Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblMap	53	82	33	0.00%	Show methods

Class EnsemblMap

Class EnsemblMap	Line # 53	Total Statements 82	Complexity 33	TOTAL Coverage 0.00%
EnsemblMap()   EnsemblMap()	6666	1.01	1.01	0.0 0.00%
EnsemblMap(String)   EnsemblMap(String)	7676	1.01	1.01	0.0 0.00%
getDbName() : String   getDbName() : String	8181	1.01	1.01	0.0 0.00%
getSequenceRecords(String) : AlignmentI   getSequenceRecords(String) : AlignmentI	8787	1.01	1.01	0.0 0.00%
getAssemblyMapUrl(String,String,String,String,int,int) : URL   getAssemblyMapUrl(String,String,String,String,int,int) : URL	107107	6.06	4.04	0.0 0.00%
useGetRequest() : boolean   useGetRequest() : boolean	125125	1.01	1.01	0.0 0.00%
getUrl(List<String>) : URL   getUrl(List<String>) : URL	131131	1.01	1.01	0.0 0.00%
getAssemblyMapping(String,String,String,String,int[]) : int[]   getAssemblyMapping(String,String,String,String,int[]) : int[]	149149	6.06	2.02	0.0 0.00%
parseAssemblyMappingResponse(URL) : int[]   parseAssemblyMappingResponse(URL) : int[]	180180	15.015	5.05	0.0 0.00%
getCdsMapping(String,String,int,int) : GeneLociI   getCdsMapping(String,String,int,int) : GeneLociI	228228	1.01	1.01	0.0 0.00%
getCdnaMapping(String,String,int,int) : GeneLociI   getCdnaMapping(String,String,int,int) : GeneLociI	246246	1.01	1.01	0.0 0.00%
getIdMapping(String,String,int,int,String) : GeneLociI   getIdMapping(String,String,int,int,String) : GeneLociI	252252	9.09	3.03	0.0 0.00%
getIdMapUrl(String,String,int,int,String) : URL   getIdMapUrl(String,String,int,int,String) : URL	285285	2.02	1.01	0.0 0.00%
parseIdMappingResponse(URL,String,String) : GeneLociI   parseIdMappingResponse(URL,String,String) : GeneLociI	314314	36.036	10.010	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 jalview.datamodel.AlignmentI;
24		import jalview.datamodel.DBRefSource;
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.ArrayList;
34		import java.util.Collections;
35		import java.util.Iterator;
36		import java.util.List;
37		import java.util.Map;
38
39		import org.json.simple.parser.ParseException;
40
41		/**
42		* A client for the Ensembl REST service /map endpoint, to convert from
43		* coordinates of one genome assembly to another.
44		* <p>
45		* Note that species and assembly identifiers passed to this class must be valid
46		* in Ensembl. They are not case sensitive.
47		*
48		* @author gmcarstairs
49		* @see https://rest.ensembl.org/documentation/info/assembly_map
50		* @see https://rest.ensembl.org/info/assembly/human?content-type=text/xml
51		* @see https://rest.ensembl.org/info/species?content-type=text/xml
52		*/
		0% Uncovered Elements: 122 (122) Complexity: 33 Complexity Density: 0.4
53		public class EnsemblMap extends EnsemblRestClient
54		{
55		private static final String MAPPED = "mapped";
56
57		private static final String MAPPINGS = "mappings";
58
59		private static final String CDS = "cds";
60
61		private static final String CDNA = "cdna";
62
63		/**
64		* Default constructor (to use rest.ensembl.org)
65		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
66	0	public EnsemblMap()...
67		{
68	0	super();
69		}
70
71		/**
72		* Constructor given the target domain to fetch data from
73		*
74		* @param
75		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
76	0	public EnsemblMap(String domain)...
77		{
78	0	super(domain);
79		}
80
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
81	0	@Override...
82		public String getDbName()
83		{
84	0	return DBRefSource.ENSEMBL;
85		}
86
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
87	0	@Override...
88		public AlignmentI getSequenceRecords(String queries) throws Exception
89		{
90	0	return null; // not used
91		}
92
93		/**
94		* Constructs a URL of the format <code>
95		* http://rest.ensembl.org/map/human/GRCh38/17:45051610..45109016:1/GRCh37?content-type=application/json
96		* </code>
97		*
98		* @param species
99		* @param chromosome
100		* @param fromRef
101		* @param toRef
102		* @param startPos
103		* @param endPos
104		* @return
105		* @throws MalformedURLException
106		*/
		0% Uncovered Elements: 12 (12) Complexity: 4 Complexity Density: 0.67
107	0	protected URL getAssemblyMapUrl(String species, String chromosome, String fromRef,...
