X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModelTest.java;h=af02d5e3d85fd0d215485bb2f6abc38ec0fa29d7;hb=3b3c59cfa50e942d2fa5b367b7117cade9459ce7;hp=84df5126af4fab14bc007afc92a74279792d498c;hpb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;p=jalview.git diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java index 84df512..af02d5e 100644 --- a/test/jalview/structures/models/AAStructureBindingModelTest.java +++ b/test/jalview/structures/models/AAStructureBindingModelTest.java @@ -20,23 +20,33 @@ */ package jalview.structures.models; +import static org.testng.Assert.assertFalse; 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.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.PDBEntry.Type; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; import jalview.gui.JvOptionPane; -import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; +import jalview.io.FileFormats; +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.io.IOException; import java.util.Arrays; +import java.util.BitSet; import java.util.List; import org.testng.annotations.BeforeClass; @@ -90,6 +100,150 @@ public class AAStructureBindingModelTest + "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"; + /** + * Multichain PDB with identical sequences imported - Binding should correctly + * recover chain mappings for each derived sequence + */ + private static final String PDB_4_MC = "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 1030 CA MET B 1 18.869 -7.572 3.432 1.00 31.52 C \n" + + "ATOM 1038 CA LYS B 2 19.182 -10.025 6.313 1.00 26.41 C \n" + + "ATOM 1047 CA LYS B 3 17.107 -12.963 7.534 1.00 19.71 C \n" + + "ATOM 1056 CA LEU B 4 16.142 -13.579 11.164 1.00 14.81 C \n" + + "ATOM 1064 CA GLN B 5 14.648 -17.005 11.785 1.00 13.38 C \n"; + + // TODO: JAL-2227 - import mmCIF PISA assembly & identify master/copy chains + + @Test(groups= {"Functional"}) + public void testImportPDBPreservesChainMappings() throws IOException + { + AlignmentI importedAl = new jalview.io.FormatAdapter().readFile( + PDB_4_MC, DataSourceType.PASTE, FileFormats.getInstance() + .forName(jalview.io.FileFormat.PDB.toString())); + // ideally, we would match on the actual data for the 'File' handle for + // pasted files, + // see JAL-623 - pasting is still not correctly handled... + PDBEntry importedPDB = new PDBEntry("3A6S", "", Type.PDB, + "Paste"); + AAStructureBindingModel binder = new AAStructureBindingModel( + new StructureSelectionManager(), new PDBEntry[] + { importedPDB }, + new SequenceI[][] + { importedAl.getSequencesArray() }, null) + { + + @Override + public void updateColours(Object source) + { + // TODO Auto-generated method stub + + } + + @Override + public void releaseReferences(Object svl) + { + // TODO Auto-generated method stub + + } + + @Override + public String[] getStructureFiles() + { + // TODO Auto-generated method stub + return null; + } + + @Override + public String superposeStructures(AlignmentI[] alignments, + int[] structureIndices, HiddenColumns[] hiddenCols) + { + // TODO Auto-generated method stub + return null; + } + + @Override + public void setJalviewColourScheme(ColourSchemeI cs) + { + // TODO Auto-generated method stub + + } + + @Override + public void setBackgroundColour(Color col) + { + // TODO Auto-generated method stub + + } + + @Override + public void highlightAtoms(List atoms) + { + // TODO Auto-generated method stub + + } + + @Override + public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment) + { + // TODO Auto-generated method stub + return null; + } + + @Override + public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment) + { + // TODO Auto-generated method stub + return null; + } + + @Override + protected StructureMappingcommandSet[] getColourBySequenceCommands( + String[] files, SequenceRenderer sr, AlignmentViewPanel avp) + { + // TODO Auto-generated method stub + return null; + } + + @Override + public List getChainNames() + { + // TODO Auto-generated method stub + return null; + } + + @Override + protected void colourBySequence( + StructureMappingcommandSet[] colourBySequenceCommands) + { + // TODO Auto-generated method stub + + } + + @Override + public void colourByCharge() + { + // TODO Auto-generated method stub + + } + + @Override + public void colourByChain() + { + // TODO Auto-generated method stub + + } + }; + String[][] chains = binder.getChains(); + assertFalse(chains == null || chains[0] == null, + "No chains discovered by binding"); + assertEquals(2, chains[0].length); + assertEquals("A", chains[0][0]); + assertEquals("B", chains[0][1]); + } AAStructureBindingModel testee; AlignmentI al = null; @@ -121,16 +275,16 @@ public class AAStructureBindingModelTest StructureSelectionManager ssm = new StructureSelectionManager(); ssm.setMapping(new SequenceI[] { seq1a, seq1b }, null, PDB_1, - AppletFormatAdapter.PASTE); + DataSourceType.PASTE, null); ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2, - AppletFormatAdapter.PASTE); + DataSourceType.PASTE, null); ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3, - AppletFormatAdapter.PASTE); + DataSourceType.PASTE, null); testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, null) { @Override - public String[] getPdbFile() + public String[] getStructureFiles() { return new String[] { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" }; } @@ -155,6 +309,60 @@ public class AAStructureBindingModelTest { return null; } + + @Override + public void setJalviewColourScheme(ColourSchemeI cs) + { + } + + @Override + public String superposeStructures(AlignmentI[] als, int[] alm, + HiddenColumns[] 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; + } }; } @@ -168,17 +376,20 @@ public class AAStructureBindingModelTest /* * create a data bean to hold data per structure file */ - SuperposeData[] structs = new SuperposeData[testee.getPdbFile().length]; + SuperposeData[] structs = new SuperposeData[testee.getStructureFiles().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); @@ -188,12 +399,12 @@ 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 third sequence - assertFalse(matched[3]); // gap in fourth sequence - assertTrue(matched[4]); - assertTrue(matched[5]); // gap in second sequence + 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); @@ -218,13 +429,17 @@ 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); @@ -232,11 +447,11 @@ 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)); } }