A B C D G H I M N P R S T V 

A

addHeader(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
 
ALGEBRAIC_RULE - Static variable in class de.unirostock.sems.bives.sbml.parser.SBMLRule
 
annotatePatch() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffInterpreter
 
ASSIGNMENT_RULE - Static variable in class de.unirostock.sems.bives.sbml.parser.SBMLRule
 

B

BivesSBMLParseException - Exception in de.unirostock.sems.bives.sbml.exception
 
BivesSBMLParseException(String) - Constructor for exception de.unirostock.sems.bives.sbml.exception.BivesSBMLParseException
 

C

canBeReactantOrProduct() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
 
canHaveAssignmentRule() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
 
connect() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLConnector
 
connect() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLConnectorPreprocessor
 

D

de.unirostock.sems.bives.sbml.algorithm - package de.unirostock.sems.bives.sbml.algorithm
 
de.unirostock.sems.bives.sbml.api - package de.unirostock.sems.bives.sbml.api
 
de.unirostock.sems.bives.sbml.exception - package de.unirostock.sems.bives.sbml.exception
 
de.unirostock.sems.bives.sbml.parser - package de.unirostock.sems.bives.sbml.parser
 
doc1 - Variable in class de.unirostock.sems.bives.sbml.api.SBMLDiff
 
doc1 - Variable in class de.unirostock.sems.bives.sbml.api.SBMLSingle
 
doc2 - Variable in class de.unirostock.sems.bives.sbml.api.SBMLDiff
 
documentNode - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject
 

G

generateHTMLReport() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
 
getAnnotation() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSBase
 
getCompartment(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getCompartment() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
 
getCompartment() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
 
getCompartments() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getCompartmentType(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getCompartmentTypes() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getConstraints() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getCRNDotGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff
 
getCRNDotGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle
 
getCRNGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff
 
getCRNGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle
 
getCRNGraphML() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff
 
getCRNGraphML() - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle
 
getCRNJsonGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff
 
getCRNJsonGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle
 
getDocumentNode() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject
 
getEvents() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getFromNode(TreeNode) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getFunctionDefinitions() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getHierarchyDotGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff
 
getHierarchyDotGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle
 
getHierarchyGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff
 
getHierarchyGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle
 
getHierarchyGraphML() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff
 
getHierarchyGraphML() - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle
 
getHierarchyJsonGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff
 
getHierarchyJsonGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle
 
getHTMLReport() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff
 
getID() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject
 
getID() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getInitialAmount() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
Returns the initial amount of this species or null if not defined.
getInitialAssignments() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getInitialConcentration() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
Returns the initial concentration of this species or null if not defined.
getKineticLaw() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
 
getLevel() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDocument
 
getListOfModifiersNode() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
 
getListOfProductsNode() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
 
getListOfReactantsNode() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
 
getMarkDownReport() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff
 
getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLConstraint
 
getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventAssignment
 
getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventDelay
 
getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventPriority
 
getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventTrigger
 
getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLFunctionDefinition
 
getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLInitialAssignment
 
getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLKineticLaw
 
getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLRule
 
getMessage() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLConstraint
 
getMetaId() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSBase
 
getModel() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDocument
 
getModel() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject
 
getModelID() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLValidator
 
getModifiers() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
 
getName() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject
 
getName() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getNameAndId() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject
Gets the name (if defined) and the id as NAME (ID)
getNameOrId() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject
Gets the name (if defined) or the id (if name undefined).
getNotes() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSBase
 
getParameter(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getParameters() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getProducts() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
 
getReactants() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
 
getReaction(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getReactions() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getReport() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffInterpreter
 
getReport(Typesetting) - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff
 
getReStructuredTextReport() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff
 
getRules() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getRuleType() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLRule
 
getSBOTerm() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSBase
 
getSidName(SBMLSBase) - Static method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getSpecies(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getSpecies() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getSpecies() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference
 
getSpeciesReference(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getSpeciesType(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getSpeciesTypes() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getSymbol() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLInitialAssignment
 
getTreeDocument() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDocument
 
getUnitDefinition(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getUnitDefinitions() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
getValue() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLParameter
 
getVariable() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLAssignmentRule
 
getVariable() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventAssignment
 
getVariable() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLRateRule
 
getVersion() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDocument
 
graphProducer - Variable in class de.unirostock.sems.bives.sbml.api.SBMLDiff
 
graphProducer - Variable in class de.unirostock.sems.bives.sbml.api.SBMLSingle
 

H

hasBoundaryCondition() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
 
hasOnlySubstanceUnits() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
 

I

id - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject
 
id - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference
 
init(TreeDocument, TreeDocument) - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLConnector
 
init(TreeDocument, TreeDocument) - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLConnectorPreprocessor
 
