X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModelTest.java;h=1325513003c67949f96a8f4baeba21ae617d0e6d;hb=d980f203d66517042c7d2707ec300c653cae1892;hp=e82bfea01a9dd40cca29405c17ecfe0394fc9406;hpb=80edaa84d6d9beac9f0d2c71b50b7b56fd393427;p=jalview.git diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java index e82bfea..1325513 100644 --- a/test/jalview/structures/models/AAStructureBindingModelTest.java +++ b/test/jalview/structures/models/AAStructureBindingModelTest.java @@ -30,7 +30,8 @@ import jalview.datamodel.PDBEntry; 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; @@ -38,6 +39,7 @@ 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; @@ -49,26 +51,44 @@ 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; @@ -80,39 +100,39 @@ public class AAStructureBindingModelTest @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" }; } @@ -130,6 +150,12 @@ public class AAStructureBindingModelTest public void highlightAtoms(List atoms) { } + + @Override + public List getChainNames() + { + return null; + } }; } @@ -140,7 +166,10 @@ public class AAStructureBindingModelTest @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()); @@ -162,10 +191,23 @@ public class AAStructureBindingModelTest */ 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" })