- about - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- ABOVE - org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm.RelativePosition
-
- abs(double, MathContainer) - Static method in class org.sbml.jsbml.ASTNode
-
Creates and returns an
ASTNode
that computes the absolute value
of the given double value.
- abs(int, MathContainer) - Static method in class org.sbml.jsbml.ASTNode
-
Creates and returns an
ASTNode
that computes the absolute value
of the given integer value.
- 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
-
- abs(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
The absolute value represented by the given
ASTNode
.
- abs(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- abs(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- abs(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- abs(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- abs(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- abs(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
The absolute value represented by the given
ASTNode2
.
- abs(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- abs(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- abs(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- abs(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- ABS - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- absoluteCx - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- absoluteCy - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- absoluteCz - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- absoluteFx - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- absoluteFy - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- absoluteFz - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- absoluteHeight - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- absoluteR - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- absoluteRx - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- absoluteRy - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- absoluteValue - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
Refers to the absolute part of a RelAbsVector
- absoluteWidth - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- absoluteX - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- absoluteX1 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- absoluteX2 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- absoluteY - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- absoluteY1 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- absoluteY2 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- absoluteZ - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- absoluteZ1 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- absoluteZ2 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- AbstractASTNode - Class in org.sbml.jsbml.math
-
A node in the Abstract Syntax Tree (AST) representation
of a mathematical expression.
- AbstractASTNode() - Constructor for class org.sbml.jsbml.math.AbstractASTNode
-
- AbstractASTNode(ASTNode2) - Constructor for class org.sbml.jsbml.math.AbstractASTNode
-
- AbstractASTNode(MathContainer) - Constructor for class org.sbml.jsbml.math.AbstractASTNode
-
- AbstractASTNodePlugin - Class in org.sbml.jsbml.ext
-
- AbstractASTNodePlugin() - Constructor for class org.sbml.jsbml.ext.AbstractASTNodePlugin
-
- AbstractASTNodePlugin(ASTNode) - Constructor for class org.sbml.jsbml.ext.AbstractASTNodePlugin
-
- AbstractASTNodePlugin(ASTNodePlugin) - Constructor for class org.sbml.jsbml.ext.AbstractASTNodePlugin
-
This method will need to be further tested
- AbstractConstraint<T> - Class in org.sbml.jsbml.validator.offline.constraints
-
Abstract generic mother class for all the constraints.
- AbstractConstraintDeclaration - Class in org.sbml.jsbml.validator.offline.constraints
-
Abstract mother class for all constraints declarations.
- AbstractConstraintDeclaration() - Constructor for class org.sbml.jsbml.validator.offline.constraints.AbstractConstraintDeclaration
-
- AbstractDistribSBase - Class in org.sbml.jsbml.ext.distrib
-
- AbstractDistribSBase() - Constructor for class org.sbml.jsbml.ext.distrib.AbstractDistribSBase
-
- AbstractDistribSBase(int, int) - Constructor for class org.sbml.jsbml.ext.distrib.AbstractDistribSBase
-
- AbstractDistribSBase(String) - Constructor for class org.sbml.jsbml.ext.distrib.AbstractDistribSBase
-
- AbstractDistribSBase(String, int, int) - Constructor for class org.sbml.jsbml.ext.distrib.AbstractDistribSBase
-
- AbstractDistribSBase(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.distrib.AbstractDistribSBase
-
- AbstractDistribSBase(AbstractDistribSBase) - Constructor for class org.sbml.jsbml.ext.distrib.AbstractDistribSBase
-
- AbstractFBCSBasePlugin - Class in org.sbml.jsbml.ext.fbc
-
Represents the basic properties of all
SBasePlugin
in the FBC package.
- AbstractFBCSBasePlugin() - Constructor for class org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin
-
- AbstractFBCSBasePlugin(AbstractFBCSBasePlugin) - Constructor for class org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin
-
- AbstractFBCSBasePlugin(SBase) - Constructor for class org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin
-
- AbstractLayoutBuilder<P,NodeT,ArcT> - Class in org.sbml.jsbml.ext.render.director
-
- AbstractLayoutBuilder() - Constructor for class org.sbml.jsbml.ext.render.director.AbstractLayoutBuilder
-
- AbstractMathContainer - Class in org.sbml.jsbml
-
Base class for all the SBML components which contain MathML nodes.
- AbstractMathContainer() - Constructor for class org.sbml.jsbml.AbstractMathContainer
-
Creates a MathContainer instance.
- AbstractMathContainer(int, int) - Constructor for class org.sbml.jsbml.AbstractMathContainer
-
Creates a MathContainer instance from a level and version.
- AbstractMathContainer(String, int, int) - Constructor for class org.sbml.jsbml.AbstractMathContainer
-
- AbstractMathContainer(AbstractMathContainer) - Constructor for class org.sbml.jsbml.AbstractMathContainer
-
Creates a MathContainer instance from a given MathContainer.
- AbstractMathContainer(ASTNode, int, int) - Constructor for class org.sbml.jsbml.AbstractMathContainer
-
Creates a MathContainer instance from an ASTNode, level and version.
- AbstractNamedSBase - Class in org.sbml.jsbml
-
Base abstract class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
- AbstractNamedSBase() - Constructor for class org.sbml.jsbml.AbstractNamedSBase
-
- AbstractNamedSBase(int, int) - Constructor for class org.sbml.jsbml.AbstractNamedSBase
-
- AbstractNamedSBase(String) - Constructor for class org.sbml.jsbml.AbstractNamedSBase
-
- AbstractNamedSBase(String, int, int) - Constructor for class org.sbml.jsbml.AbstractNamedSBase
-
- AbstractNamedSBase(String, String, int, int) - Constructor for class org.sbml.jsbml.AbstractNamedSBase
-
Creates an AbctractNamedSBase from an id, name, level and version.
- AbstractNamedSBase(AbstractNamedSBase) - Constructor for class org.sbml.jsbml.AbstractNamedSBase
-
- AbstractNamedSBaseRef - Class in org.sbml.jsbml.ext.comp
-
This abstract class is used by Deletion and Port classes.
- AbstractNamedSBaseRef() - Constructor for class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef
-
- AbstractNamedSBaseRef(int, int) - Constructor for class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef
-
- AbstractNamedSBaseRef(String) - Constructor for class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef
-
- AbstractNamedSBaseRef(String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef
-
- AbstractNamedSBaseRef(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef
-
- AbstractNamedSBaseRef(AbstractNamedSBaseRef) - Constructor for class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef
-
- AbstractNamedSBaseWithUnit - Class in org.sbml.jsbml
-
- AbstractNamedSBaseWithUnit() - Constructor for class org.sbml.jsbml.AbstractNamedSBaseWithUnit
-
Initializes a new object of type
AbstractNamedSBaseWithUnit
whose
identifier and name are set to
null
and whose level and
version are set to -1 each.
- AbstractNamedSBaseWithUnit(int, int) - Constructor for class org.sbml.jsbml.AbstractNamedSBaseWithUnit
-
- AbstractNamedSBaseWithUnit(String) - Constructor for class org.sbml.jsbml.AbstractNamedSBaseWithUnit
-
- AbstractNamedSBaseWithUnit(String, int, int) - Constructor for class org.sbml.jsbml.AbstractNamedSBaseWithUnit
-
- AbstractNamedSBaseWithUnit(String, String, int, int) - Constructor for class org.sbml.jsbml.AbstractNamedSBaseWithUnit
-
- AbstractNamedSBaseWithUnit(AbstractNamedSBaseWithUnit) - Constructor for class org.sbml.jsbml.AbstractNamedSBaseWithUnit
-
- AbstractReaderWriter - Class in org.sbml.jsbml.xml.parsers
-
Contains some code shared by most of the L3 packages parsers.
- AbstractReaderWriter() - Constructor for class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
-
- AbstractReferenceGlyph - Class in org.sbml.jsbml.ext.layout
-
Abstract super class for all kinds of glyphs that graphically represent an
instance of
NamedSBase
.
- AbstractReferenceGlyph() - Constructor for class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph
-
- AbstractReferenceGlyph(int, int) - Constructor for class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph
-
- AbstractReferenceGlyph(String) - Constructor for class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph
-
- AbstractReferenceGlyph(String, int, int) - Constructor for class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph
-
- AbstractReferenceGlyph(AbstractReferenceGlyph) - Constructor for class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph
-
- AbstractRenderPlugin - Class in org.sbml.jsbml.ext.render
-
- AbstractRenderPlugin() - Constructor for class org.sbml.jsbml.ext.render.AbstractRenderPlugin
-
Creates a AbstractRenderPlugin instance.
- AbstractRenderPlugin(AbstractRenderPlugin) - Constructor for class org.sbml.jsbml.ext.render.AbstractRenderPlugin
-
Clone constructor
- AbstractRenderPlugin(SBase) - Constructor for class org.sbml.jsbml.ext.render.AbstractRenderPlugin
-
Creates an AbstractRenderPlugin instance
- AbstractSBase - Class in org.sbml.jsbml
-
The base class for each
SBase
component.
- AbstractSBase() - Constructor for class org.sbml.jsbml.AbstractSBase
-
Creates an AbstractSBase instance.
- AbstractSBase(int, int) - Constructor for class org.sbml.jsbml.AbstractSBase
-
Creates an
AbstractSBase
instance with the given SBML Level and
Version.
- AbstractSBase(String) - Constructor for class org.sbml.jsbml.AbstractSBase
-
- AbstractSBase(String, int, int) - Constructor for class org.sbml.jsbml.AbstractSBase
-
- AbstractSBase(String, String, int, int) - Constructor for class org.sbml.jsbml.AbstractSBase
-
- AbstractSBase(SBase) - Constructor for class org.sbml.jsbml.AbstractSBase
-
- AbstractSBasePlugin - Class in org.sbml.jsbml.ext
-
- AbstractSBasePlugin() - Constructor for class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- AbstractSBasePlugin(SBasePlugin) - Constructor for class org.sbml.jsbml.ext.AbstractSBasePlugin
-
This method will need to be further tested
- AbstractSBasePlugin(SBase) - Constructor for class org.sbml.jsbml.ext.AbstractSBasePlugin
-
- AbstractSBGNnode<T> - Class in org.sbml.jsbml.ext.render.director
-
- AbstractSBGNnode() - Constructor for class org.sbml.jsbml.ext.render.director.AbstractSBGNnode
-
- AbstractSBGNNodeWithCloneMarker<T> - Class in org.sbml.jsbml.ext.render.director
-
- AbstractSBGNNodeWithCloneMarker() - Constructor for class org.sbml.jsbml.ext.render.director.AbstractSBGNNodeWithCloneMarker
-
- AbstractSBGNProcessNode<T> - Class in org.sbml.jsbml.ext.render.director
-
- AbstractSBGNProcessNode() - Constructor for class org.sbml.jsbml.ext.render.director.AbstractSBGNProcessNode
-
- AbstractSpatialNamedSBase - Class in org.sbml.jsbml.ext.spatial
-
The base class for each spatial class.
