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.analysis;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.fail;
26 import jalview.analysis.SecStrConsensus.SimpleBP;
28 import java.util.Vector;
30 import org.testng.annotations.Test;
34 @Test(groups = { "Functional" })
35 public void testGetSimpleBPs() throws WUSSParseException
37 String rna = "([{})]"; // JAL-1081 example
38 Vector<SimpleBP> bps = Rna.GetSimpleBPs(rna);
39 assertEquals(3, bps.size());
42 * the base pairs are added in the order in which the matching base is found
44 assertEquals(2, bps.get(0).bp5); // {
45 assertEquals(3, bps.get(0).bp3); // }
46 assertEquals(0, bps.get(1).bp5); // (
47 assertEquals(4, bps.get(1).bp3); // )
48 assertEquals(1, bps.get(2).bp5); // [
49 assertEquals(5, bps.get(2).bp3); // ]
52 @Test(groups = { "Functional" })
53 public void testGetSimpleBPs_unmatchedOpener()
55 String rna = "(([{})]";
58 Rna.GetSimpleBPs(rna);
59 fail("expected exception");
60 } catch (WUSSParseException e)
66 @Test(groups = { "Functional" })
67 public void testGetSimpleBPs_unmatchedCloser()
69 String rna = "([{})]]";
72 Rna.GetSimpleBPs(rna);
73 fail("expected exception");
74 } catch (WUSSParseException e)