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.jmol.c.STR;
37 import org.testng.annotations.BeforeMethod;
38 import org.testng.annotations.Test;
40 import MCview.PDBfile;
46 public class PDBFileWithJmolTest
49 * 1GAQ has been reduced to alpha carbons only
50 * 1QCF is the full PDB file including headers, HETATM etc
52 String[] testFile = new String[] { "./examples/1GAQ.txt",
53 "./test/jalview/ext/jmol/1QCF.pdb" }; // ,
56 // a modified and very cut-down extract of 4UJ4
57 String pdbWithChainBreak =
58 "HEADER TRANSPORT PROTEIN 08-APR-15 4UJ4\n" +
59 // chain B has missing residues; these should all go in the same sequence:
60 "ATOM 1909 CA VAL B 358 21.329 -19.739 -67.740 1.00201.05 C\n" +
61 "ATOM 1916 CA GLY B 359 21.694 -23.563 -67.661 1.00198.09 C\n" +
62 "ATOM 1920 CA LYS B 367 32.471 -12.135 -77.100 1.00257.97 C\n" +
63 "ATOM 1925 CA ALA B 368 31.032 -9.324 -74.946 1.00276.01 C\n" +
64 // switch to chain C; should be a separate sequence
65 "ATOM 1930 CA SER C 369 32.589 -7.517 -71.978 1.00265.44 C\n" +
66 "ATOM 1936 CA ALA C 370 31.650 -6.849 -68.346 1.00249.48 C\n";
70 // a very cut-down extract of 1ejg
71 String pdbWithAltLoc =
72 "HEADER TRANSPORT PROTEIN 08-APR-15 1EJG\n" +
73 "ATOM 448 CA ALA A 24 6.619 16.195 1.970 1.00 1.65 C\n" +
74 "ATOM 458 CA ALEU A 25 3.048 14.822 1.781 0.57 1.48 C\n" +
75 // alternative residue 25 entries (with ILE instead of LEU) should be ignored:
76 "ATOM 478 CA BILE A 25 3.048 14.822 1.781 0.21 1.48 C\n" +
77 // including the next altloc causes the unit test to fail but it works with the full file
79 // "ATOM 479 CA CILE A 25 3.048 14.822 1.781 0.22 1.48 C\n" +
80 "ATOM 512 CA CYS A 26 4.137 11.461 3.154 1.00 1.52 C\n";
83 @BeforeMethod(alwaysRun = true)
86 Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
87 Boolean.TRUE.toString());
88 Cache.applicationProperties.setProperty("ADD_SS_ANN",
89 Boolean.TRUE.toString());
92 @Test(groups = { "Functional" })
93 public void testAlignmentLoader() throws Exception
95 for (String f : testFile)
97 FileLoader fl = new jalview.io.FileLoader(false);
99 .LoadFileWaitTillLoaded(f, AppletFormatAdapter.FILE);
100 validateSecStrRows(af.getViewport().getAlignment());
104 @Test(groups = { "Functional" })
105 public void testFileParser() throws Exception
107 for (String pdbStr : testFile)
109 PDBfile mctest = new PDBfile(false, false, false, pdbStr,
110 AppletFormatAdapter.FILE);
111 PDBFileWithJmol jtest = new PDBFileWithJmol(pdbStr,
112 jalview.io.AppletFormatAdapter.FILE);
113 Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
116 "No sequences extracted from testfile\n"
117 + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
118 : "(No warnings raised)"), seqs != null
120 for (SequenceI sq : seqs)
122 assertEquals("JMol didn't process " + pdbStr
123 + " to the same sequence as MCView",
124 sq.getSequenceAsString(), mcseqs.remove(0)
125 .getSequenceAsString());
126 AlignmentI al = new Alignment(new SequenceI[] { sq });
127 validateSecStrRows(al);
132 private void validateSecStrRows(AlignmentI al)
134 if (!al.isNucleotide())
136 for (SequenceI asq : al.getSequences())
139 boolean hasDs = false;
140 while (sq.getDatasetSequence() != null
