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

A

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

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

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

accept(SBase) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

addConstantId(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

Add an id to the list

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

Adds a new Dimension to the listOfDimensions.

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ArraysSBasePluginConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DimensionConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.IndexConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ArraysSBasePluginConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DimensionConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.IndexConstraints

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

Adds a new Index to the listOfIndices.

addValue(String, double) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

Adds a new string,double pair to the idToValue.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

arrayDimension - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants

ArraysCompiler - Class in org.sbml.jsbml.ext.arrays.compiler

This compiler is used to evaluate an ASTNode object to a real number.

ArraysCompiler() - Constructor for class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

Constructs an ArraysCompiler object.

ArraysCompiler(ArraysCompiler) - Constructor for class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

Clone constructor

ArraysConstants - Class in org.sbml.jsbml.ext.arrays

This is where the constants that are frequently used in the arrays package are defined.

ArraysConstants() - Constructor for class org.sbml.jsbml.ext.arrays.ArraysConstants

ArraysConstraint - Class in org.sbml.jsbml.ext.arrays.validator.constraints

An ArraysConstraint object ensures that a given Model doesn't violate a certain validation rule defined in the arrays specification.

ArraysConstraint() - Constructor for class org.sbml.jsbml.ext.arrays.validator.constraints.ArraysConstraint

Constructs an ArraysConstraint.

ArraysConstraint(Model) - Constructor for class org.sbml.jsbml.ext.arrays.validator.constraints.ArraysConstraint

Constructs an ArraysConstraint with a model.

ArraysFlattening - Class in org.sbml.jsbml.ext.arrays.flattening

ArraysFlattening() - Constructor for class org.sbml.jsbml.ext.arrays.flattening.ArraysFlattening

ArraysMath - Class in org.sbml.jsbml.ext.arrays.util

ArraysMath() - Constructor for class org.sbml.jsbml.ext.arrays.util.ArraysMath

ArraysMathCheck - Class in org.sbml.jsbml.ext.arrays.validator.constraints

ArraysMathCheck(Model, MathContainer) - Constructor for class org.sbml.jsbml.ext.arrays.validator.constraints.ArraysMathCheck

ArraysMathValidator - Class in org.sbml.jsbml.ext.arrays.validator

This checks a given MathContainer object math is in accordance with the arrays package specification.

ArraysMathValidator() - Constructor for class org.sbml.jsbml.ext.arrays.validator.ArraysMathValidator

ArraysParser - Class in org.sbml.jsbml.xml.parsers

ArraysParser() - Constructor for class org.sbml.jsbml.xml.parsers.ArraysParser

ArraysSBasePlugin - Class in org.sbml.jsbml.ext.arrays

The ArraysSBasePlugin class extends the SBase class by adding an optional ListOfDimensions child and a single optional Index child.

ArraysSBasePlugin() - Constructor for class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Creates an new ArraysSBasePlugin instance.

ArraysSBasePlugin(SBase) - Constructor for class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Creates an new ArraysSBasePlugin instance.

ArraysSBasePlugin(ArraysSBasePlugin) - Constructor for class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Clone constructor

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

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

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

Contains some utility methods for the Arrays package validation.

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

ArraysValidator - Class in org.sbml.jsbml.ext.arrays.validator

The ArraysValidator is used to ensure that an SBMLDocument does not violate any validation rules specified in the Arrays Package Specifications.

ArraysValidator() - Constructor for class org.sbml.jsbml.ext.arrays.validator.ArraysValidator

C

canHaveDimension(SBase) - Static method in class org.sbml.jsbml.ext.arrays.validator.ExtendedSBaseValidator

Checks if this SBase can have a list of Dimension.