- AbstractSpatialNamedSBase() - Constructor for class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase
-
- AbstractSpatialNamedSBase(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase
-
- AbstractSpatialNamedSBase(String) - Constructor for class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase
-
- AbstractSpatialNamedSBase(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase
-
- AbstractSpatialNamedSBase(SpatialNamedSBase) - Constructor for class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase
-
- AbstractSpatialSBasePlugin - Class in org.sbml.jsbml.ext.spatial
-
- AbstractSpatialSBasePlugin() - Constructor for class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin
-
- AbstractSpatialSBasePlugin(AbstractSpatialSBasePlugin) - Constructor for class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin
-
- AbstractSpatialSBasePlugin(SBase) - Constructor for class org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin
-
- AbstractTreeNode - Class in org.sbml.jsbml
-
A basic implementation of the TreeNode
interface.
- AbstractTreeNode() - Constructor for class org.sbml.jsbml.AbstractTreeNode
-
- AbstractTreeNode(TreeNode) - Constructor for class org.sbml.jsbml.AbstractTreeNode
-
Constructor for cloning.
- AbstractValidationFunction<T> - Class in org.sbml.jsbml.validator.offline.constraints
-
- AbstractValidationFunction() - Constructor for class org.sbml.jsbml.validator.offline.constraints.AbstractValidationFunction
-
- accept(SBase) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin
-
- accept(SBase) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin
-
- accept(SBase) - Method in class org.sbml.jsbml.ext.spatial.SpatialModelPlugin
-
- accept(SBase) - Method in class org.sbml.jsbml.KineticLaw
-
- accept(SBase) - Method in class org.sbml.jsbml.Model
-
- accept(SBase) - Method in interface org.sbml.jsbml.util.IdManager
-
Returns true if this
IdManager
can register or unregister
the given
SBase
.
- accepts(Object) - Method in class org.sbml.jsbml.ext.layout.NamedSBaseReferenceFilter
-
- accepts(Object) - Method in class org.sbml.jsbml.util.filters.AndFilter
-
- accepts(Object) - Method in class org.sbml.jsbml.util.filters.AssignmentVariableFilter
-
- accepts(Object) - Method in class org.sbml.jsbml.util.filters.BoundaryConditionFilter
-
- accepts(Object) - Method in class org.sbml.jsbml.util.filters.CVTermFilter
-
- accepts(Object) - Method in interface org.sbml.jsbml.util.filters.Filter
-
This method checks whether the given object is of the correct type and
has the desired properties set to be acceptable.
- accepts(Object) - Method in class org.sbml.jsbml.util.filters.IdenticalUnitDefinitionFilter
-
- accepts(Object) - Method in class org.sbml.jsbml.util.filters.IdFilter
-
- accepts(Object) - Method in class org.sbml.jsbml.util.filters.MetaIdFilter
-
- accepts(Object) - Method in class org.sbml.jsbml.util.filters.NameFilter
-
- accepts(Object) - Method in class org.sbml.jsbml.util.filters.OrFilter
-
- accepts(Object) - Method in class org.sbml.jsbml.util.filters.SBOFilter
-
- accepts(Object) - Method in class org.sbml.jsbml.util.filters.SIdFilter
-
- accepts(Object) - Method in class org.sbml.jsbml.util.filters.SpeciesReferenceFilter
-
- accepts(Object) - Method in class org.sbml.jsbml.util.filters.XMLNodeFilter
-
- ACTIVATOR - org.sbml.jsbml.ext.layout.SpeciesReferenceRole
-
- activeObjective - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
-
- add(int, T) - Method in class org.sbml.jsbml.ListOf
-
- add(String) - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
Appends an XML namespace URI with an empty prefix to this list of namespace
declarations.
- add(String, String) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Adds an attribute (a name/value pair) to this
XMLAttributes
set optionally
with a prefix and URI defining a namespace.
- add(String, String) - Method in class org.sbml.jsbml.xml.XMLNamespaces
-
Appends an XML namespace prefix and URI pair to this list of namespace
declarations.
- add(String, String, String) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Adds an attribute (a name/value pair) to this
XMLAttributes
set optionally
with a prefix and URI defining a namespace.
- add(String, String, String, String) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
Adds an attribute (a name/value pair) to this
XMLAttributes
set optionally
with a prefix and URI defining a namespace.
- add(Layout) - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin
-
Adds the given
Layout
to the listOfLayouts.
- add(SBMLError) - Method in class org.sbml.jsbml.SBMLErrorLog
-
Adds an error.
- add(Option) - Method in class org.sbml.jsbml.SBMLErrorLog
-
Adds an option.
- add(AnyConstraint<T>) - Method in class org.sbml.jsbml.validator.offline.constraints.ConstraintGroup
-
Adds a constraint to the group.
- add(XMLTriple, String) - Method in class org.sbml.jsbml.xml.XMLAttributes
-
- add(T) - Method in class org.sbml.jsbml.ListOf
-
- addAdditionalGraphicalObject(GraphicalObject) - Method in class org.sbml.jsbml.ext.layout.Layout
-
- addAdjacentDomain(AdjacentDomains) - Method in class org.sbml.jsbml.ext.spatial.Geometry
-
- addAll(int, Collection<? extends T>) - Method in class org.sbml.jsbml.ListOf
-
- addAll(Collection<? extends T>) - Method in class org.sbml.jsbml.ListOf
-
- addAllAssociations(List<Association>) - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator
-
Sets the given ListOf<Association>
.
- addAllChangeListeners(Collection<TreeNodeChangeListener>) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- addAllChangeListeners(Collection<TreeNodeChangeListener>) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- addAllChangeListeners(Collection<TreeNodeChangeListener>) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- addAllChangeListeners(Collection<TreeNodeChangeListener>, boolean) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- addAllChangeListeners(Collection<TreeNodeChangeListener>, boolean) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- addAllChangeListeners(Collection<TreeNodeChangeListener>, boolean) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- addAnalyticVolume(AnalyticVolume) - Method in class org.sbml.jsbml.ext.spatial.AnalyticGeometry
-
- addAssociation(Association) - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator
-
- addAttr(String, String) - Method in class org.sbml.jsbml.xml.XMLToken
-
Adds an attribute to the attribute set in this
XMLToken
optionally
with a prefix and URI defining a namespace.
- addAttr(String, String, String) - Method in class org.sbml.jsbml.xml.XMLToken
-
Adds an attribute to the attribute set in this
XMLToken
optionally
with a prefix and URI defining a namespace.
- addAttr(String, String, String, String) - Method in class org.sbml.jsbml.xml.XMLToken
-
Adds an attribute to the attribute set in this
XMLToken
optionally
with a prefix and URI defining a namespace.
- addAttr(XMLTriple, String) - Method in class org.sbml.jsbml.xml.XMLToken
-
Adds an attribute with the given
XMLTriple
/value pair to the attribute set
in this
XMLToken
.
- addAttributes(Map<String, String>) - Method in class org.sbml.jsbml.xml.stax.SBMLObjectForXML
-
Adds an attribute to this attributes HashMap.
- addChangedMath(ChangedMath) - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin
-
- addChild(ASTNode) - Method in class org.sbml.jsbml.ASTNode
-
Adds a child to this node.
- addChild(Association) - Method in class org.sbml.jsbml.ext.fbc.LogicalOperator
-
- addChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
Adds a child to this node.
- addChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTFunction
-
Adds a child to this node.
- addChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTLogarithmNode
-
- addChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- addChild(CycleDetectionTreeNode) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.CycleDetectionTreeNode
-
- addChild(XMLNode) - Method in class org.sbml.jsbml.xml.XMLNode
-
- addChildElement(Transformation2D) - Method in class org.sbml.jsbml.ext.render.RenderGroup
-
Adds the given element to the end of the list of children elements.
- addColorDefinition(ColorDefinition) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase
-
- addCompartment(Compartment) - Method in class org.sbml.jsbml.Model
-
Adds a Compartment instance to the listOfCompartments of this Model.
- addCompartmentGlyph(CompartmentGlyph) - Method in class org.sbml.jsbml.ext.layout.Layout
-
- addCompartmentReference(CompartmentReference) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin
-
- addCompartmentType(CompartmentType) - Method in class org.sbml.jsbml.Model
-
- addConstantId(String) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
-
Add an id to the list
- addConstraint(Constraint) - Method in class org.sbml.jsbml.Model
-
- addCoordinateComponent(CoordinateComponent) - Method in class org.sbml.jsbml.ext.spatial.Geometry
-
- addCreator(Creator) - Method in class org.sbml.jsbml.History
-
- addCSGNode(CSGNode) - Method in class org.sbml.jsbml.ext.spatial.CSGSetOperator
-
Adds a new
CSGNode
to the listOfCSGNodes.
- addCSGObject(CSGObject) - Method in class org.sbml.jsbml.ext.spatial.CSGeometry
-
Adds a new
CSGObject
to the listOfCSGObjects.
- addCurveSegment(int, CurveSegment) - Method in class org.sbml.jsbml.ext.layout.Curve
-
- addCurveSegment(int, CurveSegment) - Method in interface org.sbml.jsbml.ext.layout.ICurve
-
- addCurveSegment(int, CurveSegment) - Method in class org.sbml.jsbml.ext.render.Polygon
-
- addCurveSegment(int, CurveSegment) - Method in class org.sbml.jsbml.ext.render.RenderCurve
-
- addCurveSegment(CurveSegment) - Method in class org.sbml.jsbml.ext.layout.Curve
-
- addCurveSegment(CurveSegment) - Method in interface org.sbml.jsbml.ext.layout.ICurve
-
- addCurveSegment(CurveSegment) - Method in class org.sbml.jsbml.ext.render.Polygon
-
- addCurveSegment(CurveSegment) - Method in class org.sbml.jsbml.ext.render.RenderCurve
-
- addCVTerm - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- addCVTerm(CVTerm) - Method in class org.sbml.jsbml.AbstractSBase
-
- addCVTerm(CVTerm) - Method in class org.sbml.jsbml.Annotation
-
- addCVTerm(CVTerm) - Method in interface org.sbml.jsbml.SBase
-
- addDeclaredNamespace - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- addDeclaredNamespace(String, String) - Method in class org.sbml.jsbml.AbstractSBase
-
Adds an additional name space to the set of declared namespaces of this
SBase
.
- addDeclaredNamespace(String, String) - Method in class org.sbml.jsbml.Annotation
-
Adds an additional namespace to the set of declared namespaces of this
SBase
.
- addDeclaredNamespace(String, String) - Method in interface org.sbml.jsbml.SBase
-
Adds an additional name space to the set of declared namespaces of this
SBase
.
- addDeletion(Deletion) - Method in class org.sbml.jsbml.ext.comp.Submodel
-
Adds a new
Deletion
to the listOfDeletions.
- addDimension(Dimension) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin
-
Adds a new
Dimension
to the listOfDimensions.
- addDomain(Domain) - Method in class org.sbml.jsbml.ext.spatial.Geometry
-
Adds a new
Domain
to the listOfDomains.
