Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ScoreModels	36	31	17	0.00%	Show methods

Class ScoreModels

Class ScoreModels	Line # 36	Total Statements 31	Complexity 17	TOTAL Coverage 0.00%
getInstance() : ScoreModels   getInstance() : ScoreModels	5656	3.03	2.02	0.0 0.00%
ScoreModels()   ScoreModels()	7777	8.08	1.01	0.0 0.00%
loadScoreMatrix(String,boolean) : ScoreMatrix   loadScoreMatrix(String,boolean) : ScoreMatrix	102102	8.08	3.03	0.0 0.00%
getModels() : Iterable<ScoreModelI>   getModels() : Iterable<ScoreModelI>	130130	1.01	1.01	0.0 0.00%
getScoreModel(String,AlignmentViewPanel) : ScoreModelI   getScoreModel(String,AlignmentViewPanel) : ScoreModelI	145145	2.02	2.02	0.0 0.00%
registerScoreModel(ScoreModelI) : void   registerScoreModel(ScoreModelI) : void	151151	4.04	2.02	0.0 0.00%
reset() : void   reset() : void	165165	1.01	1.01	0.0 0.00%
getDefaultModel(boolean) : ScoreMatrix   getDefaultModel(boolean) : ScoreMatrix	177177	1.01	2.02	0.0 0.00%
getBlosum62() : ScoreMatrix   getBlosum62() : ScoreMatrix	182182	1.01	1.01	0.0 0.00%
getPam250() : ScoreMatrix   getPam250() : ScoreMatrix	187187	1.01	1.01	0.0 0.00%
getSecondaryStructureMatrix() : ScoreMatrix   getSecondaryStructureMatrix() : ScoreMatrix	196196	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.io.DataSourceType;
26		import jalview.io.FileParse;
27		import jalview.io.ScoreMatrixFile;
28
29		import java.io.IOException;
30		import java.util.LinkedHashMap;
31		import java.util.Map;
32
33		/**
34		* A class that can register and serve instances of ScoreModelI
35		*/
		0% Uncovered Elements: 52 (52) Complexity: 17 Complexity Density: 0.55
36		public class ScoreModels
37		{
38		private final ScoreMatrix BLOSUM62;
39
40		private final ScoreMatrix PAM250;
41
42		private final ScoreMatrix DNA;
43
44		private final ScoreMatrix SECONDARYSTRUCTURE;
45
46		private static ScoreModels instance;
47
48		private Map<String, ScoreModelI> models;
49
50		/**
51		* Answers the singleton instance of this class, with lazy initialisation
52		* (built-in score models are loaded on the first call to this method)
53		*
54		* @return
55		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
56	0	public static ScoreModels getInstance()...
57		{
58	0	if (instance == null)
59		{
60	0	instance = new ScoreModels();
61		}
62	0	return instance;
63		}
64
65		/**
66		* Private constructor to enforce use of singleton. Registers Jalview's
67		* "built-in" score models:
68		* <ul>
69		* <li>BLOSUM62</li>
70		* <li>PAM250</li>
71		* <li>PID</li>
72		* <li>DNA</li>
73		* <li>Sequence Feature Similarity</li> *
74		* <li>Secondary Structure Similarity</li>
75		* </ul>
76		*/
		0% Uncovered Elements: 8 (8) Complexity: 1 Complexity Density: 0.12
77	0	private ScoreModels()...
78		{
79		/*
80		* using LinkedHashMap keeps models ordered as added
81		*/
82	0	models = new LinkedHashMap<>();
83	0	BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm",true);
84	0	PAM250 = loadScoreMatrix("scoreModel/pam250.scm",true);
85	0	DNA = loadScoreMatrix("scoreModel/dna.scm",true);
86	0	registerScoreModel(new PIDModel());
87	0	registerScoreModel(new FeatureDistanceModel());
88	0	SECONDARYSTRUCTURE = loadScoreMatrix(
89		"scoreModel/secondarystructure.scm",false);
90	0	registerScoreModel(new SecondaryStructureDistanceModel());
91
92		}
93
94		/**
95		* Tries to load a score matrix from the given resource file, and if
96		* successful, optionally registers it.
97		*
98		* @param resourcePath
99		* @param register (if true)
100		* @return loaded matrix
101		*/
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.38
102	0	ScoreMatrix loadScoreMatrix(String resourcePath, boolean register)...
103		{
104	0	try
105		{
106		/*
107		* delegate parsing to ScoreMatrixFile
108		*/
109	0	FileParse fp = new FileParse(resourcePath,
110		DataSourceType.CLASSLOADER);
111	0	ScoreMatrix sm = new ScoreMatrixFile(fp).parseMatrix();
112	0	if (register) {
113	0	registerScoreModel(sm);
114		}
115	0	return sm;
116		} catch (IOException e)
117		{
118	0	jalview.bin.Console.errPrintln(
119		"Error reading " + resourcePath + ": " + e.getMessage());
120		}
121	0	return null;
122		}
123
124		/**
125		* Answers an iterable set of the registered score models. Currently these are
126		* returned in the order in which they were registered.
127		*
128		* @return
129		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
130	0	public Iterable<ScoreModelI> getModels()...
131		{
132	0	return models.values();
133		}
134
135		/**
136		* Returns an instance of a score model for the given name. If the model is of
137		* 'view dependent' type (e.g. feature similarity), instantiates a new
138		* instance configured for the given view. Otherwise returns a cached instance
139		* of the score model.
140		*
141		* @param name
142		* @param avp
143		* @return
144		*/
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
145	0	public ScoreModelI getScoreModel(String name, AlignmentViewPanel avp)...
146		{
147	0	ScoreModelI model = models.get(name);
148	0	return model == null ? null : model.getInstance(avp);
149		}
150
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
151	0	public void registerScoreModel(ScoreModelI sm)...
152		{
153	0	ScoreModelI sm2 = models.get(sm.getName());
154	0	if (sm2 != null)
155		{
156	0	jalview.bin.Console.errPrintln(
157		"Warning: replacing score model " + sm2.getName());
158		}
159	0	models.put(sm.getName(), sm);
160		}
161
162		/**
163		* Resets to just the built-in score models
164		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
165	0	public void reset()...
166		{
167	0	instance = new ScoreModels();
168		}
169
170		/**
171		* Returns the default peptide or nucleotide score model, currently BLOSUM62
172		* or DNA
173		*
174		* @param forPeptide
175		* @return
176		*/
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
177	0	public ScoreMatrix getDefaultModel(boolean forPeptide)...
178		{
179	0	return forPeptide ? BLOSUM62 : DNA;
180		}
181
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
182	0	public ScoreMatrix getBlosum62()...
183		{
184	0	return BLOSUM62;
185		}
186
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
187	0	public ScoreMatrix getPam250()...
188		{
189	0	return PAM250;
190		}
191
192		/**
193		* get currently configured matrix for comparing secondary structure
194		* @return
195		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
196	0	public ScoreMatrix getSecondaryStructureMatrix()...
197		{
198	0	return SECONDARYSTRUCTURE;
199		}
200		}