sbml2.KineticLaw

getSubstanceUnits(Model) - Method in class jigcell.sbml2.KineticLaw

getSubstanceUnits() - Method in class jigcell.sbml2.Species

getSubstanceUnits(Model) - Method in class jigcell.sbml2.Species

GetSuffix(int) - Method in class jigcell.sbml2.jep.JavaCharStream

getSymbolToIdMap() - Method in class jigcell.sbml2.math.SymbolTable

getTimeUnits() - Method in class jigcell.sbml2.Event

getTimeUnits(Model) - Method in class jigcell.sbml2.Event

getTimeUnits() - Method in class jigcell.sbml2.KineticLaw

getTimeUnits(Model) - Method in class jigcell.sbml2.KineticLaw

getToken(int) - Method in class jigcell.sbml2.jep.Parser

getToObjectElement() - Method in class jigcell.sbml2.Link

getToObjectReference() - Method in class jigcell.sbml2.Link

getTopNode() - Method in class jigcell.sbml2.jep.JEP

Returns the top node of the expression tree.

getTrigger() - Method in class jigcell.sbml2.Event

getTriggerElement() - Method in class jigcell.sbml2.Event

getType() - Method in class jigcell.sbml2.Instance

getUnitDefinitions() - Method in class jigcell.sbml2.Model

getUnitDefinitionsElement() - Method in class jigcell.sbml2.Model

getUnits() - Method in class jigcell.sbml2.Compartment

getUnits(Model) - Method in class jigcell.sbml2.Compartment

getUnits() - Method in class jigcell.sbml2.Parameter

getUnits(Model) - Method in class jigcell.sbml2.Parameter

getUnits() - Method in class jigcell.sbml2.UnitDefinition

List[Unit] of units combined in this definition.

getUnitsElement() - Method in class jigcell.sbml2.UnitDefinition

getUri() - Method in class jigcell.sbml2.math.Node

getValue() - Method in class jigcell.sbml2.jep.ASTConstant

getValue(Node, Vector) - Method in class jigcell.sbml2.jep.EvaluatorVisitor

Returns the value of the expression as an object.

getValue() - Method in class jigcell.sbml2.math.Node

getValue() - Method in class jigcell.sbml2.Parameter

getVariable() - Method in class jigcell.sbml2.EventAssignment

getVariable(Model) - Method in class jigcell.sbml2.EventAssignment

getVariable() - Method in class jigcell.sbml2.VariableRule

getVariable(Model) - Method in class jigcell.sbml2.VariableRule

getVariables() - Method in class jigcell.sbml2.jep.JEP

getVariablesInExpression(String) - Method in class jigcell.sbml2.jep.JEP

Gets the variables in the given equation.

getVersion() - Method in class jigcell.sbml2.SBMLLevel2Document

GLOBAL - Static variable in class jigcell.sbml2.Model

GT - Static variable in interface jigcell.sbml2.jep.ParserConstants

H

hasError() - Method in class jigcell.sbml2.jep.JEP

Returns true if an error occured during the most recent action (parsing or evaluation).

hashCode() - Method in class jigcell.sbml2.Unit

hashTable - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

hasLocalParameters() - Method in class jigcell.sbml2.Model

hasOnlySubstanceUnits - Variable in class jigcell.sbml2.Species

hexval(char) - Static method in class jigcell.sbml2.jep.JavaCharStream

href - Variable in class jigcell.sbml2.Instance

I

id - Variable in class jigcell.sbml2.jep.SimpleNode

id - Variable in class jigcell.sbml2.SBaseId

ID_END - Static variable in class jigcell.sbml2.math.SymbolTable

ID_START - Static variable in class jigcell.sbml2.math.SymbolTable

ID_WIDTH - Static variable in class jigcell.sbml2.math.SymbolTable

idCol - Variable in class jigcell.sbml2.math.SymbolTable

Identifier() - Method in class jigcell.sbml2.jep.Parser

IDENTIFIER - Static variable in interface jigcell.sbml2.jep.ParserConstants

IDENTITY - Static variable in class jigcell.sbml2.math.SymbolTable.Mode

idNameMap - Variable in class jigcell.sbml2.math.SymbolTable

IF - Static variable in interface jigcell.sbml2.jep.ParserConstants

illegalSpecies - Variable in class jigcell.sbml2.ConservationRelationFinder

image - Variable in class jigcell.sbml2.jep.ParserTokenManager

image - Variable in class jigcell.sbml2.jep.Token

The string image of the token.

implicitMul - Variable in class jigcell.sbml2.jep.JEP

Implicit multiplication option

inBuf - Variable in class jigcell.sbml2.jep.JavaCharStream

indent - Variable in class jigcell.sbml2.jep.ParserDumpVisitor

indent - Variable in class jigcell.sbml2.XMLPrinter

indentString() - Method in class jigcell.sbml2.jep.ParserDumpVisitor

InfixExpression - Class in jigcell.sbml2.math

This code is licensed under the DARPA BioCOMP Open Source License.

InfixExpression(SymbolTable, SymbolTable, Node, int) - Constructor for class jigcell.sbml2.math.InfixExpression

InfixExpression(SymbolTable, SymbolTable, Node) - Constructor for class jigcell.sbml2.math.InfixExpression

InfixExpression(SymbolTable, SymbolTable, MathMLExpression) - Constructor for class jigcell.sbml2.math.InfixExpression

InfixExpression(SymbolTable, MathMLExpression) - Constructor for class jigcell.sbml2.math.InfixExpression

InfixExpression(SymbolTable, Node) - Constructor for class jigcell.sbml2.math.InfixExpression

InfixExpression(MathMLExpression) - Constructor for class jigcell.sbml2.math.InfixExpression

InfixExpression(Node) - Constructor for class jigcell.sbml2.math.InfixExpression

InfixExpression(Node, int) - Constructor for class jigcell.sbml2.math.InfixExpression

initFunTab() - Method in class jigcell.sbml2.jep.JEP

Creates a new FunctionTable object as funTab.

initialAmount - Variable in class jigcell.sbml2.Species

initialConcentration - Variable in class jigcell.sbml2.Species

initMaps() - Static method in class jigcell.sbml2.math.InfixExpression

input_stream - Variable in class jigcell.sbml2.jep.ParserTokenManager

inputStream - Variable in class jigcell.sbml2.jep.JavaCharStream

insertFunction(String) - Static method in class jigcell.sbml2.math.MathMLConvertor

insertFunction(String) - Method in class jigcell.sbml2.math.MathMLConvertorSAX

Instance - Class in jigcell.sbml2

Instances indicate that a copy of a model is being instantiated within the current model.

Instance() - Constructor for class jigcell.sbml2.Instance

Instance(Instance) - Constructor for class jigcell.sbml2.Instance

Creates a copy of this existing object.

Instance(Model) - Constructor for class jigcell.sbml2.Instance

Instance(String, String) - Constructor for class jigcell.sbml2.Instance

INSTANCE - Static variable in class jigcell.sbml2.Model

instances - Variable in class jigcell.sbml2.Model

instancesElement - Variable in class jigcell.sbml2.Model

INTEGER - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

INTEGER_LITERAL - Static variable in interface jigcell.sbml2.jep.ParserConstants

INTEGERSEP - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

INVALID_LEXICAL_STATE - Static variable in error jigcell.sbml2.jep.TokenMgrError

Tried to change to an invalid lexical state.

isBaseUnit() - Method in class jigcell.sbml2.Unit

isBoundaryCondition() - Method in class jigcell.sbml2.Species

isChargeSet() - Method in class jigcell.sbml2.Species

isConstant() - Method in class jigcell.sbml2.Compartment

isConstant() - Method in class jigcell.sbml2.Parameter

isConstant() - Method in class jigcell.sbml2.Species

isFast() - Method in class jigcell.sbml2.Reaction

isFastSet() - Method in class jigcell.sbml2.Reaction

isFunction(String) - Method in class jigcell.sbml2.jep.JEP

isLambda - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

isLambdaFunction() - Method in class jigcell.sbml2.math.MathMLExpression

isMathMLFunction(String) - Static method in class jigcell.sbml2.jep.JEP

isNameSet() - Method in class jigcell.sbml2.SBaseId

isRatelaw - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

isReversible() - Method in class jigcell.sbml2.Reaction

isSetByEvent(Model) - Method in class jigcell.sbml2.Species

isSetByRule(Model) - Method in class jigcell.sbml2.Species

isValid(Model) - Method in class jigcell.sbml2.Compartment

isValid(Model) - Method in class jigcell.sbml2.Event

isValid(Model) - Method in class jigcell.sbml2.EventAssignment

isValid(Model) - Method in class jigcell.sbml2.KineticLaw

isValid(Model) - Method in class jigcell.sbml2.Parameter

isValid(Model) - Method in class jigcell.sbml2.SBase

isValid(Model) - Method in class jigcell.sbml2.SBaseId

isValid(Model) - Method in class jigcell.sbml2.SBMLLevel2Document

isValid(Model) - Method in class jigcell.sbml2.SimpleObjectReference

isValid(Model) - Method in class jigcell.sbml2.SimpleSpeciesReference

isValid(Model) - Method in class jigcell.sbml2.Species

isValid(Model) - Method in class jigcell.sbml2.VariableRule

isValidAreaUnit(UnitDefinition) - Static method in class jigcell.sbml2.UnitDefinition

isValidId(String) - Static method in class jigcell.sbml2.SBaseId

isValidLengthUnit(UnitDefinition) - Static method in class jigcell.sbml2.UnitDefinition

isValidSpatialSizeUnit(UnitDefinition, int) - Static method in class jigcell.sbml2.UnitDefinition

isValidSubstanceUnit(UnitDefinition) - Static method in class jigcell.sbml2.UnitDefinition

isValidTimeUnit(UnitDefinition) - Static method in class jigcell.sbml2.UnitDefinition

isValidVolumeUnit(UnitDefinition) - Static method in class jigcell.sbml2.UnitDefinition

iterator() - Method in class jigcell.sbml2.Annotations

iterator() - Method in class jigcell.sbml2.Notes

J

JavaCharStream - Class in jigcell.sbml2.jep

An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (with java-like unicode escape processing).

JavaCharStream(Reader, int, int, int) - Constructor for class jigcell.sbml2.jep.JavaCharStream

JavaCharStream(Reader, int, int) - Constructor for class jigcell.sbml2.jep.JavaCharStream

JavaCharStream(Reader) - Constructor for class jigcell.sbml2.jep.JavaCharStream

JavaCharStream(InputStream, int, int, int) - Constructor for class jigcell.sbml2.jep.JavaCharStream

JavaCharStream(InputStream, int, int) - Constructor for class jigcell.sbml2.jep.JavaCharStream

JavaCharStream(InputStream) - Constructor for class jigcell.sbml2.jep.JavaCharStream

JEP - Class in jigcell.sbml2.jep

The JEP class is the main interface with which the user should interact.

JEP() - Constructor for class jigcell.sbml2.jep.JEP

Creates a new JEP instance with the default settings.

