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

A

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.FunctionTermConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InputConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.OutputConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.QualitativeSpeciesConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.QualModelPluginConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TransitionConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.FunctionTermConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InputConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.OutputConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.QualitativeSpeciesConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.QualModelPluginConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TransitionConstraints

addFunctionTerm(FunctionTerm) - Method in class org.sbml.jsbml.ext.qual.Transition

addInput(Input) - Method in class org.sbml.jsbml.ext.qual.Transition

addOutput(Output) - Method in class org.sbml.jsbml.ext.qual.Transition

addQualitativeSpecies(QualitativeSpecies) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Adds a QualitativeSpecies to the model.

addSpecies(QualitativeSpecies) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Adds a QualitativeSpecies instance to the listOfSpecies of this Model.

addTransition(Transition) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

assignmentLevel - org.sbml.jsbml.ext.qual.OutputTransitionEffect

The level of the QualitativeSpecies is set to the resultLevel of the selected term.

C

clone() - Method in class org.sbml.jsbml.ext.qual.FunctionTerm

clone() - Method in class org.sbml.jsbml.ext.qual.Input

clone() - Method in class org.sbml.jsbml.ext.qual.Output

clone() - Method in class org.sbml.jsbml.ext.qual.QualConstants

clone() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

clone() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

clone() - Method in class org.sbml.jsbml.ext.qual.Transition

compartment - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

constant - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

consumption - org.sbml.jsbml.ext.qual.InputTransitionEffect

The level of the QualitativeSpecies is decreased by the resultLevel of the selected term possibly modified by the thresholdLevel of the Input.

containsQualitativeSpecies(QualitativeSpecies) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Returns true if qs is already part of this QualModelPlugin

containsUndeclaredUnits() - Method in class org.sbml.jsbml.ext.qual.Input

containsUndeclaredUnits() - Method in class org.sbml.jsbml.ext.qual.Output

createFunctionTerm() - Method in class org.sbml.jsbml.ext.qual.Transition

Creates a new instance of FunctionTerm and adds it to this Transition's Transition.listOfFunctionTerms.

createFunctionTerm(ASTNode) - Method in class org.sbml.jsbml.ext.qual.Transition

Creates a new instance of FunctionTerm with the given mathematical expression (encoded in an ASTNode) and adds it to this Transition's Transition.listOfFunctionTerms.

createInput() - Method in class org.sbml.jsbml.ext.qual.Transition

createInput(String) - Method in class org.sbml.jsbml.ext.qual.Transition

createInput(String, String, InputTransitionEffect) - Method in class org.sbml.jsbml.ext.qual.Transition

createInput(String, QualitativeSpecies, InputTransitionEffect) - Method in class org.sbml.jsbml.ext.qual.Transition

createOutput() - Method in class org.sbml.jsbml.ext.qual.Transition

createOutput(String) - Method in class org.sbml.jsbml.ext.qual.Transition

createOutput(String, String, OutputTransitionEffect) - Method in class org.sbml.jsbml.ext.qual.Transition

createOutput(String, QualitativeSpecies, OutputTransitionEffect) - Method in class org.sbml.jsbml.ext.qual.Transition

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

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

createQualitativeSpecies() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Creates a new QualitativeSpecies inside this QualModelPlugin and returns it.

createQualitativeSpecies(String) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Creates a new QualitativeSpecies inside this QualModelPlugin and returns it.

createQualitativeSpecies(String, String, boolean) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Creates a new QualitativeSpecies inside this QualModelPlugin and returns it.

createQualitativeSpecies(String, String, Species) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Creates a new QualitativeSpecies, based on an existing Species, adds it to this QualModelPlugin and returns it.

createQualitativeSpecies(String, Compartment) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Creates a new Species inside this Model and returns it.

createQualitativeSpecies(String, Compartment, boolean) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Creates a new QualitativeSpecies inside this QualModelPlugin and returns it.

createTransition() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Creates a new Transition inside this QualModelPlugin and returns it.

createTransition(String) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Creates a new Transition inside this QualModelPlugin and returns it.

createTransition(String, Input, Output) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Creates a new Transition inside this QualModelPlugin and returns it.

