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package jalview.structures.models; |
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import static org.testng.Assert.assertFalse; |
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import static org.testng.AssertJUnit.assertEquals; |
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import static org.testng.AssertJUnit.assertTrue; |
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import jalview.api.AlignmentViewPanel; |
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import jalview.api.FeatureRenderer; |
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import jalview.api.SequenceRenderer; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.HiddenColumns; |
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import jalview.datamodel.PDBEntry; |
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import jalview.datamodel.PDBEntry.Type; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.JvOptionPane; |
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import jalview.io.DataSourceType; |
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import jalview.io.FileFormats; |
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import jalview.schemes.ColourSchemeI; |
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import jalview.structure.AtomSpec; |
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import jalview.structure.StructureMappingcommandSet; |
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import jalview.structure.StructureSelectionManager; |
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import jalview.structures.models.AAStructureBindingModel.SuperposeData; |
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import java.awt.Color; |
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import java.io.IOException; |
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import java.util.Arrays; |
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import java.util.BitSet; |
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import java.util.List; |
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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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@author |
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| 68.3% |
Uncovered Elements: 38 (120) |
Complexity: 37 |
Complexity Density: 0.47 |
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public class AAStructureBindingModelTest |
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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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private static final String PDB_1 = "HEADER COMPLEX (ANTI-ONCOGENE/ANKYRIN REPEATS) 30-SEP-96 1YCS \n" |
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+ "ATOM 2 CA VAL A 97 24.134 4.926 45.821 1.00 47.43 C \n" |
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+ "ATOM 9 CA PRO A 98 25.135 8.584 46.217 1.00 41.60 C \n" |
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+ "ATOM 16 CA SER A 99 28.243 9.596 44.271 1.00 39.63 C \n" |
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+ "ATOM 22 CA GLN A 100 31.488 10.133 46.156 1.00 35.60 C \n" |
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+ "ATOM 31 CA LYS A 102 33.323 11.587 43.115 1.00 41.69 C \n" |
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+ "ATOM 1857 CA GLU B 374 9.193 -16.005 95.870 1.00 54.22 C \n" |
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+ "ATOM 1866 CA ILE B 375 7.101 -14.921 92.847 1.00 46.82 C \n" |
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+ "ATOM 1874 CA VAL B 376 10.251 -13.625 91.155 1.00 47.80 C \n" |
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+ "ATOM 1881 CA LYS B 377 11.767 -17.068 91.763 1.00 50.21 C \n" |
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+ "ATOM 1890 CA PHE B 378 8.665 -18.948 90.632 1.00 44.85 C \n"; |
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private static final String PDB_2 = "HEADER HYDROLASE 09-SEP-09 3A6S \n" |
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+ "ATOM 2 CA MET B 1 15.366 -11.648 24.854 1.00 32.05 C \n" |
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+ "ATOM 10 CA LYS B 2 16.846 -9.215 22.340 1.00 25.68 C \n" |
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+ "ATOM 19 CA LYS B 3 15.412 -6.335 20.343 1.00 19.42 C \n" |
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+ "ATOM 28 CA LEU B 4 15.629 -5.719 16.616 1.00 15.49 C \n" |
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+ "ATOM 36 CA GLN B 5 14.412 -2.295 15.567 1.00 12.19 C \n"; |
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private static final String PDB_3 = "HEADER STRUCTURAL GENOMICS 04-MAR-03 1OOT \n" |
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+ "ATOM 2 CA SER A 7 29.427 3.330 -6.578 1.00 32.50 C \n" |
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+ "ATOM 8 CA PRO A 8 29.975 3.340 -2.797 1.00 17.62 C \n" |
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+ "ATOM 16 CA ALYS A 9 26.958 3.024 -0.410 0.50 8.78 C \n" |
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+ "ATOM 33 CA ALA A 10 26.790 4.320 3.172 1.00 11.98 C \n" |
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+ "ATOM 39 CA AVAL A 12 24.424 3.853 6.106 0.50 13.83 C \n"; |
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private static final String PDB_4_MC = "HEADER HYDROLASE 09-SEP-09 3A6S \n" |
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+ "ATOM 2 CA MET A 1 15.366 -11.648 24.854 1.00 32.05 C \n" |
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+ "ATOM 10 CA LYS A 2 16.846 -9.215 22.340 1.00 25.68 C \n" |
