JSBML
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PACKAGE_VERSION - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants
 
PACKAGE_VERSION_MISMATCH_MSG - Static variable in exception org.sbml.jsbml.LevelVersionError
Message to display in cases that two objects do not have identical package version attributes.
PackageDisabler - Class in org.sbml.jsbml.util
 
PackageDisabler(SBMLDocument) - Constructor for class org.sbml.jsbml.util.PackageDisabler
Instantiates a PackageDisabler on the given SBMLDocument
packageDisplayName - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
 
packageName - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants
 
packageName - Static variable in class org.sbml.jsbml.ext.comp.CompConstants
 
packageName - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants
 
packageName - Static variable in class org.sbml.jsbml.ext.fbc.FBCConstants
 
packageName - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants
 
packageName - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
 
packageName - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
 
packageName - Static variable in class org.sbml.jsbml.ext.qual.QualConstants
 
packageName - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
 
packageName - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
 
packageName - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
PackageParser - Interface in org.sbml.jsbml.xml.parsers
Interface that define some common methods that the parsers for SBML packages need to implement in order to provide some basic information about them.
PackageUtil - Class in org.sbml.jsbml.xml.parsers
 
PackageUtil() - Constructor for class org.sbml.jsbml.xml.parsers.PackageUtil
 
packageVersion - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
packageVersionMismatchMessage(SBasePlugin, SBase) - Static method in exception org.sbml.jsbml.LevelVersionError
Creates an error message showing the different package versions of the given SBase elements.
packageVersionMismatchMessage(SBase, SBase) - Static method in exception org.sbml.jsbml.LevelVersionError
Creates an error message showing the different package versions of the given SBase elements.
PAD - org.sbml.jsbml.ext.render.GradientBase.Spread
the gradient color at the endpoint of the vector defines how the gradient is continued beyond that point
Pair<L,V> - Class in org.sbml.jsbml.util
A general implementation of a 2-tuple, i.e., two arbitrary objects.
Pair() - Constructor for class org.sbml.jsbml.util.Pair
 
Pair(L, V) - Constructor for class org.sbml.jsbml.util.Pair
 
Pair(Pair<L, V>) - Constructor for class org.sbml.jsbml.util.Pair
 
pairOf(L, V) - Static method in class org.sbml.jsbml.util.Pair
Can be used for static import in your class to easily create Pairs of arbitrary data types with a simple method call, e.g., pairOf(1, 2).
Parameter - Class in org.sbml.jsbml
Represents a globally valid parameter in the model, i.e., a variable that may change during a simulation or that provides a constant value.
Parameter() - Constructor for class org.sbml.jsbml.Parameter
Creates a Parameter instance.
Parameter(int, int) - Constructor for class org.sbml.jsbml.Parameter
Creates a Parameter instance from a level and version.
Parameter(String) - Constructor for class org.sbml.jsbml.Parameter
Creates a Parameter instance from an id.
Parameter(String, int, int) - Constructor for class org.sbml.jsbml.Parameter
Creates a Parameter instance from an id, level and version.
Parameter(LocalParameter) - Constructor for class org.sbml.jsbml.Parameter
Creates a Parameter instance from a given LocalParameter.
Parameter(Parameter) - Constructor for class org.sbml.jsbml.Parameter
Creates a Parameter instance from a given Parameter.
ParameterConstraints - Class in org.sbml.jsbml.validator.offline.constraints
 
ParameterConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.ParameterConstraints
 
ParameterShouldHaveUnits - org.sbml.jsbml.SBMLException.Code
It's best to declare units for every parameter in a model
ParameterType - Class in org.sbml.jsbml.ext.spatial
Top level class for all possible child of a SpatialParameterPlugin.
ParameterType() - Constructor for class org.sbml.jsbml.ext.spatial.ParameterType
Creates a new ParameterType instance.
ParameterType(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.ParameterType
Creates a new ParameterType instance.
ParameterType(ParameterType) - Constructor for class org.sbml.jsbml.ext.spatial.ParameterType
Creates a new ParameterType instance.
parametricGeometry - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
 
