- data - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- DataKind - Enum in org.sbml.jsbml.ext.spatial
-
This enum type was created following the specifications defined in Spatial Package v0.90.
- dataType - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- DateProcessor - Class in org.sbml.jsbml.xml.stax
-
Format time to W3DTF
- DateProcessor() - Constructor for class org.sbml.jsbml.xml.stax.DateProcessor
-
- debug(String) - Method in class org.sbml.jsbml.xml.stax.XMLLogger
-
- debugStream - Variable in class org.sbml.jsbml.math.parser.FormulaParserASTNode2TokenManager
-
Debug output.
- debugStream - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2TokenManager
-
Debug output.
- debugStream - Variable in class org.sbml.jsbml.math.parser.FormulaParserLL3TokenManager
-
Debug output.
- debugStream - Variable in class org.sbml.jsbml.math.parser.FormulaParserTokenManager
-
Debug output.
- debugStream - Variable in class org.sbml.jsbml.text.parser.CobraFormulaParserTokenManager
-
Debug output.
- debugStream - Variable in class org.sbml.jsbml.text.parser.FormulaParserASTNode2TokenManager
-
Debug output.
- debugStream - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2TokenManager
-
Debug output.
- debugStream - Variable in class org.sbml.jsbml.text.parser.FormulaParserLL3TokenManager
-
Debug output.
- debugStream - Variable in class org.sbml.jsbml.text.parser.FormulaParserTokenManager
-
Debug output.
- DECIMAL_FORMAT - Static variable in class org.sbml.jsbml.util.StringTools
-
- decodeStringToArrayDouble(String) - Static method in class org.sbml.jsbml.ext.render.XMLTools
-
- decodeStringToArrayShort(String) - Static method in class org.sbml.jsbml.ext.render.XMLTools
-
- decodeStringToColor(String) - Static method in class org.sbml.jsbml.ext.render.XMLTools
-
- DEFAULT - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
Lexical state.
- DEFAULT - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
Lexical state.
- DEFAULT - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
Lexical state.
- DEFAULT - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
Lexical state.
- DEFAULT - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
Lexical state.
- DEFAULT - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
Lexical state.
- DEFAULT - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
Lexical state.
- DEFAULT - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
Lexical state.
- DEFAULT - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
Lexical state.
- DEFAULT_GENE_ASSOCIATION_SPELLING - Static variable in class org.sbml.jsbml.ext.fbc.CobraConstants
-
- DEFAULT_LOWER_BOUND_NAME - Static variable in class org.sbml.jsbml.ext.fbc.CobraConstants
-
- DEFAULT_POST_MESSAGE - Static variable in class org.sbml.jsbml.validator.offline.i18n.SBMLErrorPostMessage
-
- DEFAULT_POST_MESSAGE_KINETIC_LAW - Static variable in class org.sbml.jsbml.validator.offline.i18n.SBMLErrorPostMessage
-
- DEFAULT_POST_MESSAGE_WITH_ID - Static variable in class org.sbml.jsbml.validator.offline.i18n.SBMLErrorPostMessage
-
- DEFAULT_POST_MESSAGE_WITH_METAID - Static variable in class org.sbml.jsbml.validator.offline.i18n.SBMLErrorPostMessage
-
- DEFAULT_POST_MESSAGE_WITH_SYMBOL - Static variable in class org.sbml.jsbml.validator.offline.i18n.SBMLErrorPostMessage
-
- DEFAULT_POST_MESSAGE_WITH_VARIABLE - Static variable in class org.sbml.jsbml.validator.offline.i18n.SBMLErrorPostMessage
-
- DEFAULT_UPPER_BOUND_NAME - Static variable in class org.sbml.jsbml.ext.fbc.CobraConstants
-
- default_z - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
For DefaultValues
- defaultTerm - Static variable in class org.sbml.jsbml.ext.qual.QualConstants
-
- defaultValues - Static variable in class org.sbml.jsbml.ext.render.RenderConstants
-
- DefaultValues - Class in org.sbml.jsbml.ext.render
-
- DefaultValues() - Constructor for class org.sbml.jsbml.ext.render.DefaultValues
-
Creates an DefaultValues instance
- DefaultValues(int, int) - Constructor for class org.sbml.jsbml.ext.render.DefaultValues
-
Creates a DefaultValues instance with a level and version.
