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

A

addChild(CellMLHierarchyNode) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLHierarchyNode

Adds a child node.

addComponent(CellMLComponent) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLModel

Adds a component.

addPrivateInterfaceConnection(CellMLVariable) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

Adds the private interface connection to annother CellML variable.

addPublicInterfaceConnection(CellMLVariable) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

Adds a public interface connection to annother CellML variable.

addUnit(CellMLComponent, CellMLUserUnit, boolean) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLUnitDictionary

Adds a unit.

addUnit(CellMLUserUnit, boolean) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLModel

Adds a unit.

annotateDeletion(TreeNode, Element, ChangeFactory) - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLDiffAnnotator

annotateInsertion(TreeNode, Element, ChangeFactory) - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLDiffAnnotator

annotateMove(TreeNode, TreeNode, Element, ChangeFactory, boolean) - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLDiffAnnotator

annotatePatch(String, ChangeFactory) - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLDiffAnnotator

annotateUpdateAttribute(TreeNode, TreeNode, String, Element, ChangeFactory) - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLDiffAnnotator

annotateUpdateText(TextNode, TextNode, Element, ChangeFactory) - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLDiffAnnotator

associateRdfDescription(RDFDescription) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLDocument

Associate an rdf description.

associateRdfDescription(RDFDescription) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLEntity

Associate an rdf description.

B

BaseQuantity(CellMLUnit) - Constructor for class de.unirostock.sems.bives.cellml.parser.CellMLUserUnit.BaseQuantity

Instantiates a new base quantity.

BaseQuantity(DocumentNode) - Constructor for class de.unirostock.sems.bives.cellml.parser.CellMLUserUnit.BaseQuantity

Instantiates a new base quantity.

BivesCellMLParseException - Exception in de.unirostock.sems.bives.cellml.exception

The Class BivesCellMLParseException.

BivesCellMLParseException(String) - Constructor for exception de.unirostock.sems.bives.cellml.exception.BivesCellMLParseException

Instantiates a new BiVeS exception signalling an error while parsing a CellML document.

C

CellMLComponent - Class in de.unirostock.sems.bives.cellml.parser

The Class CellMLComponent representing a single component in a CellML model.

CellMLComponent(CellMLModel, DocumentNode) - Constructor for class de.unirostock.sems.bives.cellml.parser.CellMLComponent

Instantiates a new CellML component.

CellMLConnection - Class in de.unirostock.sems.bives.cellml.parser

The Class CellMLConnection to parse connections inside CellML models.

CellMLConnection() - Constructor for class de.unirostock.sems.bives.cellml.parser.CellMLConnection

CellMLConnection.ConnectedComponents - Class in de.unirostock.sems.bives.cellml.parser

The Class ConnectedComponents representing a connection of two components.

CellMLConnector - Class in de.unirostock.sems.bives.cellml.algorithm

The Class CellMLConnector to connect CellML documents.

CellMLConnector(Connector) - Constructor for class de.unirostock.sems.bives.cellml.algorithm.CellMLConnector

Instantiates a new CellML connector.

CellMLConnector(Connector, boolean, boolean, boolean) - Constructor for class de.unirostock.sems.bives.cellml.algorithm.CellMLConnector

Instantiates a new CellML connector.

CellMLConnector(CellMLDocument, CellMLDocument) - Constructor for class de.unirostock.sems.bives.cellml.algorithm.CellMLConnector

Instantiates a new CellML connector.

CellMLConnector(CellMLDocument, CellMLDocument, boolean, boolean, boolean) - Constructor for class de.unirostock.sems.bives.cellml.algorithm.CellMLConnector

Instantiates a new CellML connector.

CellMLConnectorPreprocessor - Class in de.unirostock.sems.bives.cellml.algorithm

The Class CellMLConnectorPreprocessor to pre-compute a mapping.

CellMLConnectorPreprocessor(Connector) - Constructor for class de.unirostock.sems.bives.cellml.algorithm.CellMLConnectorPreprocessor

Instantiates a new CellML connector preprocessor.

CellMLConnectorPreprocessor(Connector, boolean, boolean, boolean) - Constructor for class de.unirostock.sems.bives.cellml.algorithm.CellMLConnectorPreprocessor

Instantiates a new CellML connector preprocessor.