JEP(boolean, boolean, boolean, NumberFactory) - Constructor for class jigcell.sbml2.jep.JEP

Creates a new JEP instance with custom settings.

jep - Variable in class jigcell.sbml2.jep.Parser

jigcell.sbml2 - package jigcell.sbml2

jigcell.sbml2.jep - package jigcell.sbml2.jep

jigcell.sbml2.jep.function - package jigcell.sbml2.jep.function

jigcell.sbml2.jep.type - package jigcell.sbml2.jep.type

jigcell.sbml2.math - package jigcell.sbml2.math

jigcell.sbml2.tests - package jigcell.sbml2.tests

jj_2_1(int) - Method in class jigcell.sbml2.jep.Parser

jj_2_2(int) - Method in class jigcell.sbml2.jep.Parser

jj_2_3(int) - Method in class jigcell.sbml2.jep.Parser

jj_2_4(int) - Method in class jigcell.sbml2.jep.Parser

jj_2_rtns - Variable in class jigcell.sbml2.jep.Parser

jj_3_1() - Method in class jigcell.sbml2.jep.Parser

jj_3_2() - Method in class jigcell.sbml2.jep.Parser

jj_3_3() - Method in class jigcell.sbml2.jep.Parser

jj_3_4() - Method in class jigcell.sbml2.jep.Parser

jj_3R_10() - Method in class jigcell.sbml2.jep.Parser

jj_3R_11() - Method in class jigcell.sbml2.jep.Parser

jj_3R_12() - Method in class jigcell.sbml2.jep.Parser

jj_3R_13() - Method in class jigcell.sbml2.jep.Parser

jj_3R_14() - Method in class jigcell.sbml2.jep.Parser

jj_3R_15() - Method in class jigcell.sbml2.jep.Parser

jj_3R_16() - Method in class jigcell.sbml2.jep.Parser

jj_3R_17() - Method in class jigcell.sbml2.jep.Parser

jj_3R_18() - Method in class jigcell.sbml2.jep.Parser

jj_3R_19() - Method in class jigcell.sbml2.jep.Parser

jj_3R_20() - Method in class jigcell.sbml2.jep.Parser

jj_3R_21() - Method in class jigcell.sbml2.jep.Parser

jj_3R_22() - Method in class jigcell.sbml2.jep.Parser

jj_3R_23() - Method in class jigcell.sbml2.jep.Parser

jj_3R_24() - Method in class jigcell.sbml2.jep.Parser

jj_3R_25() - Method in class jigcell.sbml2.jep.Parser

jj_3R_26() - Method in class jigcell.sbml2.jep.Parser

jj_3R_6() - Method in class jigcell.sbml2.jep.Parser

jj_3R_7() - Method in class jigcell.sbml2.jep.Parser

jj_3R_8() - Method in class jigcell.sbml2.jep.Parser

jj_3R_9() - Method in class jigcell.sbml2.jep.Parser

jj_add_error_token(int, int) - Method in class jigcell.sbml2.jep.Parser

jj_consume_token(int) - Method in class jigcell.sbml2.jep.Parser

jj_endpos - Variable in class jigcell.sbml2.jep.Parser

jj_expentries - Variable in class jigcell.sbml2.jep.Parser

jj_expentry - Variable in class jigcell.sbml2.jep.Parser

jj_gc - Variable in class jigcell.sbml2.jep.Parser

jj_gen - Variable in class jigcell.sbml2.jep.Parser

jj_input_stream - Variable in class jigcell.sbml2.jep.Parser

jj_kind - Variable in class jigcell.sbml2.jep.Parser

jj_la - Variable in class jigcell.sbml2.jep.Parser

jj_la1 - Variable in class jigcell.sbml2.jep.Parser

jj_la1_0 - Variable in class jigcell.sbml2.jep.Parser

jj_la1_1 - Variable in class jigcell.sbml2.jep.Parser

jj_lastpos - Variable in class jigcell.sbml2.jep.Parser

jj_lasttokens - Variable in class jigcell.sbml2.jep.Parser

jj_nt - Variable in class jigcell.sbml2.jep.Parser

jj_ntk - Variable in class jigcell.sbml2.jep.Parser

jj_ntk() - Method in class jigcell.sbml2.jep.Parser

jj_rescan - Variable in class jigcell.sbml2.jep.Parser

jj_rescan_token() - Method in class jigcell.sbml2.jep.Parser

jj_save(int, int) - Method in class jigcell.sbml2.jep.Parser

jj_scan_token(int) - Method in class jigcell.sbml2.jep.Parser

jj_scanpos - Variable in class jigcell.sbml2.jep.Parser

jj_semLA - Variable in class jigcell.sbml2.jep.Parser

jjAddStates(int, int) - Method in class jigcell.sbml2.jep.ParserTokenManager

jjbeenHere - Variable in class jigcell.sbml2.jep.ParserTokenManager

jjbitVec0 - Static variable in class jigcell.sbml2.jep.ParserTokenManager

jjbitVec2 - Static variable in class jigcell.sbml2.jep.ParserTokenManager

jjbitVec3 - Static variable in class jigcell.sbml2.jep.ParserTokenManager

jjCanMove_0(int, int, int, long, long) - Static method in class jigcell.sbml2.jep.ParserTokenManager

jjCheckNAdd(int) - Method in class jigcell.sbml2.jep.ParserTokenManager

jjCheckNAddStates(int, int) - Method in class jigcell.sbml2.jep.ParserTokenManager

jjCheckNAddStates(int) - Method in class jigcell.sbml2.jep.ParserTokenManager

jjCheckNAddTwoStates(int, int) - Method in class jigcell.sbml2.jep.ParserTokenManager

jjemptyColNo - Variable in class jigcell.sbml2.jep.ParserTokenManager

jjemptyLineNo - Variable in class jigcell.sbml2.jep.ParserTokenManager

jjFillToken() - Method in class jigcell.sbml2.jep.ParserTokenManager

jjimageLen - Variable in class jigcell.sbml2.jep.ParserTokenManager

jjmatchedKind - Variable in class jigcell.sbml2.jep.ParserTokenManager

jjmatchedPos - Variable in class jigcell.sbml2.jep.ParserTokenManager

jjMoveNfa_0(int, int) - Method in class jigcell.sbml2.jep.ParserTokenManager

jjMoveStringLiteralDfa0_0() - Method in class jigcell.sbml2.jep.ParserTokenManager

jjMoveStringLiteralDfa1_0(long) - Method in class jigcell.sbml2.jep.ParserTokenManager

jjMoveStringLiteralDfa2_0(long, long) - Method in class jigcell.sbml2.jep.ParserTokenManager

jjMoveStringLiteralDfa3_0(long, long) - Method in class jigcell.sbml2.jep.ParserTokenManager

jjMoveStringLiteralDfa4_0(long, long) - Method in class jigcell.sbml2.jep.ParserTokenManager

jjMoveStringLiteralDfa5_0(long, long) - Method in class jigcell.sbml2.jep.ParserTokenManager

jjnewStateCnt - Variable in class jigcell.sbml2.jep.ParserTokenManager

jjnextStates - Static variable in class jigcell.sbml2.jep.ParserTokenManager

jjround - Variable in class jigcell.sbml2.jep.ParserTokenManager

jjrounds - Variable in class jigcell.sbml2.jep.ParserTokenManager

jjStartNfa_0(int, long) - Method in class jigcell.sbml2.jep.ParserTokenManager

jjStartNfaWithStates_0(int, int, int) - Method in class jigcell.sbml2.jep.ParserTokenManager

jjstateSet - Variable in class jigcell.sbml2.jep.ParserTokenManager

jjStopAtPos(int, int) - Method in class jigcell.sbml2.jep.ParserTokenManager

jjStopStringLiteralDfa_0(int, long) - Method in class jigcell.sbml2.jep.ParserTokenManager

jjstrLiteralImages - Static variable in class jigcell.sbml2.jep.ParserTokenManager

jjtAccept(ParserVisitor, Object) - Method in class jigcell.sbml2.jep.ASTConstant

Accept the visitor.

jjtAccept(ParserVisitor, Object) - Method in class jigcell.sbml2.jep.ASTElse

Accept the visitor.

jjtAccept(ParserVisitor, Object) - Method in class jigcell.sbml2.jep.ASTElseIfThen

Accept the visitor.

jjtAccept(ParserVisitor, Object) - Method in class jigcell.sbml2.jep.ASTFunNode

Accept the visitor.

jjtAccept(ParserVisitor, Object) - Method in class jigcell.sbml2.jep.ASTIfThen

Accept the visitor.

jjtAccept(ParserVisitor, Object) - Method in class jigcell.sbml2.jep.ASTPiecewise

Accept the visitor.

jjtAccept(ParserVisitor, Object) - Method in class jigcell.sbml2.jep.ASTStart

Accept the visitor.

jjtAccept(ParserVisitor, Object) - Method in class jigcell.sbml2.jep.ASTVarNode

Accept the visitor.

jjtAccept(ParserVisitor, Object) - Method in interface jigcell.sbml2.jep.Node

Accept the visitor.

jjtAccept(ParserVisitor, Object) - Method in class jigcell.sbml2.jep.SimpleNode

Accept the visitor.

jjtAddChild(Node, int) - Method in interface jigcell.sbml2.jep.Node

This method tells the node to add its argument to the node's list of children.

jjtAddChild(Node, int) - Method in class jigcell.sbml2.jep.SimpleNode

jjtClose() - Method in interface jigcell.sbml2.jep.Node

This method is called after all the child nodes have been added.

jjtClose() - Method in class jigcell.sbml2.jep.SimpleNode

JJTCONSTANT - Static variable in interface jigcell.sbml2.jep.ParserTreeConstants

JJTELSE - Static variable in interface jigcell.sbml2.jep.ParserTreeConstants

JJTELSEIFTHEN - Static variable in interface jigcell.sbml2.jep.ParserTreeConstants

JJTFUNNODE - Static variable in interface jigcell.sbml2.jep.ParserTreeConstants

jjtGetChild(int) - Method in interface jigcell.sbml2.jep.Node

This method returns a child node.

jjtGetChild(int) - Method in class jigcell.sbml2.jep.SimpleNode

jjtGetNumChildren() - Method in interface jigcell.sbml2.jep.Node

Return the number of children the node has.

jjtGetNumChildren() - Method in class jigcell.sbml2.jep.SimpleNode

jjtGetParent() - Method in interface jigcell.sbml2.jep.Node

jjtGetParent() - Method in class jigcell.sbml2.jep.SimpleNode

JJTIFTHEN - Static variable in interface jigcell.sbml2.jep.ParserTreeConstants

jjtNodeName - Static variable in interface jigcell.sbml2.jep.ParserTreeConstants

jjtOpen() - Method in interface jigcell.sbml2.jep.Node

This method is called after the node has been made the current node.

jjtOpen() - Method in class jigcell.sbml2.jep.SimpleNode

jjtoSkip - Static variable in class jigcell.sbml2.jep.ParserTokenManager

jjtoToken - Static variable in class jigcell.sbml2.jep.ParserTokenManager

JJTParserState - Class in jigcell.sbml2.jep

JJTParserState() - Constructor for class jigcell.sbml2.jep.JJTParserState

JJTPIECEWISE - Static variable in interface jigcell.sbml2.jep.ParserTreeConstants

jjtree - Variable in class jigcell.sbml2.jep.Parser

jjtSetParent(Node) - Method in interface jigcell.sbml2.jep.Node

This pair of methods are used to inform the node of its parent.

jjtSetParent(Node) - Method in class jigcell.sbml2.jep.SimpleNode

JJTSTART - Static variable in interface jigcell.sbml2.jep.ParserTreeConstants

JJTVARNODE - Static variable in interface jigcell.sbml2.jep.ParserTreeConstants

JJTVOID - Static variable in interface jigcell.sbml2.jep.ParserTreeConstants

K

kind - Variable in class jigcell.sbml2.jep.Token

An integer that describes the kind of this token.

kind - Variable in class jigcell.sbml2.Unit

KineticLaw - Class in jigcell.sbml2

Describes the rate at which a reaction takes place.

KineticLaw() - Constructor for class jigcell.sbml2.KineticLaw

KineticLaw(KineticLaw) - Constructor for class jigcell.sbml2.KineticLaw

Creates a copy of this existing object.

KineticLaw(String) - Constructor for class jigcell.sbml2.KineticLaw

kineticLaw - Variable in class jigcell.sbml2.Reaction

L

lambdaFunction - Variable in class jigcell.sbml2.math.MathMLExpression

lambdaGiven - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

LE - Static variable in interface jigcell.sbml2.jep.ParserConstants

left - Variable in class jigcell.sbml2.math.MathMLExpression.Equation

lengthOfMatch - Variable in class jigcell.sbml2.jep.ParserTokenManager

LETTER - Static variable in interface jigcell.sbml2.jep.ParserConstants

LEXICAL_ERROR - Static variable in error jigcell.sbml2.jep.TokenMgrError

Lexical error occured.

LexicalError(boolean, int, int, int, String, char) - Static method in error jigcell.sbml2.jep.TokenMgrError

Returns a detailed message for the Error when it is thrown by the token manager to indicate a lexical error.

lexStateNames - Static variable in class jigcell.sbml2.jep.ParserTokenManager

line - Variable in class jigcell.sbml2.jep.JavaCharStream

Link - Class in jigcell.sbml2

Links two components together for use in a composition hierarchy.

Link() - Constructor for class jigcell.sbml2.Link

Link(Link) - Constructor for class jigcell.sbml2.Link

Creates a copy of this existing object.

Link(String, String) - Constructor for class jigcell.sbml2.Link

links - Variable in class jigcell.sbml2.Model

linksElement - Variable in class jigcell.sbml2.Model

localName - Variable in class jigcell.sbml2.math.Node

localSymbols - Variable in class jigcell.sbml2.math.InfixExpression

localText - Variable in class jigcell.sbml2.XMLReader

lookForFunctionArgs - Variable in class jigcell.sbml2.math.MathMLExpression

lookingAhead - Variable in class jigcell.sbml2.jep.Parser

lookupFortranNameIndex(String) - Method in class jigcell.sbml2.math.SymbolTable

Finds fname in fortranNameColRev.

lookupId(String) - Method in class jigcell.sbml2.math.SymbolTable

Returns the id for the JigCell name.

lookupName(String) - Method in class jigcell.sbml2.math.SymbolTable

Returns the JigCell name for id.

lookupSymbol(String) - Method in class jigcell.sbml2.math.SymbolTable

Find the fortranName for name.

lookupSymbolById(String) - Method in class jigcell.sbml2.math.SymbolTable

Returns the Fortran name for id.

lookupSymbolIndex(String, ArrayList) - Method in class jigcell.sbml2.math.SymbolTable

Finds the index of name in the internal symbol table.

lookupSymbols - Variable in class jigcell.sbml2.math.InfixExpression

LOOP_DETECTED - Static variable in error jigcell.sbml2.jep.TokenMgrError

Detected (and bailed out of) an infinite loop in the token manager.

