2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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
36 public class TestAlignSeq
41 * @throws java.lang.Exception
44 public void setUp() throws Exception
46 s1 = new Sequence("Seq1","ASDFAQQQRRRSSS");
48 s2 = new Sequence("Seq2","ASDFA");
50 s3 = new Sequence("Seq1","SDFAQQQSSS");
56 * simple test that mapping from alignment corresponds identical positions.
58 public void TestGetMappingForS1()
60 jalview.analysis.AlignSeq as = jalview.analysis.AlignSeq.doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
61 System.out.println("s1: "+as.getAStr1());
62 System.out.println("s2: "+as.getAStr2());
64 Mapping s1tos2=as.getMappingFromS1(false);
65 System.out.println(s1tos2.getMap().toString());
66 for (int i=s2.getStart();i<s2.getEnd();i++)
68 System.out.println("Position in s2: "+i +" maps to position in s1: "+s1tos2.getPosition(i));
69 assertTrue("",s2.getCharAt(i)==s1.getCharAt(s1tos2.getPosition(i)));