A B C D E F G H I K M N O P R S T U V
All Classes All Packages
All Classes All Packages
All Classes All Packages
A
- addHeader(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
-
Adds the header.
- addOntologyLink(String, String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSBase
-
Adds an link into an ontology.
- ALGEBRAIC_RULE - Static variable in class de.unirostock.sems.bives.sbml.parser.SBMLRule
-
The flag ALGEBRAIC_RULE.
- annotateDeletion(TreeNode, Element, ChangeFactory) - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
- annotateInsertion(TreeNode, Element, ChangeFactory) - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
- annotateMove(TreeNode, TreeNode, Element, ChangeFactory, boolean) - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
- annotatePatch(String, ChangeFactory) - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
- annotateUpdateAttribute(TreeNode, TreeNode, String, Element, ChangeFactory) - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
- annotateUpdateText(TextNode, TextNode, Element, ChangeFactory) - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
- annotationPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
-
The XPATH to a machine readable annotation.
- ASSIGNMENT_RULE - Static variable in class de.unirostock.sems.bives.sbml.parser.SBMLRule
-
The flag ASSIGNMENT_RULE.
B
- BASE_UNITS - Static variable in class de.unirostock.sems.bives.sbml.parser.SBMLUnit
-
those are BASE_UNITS.
- BivesSBMLParseException - Exception in de.unirostock.sems.bives.sbml.exception
-
The Class BivesSBMLParseException.
- BivesSBMLParseException(String) - Constructor for exception de.unirostock.sems.bives.sbml.exception.BivesSBMLParseException
-
Instantiates a new BiVeS exception signalling an error while parsing an SBML document.
C
- canBeReactantOrProduct() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
-
Can this species take part in a reaction as a reactant or product?
- canHaveAssignmentRule() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
-
Is this species allowed to have an assignment rule.
- connect() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLConnector
- connect() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLConnectorPreprocessor
- contributorPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
-
The XPATH to a machine readable annotation.
- creationDatePath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
-
The XPATH to a machine readable annotation.
- creatorPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
-
The XPATH to a machine readable annotation.
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
- descriptionPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
-
The XPATH to a human readable annotation.
- doc - Variable in class de.unirostock.sems.bives.sbml.api.SBMLSingle
-
The doc.
- doc1 - Variable in class de.unirostock.sems.bives.sbml.api.SBMLDiff
-
The original document.
- doc2 - Variable in class de.unirostock.sems.bives.sbml.api.SBMLDiff
-
The modified document.
- documentNode - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject
-
The document node.
E
- eventPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
-
The XPATH to an event definition.
- extractOntologyLinks(DocumentNode, SBMLModel) - Static method in class de.unirostock.sems.bives.sbml.parser.SBMLMeta
-
Extract ontology links from an annotation element.
F
- flagMetaModifcations(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSBase
-
Flags occuring modifcations of the meta information (notes, annotations) to the given MarkupElement.
- flatten() - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle
- flatten() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDocument
- functionPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
-
The XPATH to a function definition.
G
- generateHTMLReport() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
-
Generate html report.
- getAnnotation() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSBase
-
Gets the annotation.
- getCompartment() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
-
Gets the compartment.
- getCompartment() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
-
Gets the compartment that hosts this species.
- getCompartment(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets the compartment.
- getCompartments() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets the compartments.
- getCompartmentType(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets the compartment type.
- getCompartmentTypes() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets the compartment types.
- getConstraints() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets the constraints.
- getDocument() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLValidator
- getDocument() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets the SBML document.
- getDocumentNode() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject
-
Gets the document node.
- getEvents() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets the events.
- getFromMetaId(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets an entity given its meta id.
- getFromNode(TreeNode) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets an entity given its tree node.
- getFunctionDefinitions() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets the function definitions.
- 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
-
Gets the id.
- getID() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets the id of the model.
- 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
-
Gets the initial assignments.
- 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
-
Gets the kinetic law.
