Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
AAFrequencyTest	37	120	7	15	0.882812588.3%	Show methods

Class AAFrequencyTest

Class AAFrequencyTest	Line # 37	Total Statements 120	Complexity 7	Uncovered Elements 15	TOTAL Coverage 0.882812588.3%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4040	2.02	1.01	0.00	1.0 1.0100%
testCalculate_noProfile() : void   testCalculate_noProfile() : void	4747	33.033	1.01	0.00	1.0 1.0100%
testCalculate_withProfile() : void   testCalculate_withProfile() : void	9696	25.025	1.01	0.00	1.0 1.0100%
testCalculate_withProfileTiming() : void   testCalculate_withProfileTiming() : void	131131	12.012	2.02	14.014	0.0 0.00%
testCompleteConsensus_includeGaps_showLogo() : void   testCompleteConsensus_includeGaps_showLogo() : void	159159	24.024	1.01	0.00	1.0 1.0100%
testCompleteConsensus_ignoreGaps_noLogo() : void   testCompleteConsensus_ignoreGaps_noLogo() : void	200200	24.024	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.265625	jalview.analysis.AAFrequencyTest.testCalculate_noProfilejalview.analysis.AAFrequencyTest.testCalculate_noProfile	1PASS
	0.203125	jalview.analysis.AAFrequencyTest.testCalculate_withProfilejalview.analysis.AAFrequencyTest.testCalculate_withProfile	1PASS
	0.1953125	jalview.analysis.AAFrequencyTest.testCompleteConsensus_includeGaps_showLogojalview.analysis.AAFrequencyTest.testCompleteConsensus_includeGaps_showLogo	1PASS
	0.1953125	jalview.analysis.AAFrequencyTest.testCompleteConsensus_ignoreGaps_noLogojalview.analysis.AAFrequencyTest.testCompleteConsensus_ignoreGaps_noLogo	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;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertNull;
25
26		import jalview.datamodel.AlignmentAnnotation;
27		import jalview.datamodel.Annotation;
28		import jalview.datamodel.ProfileI;
29		import jalview.datamodel.ProfilesI;
30		import jalview.datamodel.Sequence;
31		import jalview.datamodel.SequenceI;
32		import jalview.gui.JvOptionPane;
33
34		import org.testng.annotations.BeforeClass;
35		import org.testng.annotations.Test;
36
		88.3% Uncovered Elements: 15 (128) Complexity: 7 Complexity Density: 0.06
37		public class AAFrequencyTest
38		{
39
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
40	1	@BeforeClass(alwaysRun = true)...
41		public void setUpJvOptionPane()
42		{
43	1	JvOptionPane.setInteractiveMode(false);
44	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
45		}
46
		100% Uncovered Elements: 0 (33) Complexity: 1 Complexity Density: 0.03 1PASS
47	1	@Test(groups = { "Functional" })...
