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;
29 import jalview.gui.JvOptionPane;
31 import java.io.IOException;
32 import java.util.ArrayList;
33 import java.util.List;
35 import org.testng.annotations.BeforeClass;
36 import org.testng.annotations.DataProvider;
37 import org.testng.annotations.Test;
39 public class FormatAdapterTest
42 @BeforeClass(alwaysRun = true)
43 public void setUpJvOptionPane()
45 JvOptionPane.setInteractiveMode(false);
46 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
50 * Test saving and re-reading in a specified format
54 @Test(groups = { "Functional" }, dataProvider = "formats")
55 public void testRoundTrip(FileFormatI format) throws IOException
60 if (format == FileFormat.HMMER3)
62 al = new FormatAdapter().readFile("examples/uniref50.hmm",
63 DataSourceType.FILE, FileFormat.HMMER3);
67 al = new FormatAdapter().readFile("examples/uniref50.fa",
68 DataSourceType.FILE, FileFormat.Fasta);
72 * 'gap' is the gap character used in the alignment data file here,
73 * not the user preferred gap character
75 char gap = al.getGapCharacter();
78 SequenceI[] seqs = al.getSequencesArray();
79 String formatted = new FormatAdapter().formatSequences(format, al,
82 AlignmentI reloaded = new FormatAdapter().readFile(formatted,
83 DataSourceType.PASTE, format);
84 List<SequenceI> reread = reloaded.getSequences();
85 assertEquals("Wrong number of reloaded sequences", seqs.length,
90 for (SequenceI seq : reread)
92 String sequenceString = seq.getSequenceAsString();
95 * special case: MSF always uses '.' as gap character
97 sequenceString = adjustForGapTreatment(sequenceString, gap, format);
99 String.format("Sequence %d: %s", i, seqs[i].getName()),
100 seqs[i].getSequenceAsString(), sequenceString);
103 } catch (IOException e)
106 .format("Format %s failed with %s", format, e.getMessage()));
111 * Optionally change the gap character in the string to the given character,
112 * depending on the sequence file format
114 * @param sequenceString
115 * a sequence (as written in 'format' format)
117 * the sequence's original gap character
121 String adjustForGapTreatment(String sequenceString, char gap,
124 if (FileFormat.MSF.equals(format))
127 * MSF forces gap character to '.', so change it back
128 * for comparison purposes
130 sequenceString = sequenceString.replace('.', gap);
132 return sequenceString;
136 * Data provider that serves alignment formats that are both readable and
141 @DataProvider(name = "formats")
142 static Object[][] getFormats()
144 List<FileFormatI> both = new ArrayList<>();
145 for (FileFormatI format : FileFormats.getInstance().getFormats())
147 if (format.isReadable() && format.isWritable()
148 && format.isTextFormat())
154 Object[][] formats = new Object[both.size()][];
156 for (FileFormatI format : both)
158 formats[i] = new Object[] { format };
165 * Enable this to isolate testing to a single file format
167 * @throws IOException
169 @Test(groups = { "Functional" }, enabled = false)
170 public void testOneFormatRoundTrip() throws IOException
172 testRoundTrip(FileFormat.Json);