- addDomainType(DomainType) - Method in class org.sbml.jsbml.ext.spatial.Geometry
-
- addDynElement(DynElement) - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin
-
- addElement(RenderPoint) - Method in class org.sbml.jsbml.ext.render.Polygon
-
- addElement(RenderPoint) - Method in class org.sbml.jsbml.ext.render.RenderCurve
-
- addElement(Transformation2D) - Method in class org.sbml.jsbml.ext.render.RenderGroup
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AdjacentDomainsConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AdvectionCoefficientConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AlgebraicRuleConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AnalyticGeometryConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AnalyticVolumeConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AndConstraints
-
- 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.AssignmentConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AssignmentRuleConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ASTNodeConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BindingSiteSpeciesTypeConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BoundaryConditionConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BoundaryConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BoundingBoxConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ColorDefinitionConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentGlyphConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentMappingConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentReferenceConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentTypeConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompModelPluginConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompSBasePluginConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompSBMLDocumentPluginConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ConstraintConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in interface org.sbml.jsbml.validator.offline.constraints.ConstraintDeclaration
-
Adds all error codes which are needed for a check the attribute to the
set.
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CoordinateComponentConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGeometryConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGHomogeneousTransformationConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGObjectConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGPrimitiveConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGRotationConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGScaleConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGSetOperatorConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGTranslationConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CubicBezierConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CurveConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DefaultValuesConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DelayConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DeletionConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DiffusionCoefficientConstraints
-
- 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.DimensionsConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DomainConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DomainTypeConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.EllipseConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.EventAssignmentConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.EventConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ExplicitRuleConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ExternalModelDefinitionConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.FBCReactionPluginConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.FunctionDefinitionConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.FunctionTermConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeneProductConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeneralGlyphConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeometryConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeometryDefinitionConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GlobalRenderInformationConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GradientBaseConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GradientStopConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GraphicalObjectConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GraphicalPrimitive1DConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GraphicalPrimitive2DConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ImageConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.IndexConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InitialAssignmentConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InputConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InSpeciesTypeBondConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InteriorPointConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.KineticLawConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LayoutConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LayoutModelPluginConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LinearGradientConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LineEndingConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LineSegmentConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LocalParameterConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LocalRenderInformationConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LocalStyleConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MathContainerConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MixedGeometryConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ModelConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiCompartmentPluginConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiModelPluginConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiSpeciesTypeConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ObjectiveConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.OrConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.OrdinalMappingConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.OutputConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ParameterConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ParametricGeometryConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ParametricObjectConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PointConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PolygonConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PortConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PossibleSpeciesFeatureValueConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PriorityConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.QualitativeSpeciesConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.QualModelPluginConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RadialGradientConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RateRuleConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReactionConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReactionGlyphConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RectangleConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReferenceGlyphConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderCubicBezierConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderCurveConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderGraphicalObjectPluginConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderGroupConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderInformationBaseConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderLayoutPluginConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderListOfLayoutsPluginConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderPointConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReplacedByConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReplacedElementConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RuleConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SampledFieldConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SampledFieldGeometryConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SampledVolumeConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseRefConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseWithDerivedUnitConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseWithUnitConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBMLDocumentConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SimpleSpeciesReferenceConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialCompartmentPluginConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialModelPluginConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialParameterPluginConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialPointsConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialReactionPluginConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialSpeciesPluginConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialSymbolReferenceConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesFeatureTypeConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesGlyphConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesReferenceConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesReferenceGlyphConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeComponentIndexConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeInstanceConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.StyleConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SubmodelConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TextConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TextGlyphConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.Transformation2DConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TransformationComponentConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TransformationConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TransitionConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TreeNodeConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TriggerConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.UnitConstraints
-
- addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.UnitDefinitionConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AdjacentDomainsConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AdvectionCoefficientConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AlgebraicRuleConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AnalyticGeometryConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AnalyticVolumeConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AndConstraints
-
- 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.AssignmentConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.AssignmentRuleConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ASTNodeConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BindingSiteSpeciesTypeConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BoundaryConditionConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BoundaryConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BoundingBoxConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ColorDefinitionConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentGlyphConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentMappingConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentReferenceConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentTypeConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompModelPluginConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompSBasePluginConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompSBMLDocumentPluginConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ConstraintConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in interface org.sbml.jsbml.validator.offline.constraints.ConstraintDeclaration
-
Adds all error codes which are needed for a check in this category to the
set.
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CoordinateComponentConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGeometryConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGHomogeneousTransformationConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGObjectConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGPrimitiveConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGRotationConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGScaleConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGSetOperatorConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CSGTranslationConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CubicBezierConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CurveConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DefaultValuesConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DelayConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DeletionConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DiffusionCoefficientConstraints
-
- 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.DimensionsConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DomainConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.DomainTypeConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.EllipseConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.EventAssignmentConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.EventConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ExplicitRuleConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ExternalModelDefinitionConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.FBCReactionPluginConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.FunctionDefinitionConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.FunctionTermConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeneProductConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeneralGlyphConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeometryConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GeometryDefinitionConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GlobalRenderInformationConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GradientBaseConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GradientStopConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GraphicalObjectConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GraphicalPrimitive1DConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.GraphicalPrimitive2DConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ImageConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, 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.InitialAssignmentConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InputConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InSpeciesTypeBondConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InteriorPointConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.KineticLawConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LayoutConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LayoutModelPluginConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LinearGradientConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LineEndingConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LineSegmentConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LocalParameterConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LocalRenderInformationConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.LocalStyleConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MathContainerConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MixedGeometryConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ModelConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiCompartmentPluginConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiModelPluginConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiSpeciesTypeConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ObjectiveConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.OrConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.OrdinalMappingConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.OutputConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ParameterConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ParametricGeometryConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ParametricObjectConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PointConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PolygonConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PortConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PossibleSpeciesFeatureValueConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PriorityConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.QualitativeSpeciesConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.QualModelPluginConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RadialGradientConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RateRuleConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReactionConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReactionGlyphConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RectangleConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReferenceGlyphConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderCubicBezierConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderCurveConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderGraphicalObjectPluginConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderGroupConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderInformationBaseConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderLayoutPluginConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderListOfLayoutsPluginConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RenderPointConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReplacedByConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.ReplacedElementConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.RuleConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SampledFieldConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SampledFieldGeometryConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SampledVolumeConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseRefConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseWithDerivedUnitConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBaseWithUnitConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SBMLDocumentConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SimpleSpeciesReferenceConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialCompartmentPluginConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialModelPluginConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialParameterPluginConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialPointsConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialReactionPluginConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialSpeciesPluginConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpatialSymbolReferenceConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesFeatureTypeConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesGlyphConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesReferenceConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesReferenceGlyphConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeComponentIndexConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeInstanceConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.StyleConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SubmodelConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TextConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TextGlyphConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.Transformation2DConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TransformationComponentConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TransformationConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TransitionConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TreeNodeConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TriggerConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.UnitConstraints
-
- addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.UnitDefinitionConstraints
-
- addEvent(Event) - Method in class org.sbml.jsbml.Model
-
Adds an
Event
instance to the listOfEvents of this Model.
- addEventAssignment(EventAssignment) - Method in class org.sbml.jsbml.Event
-
- addExtension - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- addExtension(String, ASTNodePlugin) - Method in class org.sbml.jsbml.ASTNode
-
- addExtension(String, SBasePlugin) - Method in class org.sbml.jsbml.AbstractSBase
-
- addExtension(String, SBasePlugin) - Method in interface org.sbml.jsbml.SBase
-
- addExternalModelDefinition(ExternalModelDefinition) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin
-
- addFilter(Filter) - Method in class org.sbml.jsbml.util.filters.AndFilter
-
- addFluxBound(FluxBound) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
-
- addFluxObjective(FluxObjective) - Method in class org.sbml.jsbml.ext.fbc.Objective
-
- addFunctionDefinition(FunctionDefinition) - Method in class org.sbml.jsbml.Model
-
- addFunctionTerm(FunctionTerm) - Method in class org.sbml.jsbml.ext.qual.Transition
-
- addGeneProduct(GeneProduct) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
-
- addGeneralGlyph(GeneralGlyph) - Method in class org.sbml.jsbml.ext.layout.Layout
-
- addGeometryDefinition(GeometryDefinition) - Method in class org.sbml.jsbml.ext.spatial.Geometry
-
- addGeometryDefinition(GeometryDefinition) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry
-
- addGlobalRenderInformation(GlobalRenderInformation) - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin
-
- addGradientBase(GradientBase) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase
-
- addGradientStop(GradientStop) - Method in class org.sbml.jsbml.ext.render.GradientBase
-
- addGraphicalObject(GraphicalObject) - Method in class org.sbml.jsbml.ext.layout.Layout
-
- addGroup(Group) - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin
-
Adds a new element to the listOfGroups.
- addIndex(Index) - Method in class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin
-
Adds a new
Index
to the listOfIndices.
- addInitialAssignment(InitialAssignment) - Method in class org.sbml.jsbml.Model
-
Adds an InitialAssignment instance to the listOfInitialAssignments of this
Model.
- addInput(Input) - Method in class org.sbml.jsbml.ext.qual.Transition
-
- addInSpeciesTypeBond(InSpeciesTypeBond) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType
-
- addInteriorPoint(InteriorPoint) - Method in class org.sbml.jsbml.ext.spatial.Domain
-
- addLayout(Layout) - Method in class org.sbml.jsbml.ext.layout.LayoutModelPlugin
-
Adds the given
Layout
to the listOfLayouts.
- addLayoutedEdge(SpeciesReferenceGlyph, ReactionGlyph) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm
-
Add a layouted edge to the input of the algorithm.
- addLayoutedGlyph(GraphicalObject) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm
-
Add a fully layouted glyph (i.e. glyph with boundingbox, dimensions and
position) to the input of the algorithm.
- addLineEnding(LineEnding) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase
-
- addLocalParameter(LocalParameter) - Method in class org.sbml.jsbml.KineticLaw
-
Adds a copy of the given Parameter object to the list of local parameters
in this KineticLaw.
