Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PIDModel	37	61	34	0.065420566.5%	Show methods

Class PIDModel

Class PIDModel	Line # 37	Total Statements 61	Complexity 34	TOTAL Coverage 0.065420566.5%
PIDModel()   PIDModel()	4545	0.00	1.01	-1.0 -1.0 -
getName() : String   getName() : String	4949	1.01	1.01	1.0 1.0100%
getDescription() : String   getDescription() : String	5959	1.01	1.01	0.0 0.00%
isDNA() : boolean   isDNA() : boolean	6565	1.01	1.01	1.0 1.0100%
isProtein() : boolean   isProtein() : boolean	7171	1.01	1.01	1.0 1.0100%
getPairwiseScore(char,char) : float   getPairwiseScore(char,char) : float	8181	5.05	3.03	0.0 0.00%
toUpper(char) : char   toUpper(char) : char	9696	3.03	3.03	0.0 0.00%
findSimilarities(AlignmentView,SimilarityParamsI) : MatrixI   findSimilarities(AlignmentView,SimilarityParamsI) : MatrixI	111111	4.04	1.01	0.0 0.00%
findDistances(AlignmentView,SimilarityParamsI) : MatrixI   findDistances(AlignmentView,SimilarityParamsI) : MatrixI	130130	4.04	2.02	0.0 0.00%
findSimilarities(String[],SimilarityParamsI) : MatrixI   findSimilarities(String[],SimilarityParamsI) : MatrixI	152152	7.07	3.03	0.0 0.00%
computePID(String,String,SimilarityParamsI) : double   computePID(String,String,SimilarityParamsI) : double	180180	33.033	16.016	0.0 0.00%
getInstance(AlignmentViewPanel) : ScoreModelI   getInstance(AlignmentViewPanel) : ScoreModelI	260260	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.056074765	jalview.gui.CalculationChooserTest.testGetApplicableScoreModelsjalview.gui.CalculationChooserTest.testGetApplicableScoreModels	1PASS

 

