jalviewX
File SequenceOntologyI.java
Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| SequenceOntologyI | 25 | 0 | 0 | 0 |
Contributing tests
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| 1 | /* | |
| 2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
| 3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
| 4 | * | |
| 5 | * This file is part of Jalview. | |
| 6 | * | |
| 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. | |
| 11 | * | |
| 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. | |
| 16 | * | |
| 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. | |
| 20 | */ | |
| 21 | package jalview.io.gff; | |
| 22 | ||
| 23 | import java.util.List; | |
| 24 | ||
| 25 | public interface SequenceOntologyI | |
| 26 | { | |
| 27 | /* | |
| 28 | * selected commonly used values for quick reference | |
| 29 | */ | |
| 30 | // SO:0000104 | |
| 31 | public static final String POLYPEPTIDE = "polypeptide"; | |
| 32 | ||
| 33 | // SO:0000349 | |
| 34 | public static final String PROTEIN_MATCH = "protein_match"; | |
| 35 | ||
| 36 | // SO:0000347 | |
| 37 | public static final String NUCLEOTIDE_MATCH = "nucleotide_match"; | |
| 38 | ||
| 39 | // SO:0000316 | |
| 40 | public static final String CDS = "CDS"; | |
| 41 | ||
| 42 | // SO:0001060 | |
| 43 | public static final String SEQUENCE_VARIANT = "sequence_variant"; | |
| 44 | ||
| 45 | // SO:0001819 | |
| 46 | public static final String SYNONYMOUS_VARIANT = "synonymous_variant"; | |
| 47 | ||
| 48 | // SO:0001992 | |
| 49 | public static final String NONSYNONYMOUS_VARIANT = "nonsynonymous_variant"; | |
| 50 | ||
| 51 | // SO:0001587 | |
| 52 | public static final String STOP_GAINED = "stop_gained"; | |
| 53 | ||
| 54 | // SO:0000147 | |
| 55 | public static final String EXON = "exon"; | |
| 56 | ||
| 57 | // SO:0000673 | |
| 58 | public static final String TRANSCRIPT = "transcript"; | |
| 59 | ||
| 60 | // SO:0001621 isA sequence_variant but used in Ensembl as a transcript | |
| 61 | public static final String NMD_TRANSCRIPT_VARIANT = "NMD_transcript_variant"; | |
| 62 | ||
| 63 | // SO:0000704 | |
| 64 | public static final String GENE = "gene"; | |
| 65 | ||
| 66 | public boolean isA(String childTerm, String parentTerm); | |
| 67 | ||
| 68 | /** | |
| 69 | * Returns a sorted list of all valid terms queried for (i.e. terms processed | |
| 70 | * which were valid in the SO), using the friendly description. | |
| 71 | * | |
| 72 | * This can be used to check that any hard-coded stand-in for the full SO | |
| 73 | * includes all the terms needed for correct processing. | |
| 74 | * | |
| 75 | * @return | |
| 76 | */ | |
| 77 | public List<String> termsFound(); | |
| 78 | ||
| 79 | /** | |
| 80 | * Returns a sorted list of all invalid terms queried for (i.e. terms | |
| 81 | * processed which were not found in the SO), using the friendly description. | |
| 82 | * | |
| 83 | * This can be used to report any 'non-compliance' in data, and/or to report | |
| 84 | * valid terms missing from any hard-coded stand-in for the full SO. | |
| 85 | * | |
| 86 | * @return | |
| 87 | */ | |
| 88 | public List<String> termsNotFound(); | |
| 89 | } |