- DefaultValues(DefaultValues) - Constructor for class org.sbml.jsbml.ext.render.DefaultValues
-
Clone constructor
- DefaultValuesConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- DefaultValuesConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.DefaultValuesConstraints
-
- definitionURL - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants
-
- definitionURL - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- deflated - org.sbml.jsbml.ext.spatial.CompressionKind
-
If the deflation algorithm was used to compress the text version of the data
- degreesOfFreedom - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants
-
- delay(String, ASTNode, ASTNode, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.ArraysCompiler
-
- delay(String, ASTNode, ASTNode, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.StaticallyComputableCompiler
-
- delay(String, ASTNode, ASTNode, String) - Method in class org.sbml.jsbml.ext.arrays.compiler.VectorCompiler
-
- delay(String, ASTNode, ASTNode, String) - Method in interface org.sbml.jsbml.util.compilers.ASTNodeCompiler
-
Evaluates delay functions.
- delay(String, ASTNode, ASTNode, String) - Method in class org.sbml.jsbml.util.compilers.FindUnitsCompiler
-
- delay(String, ASTNode, ASTNode, String) - Method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
- delay(String, ASTNode, ASTNode, String) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
- delay(String, ASTNode, ASTNode, String) - Method in class org.sbml.jsbml.util.compilers.MathMLCompiler
-
Deprecated.
- delay(String, ASTNode, ASTNode, String) - Method in class org.sbml.jsbml.util.compilers.UnitsCompiler
-
- delay(String, ASTNode2, ASTNode2) - Method in interface org.sbml.jsbml.math.compiler.ASTNode2Compiler
-
Evaluates delay functions.
- delay(String, ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FindUnitsCompiler
-
- delay(String, ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
- delay(String, ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
- delay(String, ASTNode2, ASTNode2) - Method in class org.sbml.jsbml.math.compiler.UnitsCompiler
-
- Delay - Class in org.sbml.jsbml
-
Represents the delay subnode of an event element.
- Delay() - Constructor for class org.sbml.jsbml.Delay
-
Creates a Delay instance.
- Delay(int, int) - Constructor for class org.sbml.jsbml.Delay
-
Creates a Delay instance from a level and version.
- Delay(ASTNode, int, int) - Constructor for class org.sbml.jsbml.Delay
-
Creates a
Delay instance from an
ASTNode, level and version.
- Delay(Delay) - Constructor for class org.sbml.jsbml.Delay
-
Creates a Delay instance from a given Delay.
- DelayConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- DelayConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.DelayConstraints
-
- DelayUnitsNotTime - org.sbml.jsbml.SBMLException.Code
-
Units of delay are not units of time
- deletion - Static variable in class org.sbml.jsbml.ext.comp.CompConstants
-
- Deletion - Class in org.sbml.jsbml.ext.comp
-
Defines a deletion operation to
be applied when a submodel instantiates a model definition.
- Deletion() - Constructor for class org.sbml.jsbml.ext.comp.Deletion
-
Creates an Deletion instance
- Deletion(int, int) - Constructor for class org.sbml.jsbml.ext.comp.Deletion
-
Creates a Deletion instance with a level and version.
- Deletion(String) - Constructor for class org.sbml.jsbml.ext.comp.Deletion
-
Creates a new
Deletion instance with an id.
- Deletion(String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.Deletion
-
Creates a Deletion instance with an id, level, and version.
- Deletion(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.Deletion
-
Creates a Deletion instance with an id, name, level, and version.
- Deletion(Deletion) - Constructor for class org.sbml.jsbml.ext.comp.Deletion
-
Clone constructor
- DeletionConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- DeletionConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.DeletionConstraints
-
- denominator - Static variable in class org.sbml.jsbml.util.TreeNodeChangeEvent
-
- denotedSpeciesTypeComponentIndex - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants
-
- depth - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
-
- deriveUnit() - Method in class org.sbml.jsbml.ASTNode
-
Evaluates recursively this ASTNode and creates a new UnitDefinition with
respect of all referenced elements.
- deriveUnit() - Method in class org.sbml.jsbml.math.ASTCnNumberNode
-
Evaluates recursively this
ASTCnNumberNode and creates a new
UnitDefinition with respect to all referenced elements.
- descriptionBegin - Static variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
Surrounded by new line symbols.
- descriptionBegin - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
Surrounded by new line symbols.