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+ "ATOM 19 CA LYS A 3 15.412 -6.335 20.343 1.00 19.42 C \n" |
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+ "ATOM 28 CA LEU A 4 15.629 -5.719 16.616 1.00 15.49 C \n" |
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+ "ATOM 36 CA GLN A 5 14.412 -2.295 15.567 1.00 12.19 C \n" |
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+ "ATOM 1030 CA MET B 1 18.869 -7.572 3.432 1.00 31.52 C \n" |
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+ "ATOM 1038 CA LYS B 2 19.182 -10.025 6.313 1.00 26.41 C \n" |
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+ "ATOM 1047 CA LYS B 3 17.107 -12.963 7.534 1.00 19.71 C \n" |
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+ "ATOM 1056 CA LEU B 4 16.142 -13.579 11.164 1.00 14.81 C \n" |
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+ "ATOM 1064 CA GLN B 5 14.648 -17.005 11.785 1.00 13.38 C \n"; |
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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 testImportPDBPreservesChainMappings() throws IOException |
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{ |
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AlignmentI importedAl = new jalview.io.FormatAdapter().readFile( |
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PDB_4_MC, DataSourceType.PASTE, FileFormats.getInstance() |
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.forName(jalview.io.FileFormat.PDB.toString())); |
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PDBEntry importedPDB = new PDBEntry("3A6S", "", Type.PDB, |
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"Paste"); |
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AAStructureBindingModel binder = new AAStructureBindingModel( |
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new StructureSelectionManager(), new PDBEntry[] |
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{ importedPDB }, |
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new SequenceI[][] |
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{ importedAl.getSequencesArray() }, null) |
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{ |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
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@Override... |
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public void updateColours(Object source) |
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{ |
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} |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
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@Override... |
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public void releaseReferences(Object svl) |
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{ |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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@Override... |
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public String[] getStructureFiles() |
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{ |
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return null; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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@Override... |
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public String superposeStructures(AlignmentI[] alignments, |
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int[] structureIndices, HiddenColumns[] hiddenCols) |
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{ |
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return null; |
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} |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
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0 |
@Override... |
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public void setJalviewColourScheme(ColourSchemeI cs) |
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{ |
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} |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
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@Override... |
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public void setBackgroundColour(Color col) |
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{ |
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} |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
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@Override... |
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public void highlightAtoms(List<AtomSpec> atoms) |
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{ |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
@Override... |
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public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment) |
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{ |
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return null; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
@Override... |
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public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment) |
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{ |
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return null; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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protected StructureMappingcommandSet[] getColourBySequenceCommands( |
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String[] files, SequenceRenderer sr, AlignmentViewPanel avp) |
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{ |
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return null; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
@Override... |
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public List<String> getChainNames() |
