Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblLookup	47	60	28	0.00%	Show methods

Class EnsemblLookup

Class EnsemblLookup	Line # 47	Total Statements 60	Complexity 28	TOTAL Coverage 0.00%
EnsemblLookup()   EnsemblLookup()	5454	1.01	1.01	0.0 0.00%
EnsemblLookup(String)   EnsemblLookup(String)	6464	1.01	1.01	0.0 0.00%
getDbName() : String   getDbName() : String	6969	1.01	1.01	0.0 0.00%
getSequenceRecords(String) : AlignmentI   getSequenceRecords(String) : AlignmentI	7575	1.01	1.01	0.0 0.00%
getUrl(List<String>) : URL   getUrl(List<String>) : URL	8181	2.02	1.01	0.0 0.00%
getUrl(String,String) : URL   getUrl(String,String) : URL	9696	6.06	3.03	0.0 0.00%
useGetRequest() : boolean   useGetRequest() : boolean	114114	1.01	1.01	0.0 0.00%
getGeneId(String) : String   getGeneId(String) : String	127127	1.01	1.01	0.0 0.00%
getGeneId(String,String) : String   getGeneId(String,String) : String	140140	1.01	1.01	0.0 0.00%
parseGeneId(Map<String, Object>) : String   parseGeneId(Map<String, Object>) : String	154154	12.012	5.05	0.0 0.00%
getSpecies(String) : String   getSpecies(String) : String	189189	7.07	3.03	0.0 0.00%
getResult(String,String) : Map<String, Object>   getResult(String,String) : Map<String, Object>	213213	5.05	2.02	0.0 0.00%
getGeneLoci(String) : GeneLociI   getGeneLoci(String) : GeneLociI	238238	1.01	1.01	0.0 0.00%
parseGeneLoci(Map<String, Object>) : GeneLociI   parseGeneLoci(Map<String, Object>) : GeneLociI	251251	20.020	6.06	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.bin.Console;
24		import jalview.datamodel.AlignmentI;
25		import jalview.datamodel.GeneLociI;
26		import jalview.datamodel.GeneLocus;
27		import jalview.datamodel.Mapping;
28		import jalview.util.MapList;
29
30		import java.io.IOException;
31		import java.net.MalformedURLException;
32		import java.net.URL;
33		import java.util.Arrays;
34		import java.util.Collections;
35		import java.util.List;
36		import java.util.Map;
37
38		import org.json.simple.parser.ParseException;
39
40		/**
41		* A client for the Ensembl /lookup REST endpoint, used to find the gene
42		* identifier given a gene, transcript or protein identifier, or to extract the
43		* species or chromosomal coordinates from the same service response
44		*
45		* @author gmcarstairs
46		*/
		0% Uncovered Elements: 96 (96) Complexity: 28 Complexity Density: 0.47
47		public class EnsemblLookup extends EnsemblRestClient
48		{
49		private static final String SPECIES = "species";
50
51		/**
52		* Default constructor (to use rest.ensembl.org)
53		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
54	0	public EnsemblLookup()...
55		{
56	0	super();
57		}
58
59		/**
60		* Constructor given the target domain to fetch data from
61		*
62		* @param
63		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
64	0	public EnsemblLookup(String d)...
65		{
66	0	super(d);
67		}
68
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
69	0	@Override...
70		public String getDbName()
71		{
72	0	return "ENSEMBL";
73		}
74
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
75	0	@Override...
76		public AlignmentI getSequenceRecords(String queries) throws Exception
77		{
78	0	return null;
79		}
80
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
81	0	@Override...
82		protected URL getUrl(List<String> ids) throws MalformedURLException
83		{
84	0	String identifier = ids.get(0);
85	0	return getUrl(identifier, null);
86		}
87
88		/**
89		* Gets the url for lookup of the given identifier, optionally with objectType
90		* also specified in the request
91		*
92		* @param identifier
93		* @param objectType
94		* @return
95		*/
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.5
96	0	protected URL getUrl(String identifier, String objectType)...
97		{
98	0	String url = getDomain() + "/lookup/id/" + identifier
99		+ CONTENT_TYPE_JSON;
100	0	if (objectType != null)
101		{
102	0	url += "&" + OBJECT_TYPE + "=" + objectType;
103		}
104
105	0	try
106		{
107	0	return new URL(url);
108		} catch (MalformedURLException e)
109		{
110	0	return null;
111		}
112		}
113
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
114	0	@Override...
115		protected boolean useGetRequest()
116		{
117	0	return true;
118		}
119
120		/**
121		* Returns the gene id related to the given identifier (which may be for a
122		* gene, transcript or protein), or null if none is found
123		*
124		* @param identifier
125		* @return
126		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
127	0	public String getGeneId(String identifier)...
128		{
129	0	return getGeneId(identifier, null);
130		}
131
132		/**
133		* Returns the gene id related to the given identifier (which may be for a
134		* gene, transcript or protein), or null if none is found
135		*
136		* @param identifier
137		* @param objectType
138		* @return
139		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
140	0	public String getGeneId(String identifier, String objectType)...
