jalviewX
File DBRefSource.java
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| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| DBRefSource | 43 | 9 | 4 | 1 |
Contributing tests
This file is covered by 58 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.datamodel; | |
| 22 | ||
| 23 | import java.lang.reflect.Field; | |
| 24 | import java.util.ArrayList; | |
| 25 | import java.util.List; | |
| 26 | ||
| 27 | /** | |
| 28 | * BH 2018 SwingJS note: If additional final static Strings are added to this | |
| 29 | * file, they should be added to public static final String[] allTypes. | |
| 30 | * | |
| 31 | * Defines internal constants for unambiguous annotation of DbRefEntry source | |
| 32 | * strings and describing the data retrieved from external database sources (see | |
| 33 | * jalview.ws.DbSourcProxy) <br/> | |
| 34 | * TODO: replace with ontology to allow recognition of particular attributes | |
| 35 | * (e.g. protein coding, alignment (ortholog db, paralog db, domain db), | |
| 36 | * genomic, transcriptomic, 3D structure providing (PDB, MODBASE, etc) ..). | |
| 37 | * | |
| 38 | * | |
| 39 | * | |
| 40 | * @author JimP | |
| 41 | * | |
| 42 | */ | |
| 43 | public class DBRefSource | |
| 44 | { | |
| 45 | ||
| 46 | ||
| 47 | ||
| 48 | /** | |
| 49 | * UNIPROT Accession Number | |
| 50 | */ | |
| 51 | public static final String UNIPROT = "UNIPROT"; | |
| 52 | ||
| 53 | /** | |
| 54 | * UNIPROT Entry Name | |
| 55 | */ | |
| 56 | public static final String UP_NAME = "UNIPROT_NAME".toUpperCase(); | |
| 57 | ||
| 58 | /** | |
| 59 | * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products. | |
| 60 | */ | |
| 61 | public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase(); | |
| 62 | ||
| 63 | public static final String EMBLCDSProduct = "EMBLCDSProtein".toUpperCase(); | |
| 64 | ||
| 65 | ||
| 66 | /** | |
| 67 | * PDB Entry Code | |
| 68 | */ | |
| 69 | public static final String PDB = "PDB"; | |
| 70 | ||
| 71 | /** | |
| 72 | * EMBL ID | |
| 73 | */ | |
| 74 | public static final String EMBL = "EMBL"; | |
| 75 | ||
| 76 | /** | |
| 77 | * EMBLCDS ID | |
| 78 | */ | |
| 79 | public static final String EMBLCDS = "EMBLCDS"; | |
| 80 | ||
| 81 | ||
| 82 | /** | |
| 83 | * PFAM ID | |
| 84 | */ | |
| 85 | public static final String PFAM = "PFAM"; | |
| 86 | ||
| 87 | /** | |
| 88 | * RFAM ID | |
| 89 | */ | |
| 90 | public static final String RFAM = "RFAM"; | |
| 91 | ||
| 92 | /** | |
| 93 | * GeneDB ID | |
| 94 | */ | |
| 95 | public static final String GENEDB = "GeneDB".toUpperCase(); | |
| 96 | ||
| 97 | ||
| 98 | /** | |
| 99 | * Ensembl | |
| 100 | */ | |
| 101 | public static final String ENSEMBL = "ENSEMBL"; | |
| 102 | ||
| 103 | public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES"; | |
| 104 | ||
| 105 | ||
| 106 | /** | |
| 107 | * List of databases whose sequences might have coding regions annotated | |
| 108 | */ | |
| 109 | public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB, | |
| 110 | ENSEMBL, ENSEMBLGENOMES }; | |
| 111 | ||
| 112 | public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL }; | |
| 113 | ||
| 114 | public static final String[] PROTEINDBS = { UNIPROT, UNIPROTKB, | |
| 115 | EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein | |
| 116 | ||
| 117 | ||
| 118 | public static final String[] allTypes = new String[] { | |
| 119 | UNIPROT, UP_NAME, UNIPROTKB, | |
| 120 | EMBLCDSProduct, PDB, EMBL, | |
| 121 | EMBLCDS, PFAM, RFAM, | |
| 122 | GENEDB, ENSEMBL, ENSEMBLGENOMES | |
| 123 | }; | |
| 124 | ||
| 125 | ||
| 126 | public static String[] allSourcesFromReflection; | |
| 127 | ||
| 128 | 4562 |  public static String[] allSources() |
| 129 | ||
| 130 | { | |
| 131 | /** | |
| 132 | * @j2sNative | |
| 133 | * | |
| 134 | * return C$.allTypes; | |
| 135 | * | |
| 136 | */ | |
| 137 | ||
| 138 | { | |
| 139 | 4562 | if (allSourcesFromReflection == null) |
| 140 | { | |
| 141 | 1 | List<String> src = new ArrayList<>(); |
| 142 | 1 | for (Field f : DBRefSource.class.getFields()) |
| 143 | { | |
| 144 | 18 | if (String.class.equals(f.getType())) |
| 145 | { | |
| 146 | 12 | try |
| 147 | { | |
| 148 | 12 | src.add((String) f.get(null)); |
| 149 | } catch (Exception x) | |
| 150 | { | |
| 151 | 0 | x.printStackTrace(); |
| 152 | } | |
| 153 | } | |
| 154 | } | |
| 155 | 1 | allSourcesFromReflection = src.toArray(new String[0]); |
| 156 | } | |
| 157 | 4562 | return allSourcesFromReflection; |
| 158 | } | |
| 159 | } | |
| 160 | ||
| 161 | ||
| 162 | } |