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.AlignmentI;
24 import jalview.gui.JvOptionPane;
26 import java.io.IOException;
28 import org.testng.Assert;
29 import org.testng.annotations.BeforeClass;
30 import org.testng.annotations.Test;
32 public class PfamFormatInputTest
35 @BeforeClass(alwaysRun = true)
36 public void setUpJvOptionPane()
38 JvOptionPane.setInteractiveMode(false);
39 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
42 @Test(groups = "Functional")
43 public void testPfamFormatNoLimits() throws IOException
45 AlignmentI al = new AppletFormatAdapter().readFile("ASEQ"
46 + '\t' + "...--FFAFAFF--", AppletFormatAdapter.PASTE, "PFAM");
47 Assert.assertEquals(1, al.getHeight(), "Wrong number of sequences");
48 Assert.assertTrue(al.hasValidSequence(),
49 "Didn't extract limits from PFAM ID");
52 @Test(groups = "Functional")
53 public void testPfamFormatValidLimits() throws IOException
55 AlignmentI al = new AppletFormatAdapter().readFile(
56 "ASEQ/15-25" + '\t' + "...--FFAFAFF--",
57 AppletFormatAdapter.PASTE, "PFAM");
58 Assert.assertEquals(1, al.getHeight(), "Wrong number of sequences");
59 Assert.assertTrue(al.hasValidSequence(),
60 "Didn't extract limits from PFAM ID");