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

A

accept(SBase) - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

addDistribInput(DistribInput) - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

Adds a new DistribInput to the listOfDistribInputs.

C

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

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

clones this class

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

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

clones this class

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

createDistribInput() - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

Creates a new DistribInput element and adds it to the ListOfDistribInputs list.

createDistribInput(String) - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

Creates a new DistribInput element and adds it to the ListOfDistribInputs list.

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.

createDrawFromDistribution() - Method in class org.sbml.jsbml.ext.distrib.DistribFunctionDefinitionPlugin

Creates and Sets a new drawFromDistribution instance.

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

createPluginFor(ASTNode) - 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 and Sets a new Uncertainty instance.

D

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

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

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

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

Creates a new DistribFunctionDefinitionPlugin instance.

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

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

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

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

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

Creates an DistribInput instance

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

Creates a DistribInput instance with an id.

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

Creates a DistribInput instance with a level and version.

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

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

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

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

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

Clone constructor

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(SBase) - 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.

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

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

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

Creates a DrawFromDistribution instance

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

Creates a DrawFromDistribution instance with a level and version.

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

Clone constructor

E

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

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

G

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

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

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

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

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

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

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

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

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

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

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

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

getDistribInput(int) - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

Gets an element from the listOfDistribInputs at the given index.

getDistribInput(String) - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

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

getDistribInputCount() - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

Returns the number of DistribInputs in this DrawFromDistribution.

getDrawFromDistribution() - Method in class org.sbml.jsbml.ext.distrib.DistribFunctionDefinitionPlugin

Returns the value of drawFromDistribution

getIndex() - Method in class org.sbml.jsbml.ext.distrib.DistribInput

Returns the value of index

getListOfDistribInputs() - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

Returns the listOfDistribInputs.

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

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

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

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

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

getNumDistribInputs() - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

Returns the number of DistribInputs in this DrawFromDistribution.

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

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.DistribFunctionDefinitionPlugin

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

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

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

Returns the value of DistribSBasePlugin.uncertainty.

getUncertML() - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

Returns the value of uncertML

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

Returns the value of Uncertainty.uncertML.

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

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

H

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

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

I

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

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

Initializes the default values using the namespace.

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

Initializes the default values using the namespace.

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

Initializes the default values using the namespace.

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

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

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

isSetDrawFromDistribution() - Method in class org.sbml.jsbml.ext.distrib.DistribFunctionDefinitionPlugin

Returns whether drawFromDistribution is set

isSetIndex() - Method in class org.sbml.jsbml.ext.distrib.DistribInput

Returns whether index is set

isSetListOfDistribInputs() - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

Returns true, if listOfDistribInputs contains at least one element.

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

Returns whether DistribSBasePlugin.uncertainty is set.

isSetUncertML() - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

Returns whether uncertML is set

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

Returns whether Uncertainty.uncertML is set.

L

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

M

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

main(String[]) - Static method in class org.sbml.jsbml.xml.parsers.DistribParser

Tests this class

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

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

processCharactersOf(String, String, 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.DistribParser

processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.UncertMLXMLNodeReader

R

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

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

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

register(SBase) - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

removeDistribInput(DistribInput) - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

Removes an element from the listOfDistribInputs.

removeDistribInput(String) - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

Removes an element from the listOfDistribInputs.

removeDistribInput(int) - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

Removes an element from the listOfDistribInputs at the given index.

S

setDrawFromDistribution(DrawFromDistribution) - Method in class org.sbml.jsbml.ext.distrib.DistribFunctionDefinitionPlugin

Sets the value of drawFromDistribution

setIndex(int) - Method in class org.sbml.jsbml.ext.distrib.DistribInput

Sets the value of index

setListOfDistribInputs(ListOf<DistribInput>) - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

Sets the given ListOf<DistribInput>.

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

Sets the value of uncertainty

setUncertML(XMLNode) - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

Sets the value of uncertML

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

Sets the value of uncertML

shortLabel - 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

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

Creates an Uncertainty instance

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

Creates a Uncertainty instance with an id.

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

Creates a Uncertainty instance with a level and version.

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

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

UncertMLXMLNodeReader - Class in org.sbml.jsbml.xml.parsers

A XMLNodeReader can be used to store any XML into an XMLNode.

UncertMLXMLNodeReader() - Constructor for class org.sbml.jsbml.xml.parsers.UncertMLXMLNodeReader

unregister(SBase) - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

unsetDrawFromDistribution() - Method in class org.sbml.jsbml.ext.distrib.DistribFunctionDefinitionPlugin

Unsets the variable drawFromDistribution

unsetIndex() - Method in class org.sbml.jsbml.ext.distrib.DistribInput

Unsets the variable index

unsetListOfDistribInputs() - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

Returns true, if listOfDistribInputs contain at least one element, otherwise false.

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

Unsets the variable uncertainty.

unsetUncertML() - Method in class org.sbml.jsbml.ext.distrib.DrawFromDistribution

Unsets the variable uncertML

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

Unsets the variable uncertML.

W

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

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

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

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