*/
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.AlignViewportI;
import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
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.schemes.ColourSchemeI;
+import jalview.io.FileFormats;
+import jalview.io.FileLoader;
+import jalview.schemes.JalviewColourScheme;
import jalview.structure.AtomSpec;
-import jalview.structure.StructureMappingcommandSet;
+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.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;
+import junit.extensions.PA;
/**
* Unit tests for non-abstract methods of abstract base class
+ "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<AtomSpec> atoms)
+ {
+ }
+
+ @Override
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
+ {
+ return null;
+ }
+
+ @Override
+ protected List<String> 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;
StructureSelectionManager ssm = new StructureSelectionManager();
ssm.setMapping(new SequenceI[] { seq1a, seq1b }, null, PDB_1,
- DataSourceType.PASTE);
+ DataSourceType.PASTE, null);
ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2,
- DataSourceType.PASTE);
+ DataSourceType.PASTE, null);
ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3,
- DataSourceType.PASTE);
+ DataSourceType.PASTE, null);
+
+ testee = newBindingModel(pdbFiles, seqs, ssm, null);
+ }
- testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, 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
}
@Override
- public List<String> 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)
+ public SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel avp)
{
+ return avp == null ? null
+ : new jalview.gui.SequenceRenderer(
+ avp.getAlignViewport());
}
@Override
- protected StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, FeatureRenderer fr,
- AlignViewportI viewport)
+ protected List<String> 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 FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+ protected String getModelIdForFile(String pdbfile)
{
- return null;
+ for (int i = 0; i < this.getPdbCount(); i++)
+ {
+ if (pdbfile.equals(this.getPdbEntry(i).getFile()))
+ {
+ return String.valueOf(i);
+ }
+ }
+ return "";
}
@Override
- public SequenceRenderer getSequenceRenderer(
- AlignmentViewPanel alignment)
+ protected ViewerType getViewerType()
{
return null;
}
-
- @Override
- protected void colourBySequence(
- StructureMappingcommandSet[] colourBySequenceCommands)
- {
- }
-
- @Override
- public void colourByChain()
- {
- }
-
- @Override
- public void colourByCharge()
- {
- }
};
+ PA.setValue(model, "commandGenerator", new ChimeraCommands());
+ return model;
}
/**
/*
* 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 BitSet of 'superposable columns' to true (would be false for
int refStructure = testee
.findSuperposableResidues(al, matched, structs);
- assertEquals(0, refStructure);
+ assertEquals(refStructure, 0);
/*
* only ungapped, structure-mapped columns are superposable
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
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));
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<Integer, int[]> 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<Object, AtomSpecModel> 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
git://source.jalview.org / jalview.git / blobdiff