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{ |
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215 |
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return null; |
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} |
217 |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
218 |
0 |
@Override... |
219 |
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protected void colourBySequence( |
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StructureMappingcommandSet[] colourBySequenceCommands) |
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{ |
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223 |
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} |
225 |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
226 |
0 |
@Override... |
227 |
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public void colourByCharge() |
228 |
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{ |
229 |
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230 |
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231 |
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} |
232 |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
233 |
0 |
@Override... |
234 |
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public void colourByChain() |
235 |
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{ |
236 |
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237 |
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238 |
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} |
239 |
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}; |
240 |
1 |
String[][] chains = binder.getChains(); |
241 |
1 |
assertFalse(chains == null || chains[0] == null, |
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"No chains discovered by binding"); |
243 |
1 |
assertEquals(2, chains[0].length); |
244 |
1 |
assertEquals("A", chains[0][0]); |
245 |
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assertEquals("B", chains[0][1]); |
246 |
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} |
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AAStructureBindingModel testee; |
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AlignmentI al = null; |
250 |
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253 |
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| 100% |
Uncovered Elements: 0 (19) |
Complexity: 1 |
Complexity Density: 0.05 |
|
254 |
3 |
@BeforeMethod(alwaysRun = true)... |
255 |
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public void setUp() |
256 |
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{ |
257 |
3 |
SequenceI seq1a = new Sequence("1YCS|A", "-VPSQK"); |
258 |
3 |
SequenceI seq1b = new Sequence("1YCS|B", "EIVKF-"); |
259 |
3 |
SequenceI seq2 = new Sequence("3A6S", "MK-KLQ"); |
260 |
3 |
SequenceI seq3 = new Sequence("1OOT", "SPK-AV"); |
261 |
3 |
al = new Alignment(new SequenceI[] { seq1a, seq1b, seq2, seq3 }); |
262 |
3 |
al.setDataset(null); |
263 |
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264 |
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265 |
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266 |
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267 |
3 |
PDBEntry[] pdbFiles = new PDBEntry[3]; |
268 |
3 |
pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "INLINE1YCS"); |
269 |
3 |
pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "INLINE3A6S"); |
270 |
3 |
pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "INLINE1OOT"); |
271 |
3 |
SequenceI[][] seqs = new SequenceI[3][]; |
272 |
3 |
seqs[0] = new SequenceI[] { seq1a, seq1b }; |
273 |
3 |
seqs[1] = new SequenceI[] { seq2 }; |
274 |
3 |
seqs[2] = new SequenceI[] { seq3 }; |
275 |
3 |
StructureSelectionManager ssm = new StructureSelectionManager(); |
276 |
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|
277 |
3 |
ssm.setMapping(new SequenceI[] { seq1a, seq1b }, null, PDB_1, |
278 |
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DataSourceType.PASTE, null); |
279 |
3 |
ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2, |
280 |
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DataSourceType.PASTE, null); |
281 |
3 |
ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3, |
282 |
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DataSourceType.PASTE, null); |
283 |
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|
284 |
3 |
testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, null) |
285 |
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{ |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
286 |
3 |
@Override... |
287 |
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public String[] getStructureFiles() |
288 |
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{ |
289 |
3 |
return new String[] { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" }; |
290 |
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} |
291 |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
292 |
0 |
@Override... |
293 |
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public void updateColours(Object source) |
294 |
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{ |
295 |
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} |
296 |
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|
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
297 |
0 |
@Override... |
298 |
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public void releaseReferences(Object svl) |
299 |
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{ |
300 |
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} |
301 |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
302 |
0 |
@Override... |
303 |
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public void highlightAtoms(List<AtomSpec> atoms) |