D

defaultTerm - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

dual - org.sbml.jsbml.ext.qual.Sign

E

equals(Object) - Method in class org.sbml.jsbml.ext.qual.FunctionTerm

equals(Object) - Method in class org.sbml.jsbml.ext.qual.Input

equals(Object) - Method in class org.sbml.jsbml.ext.qual.Output

equals(Object) - Method in class org.sbml.jsbml.ext.qual.QualConstants

equals(Object) - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

equals(Object) - Method in class org.sbml.jsbml.ext.qual.Transition

F

FunctionTerm - Class in org.sbml.jsbml.ext.qual

Each FunctionTerm is also associated with a result and in addition to a Boolean function inside a Math element that can be used to set the conditions under which this term is selected.

FunctionTerm() - Constructor for class org.sbml.jsbml.ext.qual.FunctionTerm

Creates a new FunctionTerm instance.

FunctionTerm(int, int) - Constructor for class org.sbml.jsbml.ext.qual.FunctionTerm

Creates a new FunctionTerm instance.

FunctionTerm(ASTNode, int, int) - Constructor for class org.sbml.jsbml.ext.qual.FunctionTerm

Creates a new FunctionTerm instance.

FunctionTerm(FunctionTerm) - Constructor for class org.sbml.jsbml.ext.qual.FunctionTerm

Creates a FunctionTerm instance from a given FunctionTerm.

FunctionTermConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the FunctionTerm class.

FunctionTermConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.FunctionTermConstraints

G

getAllowsChildren() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.qual.Transition

getChildCount() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.qual.Transition

getCompartment() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

getCompartmentInstance() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

getConstant() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

getDerivedUnitDefinition() - Method in class org.sbml.jsbml.ext.qual.Input

getDerivedUnitDefinition() - Method in class org.sbml.jsbml.ext.qual.Output

getDerivedUnits() - Method in class org.sbml.jsbml.ext.qual.Input

getDerivedUnits() - Method in class org.sbml.jsbml.ext.qual.Output

getFunctionTermCount() - Method in class org.sbml.jsbml.ext.qual.Transition

getInitialLevel() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

getInputCount() - Method in class org.sbml.jsbml.ext.qual.Transition

getListOfFunctionTerms() - Method in class org.sbml.jsbml.ext.qual.Transition

getListOfInputs() - Method in class org.sbml.jsbml.ext.qual.Transition

getListOfOutputs() - Method in class org.sbml.jsbml.ext.qual.Transition

getListOfQualitativeSpecies() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

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

getListOfTransitions() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

getMaxLevel() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

getModel() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Returns the Model

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

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

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

getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.qual.QualConstants

Returns a namespace URI corresponding to the given level and version.

getNumQualitativeSpecies() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Returns the number of QualitativeSpecies of this QualModelPlugin.

getNumTransitions() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Returns the number of Transition of this QualModelPlugin.

getOutputCount() - Method in class org.sbml.jsbml.ext.qual.Transition

getOutputLevel() - Method in class org.sbml.jsbml.ext.qual.Output

Returns the outputLevel.

getPackageName() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

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

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

getParent() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

getParentSBMLObject() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

getPrefix() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

getQualitativeSpecies() - Method in class org.sbml.jsbml.ext.qual.Input

getQualitativeSpecies() - Method in class org.sbml.jsbml.ext.qual.Output

Returns the qualitativeSpecies

getQualitativeSpecies(int) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Gets the ith QualitativeSpecies.

getQualitativeSpecies(String) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Gets the QualitativeSpecies that has the given id.

getQualitativeSpeciesCount() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Returns the number of QualitativeSpecies objects in this QualModelPlugin.

getQualitativeSpeciesInstance() - Method in class org.sbml.jsbml.ext.qual.Input

getQualitativeSpeciesInstance() - Method in class org.sbml.jsbml.ext.qual.Output

getResultLevel() - Method in class org.sbml.jsbml.ext.qual.FunctionTerm

Returns the resultLevel if it is set, otherwise throw a PropertyUndefinedError Exception.

