X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModelTest.java;h=16452a57f4754ce4c8afdf669e27557cdc0dac13;hb=9dabc02511e3a334a5749a504f57f69d6c9017bd;hp=af02d5e3d85fd0d215485bb2f6abc38ec0fa29d7;hpb=14193747f3831242bc7dfac12394eb20eb0ba480;p=jalview.git diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java index af02d5e..16452a5 100644 --- a/test/jalview/structures/models/AAStructureBindingModelTest.java +++ b/test/jalview/structures/models/AAStructureBindingModelTest.java @@ -20,38 +20,45 @@ */ 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.AssertJUnit.assertTrue; +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.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.schemes.JalviewColourScheme; import jalview.structure.AtomSpec; -import jalview.structure.StructureMappingcommandSet; +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 @@ -139,110 +146,55 @@ public class AAStructureBindingModelTest @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) + protected List executeCommand(StructureCommandI command, + boolean getReply) { - // TODO Auto-generated method stub return null; } - + @Override - protected StructureMappingcommandSet[] getColourBySequenceCommands( - String[] files, SequenceRenderer sr, AlignmentViewPanel avp) + protected String getModelIdForFile(String chainId) { - // TODO Auto-generated method stub - return null; + return ""; } - + @Override - public List getChainNames() + protected ViewerType getViewerType() { - // 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]); + assertEquals(chains[0].length, 2); + assertEquals(chains[0][0], "A"); + assertEquals(chains[0][1], "B"); } AAStructureBindingModel testee; @@ -281,7 +233,22 @@ 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); + } + + /** + * A helper method to construct the test target object + * + * @param pdbFiles + * @param seqs + * @param ssm + */ + protected AAStructureBindingModel newBindingModel(PDBEntry[] pdbFiles, + SequenceI[][] seqs, + StructureSelectionManager ssm) + { + AAStructureBindingModel model = new AAStructureBindingModel(ssm, + pdbFiles, seqs, null) { @Override public String[] getStructureFiles() @@ -305,36 +272,6 @@ public class AAStructureBindingModelTest } @Override - public List getChainNames() - { - 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) { @@ -342,28 +279,37 @@ public class AAStructureBindingModelTest } @Override - protected void colourBySequence( - StructureMappingcommandSet[] colourBySequenceCommands) - { - } - - @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; } /** @@ -376,10 +322,10 @@ 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 @@ -394,7 +340,7 @@ public class AAStructureBindingModelTest int refStructure = testee .findSuperposableResidues(al, matched, structs); - assertEquals(0, refStructure); + assertEquals(refStructure, 0); /* * only ungapped, structure-mapped columns are superposable @@ -406,27 +352,28 @@ 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 @@ -444,7 +391,7 @@ 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)); @@ -454,4 +401,100 @@ 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 + */ + SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG"); + SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS"); + AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 }); + AlignFrame af = new AlignFrame(al, 800, 500); + 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); + SequenceRenderer sr = new jalview.gui.SequenceRenderer( + af.getViewport()); + SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } }; + String[] files = new String[] { "seq1.pdb", "seq2.pdb" }; + 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); + + /* + * method under test builds a map of structures residues by colour + * verify the map holds what it should + */ + Map colours = binding.buildColoursMap(ssm, files, + seqs, sr, 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