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package jalview.ext.jmol; |
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import static org.testng.AssertJUnit.assertEquals; |
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import static org.testng.AssertJUnit.assertNotNull; |
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import static org.testng.AssertJUnit.assertTrue; |
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import jalview.bin.Cache; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.AlignFrame; |
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import jalview.gui.JvOptionPane; |
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import jalview.io.DataSourceType; |
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import jalview.io.FileLoader; |
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import jalview.structure.StructureImportSettings; |
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import jalview.structure.StructureImportSettings.StructureParser; |
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import java.util.Vector; |
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import org.jmol.c.STR; |
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import org.testng.annotations.BeforeClass; |
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import org.testng.annotations.BeforeMethod; |
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import org.testng.annotations.Test; |
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import mc_view.PDBfile; |
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@author |
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| 63.4% |
Uncovered Elements: 37 (101) |
Complexity: 15 |
Complexity Density: 0.18 |
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public class JmolParserTest |
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{ |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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@BeforeClass(alwaysRun = true)... |
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public void setUpJvOptionPane() |
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{ |
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JvOptionPane.setInteractiveMode(false); |
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JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
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} |
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String[] testFile = new String[] { "./examples/1GAQ.txt", |
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"./test/jalview/ext/jmol/1xyz.pdb", |
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"./test/jalview/ext/jmol/1qcf.pdb" }; |
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String pastePDBDataWithChainBreak = |
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"HEADER TRANSPORT PROTEIN 08-APR-15 4UJ4\n" + |
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"ATOM 1909 CA VAL B 358 21.329 -19.739 -67.740 1.00201.05 C\n" + |
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"ATOM 1916 CA GLY B 359 21.694 -23.563 -67.661 1.00198.09 C\n" + |
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"ATOM 1920 CA LYS B 367 32.471 -12.135 -77.100 1.00257.97 C\n" + |
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"ATOM 1925 CA ALA B 368 31.032 -9.324 -74.946 1.00276.01 C\n" + |
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"ATOM 1930 CA SER C 369 32.589 -7.517 -71.978 1.00265.44 C\n" + |
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"ATOM 1936 CA ALA C 370 31.650 -6.849 -68.346 1.00249.48 C\n"; |
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String pdbWithAltLoc = |
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"HEADER TRANSPORT PROTEIN 08-APR-15 1EJG\n" + |
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"ATOM 448 CA ALA A 24 6.619 16.195 1.970 1.00 1.65 C\n" + |
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"ATOM 458 CA ALEU A 25 3.048 14.822 1.781 0.57 1.48 C\n" + |
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"ATOM 478 CA BILE A 25 3.048 14.822 1.781 0.21 1.48 C\n" + |
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"ATOM 512 CA CYS A 26 4.137 11.461 3.154 1.00 1.52 C\n"; |
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| 100% |
Uncovered Elements: 0 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
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@BeforeMethod(alwaysRun = true)... |
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public void setUp() |
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{ |
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Cache.loadProperties("test/jalview/io/testProps.jvprops"); |
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Cache.applicationProperties.setProperty("STRUCT_FROM_PDB", |
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Boolean.TRUE.toString()); |
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Cache.applicationProperties.setProperty("ADD_TEMPFACT_ANN", |
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Boolean.FALSE.toString()); |
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Cache.applicationProperties.setProperty("ADD_SS_ANN", |
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Boolean.TRUE.toString()); |
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StructureImportSettings.setDefaultStructureFileFormat("PDB"); |
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StructureImportSettings |
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.setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER); |
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} |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
3FAIL
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@Test(groups = { "Functional" })... |
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public void testAlignmentLoader() throws Exception |
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{ |
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for (String f : testFile) |
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{ |
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FileLoader fl = new jalview.io.FileLoader(false); |
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AlignFrame af = fl.LoadFileWaitTillLoaded(f, DataSourceType.FILE); |
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validateSecStrRows(af.getViewport().getAlignment()); |
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} |
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} |
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| 0% |
Uncovered Elements: 11 (11) |
Complexity: 2 |
Complexity Density: 0.22 |
3FAIL
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@Test(groups = { "Functional" })... |
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public void testFileParser() throws Exception |
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{ |
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for (String pdbStr : testFile) |
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{ |
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PDBfile mctest = new PDBfile(false, false, false, pdbStr, |
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DataSourceType.FILE); |
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JmolParser jtest = new JmolParser(pdbStr, DataSourceType.FILE); |
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Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs(); |
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assertTrue( |
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"No sequences extracted from testfile\n" |
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+ (jtest.hasWarningMessage() ? jtest.getWarningMessage() |
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: "(No warnings raised)"), seqs != null |
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&& seqs.size() > 0); |
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for (SequenceI sq : seqs) |
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{ |
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assertEquals("JMol didn't process " + pdbStr |
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+ " to the same sequence as MCView", |
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sq.getSequenceAsString(), mcseqs.remove(0) |
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.getSequenceAsString()); |
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AlignmentI al = new Alignment(new SequenceI[] { sq }); |
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validateSecStrRows(al); |
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} |
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} |
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} |
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| 0% |
Uncovered Elements: 16 (16) |
Complexity: 5 |
Complexity Density: 0.5 |
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private void validateSecStrRows(AlignmentI al)... |
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{ |
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if (!al.isNucleotide()) |
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{ |
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for (SequenceI asq : al.getSequences()) |
