Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblFeatures	48	64	25	0.00%	Show methods

Class EnsemblFeatures

Class EnsemblFeatures	Line # 48	Total Statements 64	Complexity 25	TOTAL Coverage 0.00%
EnsemblFeatures()   EnsemblFeatures()	6060	1.01	1.01	0.0 0.00%
EnsemblFeatures(String)   EnsemblFeatures(String)	7070	1.01	1.01	0.0 0.00%
getDbName() : String   getDbName() : String	7575	1.01	1.01	0.0 0.00%
getSequenceRecords(String) : AlignmentI   getSequenceRecords(String) : AlignmentI	8888	6.06	2.02	0.0 0.00%
parseFeaturesJson(List<String>) : SequenceI   parseFeaturesJson(List<String>) : SequenceI	109109	33.033	9.09	0.0 0.00%
getFirstNotNull(Map<String, Object>,String) : String   getFirstNotNull(Map<String, Object>,String) : String	191191	7.07	4.04	0.0 0.00%
setFeatureAttribute(SequenceFeature,Map<String, Object>,String) : void   setFeatureAttribute(SequenceFeature,Map<String, Object>,String) : void	219219	3.03	2.02	0.0 0.00%
getUrl(List<String>) : URL   getUrl(List<String>) : URL	235235	7.07	1.01	0.0 0.00%
useGetRequest() : boolean   useGetRequest() : boolean	265265	1.01	1.01	0.0 0.00%
getRequestMimeType() : String   getRequestMimeType() : String	275275	1.01	1.01	0.0 0.00%
getResponseMimeType() : String   getResponseMimeType() : String	284284	1.01	1.01	0.0 0.00%
getSequenceRecords(String,EnsemblFeatureType[]) : AlignmentI   getSequenceRecords(String,EnsemblFeatureType[]) : AlignmentI	299299	2.02	1.01	0.0 0.00%

 

