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Coverage Report

  1. Project Clover database Wed Nov 12 2025 09:00:47 GMT
  2. Package jalview.datamodel

File VisibleRowsIteratorTest.java

 

Code metrics

22
58
11
1
243
160
22
0.38
5.27
11
2

Classes

Class Line # Actions
VisibleRowsIteratorTest 33 58 22
0.9560439695.6%
 

Contributing tests

This file is covered by 9 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   
 
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 toggle @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 toggle @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 toggle @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 toggle @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 toggle @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 toggle @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 toggle @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 toggle @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 toggle @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 toggle @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 toggle 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    }
  • Report generated by OpenClover v 4.4.1 on Wed Nov 12 2025 09:10:40 GMT using coverage data from Wed Nov 12 2025 09:10:27 GMT.
  • OpenClover is free and open-source software.