Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblFeatures	50	64	25	0.00%	Show methods

Class EnsemblFeatures

Class EnsemblFeatures	Line # 50	Total Statements 64	Complexity 25	TOTAL Coverage 0.00%
EnsemblFeatures()   EnsemblFeatures()	6262	1.01	1.01	0.0 0.00%
EnsemblFeatures(String)   EnsemblFeatures(String)	7272	1.01	1.01	0.0 0.00%
getDbName() : String   getDbName() : String	7777	1.01	1.01	0.0 0.00%
getSequenceRecords(String) : AlignmentI   getSequenceRecords(String) : AlignmentI	9090	6.06	2.02	0.0 0.00%
parseFeaturesJson(List<String>) : SequenceI   parseFeaturesJson(List<String>) : SequenceI	111111	33.033	9.09	0.0 0.00%
getFirstNotNull(Map<String, Object>,String) : String   getFirstNotNull(Map<String, Object>,String) : String	193193	7.07	4.04	0.0 0.00%
setFeatureAttribute(SequenceFeature,Map<String, Object>,String) : void   setFeatureAttribute(SequenceFeature,Map<String, Object>,String) : void	221221	3.03	2.02	0.0 0.00%
getUrl(List<String>) : URL   getUrl(List<String>) : URL	237237	7.07	1.01	0.0 0.00%
useGetRequest() : boolean   useGetRequest() : boolean	267267	1.01	1.01	0.0 0.00%
getRequestMimeType() : String   getRequestMimeType() : String	277277	1.01	1.01	0.0 0.00%
getResponseMimeType() : String   getResponseMimeType() : String	286286	1.01	1.01	0.0 0.00%
getSequenceRecords(String,EnsemblFeatureType[]) : AlignmentI   getSequenceRecords(String,EnsemblFeatureType[]) : AlignmentI	301301	2.02	1.01	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.datamodel.Sequence;
26		import jalview.datamodel.SequenceFeature;
27		import jalview.datamodel.SequenceI;
28		import jalview.io.gff.SequenceOntologyI;
29		import jalview.util.JSONUtils;
30		import jalview.util.Platform;
31
32		import java.io.BufferedReader;
33		import java.io.IOException;
34		import java.net.MalformedURLException;
35		import java.net.URL;
36		import java.util.ArrayList;
37		import java.util.Iterator;
38		import java.util.List;
39		import java.util.Map;
40
41		import org.json.simple.parser.ParseException;
42
43		/**
44		* A client for fetching and processing Ensembl feature data in GFF format by
45		* calling the overlap REST service
46		*
47		* @author gmcarstairs
48		* @see http://rest.ensembl.org/documentation/info/overlap_id
49		*/
		0% Uncovered Elements: 98 (98) Complexity: 25 Complexity Density: 0.39
50		class EnsemblFeatures extends EnsemblRestClient
51		{
52		/*
53		* The default features to retrieve from Ensembl
54		* can override in getSequenceRecords parameter
55		*/
56		private EnsemblFeatureType[] featuresWanted = { EnsemblFeatureType.cds,
57		EnsemblFeatureType.exon, EnsemblFeatureType.variation };
58
59		/**
60		* Default constructor (to use rest.ensembl.org)
61		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
62	0	public EnsemblFeatures()...
63		{
64	0	super();
65		}
66
67		/**
68		* Constructor given the target domain to fetch data from
69		*
70		* @param d
71		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
72	0	public EnsemblFeatures(String d)...
73		{
74	0	super(d);
75		}
76
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
77	0	@Override...
78		public String getDbName()
79		{
80	0	return "ENSEMBL (features)";
81		}
82
83		/**
84		* Makes a query to the REST overlap endpoint for the given sequence
85		* identifier. This returns an 'alignment' consisting of one 'dummy sequence'
86		* (the genomic sequence for which overlap features are returned by the
87		* service). This sequence will have on it sequence features which are the
88		* real information of interest, such as CDS regions or sequence variations.
89		*/
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
90	0	@Override...
91		public AlignmentI getSequenceRecords(String query) throws IOException
92		{
93		// TODO: use a vararg String... for getSequenceRecords instead?
94
95	0	List<String> queries = new ArrayList<>();
96	0	queries.add(query);
97	0	SequenceI seq = parseFeaturesJson(queries);
98	0	if (seq == null)
99	0	return null;
100	0	return new Alignment(new SequenceI[] { seq });
101
102		}
103
104		/**
105		* Parses the JSON response into Jalview sequence features and attaches them
106		* to a dummy sequence
107		*
108		* @param br
109		* @return
110		*/
		0% Uncovered Elements: 45 (45) Complexity: 9 Complexity Density: 0.27
111	0	@SuppressWarnings("unchecked")...
