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.assertTrue;
25 import org.junit.Test;
27 import jalview.datamodel.Alignment;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.Sequence;
30 import jalview.datamodel.SequenceI;
31 import jalview.io.AppletFormatAdapter;
33 public class AlignmentUtilsTests
35 public static Sequence ts=new Sequence("short","ASDASDASDASDASDASDASDASDASDASDASDASDASD");
37 public void testExpandFlanks()
39 AlignmentI al = new Alignment(new Sequence[] {});
40 for (int i=4;i<14;i+=3)
42 SequenceI s1=ts.deriveSequence().getSubSequence(i, i+7);
45 System.out.println(new AppletFormatAdapter().formatSequences("Clustal", al, true));
46 for (int flnk=-1;flnk<25; flnk++)
49 System.out.println("\nFlank size: "+flnk);
50 System.out.println(new AppletFormatAdapter().formatSequences("Clustal", exp=AlignmentUtils.expandContext(al, flnk), true));
52 for (SequenceI sq:exp.getSequences())
54 String ung = sq.getSequenceAsString().replaceAll("-+", "");
55 assertTrue("Flanking sequence not the same as original dataset sequence.\n"+ung+"\n"+sq.getDatasetSequence().getSequenceAsString(),ung.equalsIgnoreCase(sq.getDatasetSequence().getSequenceAsString()));