import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
import jalview.structure.AtomSpec;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel.SuperposeData;
import java.util.Arrays;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
*/
public class AAStructureBindingModelTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ /*
+ * Scenario: Jalview has 4 sequences, corresponding to 1YCS (chains A and B), 3A6S|B, 1OOT|A
+ */
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";
+ // artificial jump in residue numbering to prove it is correctly
+ // mapped:
+ + "ATOM 31 CA LYS A 102 33.323 11.587 43.115 1.00 41.69 C \n"
+ + "ATOM 1857 CA GLU B 374 9.193 -16.005 95.870 1.00 54.22 C \n"
+ + "ATOM 1866 CA ILE B 375 7.101 -14.921 92.847 1.00 46.82 C \n"
+ + "ATOM 1874 CA VAL B 376 10.251 -13.625 91.155 1.00 47.80 C \n"
+ + "ATOM 1881 CA LYS B 377 11.767 -17.068 91.763 1.00 50.21 C \n"
+ + "ATOM 1890 CA PHE B 378 8.665 -18.948 90.632 1.00 44.85 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";
+ + "ATOM 2 CA MET B 1 15.366 -11.648 24.854 1.00 32.05 C \n"
+ + "ATOM 10 CA LYS B 2 16.846 -9.215 22.340 1.00 25.68 C \n"
+ + "ATOM 19 CA LYS B 3 15.412 -6.335 20.343 1.00 19.42 C \n"
+ + "ATOM 28 CA LEU B 4 15.629 -5.719 16.616 1.00 15.49 C \n"
+ + "ATOM 36 CA GLN B 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";
+ + "ATOM 2 CA SER A 7 29.427 3.330 -6.578 1.00 32.50 C \n"
+ + "ATOM 8 CA PRO A 8 29.975 3.340 -2.797 1.00 17.62 C \n"
+ + "ATOM 16 CA ALYS A 9 26.958 3.024 -0.410 0.50 8.78 C \n"
+ + "ATOM 33 CA ALA A 10 26.790 4.320 3.172 1.00 11.98 C \n"
+ + "ATOM 39 CA AVAL A 12 24.424 3.853 6.106 0.50 13.83 C \n";
AAStructureBindingModel testee;
@BeforeMethod(alwaysRun = true)
public void setUp()
{
- SequenceI seq1 = new Sequence("1YCS", "-VPSQK");
+ SequenceI seq1a = new Sequence("1YCS|A", "-VPSQK");
+ SequenceI seq1b = new Sequence("1YCS|B", "EIVKF-");
SequenceI seq2 = new Sequence("3A6S", "MK-KLQ");
SequenceI seq3 = new Sequence("1OOT", "SPK-AV");
- al = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+ al = new Alignment(new SequenceI[] { seq1a, seq1b, seq2, seq3 });
al.setDataset(null);
+ /*
+ * give pdb files the name generated by Jalview for PASTE source
+ */
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][];
+ pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "INLINE1YCS");
+ pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "INLINE3A6S");
+ pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "INLINE1OOT");
SequenceI[][] seqs = new SequenceI[3][];
- seqs[0] = new SequenceI[] { seq1 };
+ seqs[0] = new SequenceI[] { seq1a, seq1b };
seqs[1] = new SequenceI[] { seq2 };
seqs[2] = new SequenceI[] { seq3 };
StructureSelectionManager ssm = new StructureSelectionManager();
- ssm.setMapping(new SequenceI[] { seq1 }, null, PDB_1,
- AppletFormatAdapter.PASTE, null);
+ ssm.setMapping(new SequenceI[] { seq1a, seq1b }, null, PDB_1,
+ DataSourceType.PASTE, null);
ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2,
- AppletFormatAdapter.PASTE, null);
+ DataSourceType.PASTE, null);
ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3,
- AppletFormatAdapter.PASTE, null);
+ DataSourceType.PASTE, null);
+
- testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, chains, null)
+ testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, null)
{
@Override
public String[] getPdbFile()
{
- /*
- * fudge 'filenames' to match those generated when PDBFile parses PASTE
- * data
- */
return new String[] { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" };
}
public void highlightAtoms(List<AtomSpec> atoms)
{
}
+
+ @Override
+ public List<String> getChainNames()
+ {
+ return null;
+ }
};
}
@Test(groups = { "Functional" })
public void testFindSuperposableResidues()
{
- SuperposeData[] structs = new SuperposeData[al.getHeight()];
+ /*
+ * create a data bean to hold data per structure file
+ */
+ SuperposeData[] structs = new SuperposeData[testee.getPdbFile().length];
for (int i = 0; i < structs.length; i++)
{
structs[i] = testee.new SuperposeData(al.getWidth());
*/
assertFalse(matched[0]); // gap in first sequence
assertTrue(matched[1]);
- assertFalse(matched[2]); // gap in second sequence
- assertFalse(matched[3]); // gap in third sequence
+ assertFalse(matched[2]); // gap in third sequence
+ assertFalse(matched[3]); // gap in fourth sequence
assertTrue(matched[4]);
- assertTrue(matched[5]);
+ assertTrue(matched[5]); // gap in second sequence
+
+ assertEquals("1YCS", structs[0].pdbId);
+ assertEquals("3A6S", structs[1].pdbId);
+ assertEquals("1OOT", structs[2].pdbId);
+ assertEquals("A", structs[0].chain); // ? struct has chains A _and_ B
+ assertEquals("B", structs[1].chain);
+ assertEquals("A", structs[2].chain);
+ // the 0's for unsuperposable positions propagate down the columns:
+ assertEquals("[0, 97, 98, 99, 100, 102]",
+ Arrays.toString(structs[0].pdbResNo));
+ assertEquals("[0, 2, 0, 3, 4, 5]", Arrays.toString(structs[1].pdbResNo));
+ assertEquals("[0, 8, 0, 0, 10, 12]",
+ Arrays.toString(structs[2].pdbResNo));
}
@Test(groups = { "Functional" })
git://source.jalview.org / jalview.git / blobdiff