108		String toRef, int startPos, int endPos)
109		throws MalformedURLException
110		{
111		/*
112		* start-end might be reverse strand - present forwards to the service
113		*/
114	0	boolean forward = startPos <= endPos;
115	0	int start = forward ? startPos : endPos;
116	0	int end = forward ? endPos : startPos;
117	0	String strand = forward ? "1" : "-1";
118	0	String url = String.format(
119		"%s/map/%s/%s/%s:%d..%d:%s/%s?content-type=application/json",
120		getDomain(), species, fromRef, chromosome, start, end, strand,
121		toRef);
122	0	return new URL(url);
123		}
124
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
125	0	@Override...
126		protected boolean useGetRequest()
127		{
128	0	return true;
129		}
130
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
131	0	@Override...
132		protected URL getUrl(List<String> ids) throws MalformedURLException
133		{
134	0	return null; // not used
135		}
136
137		/**
138		* Calls the REST /map service to get the chromosomal coordinates (start/end)
139		* in 'toRef' that corresponding to the (start/end) queryRange in 'fromRef'
140		*
141		* @param species
142		* @param chromosome
143		* @param fromRef
144		* @param toRef
145		* @param queryRange
146		* @return
147		* @see http://rest.ensemblgenomes.org/documentation/info/assembly_map
148		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.33
149	0	public int[] getAssemblyMapping(String species, String chromosome,...
150		String fromRef, String toRef, int[] queryRange)
151		{
152	0	URL url = null;
153	0	try
154		{
155	0	url = getAssemblyMapUrl(species, chromosome, fromRef, toRef, queryRange[0],
156		queryRange[1]);
157	0	return (parseAssemblyMappingResponse(url));
158		} catch (Throwable t)
159		{
160	0	System.out.println("Error calling " + url + ": " + t.getMessage());
161	0	return null;
162		}
163		}
164
165		/**
166		* Parses the JSON response from the /map/&lt;species&gt;/ REST service. The
167		* format is (with some fields omitted)
168		*
169		* <pre>
170		* {"mappings":
171		* [{
172		* "original": {"end":45109016,"start":45051610},
173		* "mapped" : {"end":43186384,"start":43128978}
174		* }] }
175		* </pre>
176		*
177		* @param br
178		* @return
179		*/
		0% Uncovered Elements: 21 (21) Complexity: 5 Complexity Density: 0.33
180	0	@SuppressWarnings("unchecked")...
181		protected int[] parseAssemblyMappingResponse(URL url)
182		{
183	0	int[] result = null;
184
185	0	try
186		{
187	0	Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1, MODE_ITERATOR, MAPPINGS);
188	0	if (rvals == null)
189		{
190	0	return null;
191		}
192	0	while (rvals.hasNext())
193		{
194		// todo check for "mapped"
195	0	Map<String, Object> val = (Map<String, Object>) rvals.next();
196	0	Map<String, Object> mapped = (Map<String, Object>) val.get(MAPPED);
197	0	int start = Integer.parseInt(mapped.get("start").toString());
198	0	int end = Integer.parseInt(mapped.get("end").toString());
199	0	String strand = mapped.get("strand").toString();
200	0	if ("1".equals(strand))
201		{
202	0	result = new int[] { start, end };
203		}
204		else
205		{
206	0	result = new int[] { end, start };
207		}
208		}
209		} catch (IOException | ParseException | NumberFormatException e)
210		{
211		// ignore
212		}
213	0	return result;
214		}
215
216		/**
217		* Calls the REST /map/cds/id service, and returns a DBRefEntry holding the
218		* returned chromosomal coordinates, or returns null if the call fails
219		*
220		* @param division
221		* e.g. Ensembl, EnsemblMetazoa
222		* @param accession
223		* e.g. ENST00000592782, Y55B1AR.1.1
224		* @param start
225		* @param end
226		* @return
227		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
228	0	public GeneLociI getCdsMapping(String division, String accession,...
229		int start, int end)
230		{
231	0	return getIdMapping(division, accession, start, end, CDS);
232		}
233
234		/**
235		* Calls the REST /map/cdna/id service, and returns a DBRefEntry holding the
236		* returned chromosomal coordinates, or returns null if the call fails
237		*
238		* @param division
239		* e.g. Ensembl, EnsemblMetazoa
240		* @param accession
241		* e.g. ENST00000592782, Y55B1AR.1.1
242		* @param start
243		* @param end
244		* @return
245		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
246	0	public GeneLociI getCdnaMapping(String division, String accession,...
247		int start, int end)
248		{
249	0	return getIdMapping(division, accession, start, end, CDNA);
250		}
251
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.33
252	0	GeneLociI getIdMapping(String division, String accession, int start,...
