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.assertEquals;
24 import static org.junit.Assert.assertTrue;
25 import jalview.datamodel.Alignment;
26 import jalview.datamodel.AlignmentI;
27 import jalview.datamodel.SequenceI;
28 import jalview.gui.AlignFrame;
29 import jalview.io.AppletFormatAdapter;
30 import jalview.io.FileLoader;
32 import java.util.Vector;
34 import org.junit.Test;
36 import MCview.PDBfile;
42 public class PDBFileWithJmolTest
44 String[] testFile = new String[]
45 { "./examples/1GAQ.txt", "./test/jalview/ext/jmol/1QCF.pdb" }; // ,
47 // "./examples/DNMT1_MOUSE.pdb"
51 public void testAlignmentLoader() throws Exception
53 for (String f : testFile)
55 FileLoader fl = new jalview.io.FileLoader(false);
57 .LoadFileWaitTillLoaded(f, AppletFormatAdapter.FILE);
58 validateSecStrRows(af.getViewport().getAlignment());
63 public void testFileParser() throws Exception
65 for (String pdbStr : testFile)
67 PDBfile mctest = new PDBfile(false, false, false, pdbStr,
68 AppletFormatAdapter.FILE);
69 PDBFileWithJmol jtest = new PDBFileWithJmol(pdbStr,
70 jalview.io.AppletFormatAdapter.FILE);
71 Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
74 "No sequences extracted from testfile\n"
75 + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
76 : "(No warnings raised)"), seqs != null
78 for (SequenceI sq : seqs)
80 assertEquals("JMol didn't process " + pdbStr
81 + " to the same sequence as MCView",
82 sq.getSequenceAsString(), mcseqs.remove(0)
83 .getSequenceAsString());
84 AlignmentI al = new Alignment(new SequenceI[]
86 validateSecStrRows(al);
92 private void validateSecStrRows(AlignmentI al)
94 if (!al.isNucleotide())
96 for (SequenceI asq : al.getSequences())
99 boolean hasDs = false;
100 while (sq.getDatasetSequence() != null
101 && sq.getAnnotation() == null)
103 sq = sq.getDatasetSequence();
106 checkFirstAAIsAssoc(sq);
109 // also verify if alignment sequence has annotation on it
110 // that is correctly mapped
111 checkFirstAAIsAssoc(asq);
117 private void checkFirstAAIsAssoc(SequenceI sq)
119 assertTrue("No secondary structure assigned for protein sequence.",
120 sq.getAnnotation() != null && sq.getAnnotation().length >= 1
121 && sq.getAnnotation()[0].hasIcons);
123 "Secondary structure not associated for sequence "
124 + sq.getName(), sq.getAnnotation()[0].sequenceRef == sq);