1 package jalview.io.gff;
5 public interface SequenceOntologyI
8 * selected commonly used values for quick reference
10 public static final String POLYPEPTIDE = "polypeptide";
12 public static final String PROTEIN_MATCH = "protein_match";
14 public static final String NUCLEOTIDE_MATCH = "nucleotide_match";
17 public static final String CDS = "CDS";
20 public static final String SEQUENCE_VARIANT = "sequence_variant";
23 public static final String EXON = "exon";
26 public static final String TRANSCRIPT = "transcript";
29 public static final String GENE = "gene";
31 public boolean isA(String childTerm, String parentTerm);
34 * Returns a sorted list of all valid terms queried for (i.e. terms processed
35 * which were valid in the SO), using the friendly description.
37 * This can be used to check that any hard-coded stand-in for the full SO
38 * includes all the terms needed for correct processing.
42 public List<String> termsFound();
45 * Returns a sorted list of all invalid terms queried for (i.e. terms
46 * processed which were not found in the SO), using the friendly description.
48 * This can be used to report any 'non-compliance' in data, and/or to report
49 * valid terms missing from any hard-coded stand-in for the full SO.
53 public List<String> termsNotFound();