48		public void testCalculate_noProfile()
49		{
50	1	SequenceI seq1 = new Sequence("Seq1", "CAG-T");
51	1	SequenceI seq2 = new Sequence("Seq2", "CAC-T");
52	1	SequenceI seq3 = new Sequence("Seq3", "C---G");
53	1	SequenceI seq4 = new Sequence("Seq4", "CA--t");
54	1	SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
55	1	int width = seq1.getLength();
56	1	ProfilesI result = AAFrequency.calculate(seqs, width, 0, width,
57		false);
58
59		// col 0 is 100% C
60	1	ProfileI col = result.get(0);
61	1	assertEquals(100f, col.getPercentageIdentity(false));
62	1	assertEquals(100f, col.getPercentageIdentity(true));
63	1	assertEquals(4, col.getMaxCount());
64	1	assertEquals("C", col.getModalResidue());
65	1	assertNull(col.getCounts());
66
67		// col 1 is 75% A
68	1	col = result.get(1);
69	1	assertEquals(75f, col.getPercentageIdentity(false));
70	1	assertEquals(100f, col.getPercentageIdentity(true));
71	1	assertEquals(3, col.getMaxCount());
72	1	assertEquals("A", col.getModalResidue());
73
74		// col 2 is 50% G 50% C or 25/25 counting gaps
75	1	col = result.get(2);
76	1	assertEquals(25f, col.getPercentageIdentity(false));
77	1	assertEquals(50f, col.getPercentageIdentity(true));
78	1	assertEquals(1, col.getMaxCount());
79	1	assertEquals("CG", col.getModalResidue());
80
81		// col 3 is all gaps
82	1	col = result.get(3);
83	1	assertEquals(0f, col.getPercentageIdentity(false));
84	1	assertEquals(0f, col.getPercentageIdentity(true));
85	1	assertEquals(0, col.getMaxCount());
86	1	assertEquals("", col.getModalResidue());
87
88		// col 4 is 75% T 25% G
89	1	col = result.get(4);
90	1	assertEquals(75f, col.getPercentageIdentity(false));
91	1	assertEquals(75f, col.getPercentageIdentity(true));
92	1	assertEquals(3, col.getMaxCount());
93	1	assertEquals("T", col.getModalResidue());
94		}
95
		100% Uncovered Elements: 0 (25) Complexity: 1 Complexity Density: 0.04 1PASS
96	1	@Test(groups = { "Functional" })...
97		public void testCalculate_withProfile()
98		{
99	1	SequenceI seq1 = new Sequence("Seq1", "CAGT");
100	1	SequenceI seq2 = new Sequence("Seq2", "CACT");
101	1	SequenceI seq3 = new Sequence("Seq3", "C--G");
102	1	SequenceI seq4 = new Sequence("Seq4", "CA-t");
103	1	SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
104	1	int width = seq1.getLength();
105	1	ProfilesI result = AAFrequency.calculate(seqs, width, 0, width,
106		true);
107
108	1	ProfileI profile = result.get(0);
109	1	assertEquals(4, profile.getCounts().getCount('C'));
110	1	assertEquals(4, profile.getHeight());
111	1	assertEquals(4, profile.getNonGapped());
112
113	1	profile = result.get(1);
114	1	assertEquals(3, profile.getCounts().getCount('A'));
115	1	assertEquals(4, profile.getHeight());
116	1	assertEquals(3, profile.getNonGapped());
117
118	1	profile = result.get(2);
119	1	assertEquals(1, profile.getCounts().getCount('C'));
120	1	assertEquals(1, profile.getCounts().getCount('G'));
121	1	assertEquals(4, profile.getHeight());
122	1	assertEquals(2, profile.getNonGapped());
123
124	1	profile = result.get(3);
125	1	assertEquals(3, profile.getCounts().getCount('T'));
126	1	assertEquals(1, profile.getCounts().getCount('G'));
127	1	assertEquals(4, profile.getHeight());
128	1	assertEquals(4, profile.getNonGapped());
129		}
130
		0% Uncovered Elements: 14 (14) Complexity: 2 Complexity Density: 0.17 1PASS
131	0	@Test(groups = { "Functional" }, enabled = false)...
132		public void testCalculate_withProfileTiming()
133		{
134	0	SequenceI seq1 = new Sequence("Seq1", "CAGT");
135	0	SequenceI seq2 = new Sequence("Seq2", "CACT");
136	0	SequenceI seq3 = new Sequence("Seq3", "C--G");
137	0	SequenceI seq4 = new Sequence("Seq4", "CA-t");
138	0	SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
139
140		// ensure class loaded and initialised
141	0	int width = seq1.getLength();
142	0	AAFrequency.calculate(seqs, width, 0, width, true);
143
144	0	int reps = 100000;
145	0	long start = System.currentTimeMillis();
146	0	for (int i = 0; i < reps; i++)
147		{
148	0	AAFrequency.calculate(seqs, width, 0, width, true);
149		}
150	0	System.out.println(System.currentTimeMillis() - start);
151		}
152
153		/**
154		* Test generation of consensus annotation with options 'include gaps'
155		* (profile percentages are of all sequences, whether gapped or not), and
156		* 'show logo' (the full profile with all residue percentages is reported in
157		* the description for the tooltip)
158		*/
		100% Uncovered Elements: 0 (24) Complexity: 1 Complexity Density: 0.04 1PASS
159	1	@Test(groups = { "Functional" })...
