Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SequenceFetcher	46	22	8	0.00%	Show methods

Class SequenceFetcher

Class SequenceFetcher	Line # 46	Total Statements 22	Complexity 8	TOTAL Coverage 0.00%
setMockFetcher(SequenceFetcher) : void   setMockFetcher(SequenceFetcher) : void	6161	1.01	1.01	0.0 0.00%
getInstance() : SequenceFetcher   getInstance() : SequenceFetcher	7272	1.01	2.02	0.0 0.00%
SequenceFetcher()   SequenceFetcher()	8484	8.08	1.01	0.0 0.00%
getNonAlignmentSources() : String[]   getNonAlignmentSources() : String[]	106106	12.012	4.04	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.ws;
22
23		import jalview.bin.ApplicationSingletonProvider;
24		import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
25		import jalview.ext.ensembl.EnsemblGene;
26		import jalview.ws.dbsources.EBIAlfaFold;
27		import jalview.ws.dbsources.EmblCdsSource;
28		import jalview.ws.dbsources.EmblSource;
29		import jalview.ws.dbsources.Pdb;
30		import jalview.ws.dbsources.PfamFull;
31		import jalview.ws.dbsources.PfamSeed;
32		import jalview.ws.dbsources.RfamSeed;
33		import jalview.ws.dbsources.TDBeacons;
34		import jalview.ws.dbsources.Uniprot;
35		import jalview.ws.seqfetcher.ASequenceFetcher;
36		import jalview.ws.seqfetcher.DbSourceProxy;
37
38		import java.util.ArrayList;
39		import java.util.Collections;
40		import java.util.List;
41
42		/**
43		* This implements the run-time discovery of sequence database clients.
44		*
45		*/
		0% Uncovered Elements: 34 (34) Complexity: 8 Complexity Density: 0.36
46		public class SequenceFetcher extends ASequenceFetcher implements ApplicationSingletonI
47		{
48		/*
49		* set a mock fetcher here for testing only - reset to null afterwards
50		*/
51		private static SequenceFetcher mockFetcher;
52
53		/**
54		* Set the instance object to use (intended for unit testing with mock
55		* objects).
56		*
57		* Be sure to reset to null in the tearDown method of any tests!
58		*
59		* @param sf
60		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
61	0	public static void setMockFetcher(SequenceFetcher sf)...
62		{
63	0	mockFetcher = sf;
64		}
65
66		/**
67		* Returns a new SequenceFetcher singleton, or a mock object if one has been
68		* set.
69		*
70		* @return
71		*/
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
72	0	public static SequenceFetcher getInstance()...
73		{
74	0	return mockFetcher != null ? mockFetcher
75		: ApplicationSingletonProvider.getInstance(SequenceFetcher.class);
76		}
77
78		/**
79		* Thread safe construction of database proxies TODO: extend to a configurable
80		* database plugin mechanism where classes are instantiated by reflection and
81		* queried for their DbRefSource and version association.
82		*
83		*/
		0% Uncovered Elements: 8 (8) Complexity: 1 Complexity Density: 0.12
84	0	public SequenceFetcher()...
85		{
86	0	addDBRefSourceImpl(EnsemblGene.class);
87		// addDBRefSourceImpl(EnsemblGenomes.class);
88	0	addDBRefSourceImpl(EmblSource.class);
89	0	addDBRefSourceImpl(EmblCdsSource.class);
90	0	addDBRefSourceImpl(Uniprot.class);
91		// not a sequence source yet
92		// addDBRefSourceImpl(TDBeacons.class);
93	0	addDBRefSourceImpl(Pdb.class);
94	0	addDBRefSourceImpl(PfamFull.class);
95	0	addDBRefSourceImpl(PfamSeed.class);
96	0	addDBRefSourceImpl(RfamSeed.class);
97		// Technically not a database cross reference we fetch directly
98		// Useful for AlphaFold debugging
99		// addDBRefSourceImpl(EBIAlfaFold.class);
100		}
101
102		/**
103		* return an ordered list of database sources excluding alignment only
104		* databases
105		*/
		0% Uncovered Elements: 18 (18) Complexity: 4 Complexity Density: 0.33
106	0	public String[] getNonAlignmentSources()...
107		{
108	0	String[] srcs = this.getSupportedDb();
109	0	List<String> src = new ArrayList<>();
110
111	0	for (int i = 0; i < srcs.length; i++)
112		{
113	0	boolean accept = true;
114	0	for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
115		{
116		// Skip the alignment databases for the moment - they're not useful for
117		// verifying a single sequence against its reference source
118	0	if (dbs.isAlignmentSource())
119		{
120	0	accept = false;
121	0	break;
122		}
123		}
124	0	if (accept)
125		{
126	0	src.add(srcs[i]);
127		}
128		}
129
130	0	Collections.sort(src, String.CASE_INSENSITIVE_ORDER);
131	0	return src.toArray(new String[src.size()]);
132		}
133		}