Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblInfo	39	20	13	0.00%	Show methods

Class EnsemblInfo

Class EnsemblInfo	Line # 39	Total Statements 20	Complexity 13	TOTAL Coverage 0.00%
getDbName() : String   getDbName() : String	5959	1.01	1.01	0.0 0.00%
getSequenceRecords(String) : AlignmentI   getSequenceRecords(String) : AlignmentI	6565	1.01	1.01	0.0 0.00%
getUrl(List<String>) : URL   getUrl(List<String>) : URL	7171	1.01	1.01	0.0 0.00%
useGetRequest() : boolean   useGetRequest() : boolean	7777	1.01	1.01	0.0 0.00%
getDomain(String) : String   getDomain(String) : String	9191	3.03	2.02	0.0 0.00%
fetchDivisions() : void   fetchDivisions() : void	104104	9.09	4.04	0.0 0.00%
getDivisionsUrl(String) : URL   getDivisionsUrl(String) : URL	136136	1.01	1.01	0.0 0.00%
getDivisions() : Set<String>   getDivisions() : Set<String>	147147	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 jalview.datamodel.AlignmentI;
24		import jalview.datamodel.DBRefSource;
25		import jalview.util.JSONUtils;
26
27		import java.io.BufferedReader;
28		import java.io.IOException;
29		import java.net.MalformedURLException;
30		import java.net.URL;
31		import java.util.HashMap;
32		import java.util.Iterator;
33		import java.util.List;
34		import java.util.Map;
35		import java.util.Set;
36
37		import org.json.simple.parser.ParseException;
38
		0% Uncovered Elements: 36 (36) Complexity: 13 Complexity Density: 0.65
39		public class EnsemblInfo extends EnsemblRestClient
40		{
41
42		/*
43		* cached results of REST /info/divisions service, currently
44		* <pre>
45		* {
46		* { "ENSEMBLFUNGI", "http://rest.ensemblgenomes.org"},
47		* "ENSEMBLBACTERIA", "http://rest.ensemblgenomes.org"},
48		* "ENSEMBLPROTISTS", "http://rest.ensemblgenomes.org"},
49		* "ENSEMBLMETAZOA", "http://rest.ensemblgenomes.org"},
50		* "ENSEMBLPLANTS", "http://rest.ensemblgenomes.org"},
51		* "ENSEMBL", "http://rest.ensembl.org" }
52		* }
53		* </pre>
54		* The values for EnsemblGenomes are retrieved by a REST call, that for
55		* Ensembl is added programmatically for convenience of lookup
56		*/
57		private static Map<String, String> divisions;
58
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
59	0	@Override...
60		public String getDbName()
61		{
62	0	return "ENSEMBL";
63		}
64
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
65	0	@Override...
66		public AlignmentI getSequenceRecords(String queries) throws Exception
67		{
68	0	return null;
69		}
70
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
71	0	@Override...
72		protected URL getUrl(List<String> ids) throws MalformedURLException
73		{
74	0	return null;
75		}
76
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
77	0	@Override...
78		protected boolean useGetRequest()
79		{
80	0	return true;
81		}
82
83		/**
84		* Answers the domain (http://rest.ensembl.org or
85		* http://rest.ensemblgenomes.org) for the given division, or null if not
86		* recognised by Ensembl.
87		*
88		* @param division
89		* @return
90		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
91	0	public String getDomain(String division)...
92		{
93	0	if (divisions == null)
94		{
95	0	fetchDivisions();
96		}
97	0	return divisions.get(division.toUpperCase());
98		}
99
100		/**
101		* On first request only, populate the lookup map by fetching the list of
102		* divisions known to EnsemblGenomes.
103		*/
		0% Uncovered Elements: 13 (13) Complexity: 4 Complexity Density: 0.44
104	0	void fetchDivisions()...
105		{
106	0	divisions = new HashMap<>();
107
108		/*
109		* for convenience, pre-fill ensembl.org as the domain for "ENSEMBL"
110		*/
111	0	divisions.put(DBRefSource.ENSEMBL.toUpperCase(), ensemblDomain);
112	0	try
113		{
114	0	@SuppressWarnings("unchecked")
115		Iterator<Object> rvals = (Iterator<Object>) getJSON(getDivisionsUrl(ensemblGenomesDomain), null, -1, MODE_ITERATOR, null);
116	0	if (rvals == null)
117	0	return;
118	0	while (rvals.hasNext())
119		{
120	0	String division = rvals.next().toString();
121	0	divisions.put(division.toUpperCase(), ensemblGenomesDomain);
122		}
123		} catch (IOException | ParseException | NumberFormatException e)
124		{
125		// ignore
126		}
127		}
128
129		/**
130		* Constructs the URL for the EnsemblGenomes /info/divisions REST service
131		* @param domain TODO
132		*
133		* @return
134		* @throws MalformedURLException
135		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
136	0	URL getDivisionsUrl(String domain) throws MalformedURLException...
137		{
138	0	return new URL(domain
139		+ "/info/divisions?content-type=application/json");
140		}
141
142		/**
143		* Returns the set of 'divisions' recognised by Ensembl or EnsemblGenomes
144		*
145		* @return
146		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
147	0	public Set<String> getDivisions() {...
148	0	if (divisions == null)
149		{
150	0	fetchDivisions();
151		}
152
153	0	return divisions.keySet();
154		}
155		}