304 |
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{ |
305 |
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} |
306 |
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|
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
307 |
0 |
@Override... |
308 |
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public List<String> getChainNames() |
309 |
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{ |
310 |
0 |
return null; |
311 |
|
} |
312 |
|
|
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|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
313 |
0 |
@Override... |
314 |
|
public void setJalviewColourScheme(ColourSchemeI cs) |
315 |
|
{ |
316 |
|
} |
317 |
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|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
318 |
0 |
@Override... |
319 |
|
public String superposeStructures(AlignmentI[] als, int[] alm, |
320 |
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HiddenColumns[] alc) |
321 |
|
{ |
322 |
0 |
return null; |
323 |
|
} |
324 |
|
|
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|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
325 |
0 |
@Override... |
326 |
|
public void setBackgroundColour(Color col) |
327 |
|
{ |
328 |
|
} |
329 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
330 |
0 |
@Override... |
331 |
|
protected StructureMappingcommandSet[] getColourBySequenceCommands( |
332 |
|
String[] files, SequenceRenderer sr, AlignmentViewPanel avp) |
333 |
|
{ |
334 |
0 |
return null; |
335 |
|
} |
336 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
337 |
0 |
@Override... |
338 |
|
public SequenceRenderer getSequenceRenderer( |
339 |
|
AlignmentViewPanel alignment) |
340 |
|
{ |
341 |
0 |
return null; |
342 |
|
} |
343 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
344 |
0 |
@Override... |
345 |
|
protected void colourBySequence( |
346 |
|
StructureMappingcommandSet[] colourBySequenceCommands) |
347 |
|
{ |
348 |
|
} |
349 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
350 |
0 |
@Override... |
351 |
|
public void colourByChain() |
352 |
|
{ |
353 |
|
} |
354 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
355 |
0 |
@Override... |
356 |
|
public void colourByCharge() |
357 |
|
{ |
358 |
|
} |
359 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
360 |
0 |
@Override... |
361 |
|
public FeatureRenderer getFeatureRenderer( |
362 |
|
AlignmentViewPanel alignment) |
363 |
|
{ |
364 |
0 |
return null; |
365 |
|
} |
366 |
|
}; |
367 |
|
} |
368 |
|
|
369 |
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|
370 |
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|
371 |
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|
372 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (27) |
Complexity: 3 |
Complexity Density: 0.13 |
1PASS
|
|
373 |
1 |
@Test(groups = { "Functional" })... |
374 |
|
public void testFindSuperposableResidues() |
375 |
|
{ |
376 |
|
|
377 |
|
|
378 |
|
|
379 |
1 |
SuperposeData[] structs = new SuperposeData[testee.getStructureFiles().length]; |
380 |
4 |
for (int i = 0; i < structs.length; i++) |
381 |
|
{ |
382 |
3 |
structs[i] = testee.new SuperposeData(al.getWidth()); |
383 |
|
} |
384 |
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|
385 |
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|
386 |
|
|
387 |
|
|
388 |
1 |
BitSet matched = new BitSet(); |
389 |
7 |
for (int i = 0; i < al.getWidth(); i++) |
390 |
|
{ |
391 |
6 |
matched.set(i); |
392 |
|
} |
393 |
|
|
394 |
1 |
int refStructure = testee |
395 |
|
.findSuperposableResidues(al, matched, structs); |
396 |
|
|
397 |
1 |
assertEquals(0, refStructure); |
398 |
|
|
399 |
|
|
400 |
|
|
401 |
|
|
402 |
1 |
assertFalse(matched.get(0)); |
403 |
1 |
assertTrue(matched.get(1)); |
404 |
1 |
assertFalse(matched.get(2)); |
405 |
1 |
assertFalse(matched.get(3)); |
406 |
1 |
assertTrue(matched.get(4)); |
407 |
1 |
assertTrue(matched.get(5)); |
408 |
|
|
409 |
1 |
assertEquals("1YCS", structs[0].pdbId); |
410 |
1 |
assertEquals("3A6S", structs[1].pdbId); |
411 |
1 |
assertEquals("1OOT", structs[2].pdbId); |
412 |
1 |
assertEquals("A", structs[0].chain); |
413 |
1 |
assertEquals("B", structs[1].chain); |
414 |
1 |
assertEquals("A", structs[2].chain); |
415 |
|
|
416 |
1 |
assertEquals("[0, 97, 98, 99, 100, 102]", |
417 |
|
Arrays.toString(structs[0].pdbResNo)); |
418 |
1 |
assertEquals("[0, 2, 0, 3, 4, 5]", Arrays.toString(structs[1].pdbResNo)); |
419 |
1 |
assertEquals("[0, 8, 0, 0, 10, 12]", |
420 |
|
Arrays.toString(structs[2].pdbResNo)); |
421 |
|
} |
422 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (19) |
Complexity: 3 |
Complexity Density: 0.2 |
1PASS
|
|
423 |
1 |
@Test(groups = { "Functional" })... |
424 |
|
public void testFindSuperposableResidues_hiddenColumn() |
425 |
|
{ |
426 |
1 |
SuperposeData[] structs = new SuperposeData[al.getHeight()]; |
427 |
5 |
for (int i = 0; i < structs.length; i++) |
428 |
|
{ |
429 |
4 |
structs[i] = testee.new SuperposeData(al.getWidth()); |
430 |
|
} |
431 |
|
|
432 |
|
|
433 |
|
|
434 |
|
|
435 |
1 |
BitSet matched = new BitSet(); |
436 |
7 |
for (int i = 0; i < al.getWidth(); i++) |
437 |
|
{ |
438 |
6 |
matched.set(i); |
439 |
|
} |
440 |
|
|
441 |
|
|
442 |
1 |
matched.clear(4); |
443 |
|
|
444 |
1 |
int refStructure = testee |
445 |
|
.findSuperposableResidues(al, matched, structs); |
446 |
|
|
447 |
1 |
assertEquals(0, refStructure); |
448 |
|
|
449 |
|
|
450 |
1 |
assertFalse(matched.get(0)); |
451 |
1 |
assertTrue(matched.get(1)); |
452 |
1 |
assertFalse(matched.get(2)); |
453 |
1 |
assertFalse(matched.get(3)); |
454 |
1 |
assertFalse(matched.get(4)); |
455 |
1 |
assertTrue(matched.get(5)); |
456 |
|
} |
457 |
|
} |