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 java.io.IOException;
24		import java.net.MalformedURLException;
25		import java.net.URL;
26		import java.util.ArrayList;
27		import java.util.Iterator;
28		import java.util.List;
29		import java.util.Map;
30
31		import org.json.simple.parser.ParseException;
32
33		import jalview.datamodel.Alignment;
34		import jalview.datamodel.AlignmentI;
35		import jalview.datamodel.Sequence;
36		import jalview.datamodel.SequenceFeature;
37		import jalview.datamodel.SequenceI;
38		import jalview.io.gff.SequenceOntologyI;
39		import jalview.util.JSONUtils;
40
41		/**
42		* A client for fetching and processing Ensembl feature data in GFF format by
43		* calling the overlap REST service
44		*
45		* @author gmcarstairs
46		* @see http://rest.ensembl.org/documentation/info/overlap_id
47		*/
		0% Uncovered Elements: 98 (98) Complexity: 25 Complexity Density: 0.39
48		class EnsemblFeatures extends EnsemblRestClient
49		{
50		/*
51		* The default features to retrieve from Ensembl
52		* can override in getSequenceRecords parameter
53		*/
54		private EnsemblFeatureType[] featuresWanted = { EnsemblFeatureType.cds,
55		EnsemblFeatureType.exon, EnsemblFeatureType.variation };
56
57		/**
58		* Default constructor (to use rest.ensembl.org)
59		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
60	0	public EnsemblFeatures()...
61		{
62	0	super();
63		}
64
65		/**
66		* Constructor given the target domain to fetch data from
67		*
68		* @param d
69		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
70	0	public EnsemblFeatures(String d)...
71		{
72	0	super(d);
73		}
74
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
75	0	@Override...
76		public String getDbName()
77		{
78	0	return "ENSEMBL (features)";
79		}
80
81		/**
82		* Makes a query to the REST overlap endpoint for the given sequence
83		* identifier. This returns an 'alignment' consisting of one 'dummy sequence'
84		* (the genomic sequence for which overlap features are returned by the
85		* service). This sequence will have on it sequence features which are the
86		* real information of interest, such as CDS regions or sequence variations.
87		*/
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
88	0	@Override...
89		public AlignmentI getSequenceRecords(String query) throws IOException
90		{
91		// TODO: use a vararg String... for getSequenceRecords instead?
92
93	0	List<String> queries = new ArrayList<>();
94	0	queries.add(query);
95	0	SequenceI seq = parseFeaturesJson(queries);
96	0	if (seq == null)
97	0	return null;
98	0	return new Alignment(new SequenceI[] { seq });
99
100		}
101
102		/**
103		* Parses the JSON response into Jalview sequence features and attaches them
104		* to a dummy sequence
105		*
106		* @param br
107		* @return
108		*/
		0% Uncovered Elements: 45 (45) Complexity: 9 Complexity Density: 0.27
109	0	@SuppressWarnings("unchecked")...
110		private SequenceI parseFeaturesJson(List<String> queries)
111		{
112	0	SequenceI seq = new Sequence("Dummy", "");
113	0	try
114		{
115	0	Iterator<Object> rvals = (Iterator<Object>) getJSON(null, queries, -1,
116		MODE_ITERATOR, null);
117	0	if (rvals == null)
118		{
119	0	return null;
120		}
121	0	while (rvals.hasNext())
122		{
123	0	try
124		{
125	0	Map<String, Object> obj = (Map<String, Object>) rvals.next();
126	0	String type = obj.get("feature_type").toString();
127	0	int start = Integer.parseInt(obj.get("start").toString());
128	0	int end = Integer.parseInt(obj.get("end").toString());
129	0	String source = obj.get("source").toString();
130	0	String strand = obj.get("strand").toString();
131	0	Object phase = obj.get("phase");
132	0	String alleles = JSONUtils
133		.arrayToStringList((List<Object>) obj.get("alleles"));
134	0	String clinSig = JSONUtils.arrayToStringList(
135		(List<Object>) obj.get("clinical_significance"));
136
137		/*
138		* convert 'variation' to 'sequence_variant', and 'cds' to 'CDS'
139		* so as to have a valid SO term for the feature type
140		* ('gene', 'exon', 'transcript' don't need any conversion)
141		*/
142	0	if ("variation".equals(type))
143		{
144	0	type = SequenceOntologyI.SEQUENCE_VARIANT;
145		}
146	0	else if (SequenceOntologyI.CDS.equalsIgnoreCase((type)))
147		{
148	0	type = SequenceOntologyI.CDS;
149		}
150
151	0	String desc = getFirstNotNull(obj, "alleles", "external_name",
152		JSON_ID);
153	0	SequenceFeature sf = new SequenceFeature(type, desc, start, end,
154		source);
155	0	sf.setStrand("1".equals(strand) ? "+" : "-");
156	0	if (phase != null)
157		{
158	0	sf.setPhase(phase.toString());
159		}
160	0	setFeatureAttribute(sf, obj, "id");
161	0	setFeatureAttribute(sf, obj, "Parent");
162	0	setFeatureAttribute(sf, obj, "consequence_type");
163	0	sf.setValue("alleles", alleles);
164	0	sf.setValue("clinical_significance", clinSig);
165
166	0	seq.addSequenceFeature(sf);
167
168		} catch (Throwable t)
169		{
170		// ignore - keep trying other features
171		}
172		}
173		} catch (ParseException | IOException e)
174		{
175	0	e.printStackTrace();
176		// ignore
177		}
178
179	0	return seq;
180		}
181
182		/**
183		* Returns the first non-null attribute found (if any) as a string, formatted
184		* suitably for display as feature description or tooltip. Answers null if
185		* none of the attribute keys is present.
186		*
187		* @param obj
188		* @param keys
189		* @return
190		*/
		0% Uncovered Elements: 13 (13) Complexity: 4 Complexity Density: 0.57
191	0	@SuppressWarnings("unchecked")...
192		protected String getFirstNotNull(Map<String, Object> obj, String... keys)
193		{
194	0	for (String key : keys)
195		{
196	0	Object val = obj.get(key);
197	0	if (val != null)
198		{
199	0	String s = val instanceof List<?>
200		? JSONUtils.arrayToStringList((List<Object>) val)
201		: val.toString();
202	0	if (!s.isEmpty())
203		{
204	0	return s;
205		}
206		}
207		}
208	0	return null;
209		}
210
211		/**
212		* A helper method that reads the 'key' entry in the JSON object, and if not
213		* null, sets its string value as an attribute on the sequence feature
214		*
215		* @param sf
216		* @param obj
217		* @param key
218		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
219	0	protected void setFeatureAttribute(SequenceFeature sf,...
220		Map<String, Object> obj, String key)
221		{
222	0	Object object = obj.get(key);
223	0	if (object != null)
224		{
225	0	sf.setValue(key, object.toString());
226		}
227		}
228
229		/**
230		* Returns a URL for the REST overlap endpoint
231		*
232		* @param ids
233		* @return
234		*/
		0% Uncovered Elements: 7 (7) Complexity: 1 Complexity Density: 0.14
235	0	@Override...
236		protected URL getUrl(List<String> ids) throws MalformedURLException
237		{
238	0	StringBuffer urlstring = new StringBuffer(128);
239	0	urlstring.append(getDomain()).append("/overlap/id/").append(ids.get(0));
240
241		// @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
242	0	urlstring.append("?content-type=" + getResponseMimeType());
243
244		/*
245		* specify object_type=gene in case is shared by transcript and/or protein;
246		* currently only fetching features for gene sequences;
247		* refactor in future if needed to fetch for transcripts
248		*/
249	0	urlstring.append("&").append(OBJECT_TYPE).append("=")
250		.append(OBJECT_TYPE_GENE);
251
252		/*
253		* specify features to retrieve
254		* @see http://rest.ensembl.org/documentation/info/overlap_id
255		* could make the list a configurable entry in .jalview_properties
256		*/
257	0	for (EnsemblFeatureType feature : featuresWanted)
258		{
259	0	urlstring.append("&feature=").append(feature.name());
260		}
261
262	0	return new URL(urlstring.toString());
263		}
264
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
265	0	@Override...
266		protected boolean useGetRequest()
267		{
268	0	return true;
269		}
270
271		/**
272		* Returns the MIME type for GFF3. For GET requests the Content-type header
273		* describes the required encoding of the response.
274		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
275	0	@Override...
276		protected String getRequestMimeType()
277		{
278	0	return "application/json";
279		}
280
281		/**
282		* Returns the MIME type wanted for the response
283		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
284	0	@Override...
285		protected String getResponseMimeType()
286		{
287	0	return "application/json";
288		}
289
290		/**
291		* Overloaded method that allows a list of features to retrieve to be
292		* specified
293		*
294		* @param accId
295		* @param features
296		* @return
297		* @throws IOException
298		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
299	0	protected AlignmentI getSequenceRecords(String accId,...
300		EnsemblFeatureType[] features) throws IOException
301		{
302	0	featuresWanted = features;
303	0	return getSequenceRecords(accId);
304		}
305		}