CellMLConnectorPreprocessor(CellMLDocument, CellMLDocument) - Constructor for class de.unirostock.sems.bives.cellml.algorithm.CellMLConnectorPreprocessor

Instantiates a new CellML connector preprocessor.

CellMLConnectorPreprocessor(CellMLDocument, CellMLDocument, boolean, boolean, boolean) - Constructor for class de.unirostock.sems.bives.cellml.algorithm.CellMLConnectorPreprocessor

Instantiates a new CellML connector preprocessor.

CellMLDiff - Class in de.unirostock.sems.bives.cellml.api

The Class CellMLDiff to compare two CellML models.

CellMLDiff(CellMLDocument, CellMLDocument) - Constructor for class de.unirostock.sems.bives.cellml.api.CellMLDiff

Instantiates a new CellML differ.

CellMLDiff(CellMLDocument, CellMLDocument, DiffAnnotator) - Constructor for class de.unirostock.sems.bives.cellml.api.CellMLDiff

Instantiates a new CellML differ.

CellMLDiff(TreeDocument, TreeDocument) - Constructor for class de.unirostock.sems.bives.cellml.api.CellMLDiff

Instantiates a new CellML differ.

CellMLDiff(TreeDocument, TreeDocument, DiffAnnotator) - Constructor for class de.unirostock.sems.bives.cellml.api.CellMLDiff

Instantiates a new CellML differ.

CellMLDiff(File, File) - Constructor for class de.unirostock.sems.bives.cellml.api.CellMLDiff

Instantiates a new CellML differ.

CellMLDiff(File, File, DiffAnnotator) - Constructor for class de.unirostock.sems.bives.cellml.api.CellMLDiff

Instantiates a new CellML differ.

CellMLDiff(String, String) - Constructor for class de.unirostock.sems.bives.cellml.api.CellMLDiff

Instantiates a new CellML differ.

CellMLDiff(String, String, DiffAnnotator) - Constructor for class de.unirostock.sems.bives.cellml.api.CellMLDiff

Instantiates a new CellML differ.

CellMLDiffAnnotator - Class in de.unirostock.sems.bives.cellml.algorithm

CellMLDiffAnnotator() - Constructor for class de.unirostock.sems.bives.cellml.algorithm.CellMLDiffAnnotator

CellMLDiffInterpreter - Class in de.unirostock.sems.bives.cellml.algorithm

The Class CellMLDiffInterpreter to interpret a mapping of CellML models.

CellMLDiffInterpreter(SimpleConnectionManager, CellMLDocument, CellMLDocument) - Constructor for class de.unirostock.sems.bives.cellml.algorithm.CellMLDiffInterpreter

Instantiates a new CellML diff interpreter.

CellMLDocument - Class in de.unirostock.sems.bives.cellml.parser

The Class CellMLDocument representing a document containing a CellML model.

CellMLDocument(TreeDocument) - Constructor for class de.unirostock.sems.bives.cellml.parser.CellMLDocument

Instantiates a new cell ml document.

CellMLEntity - Class in de.unirostock.sems.bives.cellml.parser

The Class CellMLEntity representing an entity in a CellML model.

CellMLEntity(DocumentNode, CellMLModel) - Constructor for class de.unirostock.sems.bives.cellml.parser.CellMLEntity

Instantiates a new CellML entity.

CellMLGraphProducer - Class in de.unirostock.sems.bives.cellml.algorithm

The Class CellMLGraphProducer to create the graphs.

CellMLGraphProducer(SimpleConnectionManager, CellMLDocument, CellMLDocument) - Constructor for class de.unirostock.sems.bives.cellml.algorithm.CellMLGraphProducer

Instantiates a new CellML graph producer for difference graphs.

CellMLGraphProducer(CellMLDocument) - Constructor for class de.unirostock.sems.bives.cellml.algorithm.CellMLGraphProducer

Instantiates a new CellML graph producer for single document graphs.

CellMLHierarchy - Class in de.unirostock.sems.bives.cellml.parser

The Class CellMLHierarchy representing the hierarchy of CellML components.

