X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModelTest.java;h=aea12b41eec768b6f328655abe61c964f40e4bfb;hb=8a43b8353b89a47002ef17c959ed61281fc4d826;hp=0bb1dafdc0d4d2f1bce8b2f10b3648dec2417174;hpb=55bfdb07355198ae1a1a8b5e14933b4669113ca6;p=jalview.git diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java index 0bb1daf..aea12b4 100644 --- a/test/jalview/structures/models/AAStructureBindingModelTest.java +++ b/test/jalview/structures/models/AAStructureBindingModelTest.java @@ -20,37 +20,46 @@ */ package jalview.structures.models; +import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertFalse; -import static org.testng.AssertJUnit.assertEquals; +import static org.testng.Assert.assertNotNull; import static org.testng.AssertJUnit.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.FeatureRenderer; import jalview.api.SequenceRenderer; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; -import jalview.datamodel.HiddenColumns; +import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; import jalview.datamodel.PDBEntry.Type; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; +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.schemes.ColourSchemeI; +import jalview.io.FileLoader; +import jalview.schemes.JalviewColourScheme; import jalview.structure.AtomSpec; +import jalview.structure.AtomSpecModel; +import jalview.structure.StructureCommandI; +import jalview.structure.StructureMapping; 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; -import org.testng.annotations.BeforeMethod; -import org.testng.annotations.Test; +import junit.extensions.PA; /** * Unit tests for non-abstract methods of abstract base class @@ -126,86 +135,19 @@ public class AAStructureBindingModelTest // 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[] + PDBEntry importedPDB = new PDBEntry("3A6S", "", Type.PDB, "Paste"); + AAStructureBindingModel binder = newBindingModel(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 String superposeStructures(AlignmentI[] alignments, - int[] structureIndices, HiddenColumns[] hiddenCols) - { - return null; - } - - @Override - public void setJalviewColourScheme(ColourSchemeI cs) - { - } - - @Override - public void setBackgroundColour(Color col) - { - } - - @Override - public void highlightAtoms(List atoms) - { - } - - @Override - public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment) - { - return null; - } - - @Override - public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment) - { - return null; - } - - @Override - protected void colourBySequence(AlignmentViewPanel avp) - { - } - - @Override - public void colourByCharge() - { - } - - @Override - public void colourByChain() - { - } - }; + { importedAl.getSequencesArray() }, + new StructureSelectionManager(), null); + 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]); + assertEquals(chains[0].length, 2); + assertEquals(chains[0][0], "A"); + assertEquals(chains[0][1], "B"); } AAStructureBindingModel testee; @@ -244,12 +186,33 @@ public class AAStructureBindingModelTest ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3, DataSourceType.PASTE, null); - testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, null) + testee = newBindingModel(pdbFiles, seqs, ssm, 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[] 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 @@ -268,51 +231,51 @@ public class AAStructureBindingModelTest } @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 public SequenceRenderer getSequenceRenderer( - AlignmentViewPanel alignment) + AlignmentViewPanel avp) { - return null; + return avp == null ? null + : new jalview.gui.SequenceRenderer( + avp.getAlignViewport()); } @Override - protected void colourBySequence(AlignmentViewPanel avp) - { - } - - @Override - public void colourByChain() + 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 - public void colourByCharge() + 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 - public FeatureRenderer getFeatureRenderer( - AlignmentViewPanel alignment) + protected ViewerType getViewerType() { return null; } }; + PA.setValue(model, "commandGenerator", new ChimeraCommands()); + return model; } /** @@ -325,10 +288,10 @@ public class AAStructureBindingModelTest /* * create a data bean to hold data per structure file */ - SuperposeData[] structs = new SuperposeData[testee.getStructureFiles().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 BitSet of 'superposable columns' to true (would be false for @@ -343,7 +306,7 @@ public class AAStructureBindingModelTest int refStructure = testee .findSuperposableResidues(al, matched, structs); - assertEquals(0, refStructure); + assertEquals(refStructure, 0); /* * only ungapped, structure-mapped columns are superposable @@ -355,27 +318,28 @@ public class AAStructureBindingModelTest 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); + 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 BitSet of 'superposable columns' to true (would be false for @@ -393,7 +357,7 @@ public class AAStructureBindingModelTest int refStructure = testee .findSuperposableResidues(al, matched, structs); - assertEquals(0, refStructure); + assertEquals(refStructure, 0); // only ungapped, structure-mapped columns are not superposable assertFalse(matched.get(0)); @@ -403,4 +367,100 @@ public class AAStructureBindingModelTest 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, false), "#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, false), "#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, false), "#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, false), "#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, false), + "#0:26-30.A|#1:26-30.B"); + } +} \ No newline at end of file