Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SequenceOntologyFactory	34	4	5	0.00%	Show methods

Class SequenceOntologyFactory

Class SequenceOntologyFactory	Line # 34	Total Statements 4	Complexity 5	TOTAL Coverage 0.00%
getInstance() : SequenceOntologyFactory   getInstance() : SequenceOntologyFactory	4545	1.01	1.01	0.0 0.00%
SequenceOntologyFactory()   SequenceOntologyFactory()	5151	0.00	1.01	-1.0 -1.0 -
getSequenceOntology() : SequenceOntologyI   getSequenceOntology() : SequenceOntologyI	6262	2.02	2.02	0.0 0.00%
setSequenceOntology(SequenceOntologyI) : void   setSequenceOntology(SequenceOntologyI) : void	7575	1.01	1.01	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.io.gff;
22
23		import jalview.bin.ApplicationSingletonProvider;
24		import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
25
26		/**
27		* A factory class that returns a model of the Sequence Ontology. By default a
28		* hard-coded subset is used (for the applet, or testing), or setInstance() can
29		* be used to set full Ontology data.
30		*
31		* @author gmcarstairs
32		*
33		*/
		0% Uncovered Elements: 10 (10) Complexity: 5 Complexity Density: 1.25
34		public class SequenceOntologyFactory implements ApplicationSingletonI
35		{
36		/**
37		* Answers an instance of this class for the current application context. Note
38		* that this supports running two JS 'applets' on the same page, one with the
39		* full Sequence Ontology (USE_FULL_SO = true) and one with a hard-coded
40		* subset (USE_FULL_SO = false). If this is overkill, could change this method
41		* to just return a common static instance.
42		*
43		* @return
44		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
45	0	private static synchronized SequenceOntologyFactory getInstance()...
46		{
47	0	return ApplicationSingletonProvider
48		.getInstance(SequenceOntologyFactory.class);
49		}
50
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
51	0	private SequenceOntologyFactory()...
52		{
53		// private singleton
54		}
55
56
57		/**
58		* Answers the configured model of the Sequence Ontology.
59		*
60		* @return
61		*/
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
62	0	public static synchronized SequenceOntologyI getSequenceOntology()...
63		{
64	0	SequenceOntologyFactory f = getInstance();
65	0	return (f.sequenceOntology == null
66		? f.sequenceOntology = new SequenceOntologyLite()
67		: f.sequenceOntology);
68		}
69
70		/**
71		* For testng only
72		*
73		* @param so
74		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
75	0	public static void setSequenceOntology(SequenceOntologyI so)...
76		{
77	0	getInstance().sequenceOntology = so;
78		}
79
80
81		private SequenceOntologyI sequenceOntology;
82
83		}