LT - Static variable in interface jigcell.sbml2.jep.ParserConstants

M

main(String[]) - Static method in class jigcell.sbml2.tests.AlgebraicModelTests

Starts a new test suite run.

main(String[]) - Static method in class jigcell.sbml2.tests.AlgebraicModelTests2

Starts a new test suite run.

main(String[]) - Static method in class jigcell.sbml2.tests.AssignmentModelTests

Starts a new test suite run.

main(String[]) - Static method in class jigcell.sbml2.tests.AssignmentModelTests2

Starts a new test suite run.

main(String[]) - Static method in class jigcell.sbml2.tests.BoundaryModelTests

Starts a new test suite run.

main(String[]) - Static method in class jigcell.sbml2.tests.BoundaryModelTests2

Starts a new test suite run.

main(String[]) - Static method in class jigcell.sbml2.tests.BranchModelTests

Starts a new test suite run.

main(String[]) - Static method in class jigcell.sbml2.tests.BranchModelTests2

Starts a new test suite run.

main(String[]) - Static method in class jigcell.sbml2.tests.CompartmentModelTests

Starts a new test suite run.

main(String[]) - Static method in class jigcell.sbml2.tests.CompartmentModelTests2

Starts a new test suite run.

main(String[]) - Static method in class jigcell.sbml2.tests.DelayModelTests

Starts a new test suite run.

main(String[]) - Static method in class jigcell.sbml2.tests.DelayModelTests2

Starts a new test suite run.

main(String[]) - Static method in class jigcell.sbml2.tests.EventModelTests

Starts a new test suite run.

main(String[]) - Static method in class jigcell.sbml2.tests.EventModelTests2

Starts a new test suite run.

main(String[]) - Static method in class jigcell.sbml2.tests.FunctionModelTests

Starts a new test suite run.

main(String[]) - Static method in class jigcell.sbml2.tests.FunctionModelTests2

Starts a new test suite run.

main(String[]) - Static method in class jigcell.sbml2.tests.ODEModelTests

Starts a new test suite run.

main(String[]) - Static method in class jigcell.sbml2.tests.ODEModelTests2

Starts a new test suite run.

main(String[]) - Static method in class jigcell.sbml2.tests.Tests

Starts a new test suite run.

main(String[]) - Static method in class jigcell.sbml2.tests.UnitModelTests

Starts a new test suite run.

main(String[]) - Static method in class jigcell.sbml2.tests.UnitModelTests2

Starts a new test suite run.

makeFortranCharacterSafe_(String, int, boolean, char) - Static method in class jigcell.sbml2.math.SymbolTable

Makes a string safe as a Fortran character string.

makeFortranIdSafe(String) - Method in class jigcell.sbml2.math.SymbolTable

Convert a string to a Fortran safe identifier.

makeFortranIdSafe_(String, int) - Static method in class jigcell.sbml2.math.SymbolTable

makeFortranSafe(String) - Method in class jigcell.sbml2.math.SymbolTable

Returns a Fortran safe string according to mode

makeFortranSafe(String, SymbolTable.Mode) - Method in class jigcell.sbml2.math.SymbolTable

Makes string Fortran safe according to mode.

makeFortranSafe(String, SymbolTable.Mode, int) - Method in class jigcell.sbml2.math.SymbolTable

makeFortranSafe(String, SymbolTable.Mode, int, boolean, char) - Static method in class jigcell.sbml2.math.SymbolTable

Makes string Fortran safe according to mode and maxLength.

map - Static variable in class jigcell.sbml2.math.InfixExpression

marks - Variable in class jigcell.sbml2.jep.JJTParserState

math - Variable in class jigcell.sbml2.EventAssignment

math - Variable in class jigcell.sbml2.FunctionDefinition

math - Variable in class jigcell.sbml2.KineticLaw

math - Variable in class jigcell.sbml2.Rule

MATH - Static variable in class jigcell.sbml2.SBMLLevel2Reader

math - Variable in class jigcell.sbml2.StoichiometryMath

MathElement - Class in jigcell.sbml2.math

A class that holds a user or program defined value.

MathElement() - Constructor for class jigcell.sbml2.math.MathElement

Creates a new instance of MathElement

MathElement(String) - Constructor for class jigcell.sbml2.math.MathElement

MathElement - Interface in jigcell.sbml2

An element that contains MathML.

mathML - Static variable in class jigcell.sbml2.math.MathMLConvertorSAX

mathML - Variable in class jigcell.sbml2.math.MathMLExpression

MathMLConvertor - Class in jigcell.sbml2.math

A class for converting MathML to normal math.

MathMLConvertor() - Constructor for class jigcell.sbml2.math.MathMLConvertor

Creates a new instance of MathMLConvertor

MathMLConvertorSAX - Class in jigcell.sbml2.math

This code is licensed under the DARPA BioCOMP Open Source License.

MathMLConvertorSAX() - Constructor for class jigcell.sbml2.math.MathMLConvertorSAX

MathMLConvertorSAX(String, boolean, boolean) - Constructor for class jigcell.sbml2.math.MathMLConvertorSAX

Creates a new instance of MathMLConvertorSAX

MathMLConvertorSAX.MyErrorHandler - Class in jigcell.sbml2.math

MathMLConvertorSAX.MyErrorHandler(PrintStream) - Constructor for class jigcell.sbml2.math.MathMLConvertorSAX.MyErrorHandler

MathMLExpression - Class in jigcell.sbml2.math

This code is licensed under the DARPA BioCOMP Open Source License.

MathMLExpression(String) - Constructor for class jigcell.sbml2.math.MathMLExpression

MathMLExpression.Equation - Class in jigcell.sbml2.math

Used as a return value in solve.

MathMLExpression.Equation() - Constructor for class jigcell.sbml2.math.MathMLExpression.Equation

MathMLExpression.MathMLHandler - Class in jigcell.sbml2.math

Receives events from SAX and builds a parse tree.

MathMLExpression.MathMLHandler() - Constructor for class jigcell.sbml2.math.MathMLExpression.MathMLHandler

MathMLExpression.NoVarTree - Class in jigcell.sbml2.math

Used as a return value in removeVar from tree.

MathMLExpression.NoVarTree() - Constructor for class jigcell.sbml2.math.MathMLExpression.NoVarTree

mathMLFunctions - Static variable in class jigcell.sbml2.jep.JEP

MathML functions

mathMLParseTree - Variable in class jigcell.sbml2.math.MathMLExpression

maxLength - Variable in class jigcell.sbml2.math.SymbolTable

maxLength - Variable in class jigcell.sbml2.math.SymbolTable.Mode

maxLength() - Method in class jigcell.sbml2.math.SymbolTable.Mode

maxNextCharInd - Variable in class jigcell.sbml2.jep.JavaCharStream

mergeExpression(ArrayList, String, int, String) - Static method in class jigcell.sbml2.math.InfixExpression

Merges strings in expression and addes line breaks to maintain a width no greater than width.

metaid - Variable in class jigcell.sbml2.SBase

MINUS - Static variable in interface jigcell.sbml2.jep.ParserConstants

mk - Variable in class jigcell.sbml2.jep.JJTParserState

mode - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

mode - Variable in class jigcell.sbml2.math.SymbolTable

mode - Variable in class jigcell.sbml2.XMLReader

Model - Class in jigcell.sbml2

The highest level construct in an SBML document.

Model() - Constructor for class jigcell.sbml2.Model

Model(String) - Constructor for class jigcell.sbml2.Model

model - Variable in class jigcell.sbml2.SBMLLevel2Document

model - Variable in class jigcell.sbml2.tests.SBMLModelTests

ModelGenerator - Class in jigcell.sbml2.tests

Automated generators for creating random SBML models.

ModelGenerator() - Constructor for class jigcell.sbml2.tests.ModelGenerator

modelName - Variable in class jigcell.sbml2.tests.SBMLModelTests

models - Variable in class jigcell.sbml2.Model

modelsElement - Variable in class jigcell.sbml2.Model

modifier - Variable in class jigcell.sbml2.Reaction

modifiersElement - Variable in class jigcell.sbml2.Reaction

ModifierSpeciesReference - Class in jigcell.sbml2

A reference to a species contained in the model.

ModifierSpeciesReference() - Constructor for class jigcell.sbml2.ModifierSpeciesReference

ModifierSpeciesReference(ModifierSpeciesReference) - Constructor for class jigcell.sbml2.ModifierSpeciesReference

Creates a copy of this existing object.

ModifierSpeciesReference(Species) - Constructor for class jigcell.sbml2.ModifierSpeciesReference

modifyMap(String, String) - Static method in class jigcell.sbml2.math.InfixExpression

Changes the function map to map function to targetFunction.

MUL - Static variable in interface jigcell.sbml2.jep.ParserConstants

MultiplicativeExpression() - Method in class jigcell.sbml2.jep.Parser

multiplier - Variable in class jigcell.sbml2.Unit

multiplyAndAddToRow(double[][], int, int, int, double) - Static method in class jigcell.sbml2.ConservationRelationFinder

multiplyRow(double[][], int, int, double) - Static method in class jigcell.sbml2.ConservationRelationFinder

N

name - Variable in class jigcell.sbml2.jep.ASTFunNode

Name of the function

name - Variable in class jigcell.sbml2.math.SymbolTable.Mode

name - Variable in class jigcell.sbml2.SBaseId

name - Variable in class jigcell.sbml2.Unit

name - Variable in class jigcell.sbml2.XMLPrinter

nameCol - Variable in class jigcell.sbml2.math.SymbolTable

nameColRev - Variable in class jigcell.sbml2.math.SymbolTable

NAMESPACE_MATHML - Static variable in class jigcell.sbml2.SBMLLevel2Reader

NAMESPACE_RDF - Static variable in class jigcell.sbml2.SBMLLevel2Reader

NAMESPACE_SBML - Static variable in class jigcell.sbml2.SBMLLevel2Reader

namespacePrefixToURI - Variable in class jigcell.sbml2.XMLReader

NE - Static variable in interface jigcell.sbml2.jep.ParserConstants

newToken(int) - Static method in class jigcell.sbml2.jep.Token

Returns a new Token object, by default.

next - Variable in class jigcell.sbml2.jep.Parser.JJCalls

next - Variable in class jigcell.sbml2.jep.Token

A reference to the next regular (non-special) token from the input stream.

nextCharBuf - Variable in class jigcell.sbml2.jep.JavaCharStream

nextCharInd - Variable in class jigcell.sbml2.jep.JavaCharStream

Node - Interface in jigcell.sbml2.jep

Node - Class in jigcell.sbml2.math

Represents a node in a parse tree based on XML (in particular MathML).

Node(Node) - Constructor for class jigcell.sbml2.math.Node

Node(Node, String, Node[]) - Constructor for class jigcell.sbml2.math.Node

Node(Node, String, String, String, Attributes) - Constructor for class jigcell.sbml2.math.Node

Node(String, String, String, Attributes) - Constructor for class jigcell.sbml2.math.Node

Node(String, String, Node[]) - Constructor for class jigcell.sbml2.math.Node

Node(String, String, Node, Node) - Constructor for class jigcell.sbml2.math.Node

Node(String, String, Node) - Constructor for class jigcell.sbml2.math.Node

Node(String, String) - Constructor for class jigcell.sbml2.math.Node

Node() - Constructor for class jigcell.sbml2.math.Node

node_created - Variable in class jigcell.sbml2.jep.JJTParserState

nodeArity() - Method in class jigcell.sbml2.jep.JJTParserState

nodeCreated() - Method in class jigcell.sbml2.jep.JJTParserState

nodes - Variable in class jigcell.sbml2.jep.JJTParserState

NORMAL - Static variable in class jigcell.sbml2.math.InfixExpression

NORMAL - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

NORMAL - Static variable in class jigcell.sbml2.XMLReader

NOT - Static variable in interface jigcell.sbml2.jep.ParserConstants

NotConnectiveCondition() - Method in class jigcell.sbml2.jep.Parser

Notes - Class in jigcell.sbml2

Stores the note metadata for an SBML node.