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

getSign() - Method in class org.sbml.jsbml.ext.qual.Input

getSource() - Method in class org.sbml.jsbml.ext.qual.QualConstants

getThresholdLevel() - Method in class org.sbml.jsbml.ext.qual.Input

getTransition(int) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Gets the ith Transition.

getTransition(String) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Gets the Transition that has the given id.

getTransitionCount() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Returns the number of Transition objects in this QualModelPlugin.

getTransitionEffect() - Method in class org.sbml.jsbml.ext.qual.Input

getTransitionEffect() - Method in class org.sbml.jsbml.ext.qual.Output

Returns the transitionEffect

getURI() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.FunctionTermConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InputConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.OutputConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.QualitativeSpeciesConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.QualModelPluginConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.TransitionConstraints

H

hashCode() - Method in class org.sbml.jsbml.ext.qual.FunctionTerm

hashCode() - Method in class org.sbml.jsbml.ext.qual.Input

hashCode() - Method in class org.sbml.jsbml.ext.qual.Output

hashCode() - Method in class org.sbml.jsbml.ext.qual.QualConstants

hashCode() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

hashCode() - Method in class org.sbml.jsbml.ext.qual.Transition

I

initDefaults() - Method in class org.sbml.jsbml.ext.qual.FunctionTerm

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.qual.Input

initDefaults() - Method in class org.sbml.jsbml.ext.qual.Output

initDefaults() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

initDefaults() - Method in class org.sbml.jsbml.ext.qual.Transition

initialLevel - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

Input - Class in org.sbml.jsbml.ext.qual

Each Input refers to a QualitativeSpecies that participates in the corresponding Transition.

Input() - Constructor for class org.sbml.jsbml.ext.qual.Input

Creates a new Input instance.

Input(int, int) - Constructor for class org.sbml.jsbml.ext.qual.Input

Creates a new Input instance.

Input(String) - Constructor for class org.sbml.jsbml.ext.qual.Input

Creates a new Input instance.

Input(String, int, int) - Constructor for class org.sbml.jsbml.ext.qual.Input

Creates a new Input instance.

Input(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.qual.Input

Creates a new Input instance.

Input(String, QualitativeSpecies, InputTransitionEffect) - Constructor for class org.sbml.jsbml.ext.qual.Input

Creates a new Input instance.

Input(Input) - Constructor for class org.sbml.jsbml.ext.qual.Input

Creates a new Input instance cloned from the given Input.

InputConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the Input class.

InputConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.InputConstraints

InputTransitionEffect - Enum in org.sbml.jsbml.ext.qual

The transitionInputEffect is an enumeration of values used to indicate the effect of an Input Transition within the system.

isCompartmentMandatory() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

isDefaultTerm() - Method in class org.sbml.jsbml.ext.qual.FunctionTerm

Returns true if it is a defaultTerm.

isIdMandatory() - Method in class org.sbml.jsbml.ext.qual.Input

isIdMandatory() - Method in class org.sbml.jsbml.ext.qual.Output

isIdMandatory() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

isIdMandatory() - Method in class org.sbml.jsbml.ext.qual.Transition

isInitialLevelMandatory() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

isListOfFunctionTermsMandatory() - Method in class org.sbml.jsbml.ext.qual.Transition

isListOfInputsMandatory() - Method in class org.sbml.jsbml.ext.qual.Transition

isListOfOutputsMandatory() - Method in class org.sbml.jsbml.ext.qual.Transition

isMaxLevelMandatory() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

isOutputLevelMandatory() - Method in class org.sbml.jsbml.ext.qual.Output

isQualitativeSpeciesMandatory() - Method in class org.sbml.jsbml.ext.qual.Input

isQualitativeSpeciesMandatory() - Method in class org.sbml.jsbml.ext.qual.Output

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

isResultLevelMandatory() - Method in class org.sbml.jsbml.ext.qual.FunctionTerm

Returns false, resultLevel is not mandatory.

