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

A

AbstractDistribSBase - Class in org.sbml.jsbml.ext.distrib

AbstractDistribSBase() - Constructor for class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

Creates a new instance of AbstractDistribSBase

AbstractDistribSBase(int, int) - Constructor for class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

Creates a new instance of AbstractDistribSBase

AbstractDistribSBase(String) - Constructor for class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

Creates a new instance of AbstractDistribSBase

AbstractDistribSBase(String, int, int) - Constructor for class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

Creates a new instance of AbstractDistribSBase

AbstractDistribSBase(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

Creates a new instance of AbstractDistribSBase

AbstractDistribSBase(AbstractDistribSBase) - Constructor for class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

Creates a new instance of AbstractDistribSBase

addUncertainty(Uncertainty) - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

Adds a new Uncertainty to the DistribSBasePlugin.listOfUncertainties.

addUncertParameter(UncertParameter) - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Adds a new UncertParameter to the Uncertainty.listOfUncertParameters.

addUncertParameter(UncertParameter) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Adds a new UncertParameter to the UncertParameter.listOfUncertParameters.

C

clone() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

clone() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

clone() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Clones this class

clone() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

clones this class

coefficientOfVariation - org.sbml.jsbml.ext.distrib.UncertParameter.Type

For a random variable with mean μ and strictly positive standard deviation σ, the coefficient of variation is defined as the ratio (σ / |μ|).One benefit of using the coefficient of variation rather than the standard deviation is that it is unitless.

confidenceInterval - org.sbml.jsbml.ext.distrib.UncertParameter.Type

For a univariate random variable x, a confidence interval is a range [a, b], a < b, so that x lies between a and b with given probability.

containsUndeclaredUnits() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

createDistribution(FunctionDefinition, String, String[], String[]) - Static method in class org.sbml.jsbml.ext.distrib.util.DistribModelBuilder

Creates the constructs needed for the given distribution in the distrib package.

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

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

createRange(SBase, String, String) - Static method in class org.sbml.jsbml.ext.distrib.util.DistribModelBuilder

Creates the constructs needed for a uncertml Range.

createStatisticsCollection(SBase, String[], String[], String[]) - Static method in class org.sbml.jsbml.ext.distrib.util.DistribModelBuilder

Creates the constructs needed for a StatisticsCollection.

createStatisticsCollection(SBase, String[], String[], String[], String[], String[]) - Static method in class org.sbml.jsbml.ext.distrib.util.DistribModelBuilder

Creates the constructs needed for a StatisticsCollection.

createUncertainty() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

Creates a new Uncertainty element and adds it to the DistribSBasePlugin.listOfUncertainties list.

createUncertainty(String) - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

Creates a new Uncertainty element and adds it to the DistribSBasePlugin.listOfUncertainties list.

createUncertParameter() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Creates a new UncertParameter element and adds it to the Uncertainty.listOfUncertParameters list.

createUncertParameter() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Creates a new UncertParameter element and adds it to the UncertParameter.listOfUncertParameters list.

createUncertParameter(String) - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Creates a new UncertParameter element and adds it to the Uncertainty.listOfUncertParameters list.

createUncertParameter(String) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Creates a new UncertParameter element and adds it to the UncertParameter.listOfUncertParameters list.

createUncertSpan() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Creates a new UncertSpan element and adds it to the Uncertainty.listOfUncertParameters list.

createUncertSpan(String) - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Creates a new UncertSpan element and adds it to the Uncertainty.listOfUncertParameters list.

credibleInterval - org.sbml.jsbml.ext.distrib.UncertParameter.Type

In Bayesian statistics, a credible interval is similar to a confidence interval determined from the posterior distribution of a random variable x.

D

definitionURL - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

degreesOfFreedom - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

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

Creates a new DistribSBasePlugin instance.

DistribSBasePlugin(DistribSBasePlugin) - Constructor for class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

Creates a new DistribSBasePlugin instance, cloned from the input parameter.

DistribSBasePlugin(SBase) - Constructor for class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

Creates a new DistribSBasePlugin instance.