Notes() - Constructor for class jigcell.sbml2.Notes

notes - Variable in class jigcell.sbml2.Notes

notes - Variable in class jigcell.sbml2.SBase

NOTES - Static variable in class jigcell.sbml2.SBMLLevel2Reader

numArgumentsExpected - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

numberFactory - Variable in class jigcell.sbml2.jep.JEP

Number factory

NumberFactory - Interface in jigcell.sbml2.jep.type

This interface can be implemented to create numbers of any object type.

numberOfParameters - Variable in class jigcell.sbml2.jep.function.PostfixMathCommand

Number of parameters a the function requires.

O

object - Variable in class jigcell.sbml2.SimpleObjectReference

ODEModelTests - Class in jigcell.sbml2.tests

A collection of tests to exercise the reference model for odes.

ODEModelTests(String) - Constructor for class jigcell.sbml2.tests.ODEModelTests

Creates a new test for the reference model for odes.

ODEModelTests2 - Class in jigcell.sbml2.tests

A collection of tests to exercise the reference model for odes.

ODEModelTests2(String) - Constructor for class jigcell.sbml2.tests.ODEModelTests2

Creates a new test for the reference model for odes.

offset - Variable in class jigcell.sbml2.Unit

openNodeScope(Node) - Method in class jigcell.sbml2.jep.JJTParserState

OR - Static variable in interface jigcell.sbml2.jep.ParserConstants

order - Static variable in class jigcell.sbml2.math.InfixExpression

order - Variable in class jigcell.sbml2.math.MathMLConvertor

out - Variable in class jigcell.sbml2.math.MathMLConvertorSAX.MyErrorHandler

Error handler output goes here

outside - Variable in class jigcell.sbml2.Compartment

P

padCharacter - Variable in class jigcell.sbml2.math.SymbolTable

padToLength - Variable in class jigcell.sbml2.math.SymbolTable

parameter - Variable in class jigcell.sbml2.KineticLaw

PARAMETER - Static variable in class jigcell.sbml2.Model

Parameter - Class in jigcell.sbml2

Declares a variable for use in mathematical formulas in an SBML model definition.

Parameter() - Constructor for class jigcell.sbml2.Parameter

Parameter(Parameter) - Constructor for class jigcell.sbml2.Parameter

Creates a copy of this existing object.

Parameter(String, String) - Constructor for class jigcell.sbml2.Parameter

Parameter(String, String, double) - Constructor for class jigcell.sbml2.Parameter

parameterElement - Variable in class jigcell.sbml2.KineticLaw

parameters - Variable in class jigcell.sbml2.Model

parametersElement - Variable in class jigcell.sbml2.Model

parent - Variable in class jigcell.sbml2.jep.SimpleNode

parent - Variable in class jigcell.sbml2.math.Node

parent - Variable in class jigcell.sbml2.math.SBMLNode

parse(Attributes) - Method in class jigcell.sbml2.Compartment

parse(Attributes) - Method in class jigcell.sbml2.Event

parse(Attributes) - Method in class jigcell.sbml2.EventAssignment

parse(Attributes) - Method in class jigcell.sbml2.Instance

parse(Attributes) - Method in class jigcell.sbml2.KineticLaw

parse(Attributes) - Method in class jigcell.sbml2.Link

parse(InputSource) - Method in class jigcell.sbml2.math.MathMLExpression

parse(Attributes) - Method in class jigcell.sbml2.Parameter

parse(Attributes) - Method in class jigcell.sbml2.Reaction

parse(Attributes) - Method in class jigcell.sbml2.SBase

parse(Attributes) - Method in class jigcell.sbml2.SBaseId

parse(Attributes) - Method in class jigcell.sbml2.SBMLLevel2Document

parse(Attributes) - Method in class jigcell.sbml2.SimpleObjectReference

parse(Attributes) - Method in class jigcell.sbml2.SimpleSpeciesReference

parse(Attributes) - Method in class jigcell.sbml2.Species

parse(Attributes) - Method in class jigcell.sbml2.SpeciesReference

parse(Attributes) - Method in class jigcell.sbml2.Unit

parse(Attributes) - Method in class jigcell.sbml2.VariableRule

parse(Attributes) - Method in class jigcell.sbml2.XMLElement

ParseException - Exception in jigcell.sbml2.jep

This exception is thrown when parse errors are encountered.

ParseException(Token, int[][], String[]) - Constructor for exception jigcell.sbml2.jep.ParseException

This constructor is used by the method "generateParseException" in the generated parser.

ParseException() - Constructor for exception jigcell.sbml2.jep.ParseException

The following constructors are for use by you for whatever purpose you can think of.

ParseException(String) - Constructor for exception jigcell.sbml2.jep.ParseException

parseExpression(String) - Method in class jigcell.sbml2.jep.JEP

Parses the expression.

parser - Variable in class jigcell.sbml2.jep.JEP

The parser object

Parser - Class in jigcell.sbml2.jep

Parser(InputStream) - Constructor for class jigcell.sbml2.jep.Parser

Parser(Reader) - Constructor for class jigcell.sbml2.jep.Parser

Parser(ParserTokenManager) - Constructor for class jigcell.sbml2.jep.Parser

parser - Variable in class jigcell.sbml2.jep.SimpleNode

Parser.JJCalls - Class in jigcell.sbml2.jep

Parser.JJCalls() - Constructor for class jigcell.sbml2.jep.Parser.JJCalls

ParserConstants - Interface in jigcell.sbml2.jep

ParserDumpVisitor - Class in jigcell.sbml2.jep

ParserDumpVisitor() - Constructor for class jigcell.sbml2.jep.ParserDumpVisitor

ParserTokenManager - Class in jigcell.sbml2.jep

ParserTokenManager(JavaCharStream) - Constructor for class jigcell.sbml2.jep.ParserTokenManager

ParserTokenManager(JavaCharStream, int) - Constructor for class jigcell.sbml2.jep.ParserTokenManager

ParserTreeConstants - Interface in jigcell.sbml2.jep

ParserVisitor - Interface in jigcell.sbml2.jep

parseStream(Reader, JEP) - Method in class jigcell.sbml2.jep.Parser

PATTERN_ID - Static variable in class jigcell.sbml2.SBaseId

peek() - Method in class jigcell.sbml2.XMLReader

peekNode() - Method in class jigcell.sbml2.jep.JJTParserState

peekPastContainer() - Method in class jigcell.sbml2.XMLReader

pfmc - Variable in class jigcell.sbml2.jep.ASTFunNode

The function class used to evaluate the node

Piecewise() - Method in class jigcell.sbml2.jep.Parser

PLUS - Static variable in interface jigcell.sbml2.jep.ParserConstants

pop() - Method in class jigcell.sbml2.XMLReader

popNode() - Method in class jigcell.sbml2.jep.JJTParserState

PostfixMathCommand - Class in jigcell.sbml2.jep.function

Function classes extend this class.

PostfixMathCommand(int) - Constructor for class jigcell.sbml2.jep.function.PostfixMathCommand

Creates a new PostfixMathCommand class.

PostfixMathCommandI - Interface in jigcell.sbml2.jep.function

All function classes must implement this interface to ensure that the run() method is implemented.

POWER - Static variable in interface jigcell.sbml2.jep.ParserConstants

PowerExpression() - Method in class jigcell.sbml2.jep.Parser

prevCharIsCR - Variable in class jigcell.sbml2.jep.JavaCharStream

prevCharIsLF - Variable in class jigcell.sbml2.jep.JavaCharStream

print(XMLPrinter) - Method in class jigcell.sbml2.AlgebraicRule

print(XMLPrinter) - Method in class jigcell.sbml2.AssignmentRule

print(XMLPrinter) - Method in class jigcell.sbml2.Compartment

print(XMLPrinter, String) - Method in class jigcell.sbml2.Compartment

print(XMLPrinter) - Method in class jigcell.sbml2.Event

print(XMLPrinter, String) - Method in class jigcell.sbml2.Event

print(XMLPrinter) - Method in class jigcell.sbml2.EventAssignment

print(XMLPrinter, String) - Method in class jigcell.sbml2.EventAssignment

print(XMLPrinter) - Method in class jigcell.sbml2.FromObjectReference

print(XMLPrinter) - Method in class jigcell.sbml2.FunctionDefinition

print(XMLPrinter, String) - Method in class jigcell.sbml2.FunctionDefinition

print(XMLPrinter) - Method in class jigcell.sbml2.Instance

print(XMLPrinter, String) - Method in class jigcell.sbml2.Instance

print(XMLPrinter) - Method in class jigcell.sbml2.KineticLaw

print(XMLPrinter, String) - Method in class jigcell.sbml2.KineticLaw

print(XMLPrinter) - Method in class jigcell.sbml2.Link

print(XMLPrinter, String) - Method in class jigcell.sbml2.Link

print(XMLPrinter) - Method in class jigcell.sbml2.Model

print(XMLPrinter, String) - Method in class jigcell.sbml2.Model

print(XMLPrinter) - Method in class jigcell.sbml2.ModifierSpeciesReference

print(XMLPrinter) - Method in class jigcell.sbml2.Parameter

print(XMLPrinter, String) - Method in class jigcell.sbml2.Parameter

print(XMLPrinter) - Method in class jigcell.sbml2.RateRule

print(XMLPrinter) - Method in class jigcell.sbml2.Reaction

print(XMLPrinter, String) - Method in class jigcell.sbml2.Reaction

print(XMLPrinter, String) - Method in class jigcell.sbml2.Rule

print(XMLPrinter, String) - Method in class jigcell.sbml2.SBase

print(XMLPrinter, String) - Method in class jigcell.sbml2.SBaseId

print(XMLPrinter) - Method in class jigcell.sbml2.SBMLLevel2Document

print(XMLPrinter, String) - Method in class jigcell.sbml2.SBMLLevel2Document

print(XMLPrinter, String) - Method in class jigcell.sbml2.SimpleObjectReference

print(XMLPrinter, String) - Method in class jigcell.sbml2.SimpleSpeciesReference

print(XMLPrinter) - Method in class jigcell.sbml2.Species

print(XMLPrinter, String) - Method in class jigcell.sbml2.Species

print(XMLPrinter) - Method in class jigcell.sbml2.SpeciesReference

print(XMLPrinter, String) - Method in class jigcell.sbml2.SpeciesReference

print(XMLPrinter) - Method in class jigcell.sbml2.StoichiometryMath

print(XMLPrinter, String) - Method in class jigcell.sbml2.StoichiometryMath

print(XMLPrinter) - Method in class jigcell.sbml2.SubObjectReference

print(XMLPrinter) - Method in class jigcell.sbml2.ToObjectReference

print(XMLPrinter) - Method in class jigcell.sbml2.Unit

print(XMLPrinter, String) - Method in class jigcell.sbml2.Unit

print(XMLPrinter) - Method in class jigcell.sbml2.UnitDefinition

print(XMLPrinter, String) - Method in class jigcell.sbml2.UnitDefinition

print(XMLPrinter, String) - Method in class jigcell.sbml2.VariableRule

print(XMLPrinter) - Method in class jigcell.sbml2.XMLElement

print(XMLPrinter, String) - Method in class jigcell.sbml2.XMLElement

printParseTree(Node) - Static method in class jigcell.sbml2.math.MathMLExpression

product - Variable in class jigcell.sbml2.Reaction

productsElement - Variable in class jigcell.sbml2.Reaction

push(XMLElement) - Method in class jigcell.sbml2.XMLReader

pushNode(Node) - Method in class jigcell.sbml2.jep.JJTParserState

Q

qName - Variable in class jigcell.sbml2.math.Node

quote(String) - Static method in class jigcell.sbml2.XMLPrinter

R

RateRule - Class in jigcell.sbml2

A rule dx/dt=f(W) where x is a variable and f is an arbitrary function.

RateRule() - Constructor for class jigcell.sbml2.RateRule

RateRule(RateRule) - Constructor for class jigcell.sbml2.RateRule

Creates a copy of this existing object.

RATIONAL - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

RATIONALSEP - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

rdf - Variable in class jigcell.sbml2.SBase

RDF - Static variable in class jigcell.sbml2.SBMLLevel2Reader

reactant - Variable in class jigcell.sbml2.Reaction

reactantsElement - Variable in class jigcell.sbml2.Reaction

REACTION - Static variable in class jigcell.sbml2.Model

Reaction - Class in jigcell.sbml2

A transformation, transport, or binding process that changes the amount of one or more species.

Reaction() - Constructor for class jigcell.sbml2.Reaction

Reaction(Reaction) - Constructor for class jigcell.sbml2.Reaction

Creates a copy of this existing object.

