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.*;
24 import jalview.datamodel.Mapping;
25 import jalview.datamodel.Sequence;
26 import jalview.datamodel.SequenceI;
28 import org.junit.Before;
29 import org.junit.Test;
32 * Test the alignment -> Mapping routines
37 public class TestAlignSeq
43 * @throws java.lang.Exception
46 public void setUp() throws Exception
48 s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS");
50 s2 = new Sequence("Seq2", "ASDFA");
52 s3 = new Sequence("Seq1", "SDFAQQQSSS");
58 * simple test that mapping from alignment corresponds identical positions.
60 public void TestGetMappingForS1()
62 jalview.analysis.AlignSeq as = jalview.analysis.AlignSeq
63 .doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
64 System.out.println("s1: " + as.getAStr1());
65 System.out.println("s2: " + as.getAStr2());
67 Mapping s1tos2 = as.getMappingFromS1(false);
68 System.out.println(s1tos2.getMap().toString());
69 for (int i = s2.getStart(); i < s2.getEnd(); i++)
71 System.out.println("Position in s2: " + i
72 + " maps to position in s1: " + s1tos2.getPosition(i));
73 assertTrue("", s2.getCharAt(i) == s1.getCharAt(s1tos2.getPosition(i)));