ParametricGeometry - Class in org.sbml.jsbml.ext.spatial
 
ParametricGeometry() - Constructor for class org.sbml.jsbml.ext.spatial.ParametricGeometry
 
ParametricGeometry(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.ParametricGeometry
 
ParametricGeometry(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.ParametricGeometry
 
ParametricGeometry(ParametricGeometry) - Constructor for class org.sbml.jsbml.ext.spatial.ParametricGeometry
 
ParametricGeometryConstraints - Class in org.sbml.jsbml.validator.offline.constraints
Defines validation rules (as ValidationFunction instances) for the ParametricGeometry class.
ParametricGeometryConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.ParametricGeometryConstraints
 
parametricObject - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
 
ParametricObject - Class in org.sbml.jsbml.ext.spatial
 
ParametricObject() - Constructor for class org.sbml.jsbml.ext.spatial.ParametricObject
 
ParametricObject(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.ParametricObject
 
ParametricObject(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.ParametricObject
 
ParametricObject(ParametricObject) - Constructor for class org.sbml.jsbml.ext.spatial.ParametricObject
 
ParametricObjectConstraints - Class in org.sbml.jsbml.validator.offline.constraints
Defines validation rules (as ValidationFunction instances) for the ParametricObject class.
ParametricObjectConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.ParametricObjectConstraints
 
parentSBMLObject - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
parse() - Method in class org.sbml.jsbml.math.parser.FormulaParser
 
parse() - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
 
parse() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
 
parse() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
 
parse() - Method in interface org.sbml.jsbml.math.parser.IFormulaParser
 
parse() - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
 
parse() - Method in class org.sbml.jsbml.text.parser.FormulaParser
 
parse() - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
 
parse() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
 
parse() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
 
parse() - Method in interface org.sbml.jsbml.text.parser.IFormulaParser
 
parse(InputStream, DefaultHandler, boolean) - Method in class org.sbml.jsbml.util.JAXPFacade
Parses the content of a byte stream as XML, using a nonvalidating parser and the specified SAX2 default event handler.
parse(InputStream, DefaultHandler, boolean) - Method in interface org.sbml.jsbml.util.SAX2Parser
Parses the content of a byte stream as XML, using a nonvalidating parser and the specified SAX2 default event handler.
parse(InputStream, DefaultHandler, Object[]) - Method in class org.sbml.jsbml.util.JAXPFacade
Parses the content of a byte stream as XML, using a validating parser and the specified SAX2 default event handler.
parse(InputStream, DefaultHandler, Object[]) - Method in interface org.sbml.jsbml.util.SAX2Parser
Parses the content of a byte stream as XML, using a validating parser and the specified SAX2 default event handler.
parse(Reader, DefaultHandler, boolean) - Method in class org.sbml.jsbml.util.JAXPFacade
Parses the content of a character stream as XML, using a nonvalidating parser and the specified SAX2 default event handler.
parse(Reader, DefaultHandler, boolean) - Method in interface org.sbml.jsbml.util.SAX2Parser
Parses the content of a character stream as XML, using a nonvalidating parser and the specified SAX2 default event handler.
parse(Reader, DefaultHandler, Object[]) - Method in class org.sbml.jsbml.util.JAXPFacade
Parses the content of a character stream as XML, using a validating parser and the specified SAX2 default event handler.
parse(Reader, DefaultHandler, Object[]) - Method in interface org.sbml.jsbml.util.SAX2Parser
Parses the content of a character stream as XML, using a validating parser and the specified SAX2 default event handler.
parseCobraNotes(SBase) - Static method in class org.sbml.jsbml.util.CobraUtil
Parses the notes of the given SBase element.
ParseException - Exception in org.sbml.jsbml.math.parser
This exception is thrown when parse errors are encountered.
ParseException - Exception in org.sbml.jsbml.text.parser
This exception is thrown when parse errors are encountered.
ParseException() - Constructor for exception org.sbml.jsbml.math.parser.ParseException
Creates a new ParseException instance.
ParseException() - Constructor for exception org.sbml.jsbml.text.parser.ParseException
Creates a new ParseException instance.
ParseException(String) - Constructor for exception org.sbml.jsbml.math.parser.ParseException
Creates a new ParseException instance with the given message.
ParseException(String) - Constructor for exception org.sbml.jsbml.text.parser.ParseException
Creates a new ParseException instance with the given message.
ParseException(Throwable) - Constructor for exception org.sbml.jsbml.math.parser.ParseException
Creates a new ParseException instance that will warp the given Throwable.
ParseException(Throwable) - Constructor for exception org.sbml.jsbml.text.parser.ParseException
Creates a new ParseException instance that will warp the given Throwable.
ParseException(Token, int[][], String[]) - Constructor for exception org.sbml.jsbml.math.parser.ParseException
Creates a new ParseException instance with the fields "currentToken", "expectedTokenSequences", and "tokenImage" set.
ParseException(Token, int[][], String[]) - Constructor for exception org.sbml.jsbml.text.parser.ParseException
Creates a new ParseException instance with the fields "currentToken", "expectedTokenSequences", and "tokenImage" set.
parseFontStyleItalic(String) - Static method in class org.sbml.jsbml.ext.render.XMLTools
 