Reaction(String, String) - Constructor for class jigcell.sbml2.Reaction

reactions - Variable in class jigcell.sbml2.Model

reactionsElement - Variable in class jigcell.sbml2.Model

read(Reader) - Static method in class jigcell.sbml2.SBMLLevel2Reader

read(XMLReader, Reader) - Static method in class jigcell.sbml2.XMLReader

ReadByte() - Method in class jigcell.sbml2.jep.JavaCharStream

readChar() - Method in class jigcell.sbml2.jep.JavaCharStream

readDocument(InputStream) - Static method in class jigcell.sbml2.SBMLLevel2Document

readDocument(Reader) - Static method in class jigcell.sbml2.SBMLLevel2Document

readDocument(String) - Static method in class jigcell.sbml2.SBMLLevel2Document

RealConstant() - Method in class jigcell.sbml2.jep.Parser

reduceMatrix(double[][], int, int, int) - Static method in class jigcell.sbml2.ConservationRelationFinder

ReInit(Reader, int, int, int) - Method in class jigcell.sbml2.jep.JavaCharStream

ReInit(Reader, int, int) - Method in class jigcell.sbml2.jep.JavaCharStream

ReInit(Reader) - Method in class jigcell.sbml2.jep.JavaCharStream

ReInit(InputStream, int, int, int) - Method in class jigcell.sbml2.jep.JavaCharStream

ReInit(InputStream, int, int) - Method in class jigcell.sbml2.jep.JavaCharStream

ReInit(InputStream) - Method in class jigcell.sbml2.jep.JavaCharStream

ReInit(InputStream) - Method in class jigcell.sbml2.jep.Parser

ReInit(Reader) - Method in class jigcell.sbml2.jep.Parser

ReInit(ParserTokenManager) - Method in class jigcell.sbml2.jep.Parser

ReInit(JavaCharStream) - Method in class jigcell.sbml2.jep.ParserTokenManager

ReInit(JavaCharStream, int) - Method in class jigcell.sbml2.jep.ParserTokenManager

ReInitRounds() - Method in class jigcell.sbml2.jep.ParserTokenManager

remove(int) - Method in class jigcell.sbml2.Annotations

remove(int) - Method in class jigcell.sbml2.Notes

removeAllChildren() - Method in class jigcell.sbml2.math.Node

removeChild(int) - Method in class jigcell.sbml2.math.Node

removeFunction(String) - Method in class jigcell.sbml2.jep.JEP

Removes a function from the parser.

removeVar(Node, String) - Method in class jigcell.sbml2.math.MathMLExpression

Takes a product cur and removes var from the product.

reset() - Method in class jigcell.sbml2.jep.JJTParserState

reset() - Static method in class jigcell.sbml2.math.MathMLConvertor

reset() - Method in class jigcell.sbml2.math.MathMLConvertorSAX

reverseLookupId(String) - Method in class jigcell.sbml2.math.SymbolTable

Returns the JigCell id for fortranName.

reversible - Variable in class jigcell.sbml2.Reaction

right - Variable in class jigcell.sbml2.math.MathMLExpression.Equation

root - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

root - Variable in class jigcell.sbml2.math.MathMLExpression.MathMLHandler

rootNode() - Method in class jigcell.sbml2.jep.JJTParserState

Rule - Class in jigcell.sbml2

A rule constrains a model variable according to the given equation.

Rule() - Constructor for class jigcell.sbml2.Rule

rules - Variable in class jigcell.sbml2.Model

rulesElement - Variable in class jigcell.sbml2.Model

run(Stack) - Method in class jigcell.sbml2.jep.function.PostfixMathCommand

Throws an exception because this method should never be called under normal circumstances.

run(Stack) - Method in interface jigcell.sbml2.jep.function.PostfixMathCommandI

Run the function on the stack.

S

saxConvertor - Static variable in class jigcell.sbml2.math.MathMLConvertor

SBase - Class in jigcell.sbml2

Contains the notes, annotations, and metadata for an SBML element.

SBase() - Constructor for class jigcell.sbml2.SBase

SBaseId - Class in jigcell.sbml2

An SBML element that has a name and id.

SBaseId() - Constructor for class jigcell.sbml2.SBaseId

SBaseId(String, String) - Constructor for class jigcell.sbml2.SBaseId

SBML - Static variable in class jigcell.sbml2.SBMLLevel2Reader

SBMLLevel2Document - Class in jigcell.sbml2

Represents the SBML Level 2 document that contains the model.

SBMLLevel2Document() - Constructor for class jigcell.sbml2.SBMLLevel2Document

SBMLLevel2Document(Model) - Constructor for class jigcell.sbml2.SBMLLevel2Document

SBMLLevel2Reader - Class in jigcell.sbml2

Reads an SBML Level 2 file.

SBMLLevel2Reader(SBMLLevel2Document) - Constructor for class jigcell.sbml2.SBMLLevel2Reader

SBMLModelTests - Class in jigcell.sbml2.tests

A collection of test methods for pieces of an SBML model.

SBMLModelTests(String) - Constructor for class jigcell.sbml2.tests.SBMLModelTests

Creates a new test for an SBML model.

SBMLNode - Class in jigcell.sbml2.math

A class representing a node in a parse tree.

SBMLNode(SBMLNode) - Constructor for class jigcell.sbml2.math.SBMLNode

Creates a new instance of SBMLNode

SBMLNode(SBMLNode, MathElement) - Constructor for class jigcell.sbml2.math.SBMLNode

SBMLNode(MathElement) - Constructor for class jigcell.sbml2.math.SBMLNode

sbmlString - Variable in class jigcell.sbml2.jep.ParserDumpVisitor

scale - Variable in class jigcell.sbml2.Unit

searchAndRecordIds(Set) - Method in class jigcell.sbml2.math.MathMLExpression

searchAndReplaceIds(Map) - Method in class jigcell.sbml2.math.MathMLExpression

searchListForId(List, String) - Static method in class jigcell.sbml2.SBase

searchListForName(List, String) - Static method in class jigcell.sbml2.SBase

set(int, String) - Method in class jigcell.sbml2.Annotations

set(int, String) - Method in class jigcell.sbml2.Notes

setAttributes(Attributes) - Method in class jigcell.sbml2.math.Node

setBoundaryCondition(boolean) - Method in class jigcell.sbml2.Species

Sets whether the species is on the boundary of the reaction system.

setCharge(int) - Method in class jigcell.sbml2.Species

setCompartment(String) - Method in class jigcell.sbml2.Species

setCompartment(Compartment) - Method in class jigcell.sbml2.Species

setConstant(boolean) - Method in class jigcell.sbml2.Compartment

Sets whether the compartment's volume may vary during simulation.

setConstant(boolean) - Method in class jigcell.sbml2.Parameter

Sets whether the parameter's value is constant throughout a simulation.

setConstant(boolean) - Method in class jigcell.sbml2.Species

setCurNumberOfParameters(int) - Method in class jigcell.sbml2.jep.function.PostfixMathCommand

Sets the number of current number of parameters used in the next call of run().

setCurNumberOfParameters(int) - Method in interface jigcell.sbml2.jep.function.PostfixMathCommandI

Sets the number of current number of parameters used in the next call of run().

setDebugStream(PrintStream) - Method in class jigcell.sbml2.jep.ParserTokenManager

setDelay(String) - Method in class jigcell.sbml2.Event

Sets the length of time after the event has fired that the event is executed.

setElement(MathElement) - Method in class jigcell.sbml2.math.SBMLNode

setExponent(int) - Method in class jigcell.sbml2.Unit

setFast(boolean) - Method in class jigcell.sbml2.Reaction

setFunction(String, PostfixMathCommandI) - Method in class jigcell.sbml2.jep.ASTFunNode

Sets the function for a node.

setHasOnlySubstanceUnits(boolean) - Method in class jigcell.sbml2.Species

setHref(String) - Method in class jigcell.sbml2.Instance

Sets the instance's href.

setId(String) - Method in class jigcell.sbml2.SBaseId

setImplicitMul(boolean) - Method in class jigcell.sbml2.jep.JEP

Sets the value of the implicit multiplication option.

setInitialAmount(double) - Method in class jigcell.sbml2.Species

setInitialConcentration(double) - Method in class jigcell.sbml2.Species

setKind(Unit) - Method in class jigcell.sbml2.Unit

setKineticLaw(KineticLaw) - Method in class jigcell.sbml2.Reaction

setLambdaFunction(boolean) - Method in class jigcell.sbml2.math.MathMLExpression

Tell this MathMLExpression if it represents a lambda function or not.

setLevel(int) - Method in class jigcell.sbml2.SBMLLevel2Document

setLocalName(String) - Method in class jigcell.sbml2.math.Node

setMath(String) - Method in class jigcell.sbml2.EventAssignment

setMath(String) - Method in class jigcell.sbml2.FunctionDefinition

setMath(String) - Method in class jigcell.sbml2.KineticLaw

Sets the MathML expression for this KineticLaw.

setMath(String) - Method in interface jigcell.sbml2.MathElement

setMath(String) - Method in class jigcell.sbml2.Rule

setMath(String) - Method in class jigcell.sbml2.StoichiometryMath

setMetaid(String) - Method in class jigcell.sbml2.SBase

setModel(Model) - Method in class jigcell.sbml2.SBMLLevel2Document

setMultiplier(double) - Method in class jigcell.sbml2.Unit

setName(String) - Method in class jigcell.sbml2.jep.ASTVarNode

Sets the name of the variable.

setName(String) - Method in class jigcell.sbml2.SBaseId

setNumberOfParameters(int) - Method in class jigcell.sbml2.jep.function.PostfixMathCommand

Convenience method for use with the parser to set the parameters if they have changed.

setObject(String) - Method in class jigcell.sbml2.SimpleObjectReference

setObject(SimpleObjectReference) - Method in class jigcell.sbml2.SimpleObjectReference

setOffset(double) - Method in class jigcell.sbml2.Unit

setOutside(String) - Method in class jigcell.sbml2.Compartment

setOutside(Compartment) - Method in class jigcell.sbml2.Compartment

setParent(Node) - Method in class jigcell.sbml2.math.Node

setQName(String) - Method in class jigcell.sbml2.math.Node

setRDF(String) - Method in class jigcell.sbml2.SBase

setRDF(String, String) - Method in class jigcell.sbml2.SBase

setReversible(boolean) - Method in class jigcell.sbml2.Reaction

Sets whether the reaction is reversible.

setScale(int) - Method in class jigcell.sbml2.Unit

setSize(double) - Method in class jigcell.sbml2.Compartment

setSpatialDimensions(int) - Method in class jigcell.sbml2.Compartment

Sets the number of spatial dimensions for the compartment.

setSpatialSizeUnits(String) - Method in class jigcell.sbml2.Species

setSpatialSizeUnits(UnitDefinition) - Method in class jigcell.sbml2.Species

setSpecies(String) - Method in class jigcell.sbml2.SimpleSpeciesReference

setSpecies(Species) - Method in class jigcell.sbml2.SimpleSpeciesReference

setStoichiometry(double) - Method in class jigcell.sbml2.SpeciesReference

Sets the rational stoichiometry of a reaction.

setStoichiometryMath(StoichiometryMath) - Method in class jigcell.sbml2.SpeciesReference

Sets the stoichiometry of a reaction.

setSubObjectReference(String) - Method in class jigcell.sbml2.FromObjectReference

setSubObjectReference(SubObjectReference) - Method in class jigcell.sbml2.FromObjectReference

setSubObjectReference(String) - Method in class jigcell.sbml2.ToObjectReference

setSubObjectReference(SubObjectReference) - Method in class jigcell.sbml2.ToObjectReference

setSubstanceUnits(String) - Method in class jigcell.sbml2.KineticLaw

setSubstanceUnits(UnitDefinition) - Method in class jigcell.sbml2.KineticLaw

setSubstanceUnits(String) - Method in class jigcell.sbml2.Species

setSubstanceUnits(UnitDefinition) - Method in class jigcell.sbml2.Species

setTextOfMathElement(String) - Method in class jigcell.sbml2.SBMLLevel2Reader

setTimeUnits(String) - Method in class jigcell.sbml2.Event

Sets the units of time that apply to the delay field.

setTimeUnits(UnitDefinition) - Method in class jigcell.sbml2.Event

setTimeUnits(String) - Method in class jigcell.sbml2.KineticLaw

setTimeUnits(UnitDefinition) - Method in class jigcell.sbml2.KineticLaw

setTraverse(boolean) - Method in class jigcell.sbml2.jep.JEP

Sets the value of the traverse option.

setTrigger(String) - Method in class jigcell.sbml2.Event

Sets the MathML boolean expression that defines when an event is fired on the transition from false to true.

setType(String) - Method in class jigcell.sbml2.Instance

Sets the instance's type, the default value is "simple" to indicate that only two resources are associated to each other.

setUnits(String) - Method in class jigcell.sbml2.Compartment

setUnits(UnitDefinition) - Method in class jigcell.sbml2.Compartment

setUnits(String) - Method in class jigcell.sbml2.Parameter

setUnits(UnitDefinition) - Method in class jigcell.sbml2.Parameter

setUp() - Method in class jigcell.sbml2.tests.SBMLModelTests

setUri(String) - Method in class jigcell.sbml2.math.Node

setValue(Object) - Method in class jigcell.sbml2.jep.ASTConstant

setValue(String) - Method in class jigcell.sbml2.math.MathElement

setValue(String) - Method in class jigcell.sbml2.math.Node

setValue(double) - Method in class jigcell.sbml2.Parameter

setVariable(String) - Method in class jigcell.sbml2.EventAssignment

setVariable(Compartment) - Method in class jigcell.sbml2.EventAssignment

setVariable(Parameter) - Method in class jigcell.sbml2.EventAssignment

setVariable(Species) - Method in class jigcell.sbml2.EventAssignment

setVariable(String) - Method in class jigcell.sbml2.VariableRule

setVariable(Compartment) - Method in class jigcell.sbml2.VariableRule

setVariable(Parameter) - Method in class jigcell.sbml2.VariableRule

setVariable(Species) - Method in class jigcell.sbml2.VariableRule

setVersion(int) - Method in class jigcell.sbml2.SBMLLevel2Document

SimpleNode - Class in jigcell.sbml2.jep

SimpleNode(int) - Constructor for class jigcell.sbml2.jep.SimpleNode

SimpleNode(Parser, int) - Constructor for class jigcell.sbml2.jep.SimpleNode

SimpleObjectReference - Class in jigcell.sbml2

A simple reference to an object contained in the model.