253		int end, String cdsOrCdna)
254		{
255	0	URL url = null;
256	0	try
257		{
258	0	String domain = new EnsemblInfo().getDomain(division);
259	0	if (domain != null)
260		{
261	0	url = getIdMapUrl(domain, accession, start, end, cdsOrCdna);
262	0	return (parseIdMappingResponse(url, accession, domain));
263		}
264	0	return null;
265		} catch (Throwable t)
266		{
267	0	System.out.println("Error calling " + url + ": " + t.getMessage());
268	0	return null;
269		}
270		}
271
272		/**
273		* Constructs a URL to the /map/cds/<id> or /map/cdna/<id> REST service. The
274		* REST call is to either ensembl or ensemblgenomes, as determined from the
275		* division, e.g. Ensembl or EnsemblProtists.
276		*
277		* @param domain
278		* @param accession
279		* @param start
280		* @param end
281		* @param cdsOrCdna
282		* @return
283		* @throws MalformedURLException
284		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
285	0	URL getIdMapUrl(String domain, String accession, int start, int end,...
286		String cdsOrCdna) throws MalformedURLException
287		{
288	0	String url = String
289		.format("%s/map/%s/%s/%d..%d?include_original_region=1&content-type=application/json",
290		domain, cdsOrCdna, accession, start, end);
291	0	return new URL(url);
292		}
293
294		/**
295		* Parses the JSON response from the /map/cds/ or /map/cdna REST service. The
296		* format is
297		*
298		* <pre>
299		* {"mappings":
300		* [
301		* {"assembly_name":"TAIR10","end":2501311,"seq_region_name":"1","gap":0,
302		* "strand":-1,"coord_system":"chromosome","rank":0,"start":2501114},
303		* {"assembly_name":"TAIR10","end":2500815,"seq_region_name":"1","gap":0,
304		* "strand":-1,"coord_system":"chromosome","rank":0,"start":2500714}
305		* ]
306		* }
307		* </pre>
308		*
309		* @param br
310		* @param accession
311		* @param domain
312		* @return
313		*/
		0% Uncovered Elements: 48 (48) Complexity: 10 Complexity Density: 0.28
314	0	@SuppressWarnings("unchecked")...
315		GeneLociI parseIdMappingResponse(URL url, String accession,
316		String domain)
317		{
318
319	0	try
320		{
321	0	Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1, MODE_ITERATOR, MAPPINGS);
322	0	if (rvals == null)
323		{
324	0	return null;
325		}
326	0	String assembly = null;
327	0	String chromosome = null;
328	0	int fromEnd = 0;
329	0	List<int[]> regions = new ArrayList<>();
330
331	0	while (rvals.hasNext())
332		{
333	0	Map<String, Object> val = (Map<String, Object>) rvals.next();
334	0	Map<String, Object> original = (Map<String, Object>) val.get("original");
335	0	fromEnd = Integer.parseInt(original.get("end").toString());
336
337	0	Map<String, Object> mapped = (Map<String, Object>) val.get(MAPPED);
338	0	int start = Integer.parseInt(mapped.get("start").toString());
339	0	int end = Integer.parseInt(mapped.get("end").toString());
340	0	String ass = mapped.get("assembly_name").toString();
341	0	if (assembly != null && !assembly.equals(ass))
342		{
343	0	System.err
344		.println("EnsemblMap found multiple assemblies - can't resolve");
345	0	return null;
346		}
347	0	assembly = ass;
348	0	String chr = mapped.get("seq_region_name").toString();
349	0	if (chromosome != null && !chromosome.equals(chr))
350		{
351	0	System.err
352		.println("EnsemblMap found multiple chromosomes - can't resolve");
353	0	return null;
354		}
355	0	chromosome = chr;
356	0	String strand = mapped.get("strand").toString();
357	0	if ("-1".equals(strand))
358		{
359	0	regions.add(new int[] { end, start });
360		}
361		else
362		{
363	0	regions.add(new int[] { start, end });
364		}
365		}
366
367		/*
368		* processed all mapped regions on chromosome, assemble the result,
369		* having first fetched the species id for the accession
370		*/
371	0	final String species = new EnsemblLookup(domain)
372		.getSpecies(accession);
373	0	final String as = assembly;
374	0	final String chr = chromosome;
375	0	List<int[]> fromRange = Collections.singletonList(new int[] { 1,
376		fromEnd });
377	0	Mapping mapping = new Mapping(new MapList(fromRange, regions, 1, 1));
378	0	return new GeneLocus(species == null ? "" : species, as, chr,
379		mapping);
380		} catch (IOException | ParseException | NumberFormatException e)
381		{
382		// ignore
383		}
384
385	0	return null;
386		}
387
388		}