isSetCompartment() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

isSetCompartmentInstance() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

isSetConstant() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

isSetConstantMandatory() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

isSetInitialLevel() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

isSetListOfFunctionTerms() - Method in class org.sbml.jsbml.ext.qual.Transition

isSetListOfInputs() - Method in class org.sbml.jsbml.ext.qual.Transition

isSetListOfOutputs() - Method in class org.sbml.jsbml.ext.qual.Transition

isSetListOfQualitativeSpecies() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Returns true if the listOfQualitativeSpecies is set.

isSetListOfTransitions() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

Returns true if the listOfTransitions is set.

isSetMaxLevel() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

isSetNewValue() - Method in class org.sbml.jsbml.ext.qual.QualConstants

Returns true is the new value is set.

isSetOldValue() - Method in class org.sbml.jsbml.ext.qual.QualConstants

Returns true is the old value is set.

isSetOutputLevel() - Method in class org.sbml.jsbml.ext.qual.Output

isSetQualitativeSpecies() - Method in class org.sbml.jsbml.ext.qual.Input

isSetQualitativeSpecies() - Method in class org.sbml.jsbml.ext.qual.Output

isSetResultLevel() - Method in class org.sbml.jsbml.ext.qual.FunctionTerm

Returns true if resultLevel is set.

isSetSign() - Method in class org.sbml.jsbml.ext.qual.Input

isSetSource() - Method in class org.sbml.jsbml.ext.qual.QualConstants

Returns true is the source is set.

isSetThresholdLevel() - Method in class org.sbml.jsbml.ext.qual.Input

isSetTransitionEffect() - Method in class org.sbml.jsbml.ext.qual.Input

isSetTransitionEffect() - Method in class org.sbml.jsbml.ext.qual.Output

isSignMandatory() - Method in class org.sbml.jsbml.ext.qual.Transition

isThresholdLevelMandatory() - Method in class org.sbml.jsbml.ext.qual.Input

isTransitionEffectMandatory() - Method in class org.sbml.jsbml.ext.qual.Input

isTransitionEffectMandatory() - Method in class org.sbml.jsbml.ext.qual.Output

L

listOfFunctionTerms - org.sbml.jsbml.ext.qual.QualList

listOfFunctionTerms - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

listOfInputs - org.sbml.jsbml.ext.qual.QualList

listOfInputs - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

listOfOutputs - org.sbml.jsbml.ext.qual.QualList

listOfOutputs - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

listOfQualitativeSpecies - org.sbml.jsbml.ext.qual.QualList

listOfQualitativeSpecies - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

listOfSymbolicValues - org.sbml.jsbml.ext.qual.QualList

listOfTransitions - org.sbml.jsbml.ext.qual.QualList

listOfTransitions - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

M

maxLevel - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

N

name - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

namespaces - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

namespaceURI - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

The latest namespace URI of this parser, this value can change between releases.

namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

The namespace URI of this parser for SBML level 3, version 1 and package version 1.

negative - org.sbml.jsbml.ext.qual.Sign

none - org.sbml.jsbml.ext.qual.InputTransitionEffect

Neither the level nor the symbol associated to the QualitativeSpecies is modified.

none - org.sbml.jsbml.ext.qual.QualList

O

org.sbml.jsbml.ext.qual - package org.sbml.jsbml.ext.qual

Provides classes for the Qualitative Models package.

org.sbml.jsbml.validator.offline.constraints - package org.sbml.jsbml.validator.offline.constraints

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

Output - Class in org.sbml.jsbml.ext.qual

Each Output refers to a QualitativeSpecies that participates in (is affected by) the corresponding Transition.