- addLocalRenderInformation(LocalRenderInformation) - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin
-
- addLocalStyle(LocalStyle) - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation
-
- addMember(Member) - Method in class org.sbml.jsbml.ext.groups.Group
-
- addModelDefinition(ModelDefinition) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin
-
- addModifiedDate(Date) - Method in class org.sbml.jsbml.History
-
Adds a
Date
of modification to this
History
.
- addModifier(ModifierSpeciesReference) - Method in class org.sbml.jsbml.Reaction
-
- addNamespace(String) - Method in class org.sbml.jsbml.xml.XMLToken
-
Appends an XML namespace URI to this
XMLToken
.
- addNamespace(String, String) - Method in class org.sbml.jsbml.xml.XMLToken
-
Appends an XML namespace prefix and URI pair to this
XMLToken
.
- addNamespace(String, String, String) - Method in class org.sbml.jsbml.SBMLDocument
-
- addNestedCVTerm(CVTerm) - Method in class org.sbml.jsbml.CVTerm
-
- addObjective(Objective) - Method in class org.sbml.jsbml.ext.fbc.FBCModelPlugin
-
Adds a new
Objective
to the listOfObjectives.
- addOrdinalMapping(OrdinalMapping) - Method in class org.sbml.jsbml.ext.spatial.MixedGeometry
-
- addOutput(Output) - Method in class org.sbml.jsbml.ext.qual.Transition
-
- addOutwardBindingSite(OutwardBindingSite) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin
-
- addParameter(LocalParameter) - Method in class org.sbml.jsbml.KineticLaw
-
- addParameter(Parameter) - Method in class org.sbml.jsbml.KineticLaw
-
- addParameter(Parameter) - Method in class org.sbml.jsbml.Model
-
Adds a Parameter instance to the listOfParameters of this Model.
- addParametricObject(ParametricObject) - Method in class org.sbml.jsbml.ext.spatial.ParametricGeometry
-
- addParent(CycleDetectionTreeNode) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.CycleDetectionTreeNode
-
- addPlugin(String, ASTNodePlugin) - Method in class org.sbml.jsbml.ASTNode
-
- addPlugin(String, SBasePlugin) - Method in class org.sbml.jsbml.AbstractSBase
-
- addPlugin(String, SBasePlugin) - Method in interface org.sbml.jsbml.SBase
-
- addPort(Port) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin
-
Adds a new
Port
to the listOfPorts.
- addPossibleSpeciesFeatureValue(PossibleSpeciesFeatureValue) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType
-
- addPredefinedUnitDefinitions(Model) - Static method in class org.sbml.jsbml.util.SBMLtools
-
- addProduct(SpeciesReference) - Method in class org.sbml.jsbml.Reaction
-
- addQualitativeSpecies(QualitativeSpecies) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin
-
- addReactant(SpeciesReference) - Method in class org.sbml.jsbml.Reaction
-
- addReaction(Reaction) - Method in class org.sbml.jsbml.Model
-
Adds a Reaction instance to the listOfReactions of this Model.
- addReactionGlyph(ReactionGlyph) - Method in class org.sbml.jsbml.ext.layout.Layout
-
- addReferenceGlyph(ReferenceGlyph) - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph
-
- addReplacedElement(ReplacedElement) - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin
-
Adds a new element to listOfReplacedElements.
- addResource(int, String) - Method in class org.sbml.jsbml.CVTerm
-
Adds a resource to the
CVTerm
at the specified index.
- addResource(String) - Method in class org.sbml.jsbml.CVTerm
-
Adds a resource to the
CVTerm
.
- addResources(String...) - Method in class org.sbml.jsbml.CVTerm
-
Adds list of resources to the
CVTerm
.
- addResources(CVTerm.Qualifier, String...) - Method in class org.sbml.jsbml.AbstractSBase
-
Adds all the given resources to the first
CVTerm
with the given
CVTerm.Qualifier
or, if no such term exists yet, creates one.
- addResources(CVTerm.Qualifier, String...) - Method in class org.sbml.jsbml.Annotation
-
Adds all the given resources to the first
CVTerm
with the given
CVTerm.Qualifier
or, if no such term exists yet, creates one.
- addResourceURI(String) - Method in class org.sbml.jsbml.CVTerm
-
Adds a resource to the
CVTerm
.
- addRule(Rule) - Method in class org.sbml.jsbml.Model
-
Adds a Rule instance to the listOfRules of this Model.
- addSampledField(SampledField) - Method in class org.sbml.jsbml.ext.spatial.Geometry
-
- addSampledVolume(SampledVolume) - Method in class org.sbml.jsbml.ext.spatial.SampledFieldGeometry
-
- addSemanticsAnnotation(XMLNode) - Method in class org.sbml.jsbml.ASTNode
-
Adds the given
XMLNode
as a MathML
<semantics>
element to this
ASTNode
.
- addSpatialComponent(SpatialComponent) - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin
-
- addSpecies(QualitativeSpecies) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin
-
- addSpecies(Species) - Method in class org.sbml.jsbml.Model
-
Adds a Species instance to the listOfSpecies of this Model.
- addSpeciesFeature(SpeciesFeature) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin
-
- addSpeciesFeatureType(SpeciesFeatureType) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType
-
- addSpeciesFeatureValue(SpeciesFeatureValue) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature
-
- addSpeciesGlyph(SpeciesGlyph) - Method in class org.sbml.jsbml.ext.layout.Layout
-
- addSpeciesReferenceGlyph(SpeciesReferenceGlyph) - Method in class org.sbml.jsbml.ext.layout.ReactionGlyph
-
- addSpeciesType(MultiSpeciesType) - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin
-
- addSpeciesType(SpeciesType) - Method in class org.sbml.jsbml.Model
-
- addSpeciesTypeComponentIndex(SpeciesTypeComponentIndex) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType
-
- addSpeciesTypeComponentMapInProduct(SpeciesTypeComponentMapInProduct) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin
-
- addSpeciesTypeInstance(SpeciesTypeInstance) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType
-
- addStrokeDash(Short) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D
-
- addStyle(Style) - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation
-
Adds the given style to the list of styles
- addSubGlyph(GraphicalObject) - Method in class org.sbml.jsbml.ext.layout.GeneralGlyph
-
- addSubListOfSpeciesFeature(SubListOfSpeciesFeature) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin
-
- addSubmodel(Submodel) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin
-
Adds a new
Submodel
to the listOfSubmodels.
- addTextGlyph(TextGlyph) - Method in class org.sbml.jsbml.ext.layout.Layout
-
- addTransition(Transition) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin
-
- addTreeNodeChangeListener(TreeNodeChangeListener) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- addTreeNodeChangeListener(TreeNodeChangeListener) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- addTreeNodeChangeListener(TreeNodeChangeListener) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- addTreeNodeChangeListener(TreeNodeChangeListener, boolean) - Method in class org.sbml.jsbml.AbstractTreeNode
-
- addTreeNodeChangeListener(TreeNodeChangeListener, boolean) - Method in class org.sbml.jsbml.math.ASTUnknown
-
- addTreeNodeChangeListener(TreeNodeChangeListener, boolean) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
-
- addUncertainty(Uncertainty) - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin
-
- addUncertParameter(UncertParameter) - Method in class org.sbml.jsbml.ext.distrib.Uncertainty
-
- addUncertParameter(UncertParameter) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter
-
- addUnit(String) - Method in class org.sbml.jsbml.UnitDefinition
-
- addUnit(Unit) - Method in class org.sbml.jsbml.UnitDefinition
-
- addUnit(Unit.Kind) - Method in class org.sbml.jsbml.UnitDefinition
-
- addUnitDefinition(UnitDefinition) - Method in class org.sbml.jsbml.Model
-
- addUnitDefinitionIfNotContained(Model, UnitDefinition) - Static method in class org.sbml.jsbml.JSBML
-
Adds the given
UnitDefinition
to the given model or returns the
identifier of an equivalent
UnitDefinition
that is already part
of the model.
- addUnitDefinitionOrReturnIdenticalUnit(UnitDefinition) - Method in class org.sbml.jsbml.Model
-
- addUnlayoutedEdge(SpeciesReferenceGlyph, ReactionGlyph) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm
-
Add an unlayouted edge to the input of the algorithm.
- addUnlayoutedGlyph(GraphicalObject) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm
-
Add a glyph with missing layout information (i.e. no dimensions or no
position specified) to the input of the algorithm.
- addValidationListener(ValidationListener) - Method in class org.sbml.jsbml.validator.offline.ValidationContext
-
- addValue(String, double) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
-
Adds a new string,double pair to the idToValue.
- adjacentDomains - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- AdjacentDomains - Class in org.sbml.jsbml.ext.spatial
-
- AdjacentDomains() - Constructor for class org.sbml.jsbml.ext.spatial.AdjacentDomains
-
- AdjacentDomains(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.AdjacentDomains
-
- AdjacentDomains(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.AdjacentDomains
-
- AdjacentDomains(AdjacentDomains) - Constructor for class org.sbml.jsbml.ext.spatial.AdjacentDomains
-
Clone constructor
- AdjacentDomainsConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- AdjacentDomainsConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.AdjacentDomainsConstraints
-
- adjustBeginLineColumn(int, int) - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Method to adjust line and column numbers for the start of a token.
- adjustBeginLineColumn(int, int) - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
-
Method to adjust line and column numbers for the start of a token.
- advectionCoefficient - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- AdvectionCoefficient - Class in org.sbml.jsbml.ext.spatial
-
- AdvectionCoefficient() - Constructor for class org.sbml.jsbml.ext.spatial.AdvectionCoefficient
-
- AdvectionCoefficient(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.AdvectionCoefficient
-
- AdvectionCoefficient(AdvectionCoefficient) - Constructor for class org.sbml.jsbml.ext.spatial.AdvectionCoefficient
-
- AdvectionCoefficientConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- AdvectionCoefficientConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.AdvectionCoefficientConstraints
-
- AlgebraicRule - Class in org.sbml.jsbml
-
Represents the algebraicRule XML element of a SBML file.
- AlgebraicRule() - Constructor for class org.sbml.jsbml.AlgebraicRule
-
Creates an AlgebraicRule instance.
- AlgebraicRule(int, int) - Constructor for class org.sbml.jsbml.AlgebraicRule
-
Creates an AlgebraicRule instance from level and version.
- AlgebraicRule(AlgebraicRule) - Constructor for class org.sbml.jsbml.AlgebraicRule
-
Creates an AlgebraicRule instance from a given
AlgebraicRule
instance.
- AlgebraicRule(ASTNode, int, int) - Constructor for class org.sbml.jsbml.AlgebraicRule
-
Creates an AlgebraicRule instance from math, level and version.
- AlgebraicRuleConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- AlgebraicRuleConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.AlgebraicRuleConstraints
-
- all_L3_namespaces - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
-
- ALLOW_INVALID_SBML - Static variable in class org.sbml.jsbml.JSBML
-
String that can be added to an SBase user objects, if it is associated with the value true
,
then the getters and setters will allow to set some invalid values instead of throwing exceptions.