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

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

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

check() - Method in class org.sbml.jsbml.ext.arrays.validator.constraints.ArraysConstraint

Checks if the given model doesn't violate the constraint specified by this object.

check() - Method in class org.sbml.jsbml.ext.arrays.validator.constraints.ArraysMathCheck

check() - Method in class org.sbml.jsbml.ext.arrays.validator.constraints.DimensionArrayDimCheck

check() - Method in class org.sbml.jsbml.ext.arrays.validator.constraints.DimensionIDCheck

check() - Method in class org.sbml.jsbml.ext.arrays.validator.constraints.DimensionSizeCheck

check() - Method in class org.sbml.jsbml.ext.arrays.validator.constraints.IndexArrayDimCheck

check() - Method in class org.sbml.jsbml.ext.arrays.validator.constraints.IndexAttributesCheck

check() - Method in class org.sbml.jsbml.ext.arrays.validator.constraints.SBaseWithDimensionCheck

checkListOfErrors(List<SBMLError>, int) - Static method in class org.sbml.jsbml.validator.offline.constraints.ArraysUtils

Checks the list of SBMLError to see if it contains the given error code, returns true if it is found, else otherwise.

checkVectorAssignment(Model, MathContainer) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

checkVectorMath(Model, MathContainer) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

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

clone() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

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

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

clones this class

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

clones this class

compile(Compartment) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

compile(double, int, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

compile(double, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

compile(int, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

compile(CallableSBase) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

compile(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

compile(Compartment) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

compile(double, int, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

compile(double, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

compile(int, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

compile(CallableSBase) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

compile(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

compile(Compartment) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

compile(double, int, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

compile(double, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

compile(int, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

compile(CallableSBase) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

compile(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

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

convert(SBMLDocument) - Static method in class org.sbml.jsbml.ext.arrays.flattening.ArraysFlattening

This method flattens out arrays objects of a given SBMLDocument.

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

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

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

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

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

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

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

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

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

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

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

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

createDimension() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Creates a new Dimension element and adds it to the ListOfDimensions list.

createDimension(String) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Creates a new Dimension element and adds it to the ListOfDimensions list.

createIndex() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Creates a new Index element and adds it to the listOfIndices list.

createPluginFor(SBase) - Method in class org.sbml.jsbml.xml.parsers.ArraysParser

createPluginFor(ASTNode) - Method in class org.sbml.jsbml.xml.parsers.ArraysParser

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

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

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

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

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

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

D

delay(String, ASTNode, ASTNode, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

delay(String, ASTNode, ASTNode, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

delay(String, ASTNode, ASTNode, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

dimension - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants

Dimension - Class in org.sbml.jsbml.ext.arrays

The Dimension is used to indicate the parent SBase is arrayed.

Dimension() - Constructor for class org.sbml.jsbml.ext.arrays.Dimension

Creates an Dimension instance

Dimension(String) - Constructor for class org.sbml.jsbml.ext.arrays.Dimension

Creates a Dimension instance with an id.

Dimension(int, int) - Constructor for class org.sbml.jsbml.ext.arrays.Dimension

Creates a Dimension instance with a level and version.

Dimension(String, int, int) - Constructor for class org.sbml.jsbml.ext.arrays.Dimension

Creates a Dimension instance with an id, level, and version.

Dimension(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.arrays.Dimension

Creates a Dimension instance with an id, name, level, and version.

Dimension(Dimension) - Constructor for class org.sbml.jsbml.ext.arrays.Dimension

Clone constructor

DimensionArrayDimCheck - Class in org.sbml.jsbml.ext.arrays.validator.constraints

Checks if the Dimension objects of a given SBase have valid array dimension.

DimensionArrayDimCheck(Model, SBase) - Constructor for class org.sbml.jsbml.ext.arrays.validator.constraints.DimensionArrayDimCheck

Creates a DimensionArrayDimCheck with a model and sbase.

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

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

DimensionIDCheck - Class in org.sbml.jsbml.ext.arrays.validator.constraints

DimensionIDCheck(Model, SBase) - Constructor for class org.sbml.jsbml.ext.arrays.validator.constraints.DimensionIDCheck

DimensionSizeCheck - Class in org.sbml.jsbml.ext.arrays.validator.constraints

Checks if the given Dimension object has size that is both scalar and constant.

DimensionSizeCheck(Model, Dimension) - Constructor for class org.sbml.jsbml.ext.arrays.validator.constraints.DimensionSizeCheck

DimensionValidator - Class in org.sbml.jsbml.ext.arrays.validator

Validates a given Dimension object in the context of a given model and makes sure that the dimension object is in accordance with the arrays package specification.