interprete() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffInterpreter
 
interpreter - Variable in class de.unirostock.sems.bives.sbml.api.SBMLDiff
 
isBaseUnit() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLUnitDefinition
 
isConstant() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLParameter
 
isConstant() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
 
isFast() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
 
isReversible() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
 

M

mapNode(DocumentNode, SBMLSBase) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
mapTrees() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff
 
markup(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLParameter
 
markup(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLUnit
 
markup(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLUnitDefinition
 
math - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLRule
 
modifyCompartments(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
 
modifyCompartmentTypes(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
 
modifyContraints(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
 
modifyEvents(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
 
modifyFunctions(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
 
modifyInitialAssignments(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
 
modifyParameter(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
 
modifyReaction(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
 
modifyRules(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
 
modifySpecies(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
 
modifySpeciesTypes(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
 
modifyUnits(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
 

N

name - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject
 
name - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference
 

P

processCrnA() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLGraphProducer
 
processCrnB() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLGraphProducer
 
produceCRN() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLGraphProducer
 
produceHierachyGraph() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLGraphProducer
 

R

RATE_RULE - Static variable in class de.unirostock.sems.bives.sbml.parser.SBMLRule
 
registerSpeciesReference(String, SBMLSimpleSpeciesReference) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
report(MarkupDocument, MarkupElement, boolean) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
 
report() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference
 
report() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesReference
 
reportAnnotation() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSBase
 
reportDelete(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLAlgebraicRule
 
reportDelete(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLAssignmentRule
 
reportDelete(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLCompartment
 
reportDelete(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLCompartmentType
 
reportDelete(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLConstraint
 
reportDelete(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEvent
 
reportDelete(MarkupElement, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventAssignment
 
reportDelete(MarkupElement, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventDelay
 
reportDelete(MarkupElement, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventPriority
 
reportDelete(MarkupElement, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventTrigger
 
reportDelete(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLFunctionDefinition
 
reportDelete(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLInitialAssignment
 
reportDelete(MarkupElement, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLKineticLaw
 
reportDelete(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLParameter
 
reportDelete(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLRateRule
 
reportDelete(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
 
reportDelete(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference
 
reportDelete(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
 
reportDelete(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesReference
 
reportDelete(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesType
 
reportDelete(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLUnitDefinition
 
reportInsert(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLAlgebraicRule
 
reportInsert(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLAssignmentRule
 
reportInsert(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLCompartment
 
reportInsert(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLCompartmentType
 
reportInsert(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLConstraint
 
reportInsert(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEvent
 
reportInsert(MarkupElement, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventAssignment
 
reportInsert(MarkupElement, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventDelay
 
reportInsert(MarkupElement, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventPriority
 
reportInsert(MarkupElement, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventTrigger
 
reportInsert(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLFunctionDefinition
 
reportInsert(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLInitialAssignment
 
reportInsert(MarkupElement, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLKineticLaw
 
reportInsert(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLParameter
 
reportInsert(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLRateRule
 
reportInsert(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
 
reportInsert(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference
 
reportInsert(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
 
reportInsert(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesReference
 
reportInsert(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesType
 
reportInsert(MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLUnitDefinition
 
reportMofification(ClearConnectionManager, DiffReporter, DiffReporter, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLAlgebraicRule
 
reportMofification(ClearConnectionManager, DiffReporter, DiffReporter, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLAssignmentRule
 
reportMofification(ClearConnectionManager, DiffReporter, DiffReporter, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLCompartment
 
reportMofification(ClearConnectionManager, DiffReporter, DiffReporter, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLCompartmentType
 
reportMofification(ClearConnectionManager, DiffReporter, DiffReporter, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLConstraint
 
reportMofification(ClearConnectionManager, DiffReporter, DiffReporter, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEvent
 
reportMofification(ClearConnectionManager, SBMLEventAssignment, SBMLEventAssignment, MarkupElement, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventAssignment
 
reportMofification(ClearConnectionManager, SBMLEventDelay, SBMLEventDelay, MarkupElement, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventDelay
 
reportMofification(ClearConnectionManager, SBMLEventPriority, SBMLEventPriority, MarkupElement, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventPriority
 
reportMofification(ClearConnectionManager, SBMLEventTrigger, SBMLEventTrigger, MarkupElement, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventTrigger
 
reportMofification(ClearConnectionManager, DiffReporter, DiffReporter, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLFunctionDefinition
 
reportMofification(ClearConnectionManager, DiffReporter, DiffReporter, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLInitialAssignment
 
reportMofification(ClearConnectionManager, SBMLKineticLaw, SBMLKineticLaw, MarkupElement, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLKineticLaw
 
reportMofification(ClearConnectionManager, DiffReporter, DiffReporter, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLParameter
 
reportMofification(ClearConnectionManager, DiffReporter, DiffReporter, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLRateRule
 
reportMofification(ClearConnectionManager, DiffReporter, DiffReporter, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
 
