Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
VisibleRowsIteratorTest	33	58	22	0.00%	Show methods

Class VisibleRowsIteratorTest

Class VisibleRowsIteratorTest	Line # 33	Total Statements 58	Complexity 22	TOTAL Coverage 0.00%
setup() : void   setup() : void	4545	10.010	3.03	0.0 0.00%
testHasNextAndNextWithHidden() : void   testHasNextAndNextWithHidden() : void	7171	6.06	2.02	0.0 0.00%
testHasNextAndNextNoHidden() : void   testHasNextAndNextNoHidden() : void	8888	6.06	2.02	0.0 0.00%
testHasNextAndNextStartHidden() : void   testHasNextAndNextStartHidden() : void	105105	6.06	2.02	0.0 0.00%
testHasNextAndNextEndHidden() : void   testHasNextAndNextEndHidden() : void	122122	6.06	2.02	0.0 0.00%
testLastNextWithHidden() : void   testLastNextWithHidden() : void	139139	4.04	2.02	0.0 0.00%
testLastNextNoHidden() : void   testLastNextNoHidden() : void	158158	4.04	2.02	0.0 0.00%
testLastNextStartHidden() : void   testLastNextStartHidden() : void	177177	4.04	2.02	0.0 0.00%
testLastNextEndHidden() : void   testLastNextEndHidden() : void	196196	4.04	2.02	0.0 0.00%
testRemove() : void   testRemove() : void	214214	2.02	1.01	0.0 0.00%
hideSequences(AlignmentI,Hashtable<SequenceI, SequenceCollectionI>,int,int) : void   hideSequences(AlignmentI,Hashtable<SequenceI, SequenceCollectionI>,int,int) : void	228228	6.06	2.02	0.0 0.00%

 

