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;
30 import jalview.gui.AlignFrame;
31 import jalview.io.AppletFormatAdapter;
32 import jalview.io.FileLoader;
34 import org.junit.Test;
40 public class PDBFileWithJmolTest
42 String[] testFile = new String[]
43 { "./examples/1GAQ.txt" }; // , "./examples/DNMT1_MOUSE.pdb" };
46 public void testAlignmentLoader() throws Exception
48 for (String f:testFile) {
49 FileLoader fl = new jalview.io.FileLoader(false);
50 AlignFrame af = fl.LoadFileWaitTillLoaded(f, AppletFormatAdapter.FILE);
51 validateSecStrRows(af.getViewport().getAlignment());
55 public void testFileParser() throws Exception
57 for (String pdbStr : testFile)
59 PDBFileWithJmol jtest = new PDBFileWithJmol(pdbStr,
60 jalview.io.AppletFormatAdapter.FILE);
61 Vector<SequenceI> seqs = jtest.getSeqs();
64 "No sequences extracted from testfile\n"
65 + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
66 : "(No warnings raised)"), seqs != null
68 for (SequenceI sq : seqs)
70 AlignmentI al = new Alignment(new SequenceI[]
72 validateSecStrRows(al);
77 private void validateSecStrRows(AlignmentI al)
80 if (!al.isNucleotide())
82 for (SequenceI asq : al.getSequences())
85 while (sq.getDatasetSequence()!=null && sq.getAnnotation()==null)
87 sq = asq.getDatasetSequence();
90 "No secondary structure assigned for protein sequence.",
91 sq.getAnnotation() != null
92 && sq.getAnnotation().length >= 1
93 && sq.getAnnotation()[0].hasIcons);
95 "Secondary structure not associated for sequence "
97 sq.getAnnotation()[0].sequenceRef == sq);