parseFontWeightBold(String) - Static method in class org.sbml.jsbml.ext.render.XMLTools
 
parseFormula(String) - Static method in class org.sbml.jsbml.ASTNode
Parses a text-string mathematical formula and returns a representation as an Abstract Syntax Tree.
parseFormula(String) - Static method in class org.sbml.jsbml.JSBML
Parses a text-string mathematical formula and returns a representation as an Abstract Syntax Tree.
parseFormula(String) - Static method in class org.sbml.jsbml.math.ASTFactory
Parses a text-string mathematical formula and an Abstract Syntax Tree representation.
parseFormula(String, IFormulaParser) - Static method in class org.sbml.jsbml.ASTNode
Parses a text-string mathematical formula, using the given IFormulaParser and returns a representation as an Abstract Syntax Tree.
parseGPR(Reaction, String, boolean) - Static method in class org.sbml.jsbml.ext.fbc.converters.GPRParser
Parses a gene association string as used in COBRA in SBML level 2 into a GeneProductAssociation used in SBML level 3.
parseGPR(Reaction, String, boolean, boolean) - Static method in class org.sbml.jsbml.ext.fbc.converters.GPRParser
Parses a gene association string as used in COBRA in SBML level 2 into a GeneProductAssociation used in SBML level 3.
parseMathML(String) - Static method in class org.sbml.jsbml.ASTNode
 
parseMathML(String) - Static method in class org.sbml.jsbml.math.ASTFactory
Return String representation of specified MathML file
parsePosition(String) - Static method in class org.sbml.jsbml.ext.render.XMLTools
 
ParserManager - Class in org.sbml.jsbml.xml.parsers
 
parseSBMLBoolean(String) - Static method in class org.sbml.jsbml.util.StringTools
Parses a String into a boolean following the rules of the SBML specifications, section 3.1.2.
parseSBMLBooleanStrict(String) - Static method in class org.sbml.jsbml.util.StringTools
Parses a String into a boolean following the rules of the SBML specifications, section 3.1.2.
parseSBMLDouble(String) - Static method in class org.sbml.jsbml.util.StringTools
Parses a String into a double number following the rules of the SBML specifications, section 3.1.5.
parseSBMLDoubleStrict(String) - Static method in class org.sbml.jsbml.util.StringTools
Parses a String into a double number following the rules of the SBML specifications, section 3.1.5.
parseSBMLInt(String) - Static method in class org.sbml.jsbml.util.StringTools
Parses a String into an int number following the rules of the SBML specifications, section 3.1.3.
parseSBMLShort(String) - Static method in class org.sbml.jsbml.util.StringTools
Parses a String into an short number following the rules of the SBML specifications, section 3.1.3.
parseSBMLShortStrict(String) - Static method in class org.sbml.jsbml.util.StringTools
Parses a String into an short number following the rules of the SBML specifications, section 3.1.3.
partonomy - org.sbml.jsbml.ext.groups.Group.Kind
The group represents a collection of parts, and its members have a part-of relationship to the group.
PASCAL - org.sbml.jsbml.Unit.Kind
The pascal unit.
performAction(T) - Method in class org.sbml.jsbml.util.converters.LevelVersionConverter
Executes a conversion action on the given instance of SBase.
performAction(T) - Method in class org.sbml.jsbml.util.converters.ToL3Converter
 
performAction(T) - Method in class org.sbml.jsbml.util.converters.ToL3V2Converter
 
persistent - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
PerturbingAgent<T> - Class in org.sbml.jsbml.ext.render.director
 