- allowedCnType - Static variable in class org.sbml.jsbml.validator.offline.constraints.ASTNodeConstraints
-
- allowedCsymbolURI - Static variable in class org.sbml.jsbml.validator.offline.constraints.ASTNodeConstraints
-
- allowedCsymbolURIL2 - Static variable in class org.sbml.jsbml.validator.offline.constraints.ASTNodeConstraints
-
- allowedCsymbolURIL3V1 - Static variable in class org.sbml.jsbml.validator.offline.constraints.ASTNodeConstraints
-
- alpha - org.sbml.jsbml.ext.dyn.SpatialKind
-
Refers to elemental rotation of an object about the X coordinate axis
- AMPERE - org.sbml.jsbml.Unit.Kind
-
The ampere unit.
- analyseSBMLerrorLog(List<SBMLError>) - Static method in class org.sbml.jsbml.validator.offline.LoggingValidationContext
-
Goes through the list of
SBMLError
given to determined which
check categories should be ignored.
- analyticGeometry - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- AnalyticGeometry - Class in org.sbml.jsbml.ext.spatial
-
- AnalyticGeometry() - Constructor for class org.sbml.jsbml.ext.spatial.AnalyticGeometry
-
- AnalyticGeometry(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.AnalyticGeometry
-
- AnalyticGeometry(AnalyticGeometry) - Constructor for class org.sbml.jsbml.ext.spatial.AnalyticGeometry
-
- AnalyticGeometryConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- AnalyticGeometryConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.AnalyticGeometryConstraints
-
- analyticVolume - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- AnalyticVolume - Class in org.sbml.jsbml.ext.spatial
-
- AnalyticVolume() - Constructor for class org.sbml.jsbml.ext.spatial.AnalyticVolume
-
- AnalyticVolume(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.AnalyticVolume
-
- AnalyticVolume(AnalyticVolume) - Constructor for class org.sbml.jsbml.ext.spatial.AnalyticVolume
-
- AnalyticVolumeConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- AnalyticVolumeConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.AnalyticVolumeConstraints
-
- and - org.sbml.jsbml.ext.multi.Relation
-
- and - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
-
Introduced to FBC in version 2.
- 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
-
- and(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.ConfigurableLogicalFormulaCompiler
-
- and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerLibSBML
-
- and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- and(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- and(List<ASTNode2>) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- and(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- and(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- and(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- and(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- and(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- and(ASTNode2...) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- And - Class in org.sbml.jsbml.ext.fbc
-
This class represents a set of two or more associations that are related in an order independent ‘and’
relationship.
- And() - Constructor for class org.sbml.jsbml.ext.fbc.And
-
Creates a new
And
instance.
- And(int, int) - Constructor for class org.sbml.jsbml.ext.fbc.And
-
Creates a new
And
instance.
- And(And) - Constructor for class org.sbml.jsbml.ext.fbc.And
-
Creates a new
And
instance.
- AND - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- AND - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- AND - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- AND - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- AND - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
RegularExpression Id.
- AND - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- AND - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- AND - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- AND - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- AndConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- AndConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.AndConstraints
-
- AndFilter - Class in org.sbml.jsbml.util.filters
-
A
Filter
that accepts an item only if all of its internal filters
also accept the given item.
- AndFilter() - Constructor for class org.sbml.jsbml.util.filters.AndFilter
-
- AndFilter(Filter...) - Constructor for class org.sbml.jsbml.util.filters.AndFilter
-
- anisotropic - org.sbml.jsbml.ext.spatial.DiffusionKind
-
Anisotropic
- annotation - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- Annotation - Class in org.sbml.jsbml
-
An Annotation represents the annotations of an
SBase
element.
- Annotation() - Constructor for class org.sbml.jsbml.Annotation
-
Creates an Annotation instance.
- Annotation(String) - Constructor for class org.sbml.jsbml.Annotation
-
Creates an
Annotation
instance from a
String
containing non RDF
annotation.
- Annotation(String, List<CVTerm>) - Constructor for class org.sbml.jsbml.Annotation
-
Creates an
Annotation
instance from a
String
containing
non RDF annotation and a list of
CVTerm
.
- Annotation(List<CVTerm>) - Constructor for class org.sbml.jsbml.Annotation
-
- Annotation(Annotation) - Constructor for class org.sbml.jsbml.Annotation
-
Creates a new Annotation instance by cloning the given Annotation.
- Annotation(XMLNode) - Constructor for class org.sbml.jsbml.Annotation
-
- AnnotationElement - Class in org.sbml.jsbml
-
A common super class for all those elements that can be part of an
Annotation
.
- AnnotationElement() - Constructor for class org.sbml.jsbml.AnnotationElement
-
Creates a new empty
AnnotationElement
without any children, an
empty list of
TreeNodeChangeListener
s, and a parent that is
null
.
- AnnotationElement(AnnotationElement) - Constructor for class org.sbml.jsbml.AnnotationElement
-
Clone constructor.
- annotationNameSpaces - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- AnnotationNotesNotAllowedLevel1 - org.sbml.jsbml.SBMLException.Code
-
Annotation on <sbml> not permitted in SBML Level 1
- AnnotationReader - Interface in org.sbml.jsbml.xml.parsers
-
The interface to implement for the SBML parsers reading SBML annotations.
- AnnotationWriter - Interface in org.sbml.jsbml.xml.parsers
-
The interface to implement for the SBML parsers writing SBML annotations.
- ANY - org.sbml.jsbml.ext.render.Style.Type
-
- AnyConstraint<T> - Interface in org.sbml.jsbml.validator.offline.constraints
-
Basic interface which must be implemented by every kind of constraint.
- append(String) - Method in class org.sbml.jsbml.ext.spatial.ParametricObject
-
Appends the variable data to pointIndex.
- append(String) - Method in class org.sbml.jsbml.ext.spatial.SampledField
-
Appends the variable data to samples.
- append(String) - Method in class org.sbml.jsbml.ext.spatial.SpatialPoints
-
Appends the variable data to arrayData.
- append(String) - Method in class org.sbml.jsbml.xml.XMLToken
-
Appends characters to this XML text content.
- append(StringBuffer, Object...) - Static method in class org.sbml.jsbml.util.StringTools
-
Takes the given StringBuffer as input and appends every further Object to it.
- append(StringBuilder, Object...) - Static method in class org.sbml.jsbml.util.StringTools
-
- append(T) - Method in class org.sbml.jsbml.ListOf
-
Adds item to the end of this
ListOf
.
- appendAnnotation(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- appendAnnotation(String) - Method in interface org.sbml.jsbml.SBase
-
Appends the given annotation to the 'annotation' subelement of this object.
- appendAnnotation(XMLNode) - Method in class org.sbml.jsbml.AbstractSBase
-
- appendAnnotation(XMLNode) - Method in interface org.sbml.jsbml.SBase
-
Appends the given annotation to the 'annotation' subelement of this object.
- appendCobraNotes(SBase, Properties) - Static method in class org.sbml.jsbml.util.CobraUtil
-
- appendNonRDFAnnotation(String) - Method in class org.sbml.jsbml.Annotation
-
Appends some 'annotation' to the non RDF annotation
XMLNode
of this object.
- appendNonRDFAnnotation(XMLNode) - Method in class org.sbml.jsbml.Annotation
-
- appendNotes(String) - Method in class org.sbml.jsbml.AbstractSBase
-
- appendNotes(String) - Method in interface org.sbml.jsbml.SBase
-
Appends 'notes' to the notes String of this object.
- appendNotes(XMLNode) - Method in class org.sbml.jsbml.AbstractSBase
-
Appends notes to the existing notes.
- appendNotes(XMLNode) - Method in interface org.sbml.jsbml.SBase
-
Appends 'notes' to the notes of this object.
- ApplyCiMustBeModelComponent - org.sbml.jsbml.SBMLException.Code
-
<ci>'s value is not a component in this model
- ApplyCiMustBeUserFunction - org.sbml.jsbml.SBMLException.Code
-
<ci> does not refer to a function definition
- applyToAll - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants
-
- 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
-
- arccos(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- arccos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- arccos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- arccos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- arccos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- arccos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- arccos(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- arccos(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arccos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arccos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arccos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arccos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arccos(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- arccosh(double) - Static method in class org.sbml.jsbml.util.Maths
-
Computes the arccosh of n
- 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
-
- arccosh(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- arccosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- arccosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- arccosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- arccosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- arccosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- arccosh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- arccosh(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arccosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arccosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arccosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arccosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arccosh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- arccot(double) - Static method in class org.sbml.jsbml.util.Maths
-
Computes the arcus-cotangens of a double value.
- 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
-
- arccot(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- arccot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- arccot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- arccot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- arccot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- arccot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- arccot(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- arccot(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arccot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arccot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arccot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arccot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arccot(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- arccoth(double) - Static method in class org.sbml.jsbml.util.Maths
-
Computes the arccoth of n
- 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
-
- arccoth(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- arccoth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- arccoth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- arccoth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- arccoth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- arccoth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- arccoth(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- arccoth(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arccoth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arccoth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arccoth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arccoth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arccoth(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- arccsc(double) - Static method in class org.sbml.jsbml.util.Maths
-
Computes the arccosecant of a double value
- 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
-
- arccsc(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- arccsc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- arccsc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- arccsc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- arccsc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- arccsc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- arccsc(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- arccsc(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arccsc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arccsc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arccsc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arccsc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arccsc(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- arccsch(double) - Static method in class org.sbml.jsbml.util.Maths
-
Computes the arccsch of n
- 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
-
- arccsch(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- arccsch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- arccsch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- arccsch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- arccsch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- arccsch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- arccsch(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- arccsch(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arccsch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arccsch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arccsch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arccsch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arccsch(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- arcsec(double) - Static method in class org.sbml.jsbml.util.Maths
-
Computes the arcsecant of a double value
- 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
-
- arcsec(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- arcsec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- arcsec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- arcsec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- arcsec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- arcsec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- arcsec(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- arcsec(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arcsec(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arcsec(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arcsec(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arcsec(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arcsec(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- arcsech(double) - Static method in class org.sbml.jsbml.util.Maths
-
Computes the arcsech of n
- 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
-
- arcsech(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- arcsech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- arcsech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- arcsech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- arcsech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- arcsech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- arcsech(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- arcsech(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arcsech(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arcsech(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arcsech(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arcsech(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arcsech(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
- arcsin(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- arcsin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- arcsin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- arcsin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- arcsin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- arcsin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- arcsin(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- arcsin(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arcsin(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arcsin(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arcsin(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arcsin(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arcsin(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- arcsinh(double) - Static method in class org.sbml.jsbml.util.Maths
-
Computes the arcsinh of n
- 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
-
- arcsinh(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- arcsinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- arcsinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- arcsinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- arcsinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- arcsinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- arcsinh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- arcsinh(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arcsinh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arcsinh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arcsinh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arcsinh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arcsinh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- 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
-
- arctan(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- arctan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- arctan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- arctan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- arctan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- arctan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- arctan(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- arctan(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arctan(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arctan(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arctan(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arctan(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arctan(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- arctanh(double) - Static method in class org.sbml.jsbml.util.Maths
-
Computes the arctanh of n
- 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
-
- arctanh(ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- arctanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- arctanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- arctanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- arctanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
-
- arctanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- arctanh(ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- arctanh(ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
- arctanh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- arctanh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- arctanh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- arctanh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
-
- arctanh(ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- area(int, int) - Static method in class org.sbml.jsbml.UnitDefinition
-
Returns the predefined unit for area.
