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.ext.ensembl;
23 import jalview.analysis.AlignmentUtils;
24 import jalview.bin.Cache;
25 import jalview.datamodel.DBRefSource;
26 import jalview.util.Platform;
27 import jalview.ws.seqfetcher.DbSourceProxyImpl;
29 import com.stevesoft.pat.Regex;
32 * A base class for Ensembl sequence fetchers
36 abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
38 // domain properties lookup keys:
39 protected static final String ENSEMBL_BASEURL = "ENSEMBL_BASEURL";
41 protected static final String ENSEMBL_GENOMES_BASEURL = "ENSEMBL_GENOMES_BASEURL";
43 // domain properties default values:
44 protected static final String DEFAULT_ENSEMBL_BASEURL = "https://rest.ensembl.org";
46 // ensemblgenomes REST service merged to ensembl 9th April 2019
47 protected static final String DEFAULT_ENSEMBL_GENOMES_BASEURL = DEFAULT_ENSEMBL_BASEURL;
50 * accepts ENSG/T/E/P with 11 digits
51 * or ENSMUSP or similar for other species
52 * or CCDSnnnnn.nn with at least 3 digits
54 private static final Regex ACCESSION_REGEX = Platform.newRegex(
55 "(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|"
56 + "(CCDS[0-9.]{3,}$)");
58 protected final String ensemblGenomesDomain;
60 protected final String ensemblDomain;
62 protected static final String OBJECT_TYPE_TRANSLATION = "Translation";
64 protected static final String OBJECT_TYPE_TRANSCRIPT = "Transcript";
66 protected static final String OBJECT_TYPE_GENE = "Gene";
68 protected static final String PARENT = "Parent";
70 protected static final String JSON_ID = AlignmentUtils.VARIANT_ID; // "id";
72 protected static final String OBJECT_TYPE = "object_type";
75 * possible values for the 'feature' parameter of the /overlap REST service
76 * @see http://rest.ensembl.org/documentation/info/overlap_id
78 protected enum EnsemblFeatureType
80 gene, transcript, cds, exon, repeat, simple, misc, variation,
81 somatic_variation, structural_variation, somatic_structural_variation,
82 constrained, regulatory
85 private String domain;
90 public EnsemblSequenceFetcher()
93 * the default domain names may be overridden in .jalview_properties;
94 * this allows an easy change from http to https in future if needed
96 ensemblDomain = Cache.getDefault(ENSEMBL_BASEURL,
97 DEFAULT_ENSEMBL_BASEURL).trim();
98 ensemblGenomesDomain = Cache.getDefault(ENSEMBL_GENOMES_BASEURL,
99 DEFAULT_ENSEMBL_GENOMES_BASEURL).trim();
100 domain = ensemblDomain;
104 public String getDbSource()
106 // NB ensure Uniprot xrefs are canonicalised from "Ensembl" to "ENSEMBL"
107 return DBRefSource.ENSEMBL;
111 public String getAccessionSeparator()
117 * Ensembl accession are ENST + 11 digits for human transcript, ENSG for human
118 * gene. Other species insert 3 letters e.g. ENSMUST..., ENSMUSG...
120 * @see http://www.ensembl.org/Help/View?id=151
123 public Regex getAccessionValidator()
125 return ACCESSION_REGEX;
129 public boolean isValidReference(String accession)
131 return getAccessionValidator().search(accession);
141 * Default test query is a transcript
144 public String getTestQuery()
146 // has CDS on reverse strand:
147 return "ENST00000288602";
148 // ENST00000461457 // forward strand
152 public boolean isDnaCoding()
158 * Returns the domain name to query e.g. http://rest.ensembl.org or
159 * http://rest.ensemblgenomes.org
163 protected String getDomain()
168 protected void setDomain(String d)
170 domain = d == null ? null : d.trim();