1 package jalview.datamodel.ontology;
6 public interface OntologyI
10 * Answers true if <code>childTerm</code> is the same as, or a sub-type
11 * (specialisation of) <code>parentTerm</code>, else false
17 boolean isA(String childTerm, String parentTerm);
20 * Answers those terms in the given set which are not child terms of some
21 * other term in the set. That is, returns a set of parent terms. The input
22 * set is not modified.
27 Set<String> getParentTerms(Set<String> terms);
30 * Answers a (possibly empty) list of those terms in the supplied list which
31 * are a child (directly or indirectly) of <code>parent</code>. The parent
32 * term itself is not included (even if in the input list)
38 List<String> getChildTerms(String parent, List<String> terms);
41 * Returns a sorted list of all valid terms queried for (i.e. terms processed
42 * which were valid in the SO), using the friendly description.
44 * This can be used to check that any hard-coded stand-in for the full SO
45 * includes all the terms needed for correct processing.
49 List<String> termsFound();
52 * Returns a sorted list of all invalid terms queried for (i.e. terms
53 * processed which were not found in the SO), using the friendly description.
55 * This can be used to report any 'non-compliance' in data, and/or to report
56 * valid terms missing from any hard-coded stand-in for the full SO.
60 List<String> termsNotFound();