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.junit.Assert.assertEquals;
24 import static org.junit.Assert.assertNull;
25 import static org.junit.Assert.assertTrue;
26 import jalview.datamodel.Mapping;
27 import jalview.datamodel.Sequence;
28 import jalview.datamodel.SequenceI;
30 import org.junit.Before;
31 import org.junit.Test;
34 * Test the alignment -> Mapping routines
39 public class TestAlignSeq
45 * @throws java.lang.Exception
48 public void setUp() throws Exception
50 s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS");
52 s2 = new Sequence("Seq2", "ASDFA");
54 s3 = new Sequence("Seq1", "SDFAQQQSSS");
60 * simple test that mapping from alignment corresponds identical positions.
62 public void TestGetMappingForS1()
64 jalview.analysis.AlignSeq as = jalview.analysis.AlignSeq
65 .doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
66 System.out.println("s1: " + as.getAStr1());
67 System.out.println("s2: " + as.getAStr2());
69 Mapping s1tos2 = as.getMappingFromS1(false);
70 System.out.println(s1tos2.getMap().toString());
71 for (int i = s2.getStart(); i < s2.getEnd(); i++)
73 System.out.println("Position in s2: " + i
74 + " maps to position in s1: " + s1tos2.getPosition(i));
75 assertTrue("", s2.getCharAt(i) == s1.getCharAt(s1tos2.getPosition(i)));
80 public void testExtractGaps()
82 assertNull(AlignSeq.extractGaps(null, null));
83 assertNull(AlignSeq.extractGaps(". -", null));
84 assertNull(AlignSeq.extractGaps(null, "AB-C"));
86 assertEquals("ABCD", AlignSeq.extractGaps(" .-", ". -A-B.C D."));