- getLevel() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDocument
-
Gets the level.
- getListOfModifiersNode() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
-
Gets the list of modifiers node.
- getListOfProductsNode() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
-
Gets the list of products node.
- getListOfReactantsNode() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
-
Gets the list of reactants node.
- getMarkDownReport() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff
- getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLConstraint
-
Gets the math.
- getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventAssignment
-
Gets the math.
- getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventDelay
-
Gets the math.
- getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventPriority
-
Gets the math.
- getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventTrigger
-
Gets the math.
- getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLFunctionDefinition
-
Gets the math.
- getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLInitialAssignment
-
Gets the math.
- getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLKineticLaw
-
Gets the math.
- getMath() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLRule
-
Gets the math.
- getMessage() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLConstraint
-
Gets the message.
- getMetaId() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSBase
-
Gets the meta id.
- getModel() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDocument
-
Gets the model.
- getModel() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject
-
Gets the model.
- getModifiers() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
-
Gets the modifiers.
- getName() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject
-
Gets the name.
- getName() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets the name of the model.
- 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
-
Gets the notes.
- getOntologyLinks() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSBase
-
Gets the links that point to an ontology.
- getOntologyMappings() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets the ontology mappings which group entities by there pointers into ontologies.
- getParameter(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets a specific parameter.
- getParameters() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets the parameters.
- getProducts() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
-
Gets the products.
- getReactants() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
-
Gets the reactants.
- getReaction(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets a specific reaction.
- getReactions() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets the reactions.
- getReactionsDotGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff
- getReactionsDotGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle
- getReactionsGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff
- getReactionsGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle
- getReactionsGraphML() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff
- getReactionsGraphML() - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle
- getReactionsJsonGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff
- getReactionsJsonGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLSingle
- getReactionsSbgnJsonGraph() - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff
- getReport() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffInterpreter
-
Gets the produced report.
- 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
-
Gets the rules.
- getRuleType() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLRule
-
Gets the rule type.
- getSBOTerm() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSBase
-
Gets the SBO term.
- getSidName(SBMLSBase) - Static method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets the SId.
- getSpecies() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets the species.
- getSpecies() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference
-
Gets the corresponding species.
- getSpecies(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets the species.
- getSpeciesReference(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets the species reference.
- getSpeciesType(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets the species type.
- getSpeciesTypes() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets the species types.
- getSymbol() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLInitialAssignment
-
Gets the symbol.
- getUnitDefinition(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets the unit definition.
- getUnitDefinitions() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Gets the unit definitions.
- getValue() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLParameter
-
Gets the value.
- getVariable() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLAssignmentRule
-
Gets the corresponding variable.
- getVariable() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventAssignment
-
Gets the variable of interest.
- getVariable() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLRateRule
-
Gets the variable of interest.
- getVersion() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDocument
-
Gets the version.
- graphProducer - Variable in class de.unirostock.sems.bives.sbml.api.SBMLDiff
-
The graph producer.
- graphProducer - Variable in class de.unirostock.sems.bives.sbml.api.SBMLSingle
-
The graph producer.
H
- hasBoundaryCondition() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
-
Checks for a boundary condition.
- hasOnlySubstanceUnits() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
-
Checks if this species has only substance units.
I
- id - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject
-
The id.
- id - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference
-
The id of this species reference.
- init() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLConnector
- init() - 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
-
The interpreter.
- isBaseUnit() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLUnitDefinition
-
Checks if this is a base unit.
- isConstant() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLParameter
-
Checks if the parameter is constant.
- isConstant() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
-
Checks if this species is constant.
- isFast() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
-
Checks if this reaction is fast.
- isReversible() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
-
Checks if this reaction is reversible.
K
- kineticsPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
-
The XPATH to a kinetic law.
M
- mapNode(DocumentNode, SBMLSBase) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Map node model node to its entity.
