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A

addAnnotation(Property, RDFNode) - Method in class de.unirostock.sems.comodi.Change

Adds another custom annotation describing this change.

affects(ComodiTarget) - Method in class de.unirostock.sems.comodi.Change

Adds information about the target that is affected by this change.

appliesTo(ComodiXmlEntity) - Method in class de.unirostock.sems.comodi.Change

Adds information about the XML entity that this change was applied to.

C

Change - Class in de.unirostock.sems.comodi

The Class Change representing the Change concept in COMODI.

Change(String, Model, URI, String) - Constructor for class de.unirostock.sems.comodi.Change

Instantiates a new change.

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

The Class ComodiBranchTerm -- a super class for the five different COMODI branches: XmlEntity, see ComodiXmlEntity Intention, see ComodiIntention Reason, see ComodiReason Target, see ComodiTarget

ComodiBranchTerm(String) - Constructor for class de.unirostock.sems.comodi.ComodiBranchTerm

The Constructor instantiates a new term.

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(String) - Method in class de.unirostock.sems.comodi.ChangeFactory

Creates a change encoded the subject with subjectId.

createChange(String, String) - Method in class de.unirostock.sems.comodi.ChangeFactory

Creates a new Change object for a subject.

createDeletion(String) - Method in class de.unirostock.sems.comodi.ChangeFactory

Creates a deletion encoded the subject with subjectId.

createInsertion(String) - Method in class de.unirostock.sems.comodi.ChangeFactory

Creates a insertion encoded the subject with subjectId.

createMove(String) - Method in class de.unirostock.sems.comodi.ChangeFactory

Creates a move encoded the subject with subjectId.

createPermutationOfEntities(String) - Method in class de.unirostock.sems.comodi.ChangeFactory

Creates a permutation of entities (move) encoded the subject with subjectId.

createUpdate(String) - Method in class de.unirostock.sems.comodi.ChangeFactory

Creates a update encoded the subject with subjectId.

D

de.unirostock.sems.comodi - package de.unirostock.sems.comodi

de.unirostock.sems.comodi.branches - package de.unirostock.sems.comodi.branches

F

FOAF_NS - Static variable in class de.unirostock.sems.comodi.ChangeFactory

The friend-of-a-friend namespace.

G

getAnnotaions() - Method in class de.unirostock.sems.comodi.ChangeFactory

Gets the annotations.

getAnnotationEncoding() - 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.

getAttribution() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing an attribution.

getBaseUri() - Method in class de.unirostock.sems.comodi.ChangeFactory

Gets the base URI for entities in this patch.

getChangeAsResource() - Method in class de.unirostock.sems.comodi.Change

Gets the change as an RDF resource.

getChangedSpecification() - Static method in class de.unirostock.sems.comodi.branches.ComodiReason

Gets the term representing a changed specification.

getChanges() - Method in class de.unirostock.sems.comodi.ChangeFactory

Gets all registered changes.

getComponentDefinition() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing a component definition.

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.

getElaboration() - Static method in class de.unirostock.sems.comodi.branches.ComodiIntention

Gets the term representing a elaboration.

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.

getExpansion() - Static method in class de.unirostock.sems.comodi.branches.ComodiIntention

Gets the term representing an expansion.

getFunctionDefinition() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing a function definition.

getHierarchyDefinition() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing the hierarchy of, eg., components or compartments.

getIdentifierEncoding() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing an identifiers scheme.

getKineticsDefinition() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing defintion of some kinetics.

getKnowledgeGain() - Static method in class de.unirostock.sems.comodi.branches.ComodiReason

Gets the term representing a knowledge gain.

getMathematicalModelDefinition() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing the mathematical model.

getMerge() - Static method in class de.unirostock.sems.comodi.branches.ComodiIntention

Gets the term representing a merge.

getMetaIdEncoding() - 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.

getModelAnnotation() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing the annotation layer of a model document.

getModelBehaviour() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing the behaviour of the encoded system.

getModelCuration() - Static method in class de.unirostock.sems.comodi.branches.ComodiReason

Gets the term representing a model curation.

getModelDefinition() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing the definition of the actual system.

getModelEncoding() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing the document layout.

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.

getModelSetup() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing the setup of the encoded system.

getModificationDate() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing a modification date.

getNetworkDefinition() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing the network definition.

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.

getOntologyReference() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing an ontology reference.

getParameterSetup() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing the setup of a parameter.

getParticipantDefinition() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing a participant in the reaction network.

getPerson() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing a person.

getPortDefinition() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing a port definition.

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.

getReactionNetworkDefinition() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing the reaction network.

getReversibilityDefinition() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing a reaction reversibility.

getRuleDefinition() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing a rule definition.

getSimplification() - Static method in class de.unirostock.sems.comodi.branches.ComodiIntention

Gets the term representing a simplification.

getSpeciesSetup() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing the setup of a species.

getStatements() - Method in class de.unirostock.sems.comodi.Change

Gets the RDF statements about this change.

getSubjectId(Element) - Static method in class de.unirostock.sems.comodi.ChangeFactory

Gets the subject id of an Element.

getSubjectId(DocumentNode) - Static method in class de.unirostock.sems.comodi.ChangeFactory

Gets the subject id of a DocumentNode.

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.

getTrial() - Static method in class de.unirostock.sems.comodi.branches.ComodiIntention

Gets the term representing a trial of something.

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.

getVariableConnectionDefinition() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing a variable connections.

getVariableSetup() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing the setup of a variable.

getVcardEncoding() - Static method in class de.unirostock.sems.comodi.branches.ComodiTarget

Gets the term representing the VCard scheme.

H

hasIntention(ComodiIntention) - Method in class de.unirostock.sems.comodi.Change

Adds information about the intention of this change.

hasReason(ComodiReason) - Method in class de.unirostock.sems.comodi.Change

Adds information about the reason of this change.

O

ORE_NS - Static variable in class de.unirostock.sems.comodi.ChangeFactory

The Open Archives Initiative Object Reuse and Exchange (OAI-ORE) namespace.

P

PAV_NS - Static variable in class de.unirostock.sems.comodi.ChangeFactory

The PAV namespace.

printTtl() - Method in class de.unirostock.sems.comodi.ChangeFactory

Prints the TURTLE serialisation to sysout.

printXml() - Method in class de.unirostock.sems.comodi.ChangeFactory

Prints the RDF/XML serialisation to sysout.

PROV_NS - Static variable in class de.unirostock.sems.comodi.ChangeFactory

The PROV namespace.

R

RDF_NS - Static variable in class de.unirostock.sems.comodi.ChangeFactory

The RDF namespace.

RDFS_NS - Static variable in class de.unirostock.sems.comodi.ChangeFactory

The RDF schema namespace.

W

wasTriggeredBy(String) - Method in class de.unirostock.sems.comodi.Change

Links to a change that triggered this change.

A C D F G H O P R W