- descriptionEnd - Static variable in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
Surrounded by new line symbols.
- descriptionEnd - Static variable in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
Surrounded by new line symbols.
- descriptionItem(String, Object) - Method in class org.sbml.jsbml.math.compiler.LaTeXCompiler
-
This method simplifies the process of creating descriptions.
- descriptionItem(String, Object) - Method in class org.sbml.jsbml.util.compilers.LaTeXCompiler
-
This method simplifies the process of creating descriptions.
- Detail - Class in org.sbml.jsbml.util
-
- Detail() - Constructor for class org.sbml.jsbml.util.Detail
-
- determineRole(SpeciesReferenceGlyph) - Static method in class org.sbml.jsbml.ext.render.director.LayoutDirector
-
- didValidate(AnyConstraint<?>, Object, boolean) - Method in class org.sbml.jsbml.validator.offline.ValidationContext
-
- didValidate(ValidationContext, AnyConstraint<?>, Object, boolean) - Method in class org.sbml.jsbml.validator.offline.LoggingValidationContext
-
- didValidate(ValidationContext, AnyConstraint<?>, Object, boolean) - Method in interface org.sbml.jsbml.validator.offline.ValidationListener
-
Invoked after the constraint has validated the object.
- diff(Object...) - Static method in class org.sbml.jsbml.math.compiler.FormulaCompiler
-
Returns the difference of the given elements as StringBuffer.
- diff(Object...) - Static method in class org.sbml.jsbml.util.compilers.FormulaCompiler
-
Returns the difference of the given elements as StringBuffer.
- diff(ASTNode...) - Static method in class org.sbml.jsbml.ASTNode
-
Creates a new
ASTNode of type MINUS and adds the given nodes as children
- diff(ASTNode2...) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- difference - org.sbml.jsbml.ext.spatial.SetOperation
-
- diffusionCoefficient - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- DiffusionCoefficient - Class in org.sbml.jsbml.ext.spatial
-
- DiffusionCoefficient() - Constructor for class org.sbml.jsbml.ext.spatial.DiffusionCoefficient
-
- DiffusionCoefficient(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.DiffusionCoefficient
-
- DiffusionCoefficient(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.DiffusionCoefficient
-
- DiffusionCoefficient(DiffusionCoefficient) - Constructor for class org.sbml.jsbml.ext.spatial.DiffusionCoefficient
-
- DiffusionCoefficientConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- DiffusionCoefficientConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.DiffusionCoefficientConstraints
-
- diffusionKind - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- DiffusionKind - Enum in org.sbml.jsbml.ext.spatial
-
This enum type was created following the specifications defined in Spatial Package v0.90.
- DIGIT - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- DIGIT - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- DIGIT - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- DIGIT - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- DIGIT - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
RegularExpression Id.
- DIGIT - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- DIGIT - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- DIGIT - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- DIGIT - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- dimension - Static variable in class org.sbml.jsbml.ext.arrays.ArraysConstants
-
- Dimension - Class in org.sbml.jsbml.ext.arrays
-
- Dimension() - Constructor for class org.sbml.jsbml.ext.arrays.Dimension
-
Creates an Dimension instance
- Dimension(int, int) - Constructor for class org.sbml.jsbml.ext.arrays.Dimension
-
Creates a Dimension instance with a level and version.
- Dimension(String) - Constructor for class org.sbml.jsbml.ext.arrays.Dimension
-
Creates a Dimension instance with an id.
- Dimension(String, int, int) - Constructor for class org.sbml.jsbml.ext.arrays.Dimension
-
Creates a Dimension instance with an id, level, and version.
- Dimension(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.arrays.Dimension
-
Creates a Dimension instance with an id, name, level, and version.
- Dimension(Dimension) - Constructor for class org.sbml.jsbml.ext.arrays.Dimension
-
Clone constructor
- DimensionArrayDimCheck - Class in org.sbml.jsbml.ext.arrays.validator.constraints
-
Checks if the
Dimension objects of a given
SBase have valid array dimension.
- DimensionArrayDimCheck(Model, SBase) - Constructor for class org.sbml.jsbml.ext.arrays.validator.constraints.DimensionArrayDimCheck
-
Creates a DimensionArrayDimCheck with a model and sbase.
- DimensionConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- DimensionConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.DimensionConstraints
-
- DimensionIDCheck - Class in org.sbml.jsbml.ext.arrays.validator.constraints
-
- DimensionIDCheck(Model, SBase) - Constructor for class org.sbml.jsbml.ext.arrays.validator.constraints.DimensionIDCheck
-
- DIMENSIONLESS - org.sbml.jsbml.Unit.Kind
-
A pseudo-unit indicating a dimensionless quantity.
- dimensions - Static variable in class org.sbml.jsbml.ext.layout.LayoutConstants
-
- Dimensions - Class in org.sbml.jsbml.ext.layout
-
A
Dimensions is specified via the required attributes width,
height and an optional attribute depth, all of which are of type double.
- Dimensions() - Constructor for class org.sbml.jsbml.ext.layout.Dimensions
-
- Dimensions(double, double, double, int, int) - Constructor for class org.sbml.jsbml.ext.layout.Dimensions
-
- Dimensions(int, int) - Constructor for class org.sbml.jsbml.ext.layout.Dimensions
-
- Dimensions(String, int, int) - Constructor for class org.sbml.jsbml.ext.layout.Dimensions
-
- Dimensions(Dimensions) - Constructor for class org.sbml.jsbml.ext.layout.Dimensions
-
- DimensionsConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- DimensionsConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.DimensionsConstraints
-
- DimensionSizeCheck - Class in org.sbml.jsbml.ext.arrays.validator.constraints
-
Checks if the given
Dimension object has size that is both
scalar and constant.
- DimensionSizeCheck(Model, Dimension) - Constructor for class org.sbml.jsbml.ext.arrays.validator.constraints.DimensionSizeCheck
-
- DimensionValidator - Class in org.sbml.jsbml.ext.arrays.validator
-
Validates a given
Dimension object in the context of a given model and makes sure that
the dimension object is in accordance with the arrays package specification.
- DimensionValidator() - Constructor for class org.sbml.jsbml.ext.arrays.validator.DimensionValidator
-
- Dirichlet - org.sbml.jsbml.ext.spatial.BoundaryConditionKind
-
Dirichlet
- disable_tracing() - Method in class org.sbml.jsbml.math.parser.FormulaParser
-
Disable tracing.
- disable_tracing() - Method in class org.sbml.jsbml.math.parser.FormulaParserASTNode2
-
Disable tracing.
- disable_tracing() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3
-
Disable tracing.
- disable_tracing() - Method in class org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2
-
Disable tracing.
- disable_tracing() - Method in class org.sbml.jsbml.text.parser.CobraFormulaParser
-
Disable tracing.
- disable_tracing() - Method in class org.sbml.jsbml.text.parser.FormulaParser
-
Disable tracing.
- disable_tracing() - Method in class org.sbml.jsbml.text.parser.FormulaParserASTNode2
-
Disable tracing.
- disable_tracing() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3
-
Disable tracing.
- disable_tracing() - Method in class org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2
-
Disable tracing.
- disablePackage(String) - Method in class org.sbml.jsbml.AbstractSBase
-
Disables the given SBML Level 3 package on this
SBMLDocument.
- disablePackage(String) - Method in class org.sbml.jsbml.ASTNode
-
Disables the given SBML Level 3 package on this
SBMLDocument.
- disablePackage(String) - Method in interface org.sbml.jsbml.SBase
-
Disables the given SBML Level 3 package on this
SBMLDocument.
- disablePackage(String) - Method in class org.sbml.jsbml.SBMLDocument
-
Disables the given SBML Level 3 package on this
SBMLDocument.
- disableUnused() - Method in class org.sbml.jsbml.util.PackageDisabler
-
Check namespaces for unused packages and remove them
- DisallowedDefinitionURLUse - org.sbml.jsbml.SBMLException.Code
-
Disallowed use of MathML definitionURL attribute
- DisallowedMathMLEncodingUse - org.sbml.jsbml.SBMLException.Code
-
Disallowed use of MathML encoding attribute
- DisallowedMathMLSymbol - org.sbml.jsbml.SBMLException.Code
-
Disallowed MathML symbol
- DisallowedMathTypeAttributeUse - org.sbml.jsbml.SBMLException.Code
-
Disallowed use of MathML type attribute
- DisallowedMathTypeAttributeValue - org.sbml.jsbml.SBMLException.Code
-
Disallowed MathML type attribute value
- DissociationNode<T> - Interface in org.sbml.jsbml.ext.render.director
-
- distinctAttribute - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants
-
- DISTRIB_10101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1510101:
To conform to the Distributions Package specification for SBML Level 3 Version
1, an SBML document must declare
'http://www.sbml.org/sbml/level3/version1/distrib/version1' as the XMLNamespace
to use for elements of this package.