160		public void testCompleteConsensus_includeGaps_showLogo()
161		{
162		/*
163		* first compute the profiles
164		*/
165	1	SequenceI seq1 = new Sequence("Seq1", "CAG-T");
166	1	SequenceI seq2 = new Sequence("Seq2", "CAC-T");
167	1	SequenceI seq3 = new Sequence("Seq3", "C---G");
168	1	SequenceI seq4 = new Sequence("Seq4", "CA--t");
169	1	SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
170	1	int width = seq1.getLength();
171	1	ProfilesI profiles = AAFrequency.calculate(seqs, width, 0, width, true);
172
173	1	AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
174		"PID", new Annotation[width]);
175	1	AAFrequency
176		.completeConsensus(consensus, profiles, 0, 5, false, true, 4);
177
178	1	Annotation ann = consensus.annotations[0];
179	1	assertEquals("C 100%", ann.description);
180	1	assertEquals("C", ann.displayCharacter);
181	1	ann = consensus.annotations[1];
182	1	assertEquals("A 75%", ann.description);
183	1	assertEquals("A", ann.displayCharacter);
184	1	ann = consensus.annotations[2];
185	1	assertEquals("C 25%; G 25%", ann.description);
186	1	assertEquals("+", ann.displayCharacter);
187	1	ann = consensus.annotations[3];
188	1	assertEquals("", ann.description);
189	1	assertEquals("-", ann.displayCharacter);
190	1	ann = consensus.annotations[4];
191	1	assertEquals("T 75%; G 25%", ann.description);
192	1	assertEquals("T", ann.displayCharacter);
193		}
194
195		/**
196		* Test generation of consensus annotation with options 'ignore gaps' (profile
197		* percentages are of the non-gapped sequences) and 'no logo' (only the modal
198		* residue[s] percentage is reported in the description for the tooltip)
199		*/
		100% Uncovered Elements: 0 (24) Complexity: 1 Complexity Density: 0.04 1PASS
200	1	@Test(groups = { "Functional" })...
201		public void testCompleteConsensus_ignoreGaps_noLogo()
202		{
203		/*
204		* first compute the profiles
205		*/
206	1	SequenceI seq1 = new Sequence("Seq1", "CAG-T");
207	1	SequenceI seq2 = new Sequence("Seq2", "CAC-T");
208	1	SequenceI seq3 = new Sequence("Seq3", "C---G");
209	1	SequenceI seq4 = new Sequence("Seq4", "CA--t");
210	1	SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
211	1	int width = seq1.getLength();
212	1	ProfilesI profiles = AAFrequency.calculate(seqs, width, 0, width, true);
213
214	1	AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
215		"PID", new Annotation[width]);
216	1	AAFrequency
217		.completeConsensus(consensus, profiles, 0, 5, true, false, 4);
218
219	1	Annotation ann = consensus.annotations[0];
220	1	assertEquals("C 100%", ann.description);
221	1	assertEquals("C", ann.displayCharacter);
222	1	ann = consensus.annotations[1];
223	1	assertEquals("A 100%", ann.description);
224	1	assertEquals("A", ann.displayCharacter);
225	1	ann = consensus.annotations[2];
226	1	assertEquals("[CG] 50%", ann.description);
227	1	assertEquals("+", ann.displayCharacter);
228	1	ann = consensus.annotations[3];
229	1	assertEquals("", ann.description);
230	1	assertEquals("-", ann.displayCharacter);
231	1	ann = consensus.annotations[4];
232	1	assertEquals("T 75%", ann.description);
233	1	assertEquals("T", ann.displayCharacter);
234		}
235		}