DimensionValidator() - Constructor for class org.sbml.jsbml.ext.arrays.validator.DimensionValidator

E

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

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

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

equals(Object) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

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

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

evaluateBounds(Map<String, Double>, ASTNode, double) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Checks if the math does not evaluate to a negative number or to a value greater or equal to a given size value.

evaluateIndexBounds(Model, Index) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Checks if the index math does not go out of bounds.

evaluateIndexBounds(Model, SBase, int, ASTNode, Map<String, Double>) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Checks if adding an Index object to a parent SBase object for referencing another SBase object does not cause out-of-bounds issues.

evaluateIndexBounds(Model, SBase, String, ASTNode, int) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Checks if adding an Index object to a parent SBase object for referencing another SBase object does not cause out-of-bounds issues.

evaluateSelectorBounds(Model, MathContainer) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Checks if the arguments of a selector function does not go out of bounds.

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

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

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

ExtendedSBaseValidator - Class in org.sbml.jsbml.ext.arrays.validator

Validates a given SBase object in the context of a given model and makes sure that the SBase object is in accordance with the arrays package specification.

ExtendedSBaseValidator() - Constructor for class org.sbml.jsbml.ext.arrays.validator.ExtendedSBaseValidator

F

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

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

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

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

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

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

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

frac(int, int) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

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

frac(int, int) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

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

frac(int, int) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

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

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

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

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

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

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

G

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

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

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

getAllowsChildren() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

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

Returns the value of arrayDimension

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

Returns the value of arrayDimension

getChildAt(int) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

getChildCount() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

getConstantAvogadro(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

getConstantAvogadro(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

getConstantAvogadro(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

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

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

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

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

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

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

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

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

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

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

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

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

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

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

getDimension(int) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Gets an element from the listOfDimensions at the given index.

getDimension(String) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Gets an element from the listOfDimensions, with the given id.

getDimensionByArrayDimension(int) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Gets an element from the listOfDimensions at the given arrayDimension.

getDimensionCount() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Returns the number of Dimensions in this ArraysSBasePlugin.

getDimensionSizes(Model, ArraysSBasePlugin) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Maps a dimension id to the size of the dimension object.

getElementNamespace() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

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

Returns the number of values in this ArraysCompiler.

getIndex(int) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Gets an element from the listOfIndices at the given index.

getIndex(int, String) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Gets an element from the listOfIndices based on array dimension and referenced attribute.

getIndexCount() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Returns the number of Indexs in this ArraysSBasePlugin.

getListOfDimensions() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Returns the listOfDimensions.

getListOfErrors() - Method in class org.sbml.jsbml.ext.arrays.validator.constraints.ArraysConstraint

Gets the listOfErrors after checking the model.

getListOfIndices() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Returns the listOfIndices.

getLowerBound(Map<String, Double>) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Returns the lower bound index from a collection of Dimension objects.

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

Returns the idToValue Map.

getNamespaceFor(int, int, int) - Method in class org.sbml.jsbml.xml.parsers.ArraysParser

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.ArraysParser

getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.arrays.ArraysConstants

Returns the namespace URI associated with the arrays package.

getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.ArraysParser

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

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

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

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

getNumDimensions() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Returns the number of Dimensions in this ArraysSBasePlugin.

getNumIndices() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Returns the number of Indexs in this ArraysSBasePlugin.

getPackageName() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

getPackageName() - Method in class org.sbml.jsbml.xml.parsers.ArraysParser

getPackageNamespaces() - Method in class org.sbml.jsbml.xml.parsers.ArraysParser

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

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

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

getPrefix() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

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

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

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

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

Returns the value of referencedAttribute

getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.ArraysParser

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

Returns the value of size

getSize(Model, Dimension) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Gets the size of a Dimension object.

getUpperBound(Map<String, Double>) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Returns the upper bound index from a collection of Dimension objects.

getURI() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ArraysSBasePluginConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DimensionConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.IndexConstraints

getValue(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

Gets an element from the idToValue, with the given id.

getVectorDimensionSizes(Model, ASTNode) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Returns a map containing a pair of array depth level and its size.

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

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

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

H

hashCode() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

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

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

I

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

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

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

index - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants

Index - Class in org.sbml.jsbml.ext.arrays

The Index is used to referenced an arrayed element specified in an attribute.

Index() - Constructor for class org.sbml.jsbml.ext.arrays.Index

Creates an Index instance

Index(int, int) - Constructor for class org.sbml.jsbml.ext.arrays.Index

Creates a Index instance with a level and version.