- AREA - Static variable in class org.sbml.jsbml.UnitDefinition
-
- areaUnits - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- areCompatible(UnitDefinition, UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition
-
Returns true
or false
depending on
whether two UnitDefinition objects are compatible.
- areEquivalent(Unit.Kind, Unit.Kind) - Static method in enum org.sbml.jsbml.Unit.Kind
-
Tests whether the both given unit kinds are equivalent, i.e., it also
considers METRE and METER and LITRE and LITER.
- areEquivalent(UnitDefinition, String) - Static method in class org.sbml.jsbml.UnitDefinition
-
- areEquivalent(UnitDefinition, UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition
-
Returns true or false depending on whether two
UnitDefinition
objects are equivalent.
- areEquivalent(UnitDefinition, UnitDefinition) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
Returns true or false depending on whether two
UnitDefinition
objects are equivalent.
- areEquivalent(Unit, String) - Static method in class org.sbml.jsbml.Unit
-
Checks whether the given
Unit
and the
Unit
represented by
the given
String
are equivalent.
- areEquivalent(Unit, Unit) - Static method in class org.sbml.jsbml.Unit
-
Predicate returning true or false depending on whether Unit objects are
equivalent.
- areIdentical(UnitDefinition, UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition
-
Returns
true
or
false
depending on
whether two
UnitDefinition
objects are identical.
- areIdentical(UnitDefinition, UnitDefinition) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
Returns
true
or
false
depending on
whether two
UnitDefinition
objects are identical.
- areIdentical(Unit, Unit) - Static method in class org.sbml.jsbml.Unit
-
Predicate returning true or false depending on whether two Unit objects
are identical.
- ArgsToEqNeedSameType - org.sbml.jsbml.SBMLException.Code
-
Arguments to <eq> or <neq> have inconsistent data types
- arithmeticOperation(ASTNode.Type, ASTNode2...) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- arrayData - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- arrayDataLength - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- arrayDimension - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants
-
- ARRAYS_10101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8010101:
To conform to the arrays Package specification for SBML Level 3 Version 1, an
SBML document must declare
'http://www.sbml.org/sbml/level3/version1/arrays/version1' as the XMLNamespace
to use for elements of this package.
- ARRAYS_10102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8010102:
Wherever they appear in an SBML document, elements and attributes from the
arrays Package must use the
'http://www.sbml.org/sbml/level3/version1/arrays/version1' namespace, declaring
so either explicitly or implicitly.
- ARRAYS_10201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8010201:
In all SBML documents using the arrays Package, the <sbml> object must have the
'arrays:required' attribute.
- ARRAYS_10202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8010202:
The value of attribute 'arrays:required' on the <sbml> object must be of data
type 'boolean'.
- ARRAYS_10203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8010203:
The value of attribute 'arrays:required' on the <sbml> object must be set to
'true'.
- ARRAYS_10204 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8010204:
Wherever MathML content appears in an SBML document, the MathML content must be
placed within a math element, and that math element must be either explicitly or
implicitly declared to be in the XML namespace
http://www.w3.org/1998/Math/MathML Reference: L3V1 Arrays V1 Section 3.4
- ARRAYS_10205 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8010205:
The following is a list of the additional MathML 2.0 elements permitted in the
Arrays package: vector and selector.
- ARRAYS_10206 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8010206:
The first argument of aMathML selector must be aMathML vector object or a valid
identifier to an SBase object extended with a list of Dimension objects.
- ARRAYS_10207 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8010207:
The first argument of a MathML selector must have a number of dimensions equal
to the number of arguments to the selector minus 1.
- ARRAYS_10208 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8010208:
The arguments of a MathML selector other than the first argument must be
statically computable.
- ARRAYS_10209 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8010209:
The arguments of a MathML selector other than the first argument must be
evaluated to a scalar value.
- ARRAYS_10210 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8010210:
For each possible value of each Dimension id (i.e., 0 to size-1 of the Dimension
referred to) that appears in the second and later arguments of the selector,
there should be no array out - of - bounds problems.Namely, it must evaluate to
a non - negative integer that is less than the size of the corresponding
Dimension for the object being indexed where the last argument refers to
dimension 0, next to last to dimension 1 Reference: L3V1 Arrays V1 Section 3.5
- ARRAYS_10211 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8010211:
All mathematical operations must be performed on scalar values rather than
vectors.
- ARRAYS_10212 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8010212:
For MathML operations with two or more operands involving MathML vectors or
SBase objects with a list of Dimension objects, the number of dimensions and
their sizemust agree for all operands unless the operand is a scalar type(i.e.,
it does not have a list of Dimension objects).
- ARRAYS_10213 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8010213:
No SBase is allowed to have value of type vector.
- ARRAYS_10301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8010301:
(Extends validation rule #10301 in the SBML Level 3 Core specification.
- ARRAYS_10302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8010302:
The value of a 'arrays:id' must conform to the syntax of the <sbml> data type
'SId' Reference: L3V1 Arrays V1 Section
- ARRAYS_20101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020101:
Any object derived from the extended SBase class (defined in the Arrays package)
may contain at most one instance of a ListOfDimensions.
- ARRAYS_20102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020102:
Apart from the general notes and annotations subobjects permitted on all SBML
objects, a <listOfDimensions> container object may only contain <dimension>
objects.
- ARRAYS_20103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020103:
The ListOfDimensions associated with an SBase object must have a Dimension
object with arrays:arrayDimension attribute set to 0 ... n-1 before adding a
Dimension object with arrays : arrayDimension attribute set to n.
- ARRAYS_20104 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020104:
The ListOfDimensions associated with an SBase object must not have multiple
Dimension objects with the same arrays:arrayDimension attribute.
- ARRAYS_20105 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020105:
A <listOfDimensions> object may have the optional SBML Level 3 Core attributes
'metaid' and 'sboTerm'.
- ARRAYS_20106 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020106:
ListOf objects are not permitted to have a ListOfDimensions.
- ARRAYS_20107 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020107:
InSBML Level 3 Core, Models, FunctionDefinitions, Units, UnitDefinitions,
KineticLaws, LocalParameters, Triggers, Priorities, and Delays are not permitted
to have a ListOfDimensions.
- ARRAYS_20108 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020108:
The Dimension and Index objects are not permitted to have a ListOfDimensions.
- ARRAYS_20109 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020109:
Any object derived from the extended SBase class (defined in the Arrays package)
may contain at most one instance of a ListOfIndices.
- ARRAYS_20110 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020110:
Apart from the general notes and annotations subobjects permitted on all SBML
objects, a <listOfIndices> container object may only contain <index> objects.
- ARRAYS_20111 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020111:
The ListOfIndices associated with an SBase object must have a Index object with
arrays:arrayDimension attribute set to 0, 1, .
- ARRAYS_20112 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020112:
The ListOfIndices in an SBase object must not have multiple Index objects with
the same pair of values arrays:arrayDimension and arrays:referencedAttribute
attributes.
- ARRAYS_20113 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020113:
A <listOfIndices> object may have the optional SBML Level 3 Core attributes
'metaid' and 'sboTerm'.
- ARRAYS_20114 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020114:
Only SBML objects that include defined attributes of type SIdRef are permitted
to have a ListOfIndices.
- ARRAYS_20115 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020115:
SBase objects containg SIdRef must have a ListOfIndices if the referenced SBase
is an array.
- ARRAYS_20116 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020116:
SBase objects containg SIdRef with a ListOfDimensions should have a
ListOfIndices containing as many Index objects for this particular
arrays:referencedAttribute as the number of Dimension objects the referenced
object contains.
- ARRAYS_20117 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020117:
Reference: L3V1 Arrays V1
- ARRAYS_20201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020201:
A <dimension> object may have the optional SBML Level 3 Core attributes 'metaid'
and 'sboTerm'.
- ARRAYS_20202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020202:
A <dimension> object must have the required attributes 'arrays:size' and
'arrays:arrayDimension', and may have the optional attributes 'arrays:id' and
'arrays:name'.
- ARRAYS_20203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020203:
The attribute 'arrays:arrayDimension' on a <dimension> must have a value of data
type 'integer'.
- ARRAYS_20204 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020204:
The value of the attribute 'arrays:size' of a <dimension> object must be the
identifier of an existing <sBase> object defined in the enclosing <model>
object.
- ARRAYS_20205 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020205:
The value of the Parameter referenced by the arrays:size attribute must be a
non-negative scalar constant integer.
- ARRAYS_20301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020301:
An <index> object may have the optional SBML Level 3 Core attributes 'metaid'
and 'sboTerm'.
- ARRAYS_20302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020302:
An <index> object must have the required attributes 'arrays:referencedAttribute'
and 'arrays:arrayDimension'.
- ARRAYS_20303 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020303:
The attribute 'arrays:referencedAttribute' on an <index> must have a value of
data type 'string'.
- ARRAYS_20304 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020304:
The attribute 'arrays:arrayDimension' on an <index> must have a value of data
type 'integer'.
- ARRAYS_20305 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020305:
The object referenced by the SIdRef indicated by the arrays:referencedAttribute
attribute must include an arrays:arrayDimension matching the
arrays:arrayDimension for the Index Reference: L3V1 Arrays V1 Section 3.4
- ARRAYS_20306 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020306:
An <index> object must contain one and only one instance of the ASTNode element.
- ARRAYS_20307 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020307:
The MathML math element in an Index object must be statically computable.
- ARRAYS_20308 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020308:
For each possible value of each Dimension id (i.e., 0 to size-1 of the Dimension
referred to) that appears in theMathML math element, there should be no array
out of bounds problems.
- ARRAYS_20309 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020309:
An <index> object may have the optional SBML Level 3 Core subobjects for notes
and annotations.
- ARRAYS_20402 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020402:
A <dimension> object may have the optional SBML Level 3 Core subobjects for
notes and annotations.
- ARRAYS_20403 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 8020403:
The attribute 'arrays:name' on a <dimension> must have a value of data type
'string'.
- 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
-
- ArraysSBasePlugin() - Constructor for class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin
-
- ArraysSBasePlugin(ArraysSBasePlugin) - Constructor for class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin
-
Clone constructor
- ArraysSBasePlugin(SBase) - Constructor for class org.sbml.jsbml.ext.arrays.ArraysSBasePlugin
-
- 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
-
- arrayToWhitespaceSeparatedString(String[]) - Static method in class org.sbml.jsbml.ext.render.XMLTools
-
- Assignment - Interface in org.sbml.jsbml
-
An
Assignment
can be seen as a mathematical equation with a
Variable
on the left hand side and an equation on the right hand side
that assigns a value to the
Variable
.