141 && sq.getAnnotation() == null)
143 sq = sq.getDatasetSequence();
146 checkFirstAAIsAssoc(sq);
149 // also verify if alignment sequence has annotation on it
150 // that is correctly mapped
151 checkFirstAAIsAssoc(asq);
157 private void checkFirstAAIsAssoc(SequenceI sq)
159 assertTrue("No secondary structure assigned for protein sequence.",
160 sq.getAnnotation() != null && sq.getAnnotation().length >= 1
161 && sq.getAnnotation()[0].hasIcons);
163 "Secondary structure not associated for sequence "
164 + sq.getName(), sq.getAnnotation()[0].sequenceRef == sq);
168 * Test parsing a chain with missing residues
172 @Test(groups = { "Functional" })
173 public void testParse_missingResidues() throws Exception
175 PDBfile mctest = new PDBfile(false, false, false, pdbWithChainBreak,
176 AppletFormatAdapter.PASTE);
177 PDBFileWithJmol jtest = new PDBFileWithJmol(pdbWithChainBreak,
178 jalview.io.AppletFormatAdapter.PASTE);
179 Vector<SequenceI> seqs = jtest.getSeqs();
180 Vector<SequenceI> mcseqs = mctest.getSeqs();
182 assertEquals("Failed to find 2 sequences\n", 2, seqs.size());
183 assertEquals("Failed to find 2 sequences\n", 2, mcseqs.size());
184 assertEquals("VGKA", seqs.get(0).getSequenceAsString());
185 assertEquals("VGKA", mcseqs.get(0).getSequenceAsString());
186 assertEquals("SA", seqs.get(1).getSequenceAsString());
187 assertEquals("SA", mcseqs.get(1).getSequenceAsString());
191 * Test parsing a chain with 'altloc' residues
195 @Test(groups = { "Functional" })
196 public void testParse_alternativeResidues() throws Exception
198 PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc,
199 AppletFormatAdapter.PASTE);
200 PDBFileWithJmol jtest = new PDBFileWithJmol(pdbWithAltLoc,
201 jalview.io.AppletFormatAdapter.PASTE);
202 Vector<SequenceI> seqs = jtest.getSeqs();
203 Vector<SequenceI> mcseqs = mctest.getSeqs();
205 assertEquals("Failed to find 1 sequence\n", 1, seqs.size());
206 assertEquals("Failed to find 1 sequence\n", 1, mcseqs.size());
207 assertEquals("ALC", seqs.get(0).getSequenceAsString());
208 assertEquals("ALC", mcseqs.get(0).getSequenceAsString());
211 @Test(groups = "Functional")
212 public void testSetSecondaryStructure()
214 PDBFileWithJmol testee = new PDBFileWithJmol();
215 char[] struct = new char[10];
216 char[] structCode = new char[10];
220 testee.setSecondaryStructure(STR.NONE, 0, struct, structCode);
221 testee.setSecondaryStructure(STR.HELIX, 1, struct, structCode);
222 testee.setSecondaryStructure(STR.HELIX310, 2, struct, structCode);
223 testee.setSecondaryStructure(STR.HELIXALPHA, 3, struct, structCode);
224 testee.setSecondaryStructure(STR.HELIXPI, 4, struct, structCode);
225 testee.setSecondaryStructure(STR.SHEET, 5, struct, structCode);
227 assertEquals(0, struct[0]);
228 assertEquals('H', struct[1]);
229 assertEquals('3', struct[2]);
230 assertEquals('H', struct[3]);
231 assertEquals('P', struct[4]);
232 assertEquals('E', struct[5]);
234 assertEquals(0, structCode[0]);
235 assertEquals('H', structCode[1]);
236 assertEquals('H', structCode[2]);
237 assertEquals('H', structCode[3]);
238 assertEquals('H', structCode[4]);
239 assertEquals('E', structCode[5]);