Output() - Constructor for class org.sbml.jsbml.ext.qual.Output

Creates a new Output instance.

Output(int, int) - Constructor for class org.sbml.jsbml.ext.qual.Output

Creates a new Output instance.

Output(String) - Constructor for class org.sbml.jsbml.ext.qual.Output

Creates a new Output instance.

Output(String, int, int) - Constructor for class org.sbml.jsbml.ext.qual.Output

Creates a new Output instance.

Output(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.qual.Output

Creates a new Output instance.

Output(String, QualitativeSpecies, OutputTransitionEffect) - Constructor for class org.sbml.jsbml.ext.qual.Output

Creates a new Output instance.

Output(Output) - Constructor for class org.sbml.jsbml.ext.qual.Output

Creates a new Output instance.

Output(QualitativeSpecies, OutputTransitionEffect) - Constructor for class org.sbml.jsbml.ext.qual.Output

Creates a new Output instance.

OutputConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the Output class.

OutputConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.OutputConstraints

outputLevel - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

OutputTransitionEffect - Enum in org.sbml.jsbml.ext.qual

The transitionOutputEffect is an enumeration of values used to indicate the effect of an Output Transition within the system.

P

packageName - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

positive - org.sbml.jsbml.ext.qual.Sign

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

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

production - org.sbml.jsbml.ext.qual.OutputTransitionEffect

The level of the QualitativeSpecies is increased by the resultLevel of the selected term possibly modified by the level of the Output.

Q

QualConstants - Class in org.sbml.jsbml.ext.qual

Contains some constants related to the qual package.

QualConstants(QualConstants) - Constructor for class org.sbml.jsbml.ext.qual.QualConstants

Constructs a new PropertyChangeEvent, cloned from the given qualChangeEvent.

QualConstants(SBase, String, Object, Object) - Constructor for class org.sbml.jsbml.ext.qual.QualConstants

Constructs a new PropertyChangeEvent.

QualitativeModel - Class in org.sbml.jsbml.ext.qual

Deprecated.

use QualModelPlugin instead.

QualitativeModel(QualModelPlugin) - Constructor for class org.sbml.jsbml.ext.qual.QualitativeModel

Deprecated.

use QualModelPlugin instead.

QualitativeModel(Model) - Constructor for class org.sbml.jsbml.ext.qual.QualitativeModel

Deprecated.

use QualModelPlugin instead.

qualitativeSpecies - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

QualitativeSpecies - Class in org.sbml.jsbml.ext.qual

Similarly to the Species in SBML, the components of qualitative models refer to pools of entities that are considered indistinguishable and are each located in a specific Compartment.

QualitativeSpecies() - Constructor for class org.sbml.jsbml.ext.qual.QualitativeSpecies

Creates a new QualitativeSpecies instance.

QualitativeSpecies(int, int) - Constructor for class org.sbml.jsbml.ext.qual.QualitativeSpecies

Creates a new QualitativeSpecies instance.

QualitativeSpecies(String) - Constructor for class org.sbml.jsbml.ext.qual.QualitativeSpecies

Creates a new QualitativeSpecies instance.

QualitativeSpecies(String, int, int) - Constructor for class org.sbml.jsbml.ext.qual.QualitativeSpecies

Creates a new QualitativeSpecies instance.

QualitativeSpecies(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.qual.QualitativeSpecies

Creates a new QualitativeSpecies instance.

QualitativeSpecies(QualitativeSpecies) - Constructor for class org.sbml.jsbml.ext.qual.QualitativeSpecies

Creates a new QualitativeSpecies instance.

QualitativeSpecies(Species) - Constructor for class org.sbml.jsbml.ext.qual.QualitativeSpecies

Creates a new QualitativeSpecies instance.

QualitativeSpeciesConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the QualitativeSpecies class.

QualitativeSpeciesConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.QualitativeSpeciesConstraints

QualList - Enum in org.sbml.jsbml.ext.qual

QualModelPlugin - Class in org.sbml.jsbml.ext.qual

The QualModelPlugin adds two lists, one for holding QualitativeSpecies and the other for holding Transitions.

