Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblInfo	41	20	13	0.00%	Show methods

Class EnsemblInfo

Class EnsemblInfo	Line # 41	Total Statements 20	Complexity 13	TOTAL Coverage 0.00%
getDbName() : String   getDbName() : String	6161	1.01	1.01	0.0 0.00%
getSequenceRecords(String) : AlignmentI   getSequenceRecords(String) : AlignmentI	6767	1.01	1.01	0.0 0.00%
getUrl(List<String>) : URL   getUrl(List<String>) : URL	7373	1.01	1.01	0.0 0.00%
useGetRequest() : boolean   useGetRequest() : boolean	7979	1.01	1.01	0.0 0.00%
getDomain(String) : String   getDomain(String) : String	9393	3.03	2.02	0.0 0.00%
fetchDivisions() : void   fetchDivisions() : void	106106	9.09	4.04	0.0 0.00%
getDivisionsUrl(String) : URL   getDivisionsUrl(String) : URL	144144	1.01	1.01	0.0 0.00%
getDivisions() : Set<String>   getDivisions() : Set<String>	155155	3.03	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 java.util.Locale;
24
25		import jalview.datamodel.AlignmentI;
26		import jalview.datamodel.DBRefSource;
27		import jalview.util.JSONUtils;
28
29		import java.io.BufferedReader;
30		import java.io.IOException;
31		import java.net.MalformedURLException;
32		import java.net.URL;
33		import java.util.HashMap;
34		import java.util.Iterator;
35		import java.util.List;
36		import java.util.Map;
37		import java.util.Set;
38
39		import org.json.simple.parser.ParseException;
40
		0% Uncovered Elements: 36 (36) Complexity: 13 Complexity Density: 0.65
41		public class EnsemblInfo extends EnsemblRestClient
42		{
43
44		/*
45		* cached results of REST /info/divisions service, currently
46		* <pre>
47		* {
48		* { "ENSEMBLFUNGI", "http://rest.ensemblgenomes.org"},
49		* "ENSEMBLBACTERIA", "http://rest.ensemblgenomes.org"},
50		* "ENSEMBLPROTISTS", "http://rest.ensemblgenomes.org"},
51		* "ENSEMBLMETAZOA", "http://rest.ensemblgenomes.org"},
52		* "ENSEMBLPLANTS", "http://rest.ensemblgenomes.org"},
53		* "ENSEMBL", "http://rest.ensembl.org" }
54		* }
55		* </pre>
56		* The values for EnsemblGenomes are retrieved by a REST call, that for
57		* Ensembl is added programmatically for convenience of lookup
58		*/
59		private static Map<String, String> divisions;
60
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
61	0	@Override...
62		public String getDbName()
63		{
64	0	return "ENSEMBL";
65		}
66
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
67	0	@Override...
68		public AlignmentI getSequenceRecords(String queries) throws Exception
69		{
70	0	return null;
71		}
72
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
73	0	@Override...
74		protected URL getUrl(List<String> ids) throws MalformedURLException
75		{
76	0	return null;
77		}
78
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
79	0	@Override...
80		protected boolean useGetRequest()
81		{
82	0	return true;
83		}
84
85		/**
86		* Answers the domain (http://rest.ensembl.org or
87		* http://rest.ensemblgenomes.org) for the given division, or null if not
88		* recognised by Ensembl.
89		*
90		* @param division
91		* @return
92		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
93	0	public String getDomain(String division)...
94		{
95	0	if (divisions == null)
96		{
97	0	fetchDivisions();
98		}
99	0	return divisions.get(division.toUpperCase(Locale.ROOT));
100		}
101
102		/**
103		* On first request only, populate the lookup map by fetching the list of
104		* divisions known to EnsemblGenomes.
105		*/
		0% Uncovered Elements: 13 (13) Complexity: 4 Complexity Density: 0.44
106	0	void fetchDivisions()...
107		{
108	0	divisions = new HashMap<>();
109
110		/*
111		* for convenience, pre-fill ensembl.org as the domain for "ENSEMBL"
112		*/
113	0	divisions.put(DBRefSource.ENSEMBL.toUpperCase(Locale.ROOT),
114		ensemblDomain);
115	0	try
116		{
117	0	@SuppressWarnings("unchecked")
118		Iterator<Object> rvals = (Iterator<Object>) getJSON(
119		getDivisionsUrl(ensemblGenomesDomain), null, -1,
120		MODE_ITERATOR, null);
121	0	if (rvals == null)
122	0	return;
123	0	while (rvals.hasNext())
124		{
125	0	String division = rvals.next().toString();
126	0	divisions.put(division.toUpperCase(Locale.ROOT),
127		ensemblGenomesDomain);
128		}
129		} catch (IOException | ParseException | NumberFormatException e)
130		{
131		// ignore
132		}
133		}
134
135		/**
136		* Constructs the URL for the EnsemblGenomes /info/divisions REST service
137		*
138		* @param domain
139		* TODO
140		*
141		* @return
142		* @throws MalformedURLException
143		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
144	0	URL getDivisionsUrl(String domain) throws MalformedURLException...
145		{
146	0	return new URL(
147		domain + "/info/divisions?content-type=application/json");
148		}
149
150		/**
151		* Returns the set of 'divisions' recognised by Ensembl or EnsemblGenomes
152		*
153		* @return
154		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
155	0	public Set<String> getDivisions()...
156		{
157	0	if (divisions == null)
158		{
159	0	fetchDivisions();
160		}
161
162	0	return divisions.keySet();
163		}
164		}