- DISTRIB_10102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1510102:
Wherever they appear in an SBML document, elements and attributes from the
Distributions Package must use the
'http://www.sbml.org/sbml/level3/version1/distrib/version1' namespace, declaring
so either explicitly or implicitly.
- DISTRIB_10301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1510301:
(Extends validation rule #10301 in the SBML Level 3 Core specification.
- DISTRIB_10302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1510302:
The value of a 'distrib:id' must conform to the syntax of the <sbml> data type
'SId' Reference: L3V1 Distrib V1 Section
- DISTRIB_20101 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520101:
In all SBML documents using the Distributions Package, the <sbml> object must
have the 'distrib:required' attribute.
- DISTRIB_20102 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520102:
The value of attribute 'distrib:required' on the <sbml> object must be of data
type 'boolean'.
- DISTRIB_20103 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520103:
The value of attribute 'distrib:required' on the <sbml> object must be set to
'true'.
- DISTRIB_20201 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520201:
A 'SBase' object may contain one and only one instance of the
<listOfUncertainties> element.
- DISTRIB_20202 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520202:
Apart from the general notes and annotations subobjects permitted on all SBML
objects, a <listOfUncertainties> container object may only contain <uncertainty>
objects.
- DISTRIB_20203 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520203:
A <listOfUncertainties> object may have the optional SBML Level 3 Core
attributes 'metaid' and 'sboTerm'.
- DISTRIB_20301 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520301:
An <uncertParameter> object may have the optional SBML Level 3 Core attributes
'metaid' and 'sboTerm'.
- DISTRIB_20302 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520302:
An <uncertParameter> object may have the optional SBML Level 3 Core subobjects
for notes and annotations.
- DISTRIB_20303 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520303:
An <uncertParameter> object may have the optional attributes 'distrib:value',
'distrib:var', 'distrib:units', 'distrib:type' and 'distrib:definitionURL'.
- DISTRIB_20304 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520304:
An <uncertParameter> object may contain one and only one instance of the
<listOfUncertParameters> element.
- DISTRIB_20305 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520305:
The attribute 'distrib:value' on an <uncertParameter> must have a value of data
type 'double'.
- DISTRIB_20306 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520306:
The value of the attribute 'distrib:var' of an <uncertParameter> object must be
the identifier of an existing object derived from the 'SBase' class and defined
in the enclosing <model> object.
- DISTRIB_20307 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520307:
The value of the attribute 'distrib:units' on an <uncertParameter> must have a
taken from the following: the identifier of a <unitDefinition> object in the
enclosing <model,> or one of the base units in SBML.
- DISTRIB_20308 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520308:
The value of the attribute 'distrib:type' of an <uncertParameter> object must
conform to the syntax of SBML data type 'UncertType' and may only take on the
allowed values of 'UncertType' defined in SBML; that is, the value must be one
of the following: 'distribution', 'externalParameter', 'coeffientOfVariation',
'kurtosis', 'mean', 'median', 'mode', 'sampleSize', 'skewness',
'standardDeviation', 'standardError', 'variance', 'confidenceInterval',
'credibleInterval', 'interquartileRange' or 'range'.
- DISTRIB_20309 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520309:
The attribute 'distrib:definitionURL' on an <uncertParameter> must have a value
of data type 'string'.
- DISTRIB_20310 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520310:
Apart from the general notes and annotations subobjects permitted on all SBML
objects, a <listOfUncertParameters> container object may only contain
<uncertParameter> objects.
- DISTRIB_20311 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520311:
A <listOfUncertParameters> object may have the optional SBML Level 3 Core
attributes 'metaid' and 'sboTerm'.
- DISTRIB_20401 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520401:
An <uncertainty> object may have the optional SBML Level 3 Core attributes
'metaid' and 'sboTerm'.
- DISTRIB_20402 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520402:
An <uncertainty> object may have the optional SBML Level 3 Core subobjects for
notes and annotations.
- DISTRIB_20403 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520403:
An <uncertainty> object may contain one and only one instance of the
<listOfUncertParameters> element.
