X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModelTest.java;fp=test%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModelTest.java;h=7ba22b49ddb1eba4dcf4b553602d319558fa618a;hb=2595e9d4ee0dbbd3406a98c4e49a61ccde806479;hp=bb81992c6b27494cc08e7c2790ca770fe526a2b3;hpb=e20075ba805d744d7cc4976e2b8d5e5840fb0a8d;p=jalview.git diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java index bb81992..7ba22b4 100644 --- a/test/jalview/structures/models/AAStructureBindingModelTest.java +++ b/test/jalview/structures/models/AAStructureBindingModelTest.java @@ -24,20 +24,30 @@ import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertTrue; +import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureRenderer; +import jalview.api.SequenceRenderer; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; 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.schemes.ColourSchemeI; import jalview.structure.AtomSpec; +import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; import jalview.structures.models.AAStructureBindingModel.SuperposeData; +import java.awt.Color; import java.util.Arrays; +import java.util.BitSet; import java.util.List; +import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; @@ -49,26 +59,44 @@ 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 +108,38 @@ 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); + ssm.setMapping(new SequenceI[] { seq1a, seq1b }, null, PDB_1, + DataSourceType.PASTE); ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2, - AppletFormatAdapter.PASTE); + DataSourceType.PASTE); ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3, - AppletFormatAdapter.PASTE); + DataSourceType.PASTE); - 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 +157,66 @@ public class AAStructureBindingModelTest public void highlightAtoms(List atoms) { } + + @Override + public List getChainNames() + { + return null; + } + + @Override + public void setJalviewColourScheme(ColourSchemeI cs) + { + } + + @Override + public String superposeStructures(AlignmentI[] als, int[] alm, + ColumnSelection[] alc) + { + return null; + } + + @Override + public void setBackgroundColour(Color col) + { + } + + @Override + protected StructureMappingcommandSet[] getColourBySequenceCommands( + String[] files, SequenceRenderer sr, AlignmentViewPanel avp) + { + return null; + } + + @Override + public SequenceRenderer getSequenceRenderer( + AlignmentViewPanel alignment) + { + return null; + } + + @Override + protected void colourBySequence( + StructureMappingcommandSet[] colourBySequenceCommands) + { + } + + @Override + public void colourByChain() + { + } + + @Override + public void colourByCharge() + { + } + + @Override + public FeatureRenderer getFeatureRenderer( + AlignmentViewPanel alignment) + { + return null; + } }; } @@ -140,17 +227,23 @@ 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()); } /* - * initialise array of 'superposable columns' to true (would be false for + * initialise BitSet of 'superposable columns' to true (would be false for * hidden columns) */ - boolean[] matched = new boolean[al.getWidth()]; - Arrays.fill(matched, true); + BitSet matched = new BitSet(); + for (int i = 0; i < al.getWidth(); i++) + { + matched.set(i); + } int refStructure = testee .findSuperposableResidues(al, matched, structs); @@ -160,12 +253,25 @@ public class AAStructureBindingModelTest /* * 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]); + assertFalse(matched.get(0)); // gap in first sequence + assertTrue(matched.get(1)); + assertFalse(matched.get(2)); // gap in third sequence + assertFalse(matched.get(3)); // gap in fourth sequence + assertTrue(matched.get(4)); + assertTrue(matched.get(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" }) @@ -177,13 +283,17 @@ public class AAStructureBindingModelTest structs[i] = testee.new SuperposeData(al.getWidth()); } /* - * initialise array of 'superposable columns' to true (would be false for + * initialise BitSet of 'superposable columns' to true (would be false for * hidden columns) */ - boolean[] matched = new boolean[al.getWidth()]; - Arrays.fill(matched, true); + BitSet matched = new BitSet(); + for (int i = 0; i < al.getWidth(); i++) + { + matched.set(i); + } + // treat column 5 of the alignment as hidden - matched[4] = false; + matched.clear(4); int refStructure = testee .findSuperposableResidues(al, matched, structs); @@ -191,11 +301,11 @@ public class AAStructureBindingModelTest 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]); + assertFalse(matched.get(0)); + assertTrue(matched.get(1)); + assertFalse(matched.get(2)); + assertFalse(matched.get(3)); + assertFalse(matched.get(4)); // superposable, but hidden, column + assertTrue(matched.get(5)); } }