- mapTrees(boolean, boolean, boolean) - Method in class de.unirostock.sems.bives.sbml.api.SBMLDiff
- markup() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLParameter
- markup() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLUnit
- markup() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLUnitDefinition
- math - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLRule
-
The math.
- modificationDatePath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
-
The XPATH to a machine readable annotation.
- modifyCompartments(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
-
Modify compartments.
- modifyCompartmentTypes(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
-
Modify compartment types.
- modifyContraints(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
-
Modify contraints.
- modifyEvents(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
-
Modify events.
- modifyFunctions(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
-
Modify functions.
- modifyInitialAssignments(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
-
Modify initial assignments.
- modifyParameter(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
-
Modify parameter.
- modifyReaction(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
-
Modify reaction.
- modifyRules(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
-
Modify rules.
- modifySpecies(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
-
Modify species.
- modifySpeciesTypes(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
-
Modify species types.
- modifyUnits(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
-
Modify units.
N
- name - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject
-
The name.
- name - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference
-
The name.
O
- ontologyLink - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
P
- parameterPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
-
The XPATH to a parameter.
- PREDEFINED_UNITS - Static variable in class de.unirostock.sems.bives.sbml.parser.SBMLUnit
-
those are predefined units.
- processRnA() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLGraphProducer
-
Process Reaction Network of the original document.
- processRnB() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLGraphProducer
-
Process Reaction Network of the modified document.
- produceHierarchyGraph() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLGraphProducer
- produceReactionNetwork() - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLGraphProducer
R
- RATE_RULE - Static variable in class de.unirostock.sems.bives.sbml.parser.SBMLRule
-
The flag RATE_RULE.
- reactionsModifierSpeciesReference - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
- reactionsPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
-
The XPATH to a reaction.
- reactionsSpeciesReference - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
- registerSpeciesReference(String, SBMLSimpleSpeciesReference) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Registers a species reference.
- report() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference
-
Typeset this reference.
- report() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesReference
- report(MarkupElement, boolean) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
-
Typeset this reaction.
- reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLAlgebraicRule
- reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLAssignmentRule
- reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLCompartment
- reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLCompartmentType
- reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLConstraint
- reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEvent
- reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLFunctionDefinition
- reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLInitialAssignment
- reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLParameter
- reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLRateRule
- reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
- reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference
-
Report a delete.
- reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
- reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesReference
- reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesType
- reportDelete() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLUnitDefinition
- reportDelete(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventAssignment
-
Report delete.
- reportDelete(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventDelay
-
Report delete.
- reportDelete(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventPriority
-
Report delete.
- reportDelete(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventTrigger
-
Report delete.
- reportDelete(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLKineticLaw
-
Report delete.
- reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLAlgebraicRule
- reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLAssignmentRule
- reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLCompartment
- reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLCompartmentType
- reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLConstraint
- reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEvent
- reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLFunctionDefinition
- reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLInitialAssignment
- reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLParameter
- reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLRateRule
- reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
- reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference
-
Report an insert.
- reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
- reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesReference
- reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesType
- reportInsert() - Method in class de.unirostock.sems.bives.sbml.parser.SBMLUnitDefinition
- reportInsert(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventAssignment
-
Report insert.
- reportInsert(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventDelay
-
Report insert.
- reportInsert(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventPriority
-
Report insert.
- reportInsert(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventTrigger
-
Report insert.
- reportInsert(MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLKineticLaw
-
Report insert.
- reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLAlgebraicRule
- reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLAssignmentRule
- reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLCompartment
- reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLCompartmentType
- reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLConstraint
- reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEvent
- reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLFunctionDefinition
- reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLInitialAssignment
- reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLParameter
- reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLRateRule
- reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLReaction
- reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
- reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesType
- reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLUnitDefinition
- reportModification(SimpleConnectionManager, SBMLEventAssignment, SBMLEventAssignment, MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventAssignment
-
Report modification on this entity.
