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[]	181181	15.015	5.05	0.0 0.00%
getCdsMapping(String,String,int,int) : GeneLociI   getCdsMapping(String,String,int,int) : GeneLociI	230230	1.01	1.01	0.0 0.00%
getCdnaMapping(String,String,int,int) : GeneLociI   getCdnaMapping(String,String,int,int) : GeneLociI	248248	1.01	1.01	0.0 0.00%
getIdMapping(String,String,int,int,String) : GeneLociI   getIdMapping(String,String,int,int,String) : GeneLociI	254254	9.09	3.03	0.0 0.00%
getIdMapUrl(String,String,int,int,String) : URL   getIdMapUrl(String,String,int,int,String) : URL	288288	2.02	1.01	0.0 0.00%
parseIdMappingResponse(URL,String,String) : GeneLociI   parseIdMappingResponse(URL,String,String) : GeneLociI	317317	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,...
108		String fromRef, 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,
156		queryRange[0], queryRange[1]);
157	0	return (parseAssemblyMappingResponse(url));
158		} catch (Throwable t)
159		{
160	0	jalview.bin.Console
161		.outPrintln("Error calling " + url + ": " + t.getMessage());
162	0	return null;
163		}
164		}
165
166		/**
167		* Parses the JSON response from the /map/&lt;species&gt;/ REST service. The
168		* format is (with some fields omitted)
169		*
170		* <pre>
171		* {"mappings":
172		* [{
173		* "original": {"end":45109016,"start":45051610},
174		* "mapped" : {"end":43186384,"start":43128978}
175		* }] }
176		* </pre>
177		*
178		* @param br
179		* @return
180		*/
		0% Uncovered Elements: 21 (21) Complexity: 5 Complexity Density: 0.33
181	0	@SuppressWarnings("unchecked")...
182		protected int[] parseAssemblyMappingResponse(URL url)
183		{
184	0	int[] result = null;
185
186	0	try
187		{
188	0	Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1,
189		MODE_ITERATOR, MAPPINGS);
190	0	if (rvals == null)
191		{
192	0	return null;
193		}
194	0	while (rvals.hasNext())
195		{
196		// todo check for "mapped"
197	0	Map<String, Object> val = (Map<String, Object>) rvals.next();
198	0	Map<String, Object> mapped = (Map<String, Object>) val.get(MAPPED);
199	0	int start = Integer.parseInt(mapped.get("start").toString());
200	0	int end = Integer.parseInt(mapped.get("end").toString());
201	0	String strand = mapped.get("strand").toString();
202	0	if ("1".equals(strand))
203		{
204	0	result = new int[] { start, end };
205		}
206		else
207		{
208	0	result = new int[] { end, start };
209		}
210		}
211		} catch (IOException | ParseException | NumberFormatException e)
212		{
213		// ignore
214		}
215	0	return result;
216		}
217
218		/**
219		* Calls the REST /map/cds/id service, and returns a DBRefEntry holding the
220		* returned chromosomal coordinates, or returns null if the call fails
221		*
222		* @param division
223		* e.g. Ensembl, EnsemblMetazoa
224		* @param accession
225		* e.g. ENST00000592782, Y55B1AR.1.1
226		* @param start
227		* @param end
228		* @return
229		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
230	0	public GeneLociI getCdsMapping(String division, String accession,...
231		int start, int end)
232		{
233	0	return getIdMapping(division, accession, start, end, CDS);
234		}
235
236		/**
237		* Calls the REST /map/cdna/id service, and returns a DBRefEntry holding the
238		* returned chromosomal coordinates, or returns null if the call fails
239		*
240		* @param division
241		* e.g. Ensembl, EnsemblMetazoa
242		* @param accession
243		* e.g. ENST00000592782, Y55B1AR.1.1
244		* @param start
245		* @param end
246		* @return
247		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
248	0	public GeneLociI getCdnaMapping(String division, String accession,...
249		int start, int end)
250		{
251	0	return getIdMapping(division, accession, start, end, CDNA);
252		}
253
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.33
254	0	GeneLociI getIdMapping(String division, String accession, int start,...