reportMofification(ClearConnectionManager, SBMLSimpleSpeciesReference, SBMLSimpleSpeciesReference, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference
 
reportMofification(ClearConnectionManager, DiffReporter, DiffReporter, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
 
reportMofification(ClearConnectionManager, SBMLSpeciesReference, SBMLSpeciesReference, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesReference
 
reportMofification(ClearConnectionManager, DiffReporter, DiffReporter, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesType
 
reportMofification(ClearConnectionManager, DiffReporter, DiffReporter, MarkupDocument) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLUnitDefinition
 
reportNotes() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSBase
 
resolvVariable(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventAssignment
 
resolvVariable(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLRule
 

S

SBMLAlgebraicRule - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLAlgebraicRule(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLAlgebraicRule
 
SBMLAnotation - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLAnotation(DocumentNode) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLAnotation
 
SBMLAssignmentRule - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLAssignmentRule(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLAssignmentRule
 
SBMLCompartment - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLCompartment(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLCompartment
 
SBMLCompartmentType - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLCompartmentType(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLCompartmentType
 
SBMLConnector - Class in de.unirostock.sems.bives.sbml.algorithm
 
SBMLConnector(SBMLDocument, SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLConnector
 
SBMLConnector(Connector) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLConnector
 
SBMLConnectorPreprocessor - Class in de.unirostock.sems.bives.sbml.algorithm
 
SBMLConnectorPreprocessor(SBMLDocument, SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLConnectorPreprocessor
 
SBMLConnectorPreprocessor(Connector) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLConnectorPreprocessor
 
SBMLConstraint - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLConstraint(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLConstraint
 
SBMLDiff - Class in de.unirostock.sems.bives.sbml.api
 
SBMLDiff(File, File) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLDiff
 
SBMLDiff(String, String) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLDiff
 
SBMLDiff(SBMLDocument, SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLDiff
 
SBMLDiffInterpreter - Class in de.unirostock.sems.bives.sbml.algorithm
 
SBMLDiffInterpreter(ClearConnectionManager, SBMLDocument, SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffInterpreter
 
SBMLDiffReport - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLDiffReport() - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
 
SBMLDocument - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLDocument(TreeDocument) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLDocument
 
SBMLEvent - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLEvent(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLEvent
 
SBMLEventAssignment - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLEventAssignment(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLEventAssignment
 
SBMLEventDelay - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLEventDelay(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLEventDelay
 
SBMLEventPriority - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLEventPriority(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLEventPriority
 
SBMLEventTrigger - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLEventTrigger(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLEventTrigger
 
SBMLFunctionDefinition - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLFunctionDefinition(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLFunctionDefinition
 
SBMLGenericIdNameObject - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLGenericIdNameObject(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject
 
SBMLGenericObject - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLGenericObject(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject
 
SBMLGraphProducer - Class in de.unirostock.sems.bives.sbml.algorithm
 
SBMLGraphProducer(ClearConnectionManager, SBMLDocument, SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLGraphProducer
 
SBMLGraphProducer(SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLGraphProducer
 
SBMLInitialAssignment - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLInitialAssignment(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLInitialAssignment
 
SBMLKineticLaw - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLKineticLaw(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLKineticLaw
 
SBMLListOf - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLListOf(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLListOf
 
sbmlModel - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject
 
SBMLModel - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLModel(DocumentNode, SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLModel
 
SBMLParameter - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLParameter(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLParameter
 
SBMLRateRule - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLRateRule(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLRateRule
 
SBMLReaction - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLReaction(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLReaction
 
SBMLRule - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLRule(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLRule
 
SBMLSBase - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLSBase(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLSBase
 
SBMLSimpleSpeciesReference - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLSimpleSpeciesReference(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference
 
SBMLSingle - Class in de.unirostock.sems.bives.sbml.api
 
SBMLSingle(File) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLSingle
 
SBMLSingle(String) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLSingle
 
SBMLSingle(SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLSingle
 
SBMLSpecies - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLSpecies(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
 
SBMLSpeciesReference - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLSpeciesReference(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesReference
 
SBMLSpeciesType - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLSpeciesType(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesType
 
SBMLUnit - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLUnit(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLUnit
Instantiates a new SBML unit derived from a base unit.
SBMLUnitDefinition - Class in de.unirostock.sems.bives.sbml.parser
 
SBMLUnitDefinition(String, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLUnitDefinition
Instantiates a new SBML base unit.
SBMLUnitDefinition(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLUnitDefinition
 
SBMLValidator - Class in de.unirostock.sems.bives.sbml.algorithm
TODO
SBMLValidator() - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLValidator
 
species - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference
 

T

type - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLRule
 

V

validate(TreeDocument) - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLValidator
 
validate(String) - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLValidator
 
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Copyright © 2014 SEMS project @ University of Rostock. All rights reserved.