--- /dev/null
+package jalview.structures.models;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.util.Arrays;
+import java.util.List;
+
+import org.junit.Before;
+import org.junit.Test;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel.SuperposeData;
+
+/**
+ * Unit tests for non-abstract methods of abstract base class
+ *
+ * @author gmcarstairs
+ *
+ */
+public class AAStructureBindingModelTest
+{
+ private static final String PDB_1 = "HEADER COMPLEX (ANTI-ONCOGENE/ANKYRIN REPEATS) 30-SEP-96 1YCS \n"
+ + "ATOM 2 CA VAL A 97 24.134 4.926 45.821 1.00 47.43 C \n"
+ + "ATOM 9 CA PRO A 98 25.135 8.584 46.217 1.00 41.60 C \n"
+ + "ATOM 16 CA SER A 99 28.243 9.596 44.271 1.00 39.63 C \n"
+ + "ATOM 22 CA GLN A 100 31.488 10.133 46.156 1.00 35.60 C \n"
+ + "ATOM 31 CA LYS A 101 33.323 11.587 43.115 1.00 41.69 C \n";
+
+ private static final String PDB_2 = "HEADER HYDROLASE 09-SEP-09 3A6S \n"
+ + "ATOM 2 CA MET A 1 15.366 -11.648 24.854 1.00 32.05 C \n"
+ + "ATOM 10 CA LYS A 2 16.846 -9.215 22.340 1.00 25.68 C \n"
+ + "ATOM 19 CA LYS A 3 15.412 -6.335 20.343 1.00 19.42 C \n"
+ + "ATOM 28 CA LEU A 4 15.629 -5.719 16.616 1.00 15.49 C \n"
+ + "ATOM 36 CA GLN A 5 14.412 -2.295 15.567 1.00 12.19 C \n";
+
+ private static final String PDB_3 = "HEADER STRUCTURAL GENOMICS 04-MAR-03 1OOT \n"
+ + "ATOM 2 CA SER A 1 29.427 3.330 -6.578 1.00 32.50 C \n"
+ + "ATOM 8 CA PRO A 2 29.975 3.340 -2.797 1.00 17.62 C \n"
+ + "ATOM 16 CA ALYS A 3 26.958 3.024 -0.410 0.50 8.78 C \n"
+ + "ATOM 33 CA ALA A 4 26.790 4.320 3.172 1.00 11.98 C \n"
+ + "ATOM 39 CA AVAL A 5 24.424 3.853 6.106 0.50 13.83 C \n";
+
+ AAStructureBindingModel testee;
+
+ AlignmentI al = null;
+
+ /**
+ * Set up test conditions with three aligned sequences,
+ */
+ @Before
+ public void setUp()
+ {
+ SequenceI seq1 = new Sequence("1YCS", "-VPSQK");
+ SequenceI seq2 = new Sequence("3A6S", "MK-KLQ");
+ SequenceI seq3 = new Sequence("1OOT", "SPK-AV");
+ al = new Alignment(new SequenceI[]
+ { seq1, seq2, seq3 });
+ al.setDataset(null);
+
+ PDBEntry[] pdbFiles = new PDBEntry[3];
+ pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "1YCS.pdb");
+ pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "3A6S.pdb");
+ pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "1OOT.pdb");
+ String[][] chains = new String[3][];
+ SequenceI[][] seqs = new SequenceI[3][];
+ seqs[0] = new SequenceI[]
+ { seq1 };
+ seqs[1] = new SequenceI[]
+ { seq2 };
+ seqs[2] = new SequenceI[]
+ { seq3 };
+ StructureSelectionManager ssm = new StructureSelectionManager();
+
+ ssm.setMapping(new SequenceI[]
+ { seq1 }, null, PDB_1, AppletFormatAdapter.PASTE);
+ ssm.setMapping(new SequenceI[]
+ { seq2 }, null, PDB_2, AppletFormatAdapter.PASTE);
+ ssm.setMapping(new SequenceI[]
+ { seq3 }, null, PDB_3, AppletFormatAdapter.PASTE);
+
+ testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, chains, null)
+ {
+ @Override
+ public String[] getPdbFile()
+ {
+ /*
+ * fudge 'filenames' to match those generated when PDBFile parses PASTE
+ * data
+ */
+ return new String[]
+ { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" };
+ }
+ @Override
+ public void updateColours(Object source)
+ {
+ }
+ @Override
+ public void releaseReferences(Object svl)
+ {
+ }
+ @Override
+ public void highlightAtoms(List<AtomSpec> atoms)
+ {
+ }
+ };
+ }
+
+ /**
+ * Verify that the method determines that columns 2, 5 and 6 of the aligment
+ * are alignable in structure
+ */
+ @Test
+ public void testFindSuperposableResidues()
+ {
+ SuperposeData[] structs = new SuperposeData[al.getHeight()];
+ for (int i = 0; i < structs.length; i++)
+ {
+ structs[i] = testee.new SuperposeData(al.getWidth());
+ }
+ /*
+ * initialise array of 'superposable columns' to true (would be false for
+ * hidden columns)
+ */
+ boolean[] matched = new boolean[al.getWidth()];
+ Arrays.fill(matched, true);
+
+ int refStructure = testee
+ .findSuperposableResidues(al, matched, structs);
+
+ assertEquals(0, refStructure);
+
+ /*
+ * only ungapped, structure-mapped columns are superposable
+ */
+ assertFalse(matched[0]); // gap in first sequence
+ assertTrue(matched[1]);
+ assertFalse(matched[2]); // gap in second sequence
+ assertFalse(matched[3]); // gap in third sequence
+ assertTrue(matched[4]);
+ assertTrue(matched[5]);
+ }
+
+ @Test
+ public void testFindSuperposableResidues_hiddenColumn()
+ {
+ SuperposeData[] structs = new SuperposeData[al.getHeight()];
+ for (int i = 0; i < structs.length; i++)
+ {
+ structs[i] = testee.new SuperposeData(al.getWidth());
+ }
+ /*
+ * initialise array of 'superposable columns' to true (would be false for
+ * hidden columns)
+ */
+ boolean[] matched = new boolean[al.getWidth()];
+ Arrays.fill(matched, true);
+ // treat column 5 of the alignment as hidden
+ matched[4] = false;
+
+ int refStructure = testee
+ .findSuperposableResidues(al, matched, structs);
+
+ assertEquals(0, refStructure);
+
+ // only ungapped, structure-mapped columns are not superposable
+ assertFalse(matched[0]);
+ assertTrue(matched[1]);
+ assertFalse(matched[2]);
+ assertFalse(matched[3]);
+ assertFalse(matched[4]); // superposable, but hidden, column
+ assertTrue(matched[5]);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff