2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.io.gff;
23 import java.util.List;
25 public interface SequenceOntologyI
28 * selected commonly used values for quick reference
31 public static final String POLYPEPTIDE = "polypeptide";
34 public static final String PROTEIN_MATCH = "protein_match";
37 public static final String NUCLEOTIDE_MATCH = "nucleotide_match";
40 public static final String CDS = "CDS";
43 public static final String SEQUENCE_VARIANT = "sequence_variant";
46 public static final String EXON = "exon";
49 public static final String TRANSCRIPT = "transcript";
51 // SO:0001621 isA sequence_variant but used in Ensembl as a transcript
52 public static final String NMD_TRANSCRIPT_VARIANT = "NMD_transcript_variant";
55 public static final String GENE = "gene";
57 public boolean isA(String childTerm, String parentTerm);
60 * Returns a sorted list of all valid terms queried for (i.e. terms processed
61 * which were valid in the SO), using the friendly description.
63 * This can be used to check that any hard-coded stand-in for the full SO
64 * includes all the terms needed for correct processing.
68 public List<String> termsFound();
71 * Returns a sorted list of all invalid terms queried for (i.e. terms
72 * processed which were not found in the SO), using the friendly description.
74 * This can be used to report any 'non-compliance' in data, and/or to report
75 * valid terms missing from any hard-coded stand-in for the full SO.
79 public List<String> termsNotFound();