IOntologyGraph ontologyGraph = ontologyComparator.mapOntologies().getFirst();
int similarity = (int) (ontologyComparator.getSimilarity() * 100);
final IGraphModelBuilder myGraphModelBuilder =
new GraphModelBuilder(firstOntologyGraph[0], secondOntologyGraph, ontologyGraph, similarity, this.main);
this.main.log("Visualising ontologies...");
GraphModel graphModel = myGraphModelBuilder.buildGraphModel(main.getGraphPane(), main.areUnmappedConceptsVisible(), main.areUnmappedConceptsWithSynsetsVisible());
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLOntology result = OntologyManager.saveOntologies(manager, firstOntologyManager.getOntology(), secondOntologyManager.getOntology());
onGraphModelBuilt(manager, result);
this.main.setGraphModel(graphModel);
ITreeBuilder firstTreeBuilder = new TreeBuilder(firstFile.getName(), firstOntologyGraph[0].getRoots());