Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
EnsemblFeatures	41	22	11	33	0.00%	Show methods

Class EnsemblFeatures

Class EnsemblFeatures	Line # 41	Total Statements 22	Complexity 11	Uncovered Elements 33	TOTAL Coverage 0.00%
EnsemblFeatures()   EnsemblFeatures()	5353	1.01	1.01	1.01	0.0 0.00%
EnsemblFeatures(String)   EnsemblFeatures(String)	6363	1.01	1.01	1.01	0.0 0.00%
getDbName() : String   getDbName() : String	6868	1.01	1.01	1.01	0.0 0.00%
getSequenceRecords(String) : AlignmentI   getSequenceRecords(String) : AlignmentI	8181	7.07	3.03	9.09	0.0 0.00%
getUrl(List<String>) : URL   getUrl(List<String>) : URL	102102	7.07	1.01	7.07	0.0 0.00%
useGetRequest() : boolean   useGetRequest() : boolean	132132	1.01	1.01	1.01	0.0 0.00%
getRequestMimeType(boolean) : String   getRequestMimeType(boolean) : String	142142	1.01	1.01	1.01	0.0 0.00%
getResponseMimeType() : String   getResponseMimeType() : String	151151	1.01	1.01	1.01	0.0 0.00%
getSequenceRecords(String,EnsemblFeatureType[]) : AlignmentI   getSequenceRecords(String,EnsemblFeatureType[]) : AlignmentI	166166	2.02	1.01	2.02	0.0 0.00%

 

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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.ext.ensembl;
22
23		import jalview.datamodel.Alignment;
24		import jalview.datamodel.AlignmentI;
25		import jalview.io.FeaturesFile;
26		import jalview.io.FileParse;
27
28		import java.io.IOException;
29		import java.net.MalformedURLException;
30		import java.net.URL;
31		import java.util.ArrayList;
32		import java.util.List;
33
34		/**
35		* A client for fetching and processing Ensembl feature data in GFF format by
36		* calling the overlap REST service
37		*
38		* @author gmcarstairs
39		* @see http://rest.ensembl.org/documentation/info/overlap_id
40		*/
		0% Uncovered Elements: 33 (33) Complexity: 11 Complexity Density: 0.5
41		class EnsemblFeatures extends EnsemblRestClient
42		{
43		/*
44		* The default features to retrieve from Ensembl
45		* can override in getSequenceRecords parameter
46		*/
47		private EnsemblFeatureType[] featuresWanted = { EnsemblFeatureType.cds,
48		EnsemblFeatureType.exon, EnsemblFeatureType.variation };
49
50		/**
51		* Default constructor (to use rest.ensembl.org)
52		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
53	0	public EnsemblFeatures()...
54		{
55	0	super();
56		}
57
58		/**
59		* Constructor given the target domain to fetch data from
60		*
61		* @param d
62		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
63	0	public EnsemblFeatures(String d)...
64		{
65	0	super(d);
66		}
67
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
68	0	@Override...
69		public String getDbName()
70		{
71	0	return "ENSEMBL (features)";
72		}
73
74		/**
75		* Makes a query to the REST overlap endpoint for the given sequence
76		* identifier. This returns an 'alignment' consisting of one 'dummy sequence'
77		* (the genomic sequence for which overlap features are returned by the
78		* service). This sequence will have on it sequence features which are the
79		* real information of interest, such as CDS regions or sequence variations.
80		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.43
81	0	@Override...
82		public AlignmentI getSequenceRecords(String query) throws IOException
83		{
84		// TODO: use a vararg String... for getSequenceRecords instead?
85	0	List<String> queries = new ArrayList<>();
86	0	queries.add(query);
87	0	FileParse fp = getSequenceReader(queries);
88	0	if (fp == null || !fp.isValid())
89		{
90	0	return null;
91		}
92	0	FeaturesFile fr = new FeaturesFile(fp);
93	0	return new Alignment(fr.getSeqsAsArray());
94		}
95
96		/**
97		* Returns a URL for the REST overlap endpoint
98		*
99		* @param ids
100		* @return
101		*/
		0% Uncovered Elements: 7 (7) Complexity: 1 Complexity Density: 0.14
102	0	@Override...
103		protected URL getUrl(List<String> ids) throws MalformedURLException
104		{
105	0	StringBuffer urlstring = new StringBuffer(128);
106	0	urlstring.append(getDomain()).append("/overlap/id/").append(ids.get(0));
107
108		// @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
109	0	urlstring.append("?content-type=text/x-gff3");
110
111		/*
112		* specify object_type=gene in case is shared by transcript and/or protein;
113		* currently only fetching features for gene sequences;
114		* refactor in future if needed to fetch for transcripts
115		*/
116	0	urlstring.append("&").append(OBJECT_TYPE).append("=")
117		.append(OBJECT_TYPE_GENE);
118
119		/*
120		* specify features to retrieve
121		* @see http://rest.ensembl.org/documentation/info/overlap_id
122		* could make the list a configurable entry in .jalview_properties
123		*/
124	0	for (EnsemblFeatureType feature : featuresWanted)
125		{
126	0	urlstring.append("&feature=").append(feature.name());
127		}
128
129	0	return new URL(urlstring.toString());
130		}
131
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
132	0	@Override...
133		protected boolean useGetRequest()
134		{
135	0	return true;
136		}
137
138		/**
139		* Returns the MIME type for GFF3. For GET requests the Content-type header
140		* describes the required encoding of the response.
141		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
142	0	@Override...
143		protected String getRequestMimeType(boolean multipleIds)
144		{
145	0	return "text/x-gff3";
146		}
147
148		/**
149		* Returns the MIME type for GFF3.
150		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
151	0	@Override...
152		protected String getResponseMimeType()
153		{
154	0	return "text/x-gff3";
155		}
156
157		/**
158		* Overloaded method that allows a list of features to retrieve to be
159		* specified
160		*
161		* @param accId
162		* @param features
163		* @return
164		* @throws IOException
165		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
166	0	protected AlignmentI getSequenceRecords(String accId,...
167		EnsemblFeatureType[] features) throws IOException
168		{
169	0	featuresWanted = features;
170	0	return getSequenceRecords(accId);
171		}
172		}