141		{
142	0	return parseGeneId(getResult(identifier, objectType));
143		}
144
145		/**
146		* Parses the JSON response and returns the gene identifier, or null if not
147		* found. If the returned object_type is Gene, returns the id, if Transcript
148		* returns the Parent. If it is Translation (peptide identifier), then the
149		* Parent is the transcript identifier, so we redo the search with this value.
150		*
151		* @param br
152		* @return
153		*/
		0% Uncovered Elements: 20 (20) Complexity: 5 Complexity Density: 0.42
154	0	protected String parseGeneId(Map<String, Object> val)...
155		{
156	0	if (val == null)
157		{
158	0	return null;
159		}
160	0	String geneId = null;
161	0	String type = val.get(OBJECT_TYPE).toString();
162	0	if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
163		{
164		// got the gene - just returns its id
165	0	geneId = val.get(JSON_ID).toString();
166		}
167	0	else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
168		{
169		// got the transcript - return its (Gene) Parent
170	0	geneId = val.get(PARENT).toString();
171		}
172	0	else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
173		{
174		// got the protein - get its Parent, restricted to type Transcript
175	0	String transcriptId = val.get(PARENT).toString();
176	0	geneId = getGeneId(transcriptId, OBJECT_TYPE_TRANSCRIPT);
177		}
178
179	0	return geneId;
180		}
181
182		/**
183		* Calls the Ensembl lookup REST endpoint and retrieves the 'species' for the
184		* given identifier, or null if not found
185		*
186		* @param identifier
187		* @return
188		*/
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.43
189	0	public String getSpecies(String identifier)...
190		{
191	0	String species = null;
192	0	Map<String, Object> json = getResult(identifier, null);
193	0	if (json != null)
194		{
195	0	Object o = json.get(SPECIES);
196	0	if (o != null)
197		{
198	0	species = o.toString();
199		}
200		}
201	0	return species;
202		}
203
204		/**
205		* Calls the /lookup/id rest service and returns the response as a Map<String,
206		* Object>, or null if any error
207		*
208		* @param identifier
209		* @param objectType
210		* (optional)
211		* @return
212		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.4
213	0	@SuppressWarnings("unchecked")...
214		protected Map<String, Object> getResult(String identifier,
215		String objectType)
216		{
217	0	List<String> ids = Arrays.asList(new String[] { identifier });
218
219	0	try
220		{
221	0	return (Map<String, Object>) getJSON(getUrl(identifier, objectType),
222		ids, -1, MODE_MAP, null);
223		} catch (IOException | ParseException e)
224		{
225	0	jalview.bin.Console.errPrintln("Error parsing " + identifier
226		+ " lookup response " + e.getMessage());
227	0	return null;
228		}
229		}
230
231		/**
232		* Calls the /lookup/id rest service for the given id, and if successful,
233		* parses and returns the gene's chromosomal coordinates
234		*
235		* @param geneId
236		* @return
237		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
238	0	public GeneLociI getGeneLoci(String geneId)...
239		{
240	0	return parseGeneLoci(getResult(geneId, OBJECT_TYPE_GENE));
241		}
242
243		/**
244		* Parses the /lookup/id response for species, asssembly_name,
245		* seq_region_name, start, end and returns an object that wraps them, or null
246		* if unsuccessful
247		*
248		* @param json
249		* @return
250		*/
		0% Uncovered Elements: 28 (28) Complexity: 6 Complexity Density: 0.3
251	0	GeneLociI parseGeneLoci(Map<String, Object> json)...
252		{
253	0	if (json == null)
254		{
255	0	return null;
256		}
257
258	0	try
259		{
260	0	final String species = json.get("species").toString();
261	0	final String assembly = json.get("assembly_name").toString();
262	0	final String chromosome = json.get("seq_region_name").toString();
263	0	String strand = json.get("strand").toString();
264	0	int start = Integer.parseInt(json.get("start").toString());
265	0	int end = Integer.parseInt(json.get("end").toString());
266	0	int fromEnd = end - start + 1;
267	0	boolean reverseStrand = "-1".equals(strand);
268	0	int toStart = reverseStrand ? end : start;
269	0	int toEnd = reverseStrand ? start : end;
270	0	List<int[]> fromRange = Collections
271		.singletonList(new int[]
272		{ 1, fromEnd });
273	0	List<int[]> toRange = Collections
274		.singletonList(new int[]
275		{ toStart, toEnd });
276	0	final Mapping map = new Mapping(
277		new MapList(fromRange, toRange, 1, 1));
278	0	return new GeneLocus(species == null ? "" : species, assembly,
279		chromosome, map);
280		} catch (NullPointerException | NumberFormatException e)
281		{
282	0	Console.error("Error looking up gene loci: " + e.getMessage());
283	0	e.printStackTrace();
284		}
285	0	return null;
286		}
287
288		}