Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblSequenceFetcher	36	12	11	0.00%	Show methods
EnsemblSequenceFetcher.EnsemblFeatureType	78	0	0	-1.0 -	Show methods

Class EnsemblSequenceFetcher

Class EnsemblSequenceFetcher	Line # 36	Total Statements 12	Complexity 11	TOTAL Coverage 0.00%
EnsemblSequenceFetcher()   EnsemblSequenceFetcher()	9090	3.03	1.01	0.0 0.00%
getDbSource() : String   getDbSource() : String	103103	1.01	1.01	0.0 0.00%
getAccessionSeparator() : String   getAccessionSeparator() : String	110110	1.01	1.01	0.0 0.00%
getAccessionValidator() : Regex   getAccessionValidator() : Regex	122122	1.01	1.01	0.0 0.00%
isValidReference(String) : boolean   isValidReference(String) : boolean	128128	1.01	1.01	0.0 0.00%
getTier() : int   getTier() : int	134134	1.01	1.01	0.0 0.00%
getTestQuery() : String   getTestQuery() : String	143143	1.01	1.01	0.0 0.00%
isDnaCoding() : boolean   isDnaCoding() : boolean	151151	1.01	1.01	0.0 0.00%
getDomain() : String   getDomain() : String	163163	1.01	1.01	0.0 0.00%
setDomain(String) : void   setDomain(String) : void	168168	1.01	2.02	0.0 0.00%

 

Class EnsemblSequenceFetcher.EnsemblFeatureType

Class EnsemblSequenceFetcher.EnsemblFeatureType	Line # 78	Total Statements 0	Complexity 0	TOTAL Coverage -1.0 -

 

Contributing 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.util.Platform;
27		import jalview.ws.seqfetcher.DbSourceProxyImpl;
28
29		import com.stevesoft.pat.Regex;
30
31		/**
32		* A base class for Ensembl sequence fetchers
33		*
34		* @author gmcarstairs
35		*/
		0% Uncovered Elements: 24 (24) Complexity: 11 Complexity Density: 0.92
36		abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
37		{
38		// domain properties lookup keys:
39		protected static final String ENSEMBL_BASEURL = "ENSEMBL_BASEURL";
40
41		protected static final String ENSEMBL_GENOMES_BASEURL = "ENSEMBL_GENOMES_BASEURL";
42
43		// domain properties default values:
44		protected static final String DEFAULT_ENSEMBL_BASEURL = "https://rest.ensembl.org";
45
46		// ensemblgenomes REST service merged to ensembl 9th April 2019
47		protected static final String DEFAULT_ENSEMBL_GENOMES_BASEURL = DEFAULT_ENSEMBL_BASEURL;
48
49		/*
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
53		*/
54		private static final Regex ACCESSION_REGEX = Platform.newRegex(
55		"(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|"
56		+ "(CCDS[0-9.]{3,}$)");
57
58		protected final String ensemblGenomesDomain;
59
60		protected final String ensemblDomain;
61
62		protected static final String OBJECT_TYPE_TRANSLATION = "Translation";
63
64		protected static final String OBJECT_TYPE_TRANSCRIPT = "Transcript";
65
66		protected static final String OBJECT_TYPE_GENE = "Gene";
67
68		protected static final String PARENT = "Parent";
69
70		protected static final String JSON_ID = AlignmentUtils.VARIANT_ID; // "id";
71
72		protected static final String OBJECT_TYPE = "object_type";
73
74		/*
75		* possible values for the 'feature' parameter of the /overlap REST service
76		* @see http://rest.ensembl.org/documentation/info/overlap_id
77		*/
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
78		protected enum EnsemblFeatureType
79		{
80		gene, transcript, cds, exon, repeat, simple, misc, variation,
81		somatic_variation, structural_variation, somatic_structural_variation,
82		constrained, regulatory
83		}
84
85		private String domain;
86
87		/**
88		* Constructor
89		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
90	0	public EnsemblSequenceFetcher()...
91		{
92		/*
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
95		*/
96	0	ensemblDomain = Cache
97		.getDefault(ENSEMBL_BASEURL, DEFAULT_ENSEMBL_BASEURL).trim();
98	0	ensemblGenomesDomain = Cache.getDefault(ENSEMBL_GENOMES_BASEURL,
99		DEFAULT_ENSEMBL_GENOMES_BASEURL).trim();
100	0	domain = ensemblDomain;
101		}
102
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
103	0	@Override...
104		public String getDbSource()
105		{
106		// NB ensure Uniprot xrefs are canonicalised from "Ensembl" to "ENSEMBL"
107	0	return DBRefSource.ENSEMBL;
108		}
109
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
110	0	@Override...
111		public String getAccessionSeparator()
112		{
113	0	return " ";
114		}
115
116		/**
117		* Ensembl accession are ENST + 11 digits for human transcript, ENSG for human
118		* gene. Other species insert 3 letters e.g. ENSMUST..., ENSMUSG...
119		*
120		* @see http://www.ensembl.org/Help/View?id=151
121		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
122	0	@Override...
123		public Regex getAccessionValidator()
124		{
125	0	return ACCESSION_REGEX;
126		}
127
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
128	0	@Override...
129		public boolean isValidReference(String accession)
130		{
131	0	return getAccessionValidator().search(accession);
132		}
133
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
134	0	@Override...
135		public int getTier()
136		{
137	0	return 0;
138		}
139
140		/**
141		* Default test query is a transcript
142		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
143	0	@Override...
144		public String getTestQuery()
145		{
146		// has CDS on reverse strand:
147	0	return "ENST00000288602";
148		// ENST00000461457 // forward strand
149		}
150
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
151	0	@Override...
152		public boolean isDnaCoding()
153		{
154	0	return true;
155		}
156
157		/**
158		* Returns the domain name to query e.g. http://rest.ensembl.org or
159		* http://rest.ensemblgenomes.org
160		*
161		* @return
162		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
163	0	protected String getDomain()...
164		{
165	0	return domain;
166		}
167
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
168	0	protected void setDomain(String d)...
169		{
170	0	domain = d == null ? null : d.trim();
171		}
172		}