Index(Index) - Constructor for class org.sbml.jsbml.ext.arrays.Index

Clone constructor

IndexArrayDimCheck - Class in org.sbml.jsbml.ext.arrays.validator.constraints

Checks if the Index objects of a given SBase have valid array dimension.

IndexArrayDimCheck(Model, SBase) - Constructor for class org.sbml.jsbml.ext.arrays.validator.constraints.IndexArrayDimCheck

Creates a new IndexArrayDimCheck instance with a model and sbase

IndexAttributesCheck - Class in org.sbml.jsbml.ext.arrays.validator.constraints

This checks that a given Index object references a valid referenced attribute and that it doesn't go out of bounds.

IndexAttributesCheck(Model, Index) - Constructor for class org.sbml.jsbml.ext.arrays.validator.constraints.IndexAttributesCheck

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

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

IndexValidator - Class in org.sbml.jsbml.ext.arrays.validator

Validates a given Index object in the context of a given model and makes sure that the Index object is in accordance with the arrays package specification.

IndexValidator() - Constructor for class org.sbml.jsbml.ext.arrays.validator.IndexValidator

initDefaults() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Initializes the default values using the namespace.

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

Initializes the default values using the namespace.

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

Initializes the default values using the namespace.

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

isRequired() - Method in class org.sbml.jsbml.xml.parsers.ArraysParser

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

Returns whether arrayDimension is set

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

Returns whether arrayDimension is set

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

Returns true, if idToValue contains at least one element.

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

isSetListOfDimensions() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Returns true, if listOfDimensions contains at least one element.

isSetListOfIndices() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Returns true, if listOfIndices contains at least one element.

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

Returns whether referencedAttribute is set

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

Returns whether size is set

isStaticallyComputable(Model, Index) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Determines whether a MathContainer object is statically computable.

isStaticallyComputable(Model, MathContainer) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Determines whether a MathContainer object is statically computable.

isStaticallyComputable(Model, MathContainer, String...) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Determines whether a MathContainer object is statically computable given a list of ids that can appear in the math.

isStaticallyComputable(Model, ASTNode, String...) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

Determines whether a MathContainer object is statically computable given a list of ids that can appear in the math.

isVectorBalanced(Model, MathContainer) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

isVectorOperation(ASTNode) - Static method in class org.sbml.jsbml.ext.arrays.util.ArraysMath

L

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

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

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

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

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

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

listOfDimensions - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants

listOfErrors - Variable in class org.sbml.jsbml.ext.arrays.validator.constraints.ArraysConstraint

This is used to track SBMLErrors that are detected in the model.

listOfIndices - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants

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

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

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

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

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

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

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

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

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

logFailure(int, int, int, int, int, String, String, String) - Method in class org.sbml.jsbml.ext.arrays.validator.constraints.ArraysConstraint

Logs an error when checking the given model.

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

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

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

M

math - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants

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

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

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

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

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

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

MIN_SBML_LEVEL - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants

MIN_SBML_VERSION - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants

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

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

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

model - Variable in class org.sbml.jsbml.ext.arrays.validator.constraints.ArraysConstraint

A Model to be checked.

N

namespaces - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants

namespaceURI - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants

The namespace URI of this parser, this value can change between releases.

namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants

The namespace URI of this parser for SBML level 3, version 1 and package version 1.

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

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

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

not(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

not(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

not(ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

O

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

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

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

org.sbml.jsbml.ext.arrays - package org.sbml.jsbml.ext.arrays

org.sbml.jsbml.ext.arrays.compiler - package org.sbml.jsbml.ext.arrays.compiler

org.sbml.jsbml.ext.arrays.flattening - package org.sbml.jsbml.ext.arrays.flattening

org.sbml.jsbml.ext.arrays.util - package org.sbml.jsbml.ext.arrays.util

org.sbml.jsbml.ext.arrays.validator - package org.sbml.jsbml.ext.arrays.validator

org.sbml.jsbml.ext.arrays.validator.constraints - package org.sbml.jsbml.ext.arrays.validator.constraints

org.sbml.jsbml.validator.offline.constraints - package org.sbml.jsbml.validator.offline.constraints

org.sbml.jsbml.xml.parsers - package org.sbml.jsbml.xml.parsers

P

packageName - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants

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

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

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

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

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

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

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

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

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

processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.ArraysParser

Q

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

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

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

R

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.arrays.Dimension

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.arrays.Index

referencedAttribute - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants

register(SBase) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

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

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

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

removeConstantId(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

Removes an id from the list.