CellMLHierarchy(CellMLModel) - Constructor for class de.unirostock.sems.bives.cellml.parser.CellMLHierarchy

Instantiates a new CellML hierarchy object.

CellMLHierarchyNetwork - Class in de.unirostock.sems.bives.cellml.parser

The Class CellMLHierarchyNetwork representing a hirarchical network of CellML components.

CellMLHierarchyNetwork(String, String) - Constructor for class de.unirostock.sems.bives.cellml.parser.CellMLHierarchyNetwork

Instantiates a new CellML hierarchy network.

CellMLHierarchyNode - Class in de.unirostock.sems.bives.cellml.parser

The Class CellMLHierarchyNode representing a node in a CellML Hierarchy.

CellMLHierarchyNode(CellMLComponent) - Constructor for class de.unirostock.sems.bives.cellml.parser.CellMLHierarchyNode

Instantiates a new CellML hierarchy node.

CellMLImporter - Class in de.unirostock.sems.bives.cellml.parser

The Class CellMLImporter to import entities in CellML models.

CellMLImporter(DocumentNode, CellMLModel) - Constructor for class de.unirostock.sems.bives.cellml.parser.CellMLImporter

Instantiates a new CellML importer.

CellMLModel - Class in de.unirostock.sems.bives.cellml.parser

The Class CellMLModel representing a computational model that was encoded in CellML.

CellMLModel(CellMLDocument, DocumentNode) - Constructor for class de.unirostock.sems.bives.cellml.parser.CellMLModel

Instantiates a new model.

CellMLReaction - Class in de.unirostock.sems.bives.cellml.parser

The Class CellMLReaction representing a reaction defined in a CellML model.

CellMLReaction(CellMLModel, CellMLComponent, DocumentNode) - Constructor for class de.unirostock.sems.bives.cellml.parser.CellMLReaction

Instantiates a new CellML reaction.

CellMLReactionSubstance - Class in de.unirostock.sems.bives.cellml.parser

The Class CellMLReactionSubstance representing a substance taking part in a reaction.

CellMLReactionSubstance(CellMLModel, CellMLComponent, DocumentNode) - Constructor for class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance

Instantiates a new CellML reaction substance.

CellMLReactionSubstance.Role - Class in de.unirostock.sems.bives.cellml.parser

The Class Role.

CellMLSingle - Class in de.unirostock.sems.bives.cellml.api

The Class CellMLSingle to study single CellML documents.

CellMLSingle(CellMLDocument) - Constructor for class de.unirostock.sems.bives.cellml.api.CellMLSingle

Instantiates a new object.

CellMLSingle(TreeDocument) - Constructor for class de.unirostock.sems.bives.cellml.api.CellMLSingle

Instantiates a new object.

CellMLSingle(File) - Constructor for class de.unirostock.sems.bives.cellml.api.CellMLSingle

Instantiates a new object.

CellMLSingle(String) - Constructor for class de.unirostock.sems.bives.cellml.api.CellMLSingle

Instantiates a new object.

CellMLUnit - Class in de.unirostock.sems.bives.cellml.parser

The Class CellMLUnit representing a unit in a CellML model.

CellMLUnit(CellMLModel, String, DocumentNode) - Constructor for class de.unirostock.sems.bives.cellml.parser.CellMLUnit

Instantiates a new CellML unit as defined in a CellML model.

CellMLUnitDictionary - Class in de.unirostock.sems.bives.cellml.parser

The Class CellMLUnitDictionary storing all known units.

CellMLUnitDictionary(CellMLModel) - Constructor for class de.unirostock.sems.bives.cellml.parser.CellMLUnitDictionary

Instantiates a new CellML unit dictionary.

CellMLUserUnit - Class in de.unirostock.sems.bives.cellml.parser

The Class CellMLUserUnit representing a CellML unit defined by a user.

CellMLUserUnit(CellMLModel, CellMLUnitDictionary, CellMLComponent, DocumentNode) - Constructor for class de.unirostock.sems.bives.cellml.parser.CellMLUserUnit

Instantiates a new CellML user unit.

CellMLUserUnit.BaseQuantity - Class in de.unirostock.sems.bives.cellml.parser

The Class BaseQuantity.

