X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModelTest.java;h=1a2cb84585dfafe22d09b1feb6cffe64b7a74905;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=0d0016979890f98bf845e7ba24431bf2cad22a8b;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java index 0d00169..1a2cb84 100644 --- a/test/jalview/structures/models/AAStructureBindingModelTest.java +++ b/test/jalview/structures/models/AAStructureBindingModelTest.java @@ -20,26 +20,47 @@ */ package jalview.structures.models; -import static org.testng.AssertJUnit.assertEquals; -import static org.testng.AssertJUnit.assertFalse; -import static org.testng.AssertJUnit.assertTrue; +import static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertFalse; +import static org.testng.Assert.assertNotNull; +import static org.testng.Assert.assertTrue; +import java.awt.Color; +import java.io.IOException; +import java.util.Arrays; +import java.util.BitSet; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +import org.testng.annotations.BeforeClass; +import org.testng.annotations.BeforeMethod; +import org.testng.annotations.Test; + +import jalview.api.AlignmentViewPanel; +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.ext.rbvi.chimera.ChimeraCommands; +import jalview.gui.AlignFrame; +import jalview.gui.JvOptionPane; +import jalview.gui.StructureViewer.ViewerType; +import jalview.io.DataSourceType; +import jalview.io.FileFormats; +import jalview.io.FileLoader; +import jalview.schemes.JalviewColourScheme; import jalview.structure.AtomSpec; +import jalview.structure.AtomSpecModel; +import jalview.structure.StructureCommandI; +import jalview.structure.StructureCommandsI.AtomSpecType; +import jalview.structure.StructureMapping; import jalview.structure.StructureSelectionManager; -import jalview.structures.models.AAStructureBindingModel.SuperposeData; - -import java.util.Arrays; -import java.util.List; - -import org.testng.annotations.BeforeMethod; -import org.testng.annotations.Test; +import junit.extensions.PA; /** * Unit tests for non-abstract methods of abstract base class @@ -49,6 +70,14 @@ 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 */ @@ -80,6 +109,96 @@ 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) + { + } + + @Override + public void releaseReferences(Object svl) + { + } + + @Override + public String[] getStructureFiles() + { + return null; + } + + @Override + public void highlightAtoms(List atoms) + { + } + + @Override + public SequenceRenderer getSequenceRenderer( + AlignmentViewPanel alignment) + { + return null; + } + + @Override + protected List executeCommand(StructureCommandI command, + boolean getReply) + { + return null; + } + + @Override + protected String getModelIdForFile(String chainId) + { + return ""; + } + + @Override + protected ViewerType getViewerType() + { + return null; + } + }; + String[][] chains = binder.getChains(); + assertFalse(chains == null || chains[0] == null, + "No chains discovered by binding"); + assertEquals(chains[0].length, 2); + assertEquals(chains[0][0], "A"); + assertEquals(chains[0][1], "B"); + } + AAStructureBindingModel testee; AlignmentI al = null; @@ -104,7 +223,6 @@ public class AAStructureBindingModelTest 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"); - String[][] chains = new String[3][]; SequenceI[][] seqs = new SequenceI[3][]; seqs[0] = new SequenceI[] { seq1a, seq1b }; seqs[1] = new SequenceI[] { seq2 }; @@ -112,18 +230,39 @@ 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 = newBindingModel(pdbFiles, seqs, ssm, null); + } - testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, chains, null) + /** + * A helper method to construct the test target object + * + * @param pdbFiles + * @param seqs + * @param ssm + * @param alignPanel + */ + protected AAStructureBindingModel newBindingModel(PDBEntry[] pdbFiles, + SequenceI[][] seqs, StructureSelectionManager ssm, + AlignmentViewPanel avp) + { + AAStructureBindingModel model = new AAStructureBindingModel(ssm, + pdbFiles, seqs, null) { @Override - public String[] getPdbFile() + public String[] getStructureFiles() { - return new String[] { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" }; + String[] files = new String[getPdbCount()]; + for (int i = 0; i < this.getPdbCount(); i++) + { + files[i] = getPdbEntry(i).getFile(); + } + return files; } @Override @@ -140,7 +279,46 @@ public class AAStructureBindingModelTest public void highlightAtoms(List atoms) { } + + @Override + public SequenceRenderer getSequenceRenderer(AlignmentViewPanel avp) + { + return avp == null ? null + : new jalview.gui.SequenceRenderer(avp.getAlignViewport()); + } + + @Override + protected List executeCommand(StructureCommandI command, + boolean getReply) + { + return null; + } + + /* + * for this test, let structure model ids be 0, 1, ... + * corresponding to first, second etc pdbfile + */ + @Override + protected String getModelIdForFile(String pdbfile) + { + for (int i = 0; i < this.getPdbCount(); i++) + { + if (pdbfile.equals(this.getPdbEntry(i).getFile())) + { + return String.valueOf(i); + } + } + return ""; + } + + @Override + protected ViewerType getViewerType() + { + return null; + } }; + PA.setValue(model, "commandGenerator", new ChimeraCommands()); + return model; } /** @@ -153,75 +331,187 @@ public class