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VisibleRowsIteratorTest | 33 | 58 | 22 |
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 | ||
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 | ||
45 | 1 | @BeforeClass(groups = { "Functional" }) |
46 | public void setup() | |
47 | { | |
48 | // create random alignment | |
49 | 1 | AlignmentGenerator gen = new AlignmentGenerator(false); |
50 | 1 | al = gen.generate(20, 15, 123, 5, 5); |
51 | 1 | if (!hiddenRepSequences.isEmpty()) |
52 | { | |
53 | 0 | al.getHiddenSequences().showAll(hiddenRepSequences); |
54 | } | |
55 | 1 | hideSequences(al, hiddenRepSequences, 2, 4); |
56 | ||
57 | 1 | al2 = gen.generate(20, 15, 123, 5, 5); |
58 | 1 | if (!hiddenRepSequences2.isEmpty()) |
59 | { | |
60 | 0 | al2.getHiddenSequences().showAll(hiddenRepSequences2); |
61 | } | |
62 | 1 | hideSequences(al2, hiddenRepSequences2, 0, 2); |
63 | ||
64 | 1 | 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 | */ | |
71 | 1 | @Test(groups = { "Functional" }) |
72 | public void testHasNextAndNextWithHidden() | |
73 | { | |
74 | 1 | VisibleRowsIterator it = new VisibleRowsIterator(0, 6, al); |
75 | 1 | int count = 0; |
76 | 5 | while (it.hasNext()) |
77 | { | |
78 | 4 | it.next(); |
79 | 4 | count++; |
80 | } | |
81 | 1 | 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 | */ | |
88 | 1 | @Test(groups = { "Functional" }) |
89 | public void testHasNextAndNextNoHidden() | |
90 | { | |
91 | 1 | VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al3); |
92 | 1 | int count = 0; |
93 | 5 | while (it.hasNext()) |
94 | { | |
95 | 4 | it.next(); |
96 | 4 | count++; |
97 | } | |
98 | 1 | 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 | */ | |
105 | 1 | @Test(groups = { "Functional" }) |
106 | public void testHasNextAndNextStartHidden() | |
107 | { | |
108 | 1 | VisibleRowsIterator it = new VisibleRowsIterator(0, 6, al2); |
109 | 1 | int count = 0; |
110 | 5 | while (it.hasNext()) |
111 | { | |
112 | 4 | it.next(); |
113 | 4 | count++; |
114 | } | |
115 | 1 | 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 | */ | |
122 | 1 | @Test(groups = { "Functional" }) |
123 | public void testHasNextAndNextEndHidden() | |
124 | { | |
125 | 1 | VisibleRowsIterator it = new VisibleRowsIterator(0, 4, al); |
126 | 1 | int count = 0; |
127 | 3 | while (it.hasNext()) |
128 | { | |
129 | 2 | it.next(); |
130 | 2 | count++; |
131 | } | |
132 | 1 | 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 | */ | |
139 | 1 | @Test( |
140 | groups = | |
141 | { "Functional" }, | |
142 | expectedExceptions = | |
143 | { NoSuchElementException.class }) | |
144 | public void testLastNextWithHidden() throws NoSuchElementException | |
145 | { | |
146 | 1 | VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al); |
147 | 3 | while (it.hasNext()) |
148 | { | |
149 | 2 | it.next(); |
150 | } | |
151 | 1 | it.next(); |
152 | } | |
153 | ||
154 | /* | |
155 | * Test iterator always throws NoSuchElementException at end of iteration | |
156 | * when alignment has no hidden rows | |
157 | */ | |
158 | 1 | @Test( |
159 | groups = | |
160 | { "Functional" }, | |
161 | expectedExceptions = | |
162 | { NoSuchElementException.class }) | |
163 | public void testLastNextNoHidden() throws NoSuchElementException | |
164 | { | |
165 | 1 | VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al3); |
166 | 5 | while (it.hasNext()) |
167 | { | |
168 | 4 | it.next(); |
169 | } | |
170 | 1 | it.next(); |
171 | } | |
172 | ||
173 | /* | |
174 | * Test iterator always throws NoSuchElementException at end of iteration | |
175 | * when alignment has hidden rows at start | |
176 | */ | |
177 | 1 | @Test( |
178 | groups = | |
179 | { "Functional" }, | |
180 | expectedExceptions = | |
181 | { NoSuchElementException.class }) | |
182 | public void testLastNextStartHidden() throws NoSuchElementException | |
183 | { | |
184 | 1 | VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al2); |
185 | 2 | while (it.hasNext()) |
186 | { | |
187 | 1 | it.next(); |
188 | } | |
189 | 1 | it.next(); |
190 | } | |
191 | ||
192 | /* | |
193 | * Test iterator always throws NoSuchElementException at end of iteration | |
194 | * when alignment has hidden rows at end | |
195 | */ | |
196 | 1 | @Test( |
197 | groups = | |
198 | { "Functional" }, | |
199 | expectedExceptions = | |
200 | { NoSuchElementException.class }) | |
201 | public void testLastNextEndHidden() throws NoSuchElementException | |
202 | { | |
203 | 1 | VisibleRowsIterator it = new VisibleRowsIterator(0, 4, al); |
204 | 3 | while (it.hasNext()) |
205 | { | |
206 | 2 | it.next(); |
207 | } | |
208 | 1 | it.next(); |
209 | } | |
210 | ||
211 | /* | |
212 | * Test calls to remove throw UnsupportedOperationException | |
213 | */ | |
214 | 1 | @Test( |
215 | groups = | |
216 | { "Functional" }, | |
217 | expectedExceptions = | |
218 | { UnsupportedOperationException.class }) | |
219 | public void testRemove() throws UnsupportedOperationException | |
220 | { | |
221 | 1 | VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al); |
222 | 1 | it.remove(); |
223 | } | |
224 | ||
225 | /* | |
226 | * Hide sequences between start and end | |
227 | */ | |
228 | 2 | private void hideSequences(AlignmentI alignment, |
229 | Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences, | |
230 | int start, int end) | |
231 | { | |
232 | 2 | SequenceI[] allseqs = alignment.getSequencesArray(); |
233 | 2 | SequenceGroup theseSeqs = new SequenceGroup(); |
234 | ||
235 | 8 | for (int i = start; i <= end; i++) |
236 | { | |
237 | 6 | theseSeqs.addSequence(allseqs[i], false); |
238 | 6 | alignment.getHiddenSequences().hideSequence(allseqs[i]); |
239 | } | |
240 | ||
241 | 2 | hiddenRepSequences.put(allseqs[start], theseSeqs); |
242 | } | |
243 | } |