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{ |
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SequenceI sq = asq; |
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boolean hasDs = false; |
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while (sq.getDatasetSequence() != null |
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&& sq.getAnnotation() == null) |
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{ |
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sq = sq.getDatasetSequence(); |
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hasDs = true; |
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} |
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checkFirstAAIsAssoc(sq); |
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if (hasDs) |
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{ |
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checkFirstAAIsAssoc(asq); |
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} |
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} |
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} |
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} |
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| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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private void checkFirstAAIsAssoc(SequenceI sq)... |
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{ |
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assertTrue("No secondary structure assigned for protein sequence for " |
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+ sq.getName(), |
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sq.getAnnotation() != null && sq.getAnnotation().length >= 1 |
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&& sq.getAnnotation()[0].hasIcons); |
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assertTrue( |
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"Secondary structure not associated for sequence " |
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+ sq.getName(), sq.getAnnotation()[0].sequenceRef == sq); |
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} |
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@throws |
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| 100% |
Uncovered Elements: 0 (10) |
Complexity: 1 |
Complexity Density: 0.1 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testParse_missingResidues() throws Exception |
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{ |
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PDBfile mctest = new PDBfile(false, false, false, |
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pastePDBDataWithChainBreak, DataSourceType.PASTE); |
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JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak, DataSourceType.PASTE); |
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Vector<SequenceI> seqs = jtest.getSeqs(); |
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Vector<SequenceI> mcseqs = mctest.getSeqs(); |
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assertEquals("Failed to find 2 sequences\n", 2, seqs.size()); |
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assertEquals("Failed to find 2 sequences\n", 2, mcseqs.size()); |
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assertEquals("VGKA", seqs.get(0).getSequenceAsString()); |
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assertEquals("VGKA", mcseqs.get(0).getSequenceAsString()); |
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assertEquals("SA", seqs.get(1).getSequenceAsString()); |
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assertEquals("SA", mcseqs.get(1).getSequenceAsString()); |
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} |
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@throws |
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| 100% |
Uncovered Elements: 0 (8) |
Complexity: 1 |
Complexity Density: 0.12 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testParse_alternativeResidues() throws Exception |
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{ |
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PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc, |
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DataSourceType.PASTE); |
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JmolParser jtest = new JmolParser(pdbWithAltLoc, |
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DataSourceType.PASTE); |
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Vector<SequenceI> seqs = jtest.getSeqs(); |
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Vector<SequenceI> mcseqs = mctest.getSeqs(); |
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assertEquals("Failed to find 1 sequence\n", 1, seqs.size()); |
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assertEquals("Failed to find 1 sequence\n", 1, mcseqs.size()); |
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assertEquals("ALC", seqs.get(0).getSequenceAsString()); |
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assertEquals("ALC", mcseqs.get(0).getSequenceAsString()); |
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} |
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| 100% |
Uncovered Elements: 0 (23) |
Complexity: 1 |
Complexity Density: 0.04 |
1PASS
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@Test(groups = "Functional")... |
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public void testSetSecondaryStructure() |
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{ |
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JmolParser testee = new JmolParser(); |
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char[] struct = new char[10]; |
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char[] structCode = new char[10]; |
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struct[0] = '1'; |
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structCode[0] = '1'; |
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testee.setSecondaryStructure(STR.NONE, 0, struct, structCode); |
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testee.setSecondaryStructure(STR.HELIX, 1, struct, structCode); |
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testee.setSecondaryStructure(STR.HELIX310, 2, struct, structCode); |
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testee.setSecondaryStructure(STR.HELIXALPHA, 3, struct, structCode); |
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testee.setSecondaryStructure(STR.HELIXPI, 4, struct, structCode); |
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testee.setSecondaryStructure(STR.SHEET, 5, struct, structCode); |
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assertEquals(0, struct[0]); |
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assertEquals('H', struct[1]); |
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assertEquals('3', struct[2]); |
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assertEquals('H', struct[3]); |
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assertEquals('P', struct[4]); |
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assertEquals('E', struct[5]); |
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assertEquals(0, structCode[0]); |
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assertEquals('H', structCode[1]); |
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assertEquals('H', structCode[2]); |
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assertEquals('H', structCode[3]); |
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assertEquals('H', structCode[4]); |
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assertEquals('E', structCode[5]); |
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} |
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| 100% |
Uncovered Elements: 0 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
1PASS
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1 |
@Test(groups = "Functional")... |
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public void testLocalPDBId() throws Exception |
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{ |
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JmolParser structureData; |
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structureData = new JmolParser("examples/testdata/localstruct.pdb", |
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DataSourceType.FILE); |
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assertNotNull(structureData); |
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assertNotNull(structureData.getId()); |
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assertEquals(structureData.getId(), "localstruct"); |
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assertNotNull(structureData.getSeqs()); |
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String featureGroup = structureData.getSeqs().get(0) |
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.getSequenceFeatures().get(0).featureGroup; |
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assertNotNull(featureGroup); |
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assertEquals(featureGroup, "localstruct"); |
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} |
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} |