2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertNotNull;
25 import static org.testng.AssertJUnit.fail;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.SequenceI;
30 import java.io.IOException;
31 import java.util.ArrayList;
32 import java.util.Arrays;
33 import java.util.List;
35 import org.testng.annotations.DataProvider;
36 import org.testng.annotations.Test;
38 public class FormatAdapterTest
42 * Test saving and re-reading in a specified format
46 @Test(groups = { "Functional" }, dataProvider = "formats")
47 public void testRoundTrip(String format) throws IOException
51 AlignmentI al = new FormatAdapter().readFile("examples/uniref50.fa",
52 FormatAdapter.FILE, "FASTA");
55 * 'gap' is the gap character used in the alignment data file here,
56 * not the user preferred gap character
58 char gap = al.getGapCharacter();
61 SequenceI[] seqs = al.getSequencesArray();
62 String formatted = new FormatAdapter().formatSequences(format, al,
65 AlignmentI reloaded = new FormatAdapter().readFile(formatted,
66 FormatAdapter.PASTE, format);
67 List<SequenceI> reread = reloaded.getSequences();
68 assertEquals("Wrong number of reloaded sequences", seqs.length,
72 for (SequenceI seq : reread)
74 String sequenceString = seq.getSequenceAsString();
77 * special case: MSF always uses '.' as gap character
79 sequenceString = adjustForGapTreatment(sequenceString, gap, format);
81 String.format("Sequence %d: %s", i, seqs[i].getName()),
82 seqs[i].getSequenceAsString(), sequenceString);
85 } catch (IOException e)
88 .format("Format %s failed with %s", format, e.getMessage()));
93 * Optionally change the gap character in the string to the given character,
94 * depending on the sequence file format
96 * @param sequenceString
97 * a sequence (as written in 'format' format)
99 * the sequence's original gap character
103 String adjustForGapTreatment(String sequenceString, char gap,
106 if ("MSF".equals(format))
109 * MSF forces gap character to '.', so change it back
110 * for comparison purposes
112 sequenceString = sequenceString.replace('.', gap);
114 return sequenceString;
118 * Data provider that serves alignment formats that are both readable and
123 @DataProvider(name = "formats")
124 static Object[][] getFormats()
126 List<String> both = new ArrayList<String>();
127 String[] readable = FormatAdapter.READABLE_FORMATS;
128 List<String> writeable = Arrays.asList(FormatAdapter.WRITEABLE_FORMATS);
129 for (String r : readable)
131 if (writeable.contains(r))
137 Object[][] formats = new Object[both.size()][];
139 for (String format : both)
141 formats[i] = new Object[] { format };
148 * Enable this to isolate testing to a single file format
150 * @throws IOException
152 @Test(groups = { "Functional" }, enabled = false)
153 public void testOneFormatRoundTrip() throws IOException
155 testRoundTrip("JSON");