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Coverage Report

  1. Project Clover database Wed Dec 3 2025 17:03:17 GMT
  2. Package jalview.io

File FormatAdapterTest.java

 

Code metrics

6
35
5
1
173
98
11
0.31
7
5
2.2

Classes

Class Line # Actions
FormatAdapterTest 39 35 11
0.934782693.5%
 

Contributing tests

This file is covered by 12 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.io;
22   
23    import static org.testng.AssertJUnit.assertEquals;
24    import static org.testng.AssertJUnit.assertNotNull;
25    import static org.testng.AssertJUnit.fail;
26   
27    import jalview.datamodel.AlignmentI;
28    import jalview.datamodel.SequenceI;
29    import jalview.gui.JvOptionPane;
30   
31    import java.io.IOException;
32    import java.util.ArrayList;
33    import java.util.List;
34   
35    import org.testng.annotations.BeforeClass;
36    import org.testng.annotations.DataProvider;
37    import org.testng.annotations.Test;
38   
 
39    public class FormatAdapterTest
40    {
41   
 
42  1 toggle @BeforeClass(alwaysRun = true)
43    public void setUpJvOptionPane()
44    {
45  1 JvOptionPane.setInteractiveMode(false);
46  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
47    }
48   
49    /**
50    * Test saving and re-reading in a specified format
51    *
52    * @throws IOException
53    */
 
54  12 toggle @Test(groups = { "Functional" }, dataProvider = "formats")
55    public void testRoundTrip(FileFormatI format) throws IOException
56    {
57  12 try
58    {
59  12 AlignmentI al;
60  12 if (format == FileFormat.HMMER3)
61    {
62  1 al = new FormatAdapter().readFile("examples/uniref50.hmm",
63    DataSourceType.FILE, FileFormat.HMMER3);
64    }
65    else
66    {
67  11 al = new FormatAdapter().readFile("examples/uniref50.fa",
68    DataSourceType.FILE, FileFormat.Fasta);
69    }
70   
71    /*
72    * 'gap' is the gap character used in the alignment data file here,
73    * not the user preferred gap character
74    */
75  12 char gap = al.getGapCharacter();
76  12 assertNotNull(al);
77   
78  12 SequenceI[] seqs = al.getSequencesArray();
79  12 String formatted = new FormatAdapter().formatSequences(format, al,
80    false);
81   
82  12 AlignmentI reloaded = new FormatAdapter().readFile(formatted,
83    DataSourceType.PASTE, format);
84  12 List<SequenceI> reread = reloaded.getSequences();
85  12 assertEquals("Wrong number of reloaded sequences", seqs.length,
86    reread.size());
87   
88   
89  12 int i = 0;
90  12 for (SequenceI seq : reread)
91    {
92  166 String sequenceString = seq.getSequenceAsString();
93   
94    /*
95    * special case: MSF always uses '.' as gap character
96    */
97  166 sequenceString = adjustForGapTreatment(sequenceString, gap, format);
98  166 assertEquals(String.format("Sequence %d: %s", i, seqs[i].getName()),
99    seqs[i].getSequenceAsString(), sequenceString);
100  166 i++;
101    }
102    } catch (IOException e)
103    {
104  0 fail(String.format("Format %s failed with %s", format,
105    e.getMessage()));
106    }
107    }
108   
109    /**
110    * Optionally change the gap character in the string to the given character,
111    * depending on the sequence file format
112    *
113    * @param sequenceString
114    * a sequence (as written in 'format' format)
115    * @param gap
116    * the sequence's original gap character
117    * @param format
118    * @return
119    */
 
120  166 toggle String adjustForGapTreatment(String sequenceString, char gap,
121    FileFormatI format)
122    {
123  166 if (FileFormat.MSF.equals(format))
124    {
125    /*
126    * MSF forces gap character to '.', so change it back
127    * for comparison purposes
128    */
129  15 sequenceString = sequenceString.replace('.', gap);
130    }
131  166 return sequenceString;
132    }
133   
134    /**
135    * Data provider that serves alignment formats that are both readable and
136    * (text) writable
137    *
138    * @return
139    */
 
140  1 toggle @DataProvider(name = "formats")
141    static Object[][] getFormats()
142    {
143  1 List<FileFormatI> both = new ArrayList<>();
144  1 for (FileFormatI format : FileFormats.getInstance().getFormats())
145    {
146  26 if (format.isReadable() && format.isWritable()
147    && format.isTextFormat())
148    {
149  12 both.add(format);
150    }
151    }
152   
153  1 Object[][] formats = new Object[both.size()][];
154  1 int i = 0;
155  1 for (FileFormatI format : both)
156    {
157  12 formats[i] = new Object[] { format };
158  12 i++;
159    }
160  1 return formats;
161    }
162   
163    /**
164    * Enable this to isolate testing to a single file format
165    *
166    * @throws IOException
167    */
 
168  0 toggle @Test(groups = { "Functional" }, enabled = false)
169    public void testOneFormatRoundTrip() throws IOException
170    {
171  0 testRoundTrip(FileFormat.Json);
172    }
173    }
  • Report generated by OpenClover v 4.4.1 on Wed Dec 3 2025 17:13:21 GMT using coverage data from Wed Dec 3 2025 17:13:06 GMT.
  • OpenClover is free and open-source software.