- Change - Class in de.unirostock.sems.comodi
-
The Class Change representing the Change concept in COMODI.
- Change(Element, Model, URI) - Constructor for class de.unirostock.sems.comodi.Change
-
The Constructor specifying the node in the delta and the Apache/Jena RDF
model.
- Change(DocumentNode, Model, URI) - Constructor for class de.unirostock.sems.comodi.Change
-
The Constructor specifying the node in the delta and the Apache/Jena RDF
model.
- ChangeFactory - Class in de.unirostock.sems.comodi
-
The Class ChangeFactory creating and storing changes.
- ChangeFactory(URI) - Constructor for class de.unirostock.sems.comodi.ChangeFactory
-
The Constructor specifying the base URI of the file containing the changes.
- COMODI_NS - Static variable in class de.unirostock.sems.comodi.ChangeFactory
-
The namespace of COMODI.
- ComodiBranchTerm - Class in de.unirostock.sems.comodi
-
- ComodiBranchTerm(String) - Constructor for class de.unirostock.sems.comodi.ComodiBranchTerm
-
The Constructor instantiates a new term.
- ComodiChangeType - Class in de.unirostock.sems.comodi.branches
-
The Class ComodiChangeType creating terms of COMODI's Type branch.
- ComodiChangeType(String) - Constructor for class de.unirostock.sems.comodi.branches.ComodiChangeType
-
The Constructor -- just to call the constructor of the super class.
- ComodiIntention - Class in de.unirostock.sems.comodi.branches
-
The Class ComodiIntention creating terms of COMODI's Intention branch.
- ComodiIntention(String) - Constructor for class de.unirostock.sems.comodi.branches.ComodiIntention
-
The Constructor -- just to call the constructor of the super class.
- ComodiReason - Class in de.unirostock.sems.comodi.branches
-
The Class ComodiReason creating terms of COMODI's Reason branch.
- ComodiReason(String) - Constructor for class de.unirostock.sems.comodi.branches.ComodiReason
-
The Constructor -- just to call the constructor of the super class.
- ComodiTarget - Class in de.unirostock.sems.comodi.branches
-
The Class ComodiTarget creating terms of COMODI's Target branch.
- ComodiTarget(String) - Constructor for class de.unirostock.sems.comodi.branches.ComodiTarget
-
The Constructor -- just to call the constructor of the super class.
- ComodiXmlEntity - Class in de.unirostock.sems.comodi.branches
-
The Class ComodiXmlEntity creating terms of COMODI's XmlEntity branch.
- ComodiXmlEntity(String) - Constructor for class de.unirostock.sems.comodi.branches.ComodiXmlEntity
-
The Constructor -- just to call the constructor of the super class.
- createChange(Element) - Method in class de.unirostock.sems.comodi.ChangeFactory
-
Creates a change encoded in the JDOM element node
.
- createChange(DocumentNode) - Method in class de.unirostock.sems.comodi.ChangeFactory
-
Creates a change encoded in the
DocumentNode
element
node
.
- getAnnotaions() - Method in class de.unirostock.sems.comodi.ChangeFactory
-
Gets the annotations.
- getAnnotation() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing an annotation.
- getAnnotationScheme() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing an annotation scheme.
- getAttribute() - Static method in class de.unirostock.sems.comodi.branches.ComodiXmlEntity
-
Gets the term representing an XML attribute.
- getAttributeValue() - Static method in class de.unirostock.sems.comodi.branches.ComodiChangeType
-
Gets the term representing an update of an attribute value.
- getAttribution() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing an attribution.
- getCellmlSpecification() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing the CellML specification.
- getComponentDefinition() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing a component definition.
- getComponentHierarchy() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing the component hierarchy.
- getContributor() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing a contributor.
- getCorrection() - Static method in class de.unirostock.sems.comodi.branches.ComodiIntention
-
Gets the term representing a correction.
- getCreationDate() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing a creation date.
- getCreator() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing a creator.
- getDate() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing a date.
- getDeletion() - Static method in class de.unirostock.sems.comodi.branches.ComodiChangeType
-
Gets the term representing a deletion.
- getDocumentLayout() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing the document layout.