- ASSIGNMENT_CYCLE_VALIDATION_FOUND_CYCLE_IDS - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.AssignmentCycleValidation
-
Key to store a set of ids in the
ValidationContext
so that we do not report several times the same cycle.
- AssignmentConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- AssignmentConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.AssignmentConstraints
-
- AssignmentCycleValidation - Class in org.sbml.jsbml.validator.offline.constraints.helper
-
- AssignmentCycleValidation() - Constructor for class org.sbml.jsbml.validator.offline.constraints.helper.AssignmentCycleValidation
-
- assignmentLevel - org.sbml.jsbml.ext.qual.OutputTransitionEffect
-
- AssignmentRule - Class in org.sbml.jsbml
-
Represents the assignmentRule XML element of a SBML file.
- AssignmentRule() - Constructor for class org.sbml.jsbml.AssignmentRule
-
Creates an AssignmentRule instance.
- AssignmentRule(int, int) - Constructor for class org.sbml.jsbml.AssignmentRule
-
Creates an AssignmentRule instance with the given level and version.
- AssignmentRule(AssignmentRule) - Constructor for class org.sbml.jsbml.AssignmentRule
-
Creates a cloned AssignmentRule instance from a given AssignmentRule.
- AssignmentRule(ASTNode, int, int) - Constructor for class org.sbml.jsbml.AssignmentRule
-
Creates an AssignmentRule instance from a given math, level and version.
- AssignmentRule(ASTNode, Parameter) - Constructor for class org.sbml.jsbml.AssignmentRule
-
Creates an AssignmentRule instance from a given math and Parameter.
- AssignmentRule(ASTNode, Variable) - Constructor for class org.sbml.jsbml.AssignmentRule
-
Creates an AssignmentRule instance from a given math and
Variable
.
- AssignmentRule(ExplicitRule) - Constructor for class org.sbml.jsbml.AssignmentRule
-
Creates a cloned AssignmentRule instance from a given
ExplicitRule
.
- AssignmentRule(Parameter) - Constructor for class org.sbml.jsbml.AssignmentRule
-
Creates an AssignmentRule instance from a given Parameter.
- AssignmentRule(Parameter, ASTNode) - Constructor for class org.sbml.jsbml.AssignmentRule
-
Creates an AssignmentRule instance from a given math and Parameter.
- AssignmentRule(Variable) - Constructor for class org.sbml.jsbml.AssignmentRule
-
Creates an AssignmentRule instance from a given variable.
- AssignmentRule(Variable, ASTNode) - Constructor for class org.sbml.jsbml.AssignmentRule
-
Creates an AssignmentRule instance from a given variable and math.
- AssignmentRuleConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- AssignmentRuleConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.AssignmentRuleConstraints
-
- AssignmentToConstantEntity - org.sbml.jsbml.SBMLException.Code
-
Cannot reassign a constant in an assignment rule
- AssignmentVariableFilter - Class in org.sbml.jsbml.util.filters
-
This filter only accepts instances of
Assignment
with the variable as
given in the constructor of this object.
- AssignmentVariableFilter() - Constructor for class org.sbml.jsbml.util.filters.AssignmentVariableFilter
-
- AssignmentVariableFilter(String) - Constructor for class org.sbml.jsbml.util.filters.AssignmentVariableFilter
-
- AssignRuleCompartmentMismatch - org.sbml.jsbml.SBMLException.Code
-
Mismatched units in assignment rule for compartment
- AssignRuleParameterMismatch - org.sbml.jsbml.SBMLException.Code
-
Mismatched units in assignment rule for parameter
- AssignRuleSpeciesMismatch - org.sbml.jsbml.SBMLException.Code
-
Mismatched units in assignment rule for species
- associatedSpecies - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
-
Introduced to FBC in version 2.
- association - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
-
Introduced to FBC in version 2.
- Association - Interface in org.sbml.jsbml.ext.fbc
-
Represents either
a single gene, or a collection of genes in a logical expression and is only ever instantiated as one of its subclasses:
GeneProductRef
,
And
and
Or
.
- AssociationNode<T> - Interface in org.sbml.jsbml.ext.render.director
-
- ASTArithmeticOperatorNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing an arithmetic
operator in a mathematical expression.
- ASTArithmeticOperatorNode() - Constructor for class org.sbml.jsbml.math.ASTArithmeticOperatorNode
-
- ASTArithmeticOperatorNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTArithmeticOperatorNode
-
- ASTArithmeticOperatorNode(ASTNode.Type, MathContainer) - Constructor for class org.sbml.jsbml.math.ASTArithmeticOperatorNode
-
- ASTArithmeticOperatorNode(ASTArithmeticOperatorNode) - Constructor for class org.sbml.jsbml.math.ASTArithmeticOperatorNode
-
- ASTArithmeticOperatorNode(MathContainer) - Constructor for class org.sbml.jsbml.math.ASTArithmeticOperatorNode
-
- ASTBinaryFunctionNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a function with two
parameters
- ASTBinaryFunctionNode() - Constructor for class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- ASTBinaryFunctionNode(ASTBinaryFunctionNode) - Constructor for class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- ASTBinaryFunctionNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTBinaryFunctionNode
-
- ASTBoolean - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a boolean
- ASTBoolean() - Constructor for class org.sbml.jsbml.math.ASTBoolean
-
- ASTBoolean(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTBoolean
-
- ASTBoolean(ASTBoolean) - Constructor for class org.sbml.jsbml.math.ASTBoolean
-
Copy constructor; Creates a deep copy of the given
ASTBoolean
.
- ASTCiFunctionNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a MathML ci element
in a mathematical expression.
- ASTCiFunctionNode() - Constructor for class org.sbml.jsbml.math.ASTCiFunctionNode
-
- ASTCiFunctionNode(ASTCiFunctionNode) - Constructor for class org.sbml.jsbml.math.ASTCiFunctionNode
-
- ASTCiNumberNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a MathML ci element
in a mathematical expression.
- ASTCiNumberNode() - Constructor for class org.sbml.jsbml.math.ASTCiNumberNode
-
- ASTCiNumberNode(ASTCiNumberNode) - Constructor for class org.sbml.jsbml.math.ASTCiNumberNode
-
- ASTCnExponentialNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing an exponent
in a mathematical expression
- ASTCnExponentialNode() - Constructor for class org.sbml.jsbml.math.ASTCnExponentialNode
-
- ASTCnExponentialNode(ASTCnExponentialNode) - Constructor for class org.sbml.jsbml.math.ASTCnExponentialNode
-
- ASTCnIntegerNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing an Integer
in a mathematical expression
- ASTCnIntegerNode() - Constructor for class org.sbml.jsbml.math.ASTCnIntegerNode
-
Creates a new
ASTCnIntegerNode
that lacks a pointer
to its containing
MathContainer
.
- ASTCnIntegerNode(int) - Constructor for class org.sbml.jsbml.math.ASTCnIntegerNode
-
- ASTCnIntegerNode(ASTCnIntegerNode) - Constructor for class org.sbml.jsbml.math.ASTCnIntegerNode
-
- ASTCnNumberNode<T> - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a MathML cn element in a
mathematical expression. cn elements are used to specify actual numerical
constants.
- ASTCnNumberNode() - Constructor for class org.sbml.jsbml.math.ASTCnNumberNode
-
- ASTCnNumberNode(String) - Constructor for class org.sbml.jsbml.math.ASTCnNumberNode
-
- ASTCnNumberNode(ASTCnNumberNode<T>) - Constructor for class org.sbml.jsbml.math.ASTCnNumberNode
-
- ASTCnRationalNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a rational number
in a mathematical expression
- ASTCnRationalNode() - Constructor for class org.sbml.jsbml.math.ASTCnRationalNode
-
Creates a new
ASTCnRationalNode
that lacks a pointer
to its containing
MathContainer
.
- ASTCnRationalNode(ASTCnRationalNode) - Constructor for class org.sbml.jsbml.math.ASTCnRationalNode
-
- ASTCnRealNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a real number
in a mathematical expression
- ASTCnRealNode() - Constructor for class org.sbml.jsbml.math.ASTCnRealNode
-
Creates a new
ASTCnRealNode
that lacks a pointer
to its containing
MathContainer
.
- ASTCnRealNode(double) - Constructor for class org.sbml.jsbml.math.ASTCnRealNode
-
Creates a new
ASTCnRealNode
that lacks a pointer
to its containing
MathContainer
but has the
specified real value.
- ASTCnRealNode(ASTCnRealNode) - Constructor for class org.sbml.jsbml.math.ASTCnRealNode
-
Copy constructor; Creates a deep copy of the given
ASTCnRealNode
.
- ASTConstantNumber - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a constant number
in a mathematical expression.
- ASTConstantNumber() - Constructor for class org.sbml.jsbml.math.ASTConstantNumber
-
- ASTConstantNumber(double) - Constructor for class org.sbml.jsbml.math.ASTConstantNumber
-
- ASTConstantNumber(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTConstantNumber
-
- ASTConstantNumber(ASTConstantNumber) - Constructor for class org.sbml.jsbml.math.ASTConstantNumber
-
- ASTCSymbolAvogadroNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing avogadro's number
- ASTCSymbolAvogadroNode() - Constructor for class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- ASTCSymbolAvogadroNode(ASTCSymbolAvogadroNode) - Constructor for class org.sbml.jsbml.math.ASTCSymbolAvogadroNode
-
- ASTCSymbolBaseNode - Interface in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a MathML element
that contains a definitionURL and name attribute.
- ASTCSymbolDelayNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing the delay function
- ASTCSymbolDelayNode() - Constructor for class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- ASTCSymbolDelayNode(ASTCSymbolDelayNode) - Constructor for class org.sbml.jsbml.math.ASTCSymbolDelayNode
-
- ASTCSymbolNode - Interface in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a MathML csymbol element
in a mathematical expression.
- ASTCSymbolTimeNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing the time function
- ASTCSymbolTimeNode() - Constructor for class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- ASTCSymbolTimeNode(ASTCSymbolTimeNode) - Constructor for class org.sbml.jsbml.math.ASTCSymbolTimeNode
-
- ASTDivideNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing the divide function
- ASTDivideNode() - Constructor for class org.sbml.jsbml.math.ASTDivideNode
-
- ASTDivideNode(ASTDivideNode) - Constructor for class org.sbml.jsbml.math.ASTDivideNode
-
Copy constructor; Creates a deep copy of the given
ASTDivideNode
.
- ASTDivideNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTDivideNode
-
- ASTFactory - Class in org.sbml.jsbml.math
-
A collection of static methods that can be used to create new abstract syntax
trees or alter the topology of existing ones.
- ASTFactory() - Constructor for class org.sbml.jsbml.math.ASTFactory
-
- ASTFunction - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a function
in a mathematical expression.
- ASTFunction() - Constructor for class org.sbml.jsbml.math.ASTFunction
-
- ASTFunction(ASTFunction) - Constructor for class org.sbml.jsbml.math.ASTFunction
-
Copy constructor; Creates a deep copy of the given
ASTFunction
.