- DISTRIB_20501 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520501:
An <uncertSpan> object may have the optional SBML Level 3 Core attributes
'metaid' and 'sboTerm'.
- DISTRIB_20502 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520502:
An <uncertSpan> object may have the optional SBML Level 3 Core subobjects for
notes and annotations.
- DISTRIB_20503 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520503:
An <uncertSpan> object may have the optional attributes 'distrib:varLower',
'distrib:valueLower', 'distrib:varUpper' and 'distrib:valueUpper'.
- DISTRIB_20504 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520504:
The value of the attribute 'distrib:varLower' of an <uncertSpan> object must be
the identifier of an existing object derived from the 'SBase' class and defined
in the enclosing <model> object.
- DISTRIB_20505 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520505:
The attribute 'distrib:valueLower' on an <uncertSpan> must have a value of data
type 'double'.
- DISTRIB_20506 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520506:
The value of the attribute 'distrib:varUpper' of an <uncertSpan> object must be
the identifier of an existing object derived from the 'SBase' class and defined
in the enclosing <model> object.
- DISTRIB_20507 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520507:
The attribute 'distrib:valueUpper' on an <uncertSpan> must have a value of data
type 'double'.
- DISTRIB_20601 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520601:
A <distribBase> object may have the optional SBML Level 3 Core attributes
'metaid' and 'sboTerm'.
- DISTRIB_20602 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520602:
A <distribBase> object may have the optional SBML Level 3 Core subobjects for
notes and annotations.
- DISTRIB_20603 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520603:
A <distribBase> object may have the optional attributes 'distrib:id' and
'distrib:name'.
- DISTRIB_20604 - Static variable in interface org.sbml.jsbml.validator.offline.factory.SBMLErrorCodes
-
Error code 1520604:
The attribute 'distrib:name' on a <distribBase> must have a value of data type
'string'.
- DistribConstants - Class in org.sbml.jsbml.ext.distrib
-
- DistribConstants() - Constructor for class org.sbml.jsbml.ext.distrib.DistribConstants
-
- DistribModelBuilder - Class in org.sbml.jsbml.ext.distrib.util
-
This class provides a collection of convenient methods to create SBML elements
related to the distrib package.
- DistribModelBuilder() - Constructor for class org.sbml.jsbml.ext.distrib.util.DistribModelBuilder
-
- DistribParser - Class in org.sbml.jsbml.xml.parsers
-
This class is used to parse the distrib extension package elements and
attributes.
- DistribParser() - Constructor for class org.sbml.jsbml.xml.parsers.DistribParser
-
- DistribSBasePlugin - Class in org.sbml.jsbml.ext.distrib
-
- DistribSBasePlugin() - Constructor for class org.sbml.jsbml.ext.distrib.DistribSBasePlugin
-
- DistribSBasePlugin(DistribSBasePlugin) - Constructor for class org.sbml.jsbml.ext.distrib.DistribSBasePlugin
-
- DistribSBasePlugin(SBase) - Constructor for class org.sbml.jsbml.ext.distrib.DistribSBasePlugin
-
- distribution - org.sbml.jsbml.ext.distrib.UncertParameter.Type
-
If the uncertainty is defined by a known distribution, that distribution may either be defined by using the
child math element, or by using the definitionURL .
- distribution - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants
-
- DIVIDE - org.sbml.jsbml.ASTNode.Type
-
- DIVIDE - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- DIVIDE - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserConstants
-
RegularExpression Id.
- DIVIDE - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- DIVIDE - Static variable in interface org.sbml.jsbml.math.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- DIVIDE - Static variable in interface org.sbml.jsbml.text.parser.CobraFormulaParserConstants
-
RegularExpression Id.
- DIVIDE - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserASTNode2Constants
-
RegularExpression Id.
- DIVIDE - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserConstants
-
RegularExpression Id.
- DIVIDE - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3ASTNode2Constants
-
RegularExpression Id.
- DIVIDE - Static variable in interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
-
RegularExpression Id.
- divideBy(ASTNode) - Method in class org.sbml.jsbml.ASTNode
-
Divides this node by the given node
- divideBy(CallableSBase) - Method in class org.sbml.jsbml.ASTNode
-
Divides this node by the given SBML element.
- divideBy(ASTNode2, ASTNode2) - Static method in class org.sbml.jsbml.math.ASTFactory
-
- divideBy(UnitDefinition) - Method in class org.sbml.jsbml.UnitDefinition
-
Divides this unit definition by the second unit definition.