CellMLValidator - Class in de.unirostock.sems.bives.cellml.algorithm

CellMLValidator() - Constructor for class de.unirostock.sems.bives.cellml.algorithm.CellMLValidator

CellMLVariable - Class in de.unirostock.sems.bives.cellml.parser

The Class CellMLVariable representing a variable of a CellML model.

CellMLVariable(CellMLModel, CellMLComponent, DocumentNode) - Constructor for class de.unirostock.sems.bives.cellml.parser.CellMLVariable

Instantiates a new CellML variable.

component_1 - Variable in class de.unirostock.sems.bives.cellml.parser.CellMLConnection.ConnectedComponents

component_2 - Variable in class de.unirostock.sems.bives.cellml.parser.CellMLConnection.ConnectedComponents

connect() - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLConnector

connect() - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLConnectorPreprocessor

ConnectedComponents(CellMLComponent, CellMLComponent) - Constructor for class de.unirostock.sems.bives.cellml.parser.CellMLConnection.ConnectedComponents

Instantiates a new component connection.

connectHierarchically(CellMLComponent, CellMLComponent) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLHierarchyNetwork

Connect a parent component and its child hierarchically.

containsImports() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLDocument

Does this model contain imports?

containsImports() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLModel

Does this model contain imports?.

createStandardUnit(String) - Static method in class de.unirostock.sems.bives.cellml.parser.CellMLUnit

Instantiates a standard CellML unit.

creationDatePath - Static variable in class de.unirostock.sems.bives.cellml.algorithm.CellMLDiffAnnotator

The XPATH to a machine readable annotation.

D

de.unirostock.sems.bives.cellml.algorithm - package de.unirostock.sems.bives.cellml.algorithm

de.unirostock.sems.bives.cellml.api - package de.unirostock.sems.bives.cellml.api

de.unirostock.sems.bives.cellml.exception - package de.unirostock.sems.bives.cellml.exception

de.unirostock.sems.bives.cellml.parser - package de.unirostock.sems.bives.cellml.parser

delta_variable - Variable in class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance.Role

The optional delta_variable attribute indicates which variable is used to store the change in concentration of the species represented by the variable referenced by the current variable_ref element.

direction - Variable in class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance.Role

The optional direction attribute may be used on role elements in reversible reactions.

DIRECTION_BOTH - Static variable in class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance

The Constant DIRECTION_BOTH representing a reversable reaction.

DIRECTION_FORWARD - Static variable in class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance

The Constant DIRECTION_FORWARD representing a forward reaction.

DIRECTION_REVERSE - Static variable in class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance

The Constant DIRECTION_REVERSE representing a reverse reaction.

E

exponent - Variable in class de.unirostock.sems.bives.cellml.parser.CellMLUserUnit.BaseQuantity

The exponent.

F

flagMetaModifcations(MarkupElement) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLEntity

Flags occuring modifcations of the meta information (notes, annotations) to the given MarkupElement.

flatten() - Method in class de.unirostock.sems.bives.cellml.api.CellMLSingle

flatten() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLDocument

Flatten flatten the model encoded in this document.

flatten() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLModel

Flatten this model.

G

getChildren() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLHierarchyNode

Gets the children.

getComponent() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLHierarchyNode

Gets the component behind this node.

getComponent() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLReaction

Gets the component defining this reaction.

getComponent() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

Gets the component.

getComponent(String) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLModel

Gets the component having a specified name.

getComponents() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLModel

Gets the components.

getComponentUnits(CellMLComponent) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLUnitDictionary

Gets the units defined in a certain component.

getDependencies(Map<CellMLUserUnit, List<CellMLEntity>>) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLComponent

Adds the units the variables in this component depend on to a global list of dependencies.

getDependencies(Map<CellMLUserUnit, List<CellMLEntity>>) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLUserUnit

Add the units this unit depends on to a global list of dependencies.

getDependencies(Map<CellMLUserUnit, List<CellMLEntity>>) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

Adds the unit this variable depends on to a global list of dependencies.

getDescriptions(CellMLEntity) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLModel

Gets the RDF descriptions for an entity.

getDocument() - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLValidator

getDocument() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLModel

Gets the document.