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

E

equals(Object) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

equals(Object) - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

externalParameter - org.sbml.jsbml.ext.distrib.UncertParameter.Type

This type is uniquely described by an appropriate definitionURL, and is provided to allow a modeler to encode externally-provided parameters not otherwise explicitly handled by this specification.

G

getAllowsChildren() - Method in class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

getAllowsChildren() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

getAllowsChildren() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

getChildAt(int) - Method in class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

getChildAt(int) - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

getChildAt(int) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

getChildCount() - Method in class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

getChildCount() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

getChildCount() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

getChildCount() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

getDefinitionURL() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns the value of UncertParameter.definitionURL.

getDerivedUnitDefinition() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

getDerivedUnits() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

getFormula() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Deprecated.

getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.DistribParser

getListOfUncertainties() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

Returns the DistribSBasePlugin.listOfUncertainties.

getListOfUncertParameters() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Returns the Uncertainty.listOfUncertParameters.

getListOfUncertParameters() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns the UncertParameter.listOfUncertParameters.

getMath() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

getMathMLString() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

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

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

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

getNumUncertainties() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

Returns the number of Uncertaintys in this DistribSBasePlugin.

getNumUncertParameters() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Returns the number of UncertParameters in this Uncertainty.

getNumUncertParameters() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns the number of UncertParameters in this UncertParameter.

getPackageName() - Method in class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

getPackageName() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

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

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

getPrefix() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

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

getType() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns the value of UncertParameter.type.

getUncertainty(int) - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

Gets an element from the DistribSBasePlugin.listOfUncertainties at the given index.

getUncertainty(String) - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

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

getUncertaintyCount() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

Returns the number of Uncertaintys in this DistribSBasePlugin.

getUncertParameter(int) - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Gets an element from the Uncertainty.listOfUncertParameters at the given index.

getUncertParameter(int) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Gets an element from the UncertParameter.listOfUncertParameters at the given index.

getUncertParameter(String) - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

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

getUncertParameter(String) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

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

getUncertParameterCount() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Returns the number of UncertParameters in this Uncertainty.

getUncertParameterCount() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns the number of UncertParameters in this UncertParameter.

getUnits() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns the value of UncertParameter.units.

getURI() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

getValue() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns the value of UncertParameter.value.

getValueLower() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

Returns the value of UncertSpan.valueLower.

getValueUpper() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

Returns the value of UncertSpan.valueUpper.

getVar() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns the value of UncertParameter.var.

getVarLower() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

Returns the value of UncertSpan.varLower.

getVarUpper() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

Returns the value of UncertSpan.varUpper.

H

hashCode() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

hashCode() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

I

inclusive - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

initDefaults() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

Initializes the default values using the namespace.

interquartileRange - org.sbml.jsbml.ext.distrib.UncertParameter.Type

The interquartile range is the range between the 1st and 3rd quartiles.

isIdMandatory() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

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

isSetDefinitionURL() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns whether UncertParameter.definitionURL is set.

isSetListOfUncertainties() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

Returns true if DistribSBasePlugin.listOfUncertainties contains at least one element.

isSetListOfUncertParameters() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Returns true if Uncertainty.listOfUncertParameters contains at least one element.

isSetListOfUncertParameters() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns true if UncertParameter.listOfUncertParameters contains at least one element.

isSetMath() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

isSetType() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns whether UncertParameter.type is set.

isSetUnits() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns whether UncertParameter.units is set.

isSetValue() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns whether UncertParameter.value is set.

isSetValueLower() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

Returns whether UncertSpan.valueLower is set.

isSetValueUpper() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

Returns whether UncertSpan.valueUpper is set.

isSetVar() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns whether UncertParameter.var is set.

isSetVarLower() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

Returns whether UncertSpan.varLower is set.

isSetVarUpper() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

Returns whether UncertSpan.varUpper is set.

K

kurtosis - org.sbml.jsbml.ext.distrib.UncertParameter.Type

The kurtosis of a distribution is a measure of how peaked the distribution is.