255		int end, String cdsOrCdna)
256		{
257	0	URL url = null;
258	0	try
259		{
260	0	String domain = new EnsemblInfo().getDomain(division);
261	0	if (domain != null)
262		{
263	0	url = getIdMapUrl(domain, accession, start, end, cdsOrCdna);
264	0	return (parseIdMappingResponse(url, accession, domain));
265		}
266	0	return null;
267		} catch (Throwable t)
268		{
269	0	jalview.bin.Console
270		.outPrintln("Error calling " + url + ": " + t.getMessage());
271	0	return null;
272		}
273		}
274
275		/**
276		* Constructs a URL to the /map/cds/<id> or /map/cdna/<id> REST service. The
277		* REST call is to either ensembl or ensemblgenomes, as determined from the
278		* division, e.g. Ensembl or EnsemblProtists.
279		*
280		* @param domain
281		* @param accession
282		* @param start
283		* @param end
284		* @param cdsOrCdna
285		* @return
286		* @throws MalformedURLException
287		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
288	0	URL getIdMapUrl(String domain, String accession, int start, int end,...
289		String cdsOrCdna) throws MalformedURLException
290		{
291	0	String url = String.format(
292		"%s/map/%s/%s/%d..%d?include_original_region=1&content-type=application/json",
293		domain, cdsOrCdna, accession, start, end);
294	0	return new URL(url);
295		}
296
297		/**
298		* Parses the JSON response from the /map/cds/ or /map/cdna REST service. The
299		* format is
300		*
301		* <pre>
302		* {"mappings":
303		* [
304		* {"assembly_name":"TAIR10","end":2501311,"seq_region_name":"1","gap":0,
305		* "strand":-1,"coord_system":"chromosome","rank":0,"start":2501114},
306		* {"assembly_name":"TAIR10","end":2500815,"seq_region_name":"1","gap":0,
307		* "strand":-1,"coord_system":"chromosome","rank":0,"start":2500714}
308		* ]
309		* }
310		* </pre>
311		*
312		* @param br
313		* @param accession
314		* @param domain
315		* @return
316		*/
		0% Uncovered Elements: 48 (48) Complexity: 10 Complexity Density: 0.28
317	0	@SuppressWarnings("unchecked")...
318		GeneLociI parseIdMappingResponse(URL url, String accession, String domain)
319		{
320
321	0	try
322		{
323	0	Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1,
324		MODE_ITERATOR, MAPPINGS);
325	0	if (rvals == null)
326		{
327	0	return null;
328		}
329	0	String assembly = null;
330	0	String chromosome = null;
331	0	int fromEnd = 0;
332	0	List<int[]> regions = new ArrayList<>();
333
334	0	while (rvals.hasNext())
335		{
336	0	Map<String, Object> val = (Map<String, Object>) rvals.next();
337	0	Map<String, Object> original = (Map<String, Object>) val
338		.get("original");
339	0	fromEnd = Integer.parseInt(original.get("end").toString());
340
341	0	Map<String, Object> mapped = (Map<String, Object>) val.get(MAPPED);
342	0	int start = Integer.parseInt(mapped.get("start").toString());
343	0	int end = Integer.parseInt(mapped.get("end").toString());
344	0	String ass = mapped.get("assembly_name").toString();
345	0	if (assembly != null && !assembly.equals(ass))
346		{
347	0	jalview.bin.Console.errPrintln(
348		"EnsemblMap found multiple assemblies - can't resolve");
349	0	return null;
350		}
351	0	assembly = ass;
352	0	String chr = mapped.get("seq_region_name").toString();
353	0	if (chromosome != null && !chromosome.equals(chr))
354		{
355	0	jalview.bin.Console.errPrintln(
356		"EnsemblMap found multiple chromosomes - can't resolve");
357	0	return null;
358		}
359	0	chromosome = chr;
360	0	String strand = mapped.get("strand").toString();
361	0	if ("-1".equals(strand))
362		{
363	0	regions.add(new int[] { end, start });
364		}
365		else
366		{
367	0	regions.add(new int[] { start, end });
368		}
369		}
370
371		/*
372		* processed all mapped regions on chromosome, assemble the result,
373		* having first fetched the species id for the accession
374		*/
375	0	final String species = new EnsemblLookup(domain)
376		.getSpecies(accession);
377	0	final String as = assembly;
378	0	final String chr = chromosome;
379	0	List<int[]> fromRange = Collections
380		.singletonList(new int[]
381		{ 1, fromEnd });
382	0	Mapping mapping = new Mapping(new MapList(fromRange, regions, 1, 1));
383	0	return new GeneLocus(species == null ? "" : species, as, chr,
384		mapping);
385		} catch (IOException | ParseException | NumberFormatException e)
386		{
387		// ignore
388		}
389
390	0	return null;
391		}
392
393		}