Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblSequenceFetcher	35	12	11	0.00%	Show methods
EnsemblSequenceFetcher.EnsemblFeatureType	77	0	0	-1.0 -	Show methods

Class EnsemblSequenceFetcher

Class EnsemblSequenceFetcher	Line # 35	Total Statements 12	Complexity 11	TOTAL Coverage 0.00%
EnsemblSequenceFetcher()   EnsemblSequenceFetcher()	8989	3.03	1.01	0.0 0.00%
getDbSource() : String   getDbSource() : String	102102	1.01	1.01	0.0 0.00%
getAccessionSeparator() : String   getAccessionSeparator() : String	109109	1.01	1.01	0.0 0.00%
getAccessionValidator() : Regex   getAccessionValidator() : Regex	121121	1.01	1.01	0.0 0.00%
isValidReference(String) : boolean   isValidReference(String) : boolean	127127	1.01	1.01	0.0 0.00%
getTier() : int   getTier() : int	133133	1.01	1.01	0.0 0.00%
getTestQuery() : String   getTestQuery() : String	142142	1.01	1.01	0.0 0.00%
isDnaCoding() : boolean   isDnaCoding() : boolean	150150	1.01	1.01	0.0 0.00%
getDomain() : String   getDomain() : String	162162	1.01	1.01	0.0 0.00%
setDomain(String) : void   setDomain(String) : void	167167	1.01	2.02	0.0 0.00%

 

Class EnsemblSequenceFetcher.EnsemblFeatureType

Class EnsemblSequenceFetcher.EnsemblFeatureType	Line # 77	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.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		*/
		0% Uncovered Elements: 24 (24) Complexity: 11 Complexity Density: 0.92
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		*/
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
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		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
89	0	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	0	ensemblDomain = Cache
96		.getDefault(ENSEMBL_BASEURL, DEFAULT_ENSEMBL_BASEURL).trim();
97	0	ensemblGenomesDomain = Cache.getDefault(ENSEMBL_GENOMES_BASEURL,
98		DEFAULT_ENSEMBL_GENOMES_BASEURL).trim();
99	0	domain = ensemblDomain;
100		}
101
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
102	0	@Override...
103		public String getDbSource()
104		{
105		// NB ensure Uniprot xrefs are canonicalised from "Ensembl" to "ENSEMBL"
106	0	return DBRefSource.ENSEMBL;
107		}
108
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
109	0	@Override...
110		public String getAccessionSeparator()
111		{
112	0	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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
121	0	@Override...
122		public Regex getAccessionValidator()
123		{
124	0	return ACCESSION_REGEX;
125		}
126
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
127	0	@Override...
128		public boolean isValidReference(String accession)
129		{
130	0	return getAccessionValidator().search(accession);
131		}
132
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
133	0	@Override...
134		public int getTier()
135		{
136	0	return 0;
137		}
138
139		/**
140		* Default test query is a transcript
141		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
142	0	@Override...
143		public String getTestQuery()
144		{
145		// has CDS on reverse strand:
146	0	return "ENST00000288602";
147		// ENST00000461457 // forward strand
148		}
149
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
150	0	@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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
162	0	protected String getDomain()...
163		{
164	0	return domain;
165		}
166
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
167	0	protected void setDomain(String d)...
168		{
169	0	domain = d == null ? null : d.trim();
170		}
171		}