- reportModification(SimpleConnectionManager, SBMLEventDelay, SBMLEventDelay, MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventDelay
-
Report modifications on the entity.
- reportModification(SimpleConnectionManager, SBMLEventPriority, SBMLEventPriority, MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventPriority
-
Report modifications on the entity.
- reportModification(SimpleConnectionManager, SBMLEventTrigger, SBMLEventTrigger, MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventTrigger
-
Report modifications.
- reportModification(SimpleConnectionManager, SBMLKineticLaw, SBMLKineticLaw, MarkupElement) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLKineticLaw
-
Report modification of the entities.
- reportModification(SimpleConnectionManager, SBMLSimpleSpeciesReference, SBMLSimpleSpeciesReference) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference
-
Report modification between two versions of this species reference.
- reportModification(SimpleConnectionManager, SBMLSpeciesReference, SBMLSpeciesReference) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesReference
-
Report the modifications of this species reference.
- resolveSymbol(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Resolve certain symbol.
- resolveSymbole(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Deprecated.as of version 1.3.6, replaced by
SBMLModel.resolveSymbol(String)
- resolveVariable(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLEventAssignment
-
Resolve variable.
- resolveVariable(String) - Method in class de.unirostock.sems.bives.sbml.parser.SBMLRule
-
Resolves a variable.
- rulePath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
-
The XPATH to a rule.
S
- SBMLAlgebraicRule - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLAlgebraicRule used to express equations that are neither assignments of model variables nor rates of change.
- SBMLAlgebraicRule(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLAlgebraicRule
-
Instantiates a new SBML algebraic rule.
- SBMLAnotation - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLAnotation ,a container for optional software-generated content not meant to be shown to humans.
- SBMLAnotation(DocumentNode) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLAnotation
-
Instantiates a new SBML anotation.
- SBMLAssignmentRule - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLAssignmentRule used to express equations that set the values of variables.
- SBMLAssignmentRule(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLAssignmentRule
-
Instantiates a new SBML assignment rule.
- SBMLCompartment - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLCompartment, a bounded space in which species are located.
- SBMLCompartment(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLCompartment
-
Instantiates a new SBML compartment.
- SBMLCompartmentType - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLCompartmentType, a grouping construct used to establish a relationship between multiple SBMLCompartments.
- SBMLCompartmentType(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLCompartmentType
-
Instantiates a new SBML compartment type.
- SBMLConnector - Class in de.unirostock.sems.bives.sbml.algorithm
-
The Class SBMLConnector to connect SBML documents.
- SBMLConnector(Connector) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLConnector
-
Instantiates a new SBML connector.
- SBMLConnector(Connector, boolean, boolean, boolean) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLConnector
-
Instantiates a new SBML connector.
- SBMLConnector(SBMLDocument, SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLConnector
-
Instantiates a new SBML connector.
- SBMLConnector(SBMLDocument, SBMLDocument, boolean, boolean, boolean) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLConnector
-
Instantiates a new SBML connector.
- SBMLConnectorPreprocessor - Class in de.unirostock.sems.bives.sbml.algorithm
-
The Class SBMLConnectorPreprocessor to pre-compute a mapping.
- SBMLConnectorPreprocessor(Connector) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLConnectorPreprocessor
-
Instantiates a new sBML connector preprocessor.
- SBMLConnectorPreprocessor(Connector, boolean, boolean, boolean) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLConnectorPreprocessor
-
Instantiates a new sBML connector preprocessor.
- SBMLConnectorPreprocessor(SBMLDocument, SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLConnectorPreprocessor
-
Instantiates a new sBML connector preprocessor.
- SBMLConnectorPreprocessor(SBMLDocument, SBMLDocument, boolean, boolean, boolean) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLConnectorPreprocessor
-
Instantiates a new sBML connector preprocessor.
- SBMLConstraint - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLConstraint, a mechanism for stating the assumptions under which a model is designed to operate.
- SBMLConstraint(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLConstraint
-
Instantiates a new SBML constraint.