AAStructureBindingModelTest /* * create a data bean to hold data per structure file */ - SuperposeData[] structs = new SuperposeData[testee.getPdbFile().length]; + AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[testee + .getStructureFiles().length]; for (int i = 0; i < structs.length; i++) { - structs[i] = testee.new SuperposeData(al.getWidth()); + structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(), + "0"); } /* - * 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); + int refStructure = testee.findSuperposableResidues(al, matched, + structs); - assertEquals(0, refStructure); + assertEquals(refStructure, 0); /* * 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 - - 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); + 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(structs[0].pdbId, "1YCS"); + assertEquals(structs[1].pdbId, "3A6S"); + assertEquals(structs[2].pdbId, "1OOT"); + assertEquals(structs[0].chain, "A"); // ? struct has chains A _and_ B + assertEquals(structs[1].chain, "B"); + assertEquals(structs[2].chain, "A"); // 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)); + assertEquals(Arrays.toString(structs[0].pdbResNo), + "[0, 97, 98, 99, 100, 102]"); + assertEquals(Arrays.toString(structs[1].pdbResNo), + "[0, 2, 0, 3, 4, 5]"); + assertEquals(Arrays.toString(structs[2].pdbResNo), + "[0, 8, 0, 0, 10, 12]"); } @Test(groups = { "Functional" }) public void testFindSuperposableResidues_hiddenColumn() { - SuperposeData[] structs = new SuperposeData[al.getHeight()]; + AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[al + .getHeight()]; for (int i = 0; i < structs.length; i++) { - structs[i] = testee.new SuperposeData(al.getWidth()); + structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(), + "0"); } /* - * 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); + int refStructure = testee.findSuperposableResidues(al, matched, + structs); - assertEquals(0, refStructure); + assertEquals(refStructure, 0); // 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)); + } + + @Test(groups = { "Functional" }) + public void testBuildColoursMap() + { + /* + * load these sequences, coloured by Strand propensity, + * with columns 2-4 hidden + */ + String fasta = ">seq1\nMHRSQSSSGG\n>seq2\nMVRSNGGSSS"; + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta, + DataSourceType.PASTE); + AlignmentI al = af.getViewport().getAlignment(); + af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString()); + ColumnSelection cs = new ColumnSelection(); + cs.addElement(2); + cs.addElement(3); + cs.addElement(4); + af.getViewport().setColumnSelection(cs); + af.hideSelColumns_actionPerformed(null); + SequenceI seq1 = al.getSequenceAt(0); + SequenceI seq2 = al.getSequenceAt(1); + SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } }; + PDBEntry[] pdbFiles = new PDBEntry[2]; + pdbFiles[0] = new PDBEntry("PDB1", "A", Type.PDB, "seq1.pdb"); + pdbFiles[1] = new PDBEntry("PDB2", "B", Type.PDB, "seq2.pdb"); + StructureSelectionManager ssm = new StructureSelectionManager(); + + /* + * map residues 1-10 to residues 21-30 (atoms 105-150) in structures + */ + HashMap map = new HashMap<>(); + for (int pos = 1; pos <= seq1.getLength(); pos++) + { + map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) }); + } + StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1", + "A", map, null); + ssm.addStructureMapping(sm1); + StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2", + "B", map, null); + ssm.addStructureMapping(sm2); + + AAStructureBindingModel binding = newBindingModel(pdbFiles, seqs, ssm, + af.alignPanel); + + /* + * method under test builds a map of structures residues by colour + * verify the map holds what it should + */ + Map colours = binding.buildColoursMap(ssm, seqs, + af.alignPanel); + ChimeraCommands helper = new ChimeraCommands(); + + /* + * M colour is #82827d (see strand.html help page) + * sequence residue 1 mapped to structure residue 21 + */ + Color mColor = new Color(0x82827d); + AtomSpecModel atomSpec = colours.get(mColor); + assertNotNull(atomSpec); + assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY), + "#0:21.A|#1:21.B"); + + /* + * H colour is #60609f, seq1.2 mapped to structure 0 residue 22 + */ + Color hColor = new Color(0x60609f); + atomSpec = colours.get(hColor); + assertNotNull(atomSpec); + assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY), + "#0:22.A"); + + /* + * V colour is #ffff00, seq2.2 mapped to structure 1 residue 22 + */ + Color vColor = new Color(0xffff00); + atomSpec = colours.get(vColor); + assertNotNull(atomSpec); + assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY), + "#1:22.B"); + + /* + * hidden columns are Gray (128, 128, 128) + * sequence positions 3-5 mapped to structure residues 23-25 + */ + Color gray = new Color(128, 128, 128); + atomSpec = colours.get(gray); + assertNotNull(atomSpec); + assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY), + "#0:23-25.A|#1:23-25.B"); + + /* + * S and G are both coloured #4949b6, structure residues 26-30 + */ + Color sgColour = new Color(0x4949b6); + atomSpec = colours.get(sgColour); + assertNotNull(atomSpec); + assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY), + "#0:26-30.A|#1:26-30.B"); } -} +} \ No newline at end of file