Contributing tests

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.datamodel;
22
23		import static org.testng.Assert.assertTrue;
24
25		import jalview.analysis.AlignmentGenerator;
26
27		import java.util.Hashtable;
28		import java.util.NoSuchElementException;
29
30		import org.testng.annotations.BeforeClass;
31		import org.testng.annotations.Test;
32
		0% Uncovered Elements: 91 (91) Complexity: 22 Complexity Density: 0.38
33		public class VisibleRowsIteratorTest
34		{
35		AlignmentI al;
36
37		AlignmentI al2;
38
39		AlignmentI al3;
40
41		Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
42
43		Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences2 = new Hashtable<SequenceI, SequenceCollectionI>();
44
		0% Uncovered Elements: 14 (14) Complexity: 3 Complexity Density: 0.3
45	0	@BeforeClass(groups = { "Functional" })...
46		public void setup()
47		{
48		// create random alignment
49	0	AlignmentGenerator gen = new AlignmentGenerator(false);
50	0	al = gen.generate(20, 15, 123, 5, 5);
51	0	if (!hiddenRepSequences.isEmpty())
52		{
53	0	al.getHiddenSequences().showAll(hiddenRepSequences);
54		}
55	0	hideSequences(al, hiddenRepSequences, 2, 4);
56
57	0	al2 = gen.generate(20, 15, 123, 5, 5);
58	0	if (!hiddenRepSequences2.isEmpty())
59		{
60	0	al2.getHiddenSequences().showAll(hiddenRepSequences2);
61		}
62	0	hideSequences(al2, hiddenRepSequences2, 0, 2);
63
64	0	al3 = gen.generate(20, 15, 123, 5, 5);
65		}
66
67		/*
68		* Test iterator iterates correctly through the rows
69		* when alignment has hidden rows
70		*/
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33 4-
71	0	@Test(groups = { "Functional" })...
72		public void testHasNextAndNextWithHidden()
73		{
74	0	VisibleRowsIterator it = new VisibleRowsIterator(0, 6, al);
75	0	int count = 0;
76	0	while (it.hasNext())
77		{
78	0	it.next();
79	0	count++;
80		}
81	0	assertTrue(count == 4, "hasNext() is false after 4 iterations");
82		}
83
84		/*
85		* Test iterator iterates correctly through the rows
86		* when alignment has no hidden rows
87		*/
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33 4-
88	0	@Test(groups = { "Functional" })...
89		public void testHasNextAndNextNoHidden()
90		{
91	0	VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al3);
92	0	int count = 0;
93	0	while (it.hasNext())
94		{
95	0	it.next();
96	0	count++;
97		}
98	0	assertTrue(count == 4, "hasNext() is false after 4 iterations");
99		}
100
101		/*
102		* Test iterator iterates correctly through the rows
103		* when alignment has hidden rows at start
104		*/
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33 4-
105	0	@Test(groups = { "Functional" })...
106		public void testHasNextAndNextStartHidden()
107		{
108	0	VisibleRowsIterator it = new VisibleRowsIterator(0, 6, al2);
109	0	int count = 0;
110	0	while (it.hasNext())
111		{
112	0	it.next();
113	0	count++;
114		}
115	0	assertTrue(count == 4, "hasNext() is false after 4 iterations");
116		}
117
118		/*
119		* Test iterator iterates correctly through the rows
120		* when alignment has hidden rows at end
121		*/
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33 4-
122	0	@Test(groups = { "Functional" })...
123		public void testHasNextAndNextEndHidden()
124		{
125	0	VisibleRowsIterator it = new VisibleRowsIterator(0, 4, al);
126	0	int count = 0;
127	0	while (it.hasNext())
128		{
129	0	it.next();
130	0	count++;
131		}
132	0	assertTrue(count == 2, "hasNext() is false after 2 iterations");
133		}
134
135		/*
136		* Test iterator always throws NoSuchElementException at end of iteration
137		* when alignment has hidden rows
138		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5 4-
139	0	@Test(...
140		groups =
141		{ "Functional" },
142		expectedExceptions =
143		{ NoSuchElementException.class })
144		public void testLastNextWithHidden() throws NoSuchElementException
145		{
146	0	VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al);
147	0	while (it.hasNext())
148		{
149	0	it.next();
150		}
151	0	it.next();
152		}
153
154		/*
155		* Test iterator always throws NoSuchElementException at end of iteration
156		* when alignment has no hidden rows
157		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5 4-
158	0	@Test(...
159		groups =
160		{ "Functional" },
161		expectedExceptions =
162		{ NoSuchElementException.class })
163		public void testLastNextNoHidden() throws NoSuchElementException
164		{
165	0	VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al3);
166	0	while (it.hasNext())
167		{
168	0	it.next();
169		}
170	0	it.next();
171		}
172
173		/*
174		* Test iterator always throws NoSuchElementException at end of iteration
175		* when alignment has hidden rows at start
176		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5 4-
177	0	@Test(...
178		groups =
179		{ "Functional" },
180		expectedExceptions =
181		{ NoSuchElementException.class })
182		public void testLastNextStartHidden() throws NoSuchElementException
183		{
184	0	VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al2);
185	0	while (it.hasNext())
186		{
187	0	it.next();
188		}
189	0	it.next();
190		}
191
192		/*
193		* Test iterator always throws NoSuchElementException at end of iteration
194		* when alignment has hidden rows at end
195		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5 4-
196	0	@Test(...
197		groups =
198		{ "Functional" },
199		expectedExceptions =
200		{ NoSuchElementException.class })
201		public void testLastNextEndHidden() throws NoSuchElementException
202		{
203	0	VisibleRowsIterator it = new VisibleRowsIterator(0, 4, al);
204	0	while (it.hasNext())
205		{
206	0	it.next();
207		}
208	0	it.next();
209		}
210
211		/*
212		* Test calls to remove throw UnsupportedOperationException
213		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5 4-
214	0	@Test(...
215		groups =
216		{ "Functional" },
217		expectedExceptions =
218		{ UnsupportedOperationException.class })
219		public void testRemove() throws UnsupportedOperationException
220		{
221	0	VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al);
222	0	it.remove();
223		}
224
225		/*
226		* Hide sequences between start and end
227		*/
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
228	0	private void hideSequences(AlignmentI alignment,...
229		Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences,
230		int start, int end)
231		{
232	0	SequenceI[] allseqs = alignment.getSequencesArray();
233	0	SequenceGroup theseSeqs = new SequenceGroup();
234
235	0	for (int i = start; i <= end; i++)
236		{
237	0	theseSeqs.addSequence(allseqs[i], false);
238	0	alignment.getHiddenSequences().hideSequence(allseqs[i]);
239		}
240
241	0	hiddenRepSequences.put(allseqs[start], theseSeqs);
242		}
243		}