PerturbingAgent() - Constructor for class org.sbml.jsbml.ext.render.director.PerturbingAgent
 
PieceNeedsBoolean - org.sbml.jsbml.SBMLException.Code
Second argument of <piece> must yield a boolean value
piecewise(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
 
piecewise(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
 
piecewise(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
 
piecewise(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
piecewise(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
piecewise(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
piecewise(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise
 
piecewise(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
piecewise(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
Deprecated.
 
piecewise(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
piecewise(List<ASTNode2>) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
 
piecewise(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
 
piecewise(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
 
piecewise(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
 
piecewise(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
 
piecewise(ASTNode, ASTNode...) - Static method in class org.sbml.jsbml.ASTNode
Creates a piecewise ASTNode.
piecewise(ASTQualifierNode, ASTQualifierNode...) - Static method in class org.sbml.jsbml.math.ASTFactory
Creates a piecewise ASTPiecewiseFunctionNode.
piecewise(MathContainer, ASTNode[]) - Static method in class org.sbml.jsbml.ASTNode
 
PIECEWISE_ID - Static variable in class org.sbml.jsbml.JSBML
Key used to store the real parent element for each child of a ASTNode.Type.FUNCTION_PIECEWISE ASTNode.
PiecewiseNeedsConsistentTypes - org.sbml.jsbml.SBMLException.Code
<piecewise> terms have inconsistent data types
plus(double) - Method in class org.sbml.jsbml.ASTNode
Adds a number to this node.
plus(int) - Method in class org.sbml.jsbml.ASTNode
Adds an integer number to this node.
plus(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
 
plus(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
 
plus(List<ASTNode>) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
 
plus(List<ASTNode>) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
plus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
plus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
plus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
plus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
Deprecated.
 
plus(List<ASTNode>) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
plus(List<ASTNode>) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationUnitsCompiler
 
plus(List<ASTNode2>) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
 
plus(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
 
plus(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
 
plus(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
 
plus(List<ASTNode2>) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
 
plus(ASTNode) - Method in class org.sbml.jsbml.ASTNode
Adds a given node to this node.
plus(CallableSBase) - Method in class org.sbml.jsbml.ASTNode
Adds an SBML element to this node.
plus(ASTNode2, double) - Static method in class org.sbml.jsbml.math.ASTFactory
Adds a real number to ASTNode2.
plus(ASTNode2, int) - Static method in class org.sbml.jsbml.math.ASTFactory
Adds an integer number to ASTNode2.
plus(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
Adds an ASTNode2 to an ASTNode2.
PLUS - org.sbml.jsbml.ASTNode.Type
 
PLUS - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
RegularExpression Id.
PLUS - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
RegularExpression Id.
PLUS - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
RegularExpression Id.
PLUS - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
RegularExpression Id.
PLUS - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
RegularExpression Id.
PLUS - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
RegularExpression Id.
PLUS - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
PLUS - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
RegularExpression Id.
PLUS - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
RegularExpression Id.
PN_RELATIVE_DOCKING_POINT - Static variable in class org.sbml.jsbml.ext.render.director.LayoutDirector
Constant for use as the key for relative docking points.
Point - Class in org.sbml.jsbml.ext.layout
The representation of a point in the "layout" package.
Point() - Constructor for class org.sbml.jsbml.ext.layout.Point
Creates a new Point instance with all coordinates set to Double.NaN.
Point(double, double) - Constructor for class org.sbml.jsbml.ext.layout.Point
Creates a new Point instance with the given x and y coordinates. z is set to Double.NaN.
Point(double, double, double) - Constructor for class org.sbml.jsbml.ext.layout.Point
Creates a new Point instance with the given coordinates.
Point(double, double, double, int, int) - Constructor for class org.sbml.jsbml.ext.layout.Point
Creates a new Point instance with the given coordinates and level and version.
Point(int, int) - Constructor for class org.sbml.jsbml.ext.layout.Point
Creates a new Point instance with the given level and version, all coordinates are set to Double.NaN.
Point(Point) - Constructor for class org.sbml.jsbml.ext.layout.Point
Creates a new Point instance with all attributes cloned from the given Point.
Point3D - Interface in org.sbml.jsbml.ext.render
 