- DocumentFactory - Interface in org.sbml.jsbml.util
-
* An interface for XML DOM document factories.
- domain - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- Domain - Class in org.sbml.jsbml.ext.spatial
-
- Domain() - Constructor for class org.sbml.jsbml.ext.spatial.Domain
-
- Domain(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.Domain
-
- Domain(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.Domain
-
- Domain(Domain) - Constructor for class org.sbml.jsbml.ext.spatial.Domain
-
- domain1 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- domain2 - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- DomainConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- DomainConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.DomainConstraints
-
- domainType - Static variable in class org.sbml.jsbml.ext.spatial.SpatialConstants
-
- DomainType - Class in org.sbml.jsbml.ext.spatial
-
- DomainType() - Constructor for class org.sbml.jsbml.ext.spatial.DomainType
-
- DomainType(int, int) - Constructor for class org.sbml.jsbml.ext.spatial.DomainType
-
- DomainType(String, int, int) - Constructor for class org.sbml.jsbml.ext.spatial.DomainType
-
- DomainType(DomainType) - Constructor for class org.sbml.jsbml.ext.spatial.DomainType
-
- DomainTypeConstraints - Class in org.sbml.jsbml.validator.offline.constraints
-
- DomainTypeConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.DomainTypeConstraints
-
- Done() - Method in class org.sbml.jsbml.math.parser.SimpleCharStream
-
Reset buffer when finished.
- Done() - Method in class org.sbml.jsbml.text.parser.SimpleCharStream
-
Reset buffer when finished.
- dotProduct(Point, Point) - Static method in class org.sbml.jsbml.ext.render.director.Geometry
-
Computes the dot product of the given two points
- DOUBLE - org.sbml.jsbml.ext.spatial.DataKind
-
To indicate double-precision (64-bit) floating point values
- draw(double, double, double, double, double, double) - Method in class org.sbml.jsbml.ext.render.director.AbstractSBGNNodeWithCloneMarker
-
- draw(double, double, double, double, double, double) - Method in interface org.sbml.jsbml.ext.render.director.SBGNNode
-
Method for drawing an entity pool node with the specified position and
size of a
BoundingBox
- draw(double, double, double, double, double, double, double, Point) - Method in interface org.sbml.jsbml.ext.render.director.SBGNProcessNode
-
- draw(Curve) - Method in interface org.sbml.jsbml.ext.render.director.SBGNArc
-
Draw a whole curve consisting of multiple curve segments.
- draw(Curve, double) - Method in interface org.sbml.jsbml.ext.render.director.SBGNArc
-
Draw a whole curve consisting of multiple curve segments with the given
line width.
- draw(Curve, double, Point) - Method in class org.sbml.jsbml.ext.render.director.AbstractSBGNProcessNode
-
- draw(Curve, double, Point) - Method in interface org.sbml.jsbml.ext.render.director.SBGNProcessNode
-
Draw a whole curve consisting of multiple curve segments with the given
line width.
- draw(CurveSegment, double) - Method in interface org.sbml.jsbml.ext.render.director.SBGNArc
-
Method for drawing the connecting arc, with appropriate line ending and the
given line width
- drawCurveSegment(CurveSegment, double, Point) - Method in interface org.sbml.jsbml.ext.render.director.SBGNProcessNode
-
- DT_BOOLEAN - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
- DT_NUMBER - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
- DT_STRING - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
- DT_UNKNOWN - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
- DT_VECTOR - Static variable in class org.sbml.jsbml.validator.offline.constraints.helper.ValidationTools
-
- dual - org.sbml.jsbml.ext.qual.Sign
-
- DUPLICATE_IDENTIFIER_MSG - Static variable in exception org.sbml.jsbml.IdentifierException
-
- DUPLICATE_OBJECT_ID - Static variable in class org.sbml.jsbml.JSBML
-
- DuplicateAnnotationInvalidInL2v2 - org.sbml.jsbml.SBMLException.Code
-
Duplicate top level annotations invalid for this SBML Level+Version
- DuplicateAnnotationInvalidInL2v3 - org.sbml.jsbml.SBMLException.Code
-
Duplicate top level annotations invalid for this SBML Level+Version
- DuplicateAnnotationInvalidInL2v4 - org.sbml.jsbml.SBMLException.Code
-
Duplicate top level annotations invalid for this SBML Level+Version
- DuplicateAnnotationNamespaces - org.sbml.jsbml.SBMLException.Code
-
Multiple annotations using same XML namespace
- DuplicateComponentId - org.sbml.jsbml.SBMLException.Code
-
Duplicate component identifier
- DuplicatedElementValidationFunction<T extends TreeNodeWithChangeSupport> - Class in org.sbml.jsbml.validator.offline.constraints.helper
-
Class used to check that a child XML element was not present more than once.
