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A

addChangedMath(ChangedMath) - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin
Adds a new ChangedMath to the listOfChangedMaths.

C

changedBy - Static variable in class org.sbml.jsbml.ext.req.ReqConstants
 
ChangedMath - Class in org.sbml.jsbml.ext.req
Declares which package has modified the value or the mathematical meaning of an SBase and in which way.
ChangedMath() - Constructor for class org.sbml.jsbml.ext.req.ChangedMath
Creates an ChangedMath instance
ChangedMath(String) - Constructor for class org.sbml.jsbml.ext.req.ChangedMath
Creates a ChangedMath instance with an id.
ChangedMath(int, int) - Constructor for class org.sbml.jsbml.ext.req.ChangedMath
Creates a ChangedMath instance with a level and version.
ChangedMath(String, int, int) - Constructor for class org.sbml.jsbml.ext.req.ChangedMath
Creates a ChangedMath instance with an id, level, and version.
ChangedMath(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.req.ChangedMath
Creates a ChangedMath instance with an id, name, level, and version.
ChangedMath(ChangedMath) - Constructor for class org.sbml.jsbml.ext.req.ChangedMath
Clone constructor
changedMath - Static variable in class org.sbml.jsbml.ext.req.ReqConstants
 
clone() - Method in class org.sbml.jsbml.ext.req.ChangedMath
clones this class
clone() - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin
clones this class
createChangedMath() - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin
Creates a new ChangedMath element and adds it to the ListOfMathChangeds list
createChangedMath(String) - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin
Creates a new ChangedMath element and adds it to the ListOfMathChangeds list
createPluginFor(SBase) - Method in class org.sbml.jsbml.xml.parsers.ReqParser
 
createPluginFor(ASTNode) - Method in class org.sbml.jsbml.xml.parsers.ReqParser
 

G

getAllowsChildren() - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin
 
getChangedBy() - Method in class org.sbml.jsbml.ext.req.ChangedMath
Returns the value of changedBy
getChildAt(int) - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin
 
getChildCount() - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin
 
getListOfChangedMaths() - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin
Returns the listOfChangedMaths.
getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.ReqParser
 
getNamespaceFor(int, int, int) - Method in class org.sbml.jsbml.xml.parsers.ReqParser
 
getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.ReqParser
 
getNamespaceURI(int, int, int) - Static method in class org.sbml.jsbml.ext.req.ReqConstants
Gets the namespace for this package that correspond to the given SBML level, version and the package version.
getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.ReqParser
 
getPackageName() - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin
 
getPackageName() - Method in class org.sbml.jsbml.xml.parsers.ReqParser
 
getPackageNamespaces() - Method in class org.sbml.jsbml.xml.parsers.ReqParser
 
getPrefix() - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin
 
getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.ReqParser
 
getURI() - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin
 
getViableWithoutChange() - Method in class org.sbml.jsbml.ext.req.ChangedMath
Returns the value of viableWithoutChange

I

initDefaults() - Method in class org.sbml.jsbml.ext.req.ChangedMath
Initializes the default values using the namespace.
initDefaults() - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin
Initializes the default values using the namespace.
isIdMandatory() - Method in class org.sbml.jsbml.ext.req.ChangedMath
 
isRequired() - Method in class org.sbml.jsbml.xml.parsers.ReqParser
 
isSetChangedBy() - Method in class org.sbml.jsbml.ext.req.ChangedMath
Returns whether changedBy is set
isSetListOfChangedMaths() - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin
Returns true, if listOfChangedMaths contains at least one element.
isSetViableWithoutChange() - Method in class org.sbml.jsbml.ext.req.ChangedMath
Returns whether viableWithoutChange is set
isViableWithoutChange() - Method in class org.sbml.jsbml.ext.req.ChangedMath
Returns the value of viableWithoutChange

L

listOfChangedMaths - Static variable in class org.sbml.jsbml.ext.req.ReqConstants
 

M

MIN_SBML_LEVEL - Static variable in class org.sbml.jsbml.ext.req.ReqConstants
 
MIN_SBML_VERSION - Static variable in class org.sbml.jsbml.ext.req.ReqConstants
 

N

namespaces - Static variable in class org.sbml.jsbml.ext.req.ReqConstants
 
namespaceURI - Static variable in class org.sbml.jsbml.ext.req.ReqConstants
The latest namespace URI of this parser, this value can change between releases.
namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.req.ReqConstants
The namespace URI of this parser for SBML level 3, version 1 and package version 1.

O

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

P

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

R

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.req.ChangedMath
 
readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin
 
removeChangedMath(ChangedMath) - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin
Removes an element from the listOfChangedMaths.
removeChangedMath(int) - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin
Removes an element from the listOfChangedMaths at the given index.
removeChangedMath(String) - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin
Removes an element from the listOfChangedMaths with the given id.
ReqConstants - Class in org.sbml.jsbml.ext.req
Contains some constants related to the req package.
ReqConstants() - Constructor for class org.sbml.jsbml.ext.req.ReqConstants
 
ReqParser - Class in org.sbml.jsbml.xml.parsers
A ReqParser is used to parse the req extension package elements and attributes.
ReqParser() - Constructor for class org.sbml.jsbml.xml.parsers.ReqParser
 
ReqSBasePlugin - Class in org.sbml.jsbml.ext.req
Represents the extended SBase as define in the req package.
ReqSBasePlugin() - Constructor for class org.sbml.jsbml.ext.req.ReqSBasePlugin
Creates an ReqSBasePlugin instance
ReqSBasePlugin(SBase) - Constructor for class org.sbml.jsbml.ext.req.ReqSBasePlugin
Creates a ReqSBasePlugin instance associated with the given SBase.
ReqSBasePlugin(ReqSBasePlugin) - Constructor for class org.sbml.jsbml.ext.req.ReqSBasePlugin
Clone constructor

S

setChangedBy(String) - Method in class org.sbml.jsbml.ext.req.ChangedMath
Sets the value of changedBy
setListOfChangedMaths(ListOf<ChangedMath>) - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin
Sets the given ListOf<ChangedMath>.
setViableWithoutChange(boolean) - Method in class org.sbml.jsbml.ext.req.ChangedMath
Sets the value of viableWithoutChange
shortLabel - Static variable in class org.sbml.jsbml.ext.req.ReqConstants
 

U

unsetChangedBy() - Method in class org.sbml.jsbml.ext.req.ChangedMath
Unsets the variable changedBy
unsetListOfChangedMaths() - Method in class org.sbml.jsbml.ext.req.ReqSBasePlugin
Removes all of the elements from this list of ChangedMaths.
unsetViableWithoutChange() - Method in class org.sbml.jsbml.ext.req.ChangedMath
Unsets the variable viableWithoutChange

V

viableWithoutChange - Static variable in class org.sbml.jsbml.ext.req.ReqConstants
 

W

writeElement(SBMLObjectForXML, Object) - Method in class org.sbml.jsbml.xml.parsers.ReqParser
 
writeXMLAttributes() - Method in class org.sbml.jsbml.ext.req.ChangedMath
 
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