PointConstraints - Class in org.sbml.jsbml.validator.offline.constraints
Defines validation rules (as ValidationFunction instances) for the Point class.
PointConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.PointConstraints
 
pointIndex - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
 
pointIndexLength - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
 
polygon - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
 
Polygon - Class in org.sbml.jsbml.ext.render
 
Polygon() - Constructor for class org.sbml.jsbml.ext.render.Polygon
Creates an Polygon instance
Polygon(Polygon) - Constructor for class org.sbml.jsbml.ext.render.Polygon
Clone constructor
PolygonConstraints - Class in org.sbml.jsbml.validator.offline.constraints
Defines validation rules (as ValidationFunction instances) for the Polygon class.
PolygonConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.PolygonConstraints
 
PolygonKind - Enum in org.sbml.jsbml.ext.spatial
This enum type was created following the specifications defined in Spatial Package v0.90.
polygonObject - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
 
PolygonObject - Class in org.sbml.jsbml.ext.spatial
Deprecated. 
PolygonObject() - Constructor for class org.sbml.jsbml.ext.spatial.PolygonObject
Deprecated.
 
PolygonObject(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.PolygonObject
Deprecated.
 
PolygonObject(PolygonObject) - Constructor for class org.sbml.jsbml.ext.spatial.PolygonObject
Deprecated.
 
polygonType - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
 
Port - Class in org.sbml.jsbml.ext.comp
The Port allows a modeler to design a Submodel such that other models interact with the Submodel through designated interfaces.
Port() - Constructor for class org.sbml.jsbml.ext.comp.Port
Creates an Port instance
Port(int, int) - Constructor for class org.sbml.jsbml.ext.comp.Port
Creates a Port instance with a level and version.
Port(String) - Constructor for class org.sbml.jsbml.ext.comp.Port
Creates a Port instance with an id.
Port(String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.Port
Creates a Port instance with an id, level, and version.
Port(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.Port
Creates a Port instance with an id, name, level, and version.
Port(Port) - Constructor for class org.sbml.jsbml.ext.comp.Port
Clone constructor
PortConstraints - Class in org.sbml.jsbml.validator.offline.constraints
Defines validation rules (as ValidationFunction instances) for the Port class.
PortConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.PortConstraints
 
portRef - Static variable in class org.sbml.jsbml.ext.comp.CompConstants
 
position - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
 
positioningToString(double, boolean) - Static method in class org.sbml.jsbml.ext.render.XMLTools
 
positive - org.sbml.jsbml.ext.qual.Sign
 
POSITIVE_INFINITY - Static variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
 
POSITIVE_INFINITY - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
possibleSpeciesFeatureValue - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
 
PossibleSpeciesFeatureValue - Class in org.sbml.jsbml.ext.multi
Each state feature (SpeciesFeatureType) also requires the definition of all the possible values it can take.
PossibleSpeciesFeatureValue() - Constructor for class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue
Creates an PossibleSpeciesFeatureValue instance
PossibleSpeciesFeatureValue(int, int) - Constructor for class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue
Creates a PossibleSpeciesFeatureValue instance with a level and version.
PossibleSpeciesFeatureValue(String) - Constructor for class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue
Creates a PossibleSpeciesFeatureValue instance with an id.
PossibleSpeciesFeatureValue(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue
Creates a PossibleSpeciesFeatureValue instance with an id, level, and version.
PossibleSpeciesFeatureValue(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue
Creates a PossibleSpeciesFeatureValue instance with an id, name, level, and version.
PossibleSpeciesFeatureValue(PossibleSpeciesFeatureValue) - Constructor for class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue
Clone constructor
PossibleSpeciesFeatureValueConstraints - Class in org.sbml.jsbml.validator.offline.constraints
Constraints declaration for the MultiCompartmentPlugin class.
PossibleSpeciesFeatureValueConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.PossibleSpeciesFeatureValueConstraints
 
