Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblXref	46	26	14	0.00%	Show methods

Class EnsemblXref

Class EnsemblXref	Line # 46	Total Statements 26	Complexity 14	TOTAL Coverage 0.00%
EnsemblXref(String,String,String)   EnsemblXref(String,String,String)	5858	3.03	1.01	0.0 0.00%
getDbName() : String   getDbName() : String	6666	1.01	1.01	0.0 0.00%
getSequenceRecords(String) : AlignmentI   getSequenceRecords(String) : AlignmentI	7272	1.01	1.01	0.0 0.00%
getUrl(List<String>) : URL   getUrl(List<String>) : URL	7878	1.01	1.01	0.0 0.00%
useGetRequest() : boolean   useGetRequest() : boolean	8484	1.01	1.01	0.0 0.00%
getCrossReferences(String) : List<DBRefEntry>   getCrossReferences(String) : List<DBRefEntry>	101101	14.014	6.06	0.0 0.00%
getXRefVersion() : String   getXRefVersion() : String	156156	1.01	1.01	0.0 0.00%
getUrl(String) : URL   getUrl(String) : URL	169169	4.04	2.02	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.datamodel.AlignmentI;
24		import jalview.datamodel.DBRefEntry;
25		import jalview.util.DBRefUtils;
26		import jalview.util.JSONUtils;
27
28		import java.io.BufferedReader;
29		import java.io.IOException;
30		import java.net.MalformedURLException;
31		import java.net.URL;
32		import java.util.ArrayList;
33		import java.util.Iterator;
34		import java.util.List;
35		import java.util.Map;
36
37		import org.json.simple.parser.ParseException;
38
39		/**
40		* A class to fetch cross-references from Ensembl by calling the /xrefs REST
41		* service
42		*
43		* @author gmcarstairs
44		* @see http://rest.ensembl.org/documentation/info/xref_id
45		*/
		0% Uncovered Elements: 38 (38) Complexity: 14 Complexity Density: 0.54
46		class EnsemblXref extends EnsemblRestClient
47		{
48
49		private static final String GO_GENE_ONTOLOGY = "GO";
50
51		private String dbName = "ENSEMBL (xref)";
52
53		/**
54		* Constructor given the target domain to fetch data from
55		*
56		* @param d
57		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
58	0	public EnsemblXref(String d, String dbSource, String version)...
59		{
60	0	super(d);
61	0	dbName = dbSource;
62	0	xrefVersion = dbSource + ":" + version;
63
64		}
65
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
66	0	@Override...
67		public String getDbName()
68		{
69	0	return dbName;
70		}
71
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
72	0	@Override...
73		public AlignmentI getSequenceRecords(String queries) throws Exception
74		{
75	0	return null;
76		}
77
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
78	0	@Override...
79		protected URL getUrl(List<String> ids) throws MalformedURLException
80		{
81	0	return getUrl(ids.get(0));
82		}
83
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
84	0	@Override...
85		protected boolean useGetRequest()
86		{
87	0	return true;
88		}
89
90		/**
91		* Calls the Ensembl xrefs REST endpoint and retrieves any cross-references
92		* ("primary_id") for the given identifier (Ensembl accession id) and database
93		* names. The "dbname" returned by Ensembl is canonicalised to Jalview's
94		* standard version, and a DBRefEntry constructed. Currently takes all
95		* identifiers apart from GO terms and synonyms.
96		*
97		* @param identifier
98		* an Ensembl stable identifier
99		* @return
100		*/
		0% Uncovered Elements: 18 (18) Complexity: 6 Complexity Density: 0.43
101	0	@SuppressWarnings("unchecked")...
102		public List<DBRefEntry> getCrossReferences(String identifier)
103		{
104	0	List<DBRefEntry> result = new ArrayList<>();
105	0	List<String> ids = new ArrayList<>();
106	0	ids.add(identifier);
107
108	0	try
109		{
110	0	Iterator<Object> rvals = (Iterator<Object>) getJSON(
111		getUrl(identifier), ids, -1, MODE_ITERATOR, null);
112	0	while (rvals.hasNext())
113		{
114	0	Map<String, Object> val = (Map<String, Object>) rvals.next();
115	0	String db = val.get("dbname").toString();
116	0	String id = val.get("primary_id").toString();
117	0	if (db != null && id != null && !GO_GENE_ONTOLOGY.equals(db))
118		{
119	0	db = DBRefUtils.getCanonicalName(db);
120	0	DBRefEntry dbref = new DBRefEntry(db, getXRefVersion(), id);
121	0	result.add(dbref);
122		}
123		}
124		} catch (ParseException | IOException e)
125		{
126		// ignore
127		}
128	0	return result;
129		}
130
131		// /**
132		// * Parses "primary_id" and "dbname" values from the JSON response and
133		// * constructs a DBRefEntry. Returns a list of the DBRefEntry created. Note
134		// we
135		// * don't parse "synonyms" as they appear to be either redirected or obsolete
136		// * in Uniprot.
137		// *
138		// * @param br
139		// * @return
140		// * @throws IOException
141		// */
142		// @SuppressWarnings("unchecked")
143		// protected List<DBRefEntry> parseResponse(BufferedReader br)
144		// throws IOException
145		// {
146		// return result;
147		// }
148		//
149		private String xrefVersion = "ENSEMBL:0";
150
151		/**
152		* version string for Xrefs - for 2.10, hardwired for ENSEMBL:0
153		*
154		* @return
155		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
156	0	public String getXRefVersion()...
157		{
158	0	return xrefVersion;
159		}
160
161		/**
162		* Returns the URL for the REST endpoint to fetch all cross-references for an
163		* identifier. Note this may return protein cross-references for nucleotide.
164		* Filter the returned list as required.
165		*
166		* @param identifier
167		* @return
168		*/
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 0.5
169	0	protected URL getUrl(String identifier)...
170		{
171	0	String url = getDomain() + "/xrefs/id/" + identifier + CONTENT_TYPE_JSON
172		+ "&all_levels=1";
173	0	try
174		{
175	0	return new URL(url);
176		} catch (MalformedURLException e)
177		{
178	0	return null;
179		}
180		}
181
182		}