- SBMLDiff - Class in de.unirostock.sems.bives.sbml.api
-
The Class SBMLDiff to compare two SBML models.
- SBMLDiff(SBMLDocument, SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLDiff
-
Instantiates a new SBML differ.
- SBMLDiff(SBMLDocument, SBMLDocument, DiffAnnotator) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLDiff
-
Instantiates a new SBML differ.
- SBMLDiff(TreeDocument, TreeDocument) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLDiff
-
Instantiates a new SBML differ.
- SBMLDiff(TreeDocument, TreeDocument, DiffAnnotator) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLDiff
-
Instantiates a new SBML differ.
- SBMLDiff(File, File) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLDiff
-
Instantiates a new SBML differ.
- SBMLDiff(File, File, DiffAnnotator) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLDiff
-
Instantiates a new SBML differ.
- SBMLDiff(String, String) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLDiff
-
Instantiates a new SBML differ.
- SBMLDiff(String, String, DiffAnnotator) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLDiff
-
Instantiates a new SBML differ.
- SBMLDiffAnnotator - Class in de.unirostock.sems.bives.sbml.algorithm
- SBMLDiffAnnotator() - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
- SBMLDiffInterpreter - Class in de.unirostock.sems.bives.sbml.algorithm
-
The Class SBMLDiffInterpreter to interpret a mapping of SBML models.
- SBMLDiffInterpreter(SimpleConnectionManager, SBMLDocument, SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffInterpreter
-
Instantiates a new SBML diff interpreter.
- SBMLDiffReport - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLDiffReport creates a report about the differences between two versions of an SBML document.
- SBMLDiffReport() - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLDiffReport
-
Instantiates a new sBML diff report.
- SBMLDocument - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLDocument representing a document holding an SBMLModel.
- SBMLDocument(TreeDocument) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLDocument
-
Instantiates a new SBML document.
- SBMLEvent - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLEvent describes the time and form of instantaneous, discontinuous state changes in the model.
- SBMLEvent(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLEvent
-
Instantiates a new sBML event.
- SBMLEventAssignment - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLEventAssignment.
- SBMLEventAssignment(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLEventAssignment
-
Instantiates a new SBML event assignment.
- SBMLEventDelay - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLEventDelay.
- SBMLEventDelay(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLEventDelay
-
Instantiates a new SBML event delay.
- SBMLEventPriority - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLEventPriority.
- SBMLEventPriority(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLEventPriority
-
Instantiates a new SBML event priority.
- SBMLEventTrigger - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLEventTrigger.
- SBMLEventTrigger(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLEventTrigger
-
Instantiates a new SBML event trigger.
- SBMLFunctionDefinition - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLFunctionDefinition associates an identifier with a function definition.
- SBMLFunctionDefinition(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLFunctionDefinition
-
Instantiates a new SBML function definition.
- SBMLGenericIdNameObject - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLGenericIdNameObject representing a generic object that has an id and a name.
- SBMLGenericIdNameObject(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLGenericIdNameObject
-
Instantiates a new SBML generic id-name-object.
- SBMLGenericObject - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLGenericObject representing a generic SBML object.
- SBMLGenericObject(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject
-
Instantiates a new generic SBML object.
- SBMLGraphProducer - Class in de.unirostock.sems.bives.sbml.algorithm
-
The Class SBMLGraphProducer to create the graphs.
- SBMLGraphProducer(SimpleConnectionManager, SBMLDocument, SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLGraphProducer
-
Instantiates a new SBML graph producer for difference graphs.
- SBMLGraphProducer(SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLGraphProducer
-
Instantiates a new SBML graph producer for single document graphs.
- SBMLInitialAssignment - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLInitialAssignment assigning initial values to entities in a model.
- SBMLInitialAssignment(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLInitialAssignment
-
Instantiates a new SBML initial assignment.
- SBMLKineticLaw - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLKineticLaw defines the speed at which the process defined by the reaction takes place.