SimpleObjectReference() - Constructor for class jigcell.sbml2.SimpleObjectReference

SimpleSpeciesReference - Class in jigcell.sbml2

A reference to a species contained in the model.

SimpleSpeciesReference() - Constructor for class jigcell.sbml2.SimpleSpeciesReference

simpleTree - Variable in class jigcell.sbml2.math.MathMLExpression

size() - Method in class jigcell.sbml2.Annotations

size - Variable in class jigcell.sbml2.Compartment

size() - Method in class jigcell.sbml2.Notes

solve(String) - Method in class jigcell.sbml2.math.MathMLExpression

Solves for var and returns a parse tree.

solve_(Node, String) - Method in class jigcell.sbml2.math.MathMLExpression

Internal routine for separating left and right side of equations.

sp - Variable in class jigcell.sbml2.jep.JJTParserState

spatialDimensions - Variable in class jigcell.sbml2.Compartment

spatialSizeUnits - Variable in class jigcell.sbml2.Species

specialConstructor - Variable in exception jigcell.sbml2.jep.ParseException

This variable determines which constructor was used to create this object and thereby affects the semantics of the "getMessage" method (see below).

specialToken - Variable in class jigcell.sbml2.jep.Token

This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.

SPECIES - Static variable in class jigcell.sbml2.Model

species - Variable in class jigcell.sbml2.Model

species - Variable in class jigcell.sbml2.SimpleSpeciesReference

Species - Class in jigcell.sbml2

A chemical entity that takes part in a reaction.

Species() - Constructor for class jigcell.sbml2.Species

Species(Species) - Constructor for class jigcell.sbml2.Species

Creates a copy of this existing object.

Species(String, String) - Constructor for class jigcell.sbml2.Species

speciesElement - Variable in class jigcell.sbml2.Model

speciesIds - Variable in class jigcell.sbml2.ConservationRelationFinder

SpeciesReference - Class in jigcell.sbml2

A reference to a species contained in the model.

SpeciesReference() - Constructor for class jigcell.sbml2.SpeciesReference

SpeciesReference(SpeciesReference) - Constructor for class jigcell.sbml2.SpeciesReference

Creates a copy of this existing object.

SpeciesReference(Species) - Constructor for class jigcell.sbml2.SpeciesReference

stack - Variable in class jigcell.sbml2.jep.EvaluatorVisitor

Stack used for evaluating the expression

stack - Variable in class jigcell.sbml2.XMLReader

Start() - Method in class jigcell.sbml2.jep.Parser

GRAMMAR START

startDocument() - Method in class jigcell.sbml2.math.MathMLConvertorSAX

startDocument() - Method in class jigcell.sbml2.math.MathMLExpression.MathMLHandler

startElement(String, String, String, Attributes) - Method in class jigcell.sbml2.math.MathMLConvertorSAX

startElement(String, String, String, Attributes) - Method in class jigcell.sbml2.math.MathMLExpression.MathMLHandler

startElement(String, String, String, Attributes) - Method in class jigcell.sbml2.SBMLLevel2Reader

startPrefixMapping(String, String) - Method in class jigcell.sbml2.XMLReader

startSBMLElement(String, Attributes) - Method in class jigcell.sbml2.SBMLLevel2Reader

STATIC_LEXER_ERROR - Static variable in error jigcell.sbml2.jep.TokenMgrError

An attempt wass made to create a second instance of a static token manager.

staticFlag - Static variable in class jigcell.sbml2.jep.JavaCharStream

stoichiometry - Variable in class jigcell.sbml2.SpeciesReference

stoichiometryMath - Variable in class jigcell.sbml2.SpeciesReference

StoichiometryMath - Class in jigcell.sbml2

Special element used when the stoichiometry of a species reference is given in MathML.

StoichiometryMath() - Constructor for class jigcell.sbml2.StoichiometryMath

StoichiometryMath(StoichiometryMath) - Constructor for class jigcell.sbml2.StoichiometryMath

Creates a copy of this existing object.

stoichiometryMatrix - Variable in class jigcell.sbml2.ConservationRelationFinder

stringEquals(String, String) - Method in class jigcell.sbml2.tests.SBMLModelTests

stripComments(Node) - Method in class jigcell.sbml2.math.MathMLExpression

Return a parse tree with only elements that can be translated into code.

SUBMODEL - Static variable in class jigcell.sbml2.Model

subObjectElement - Variable in class jigcell.sbml2.FromObjectReference

subObjectElement - Variable in class jigcell.sbml2.ToObjectReference

subObjectReference - Variable in class jigcell.sbml2.FromObjectReference

SubObjectReference - Class in jigcell.sbml2

A reference to a subObject contained within an object in the model.

SubObjectReference() - Constructor for class jigcell.sbml2.SubObjectReference

SubObjectReference(SubObjectReference) - Constructor for class jigcell.sbml2.SubObjectReference

Creates a copy of this existing object.

SubObjectReference(SimpleObjectReference) - Constructor for class jigcell.sbml2.SubObjectReference

SubObjectReference(String) - Constructor for class jigcell.sbml2.SubObjectReference

subObjectReference - Variable in class jigcell.sbml2.ToObjectReference

substanceUnits - Variable in class jigcell.sbml2.KineticLaw

substanceUnits - Variable in class jigcell.sbml2.Species

suite() - Static method in class jigcell.sbml2.tests.AlgebraicModelTests

All of the tests in this test.

suite() - Static method in class jigcell.sbml2.tests.AlgebraicModelTests2

All of the tests in this test.

suite() - Static method in class jigcell.sbml2.tests.AssignmentModelTests

All of the tests in this test.

suite() - Static method in class jigcell.sbml2.tests.AssignmentModelTests2

All of the tests in this test.

suite() - Static method in class jigcell.sbml2.tests.BoundaryModelTests

All of the tests in this test.

suite() - Static method in class jigcell.sbml2.tests.BoundaryModelTests2

All of the tests in this test.

suite() - Static method in class jigcell.sbml2.tests.BranchModelTests

All of the tests in this test.

suite() - Static method in class jigcell.sbml2.tests.BranchModelTests2

All of the tests in this test.

suite() - Static method in class jigcell.sbml2.tests.CompartmentModelTests

All of the tests in this test.

suite() - Static method in class jigcell.sbml2.tests.CompartmentModelTests2

All of the tests in this test.

suite() - Static method in class jigcell.sbml2.tests.DelayModelTests

All of the tests in this test.

suite() - Static method in class jigcell.sbml2.tests.DelayModelTests2

All of the tests in this test.

suite() - Static method in class jigcell.sbml2.tests.EventModelTests

All of the tests in this test.

suite() - Static method in class jigcell.sbml2.tests.EventModelTests2

All of the tests in this test.

suite() - Static method in class jigcell.sbml2.tests.FunctionModelTests

All of the tests in this test.

suite() - Static method in class jigcell.sbml2.tests.FunctionModelTests2

All of the tests in this test.

suite() - Static method in class jigcell.sbml2.tests.ODEModelTests

All of the tests in this test.

suite() - Static method in class jigcell.sbml2.tests.ODEModelTests2

All of the tests in this test.

suite() - Static method in class jigcell.sbml2.tests.Tests

A suite containing all test suites for the SBML parser.

suite() - Static method in class jigcell.sbml2.tests.UnitModelTests

All of the tests in this test.

suite() - Static method in class jigcell.sbml2.tests.UnitModelTests2

All of the tests in this test.

swapRows(double[][], int, int) - Static method in class jigcell.sbml2.ConservationRelationFinder

SwitchTo(int) - Method in class jigcell.sbml2.jep.ParserTokenManager

symbolTable - Variable in class jigcell.sbml2.math.InfixExpression

SymbolTable - Class in jigcell.sbml2.math

SymbolTable keeps track of all names and strings in a model and their translated names in Fortran.

SymbolTable() - Constructor for class jigcell.sbml2.math.SymbolTable

Create a new empty symbol table.

SymbolTable(int) - Constructor for class jigcell.sbml2.math.SymbolTable

Create a new SymbolTable object with specified maximum ID length.

SymbolTable(SymbolTable.Mode) - Constructor for class jigcell.sbml2.math.SymbolTable

Creates a new empty SymbolTable object with the specified mode.

SymbolTable(SymbolTable.Mode, int) - Constructor for class jigcell.sbml2.math.SymbolTable

Creates a new empty SymbolTable with the specified mode and maximum id length.

SymbolTable(SymbolTable.Mode, int, boolean) - Constructor for class jigcell.sbml2.math.SymbolTable

Creates a new empty SymbolTable with the specified mode and maximum id length and request to pad.

SymbolTable.Mode - Class in jigcell.sbml2.math

These constants describe the type of symbol table.

SymbolTable.Mode(String, int) - Constructor for class jigcell.sbml2.math.SymbolTable.Mode

symTab - Variable in class jigcell.sbml2.jep.JEP

Symbol Table

T

tabs - Static variable in class jigcell.sbml2.math.MathMLExpression

testCompartment(String, boolean, String, double, int, String) - Method in class jigcell.sbml2.tests.SBMLModelTests

testCompartment0() - Method in class jigcell.sbml2.tests.AlgebraicModelTests

A test for compartments.

testCompartment0() - Method in class jigcell.sbml2.tests.AssignmentModelTests

A test for compartments.

testCompartment0() - Method in class jigcell.sbml2.tests.BoundaryModelTests

A test for compartments.

testCompartment0() - Method in class jigcell.sbml2.tests.BranchModelTests

A test for compartments.

testCompartment0() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for compartments.

testCompartment0() - Method in class jigcell.sbml2.tests.DelayModelTests

A test for compartments.

testCompartment0() - Method in class jigcell.sbml2.tests.EventModelTests

A test for compartments.

testCompartment0() - Method in class jigcell.sbml2.tests.FunctionModelTests

A test for compartments.

testCompartment0() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for compartments.

testCompartment0() - Method in class jigcell.sbml2.tests.UnitModelTests

A test for compartments.

testCompartment1() - Method in class jigcell.sbml2.tests.AlgebraicModelTests

A test for compartments.

testCompartment1() - Method in class jigcell.sbml2.tests.AssignmentModelTests

A test for compartments.

testCompartment1() - Method in class jigcell.sbml2.tests.BoundaryModelTests

A test for compartments.

testCompartment1() - Method in class jigcell.sbml2.tests.BranchModelTests

A test for compartments.

testCompartment1() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for compartments.

testCompartment1() - Method in class jigcell.sbml2.tests.DelayModelTests

A test for compartments.

testCompartment1() - Method in class jigcell.sbml2.tests.EventModelTests

A test for compartments.

testCompartment1() - Method in class jigcell.sbml2.tests.FunctionModelTests

A test for compartments.

testCompartment1() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for compartments.

testCompartment1() - Method in class jigcell.sbml2.tests.UnitModelTests

A test for compartments.

testCompartment2() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for compartments.

testCompartment2() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for compartments.

testCompartment3() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for compartments.

testEvent0() - Method in class jigcell.sbml2.tests.AlgebraicModelTests

A test for events.

testEvent0() - Method in class jigcell.sbml2.tests.AssignmentModelTests

A test for events.

testEvent0() - Method in class jigcell.sbml2.tests.BoundaryModelTests

A test for events.