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

Removes an element from the listOfDimensions.

removeDimension(String) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Removes an element from the listOfDimensions.

removeDimension(int) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Removes an element from the listOfDimensions at the given index.

removeDimensionByArrayDimension(int) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Removes an element from the listOfDimensions by array dimension.

removeField(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

Removes an element from the idToValue.

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

Removes an element from the listOfIndices.

removeIndex(int) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Removes an element from the listOfIndices at the given index.

removeIndexByArrayDimension(int) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Removes an element from the listOfIndices based on array dimension.

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

root(double, ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

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

root(double, ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

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

root(double, ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

S

SBaseWithDimensionCheck - Class in org.sbml.jsbml.ext.arrays.validator.constraints

Checks that the given SBase does not have a listOfDimensions, otherwise reports an error.

SBaseWithDimensionCheck(Model, SBase) - Constructor for class org.sbml.jsbml.ext.arrays.validator.constraints.SBaseWithDimensionCheck

Creates a new SBaseWithDimensionCheck with a model and sbase.

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

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

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

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

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

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

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

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

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

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

Sets the value of arrayDimension

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

Sets the value of arrayDimension

setidToValue(Map<String, Double>) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

Sets the given map.

setIdToVector(Map<String, ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

setListOfDimensions(ListOf<Dimension>) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Sets the given ListOf<Dimension>.

setListOfIndices(ListOf<Index>) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Sets the given ListOf<Index>.

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

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

Sets the value of referencedAttribute

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

Sets the value of size

shortLabel - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants

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

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

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

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

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

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

size - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants

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

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

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

StaticallyComputableCompiler - Class in org.sbml.jsbml.ext.arrays.compiler

This compiler is used to check if an ASTNode object contains only constant values or Dimension ids.

StaticallyComputableCompiler(Model) - Constructor for class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

Constructs a new StaticallyComputableCompiler object

symbolTime(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler

symbolTime(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler

symbolTime(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

T

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

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

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

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

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

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

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

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

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

U

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

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

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

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

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

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

unregister(SBase) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

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

Unsets the variable arrayDimension

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

Unsets the variable arrayDimension

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

Returns true, if idToValue contain at least one element, otherwise false.

unsetListOfDimensions() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Returns true, if listOfDimensions contain at least one element, otherwise false.

unsetListOfIndices() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

Returns true, if listOfIndices contain at least one element, otherwise false.

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

Unsets the variable referencedAttribute

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

Unsets the variable size

V

validate(Model, MathContainer) - Static method in class org.sbml.jsbml.ext.arrays.validator.ArraysMathValidator

Validates the given SBase object.

validate(SBMLDocument) - Static method in class org.sbml.jsbml.ext.arrays.validator.ArraysValidator

Validates the given SBMLDocument

validate(SBMLDocument, boolean) - Static method in class org.sbml.jsbml.ext.arrays.validator.ArraysValidator

Validates the given SBMLDocument

validate(Model, Dimension) - Static method in class org.sbml.jsbml.ext.arrays.validator.DimensionValidator

Validates the given SBase object.

validate(Model, SBase) - Static method in class org.sbml.jsbml.ext.arrays.validator.ExtendedSBaseValidator

Validates the given SBase object.

validate(Model, Index) - Static method in class org.sbml.jsbml.ext.arrays.validator.IndexValidator

Validates the given SBase object.

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

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

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

VectorCompiler - Class in org.sbml.jsbml.ext.arrays.compiler

VectorCompiler(Model) - Constructor for class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

VectorCompiler(Model, boolean) - Constructor for class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

VectorCompiler(Model, NamedSBase, boolean) - Constructor for class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

VectorCompiler(Model, boolean, Map<String, ASTNode>) - Constructor for class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler

W

writeElement(SBMLObjectForXML, Object) - Method in class org.sbml.jsbml.xml.parsers.ArraysParser

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

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

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

X

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

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

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

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