getDocumentNode() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLEntity

Gets the document node.

getEncapsulationHierarchyNetwork() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLHierarchy

Gets the encapsulation hierarchy network.

getEncapsulationRelationship(CellMLComponent, CellMLComponent) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLHierarchy

Gets the encapsulation relationship of two components.

getEntityByMetaId(String) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLModel

Get an entity by its meta id.

getFromNode(TreeNode) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLModel

Gets an entity given a node in an XML tree.

getHierarchy() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLModel

Gets the hierarchy.

getHierarchyDotGraph() - Method in class de.unirostock.sems.bives.cellml.api.CellMLDiff

getHierarchyDotGraph() - Method in class de.unirostock.sems.bives.cellml.api.CellMLSingle

getHierarchyGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.cellml.api.CellMLDiff

getHierarchyGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.cellml.api.CellMLSingle

getHierarchyGraphML() - Method in class de.unirostock.sems.bives.cellml.api.CellMLDiff

getHierarchyGraphML() - Method in class de.unirostock.sems.bives.cellml.api.CellMLSingle

getHierarchyJsonGraph() - Method in class de.unirostock.sems.bives.cellml.api.CellMLDiff

getHierarchyJsonGraph() - Method in class de.unirostock.sems.bives.cellml.api.CellMLSingle

getHierarchyNetwork(String, String) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLHierarchy

Gets a specific hierarchy network.

getHTMLReport() - Method in class de.unirostock.sems.bives.cellml.api.CellMLDiff

getInitialValue() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

Gets the initial value, if explicitly specified by a scalar value.

getInitialValueVariable() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

Gets the initial value, if specified by a variable.

getMarkDownReport() - Method in class de.unirostock.sems.bives.cellml.api.CellMLDiff

getMath() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLComponent

Gets the mathematical equations defined in this component.

getMetaId() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLEntity

Gets the CellML meta id of this entity.

getModel() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLDocument

Gets the encoded model.

getModel() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLEntity

Gets the corresponding model.

getModelUnits() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLUnitDictionary

Gets the units defined globally in the model.

getName() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLComponent

Gets the name of this component.

getName() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLHierarchyNetwork

Gets the name of this network.

getName() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLModel

Gets the name of the model.

getName() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLUnit

Gets the name of this unit.

getName() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

Gets the name of this variable.

getNode(CellMLComponent) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLHierarchyNetwork

Gets the node that corresponds to a certain CellML component.

getNodes() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLHierarchyNetwork

Gets all nodes of this network.

getParent() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLHierarchyNode

Gets the parent node.

getPrivateInterface() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

Gets the private interface flag.

getPrivateInterfaceConnections() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

Gets the private interface connections as a list of CellML variables.

getPrivateInterfaceStr() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

Gets the textual representation (in, out, or none) of the private interface.

getPublicInterface() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

Gets the public interface flag.

getPublicInterfaceConnections() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

Gets the public interface connections as a list of CellML variables.

getPublicInterfaceStr() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

Gets the textual representation (in, out, or none) of the public interface.

getRdfBlocks() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLEntity

Gets the RDF descriptions, if there are any rooted in this entity.

getRdfDescriptions() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLEntity

Gets the rdf descriptions.

getReactions() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLComponent

Gets the reactions defined in this component.

getReactionsDotGraph() - Method in class de.unirostock.sems.bives.cellml.api.CellMLDiff

getReactionsDotGraph() - Method in class de.unirostock.sems.bives.cellml.api.CellMLSingle

getReactionsGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.cellml.api.CellMLDiff

getReactionsGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.cellml.api.CellMLSingle

getReactionsGraphML() - Method in class de.unirostock.sems.bives.cellml.api.CellMLDiff

getReactionsGraphML() - Method in class de.unirostock.sems.bives.cellml.api.CellMLSingle

getReactionsJsonGraph() - Method in class de.unirostock.sems.bives.cellml.api.CellMLDiff

getReactionsJsonGraph() - Method in class de.unirostock.sems.bives.cellml.api.CellMLSingle

getReactionsSbgnJsonGraph() - Method in class de.unirostock.sems.bives.cellml.api.CellMLDiff

getRelationship() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLHierarchyNetwork

Gets the relationship type.

getReport() - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLDiffInterpreter

Gets the produced report.

getReport(Typesetting) - Method in class de.unirostock.sems.bives.cellml.api.CellMLDiff

getReStructuredTextReport() - Method in class de.unirostock.sems.bives.cellml.api.CellMLDiff

getRoles() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance

Gets the roles of this substance.

getRootVariable() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

Gets the root variable, obtained by traversing the interface connections.

getSubstances() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLReaction

Gets the substances taking part in the reaction.

getUnit(String) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLComponent

Gets the unit.

getUnit(String, CellMLComponent) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLUnitDictionary

Gets a unit by its name.

getUnits() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLModel

Gets the units.

getVariable() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance

Gets the corresponding CellML variable.

getVariable(String) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLComponent

Gets the variable.

getVariables() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLComponent

Gets the variables of this component.

graphProducer - Variable in class de.unirostock.sems.bives.cellml.api.CellMLDiff

The graph producer.

graphProducer - Variable in class de.unirostock.sems.bives.cellml.api.CellMLSingle

The graph producer.

I

importComponent(CellMLComponent) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLModel

Import a component from another document.

importUnit(CellMLUserUnit) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLModel

Imports a unit from another document.

init() - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLConnector

init() - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLConnectorPreprocessor

INTERFACE_IN - Static variable in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

The flag INTERFACE_IN = incoming interface.

INTERFACE_NONE - Static variable in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

The flag INTERFACE_NONE = no interface.

INTERFACE_OUT - Static variable in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

The flag INTERFACE_OUT = outgoing interface.

interprete() - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLDiffInterpreter

interpreter - Variable in class de.unirostock.sems.bives.cellml.api.CellMLDiff

The interpreter.

isReversible() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLReaction

Checks if this reaction is reversible.

isStandardUnits() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLUnit

Checks if it is a standard unit.

M

mapNode(DocumentNode, CellMLEntity) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLModel

Map document node to a CellML entity.

mapTrees(boolean, boolean, boolean) - Method in class de.unirostock.sems.bives.cellml.api.CellMLDiff

markup() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLUserUnit.BaseQuantity

markup() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLUserUnit

math - Variable in class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance.Role

The role elements may also contain math elements in the MathML namespace, which define equations using MathML.

model - Variable in class de.unirostock.sems.bives.cellml.parser.CellMLEntity

The model.

modificationDatePath - Static variable in class de.unirostock.sems.bives.cellml.algorithm.CellMLDiffAnnotator

The XPATH to a machine readable annotation.

multiplier - Variable in class de.unirostock.sems.bives.cellml.parser.CellMLUserUnit.BaseQuantity

The multiplier.

N

node - Variable in class de.unirostock.sems.bives.cellml.parser.CellMLUserUnit.BaseQuantity

The document node.

O

offset - Variable in class de.unirostock.sems.bives.cellml.parser.CellMLUserUnit.BaseQuantity

The offset.

P

parse() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLImporter

Parses the import section.

parseConnection(CellMLModel, CellMLHierarchy, DocumentNode, HashMap<String, CellMLComponent>) - Static method in class de.unirostock.sems.bives.cellml.parser.CellMLConnection

Parses a connection as defined in a CellML document.

parseGroup(DocumentNode) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLHierarchy

Parses a component group.

prefix - Variable in class de.unirostock.sems.bives.cellml.parser.CellMLUserUnit.BaseQuantity

The prefix (power of ten).

processHnA() - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLGraphProducer

Process Hierarchy Network of the original document.

processHnB() - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLGraphProducer

Process Hierarchy Network of the modified document.

processRnA() - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLGraphProducer

Process Reaction Network of the original document.

processRnB() - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLGraphProducer

Process Reaction Network of the modified document.

produceHierarchyGraph() - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLGraphProducer

produceReactionNetwork() - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLGraphProducer

putNode(CellMLComponent) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLHierarchyNetwork

Install a new hierarchy node if it doesn't exist.

R

registerMetaId(String, CellMLEntity) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLModel

Register an entity by its meta id.

registerRdfBlock(RDF) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLModel

Register an rdf block.

