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 jalview.datamodel.SequenceI;
24 import jalview.gui.JvOptionPane;
26 import static org.testng.Assert.assertEquals;
27 import static org.testng.Assert.assertNotNull;
30 import java.io.IOException;
32 import org.testng.annotations.AfterClass;
33 import org.testng.annotations.BeforeClass;
34 import org.testng.annotations.Test;
36 import fr.orsay.lri.varna.utils.RNAMLParser;
37 import groovy.lang.Sequence;
39 public class RNAMLfileTest
42 @BeforeClass(alwaysRun = true)
43 public void setUpJvOptionPane()
45 JvOptionPane.setInteractiveMode(false);
46 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
49 @BeforeClass(alwaysRun = true)
50 public static void setUpBeforeClass() throws Exception
54 @AfterClass(alwaysRun = true)
55 public static void tearDownAfterClass() throws Exception
59 @Test(groups = { "Functional" })
60 public void testRnamlToStockholmIO()
62 StockholmFileTest.testFileIOwithFormat(
63 new File("examples/testdata/rna-alignment.xml"),
64 FileFormat.Stockholm, -1, -1, true, true, true);
68 @Test(groups = { "Functional" })
69 public void testRnamlSeqImport() throws IOException
71 RnamlFile parser = new RnamlFile("examples/testdata/7WKP-rna1.xml",
73 SequenceI[] seqs = parser.getSeqsAsArray();
75 assertEquals(seqs.length, 1);
76 assertEquals(seqs[0].getEnd() - seqs[0].getStart() + 1,
77 seqs[0].getSequence().length);