Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblSymbol	40	31	12	0.00%	Show methods

Class EnsemblSymbol

Class EnsemblSymbol	Line # 40	Total Statements 31	Complexity 12	TOTAL Coverage 0.00%
EnsemblSymbol(String,String,String)   EnsemblSymbol(String,String,String)	5353	1.01	1.01	0.0 0.00%
getUrl(String,Species,String) : URL   getUrl(String,Species,String) : URL	8383	8.08	2.02	0.0 0.00%
getGeneIds(String) : List<String>   getGeneIds(String) : List<String>	110110	22.022	9.09	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 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		/**
34		* A client for the Ensembl xrefs/symbol REST service;
35		*
36		* @see http://rest.ensembl.org/documentation/info/xref_external
37		* @author gmcarstairs
38		*
39		*/
		0% Uncovered Elements: 42 (42) Complexity: 12 Complexity Density: 0.39
40		public class EnsemblSymbol extends EnsemblXref
41		{
42		private static final String GENE = "gene";
43
44		private static final String TYPE = "type";
45
46		/**
47		* Constructor given the target domain to fetch data from
48		*
49		* @param domain
50		* @param dbName
51		* @param dbVersion
52		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
53	0	public EnsemblSymbol(String domain, String dbName, String dbVersion)...
54		{
55	0	super(domain, dbName, dbVersion);
56		}
57
58		// /**
59		// * Returns the first "id" value in gene identifier format from the JSON
60		// * response, or null if none found
61		// *
62		// * @param br
63		// * @return
64		// * @throws IOException
65		// */
66		// @SuppressWarnings("unchecked")
67		// protected String parseSymbolResponse(BufferedReader br) throws IOException
68		// {
69		// }
70
71		/**
72		* Constructs the URL for the REST symbol endpoint
73		*
74		* @param id
75		* the accession id (Ensembl or external)
76		* @param species
77		* a species name recognisable by Ensembl
78		* @param type
79		* an optional type to filter the response (gene, transcript,
80		* translation)
81		* @return
82		*/
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.25
83	0	protected URL getUrl(String id, Species species, String... type)...
84		{
85	0	StringBuilder sb = new StringBuilder();
86	0	sb.append(getDomain()).append("/xrefs/symbol/")
87		.append(species.toString()).append("/").append(id)
88		.append(CONTENT_TYPE_JSON);
89	0	for (String t : type)
90		{
91	0	sb.append("&object_type=").append(t);
92		}
93	0	try
94		{
95	0	String url = sb.toString();
96	0	return new URL(url);
97		} catch (MalformedURLException e)
98		{
99	0	return null;
100		}
101		}
102
103		/**
104		* Calls the Ensembl xrefs REST 'symbol' endpoint and retrieves any gene ids
105		* for the given identifier, for any known model organisms
106		*
107		* @param identifier
108		* @return
109		*/
		0% Uncovered Elements: 30 (30) Complexity: 9 Complexity Density: 0.41
110	0	@SuppressWarnings("unchecked")...
111		public List<String> getGeneIds(String identifier)
112		{
113	0	List<String> result = new ArrayList<String>();
114	0	List<String> ids = new ArrayList<String>();
115	0	ids.add(identifier);
116
117	0	String[] queries = identifier.split(getAccessionSeparator());
118	0	try
119		{
120	0	for (String query : queries)
121		{
122	0	for (Species taxon : Species.getModelOrganisms())
123		{
124	0	String geneId = null;/// parseSymbolResponse(br);
125	0	try
126		{
127	0	Iterator<Object> rvals = (Iterator<Object>) getJSON(
128		getUrl(query, taxon, GENE), ids, -1, MODE_ITERATOR,
129		null);
130	0	if (rvals == null)
131	0	continue;
132	0	while (rvals.hasNext())
133		{
134	0	Map<String, Object> val = (Map<String, Object>) rvals.next();
135	0	String id = val.get(JSON_ID).toString();
136	0	String type = val.get(TYPE).toString();
137	0	if (id != null && GENE.equals(type))
138		{
139	0	geneId = id;
140	0	break;
141		}
142		}
143		} catch (ParseException e)
144		{
145		// ignore
146		}
147
148	0	if (geneId != null && !result.contains(geneId))
149		{
150	0	result.add(geneId);
151		}
152		}
153		}
154		} catch (IOException e)
155		{
156		// ignore
157		}
158	0	return result;
159		}
160
161		}