RELATION_ENCAPSULATED - Static variable in class de.unirostock.sems.bives.cellml.parser.CellMLHierarchy

The Constant RELATION_ENCAPSULATED => component 1 is encapsulated in component 2.

RELATION_HIDDEN - Static variable in class de.unirostock.sems.bives.cellml.parser.CellMLHierarchy

The Constant RELATION_HIDDEN => components cannot see each other.

RELATION_PARENT - Static variable in class de.unirostock.sems.bives.cellml.parser.CellMLHierarchy

The Constant RELATION_PARENT => component 1 is parent of component 2 .

RELATION_SIBLING - Static variable in class de.unirostock.sems.bives.cellml.parser.CellMLHierarchy

The Constant RELATION_SIBLING => components are siblings.

renameUnit(String, String) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLUserUnit.BaseQuantity

Rename the corresponding unit.

renameUnit(String, String) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLUserUnit

Rename the corresponding unit.

renameUnit(String, String) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

Rename the corresponding unit.

reportDelete() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLReaction

reportDelete() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLUserUnit

reportDelete() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

reportInsert() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLReaction

reportInsert() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLUserUnit

reportInsert() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLReaction

reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLUserUnit

reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

resolveDirection(int) - Static method in class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance

Resolve direction of this substance.

resolveDirection(String) - Static method in class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance

Resolve direction.

resolveRole(int) - Static method in class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance

Resolve the role flag to get a textual representation.

resolveRole(String) - Static method in class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance

Resolve role as a string to get the corresponding flag.

role - Variable in class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance.Role

The role attribute must have a value of "reactant", "product", "catalyst", "activator", "inhibitor", "modifier", or "rate".

Role(CellMLModel, DocumentNode) - Constructor for class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance.Role

Instantiates a new role.

ROLE_ACTIVATOR - Static variable in class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance

The Constant ROLE_ACTIVATOR representing an activator.

ROLE_CATALYST - Static variable in class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance

The Constant ROLE_CATALYST representing a catalyst.

ROLE_INHIBITOR - Static variable in class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance

The Constant ROLE_INHIBITOR representing an inhibitor.

ROLE_MODIFIER - Static variable in class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance

The Constant ROLE_MODIFIER representing a modifier.

ROLE_PRODUCT - Static variable in class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance

The Constant ROLE_PRODUCT representing a product.

ROLE_RATE - Static variable in class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance

The Constant ROLE_RATE representing a the rate variable.

ROLE_REACTANT - Static variable in class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance

The Constant ROLE_REACTANT representing a reactant.

S

scale(String) - Static method in class de.unirostock.sems.bives.cellml.parser.CellMLUserUnit

Get the scaling factor given a textual representation.

setMetaId(String) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLEntity

Sets the meta id of this entity.

setModel(CellMLModel) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLEntity

Sets the model.

setName(String) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLComponent

Sets the name of this component.

setName(String) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLUnit

Sets the name of this unit.

setParent(CellMLHierarchyNode) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLHierarchyNode

Sets the parent node.

STANDARD_UNITS - Static variable in class de.unirostock.sems.bives.cellml.parser.CellMLUnitDictionary

The common standard units

stoichiometry - Variable in class de.unirostock.sems.bives.cellml.parser.CellMLReactionSubstance.Role

The optional stoichiometry attribute stores the stoichiometry of the current variable relative to the other reaction participants.

T

toString() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLHierarchyNode

toString() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLUnit

U

unconnect() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLComponent

Unconnect all variables in this component.

unconnect() - Method in class de.unirostock.sems.bives.cellml.parser.CellMLVariable

Unconnect all interface connections.

unit - Variable in class de.unirostock.sems.bives.cellml.parser.CellMLUserUnit.BaseQuantity

The unit.

unregisterMetaId(String) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLModel

Unregister a meta id.

V

validate(TreeDocument) - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLValidator

validate(File) - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLValidator

validate(String) - Method in class de.unirostock.sems.bives.cellml.algorithm.CellMLValidator

W

write(File) - Method in class de.unirostock.sems.bives.cellml.parser.CellMLDocument

Write the document to disk.

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