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;
25 import java.io.IOException;
27 import org.testng.Assert;
28 import org.testng.annotations.Test;
30 public class PfamFormatInputTest
33 public void testPfamFormatNoLimits() throws IOException
35 AlignmentI al = new jalview.io.AppletFormatAdapter().readFile("ASEQ"
36 + '\t' + "...--FFAFAFF--", AppletFormatAdapter.PASTE, "PFAM");
37 Assert.assertEquals(1, al.getHeight(), "Wrong number of sequences");
38 Assert.assertTrue(al.hasValidSequence(),
39 "Didn't extract limits from PFAM ID");
43 public void testPfamFormatValidLimits() throws IOException
45 AlignmentI al = new jalview.io.AppletFormatAdapter().readFile(
46 "ASEQ/15-25" + '\t' + "...--FFAFAFF--",
47 AppletFormatAdapter.PASTE, "PFAM");
48 Assert.assertEquals(1, al.getHeight(), "Wrong number of sequences");
49 Assert.assertTrue(al.hasValidSequence(),
50 "Didn't extract limits from PFAM ID");