QualModelPlugin(QualModelPlugin) - Constructor for class org.sbml.jsbml.ext.qual.QualModelPlugin

Clone constructor

QualModelPlugin(Model) - Constructor for class org.sbml.jsbml.ext.qual.QualModelPlugin

Creates a new QualModelPlugin instance

QualModelPluginConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Defines validation rules (as ValidationFunction instances) for the QualModelPlugin class.

QualModelPluginConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.QualModelPluginConstraints

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

This class is used to parse the qual extension package elements and attributes.

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

R

rank - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.qual.FunctionTerm

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.qual.Input

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.qual.Output

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

removeFunctionTerm(int) - Method in class org.sbml.jsbml.ext.qual.Transition

removeFunctionTerm(FunctionTerm) - Method in class org.sbml.jsbml.ext.qual.Transition

removeInput(int) - Method in class org.sbml.jsbml.ext.qual.Transition

removeInput(Input) - Method in class org.sbml.jsbml.ext.qual.Transition

removeOutput(int) - Method in class org.sbml.jsbml.ext.qual.Transition

removeOutput(Output) - Method in class org.sbml.jsbml.ext.qual.Transition

removeQualitativeSpecies(QualitativeSpecies) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

removeTransition(Transition) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

resultLevel - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

S

SET_20311 - Static variable in class org.sbml.jsbml.validator.offline.constraints.OutputConstraints

setCompartment(String) - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

setCompartment(Compartment) - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

setConstant(boolean) - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

Sets the constant attribute.

setDefaultTerm(boolean) - Method in class org.sbml.jsbml.ext.qual.FunctionTerm

Sets if this FunctionTerm is a defaultTerm.

setInitialLevel(int) - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

Sets the initialLevel attribute.

setListOfFunctionTerms(ListOf<FunctionTerm>) - Method in class org.sbml.jsbml.ext.qual.Transition

The Transition element contains exactly one list of FunctionTerms.

setListOfInputs(ListOf<Input>) - Method in class org.sbml.jsbml.ext.qual.Transition

The Transition element contains at most one list of Inputs.

setListOfOutputs(ListOf<Output>) - Method in class org.sbml.jsbml.ext.qual.Transition

The Transition element contains at most one list of Outputs.

setListOfQualitativeSpecies(ListOf<QualitativeSpecies>) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

QualModelPlugin may contain at most one listOfQualitativeSpecies which must contain at least on QualitativeSpecies.

setListOfTransitions(ListOf<Transition>) - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

QualModelPlugin can contain at most one listOfTransitions which must contain at least one Transition.

setMaxLevel(int) - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

Sets the maxLevel attribute.

setOutputLevel(int) - Method in class org.sbml.jsbml.ext.qual.Output

The outputLevel is a non-negative integer used along with the transitionEffect to specify the effect of the Transition on the corresponding QualitativeSpecies.

setQualitativeSpecies(String) - Method in class org.sbml.jsbml.ext.qual.Input

The required attribute qualitativeSpecies is used to identify the QualitativeSpecies that is the input of this Transition.

setQualitativeSpecies(String) - Method in class org.sbml.jsbml.ext.qual.Output

The required attribute qualitativeSpecies is used to identify the QualitativeSpecies that is the output of this Transition.

setResultLevel(int) - Method in class org.sbml.jsbml.ext.qual.FunctionTerm

The result of a term is described by a resultLevel.

setSign(Sign) - Method in class org.sbml.jsbml.ext.qual.Input

The sign of type Sign can be used as an indication as to whether the contribution of this Input is positive, negative, both (dual) or unknown.

setThresholdLevel(int) - Method in class org.sbml.jsbml.ext.qual.Input

The thresholdLevel is a non-negative integer that can be used to set the threshold level of the particular input.

setTransitionEffect(InputTransitionEffect) - Method in class org.sbml.jsbml.ext.qual.Input

