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" }; // ,
45 // "./examples/DNMT1_MOUSE.pdb"
49 public void testAlignmentLoader() throws Exception
51 for (String f : testFile)
53 FileLoader fl = new jalview.io.FileLoader(false);
55 .LoadFileWaitTillLoaded(f, AppletFormatAdapter.FILE);
56 validateSecStrRows(af.getViewport().getAlignment());
61 public void testFileParser() throws Exception
63 for (String pdbStr : testFile)
65 PDBFileWithJmol jtest = new PDBFileWithJmol(pdbStr,
66 jalview.io.AppletFormatAdapter.FILE);
67 Vector<SequenceI> seqs = jtest.getSeqs();
70 "No sequences extracted from testfile\n"
71 + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
72 : "(No warnings raised)"), seqs != null
74 for (SequenceI sq : seqs)
76 AlignmentI al = new Alignment(new SequenceI[]
78 validateSecStrRows(al);
83 private void validateSecStrRows(AlignmentI al)
85 if (!al.isNucleotide())
87 for (SequenceI asq : al.getSequences())
90 boolean hasDs = false;
91 while (sq.getDatasetSequence() != null
92 && sq.getAnnotation() == null)
94 sq = sq.getDatasetSequence();
97 checkFirstAAIsAssoc(sq);
100 // also verify if alignment sequence has annotation on it
101 // that is correctly mapped
102 checkFirstAAIsAssoc(asq);
108 private void checkFirstAAIsAssoc(SequenceI sq)
110 assertTrue("No secondary structure assigned for protein sequence.",
111 sq.getAnnotation() != null && sq.getAnnotation().length >= 1
112 && sq.getAnnotation()[0].hasIcons);
114 "Secondary structure not associated for sequence "
115 + sq.getName(), sq.getAnnotation()[0].sequenceRef == sq);