Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
EnsemblSymbol	43	41	16	57	0.00%	Show methods

Class EnsemblSymbol

Class EnsemblSymbol	Line # 43	Total Statements 41	Complexity 16	Uncovered Elements 57	TOTAL Coverage 0.00%
EnsemblSymbol(String,String,String)   EnsemblSymbol(String,String,String)	5454	1.01	1.01	1.01	0.0 0.00%
parseSymbolResponse(BufferedReader) : String   parseSymbolResponse(BufferedReader) : String	6767	13.013	5.05	17.017	0.0 0.00%
getUrl(String,Species,String) : URL   getUrl(String,Species,String) : URL	105105	8.08	2.02	8.08	0.0 0.00%
getGeneIds(String) : List<String>   getGeneIds(String) : List<String>	132132	19.019	8.08	27.027	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.BufferedReader;
24		import java.io.IOException;
25		import java.net.MalformedURLException;
26		import java.net.URL;
27		import java.util.ArrayList;
28		import java.util.Iterator;
29		import java.util.List;
30
31		import org.json.simple.JSONArray;
32		import org.json.simple.JSONObject;
33		import org.json.simple.parser.JSONParser;
34		import org.json.simple.parser.ParseException;
35
36		/**
37		* A client for the Ensembl xrefs/symbol REST service;
38		*
39		* @see http://rest.ensembl.org/documentation/info/xref_external
40		* @author gmcarstairs
41		*
42		*/
		0% Uncovered Elements: 57 (57) Complexity: 16 Complexity Density: 0.39
43		public class EnsemblSymbol extends EnsemblXref
44		{
45		private static final String GENE = "gene";
46		private static final String TYPE = "type";
47		/**
48		* Constructor given the target domain to fetch data from
49		*
50		* @param domain
51		* @param dbName
52		* @param dbVersion
53		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
54	0	public EnsemblSymbol(String domain, String dbName, String dbVersion)...
55		{
56	0	super(domain, dbName, dbVersion);
57		}
58
59		/**
60		* Returns the first "id" value in gene identifier format from the JSON
61		* response, or null if none found
62		*
63		* @param br
64		* @return
65		* @throws IOException
66		*/
		0% Uncovered Elements: 17 (17) Complexity: 5 Complexity Density: 0.38
67	0	protected String parseSymbolResponse(BufferedReader br) throws IOException...
68		{
69	0	JSONParser jp = new JSONParser();
70	0	String result = null;
71	0	try
72		{
73	0	JSONArray responses = (JSONArray) jp.parse(br);
74	0	Iterator rvals = responses.iterator();
75	0	while (rvals.hasNext())
76		{
77	0	JSONObject val = (JSONObject) rvals.next();
78	0	String id = val.get(JSON_ID).toString();
79	0	String type = val.get(TYPE).toString();
80	0	if (id != null && GENE.equals(type))
81		{
82	0	result = id;
83	0	break;
84		}
85		}
86		} catch (ParseException e)
87		{
88		// ignore
89		}
90	0	return result;
91		}
92
93		/**
94		* Constructs the URL for the REST symbol endpoint
95		*
96		* @param id
97		* the accession id (Ensembl or external)
98		* @param species
99		* a species name recognisable by Ensembl
100		* @param type
101		* an optional type to filter the response (gene, transcript,
102		* translation)
103		* @return
104		*/
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.25
105	0	protected URL getUrl(String id, Species species, String... type)...
106		{
107	0	StringBuilder sb = new StringBuilder();
108	0	sb.append(getDomain()).append("/xrefs/symbol/")
109		.append(species.toString()).append("/").append(id)
110		.append(CONTENT_TYPE_JSON);
111	0	for (String t : type)
112		{
113	0	sb.append("&object_type=").append(t);
114		}
115	0	try
116		{
117	0	String url = sb.toString();
118	0	return new URL(url);
119		} catch (MalformedURLException e)
120		{
121	0	return null;
122		}
123		}
124
125		/**
126		* Calls the Ensembl xrefs REST 'symbol' endpoint and retrieves any gene ids
127		* for the given identifier, for any known model organisms
128		*
129		* @param identifier
130		* @return
131		*/
		0% Uncovered Elements: 27 (27) Complexity: 8 Complexity Density: 0.42
132	0	public List<String> getGeneIds(String identifier)...
133		{
134	0	List<String> result = new ArrayList<String>();
135	0	List<String> ids = new ArrayList<String>();
136	0	ids.add(identifier);
137
138	0	String[] queries = identifier.split(getAccessionSeparator());
139	0	BufferedReader br = null;
140	0	try
141		{
142	0	for (String query : queries)
143		{
144	0	for (Species taxon : Species.getModelOrganisms())
145		{
146	0	URL url = getUrl(query, taxon, GENE);
147	0	if (url != null)
148		{
149	0	br = getHttpResponse(url, ids);
150	0	if (br != null)
151		{
152	0	String geneId = parseSymbolResponse(br);
153	0	if (geneId != null && !result.contains(geneId))
154		{
155	0	result.add(geneId);
156		}
157		}
158		}
159		}
160		}
161		} catch (IOException e)
162		{
163		// ignore
164		} finally
165		{
166	0	if (br != null)
167		{
168	0	try
169		{
170	0	br.close();
171		} catch (IOException e)
172		{
173		// ignore
174		}
175		}
176		}
177	0	return result;
178		}
179
180		}