L

listOfUncertainties - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

listOfUncertParameters - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

location - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

logScale - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

M

main(String[]) - Static method in class org.sbml.jsbml.ext.distrib.util.DistribModelBuilder

mean - org.sbml.jsbml.ext.distrib.UncertParameter.Type

The arithmetic mean (typically just the mean) is what is commonly called the average.

mean - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

median - org.sbml.jsbml.ext.distrib.UncertParameter.Type

The median is described as the numeric value separating the higher half of a sample (or population) from the lower half.

mode - org.sbml.jsbml.ext.distrib.UncertParameter.Type

The mode is the value that occurs the most frequently in a data set (or a probability distribution).

N

namespaces - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

namespaceURI - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

numberOfClasses - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

O

org.sbml.jsbml.ext.distrib - package org.sbml.jsbml.ext.distrib

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

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

P

processAttribute(String, String, String, String, String, 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.DistribParser

R

range - org.sbml.jsbml.ext.distrib.UncertParameter.Type

The range is the interval [a, b] so that a < b and contains all possible values of x.

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

removeUncertainty(int) - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

Removes an element from the DistribSBasePlugin.listOfUncertainties at the given index.

removeUncertainty(String) - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

Removes an element from the DistribSBasePlugin.listOfUncertainties.

removeUncertainty(Uncertainty) - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

Removes an element from the DistribSBasePlugin.listOfUncertainties.

removeUncertParameter(int) - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Removes an element from the Uncertainty.listOfUncertParameters at the given index.

removeUncertParameter(int) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Removes an element from the UncertParameter.listOfUncertParameters at the given index.

removeUncertParameter(String) - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Removes an element from the Uncertainty.listOfUncertParameters.

removeUncertParameter(String) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Removes an element from the UncertParameter.listOfUncertParameters.

removeUncertParameter(UncertParameter) - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Removes an element from the Uncertainty.listOfUncertParameters.

removeUncertParameter(UncertParameter) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Removes an element from the UncertParameter.listOfUncertParameters.

S

sampleSize - org.sbml.jsbml.ext.distrib.UncertParameter.Type

The sample size is a direct count of the number of observations made or the number of samples measured.

scale - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

setDefinitionURL(String) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Sets the value of definitionURL

setFormula(String) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Deprecated.

setListOfUncertainties(ListOf<Uncertainty>) - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

Sets the given ListOf<Uncertainty>.

setListOfUncertParameters(ListOf<UncertParameter>) - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Sets the given ListOf<UncertParameter>.

setListOfUncertParameters(ListOf<UncertParameter>) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Sets the given ListOf<UncertParameter>.

setMath(ASTNode) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

setType(UncertParameter.Type) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Sets the value of type

setUnits(String) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Sets the value of units

setValue(double) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Sets the value of value

setValueLower(double) - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

Sets the value of valueLower

setValueUpper(double) - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

Sets the value of valueUpper

setVar(String) - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Sets the value of var

setVarLower(String) - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

Sets the value of varLower

setVarUpper(String) - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

Sets the value of varUpper

shape - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

shortLabel - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

singleValueStatistic - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

skewness - org.sbml.jsbml.ext.distrib.UncertParameter.Type

The skewness of a random variable is a measure of how asymmetric the corresponding probability distribution is.

spanStatistic - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

standardDeviation - org.sbml.jsbml.ext.distrib.UncertParameter.Type

The standard deviation of a distribution or population is the square root of its variance.

standardError - org.sbml.jsbml.ext.distrib.UncertParameter.Type

The standard error is the standard deviation of estimates of a population value.

stddev - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

T

truncationLowerBound - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

truncationUpperBound - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

type - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

U

UNCERT_ML_URI_L3 - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

uncertainty - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

Uncertainty - Class in org.sbml.jsbml.ext.distrib

The Uncertainty class is a collection of zero or more statistical measures related to the uncertainty of the parent SBML element.

Uncertainty() - Constructor for class org.sbml.jsbml.ext.distrib.Uncertainty

Creates an Uncertainty instance

Uncertainty(int, int) - Constructor for class org.sbml.jsbml.ext.distrib.Uncertainty

Creates a Uncertainty instance with a level and version.

Uncertainty(String) - Constructor for class org.sbml.jsbml.ext.distrib.Uncertainty

Creates a Uncertainty instance with an id.