- SBMLKineticLaw(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLKineticLaw
-
Instantiates a new SBML kinetic law.
- SBMLListOf - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLListOf represents a list of something in SBML.
- SBMLListOf(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLListOf
-
Instantiates a new SBML list of ...
- SBMLMeta - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLMeta to handle annotations and stuff.
- SBMLMeta() - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLMeta
- sbmlModel - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLGenericObject
-
The sbml model.
- SBMLModel - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLModel representing a model encoded in SBML.
- SBMLModel(DocumentNode, SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLModel
-
Instantiates a new SBML model.
- SBMLParameter - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLParameter is used to define a symbol associated with a value; this symbol can then be used in mathematical formulas in a model.
- SBMLParameter(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLParameter
-
Instantiates a new SBML parameter.
- SBMLRateRule - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLRateRule used to express equations that determine the rates of change of variables.
- SBMLRateRule(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLRateRule
-
Instantiates a new SBML rate rule.
- SBMLReaction - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLReaction represents any kind of process that can change the quantity of one or more species in a model.
- SBMLReaction(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLReaction
-
Instantiates a new SBML reaction.
- SBMLRule - Class in de.unirostock.sems.bives.sbml.parser
-
The abstract Class SBMLRule.
- SBMLRule(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLRule
-
Instantiates a new SBML rule.
- SBMLSBase - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLSBase.
- SBMLSBase(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLSBase
-
Instantiates a new SBMLS base.
- SBMLSimpleSpeciesReference - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLSimpleSpeciesReference representing a link to a species (mainly for modifiers, parent class for substrates and products).
- SBMLSimpleSpeciesReference(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference
-
Instantiates a new SBML simple species reference.
- SBMLSingle - Class in de.unirostock.sems.bives.sbml.api
-
The Class SBMLSingle to study single SBML documents.
- SBMLSingle(SBMLDocument) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLSingle
-
Instantiates a new object to study single SBML documents.
- SBMLSingle(TreeDocument) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLSingle
-
Instantiates a new object.
- SBMLSingle(File) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLSingle
-
Instantiates a new object to study single SBML documents.
- SBMLSingle(String) - Constructor for class de.unirostock.sems.bives.sbml.api.SBMLSingle
-
Instantiates a new object to study single SBML documents.
- SBMLSpecies - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLSpecies representing a species in an SBML document.
- SBMLSpecies(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLSpecies
-
Instantiates a new SBML species.
- SBMLSpeciesReference - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLSpeciesReference representing a link to a species.
- SBMLSpeciesReference(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesReference
-
Instantiates a new SBML species reference.
- SBMLSpeciesType - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLSpeciesType representing type of species (level < 3).
- SBMLSpeciesType(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLSpeciesType
-
Instantiates a new SBML species type.
- SBMLUnit - Class in de.unirostock.sems.bives.sbml.parser
-
The Class SBMLUnit representing a factor based on a unit:
- 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
-
The Class SBMLUnitDefinition.
- SBMLUnitDefinition(DocumentNode, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLUnitDefinition
-
Instantiates a new SBML unit definition.
- SBMLUnitDefinition(String, SBMLModel) - Constructor for class de.unirostock.sems.bives.sbml.parser.SBMLUnitDefinition
-
Instantiates a new SBML base unit.
- SBMLValidator - Class in de.unirostock.sems.bives.sbml.algorithm
-
The Class SBMLValidator validates SBML code.
- SBMLValidator() - Constructor for class de.unirostock.sems.bives.sbml.algorithm.SBMLValidator
- species - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLSimpleSpeciesReference
-
The species it is linking to.
- speciesPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
-
The XPATH to a species.
T
- type - Variable in class de.unirostock.sems.bives.sbml.parser.SBMLRule
-
The type flag encoding the type of rule.
U
- unitsPath - Static variable in class de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
-
The XPATH to a reaction.
V
- validate(TreeDocument) - Method in class de.unirostock.sems.bives.sbml.algorithm.SBMLValidator
- validate(File) - 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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