112		private SequenceI parseFeaturesJson(List<String> queries)
113		{
114	0	SequenceI seq = new Sequence("Dummy", "");
115	0	try
116		{
117	0	Iterator<Object> rvals = (Iterator<Object>) getJSON(null, queries, -1,
118		MODE_ITERATOR, null);
119	0	if (rvals == null)
120		{
121	0	return null;
122		}
123	0	while (rvals.hasNext())
124		{
125	0	try
126		{
127	0	Map<String, Object> obj = (Map<String, Object>) rvals.next();
128	0	String type = obj.get("feature_type").toString();
129	0	int start = Integer.parseInt(obj.get("start").toString());
130	0	int end = Integer.parseInt(obj.get("end").toString());
131	0	String source = obj.get("source").toString();
132	0	String strand = obj.get("strand").toString();
133	0	Object phase = obj.get("phase");
134	0	String alleles = JSONUtils
135		.arrayToStringList((List<Object>) obj.get("alleles"));
136	0	String clinSig = JSONUtils.arrayToStringList(
137		(List<Object>) obj.get("clinical_significance"));
138
139		/*
140		* convert 'variation' to 'sequence_variant', and 'cds' to 'CDS'
141		* so as to have a valid SO term for the feature type
142		* ('gene', 'exon', 'transcript' don't need any conversion)
143		*/
144	0	if ("variation".equals(type))
145		{
146	0	type = SequenceOntologyI.SEQUENCE_VARIANT;
147		}
148	0	else if (SequenceOntologyI.CDS.equalsIgnoreCase((type)))
149		{
150	0	type = SequenceOntologyI.CDS;
151		}
152
153	0	String desc = getFirstNotNull(obj, "alleles", "external_name",
154		JSON_ID);
155	0	SequenceFeature sf = new SequenceFeature(type, desc, start, end,
156		source);
157	0	sf.setStrand("1".equals(strand) ? "+" : "-");
158	0	if (phase != null)
159		{
160	0	sf.setPhase(phase.toString());
161		}
162	0	setFeatureAttribute(sf, obj, "id");
163	0	setFeatureAttribute(sf, obj, "Parent");
164	0	setFeatureAttribute(sf, obj, "consequence_type");
165	0	sf.setValue("alleles", alleles);
166	0	sf.setValue("clinical_significance", clinSig);
167
168	0	seq.addSequenceFeature(sf);
169
170		} catch (Throwable t)
171		{
172		// ignore - keep trying other features
173		}
174		}
175		} catch (ParseException | IOException e)
176		{
177	0	e.printStackTrace();
178		// ignore
179		}
180
181	0	return seq;
182		}
183
184		/**
185		* Returns the first non-null attribute found (if any) as a string, formatted
186		* suitably for display as feature description or tooltip. Answers null if
187		* none of the attribute keys is present.
188		*
189		* @param obj
190		* @param keys
191		* @return
192		*/
		0% Uncovered Elements: 13 (13) Complexity: 4 Complexity Density: 0.57
193	0	@SuppressWarnings("unchecked")...
194		protected String getFirstNotNull(Map<String, Object> obj, String... keys)
195		{
196	0	for (String key : keys)
197		{
198	0	Object val = obj.get(key);
199	0	if (val != null)
200		{
201	0	String s = val instanceof List<?>
202		? JSONUtils.arrayToStringList((List<Object>) val)
203		: val.toString();
204	0	if (!s.isEmpty())
205		{
206	0	return s;
207		}
208		}
209		}
210	0	return null;
211		}
212
213		/**
214		* A helper method that reads the 'key' entry in the JSON object, and if not
215		* null, sets its string value as an attribute on the sequence feature
216		*
217		* @param sf
218		* @param obj
219		* @param key
220		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
221	0	protected void setFeatureAttribute(SequenceFeature sf,...
222		Map<String, Object> obj, String key)
223		{
224	0	Object object = obj.get(key);
225	0	if (object != null)
226		{
227	0	sf.setValue(key, object.toString());
228		}
229		}
230
231		/**
232		* Returns a URL for the REST overlap endpoint
233		*
234		* @param ids
235		* @return
236		*/
		0% Uncovered Elements: 7 (7) Complexity: 1 Complexity Density: 0.14
237	0	@Override...
238		protected URL getUrl(List<String> ids) throws MalformedURLException
239		{
240	0	StringBuffer urlstring = new StringBuffer(128);
241	0	urlstring.append(getDomain()).append("/overlap/id/").append(ids.get(0));
242
243		// @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
244	0	urlstring.append("?content-type=" + getResponseMimeType());
245
246		/*
247		* specify object_type=gene in case is shared by transcript and/or protein;
248		* currently only fetching features for gene sequences;
249		* refactor in future if needed to fetch for transcripts
250		*/
251	0	urlstring.append("&").append(OBJECT_TYPE).append("=")
252		.append(OBJECT_TYPE_GENE);
253
254		/*
255		* specify features to retrieve
256		* @see http://rest.ensembl.org/documentation/info/overlap_id
257		* could make the list a configurable entry in .jalview_properties
258		*/
259	0	for (EnsemblFeatureType feature : featuresWanted)
260		{
261	0	urlstring.append("&feature=").append(feature.name());
262		}
263
264	0	return new URL(urlstring.toString());
265		}
266
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
267	0	@Override...
268		protected boolean useGetRequest()
269		{
270	0	return true;
271		}
272
273		/**
274		* Returns the MIME type for GFF3. For GET requests the Content-type header
275		* describes the required encoding of the response.
276		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
277	0	@Override...
278		protected String getRequestMimeType()
279		{
280	0	return "application/json";
281		}
282
283		/**
284		* Returns the MIME type wanted for the response
285		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
286	0	@Override...
287		protected String getResponseMimeType()
288		{
289	0	return "application/json";
290		}
291
292		/**
293		* Overloaded method that allows a list of features to retrieve to be
294		* specified
295		*
296		* @param accId
297		* @param features
298		* @return
299		* @throws IOException
300		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
301	0	protected AlignmentI getSequenceRecords(String accId,...
302		EnsemblFeatureType[] features) throws IOException
303		{
304	0	featuresWanted = features;
305	0	return getSequenceRecords(accId);
306		}
307		}