2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.analysis;
20 import static org.junit.Assert.*;
21 import jalview.datamodel.Mapping;
22 import jalview.datamodel.Sequence;
23 import jalview.datamodel.SequenceI;
25 import org.junit.Before;
26 import org.junit.Test;
29 * Test the alignment -> Mapping routines
33 public class TestAlignSeq
38 * @throws java.lang.Exception
41 public void setUp() throws Exception
43 s1 = new Sequence("Seq1","ASDFAQQQRRRSSS");
45 s2 = new Sequence("Seq2","ASDFA");
47 s3 = new Sequence("Seq1","SDFAQQQSSS");
53 * simple test that mapping from alignment corresponds identical positions.
55 public void TestGetMappingForS1()
57 jalview.analysis.AlignSeq as = jalview.analysis.AlignSeq.doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
58 System.out.println("s1: "+as.getAStr1());
59 System.out.println("s2: "+as.getAStr2());
61 Mapping s1tos2=as.getMappingFromS1(false);
62 System.out.println(s1tos2.getMap().toString());
63 for (int i=s2.getStart();i<s2.getEnd();i++)
65 System.out.println("Position in s2: "+i +" maps to position in s1: "+s1tos2.getPosition(i));
66 assertTrue("",s2.getCharAt(i)==s1.getCharAt(s1tos2.getPosition(i)));