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.ext.jmol;
23 import static org.junit.Assert.*;
25 import java.util.Vector;
27 import jalview.datamodel.Alignment;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.SequenceI;
31 import org.junit.Test;
37 public class PDBFileWithJmolTest
41 public void test() throws Exception
43 PDBFileWithJmol jtest = new PDBFileWithJmol("./examples/1GAQ.txt",
44 jalview.io.AppletFormatAdapter.FILE);
45 Vector<SequenceI> seqs = jtest.getSeqs();
48 "No sequences extracted from testfile\n"
49 + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
50 : "(No warnings raised)"),
51 seqs != null && seqs.size() > 0);
52 for (SequenceI sq : seqs)
54 AlignmentI al = new Alignment(new SequenceI[]
56 if (!al.isNucleotide())
59 "No secondary structure assigned for protein sequence.",
60 sq.getAnnotation() != null
61 && sq.getAnnotation().length >= 1
62 && sq.getAnnotation()[0].hasIcons);