monarch-initiative/owlsim-v3

Adding ability to load individuals from in-memory data as well as off-disk.

…xt of the Ontology/OntologySourceData/OwlKnowledgebase in order to be more specific.

…via the OwlKnowledgeBase and the OntologyDataSource.

…API more self-explanatory.

…, added toString.

…r creating a BMKnowledgeBaseOWLAPIImpl - @deprecated OWLLoader.

Added new supporting classes Ontology and OntologyDataSource, OntologyLoadException to help the OwlKnowledgeBase do its thing.
OWLLoader is only partially removed from the tests at present.
Removed overly verbose logging from FilterEngine.
Added commented-out clean-up of KnowledgeBaseModule - server still fails to start with ot without this.

 into 57-loader_refactor

# Conflicts:
#	owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java

…oduced from CurieUtil.

Removed useless right-hand class types from collection initialisation. e.g. = new ArrayList<String>() -> new ArrayList<>();