Uncertainty(String, int, int) - Constructor for class org.sbml.jsbml.ext.distrib.Uncertainty

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

Uncertainty(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.distrib.Uncertainty

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

Uncertainty(Uncertainty) - Constructor for class org.sbml.jsbml.ext.distrib.Uncertainty

Clone constructor

uncertParameter - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

UncertParameter - Class in org.sbml.jsbml.ext.distrib

Defines one uncertainty statistic about the parent element.

UncertParameter() - Constructor for class org.sbml.jsbml.ext.distrib.UncertParameter

Creates an UncertParameter instance

UncertParameter(int, int) - Constructor for class org.sbml.jsbml.ext.distrib.UncertParameter

Creates a UncertParameter instance with a level and version.

UncertParameter(String) - Constructor for class org.sbml.jsbml.ext.distrib.UncertParameter

Creates a UncertParameter instance with an id.

UncertParameter(String, int, int) - Constructor for class org.sbml.jsbml.ext.distrib.UncertParameter

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

UncertParameter(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.distrib.UncertParameter

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

UncertParameter(UncertParameter) - Constructor for class org.sbml.jsbml.ext.distrib.UncertParameter

Clone constructor

UncertParameter.Type - Enum in org.sbml.jsbml.ext.distrib

The different UncertParameter and UncertSpan type values.

uncertSpan - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

UncertSpan - Class in org.sbml.jsbml.ext.distrib

The UncertSpan class defines a span of values that define an uncertainty statistic such as confidence interval or range.

UncertSpan() - Constructor for class org.sbml.jsbml.ext.distrib.UncertSpan

Creates an UncertSpan instance

UncertSpan(int, int) - Constructor for class org.sbml.jsbml.ext.distrib.UncertSpan

Creates a UncertSpan instance with a level and version.

UncertSpan(String) - Constructor for class org.sbml.jsbml.ext.distrib.UncertSpan

Creates a UncertSpan instance with an id.

UncertSpan(String, int, int) - Constructor for class org.sbml.jsbml.ext.distrib.UncertSpan

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

UncertSpan(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.distrib.UncertSpan

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

UncertSpan(UncertSpan) - Constructor for class org.sbml.jsbml.ext.distrib.UncertSpan

Clone constructor

uncertStatistics - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

uncertStatisticSpan - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

units - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

unsetDefinitionURL() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Unsets the variable definitionURL.

unsetFormula() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Deprecated.

unsetListOfUncertainties() - Method in class org.sbml.jsbml.ext.distrib.DistribSBasePlugin

Returns true if DistribSBasePlugin.listOfUncertainties contains at least one element, otherwise false.

unsetListOfUncertParameters() - Method in class org.sbml.jsbml.ext.distrib.Uncertainty

Returns true if Uncertainty.listOfUncertParameters contains at least one element, otherwise false.

unsetListOfUncertParameters() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Returns true if UncertParameter.listOfUncertParameters contains at least one element, otherwise false.

unsetMath() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

unsetType() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Unsets the variable type.

unsetUnits() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Unsets the variable units.

unsetValue() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Unsets the variable value.

unsetValueLower() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

Unsets the variable valueLower.

unsetValueUpper() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

Unsets the variable valueUpper.

unsetVar() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

Unsets the variable var.

unsetVarLower() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

Unsets the variable varLower.

unsetVarUpper() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

Unsets the variable varUpper.

V

value - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

valueLower - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

valueOf(String) - Static method in enum org.sbml.jsbml.ext.distrib.UncertParameter.Type

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.sbml.jsbml.ext.distrib.UncertParameter.Type

Returns an array containing the constants of this enum type, in the order they are declared.

valueUpper - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

var - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

variance - org.sbml.jsbml.ext.distrib.UncertParameter.Type

The variance of a random quantity (or distribution) is the average value of the square of the deviation of that variable from its mean.

variance - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

varLower - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

varUpper - Static variable in class org.sbml.jsbml.ext.distrib.DistribConstants

W

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

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.distrib.AbstractDistribSBase

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.distrib.UncertParameter

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.distrib.UncertSpan

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