- 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.
- 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(SBase, SBase) - Static method in exception org.sbml.jsbml.LevelVersionError
-
Creates an error message showing the different package versions of the given SBase elements.
- 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.
- 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
Pair
s
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
-
- Parameter(int, int) - Constructor for class org.sbml.jsbml.Parameter
-
Creates a
Parameter
instance from a level and version.
- Parameter(LocalParameter) - Constructor for class org.sbml.jsbml.Parameter
-
- Parameter(Parameter) - Constructor for class org.sbml.jsbml.Parameter
-
- Parameter(String) - Constructor for class org.sbml.jsbml.Parameter
-
- Parameter(String, int, int) - Constructor for class org.sbml.jsbml.Parameter
-
Creates a
Parameter
instance from an id, level and version.
- ParameterType - Class in org.sbml.jsbml.ext.spatial
-
- ParameterType() - Constructor for class org.sbml.jsbml.ext.spatial.ParameterType
-
- ParameterType(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.ParameterType
-
- ParameterType(ParameterType) - Constructor for class org.sbml.jsbml.ext.spatial.ParameterType
-
- ParametricGeometry - Class in org.sbml.jsbml.ext.spatial
-
- ParametricGeometry() - Constructor for class org.sbml.jsbml.ext.spatial.ParametricGeometry
-
- ParametricGeometry(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 - 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(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 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- 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, 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(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, 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(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 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 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 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(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() - Constructor for exception org.sbml.jsbml.math.parser.ParseException
-
- ParseException(String) - Constructor for exception org.sbml.jsbml.math.parser.ParseException
-
- ParseException(Throwable) - Constructor for exception org.sbml.jsbml.math.parser.ParseException
-
- ParseException - Exception in org.sbml.jsbml.text.parser
-
This exception is thrown when parse errors are encountered.
- 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.
- ParseException() - Constructor for exception org.sbml.jsbml.text.parser.ParseException
-
- ParseException(String) - Constructor for exception org.sbml.jsbml.text.parser.ParseException
-
- ParseException(Throwable) - Constructor for exception org.sbml.jsbml.text.parser.ParseException
-
- 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, 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.
- 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.
- 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.
- 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.
- 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.
- persistent - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- piecewise(ASTNode, ASTNode...) - Static method in class org.sbml.jsbml.ASTNode
-
- piecewise(MathContainer, ASTNode[]) - Static method in class org.sbml.jsbml.ASTNode
-
- 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(ASTQualifierNode, ASTQualifierNode...) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- 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(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
-
- 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(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(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- plus(ASTNode2, double) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- plus(ASTNode2, int) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- 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 - 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.
- 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
-
- 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
-
- 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
-
- pointIndex - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- pointIndexLength - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- 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
- PolygonKind - Enum in org.sbml.jsbml.ext.spatial
-
This enum type was created following the specifications defined in Spatial Package v0.90.
- PolygonObject - Class in org.sbml.jsbml.ext.spatial
-
Deprecated.
- PolygonObject() - Constructor for class org.sbml.jsbml.ext.spatial.PolygonObject
-
Deprecated.
- PolygonObject(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 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- 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(String) - Constructor for class org.sbml.jsbml.ext.comp.Port
-
Creates a Port instance with an id.
- Port(int, int) - Constructor for class org.sbml.jsbml.ext.comp.Port
-
Creates a Port instance with a level and version.
- 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
- 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_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(String) - Constructor for class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue
-
Creates a PossibleSpeciesFeatureValue instance with an id.
- PossibleSpeciesFeatureValue(int, int) - Constructor for class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue
-
Creates a PossibleSpeciesFeatureValue instance with a level and version.
- 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
- pow(ASTNode, ASTNode) - Static method in class org.sbml.jsbml.ASTNode
-
- pow(ASTNode, double) - Static method in class org.sbml.jsbml.ASTNode
-
- pow(ASTNode, int) - Static method in class org.sbml.jsbml.ASTNode
-
- pow(MathContainer, CallableSBase, CallableSBase) - Static method in class org.sbml.jsbml.ASTNode
-
Raises the given basis by the power of the given exponent.
- 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(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- pow(ASTNode2, double) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- pow(ASTNode2, int) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- 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(Object, Object) - Static method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
Returns the basis to the power of the exponent as StringBuffer.
- pow(ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- 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(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(ASTNode, ASTNode) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
- pow(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- 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(ASTNode, ASTNode) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- 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, 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
-
- 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
-
- prependChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTFunction
-
- prependChild(ASTNode2) - Method in class org.sbml.jsbml.math.ASTUnaryFunctionNode
-
- 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
-
- printErrors(PrintStream) - Method in class org.sbml.jsbml.SBMLDocument
-
Prints all the errors or warnings encountered trying to check this SBML document.
- 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.
- 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 - Class in org.sbml.jsbml
-
This class represents the priority element in SBML.
- Priority() - Constructor for class org.sbml.jsbml.Priority
-
- Priority(ASTNode, int, int) - Constructor for class org.sbml.jsbml.Priority
-
- Priority(int, int) - Constructor for class org.sbml.jsbml.Priority
-
- Priority(Priority) - Constructor for class org.sbml.jsbml.Priority
-
- priority - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- 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.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.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.UncertMLXMLNodeReader
-
- 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.SBMLCoreParser
-
- 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
-
- 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
-
- 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.UncertMLXMLNodeReader
-
- processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.XMLNodeReader
-
- processUnknownAttribute(String, String, String, Object) - Static method in class org.sbml.jsbml.xml.parsers.AbstractReaderWriter
-
- product(ASTNode2...) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- productComponent - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
-
- 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, SBase) - Constructor for exception org.sbml.jsbml.PropertyUndefinedError
-
- PropertyUndefinedError(String, SBasePlugin) - Constructor for exception org.sbml.jsbml.PropertyUndefinedError
-
- PropertyUndefinedError(String, TreeNode) - 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
-