1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.commands

File TrimRegionCommandTest.java

 

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Classes

Class
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Actions
TrimRegionCommandTest 41 43 8
1.0100%
 

Contributing tests

This file is covered by 6 tests. .

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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.commands;
22   
23    import static org.testng.AssertJUnit.assertEquals;
24   
25    import jalview.datamodel.Alignment;
26    import jalview.datamodel.AlignmentI;
27    import jalview.datamodel.Sequence;
28    import jalview.datamodel.SequenceI;
29    import jalview.gui.JvOptionPane;
30   
31    import org.testng.annotations.BeforeClass;
32    import org.testng.annotations.BeforeMethod;
33    import org.testng.annotations.Test;
34   
35    /**
36    * Unit tests for TrimRegionCommand
37    *
38    * @author gmcarstairs
39    *
40    */
 
41    public class TrimRegionCommandTest
42    {
43   
 
44  1 toggle @BeforeClass(alwaysRun = true)
45    public void setUpJvOptionPane()
46    {
47  1 JvOptionPane.setInteractiveMode(false);
48  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
49    }
50   
51    private AlignmentI al;
52   
 
53  6 toggle @BeforeMethod(alwaysRun = true)
54    public void setUp()
55    {
56  6 SequenceI[] seqs = new SequenceI[2];
57  6 seqs[0] = new Sequence("seq0", "abcde-");
58  6 seqs[1] = new Sequence("seq1", "-ghjkl");
59  6 al = new Alignment(seqs);
60  6 al.setDataset(null);
61    }
62   
63    /**
64    * Test performing, undoing and redoing a 'trim left'
65    */
 
66  1 toggle @Test(groups = { "Functional" })
67    public void testTrimLeft_withUndoAndRedo()
68    {
69  1 TrimRegionCommand cmd = new TrimRegionCommand("Remove Left", true,
70    al.getSequencesArray(), 2, al);
71  1 assertEquals(2, cmd.getSize());
72  1 assertEquals("cde-", al.getSequenceAt(0).getSequenceAsString());
73  1 assertEquals("hjkl", al.getSequenceAt(1).getSequenceAsString());
74   
75    /*
76    * undo and verify
77    */
78  1 cmd.undoCommand(new AlignmentI[] { al });
79  1 assertEquals("abcde-", al.getSequenceAt(0).getSequenceAsString());
80  1 assertEquals("-ghjkl", al.getSequenceAt(1).getSequenceAsString());
81   
82    /*
83    * redo and verify
84    */
85  1 cmd.doCommand(new AlignmentI[] { al });
86  1 assertEquals("cde-", al.getSequenceAt(0).getSequenceAsString());
87  1 assertEquals("hjkl", al.getSequenceAt(1).getSequenceAsString());
88    }
89   
90    /**
91    * Trim left of no columns - should do nothing. This is the case where the
92    * first column is selected and 'Remove Left' is selected.
93    */
 
94  1 toggle @Test(groups = { "Functional" })
95    public void testTrimLeft_noColumns()
96    {
97  1 TrimRegionCommand cmd = new TrimRegionCommand("Remove Left", true,
98    al.getSequencesArray(), 0, al);
99  1 assertEquals(0, cmd.getSize());
100  1 assertEquals("abcde-", al.getSequenceAt(0).getSequenceAsString());
101  1 assertEquals("-ghjkl", al.getSequenceAt(1).getSequenceAsString());
102    }
103   
104    /**
105    * Trim left of a single column
106    */
 
107  1 toggle @Test(groups = { "Functional" })
108    public void testTrimLeft_oneColumn()
109    {
110  1 TrimRegionCommand cmd = new TrimRegionCommand("Remove Left", true,
111    al.getSequencesArray(), 1, al);
112  1 assertEquals(1, cmd.getSize());
113  1 assertEquals("bcde-", al.getSequenceAt(0).getSequenceAsString());
114  1 assertEquals("ghjkl", al.getSequenceAt(1).getSequenceAsString());
115    }
116   
117    /**
118    * Trim right of no columns - should do nothing. This is the case where the
119    * last column is selected and 'Remove Right' is selected.
120    */
 
121  1 toggle @Test(groups = { "Functional" })
122    public void testTrimRight_noColumns()
123    {
124  1 TrimRegionCommand cmd = new TrimRegionCommand("Remove Right", false,
125    al.getSequencesArray(), 5, al);
126  1 assertEquals(0, cmd.getSize());
127  1 assertEquals("abcde-", al.getSequenceAt(0).getSequenceAsString());
128  1 assertEquals("-ghjkl", al.getSequenceAt(1).getSequenceAsString());
129    }
130   
131    /**
132    * Trim right of a single column
133    */
 
134  1 toggle @Test(groups = { "Functional" })
135    public void testTrimRight_oneColumn()
136    {
137  1 TrimRegionCommand cmd = new TrimRegionCommand("Remove Right", false,
138    al.getSequencesArray(), 4, al);
139  1 assertEquals(1, cmd.getSize());
140  1 assertEquals("abcde", al.getSequenceAt(0).getSequenceAsString());
141  1 assertEquals("-ghjk", al.getSequenceAt(1).getSequenceAsString());
142    }
143   
144    /**
145    * Test performing, undoing and redoing a 'trim right'
146    */
 
147  1 toggle @Test(groups = { "Functional" })
148    public void testTrimRight_withUndoAndRedo()
149    {
150  1 TrimRegionCommand cmd = new TrimRegionCommand("Remove Right", false,
151    al.getSequencesArray(), 2, al);
152  1 assertEquals(3, cmd.getSize());
153  1 assertEquals("abc", al.getSequenceAt(0).getSequenceAsString());
154  1 assertEquals("-gh", al.getSequenceAt(1).getSequenceAsString());
155   
156    /*
157    * undo and verify
158    */
159  1 cmd.undoCommand(new AlignmentI[] { al });
160  1 assertEquals("abcde-", al.getSequenceAt(0).getSequenceAsString());
161  1 assertEquals("-ghjkl", al.getSequenceAt(1).getSequenceAsString());
162   
163    /*
164    * redo and verify
165    */
166  1 cmd.doCommand(new AlignmentI[] { al });
167  1 assertEquals("abc", al.getSequenceAt(0).getSequenceAsString());
168  1 assertEquals("-gh", al.getSequenceAt(1).getSequenceAsString());
169    }
170    }