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Coverage Report

  1. Project Clover database Mon Nov 11 2024 17:27:16 GMT
  2. Package jalview.ext.ensembl

File EnsemblSequenceFetcher.java

 

Coverage histogram

../../../img/srcFileCovDistChart7.png
29% of files have more coverage

Code metrics

2
12
10
2
171
82
11
0.92
1.2
5
1.1

Classes

Class Line # Actions
EnsemblSequenceFetcher 35 12 11
0.708333370.8%
EnsemblSequenceFetcher.EnsemblFeatureType 77 0 0
-1.0 -
 

Contributing tests

This file is covered by 206 tests. .

Source view

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.ext.ensembl;
22   
23    import jalview.analysis.AlignmentUtils;
24    import jalview.bin.Cache;
25    import jalview.datamodel.DBRefSource;
26    import jalview.ws.seqfetcher.DbSourceProxyImpl;
27   
28    import com.stevesoft.pat.Regex;
29   
30    /**
31    * A base class for Ensembl sequence fetchers
32    *
33    * @author gmcarstairs
34    */
 
35    abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
36    {
37    // domain properties lookup keys:
38    protected static final String ENSEMBL_BASEURL = "ENSEMBL_BASEURL";
39   
40    protected static final String ENSEMBL_GENOMES_BASEURL = "ENSEMBL_GENOMES_BASEURL";
41   
42    // domain properties default values:
43    protected static final String DEFAULT_ENSEMBL_BASEURL = "https://rest.ensembl.org";
44   
45    // ensemblgenomes REST service merged to ensembl 9th April 2019
46    protected static final String DEFAULT_ENSEMBL_GENOMES_BASEURL = DEFAULT_ENSEMBL_BASEURL;
47   
48    /*
49    * accepts ENSG/T/E/P with 11 digits
50    * or ENSMUSP or similar for other species
51    * or CCDSnnnnn.nn with at least 3 digits
52    */
53    private static final Regex ACCESSION_REGEX = new Regex(
54    "(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|"
55    + "(CCDS[0-9.]{3,}$)");
56   
57    protected final String ensemblGenomesDomain;
58   
59    protected final String ensemblDomain;
60   
61    protected static final String OBJECT_TYPE_TRANSLATION = "Translation";
62   
63    protected static final String OBJECT_TYPE_TRANSCRIPT = "Transcript";
64   
65    protected static final String OBJECT_TYPE_GENE = "Gene";
66   
67    protected static final String PARENT = "Parent";
68   
69    protected static final String JSON_ID = AlignmentUtils.VARIANT_ID; // "id";
70   
71    protected static final String OBJECT_TYPE = "object_type";
72   
73    /*
74    * possible values for the 'feature' parameter of the /overlap REST service
75    * @see http://rest.ensembl.org/documentation/info/overlap_id
76    */
 
77    protected enum EnsemblFeatureType
78    {
79    gene, transcript, cds, exon, repeat, simple, misc, variation,
80    somatic_variation, structural_variation, somatic_structural_variation,
81    constrained, regulatory
82    }
83   
84    private String domain;
85   
86    /**
87    * Constructor
88    */
 
89  50 toggle public EnsemblSequenceFetcher()
90    {
91    /*
92    * the default domain names may be overridden in .jalview_properties;
93    * this allows an easy change from http to https in future if needed
94    */
95  50 ensemblDomain = Cache
96    .getDefault(ENSEMBL_BASEURL, DEFAULT_ENSEMBL_BASEURL).trim();
97  50 ensemblGenomesDomain = Cache.getDefault(ENSEMBL_GENOMES_BASEURL,
98    DEFAULT_ENSEMBL_GENOMES_BASEURL).trim();
99  50 domain = ensemblDomain;
100    }
101   
 
102  3398 toggle @Override
103    public String getDbSource()
104    {
105    // NB ensure Uniprot xrefs are canonicalised from "Ensembl" to "ENSEMBL"
106  3398 return DBRefSource.ENSEMBL;
107    }
108   
 
109  6 toggle @Override
110    public String getAccessionSeparator()
111    {
112  6 return " ";
113    }
114   
115    /**
116    * Ensembl accession are ENST + 11 digits for human transcript, ENSG for human
117    * gene. Other species insert 3 letters e.g. ENSMUST..., ENSMUSG...
118    *
119    * @see http://www.ensembl.org/Help/View?id=151
120    */
 
121  6 toggle @Override
122    public Regex getAccessionValidator()
123    {
124  6 return ACCESSION_REGEX;
125    }
126   
 
127  17 toggle @Override
128    public boolean isValidReference(String accession)
129    {
130  17 return getAccessionValidator().search(accession);
131    }
132   
 
133  0 toggle @Override
134    public int getTier()
135    {
136  0 return 0;
137    }
138   
139    /**
140    * Default test query is a transcript
141    */
 
142  0 toggle @Override
143    public String getTestQuery()
144    {
145    // has CDS on reverse strand:
146  0 return "ENST00000288602";
147    // ENST00000461457 // forward strand
148    }
149   
 
150  0 toggle @Override
151    public boolean isDnaCoding()
152    {
153  0 return true;
154    }
155   
156    /**
157    * Returns the domain name to query e.g. http://rest.ensembl.org or
158    * http://rest.ensemblgenomes.org
159    *
160    * @return
161    */
 
162  1 toggle protected String getDomain()
163    {
164  1 return domain;
165    }
166   
 
167  1 toggle protected void setDomain(String d)
168    {
169  1 domain = d == null ? null : d.trim();
170    }
171    }
  • Report generated by OpenClover v 4.4.1 on Mon Nov 11 2024 17:34:35 GMT using coverage data from Mon Nov 11 2024 17:34:16 GMT.
  • OpenClover is free and open-source software.