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.
21 package jalview.ws.dbsources;
23 import jalview.datamodel.AlignmentI;
24 import jalview.gui.JvOptionPane;
26 import org.testng.Assert;
27 import org.testng.annotations.BeforeClass;
28 import org.testng.annotations.Test;
30 public class XfamFetcherTest
33 @BeforeClass(alwaysRun = true)
34 public void setUpJvOptionPane()
36 JvOptionPane.setInteractiveMode(false);
37 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
40 @Test(groups = { "External" })
41 public void testRfamSeed() throws Exception
43 // RfamFull rff = new RfamFull();
44 RfamSeed rfs = new RfamSeed();
46 AlignmentI seedrf = rfs.getSequenceRecords(rfs.getTestQuery());
47 Assert.assertNotNull(seedrf, "Seed Alignment for " + rfs.getTestQuery()
48 + " didn't retrieve.");
49 Assert.assertTrue(seedrf.getHeight() > 1,
50 "Seed Alignment for " + rfs.getTestQuery()
51 + " didn't contain more than one sequence.");
52 Assert.assertTrue(seedrf.getProperties().size() > 0,
53 "Seed Alignment for " + rfs.getTestQuery()
54 + " didn't have any properties.");
58 @Test(groups = { "External" })
59 public void testPfamFullAndSeed() throws Exception
61 Pfam pff = new PfamFull();
62 PfamSeed pfseed = new PfamSeed();
64 AlignmentI fullpf = pff.getSequenceRecords(pff.getTestQuery());
65 Assert.assertNotNull(fullpf, "Full Alignment for " + pff.getTestQuery()
66 + " didn't retrieve.");
67 Assert.assertTrue(fullpf.getHeight() > 1,
68 "Full Alignment for " + pff.getTestQuery()
69 + " didn't have more than one sequence.");
70 AlignmentI seedpf = pfseed.getSequenceRecords(pff.getTestQuery());
71 Assert.assertNotNull(seedpf, "Seed Alignment for " + pff.getTestQuery()
72 + " didn't retrieve.");
73 Assert.assertTrue(seedpf.getProperties().size() > 0,
74 "Seed Alignment for " + pfseed.getTestQuery()
75 + " didn't have any properties.");
77 Assert.assertTrue(seedpf.getHeight() < fullpf.getHeight(),
78 "Expected Full alignment to have more sequences than seed for "
79 + pff.getTestQuery());
80 Assert.assertTrue(fullpf.getProperties().size() > 0,
81 "Full Alignment for " + pff.getTestQuery()
82 + " didn't have any properties.");