pow(Object, Object) - Static method in class org.sbml.jsbml.math.compiler.FormulaCompiler
Returns the basis to the power of the exponent as StringBuffer.
pow(Object, Object) - Static method in class org.sbml.jsbml.math.compiler.HTMLFormula
Returns the basis to the power of the exponent as StringBuffer.
pow(Object, Object) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
Returns the basis to the power of the exponent as StringBuffer.
pow(Object, Object) - Static method in class org.sbml.jsbml.util.compilers.HTMLFormula
Returns the basis to the power of the exponent as StringBuffer.
pow(ASTNode, double) - Static method in class org.sbml.jsbml.ASTNode
Creates a power ASTNode.
pow(ASTNode, int) - Static method in class org.sbml.jsbml.ASTNode
Creates a power ASTNode.
pow(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
Creates a power ASTNode.
pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
 
pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
 
pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
 
pow(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
 
pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
 
pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
 
pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
 
pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler
 
pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
Deprecated.
 
pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
 
pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationUnitsCompiler
 
pow(ASTNode2, double) - Static method in class org.sbml.jsbml.math.ASTFactory
Creates a power ASTPowerNode with an ASTNode2 basis and a real exponent.
pow(ASTNode2, int) - Static method in class org.sbml.jsbml.math.ASTFactory
Creates a power ASTPowerNode with an ASTNode2 basis and an integer exponent.
pow(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
Creates a power ASTNode2.
pow(ASTNode2, ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
 
pow(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
 
pow(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
 
pow(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
 
pow(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LibSBMLFormulaCompiler
 
pow(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
 
pow(MathContainer, CallableSBase, CallableSBase) - Static method in class org.sbml.jsbml.ASTNode
Raises the given basis by the power of the given exponent.
POWER - org.sbml.jsbml.ASTNode.Type
This ASTNode.Type represents an operation with two children: a base and an exponent.
POWER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
RegularExpression Id.
POWER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
RegularExpression Id.
POWER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
RegularExpression Id.
POWER - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
RegularExpression Id.
POWER - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
RegularExpression Id.
POWER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
RegularExpression Id.
POWER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
RegularExpression Id.
POWER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
RegularExpression Id.
POWER - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
RegularExpression Id.
prependChild(ASTNode) - Method in class org.sbml.jsbml.ASTNode
Adds the given node as a child of this ASTNode.
prependChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTBinaryFunctionNode
Adds the given node as a child of this ASTBinaryFunctionNode.
prependChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTFunction
Adds the given node as a child of this ASTFunction.
prependChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
 
preprocess(Layout) - Static method in class org.sbml.jsbml.ext.render.director.RenderProcessor
 
PrimitiveKind - Enum in org.sbml.jsbml.ext.spatial
This enum type was created following the specifications defined in Spatial Package v0.90.
primitiveType - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
 
printASTNode() - Method in class org.sbml.jsbml.ASTNode
Returns the infix formula representing this ASTNode or an empty String if there was a problem to construct the formula.
printASTNodeAsFormula(ASTNode) - Static method in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
Returns the infix formula representing this ASTNode or an empty String if there was a problem to construct the formula.
printCreator() - Method in class org.sbml.jsbml.Creator
Returns the information about the Creator as a String.
printCVTerm() - Method in class org.sbml.jsbml.CVTerm
Returns a String containing the qualifier and all the resource URIs of this CVTerm.
printErrors(PrintStream) - Method in class org.sbml.jsbml.SBMLDocument
Prints all the errors or warnings encountered trying to check this SBML document.
printSpeciesReference() - Method in class org.sbml.jsbml.SimpleSpeciesReference
Human-readable representation of this reference.
printSpeciesReference() - Method in class org.sbml.jsbml.SpeciesReference
 
