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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.