- getEncodedSystem() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing the encoded system.
- getEntityIdentifier() - Static method in class de.unirostock.sems.comodi.branches.ComodiXmlEntity
-
Gets the term representing an XML entity identifier, typically the
id
attribute.
- getEntityName() - Static method in class de.unirostock.sems.comodi.branches.ComodiXmlEntity
-
Gets the resenting an XML entity name, typically the name
attribute.
- getEventDefinition() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing an event definition.
- getExtension() - Static method in class de.unirostock.sems.comodi.branches.ComodiIntention
-
Gets the term representing an extension.
- getFunctionDefinition() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing a function definition.
- getIdentifiersScheme() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing an identifiers scheme.
- getInsertion() - Static method in class de.unirostock.sems.comodi.branches.ComodiChangeType
-
Gets the term representing an insertion.
- getKinetics() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing kinetics.
- getKnowledgeGain() - Static method in class de.unirostock.sems.comodi.branches.ComodiReason
-
Gets the term representing a knowledge gain.
- getMathematicalModel() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing the mathematical model.
- getMetaIdentifier() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing the meta identifier.
- getMismatchWithPublication() - Static method in class de.unirostock.sems.comodi.branches.ComodiReason
-
Gets the term representing a mismatch with publication.
- getModelCuration() - Static method in class de.unirostock.sems.comodi.branches.ComodiReason
-
Gets the term representing a model curation.
- getModelId() - Static method in class de.unirostock.sems.comodi.branches.ComodiXmlEntity
-
Gets the term representing a change in the model identifier.
- getModelName() - Static method in class de.unirostock.sems.comodi.branches.ComodiXmlEntity
-
Gets the representing a change in the model name.
- getModificationDate() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing a modification date.
- getMove() - Static method in class de.unirostock.sems.comodi.branches.ComodiChangeType
-
Gets the term representing a move.
- getNetwork() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing the network.
- getNode() - Static method in class de.unirostock.sems.comodi.branches.ComodiXmlEntity
-
Gets the term representing an XML node.
- getNumChanges() - Method in class de.unirostock.sems.comodi.ChangeFactory
-
Gets the number changes produced by this factory.
- getNumStatements() - Method in class de.unirostock.sems.comodi.ChangeFactory
-
Gets the number of overall statements in all changes produced by this
change factory.
- getOntologyLink() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing an ontology link.
- getParameterDefinition() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing a parameter definition.
- getPermutationOfEntities() - Static method in class de.unirostock.sems.comodi.branches.ComodiChangeType
-
Gets the term representing a permutation of entities.
- getPerson() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing a person.
- getRdfXml() - Method in class de.unirostock.sems.comodi.ChangeFactory
-
Compiles the assembled changes in an RDF/XML string.
- getReactionDefinition() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing a reaction definition.
- getReactionNetwork() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing the reaction network.
- getReactionReversibility() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing a reaction reversibility.
- getRules() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing a rule.
- getSbmlLevel() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing an SBML level.
- getSbmlSpecification() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing the SBML specification.
- getSbmlVersion() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing an SBML version.
- getSimplification() - Static method in class de.unirostock.sems.comodi.branches.ComodiIntention
-
Gets the term representing a simplification.
- getSpeciesDefinition() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing a species definition.
- getSpecification() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing a specification.
- getStatements() - Method in class de.unirostock.sems.comodi.Change
-
Gets the RDF statements about this change.
- getTerm() - Method in class de.unirostock.sems.comodi.ComodiBranchTerm
-
Gets the term.
- getText() - Static method in class de.unirostock.sems.comodi.branches.ComodiXmlEntity
-
Gets the term representing an XML text node.
- getTextualDescription() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing a textual description.
- getTypo() - Static method in class de.unirostock.sems.comodi.branches.ComodiReason
-
Gets the term representing a typo.
- getUnitDefinition() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing an unit definition.
- getUpdate() - Static method in class de.unirostock.sems.comodi.branches.ComodiChangeType
-
Gets the term representing an update.
- getVariableConnections() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing a variable connections.
- getVariableDefinition() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing a variable definition.
- getVcardScheme() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget
-
Gets the term representing the VCard scheme.