testEvent0() - Method in class jigcell.sbml2.tests.BranchModelTests

A test for events.

testEvent0() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for events.

testEvent0() - Method in class jigcell.sbml2.tests.DelayModelTests

A test for events.

testEvent0() - Method in class jigcell.sbml2.tests.EventModelTests

A test for events.

testEvent0() - Method in class jigcell.sbml2.tests.FunctionModelTests

A test for events.

testEvent0() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for odes.

testEvent0() - Method in class jigcell.sbml2.tests.UnitModelTests

A test for units.

testFunction0() - Method in class jigcell.sbml2.tests.AlgebraicModelTests

A test for function definitions.

testFunction0() - Method in class jigcell.sbml2.tests.AssignmentModelTests

A test for function definitions.

testFunction0() - Method in class jigcell.sbml2.tests.BoundaryModelTests

A test for function definitions.

testFunction0() - Method in class jigcell.sbml2.tests.BranchModelTests

A test for function definitions.

testFunction0() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for function definitions.

testFunction0() - Method in class jigcell.sbml2.tests.DelayModelTests

A test for function definitions.

testFunction0() - Method in class jigcell.sbml2.tests.EventModelTests

A test for function definitions.

testFunction0() - Method in class jigcell.sbml2.tests.FunctionModelTests

A test for function definitions.

testFunction1() - Method in class jigcell.sbml2.tests.FunctionModelTests

A test for function definitions.

testFunctionDefinition(String) - Method in class jigcell.sbml2.tests.SBMLModelTests

testModel1() - Method in class jigcell.sbml2.tests.AlgebraicModelTests

A test for model.

testModel1() - Method in class jigcell.sbml2.tests.AssignmentModelTests

A test for model.

testModel1() - Method in class jigcell.sbml2.tests.BoundaryModelTests

A test for model.

testModel1() - Method in class jigcell.sbml2.tests.BranchModelTests

A test for model.

testModel1() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for model.

testModel1() - Method in class jigcell.sbml2.tests.DelayModelTests

A test for model.

testModel1() - Method in class jigcell.sbml2.tests.EventModelTests

A test for model.

testModel1() - Method in class jigcell.sbml2.tests.FunctionModelTests

A test for model.

testModel1() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for model.

testModel1() - Method in class jigcell.sbml2.tests.UnitModelTests

A test for model.

testParameter(String, double) - Method in class jigcell.sbml2.tests.SBMLModelTests

testParameter(String, double, String, boolean) - Method in class jigcell.sbml2.tests.SBMLModelTests

testParameter(Reaction, String, double) - Method in class jigcell.sbml2.tests.SBMLModelTests

testParameter(Iterator, String, double, String, boolean) - Method in class jigcell.sbml2.tests.SBMLModelTests

testParameter0() - Method in class jigcell.sbml2.tests.AlgebraicModelTests

A test for parameters.

testParameter0() - Method in class jigcell.sbml2.tests.AssignmentModelTests

A test for parameters.

testParameter0() - Method in class jigcell.sbml2.tests.BoundaryModelTests

A test for parameters.

testParameter0() - Method in class jigcell.sbml2.tests.BranchModelTests

A test for parameters.

testParameter0() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for parameters.

testParameter0() - Method in class jigcell.sbml2.tests.DelayModelTests

A test for parameters.

testParameter0() - Method in class jigcell.sbml2.tests.EventModelTests

A test for parameters.

testParameter0() - Method in class jigcell.sbml2.tests.FunctionModelTests

A test for parameters.

testParameter0() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for parameters.

testParameter0() - Method in class jigcell.sbml2.tests.UnitModelTests

A test for parameters.

testParameter1() - Method in class jigcell.sbml2.tests.AlgebraicModelTests

A test for parameters.

testParameter1() - Method in class jigcell.sbml2.tests.AssignmentModelTests

A test for parameters.

testParameter1() - Method in class jigcell.sbml2.tests.BoundaryModelTests

A test for parameters.

testParameter1() - Method in class jigcell.sbml2.tests.DelayModelTests

A test for parameters.

testParameter1() - Method in class jigcell.sbml2.tests.EventModelTests

A test for parameters.

testParameter1() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for parameters.

testParameter1() - Method in class jigcell.sbml2.tests.UnitModelTests

A test for parameters.

testParameter2() - Method in class jigcell.sbml2.tests.BoundaryModelTests

A test for parameters.

testParameter2() - Method in class jigcell.sbml2.tests.DelayModelTests

A test for parameters.

testParameter2() - Method in class jigcell.sbml2.tests.EventModelTests

A test for parameters.

testParameter2() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for parameters.

testParameter2() - Method in class jigcell.sbml2.tests.UnitModelTests

A test for parameters.

testParameter3() - Method in class jigcell.sbml2.tests.DelayModelTests

A test for parameters.

testParameter3() - Method in class jigcell.sbml2.tests.EventModelTests

A test for parameters.

testParameter3() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for parameters.

testParameter4() - Method in class jigcell.sbml2.tests.DelayModelTests

A test for parameters.

testParameter4() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for parameters.

testParameter5() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for parameters.

testParameter6() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for parameters.

testReaction(String, Boolean, boolean) - Method in class jigcell.sbml2.tests.SBMLModelTests

testReaction0() - Method in class jigcell.sbml2.tests.AlgebraicModelTests

A test for reactions.

testReaction0() - Method in class jigcell.sbml2.tests.AssignmentModelTests

A test for reactions.

testReaction0() - Method in class jigcell.sbml2.tests.BoundaryModelTests

A test for reactions.

testReaction0() - Method in class jigcell.sbml2.tests.BranchModelTests

A test for reactions.

testReaction0() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for reactions.

testReaction0() - Method in class jigcell.sbml2.tests.DelayModelTests

A test for reactions.

testReaction0() - Method in class jigcell.sbml2.tests.EventModelTests

A test for reactions.

testReaction0() - Method in class jigcell.sbml2.tests.FunctionModelTests

A test for reactions.

testReaction0() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for reactions.

testReaction0() - Method in class jigcell.sbml2.tests.UnitModelTests

A test for reactions.

testReaction1() - Method in class jigcell.sbml2.tests.AlgebraicModelTests

A test for reactions.

testReaction1() - Method in class jigcell.sbml2.tests.AssignmentModelTests

A test for reactions.

testReaction1() - Method in class jigcell.sbml2.tests.BoundaryModelTests

A test for reactions.

testReaction1() - Method in class jigcell.sbml2.tests.BranchModelTests

A test for reactions.

testReaction1() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for reactions.

testReaction1() - Method in class jigcell.sbml2.tests.FunctionModelTests

A test for reactions.

testReaction1() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for reactions.

testReaction1() - Method in class jigcell.sbml2.tests.UnitModelTests

A test for reactions.

testReaction2() - Method in class jigcell.sbml2.tests.AlgebraicModelTests

A test for reactions.

testReaction2() - Method in class jigcell.sbml2.tests.AssignmentModelTests

A test for reactions.

testReaction2() - Method in class jigcell.sbml2.tests.BranchModelTests

A test for reactions.

testReaction2() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for reactions.

testReaction2() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for reactions.

testReaction2() - Method in class jigcell.sbml2.tests.UnitModelTests

A test for reactions.

testReaction3() - Method in class jigcell.sbml2.tests.BranchModelTests

A test for reactions.

testReaction3() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for reactions.

testReaction3() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for reactions.

testReaction3() - Method in class jigcell.sbml2.tests.UnitModelTests

A test for reactions.

testReaction4() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for reactions.

testReaction4() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for reactions.

testReactionModifier(List, String) - Method in class jigcell.sbml2.tests.SBMLModelTests

testReactionModifier(List, String, double) - Method in class jigcell.sbml2.tests.SBMLModelTests

testRule0() - Method in class jigcell.sbml2.tests.AlgebraicModelTests

A test for rules.

testRule0() - Method in class jigcell.sbml2.tests.AssignmentModelTests

A test for rules.

testRule0() - Method in class jigcell.sbml2.tests.BoundaryModelTests

A test for rules.

testRule0() - Method in class jigcell.sbml2.tests.BranchModelTests

A test for rules.

testRule0() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for rules.

testRule0() - Method in class jigcell.sbml2.tests.DelayModelTests

A test for rules.

testRule0() - Method in class jigcell.sbml2.tests.EventModelTests

A test for rules.

testRule0() - Method in class jigcell.sbml2.tests.FunctionModelTests

A test for rules.

testRule0() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for rules.

testRule0() - Method in class jigcell.sbml2.tests.UnitModelTests

A test for rules.

Tests - Class in jigcell.sbml2.tests

Test harness for all SBML parser tests.

Tests() - Constructor for class jigcell.sbml2.tests.Tests

Tests should never be instantiated.

testSpecies(String, String, double, boolean, boolean) - Method in class jigcell.sbml2.tests.SBMLModelTests

testSpecies0() - Method in class jigcell.sbml2.tests.AlgebraicModelTests

A test for species.

testSpecies0() - Method in class jigcell.sbml2.tests.AssignmentModelTests

A test for species.

testSpecies0() - Method in class jigcell.sbml2.tests.BoundaryModelTests

A test for species.

testSpecies0() - Method in class jigcell.sbml2.tests.BranchModelTests

A test for species.

testSpecies0() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for species.

testSpecies0() - Method in class jigcell.sbml2.tests.DelayModelTests

A test for species.

testSpecies0() - Method in class jigcell.sbml2.tests.EventModelTests

A test for species.

testSpecies0() - Method in class jigcell.sbml2.tests.FunctionModelTests

A test for species.

testSpecies0() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for species.

testSpecies0() - Method in class jigcell.sbml2.tests.UnitModelTests

A test for species.

testSpecies1() - Method in class jigcell.sbml2.tests.AlgebraicModelTests

A test for species.

testSpecies1() - Method in class jigcell.sbml2.tests.AssignmentModelTests

A test for species.

testSpecies1() - Method in class jigcell.sbml2.tests.BoundaryModelTests

A test for species.

testSpecies1() - Method in class jigcell.sbml2.tests.BranchModelTests

A test for species.

testSpecies1() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for species.

testSpecies1() - Method in class jigcell.sbml2.tests.DelayModelTests

A test for species.

testSpecies1() - Method in class jigcell.sbml2.tests.EventModelTests

A test for species.

testSpecies1() - Method in class jigcell.sbml2.tests.FunctionModelTests

A test for species.

testSpecies1() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for species.

testSpecies1() - Method in class jigcell.sbml2.tests.UnitModelTests

A test for species.

testSpecies2() - Method in class jigcell.sbml2.tests.AlgebraicModelTests

A test for species.

testSpecies2() - Method in class jigcell.sbml2.tests.AssignmentModelTests

A test for species.

testSpecies2() - Method in class jigcell.sbml2.tests.BoundaryModelTests

A test for species.

testSpecies2() - Method in class jigcell.sbml2.tests.BranchModelTests

A test for species.

testSpecies2() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for species.

testSpecies2() - Method in class jigcell.sbml2.tests.EventModelTests

A test for species.

testSpecies2() - Method in class jigcell.sbml2.tests.FunctionModelTests

A test for species.

testSpecies2() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for species.

testSpecies2() - Method in class jigcell.sbml2.tests.UnitModelTests

A test for species.

testSpecies3() - Method in class jigcell.sbml2.tests.AlgebraicModelTests

A test for species.

testSpecies3() - Method in class jigcell.sbml2.tests.AssignmentModelTests

A test for species.

testSpecies3() - Method in class jigcell.sbml2.tests.BoundaryModelTests

A test for species.

testSpecies3() - Method in class jigcell.sbml2.tests.BranchModelTests

A test for species.

testSpecies3() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for species.

testSpecies3() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for species.

testSpecies3() - Method in class jigcell.sbml2.tests.UnitModelTests

A test for species.

testSpecies4() - Method in class jigcell.sbml2.tests.AlgebraicModelTests

A test for species.

testSpecies4() - Method in class jigcell.sbml2.tests.AssignmentModelTests

A test for species.

testSpecies4() - Method in class jigcell.sbml2.tests.BoundaryModelTests

A test for species.

testSpecies4() - Method in class jigcell.sbml2.tests.BranchModelTests

A test for species.

testSpecies4() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for species.

testSpecies4() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for species.

testSpecies4() - Method in class jigcell.sbml2.tests.UnitModelTests

A test for species.

testSpecies5() - Method in class jigcell.sbml2.tests.AlgebraicModelTests

A test for species.

testSpecies5() - Method in class jigcell.sbml2.tests.AssignmentModelTests

A test for species.

testSpecies5() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for species.

testSpecies5() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for species.

testSpecies6() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for species.

testSpecies7() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for species.

testSpecies8() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for species.

testUnit(Unit, int, String, double, double, int) - Method in class jigcell.sbml2.tests.SBMLModelTests

testUnit0() - Method in class jigcell.sbml2.tests.AlgebraicModelTests

A test for units.

testUnit0() - Method in class jigcell.sbml2.tests.AssignmentModelTests

A test for units.

testUnit0() - Method in class jigcell.sbml2.tests.BoundaryModelTests

A test for units.

testUnit0() - Method in class jigcell.sbml2.tests.BranchModelTests

A test for units.

testUnit0() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for units.

testUnit0() - Method in class jigcell.sbml2.tests.DelayModelTests

A test for units.

testUnit0() - Method in class jigcell.sbml2.tests.EventModelTests

A test for units.

testUnit0() - Method in class jigcell.sbml2.tests.FunctionModelTests

A test for units.

testUnit0() - Method in class jigcell.sbml2.tests.ODEModelTests

A test for units.

testUnit0() - Method in class jigcell.sbml2.tests.UnitModelTests

A test for units.

testUnit1() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for units.

testUnit1() - Method in class jigcell.sbml2.tests.UnitModelTests

A test for units.

testUnit2() - Method in class jigcell.sbml2.tests.CompartmentModelTests

A test for units.

testUnit2() - Method in class jigcell.sbml2.tests.UnitModelTests

A test for units.

testUnit3() - Method in class jigcell.sbml2.tests.UnitModelTests

A test for units.

testUnitDefinition(String, int) - Method in class jigcell.sbml2.tests.SBMLModelTests

text - Variable in class jigcell.sbml2.XMLPrinter

THEN - Static variable in interface jigcell.sbml2.jep.ParserConstants

timeUnits - Variable in class jigcell.sbml2.Event

timeUnits - Variable in class jigcell.sbml2.KineticLaw

token - Variable in class jigcell.sbml2.jep.Parser

Token - Class in jigcell.sbml2.jep

Describes the input token stream.