- ASTFunction(MathContainer) - Constructor for class org.sbml.jsbml.math.ASTFunction
-
- ASTHyperbolicNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a hyperbolic function
- ASTHyperbolicNode() - Constructor for class org.sbml.jsbml.math.ASTHyperbolicNode
-
- ASTHyperbolicNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTHyperbolicNode
-
- ASTHyperbolicNode(ASTHyperbolicNode) - Constructor for class org.sbml.jsbml.math.ASTHyperbolicNode
-
- ASTLambdaFunctionNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a lambda function
in a mathematical expression.
- ASTLambdaFunctionNode() - Constructor for class org.sbml.jsbml.math.ASTLambdaFunctionNode
-
- ASTLambdaFunctionNode(ASTLambdaFunctionNode) - Constructor for class org.sbml.jsbml.math.ASTLambdaFunctionNode
-
- ASTLogarithmNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing the logarithm function
- ASTLogarithmNode() - Constructor for class org.sbml.jsbml.math.ASTLogarithmNode
-
- ASTLogarithmNode(ASTLogarithmNode) - Constructor for class org.sbml.jsbml.math.ASTLogarithmNode
-
- ASTLogarithmNode(ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTLogarithmNode
-
- ASTLogarithmNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTLogarithmNode
-
- ASTLogicalOperatorNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a logical operator
in a mathematical expression.
- ASTLogicalOperatorNode() - Constructor for class org.sbml.jsbml.math.ASTLogicalOperatorNode
-
- ASTLogicalOperatorNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTLogicalOperatorNode
-
- ASTLogicalOperatorNode(ASTLogicalOperatorNode) - Constructor for class org.sbml.jsbml.math.ASTLogicalOperatorNode
-
- ASTMinusNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing the minus operator
- ASTMinusNode() - Constructor for class org.sbml.jsbml.math.ASTMinusNode
-
- ASTMinusNode(ASTMinusNode) - Constructor for class org.sbml.jsbml.math.ASTMinusNode
-
Copy constructor; Creates a deep copy of the given
ASTMinusNode
.
- ASTMinusNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTMinusNode
-
- ASTNode - Class in org.sbml.jsbml
-
A node in the Abstract Syntax Tree (AST) representation of a mathematical
expression.
- ASTNode() - Constructor for class org.sbml.jsbml.ASTNode
-
- ASTNode(char) - Constructor for class org.sbml.jsbml.ASTNode
-
Creates a new
ASTNode
representing an operator, i.e., an internal
node.
- ASTNode(char, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode
-
Creates a new
ASTNode
representing an operator, i.e., an internal
node.
- ASTNode(double) - Constructor for class org.sbml.jsbml.ASTNode
-
- ASTNode(double, int) - Constructor for class org.sbml.jsbml.ASTNode
-
- ASTNode(double, int, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode
-
- ASTNode(double, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode
-
- ASTNode(int) - Constructor for class org.sbml.jsbml.ASTNode
-
Creates and returns a new
ASTNode
with the given integer value.
- ASTNode(int, String, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode
-
- ASTNode(int, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode
-
Creates and returns a new
ASTNode
with the given integer value for
the
given
MathContainer
as its parent SBML object.
- ASTNode(String) - Constructor for class org.sbml.jsbml.ASTNode
-
Creates and returns a new
ASTNode
with the given name.
- ASTNode(String, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode
-
Creates and returns a new
ASTNode
with the given name.
- ASTNode(ASTNode) - Constructor for class org.sbml.jsbml.ASTNode
-
Copy constructor; Creates a deep copy of the given
ASTNode
.
- ASTNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.ASTNode
-
- ASTNode(ASTNode.Type, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode
-
- ASTNode(CallableSBase) - Constructor for class org.sbml.jsbml.ASTNode
-
- ASTNode(CallableSBase, MathContainer) - Constructor for class org.sbml.jsbml.ASTNode
-
- ASTNode(ASTNode2) - Constructor for class org.sbml.jsbml.ASTNode
-
- ASTNode(MathContainer) - Constructor for class org.sbml.jsbml.ASTNode
-
- ASTNODE_CN_TYPE_ATTRIBUTE - Static variable in class org.sbml.jsbml.validator.offline.constraints.ASTNodeConstraints
-
- ASTNode.Type - Enum in org.sbml.jsbml
-
An enumeration of all possible types that can be represented by an
abstract syntax tree node.
- ASTNode2 - Interface in org.sbml.jsbml.math
-
A node in the Abstract Syntax Tree (AST) representation of a mathematical
expression.
- ASTNode2Compiler - Interface in org.sbml.jsbml.math.compiler
-
A compiler for abstract syntax trees.
- ASTNode2Value<T> - Class in org.sbml.jsbml.math.compiler
-
When interpreting
ASTNode2
s, the
ASTNode2Compiler
takes
elements of this class as arguments and performs its operations on it.
- ASTNode2Value(ASTNode2Compiler) - Constructor for class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- ASTNode2Value(UnitDefinition, ASTNode2Compiler) - Constructor for class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- ASTNode2Value(T, ASTNode2Compiler) - Constructor for class org.sbml.jsbml.math.compiler.ASTNode2Value
-
- ASTNodeCompiler - Interface in org.sbml.jsbml.util.compilers
-
A compiler for abstract syntax trees.
- ASTNodeConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
Validation constraints related to
ASTNode
.
- ASTNodeConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.ASTNodeConstraints
-
- ASTNodePlugin - Interface in org.sbml.jsbml.ext
-
Defines the methods necessary for an ASTNode
or ASTNode2
Plugin.
- astNodeToTree(ASTNode, String, String) - Static method in class org.sbml.jsbml.ASTNode
-
Returns a simple tree view of the ASTNode internal, including mainly
node type and hierarchy.
- ASTNodeValue - Class in org.sbml.jsbml.util.compilers
-
When interpreting
ASTNode
s, the
ASTNodeCompiler
takes
elements of this class as arguments and performs its operations on it.
- ASTNodeValue(boolean, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- ASTNodeValue(double, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- ASTNodeValue(float, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- ASTNodeValue(int, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- ASTNodeValue(long, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- ASTNodeValue(Number, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- ASTNodeValue(String, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- ASTNodeValue(CallableSBase, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- ASTNodeValue(UnitDefinition, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- ASTNodeValue(ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- ASTNodeValue(Node, ASTNodeCompiler) - Constructor for class org.sbml.jsbml.util.compilers.ASTNodeValue
-
- ASTNumber - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a number
in a mathematical expression.
- ASTNumber() - Constructor for class org.sbml.jsbml.math.ASTNumber
-
Creates a new
ASTNumber
that lacks a pointer
to its containing
MathContainer
.
- ASTNumber(ASTNumber) - Constructor for class org.sbml.jsbml.math.ASTNumber
-
Copy constructor; Creates a deep copy of the given
ASTNumber
.
- ASTPiecewiseFunctionNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a MathML piecewise
element in a mathematical expression.
- ASTPiecewiseFunctionNode() - Constructor for class org.sbml.jsbml.math.ASTPiecewiseFunctionNode
-
- ASTPiecewiseFunctionNode(ASTPiecewiseFunctionNode) - Constructor for class org.sbml.jsbml.math.ASTPiecewiseFunctionNode
-
- ASTPlusNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing the plus operator
- ASTPlusNode() - Constructor for class org.sbml.jsbml.math.ASTPlusNode
-
- ASTPlusNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTPlusNode
-
- ASTPlusNode(ASTPlusNode) - Constructor for class org.sbml.jsbml.math.ASTPlusNode
-
Copy constructor; Creates a deep copy of the given
ASTPlusNode
.
- ASTPowerNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing the power function
- ASTPowerNode() - Constructor for class org.sbml.jsbml.math.ASTPowerNode
-
- ASTPowerNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTPowerNode
-
Creates a new
ASTPowerNode
with the specified basis and
exponent.
- ASTPowerNode(ASTPowerNode) - Constructor for class org.sbml.jsbml.math.ASTPowerNode
-
Copy constructor; Creates a deep copy of the given
ASTPowerNode
.
- ASTQualifierNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a MathML qualifier element
in a mathematical expression.
- ASTQualifierNode() - Constructor for class org.sbml.jsbml.math.ASTQualifierNode
-
- ASTQualifierNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTQualifierNode
-
- ASTQualifierNode(ASTQualifierNode) - Constructor for class org.sbml.jsbml.math.ASTQualifierNode
-
- ASTRelationalOperatorNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a relational
operator in a mathematical expression.
- ASTRelationalOperatorNode() - Constructor for class org.sbml.jsbml.math.ASTRelationalOperatorNode
-
- ASTRelationalOperatorNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTRelationalOperatorNode
-
- ASTRelationalOperatorNode(ASTRelationalOperatorNode) - Constructor for class org.sbml.jsbml.math.ASTRelationalOperatorNode
-
- ASTRootNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a root function
- ASTRootNode() - Constructor for class org.sbml.jsbml.math.ASTRootNode
-
- ASTRootNode(ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTRootNode
-
Creates a new
ASTRootNode
with the specified radicand and
a root exponent of 2.
- ASTRootNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTRootNode
-
Creates a new
ASTRootNode
with the specified radicand and
rootExponent.
- ASTRootNode(ASTRootNode) - Constructor for class org.sbml.jsbml.math.ASTRootNode
-
Copy constructor; Creates a deep copy of the given
ASTRootNode
.
- ASTTimesNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing the times operator
- ASTTimesNode() - Constructor for class org.sbml.jsbml.math.ASTTimesNode
-
- ASTTimesNode(ASTNode2, ASTNode2) - Constructor for class org.sbml.jsbml.math.ASTTimesNode
-
- ASTTimesNode(ASTTimesNode) - Constructor for class org.sbml.jsbml.math.ASTTimesNode
-
Copy constructor; Creates a deep copy of the given
ASTTimesNode
.
- ASTTrigonometricNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a trigonometric function
- ASTTrigonometricNode() - Constructor for class org.sbml.jsbml.math.ASTTrigonometricNode
-
- ASTTrigonometricNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTTrigonometricNode
-
- ASTTrigonometricNode(ASTTrigonometricNode) - Constructor for class org.sbml.jsbml.math.ASTTrigonometricNode
-
- ASTUnaryFunctionNode - Class in org.sbml.jsbml.math
-
An Abstract Syntax Tree (AST) node representing a function with only one
parameter
- ASTUnaryFunctionNode() - Constructor for class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- ASTUnaryFunctionNode(ASTNode.Type) - Constructor for class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- ASTUnaryFunctionNode(ASTUnaryFunctionNode) - Constructor for class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- ASTUnknown - Class in org.sbml.jsbml.math
-
An
ASTNode2
with specified neutral behavior.
- AVOGADRO - org.sbml.jsbml.Unit.Kind
-
This unit is DIMENSIONLESS multiplied with Avogadro's number.
- AVOGADRO_L3V1 - Static variable in class org.sbml.jsbml.util.Maths
-
Avogadro's constant of 6.02214179 ⋅ 1023
mol-1.