Each Input has a required attribute transitionEffect of type InputTransitionEffect which describes how the QualitativeSpecies referenced by the Input is affected by the Transition.

setTransitionEffect(OutputTransitionEffect) - Method in class org.sbml.jsbml.ext.qual.Output

Each Output has a required attribute transitionEffect of type OutputTransitionEffect which describes how the QualitativeSpecies referenced by the Output is affected by the Transition.

shortLabel - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

The short name/label of the package

sign - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

Sign - Enum in org.sbml.jsbml.ext.qual

The sign is an enumeration of values used to indicate direction of an Input within the system.

T

thresholdLevel - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

Transition - Class in org.sbml.jsbml.ext.qual

A Transition defines the changes in level associated with the QualitativeSpecies that occur when a Transition is enabled.

Transition() - Constructor for class org.sbml.jsbml.ext.qual.Transition

Creates a new Transition instance.

Transition(int, int) - Constructor for class org.sbml.jsbml.ext.qual.Transition

Creates a new Transition instance.

Transition(String) - Constructor for class org.sbml.jsbml.ext.qual.Transition

Creates a new Transition instance.

Transition(String, int, int) - Constructor for class org.sbml.jsbml.ext.qual.Transition

Creates a new Transition instance.

Transition(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.qual.Transition

Creates a new Transition instance.

Transition(Transition) - Constructor for class org.sbml.jsbml.ext.qual.Transition

Creates a new Transition instance.

TransitionConstraints - Class in org.sbml.jsbml.validator.offline.constraints

TransitionConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.TransitionConstraints

transitionEffect - Static variable in class org.sbml.jsbml.ext.qual.QualConstants

U

unknown - org.sbml.jsbml.ext.qual.Sign

unsetCompartment() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

unsetConstant() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

unsetInitialLevel() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

unsetListOfFunctionTerms() - Method in class org.sbml.jsbml.ext.qual.Transition

unsetListOfInputs() - Method in class org.sbml.jsbml.ext.qual.Transition

unsetListOfOutputs() - Method in class org.sbml.jsbml.ext.qual.Transition

unsetListOfQualitativeSpecies() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

unsetListOfTransitions() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

unsetMaxLevel() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

unsetOutputLevel() - Method in class org.sbml.jsbml.ext.qual.Output

unsetQualitativeSpecies() - Method in class org.sbml.jsbml.ext.qual.Input

unsetQualitativeSpecies() - Method in class org.sbml.jsbml.ext.qual.Output

unsetResultLevel() - Method in class org.sbml.jsbml.ext.qual.FunctionTerm

Unsets the resultLevel.

unsetSign() - Method in class org.sbml.jsbml.ext.qual.Input

unsetThresholdLevel() - Method in class org.sbml.jsbml.ext.qual.Input

unsetTransitionEffect() - Method in class org.sbml.jsbml.ext.qual.Input

unsetTransitionEffect() - Method in class org.sbml.jsbml.ext.qual.Output

V

valueOf(String) - Static method in enum org.sbml.jsbml.ext.qual.InputTransitionEffect

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

valueOf(String) - Static method in enum org.sbml.jsbml.ext.qual.OutputTransitionEffect

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

valueOf(String) - Static method in enum org.sbml.jsbml.ext.qual.QualList

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

valueOf(String) - Static method in enum org.sbml.jsbml.ext.qual.Sign

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

values() - Static method in enum org.sbml.jsbml.ext.qual.InputTransitionEffect

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

values() - Static method in enum org.sbml.jsbml.ext.qual.OutputTransitionEffect

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

values() - Static method in enum org.sbml.jsbml.ext.qual.QualList

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

values() - Static method in enum org.sbml.jsbml.ext.qual.Sign

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

W

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

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.qual.FunctionTerm

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.qual.Input

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.qual.Output

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.qual.QualitativeSpecies

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.qual.QualModelPlugin

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.qual.Transition

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