Source view

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.PairwiseScoreModelI;
25		import jalview.api.analysis.ScoreModelI;
26		import jalview.api.analysis.SimilarityParamsI;
27		import jalview.datamodel.AlignmentView;
28		import jalview.math.Matrix;
29		import jalview.math.MatrixI;
30		import jalview.util.Comparison;
31
32		/**
33		* A class to provide sequence pairwise similarity based on residue identity.
34		* Instances of this class are immutable and thread-safe, so the same object is
35		* returned from calls to getInstance().
36		*/
		6.5% Uncovered Elements: 100 (107) Complexity: 34 Complexity Density: 0.56
37		public class PIDModel extends SimilarityScoreModel
38		implements PairwiseScoreModelI
39		{
40		private static final String NAME = "PID";
41
42		/**
43		* Constructor
44		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
45	21	public PIDModel()...
46		{
47		}
48
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
49	47	@Override...
50		public String getName()
51		{
52	47	return NAME;
53		}
54
55		/**
56		* Answers null for description. If a display name is needed, use getName() or
57		* an internationalized string built from the name.
58		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
59	0	@Override...
60		public String getDescription()
61		{
62	0	return null;
63		}
64
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
65	4	@Override...
66		public boolean isDNA()
67		{
68	4	return true;
69		}
70
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
71	2	@Override...
72		public boolean isProtein()
73		{
74	2	return true;
75		}
76
77		/**
78		* Answers 1 if c and d are the same residue (ignoring case), and not gap
79		* characters. Answers 0 for non-matching or gap characters.
80		*/
		0% Uncovered Elements: 7 (7) Complexity: 3 Complexity Density: 0.6
81	0	@Override...
82		public float getPairwiseScore(char c, char d)
83		{
84	0	c = toUpper(c);
85	0	d = toUpper(d);
86	0	if (c == d && !Comparison.isGap(c))
87		{
88	0	return 1f;
89		}
90	0	return 0f;
91		}
92
93		/**
94		* @param c
95		*/
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
96	0	protected static char toUpper(char c)...
97		{
98	0	if ('a' <= c && c <= 'z')
99		{
100	0	c += 'A' - 'a';
101		}
102	0	return c;
103		}
104
105		/**
106		* Computes similarity scores based on pairwise percentage identity of
107		* sequences. For consistency with Jalview 2.10.1's SeqSpace mode PCA
108		* calculation, the percentage scores are rescaled to the width of the
109		* sequences (as if counts of identical residues). This method is thread-safe.
110		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
111	0	@Override...
112		public MatrixI findSimilarities(AlignmentView seqData,
113		SimilarityParamsI options)
114		{
115	0	String[] seqs = seqData.getSequenceStrings(Comparison.GAP_DASH);
116
117	0	MatrixI result = findSimilarities(seqs, options);
118
119	0	result.multiply(seqData.getWidth() / 100d);
120
121	0	return result;
122		}
123
124		/**
125		* A distance score is computed in the usual way (by reversing the range of
126		* the similarity score results), and then rescaled to percentage values
127		* (reversing the rescaling to count values done in findSimilarities). This
128		* method is thread-safe.
129		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
130	0	@Override...
131		public MatrixI findDistances(AlignmentView seqData,
132		SimilarityParamsI options)
133		{
134	0	MatrixI result = super.findDistances(seqData, options);
135
136	0	if (seqData.getWidth() != 0)
137		{
138	0	result.multiply(100d / seqData.getWidth());
139		}
140
141	0	return result;
142		}
143
144		/**
145		* Compute percentage identity scores, using the gap treatment and
146		* normalisation specified by the options parameter
147		*
148		* @param seqs
149		* @param options
150		* @return
151		*/
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.43
152	0	protected MatrixI findSimilarities(String[] seqs,...
153		SimilarityParamsI options)
154		{
155		/*
156		* calculation is symmetric so just compute lower diagonal
157		*/
158	0	double[][] values = new double[seqs.length][seqs.length];
159	0	for (int row = 0; row < seqs.length; row++)
160		{
161	0	for (int col = row; col < seqs.length; col++)
162		{
163	0	double total = computePID(seqs[row], seqs[col], options);
164	0	values[row][col] = total;
165	0	values[col][row] = total;
166		}
167		}
168	0	return new Matrix(values);
169		}
170
171		/**
172		* Computes a percentage identity for two sequences, using the algorithm
173		* choices specified by the options parameter
174		*
175		* @param seq1
176		* @param seq2
177		* @param options
178		* @return
179		*/
		0% Uncovered Elements: 57 (57) Complexity: 16 Complexity Density: 0.48
180	0	public static double computePID(String seq1, String seq2,...
181		SimilarityParamsI options)
182		{
183	0	int len1 = seq1.length();
184	0	int len2 = seq2.length();
185	0	int width = Math.max(len1, len2);
186	0	int total = 0;
187	0	int divideBy = 0;
188
189	0	for (int i = 0; i < width; i++)
190		{
191	0	if (i >= len1 || i >= len2)
192		{
193		/*
194		* off the end of one sequence; stop if we are only matching
195		* on the shorter sequence length, else treat as trailing gap
196		*/
197	0	if (options.denominateByShortestLength())
198		{
199	0	break;
200		}
201	0	if (options.includeGaps())
202		{
203	0	divideBy++;
204		}
205	0	if (options.matchGaps())
206		{
207	0	total++;
208		}
209	0	continue;
210		}
211	0	char c1 = seq1.charAt(i);
212	0	char c2 = seq2.charAt(i);
213	0	boolean gap1 = Comparison.isGap(c1);
214	0	boolean gap2 = Comparison.isGap(c2);
215
216	0	if (gap1 && gap2)
217		{
218		/*
219		* gap-gap: include if options say so, if so
220		* have to score as identity; else ignore
221		*/
222	0	if (options.includeGappedColumns())
223		{
224	0	divideBy++;
225	0	total++;
226		}
227	0	continue;
228		}
229
230	0	if (gap1 || gap2)
231		{
232		/*
233		* gap-residue: include if options say so,
234		* count as match if options say so
235		*/
236	0	if (options.includeGaps())
237		{
238	0	divideBy++;
239		}
240	0	if (options.matchGaps())
241		{
242	0	total++;
243		}
244	0	continue;
245		}
246
247		/*
248		* remaining case is gap-residue
249		*/
250	0	if (toUpper(c1) == toUpper(c2))
251		{
252	0	total++;
253		}
254	0	divideBy++;
255		}
256
257	0	return divideBy == 0 ? 0D : 100D * total / divideBy;
258		}
259
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
260	0	@Override...
261		public ScoreModelI getInstance(AlignmentViewPanel avp)
262		{
263	0	return this;
264		}
265		}