Token() - Constructor for class jigcell.sbml2.jep.Token

token_source - Variable in class jigcell.sbml2.jep.Parser

tokenBegin - Variable in class jigcell.sbml2.jep.JavaCharStream

tokenImage - Variable in exception jigcell.sbml2.jep.ParseException

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

tokenImage - Static variable in interface jigcell.sbml2.jep.ParserConstants

TokenLexicalActions(Token) - Method in class jigcell.sbml2.jep.ParserTokenManager

TokenMgrError - Error in jigcell.sbml2.jep

TokenMgrError() - Constructor for error jigcell.sbml2.jep.TokenMgrError

TokenMgrError(String, int) - Constructor for error jigcell.sbml2.jep.TokenMgrError

TokenMgrError(boolean, int, int, int, String, char, int) - Constructor for error jigcell.sbml2.jep.TokenMgrError

toNormalMath(String, boolean, boolean) - Static method in class jigcell.sbml2.math.MathMLConvertor

Gets the normal math representation of the string.

toObjectElement - Variable in class jigcell.sbml2.Link

toObjectReference - Variable in class jigcell.sbml2.Link

ToObjectReference - Class in jigcell.sbml2

A reference to a object contained in the model.

ToObjectReference() - Constructor for class jigcell.sbml2.ToObjectReference

ToObjectReference(ToObjectReference) - Constructor for class jigcell.sbml2.ToObjectReference

Creates a copy of this existing object.

ToObjectReference(SimpleObjectReference) - Constructor for class jigcell.sbml2.ToObjectReference

ToObjectReference(String) - Constructor for class jigcell.sbml2.ToObjectReference

topNode - Variable in class jigcell.sbml2.jep.JEP

Node at the top of the parse tree

toString() - Method in class jigcell.sbml2.Annotations

The SBML for this element.

toString() - Method in class jigcell.sbml2.ConservationRelationFinder.ConservationRelation

toString() - Method in class jigcell.sbml2.jep.ASTConstant

toString() - Method in class jigcell.sbml2.jep.ASTFunNode

Returns a string containing the function name.

toString() - Method in class jigcell.sbml2.jep.ASTVarNode

Creates a string containing the variable's name

toString() - Method in class jigcell.sbml2.jep.SimpleNode

toString(String) - Method in class jigcell.sbml2.jep.SimpleNode

toString() - Method in class jigcell.sbml2.jep.Token

Returns the image.

toString() - Method in class jigcell.sbml2.math.MathElement

toString() - Method in class jigcell.sbml2.math.MathMLExpression

toString() - Method in class jigcell.sbml2.math.Node

toString(String) - Method in class jigcell.sbml2.math.Node

toString() - Method in class jigcell.sbml2.math.SymbolTable.Mode

toString() - Method in class jigcell.sbml2.Notes

The SBML for this element.

toString() - Method in class jigcell.sbml2.XMLElement

Prints this element as XML.

toString() - Method in class jigcell.sbml2.XMLPrinter

toString(StringBuffer) - Method in class jigcell.sbml2.XMLPrinter

traverse - Variable in class jigcell.sbml2.jep.JEP

Traverse option

treeOutput(SBMLNode) - Static method in class jigcell.sbml2.math.MathMLConvertor

treeWithoutVar - Variable in class jigcell.sbml2.math.MathMLExpression.NoVarTree

trigger - Variable in class jigcell.sbml2.Event

triggerElement - Variable in class jigcell.sbml2.Event

TRUE - Static variable in interface jigcell.sbml2.jep.ParserConstants

type - Variable in class jigcell.sbml2.Instance

type - Variable in class jigcell.sbml2.math.MathMLConvertorSAX

U

UnaryExpression() - Method in class jigcell.sbml2.jep.Parser

UnaryExpressionNotPlusMinus() - Method in class jigcell.sbml2.jep.Parser

Unit - Class in jigcell.sbml2

Units of measurement for quantities in an SBML model.

Unit(Unit) - Constructor for class jigcell.sbml2.Unit

Creates a copy of this existing object.

Unit(Unit, double, int, int, double) - Constructor for class jigcell.sbml2.Unit

Creates a new unit.

Unit() - Constructor for class jigcell.sbml2.Unit

Unit(String) - Constructor for class jigcell.sbml2.Unit

Creates a new base unit.

UNITDEFINITION - Static variable in class jigcell.sbml2.Model

UnitDefinition - Class in jigcell.sbml2

Gives an abbreviated name to a combination of units.

UnitDefinition() - Constructor for class jigcell.sbml2.UnitDefinition

UnitDefinition(UnitDefinition) - Constructor for class jigcell.sbml2.UnitDefinition

Creates a copy of this existing object.

UnitDefinition(String, String) - Constructor for class jigcell.sbml2.UnitDefinition

unitDefinitions - Variable in class jigcell.sbml2.Model

unitDefinitionsElement - Variable in class jigcell.sbml2.Model

UnitModelTests - Class in jigcell.sbml2.tests

A collection of tests to exercise the reference model for units.

UnitModelTests(String) - Constructor for class jigcell.sbml2.tests.UnitModelTests

Creates a new test for the reference model for units.

UnitModelTests2 - Class in jigcell.sbml2.tests

A collection of tests to exercise the reference model for units.

UnitModelTests2(String) - Constructor for class jigcell.sbml2.tests.UnitModelTests2

Creates a new test for the reference model for units.

units - Variable in class jigcell.sbml2.Compartment

units - Variable in class jigcell.sbml2.Parameter

units - Variable in class jigcell.sbml2.UnitDefinition

unitsElement - Variable in class jigcell.sbml2.UnitDefinition

unsetCharge() - Method in class jigcell.sbml2.Species

unsetFast() - Method in class jigcell.sbml2.Reaction

UpdateLineColumn(char) - Method in class jigcell.sbml2.jep.JavaCharStream

uri - Variable in class jigcell.sbml2.math.Node

V

validateConservationRelations(List) - Method in class jigcell.sbml2.ConservationRelationFinder

Checks that the given conservation relations are consistent with the conservation relations found in the model.

value - Variable in class jigcell.sbml2.jep.ASTConstant

value - Variable in class jigcell.sbml2.math.MathElement

value - Variable in class jigcell.sbml2.math.Node

value - Variable in class jigcell.sbml2.Parameter

variable - Variable in class jigcell.sbml2.EventAssignment

Variable() - Method in class jigcell.sbml2.jep.Parser

variable - Variable in class jigcell.sbml2.VariableRule

VariableRule - Class in jigcell.sbml2

A rule whose left-hand side is a variable.

VariableRule() - Constructor for class jigcell.sbml2.VariableRule

varName - Variable in class jigcell.sbml2.jep.ASTVarNode

varWasHere - Variable in class jigcell.sbml2.math.MathMLExpression.NoVarTree

visit(SimpleNode, Object) - Method in class jigcell.sbml2.jep.EvaluatorVisitor

This method should never be called when evaluation a normal expression.

visit(ASTStart, Object) - Method in class jigcell.sbml2.jep.EvaluatorVisitor

This method should never be called when evaluating a normal expression.

visit(ASTFunNode, Object) - Method in class jigcell.sbml2.jep.EvaluatorVisitor

Visit a function node.

visit(ASTVarNode, Object) - Method in class jigcell.sbml2.jep.EvaluatorVisitor

visit(ASTConstant, Object) - Method in class jigcell.sbml2.jep.EvaluatorVisitor

visit(ASTIfThen, Object) - Method in class jigcell.sbml2.jep.EvaluatorVisitor

visit(ASTElse, Object) - Method in class jigcell.sbml2.jep.EvaluatorVisitor

visit(ASTPiecewise, Object) - Method in class jigcell.sbml2.jep.EvaluatorVisitor

visit(ASTElseIfThen, Object) - Method in class jigcell.sbml2.jep.EvaluatorVisitor

visit(SimpleNode, Object) - Method in class jigcell.sbml2.jep.ParserDumpVisitor

visit(ASTPiecewise, Object) - Method in class jigcell.sbml2.jep.ParserDumpVisitor

visit(ASTStart, Object) - Method in class jigcell.sbml2.jep.ParserDumpVisitor

visit(ASTFunNode, Object) - Method in class jigcell.sbml2.jep.ParserDumpVisitor

visit(ASTVarNode, Object) - Method in class jigcell.sbml2.jep.ParserDumpVisitor

visit(ASTConstant, Object) - Method in class jigcell.sbml2.jep.ParserDumpVisitor

visit(ASTIfThen, Object) - Method in class jigcell.sbml2.jep.ParserDumpVisitor

visit(ASTElseIfThen, Object) - Method in class jigcell.sbml2.jep.ParserDumpVisitor

visit(ASTElse, Object) - Method in class jigcell.sbml2.jep.ParserDumpVisitor

visit(SimpleNode, Object) - Method in interface jigcell.sbml2.jep.ParserVisitor

visit(ASTStart, Object) - Method in interface jigcell.sbml2.jep.ParserVisitor

visit(ASTFunNode, Object) - Method in interface jigcell.sbml2.jep.ParserVisitor

visit(ASTVarNode, Object) - Method in interface jigcell.sbml2.jep.ParserVisitor

visit(ASTIfThen, Object) - Method in interface jigcell.sbml2.jep.ParserVisitor

visit(ASTElseIfThen, Object) - Method in interface jigcell.sbml2.jep.ParserVisitor

visit(ASTElse, Object) - Method in interface jigcell.sbml2.jep.ParserVisitor

visit(ASTPiecewise, Object) - Method in interface jigcell.sbml2.jep.ParserVisitor

visit(ASTConstant, Object) - Method in interface jigcell.sbml2.jep.ParserVisitor

W

warning(SAXParseException) - Method in class jigcell.sbml2.math.MathMLConvertorSAX.MyErrorHandler

wrapItem(String) - Static method in class jigcell.sbml2.Annotations

wrapItem(String) - Static method in class jigcell.sbml2.Notes

write(Writer) - Method in class jigcell.sbml2.XMLPrinter

writeDocument(OutputStream) - Method in class jigcell.sbml2.SBMLLevel2Document

writeDocument(String) - Method in class jigcell.sbml2.SBMLLevel2Document

writeDocument(Writer) - Method in class jigcell.sbml2.SBMLLevel2Document

Writes an SBML document and closes the writer.

X

XMLElement - Class in jigcell.sbml2

Base class for elements used with the XML reader and printer.

XMLElement() - Constructor for class jigcell.sbml2.XMLElement

XMLPrinter - Class in jigcell.sbml2

Used to format and print XML.

XMLPrinter(String) - Constructor for class jigcell.sbml2.XMLPrinter

XMLPrinter(XMLPrinter, String) - Constructor for class jigcell.sbml2.XMLPrinter

XMLReader - Class in jigcell.sbml2

XMLReader() - Constructor for class jigcell.sbml2.XMLReader

XOR - Static variable in interface jigcell.sbml2.jep.ParserConstants

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