printTerm(Term) - Static method in class org.sbml.jsbml.ontology.Term
Returns a String representing a term the same way as in the OBO file.
printUnit() - Method in class org.sbml.jsbml.Unit
Produces a text formula representation of this unit.
printUnits(UnitDefinition) - Static method in class org.sbml.jsbml.UnitDefinition
Returns a string that expresses the unit definition represented by this UnitDefinition object.
printUnits(UnitDefinition, boolean) - Static method in class org.sbml.jsbml.UnitDefinition
Returns a string that expresses the unit definition represented by this UnitDefinition object.
printValueAndUnit() - Method in class org.sbml.jsbml.math.compiler.ASTNode2Value
 
printValueAndUnit() - Method in class org.sbml.jsbml.util.compilers.ASTNodeValue
 
priority - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
 
Priority - Class in org.sbml.jsbml
This class represents the priority element in SBML.
Priority() - Constructor for class org.sbml.jsbml.Priority
 
Priority(int, int) - Constructor for class org.sbml.jsbml.Priority
 
Priority(ASTNode, int, int) - Constructor for class org.sbml.jsbml.Priority
 
Priority(Priority) - Constructor for class org.sbml.jsbml.Priority
 
PriorityConstraints - Class in org.sbml.jsbml.validator.offline.constraints
Defines validation rules (as ValidationFunction instances) for the Priority class.
PriorityConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.PriorityConstraints
 
processAnnotation(SBase) - Method in interface org.sbml.jsbml.xml.parsers.AnnotationReader
Process the annotation of the given SBase object.
processAnnotation(SBase) - Method in class org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser
 
processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
 
processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.DistribParser
 
processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.DynParser
 
processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.FBCParser
 
processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.LayoutParser
 
processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MultiParser
 
processAttribute(String, String, String, String, String, boolean, Object) - Method in interface org.sbml.jsbml.xml.parsers.ReadingParser
Process the XML attribute and modify 'contextObject' in consequence.
processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.RenderParser
 
processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
 
processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.SpatialParser
 
processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.XMLNodeReader
 
processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
 
processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.LayoutParser
 
processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
processCharactersOf(String, String, Object) - Method in interface org.sbml.jsbml.xml.parsers.ReadingParser
Process the text of a XML element and modify 'contextObject' in consequence.
processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.RenderParser
 
processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
 
processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.SpatialParser
 
processCharactersOf(String, String, Object) - Method in class org.sbml.jsbml.xml.parsers.XMLNodeReader
 
processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
 
processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.L3LayoutParser
 
processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.LayoutParser
 
processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
processEndDocument(SBMLDocument) - Method in interface org.sbml.jsbml.xml.parsers.ReadingParser
Process the end of the document.
processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.RenderParser
 
processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
 
processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.SpatialParser
 
processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.XMLNodeReader
 
processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
 
processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.FBCParser
 
processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.LayoutParser
 
processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.QualParser
 
processEndElement(String, String, boolean, Object) - Method in interface org.sbml.jsbml.xml.parsers.ReadingParser
Process the end of the element 'elementName'.
processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
 
processEndElement(String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.XMLNodeReader
 
processInvalidAttribute(String, String, String, String, Object) - Static method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
Process an invalid XML attribute.
processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
 
processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.LayoutParser
 
processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
processNamespace(String, String, String, String, boolean, boolean, Object) - Method in interface org.sbml.jsbml.xml.parsers.ReadingParser
Process the namespace and modify the contextObject in consequence.
processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
 
processNamespace(String, String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.XMLNodeReader
 
ProcessNode<T> - Interface in org.sbml.jsbml.ext.render.director
 
processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
 
processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.ArraysParser
 
processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.CompParser
 
processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.DistribParser
 
processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.DynParser
 
processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.FBCParser
 
processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.GroupsParser
 
processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.L3LayoutParser
 
processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.LayoutParser
 
processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLParser
Deprecated.
 
processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MathMLStaxParser
 
processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MultiParser
 
processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.QualParser
 
processStartElement(String, String, String, boolean, boolean, Object) - Method in interface org.sbml.jsbml.xml.parsers.ReadingParser
Process the XML element and modify 'contextObject' in consequence.
processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.RenderParser
 
processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.ReqParser
 
processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.SBMLCoreParser
 
processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.SpatialParser
 
processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.XMLNodeReader
 
processUnknownAttribute(String, String, String, String, Object) - Static method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
Process an unknown XML attribute.
processUnknownElement(String, String, String, Object) - Static method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
Process an unknown XML element.
product(ASTNode2...) - Static method in class org.sbml.jsbml.math.ASTFactory
Creates an ASTArithmeticOperatorNode of type ASTNode.Type.PRODUCT and adds the given nodes as children.
PRODUCT - org.sbml.jsbml.ASTNode.Type
 
PRODUCT - org.sbml.jsbml.ext.layout.SpeciesReferenceRole
 
productComponent - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
 
production - org.sbml.jsbml.ext.qual.OutputTransitionEffect
The level of the QualitativeSpecies is increased by the resultLevel of the selected term possibly modified by the level of the Output.
Production<T> - Interface in org.sbml.jsbml.ext.render.director
interface all the different graphical representations for production arcs have to implement
productSpeciesFeature - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
 
programName - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
 
programVersion - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
 
progressFinish() - Method in interface org.sbml.jsbml.util.ProgressListener
This method is called when the process is finished, irrespective of the progress/total ratio.
ProgressListener - Interface in org.sbml.jsbml.util
The listener interface for receiving progress events.
progressStart(int) - Method in interface org.sbml.jsbml.util.ProgressListener
Reports the total number of expected steps.
progressUpdate(int, String) - Method in interface org.sbml.jsbml.util.ProgressListener
Reports the current progress to this listener, i.e., progress < total.
PROPERTY_UNDEFINED_EXCEPTION_MSG - Static variable in exception org.sbml.jsbml.PropertyNotAvailableException
Message to indicate that a certain property cannot be set for the current level/version combination.
PROPERTY_UNDEFINED_EXCEPTION_MSG_SBASE - Static variable in exception org.sbml.jsbml.PropertyUndefinedError
Message to indicate that a certain property has not been set for the current SBase in its level/version combination.
PROPERTY_UNDEFINED_EXCEPTION_MSG_TREE_NODE - Static variable in exception org.sbml.jsbml.PropertyUndefinedError
Message to indicate that a certain property has not been set for the current TreeNode in its level/version combination.
propertyChange(PropertyChangeEvent) - Method in class org.sbml.jsbml.util.SimpleTreeNodeChangeListener
 
PropertyException - Exception in org.sbml.jsbml
This is an error of an undefined property or value for a property in some instance of SBase.
PropertyException() - Constructor for exception org.sbml.jsbml.PropertyException
 
PropertyException(String) - Constructor for exception org.sbml.jsbml.PropertyException
 
PropertyNotAvailableException - Exception in org.sbml.jsbml
An error that indicates that a property of an SBase is not available for the current SBML Level/Version combination.
PropertyNotAvailableException(String, SBase) - Constructor for exception org.sbml.jsbml.PropertyNotAvailableException
 
PropertyUndefinedError - Exception in org.sbml.jsbml
This PropertyException indicates that the value belonging to a mandatory property, for which there is no default value, has not been declared by the user.
PropertyUndefinedError(String, TreeNode) - Constructor for exception org.sbml.jsbml.PropertyUndefinedError
 
PropertyUndefinedError(String, SBasePlugin) - Constructor for exception org.sbml.jsbml.PropertyUndefinedError
 
PropertyUndefinedError(String, SBase) - Constructor for exception org.sbml.jsbml.PropertyUndefinedError
 
putUserObject(Object, Object) - Method in class org.sbml.jsbml.AbstractTreeNode
 
putUserObject(Object, Object) - Method in class org.sbml.jsbml.math.ASTUnknown
 
putUserObject(Object, Object) - Method in interface org.sbml.jsbml.util.TreeNodeWithChangeSupport
 
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Generated at January 5 2022
Version 1.6.1-SNAPSHOT Revision ed2d2b5c6574a3d1769c1e26e09e14e700d571fa