- DuplicatedElementValidationFunction(String) - Constructor for class org.sbml.jsbml.validator.offline.constraints.helper.DuplicatedElementValidationFunction
-
- DuplicatedMathValidationFunction<T extends MathContainer> - Class in org.sbml.jsbml.validator.offline.constraints.helper
-
Class used to check if the 'math' mathML element is duplicated.
- DuplicatedMathValidationFunction() - Constructor for class org.sbml.jsbml.validator.offline.constraints.helper.DuplicatedMathValidationFunction
-
- DuplicatedMathValidationFunction(boolean) - Constructor for class org.sbml.jsbml.validator.offline.constraints.helper.DuplicatedMathValidationFunction
-
- DuplicatedOrMissingElementValidationFunction<T extends TreeNodeWithChangeSupport> - Class in org.sbml.jsbml.validator.offline.constraints.helper
-
Class used to check that a child XML element is not missing or present more than once.
- DuplicatedOrMissingElementValidationFunction(String) - Constructor for class org.sbml.jsbml.validator.offline.constraints.helper.DuplicatedOrMissingElementValidationFunction
-
- DuplicateLocalParameterId - org.sbml.jsbml.SBMLException.Code
-
Duplicate local parameter identifier
- DuplicateMetaId - org.sbml.jsbml.SBMLException.Code
-
Duplicate metaid identifier
- DuplicateUnitDefinitionId - org.sbml.jsbml.SBMLException.Code
-
Duplicate unit definition identifier
- DynCompartmentPlugin - Class in org.sbml.jsbml.ext.dyn
-
- DynCompartmentPlugin() - Constructor for class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin
-
Empty constructor
- DynCompartmentPlugin(Compartment) - Constructor for class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin
-
Constructor
- DynCompartmentPlugin(DynCompartmentPlugin) - Constructor for class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin
-
Constructor
- DynConstants - Class in org.sbml.jsbml.ext.dyn
-
Contains some constants related to the Dynamic Structures package.
- DynConstants() - Constructor for class org.sbml.jsbml.ext.dyn.DynConstants
-
- dynElement - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants
-
- DynElement - Class in org.sbml.jsbml.ext.dyn
-
- DynElement() - Constructor for class org.sbml.jsbml.ext.dyn.DynElement
-
Empty constructor
- DynElement(int, int) - Constructor for class org.sbml.jsbml.ext.dyn.DynElement
-
Constructor
- DynElement(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.dyn.DynElement
-
Constructor
- DynElement(DynElement) - Constructor for class org.sbml.jsbml.ext.dyn.DynElement
-
Constructor
- DynEventPlugin - Class in org.sbml.jsbml.ext.dyn
-
- DynEventPlugin() - Constructor for class org.sbml.jsbml.ext.dyn.DynEventPlugin
-
Empty constructor
- DynEventPlugin(Event) - Constructor for class org.sbml.jsbml.ext.dyn.DynEventPlugin
-
Constructor
- DynEventPlugin(DynEventPlugin) - Constructor for class org.sbml.jsbml.ext.dyn.DynEventPlugin
-
Constructor
- DynParser - Class in org.sbml.jsbml.xml.parsers
-
This class is used to parse the dynamic structures extension package elements
and attributes.
- DynParser() - Constructor for class org.sbml.jsbml.xml.parsers.DynParser
-
- DynSBasePlugin - Class in org.sbml.jsbml.ext.dyn
-
- DynSBasePlugin() - Constructor for class org.sbml.jsbml.ext.dyn.DynSBasePlugin
-
Empty constructor
- DynSBasePlugin(DynSBasePlugin) - Constructor for class org.sbml.jsbml.ext.dyn.DynSBasePlugin
-
Constructor
- DynSBasePlugin(SBase) - Constructor for class org.sbml.jsbml.ext.dyn.DynSBasePlugin
-
Constructor
