Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ScoreModels	38	30	16	0.00%	Show methods

Class ScoreModels

Class ScoreModels	Line # 38	Total Statements 30	Complexity 16	TOTAL Coverage 0.00%
getInstance() : ScoreModels   getInstance() : ScoreModels	5555	1.01	1.01	0.0 0.00%
ScoreModels()   ScoreModels()	7272	9.09	1.01	0.0 0.00%
loadScoreMatrix(String,boolean) : ScoreMatrix   loadScoreMatrix(String,boolean) : ScoreMatrix	9797	8.08	3.03	0.0 0.00%
getModels() : Iterable<ScoreModelI>   getModels() : Iterable<ScoreModelI>	125125	1.01	1.01	0.0 0.00%
getScoreModel(String,AlignmentViewPanel) : ScoreModelI   getScoreModel(String,AlignmentViewPanel) : ScoreModelI	140140	2.02	2.02	0.0 0.00%
registerScoreModel(ScoreModelI) : void   registerScoreModel(ScoreModelI) : void	146146	4.04	2.02	0.0 0.00%
reset() : void   reset() : void	160160	1.01	1.01	0.0 0.00%
getDefaultModel(boolean) : ScoreMatrix   getDefaultModel(boolean) : ScoreMatrix	172172	1.01	2.02	0.0 0.00%
getBlosum62() : ScoreMatrix   getBlosum62() : ScoreMatrix	177177	1.01	1.01	0.0 0.00%
getPam250() : ScoreMatrix   getPam250() : ScoreMatrix	182182	1.01	1.01	0.0 0.00%
getSecondaryStructureMatrix() : ScoreMatrix   getSecondaryStructureMatrix() : ScoreMatrix	191191	1.01	1.01	0.0 0.00%

 

Contributing tests

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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.analysis.scoremodels;
22
23		import jalview.api.AlignmentViewPanel;
24		import jalview.api.analysis.ScoreModelI;
25		import jalview.bin.ApplicationSingletonProvider;
26		import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
27		import jalview.io.DataSourceType;
28		import jalview.io.FileParse;
29		import jalview.io.ScoreMatrixFile;
30
31		import java.io.IOException;
32		import java.util.LinkedHashMap;
33		import java.util.Map;
34
35		/**
36		* A class that can register and serve instances of ScoreModelI
37		*/
		0% Uncovered Elements: 49 (49) Complexity: 16 Complexity Density: 0.53
38		public class ScoreModels implements ApplicationSingletonI
39		{
40		private final ScoreMatrix BLOSUM62;
41
42		private final ScoreMatrix PAM250;
43
44		private final ScoreMatrix DNA;
45
46		private final ScoreMatrix SECONDARYSTRUCTURE;
47
48		private Map<String, ScoreModelI> models;
49		/**
50		* Answers the singleton instance of this class, with lazy initialisation
51		* (built-in score models are loaded on the first call to this method)
52		*
53		* @return
54		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
55	0	public static ScoreModels getInstance()...
56		{
57	0	return ApplicationSingletonProvider.getInstance(ScoreModels.class);
58		}
59
60		/**
61		* Private constructor to enforce use of singleton. Registers Jalview's
62		* "built-in" score models:
63		* <ul>
64		* <li>BLOSUM62</li>
65		* <li>PAM250</li>
66		* <li>PID</li>
67		* <li>DNA</li>
68		* <li>Sequence Feature Similarity</li> *
69		* <li>Secondary Structure Similarity</li>
70		* </ul>
71		*/
		0% Uncovered Elements: 9 (9) Complexity: 1 Complexity Density: 0.11
72	0	private ScoreModels()...
73		{
74		/*
75		* using LinkedHashMap keeps models ordered as added
76		*/
77	0	models = new LinkedHashMap<>();
78	0	BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm",true);
79	0	PAM250 = loadScoreMatrix("scoreModel/pam250.scm",true);
80	0	DNA = loadScoreMatrix("scoreModel/dna.scm",true);
81	0	registerScoreModel(new PIDModel());
82	0	registerScoreModel(new FeatureDistanceModel());
83	0	SECONDARYSTRUCTURE = loadScoreMatrix(
84		"scoreModel/secondarystructure.scm",false);
85	0	registerScoreModel(new SecondaryStructureDistanceModel());
86	0	registerScoreModel(new ValueAnnotationDistanceModel());
87		}
88
89		/**
90		* Tries to load a score matrix from the given resource file, and if
91		* successful, optionally registers it.
92		*
93		* @param resourcePath
94		* @param register (if true)
95		* @return loaded matrix
96		*/
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.38
97	0	ScoreMatrix loadScoreMatrix(String resourcePath, boolean register)...
98		{
99	0	try
100		{
101		/*
102		* delegate parsing to ScoreMatrixFile
103		*/
104	0	FileParse fp = new FileParse(resourcePath,
105		DataSourceType.CLASSLOADER);
106	0	ScoreMatrix sm = new ScoreMatrixFile(fp).parseMatrix();
107	0	if (register) {
108	0	registerScoreModel(sm);
109		}
110	0	return sm;
111		} catch (IOException e)
112		{
113	0	jalview.bin.Console.errPrintln(
114		"Error reading " + resourcePath + ": " + e.getMessage());
115		}
116	0	return null;
117		}
118
119		/**
120		* Answers an iterable set of the registered score models. Currently these are
121		* returned in the order in which they were registered.
122		*
123		* @return
124		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
125	0	public Iterable<ScoreModelI> getModels()...
126		{
127	0	return models.values();
128		}
129
130		/**
131		* Returns an instance of a score model for the given name. If the model is of
132		* 'view dependent' type (e.g. feature similarity), instantiates a new
133		* instance configured for the given view. Otherwise returns a cached instance
134		* of the score model.
135		*
136		* @param name
137		* @param avp
138		* @return
139		*/
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
140	0	public ScoreModelI getScoreModel(String name, AlignmentViewPanel avp)...
141		{
142	0	ScoreModelI model = models.get(name);
143	0	return model == null ? null : model.getInstance(avp);
144		}
145
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
146	0	public void registerScoreModel(ScoreModelI sm)...
147		{
148	0	ScoreModelI sm2 = models.get(sm.getName());
149	0	if (sm2 != null)
150		{
151	0	jalview.bin.Console.errPrintln(
152		"Warning: replacing score model " + sm2.getName());
153		}
154	0	models.put(sm.getName(), sm);
155		}
156
157		/**
158		* Resets to just the built-in score models
159		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
160	0	public void reset()...
161		{
162	0	ApplicationSingletonProvider.removeInstance(this.getClass());
163		}
164
165		/**
166		* Returns the default peptide or nucleotide score model, currently BLOSUM62
167		* or DNA
168		*
169		* @param forPeptide
170		* @return
171		*/
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
172	0	public ScoreMatrix getDefaultModel(boolean forPeptide)...
173		{
174	0	return forPeptide ? BLOSUM62 : DNA;
175		}
176
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
177	0	public ScoreMatrix getBlosum62()...
178		{
179	0	return BLOSUM62;
180		}
181
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
182	0	public ScoreMatrix getPam250()...
183		{
184	0	return PAM250;
185		}
186
187		/**
188		* get currently configured matrix for comparing secondary structure
189		* @return
190		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
191	0	public ScoreMatrix getSecondaryStructureMatrix()...
192		{
193	0	return SECONDARYSTRUCTURE;
194		}
195		}