2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertTrue;
26 import jalview.bin.Cache;
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 java.util.Vector;
36 import org.testng.annotations.BeforeMethod;
37 import org.testng.annotations.Test;
39 import MCview.PDBfile;
45 public class PDBFileWithJmolTest
48 * 1GAQ has been reduced to alpha carbons only
49 * 1QCF is the full PDB file including headers, HETATM etc
51 String[] testFile = new String[] { "./examples/1GAQ.txt",
52 "./test/jalview/ext/jmol/1QCF.pdb" }; // ,
55 // a modified and very cut-down extract of 4UJ4
56 String pdbWithChainBreak =
57 "HEADER TRANSPORT PROTEIN 08-APR-15 4UJ4\n" +
58 // chain B has missing residues; these should all go in the same sequence:
59 "ATOM 1909 CA VAL B 358 21.329 -19.739 -67.740 1.00201.05 C\n" +
60 "ATOM 1916 CA GLY B 359 21.694 -23.563 -67.661 1.00198.09 C\n" +
61 "ATOM 1920 CA LYS B 367 32.471 -12.135 -77.100 1.00257.97 C\n" +
62 "ATOM 1925 CA ALA B 368 31.032 -9.324 -74.946 1.00276.01 C\n" +
63 // switch to chain C; should be a separate sequence
64 "ATOM 1930 CA SER C 369 32.589 -7.517 -71.978 1.00265.44 C\n" +
65 "ATOM 1936 CA ALA C 370 31.650 -6.849 -68.346 1.00249.48 C\n";
69 // a very cut-down extract of 1ejg
70 String pdbWithAltLoc =
71 "HEADER TRANSPORT PROTEIN 08-APR-15 1EJG\n" +
72 "ATOM 448 CA ALA A 24 6.619 16.195 1.970 1.00 1.65 C\n" +
73 "ATOM 458 CA ALEU A 25 3.048 14.822 1.781 0.57 1.48 C\n" +
74 // alternative residue 25 entries (with ILE instead of LEU) should be ignored:
75 "ATOM 478 CA BILE A 25 3.048 14.822 1.781 0.21 1.48 C\n" +
76 // including the next altloc causes the unit test to fail but it works with the full file
78 // "ATOM 479 CA CILE A 25 3.048 14.822 1.781 0.22 1.48 C\n" +
79 "ATOM 512 CA CYS A 26 4.137 11.461 3.154 1.00 1.52 C\n";
82 @BeforeMethod(alwaysRun = true)
85 Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
86 Boolean.TRUE.toString());
87 Cache.applicationProperties.setProperty("ADD_SS_ANN",
88 Boolean.TRUE.toString());
91 @Test(groups = { "Functional" })
92 public void testAlignmentLoader() throws Exception
94 for (String f : testFile)
96 FileLoader fl = new jalview.io.FileLoader(false);
98 .LoadFileWaitTillLoaded(f, AppletFormatAdapter.FILE);
99 validateSecStrRows(af.getViewport().getAlignment());
103 @Test(groups = { "Functional" })
104 public void testFileParser() throws Exception
106 for (String pdbStr : testFile)
108 PDBfile mctest = new PDBfile(false, false, false, pdbStr,
109 AppletFormatAdapter.FILE);
110 PDBFileWithJmol jtest = new PDBFileWithJmol(pdbStr,
111 jalview.io.AppletFormatAdapter.FILE);
112 Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
115 "No sequences extracted from testfile\n"
116 + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
117 : "(No warnings raised)"), seqs != null
119 for (SequenceI sq : seqs)
121 assertEquals("JMol didn't process " + pdbStr
122 + " to the same sequence as MCView",
123 sq.getSequenceAsString(), mcseqs.remove(0)
124 .getSequenceAsString());
125 AlignmentI al = new Alignment(new SequenceI[] { sq });
126 validateSecStrRows(al);
131 private void validateSecStrRows(AlignmentI al)
133 if (!al.isNucleotide())
135 for (SequenceI asq : al.getSequences())
138 boolean hasDs = false;
139 while (sq.getDatasetSequence() != null
140 && sq.getAnnotation() == null)
142 sq = sq.getDatasetSequence();
145 checkFirstAAIsAssoc(sq);
148 // also verify if alignment sequence has annotation on it
149 // that is correctly mapped
150 checkFirstAAIsAssoc(asq);
156 private void checkFirstAAIsAssoc(SequenceI sq)
158 assertTrue("No secondary structure assigned for protein sequence.",
159 sq.getAnnotation() != null && sq.getAnnotation().length >= 1
160 && sq.getAnnotation()[0].hasIcons);
162 "Secondary structure not associated for sequence "
163 + sq.getName(), sq.getAnnotation()[0].sequenceRef == sq);
167 * Test parsing a chain with missing residues
171 @Test(groups = { "Functional" })
172 public void testParse_missingResidues() throws Exception
174 PDBfile mctest = new PDBfile(false, false, false, pdbWithChainBreak,
175 AppletFormatAdapter.PASTE);
176 PDBFileWithJmol jtest = new PDBFileWithJmol(pdbWithChainBreak,
177 jalview.io.AppletFormatAdapter.PASTE);
178 Vector<SequenceI> seqs = jtest.getSeqs();
179 Vector<SequenceI> mcseqs = mctest.getSeqs();
181 assertEquals("Failed to find 2 sequences\n", 2, seqs.size());
182 assertEquals("Failed to find 2 sequences\n", 2, mcseqs.size());
183 assertEquals("VGKA", seqs.get(0).getSequenceAsString());
184 assertEquals("VGKA", mcseqs.get(0).getSequenceAsString());
185 assertEquals("SA", seqs.get(1).getSequenceAsString());
186 assertEquals("SA", mcseqs.get(1).getSequenceAsString());
190 * Test parsing a chain with 'altloc' residues
194 @Test(groups = { "Functional" })
195 public void testParse_alternativeResidues() throws Exception
197 PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc,
198 AppletFormatAdapter.PASTE);
199 PDBFileWithJmol jtest = new PDBFileWithJmol(pdbWithAltLoc,
200 jalview.io.AppletFormatAdapter.PASTE);
201 Vector<SequenceI> seqs = jtest.getSeqs();
202 Vector<SequenceI> mcseqs = mctest.getSeqs();
204 assertEquals("Failed to find 1 sequence\n", 1, seqs.size());
205 assertEquals("Failed to find 1 sequence\n", 1, mcseqs.size());
206 assertEquals("ALC", seqs.get(0).getSequenceAsString());
207 assertEquals("ALC", mcseqs.get(0).getSequenceAsString());