+++ /dev/null
-package jalview.ext.rbvi.chimera;
-
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertNotNull;
-
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.testng.annotations.BeforeTest;
-import org.testng.annotations.Test;
-
-import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
-import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
-import jalview.gui.ChimeraViewFrame;
-import jalview.gui.JalviewChimeraBindingModel;
-import jalview.io.DataSourceType;
-import jalview.io.FileLoader;
-import jalview.structure.StructureCommandI;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
-import junit.extensions.PA;
-
-public class JalviewChimeraBindingTest
-{
- private AlignFrame af;
-
- @BeforeTest(alwaysRun = true)
- public void setup()
- {
- af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
- DataSourceType.FILE);
- }
-
- @Test(groups = "Functional")
- public void testBuildShowStructuresCommand()
- {
- AlignViewport av = af.getViewport();
- PDBEntry[] pdbs = new PDBEntry[] {};
- StructureSelectionManager ssm = new StructureSelectionManager();
- SequenceI seq1 = av.getAlignment().findSequenceMatch("FER1_SPIOL")[0];
- assertNotNull(seq1);
- SequenceI seq2 = av.getAlignment().findSequenceMatch("FER2_ARATH")[0];
- assertNotNull(seq2);
- SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
- JalviewChimeraBindingModel testee = new JalviewChimeraBindingModel(
- new ChimeraViewFrame(),
- ssm, pdbs, seqs, null);
-
- /*
- * with no structures mapped
- */
- StructureCommandI cmd = testee.buildShowStructuresCommand(av, true);
- assertEquals(cmd.getCommand(), "~display; ribbon; focus");
- cmd = testee.buildShowStructuresCommand(av, false);
- assertEquals(cmd.getCommand(), "~display; ribbon");
-
- /*
- * stub out a structure with chains A and B
- */
- Map<String, List<ChimeraModel>> chimeraMaps = (Map<String, List<ChimeraModel>>) PA
- .getValue(testee, "chimeraMaps");
- ChimeraModel model0 = new ChimeraModel("1A70", ModelType.PDB_MODEL, 0,
- 0);
- chimeraMaps.put("1a70.pdb", Arrays.asList(model0));
- ChimeraModel model1 = new ChimeraModel("4ZHO", ModelType.PDB_MODEL, 1,
- 0);
- chimeraMaps.put("4zho.pdb", Arrays.asList(model1));
-
- Map<String, String> chainFiles = (Map<String, String>) PA
- .getValue(testee, "chainFile");
- chainFiles.put("1A70:A", "1a70.pdb");
- chainFiles.put("1A70:B", "1a70.pdb");
- chainFiles.put("4ZHO:B", "4zho.pdb");
- chainFiles.put("4ZHO:C", "4zho.pdb");
-
- /*
- * map FER1_SPIOL residues 51-100 to residues 1-50 (atoms 1-250) in 1A70
- * and residues 110-147 to structure residues 60-97
- * (in fact there is no gap, added here for test purposes)
- */
- HashMap<Integer, int[]> map = new HashMap<>();
- for (int pos = 51; pos <= 100; pos++)
- {
- map.put(pos, new int[] { pos - 50, 5 * (pos - 50) });
- }
- for (int pos = 110; pos <= 147; pos++)
- {
- map.put(pos, new int[] { pos - 50, 5 * (pos - 50) });
- }
- StructureMapping sm1 = new StructureMapping(seq1, "1a70.pdb", "1A70",
- "A", map, null);
- ssm.addStructureMapping(sm1);
-
- /*
- * map FER2_ARATH residues 53-148 to residues 2-97 in 4ZHO
- */
- map = new HashMap<>();
- for (int pos = 53; pos <= 148; pos++)
- {
- map.put(pos, new int[] { pos - 51, 5 * (pos - 51) });
- }
- StructureMapping sm2 = new StructureMapping(seq2, "4zho.pdb", "4ZHO",
- "B", map, null);
- ssm.addStructureMapping(sm2);
-
- /*
- * select chain A only (hide chain B)
- */
- List<String> chainsToHide = (List<String>) PA.getValue(testee, "chainsToHide");
- chainsToHide.add("1A70:B");
- chainsToHide.add("4ZHO:C");
- cmd = testee.buildShowStructuresCommand(av, false);
- assertEquals(cmd.getCommand(),
- "~display; ribbon; ~ribbon #0:.B; ~ribbon #1:.C");
-
- /*
- * show alignment only, no chains hidden
- */
- chainsToHide.clear();
- testee.setShowAlignmentOnly(true);
- cmd = testee.buildShowStructuresCommand(av, false);
- assertEquals(cmd
- .getCommand(),
- "~display; ~ribbon; ribbon #0:1-50.A,60-97.A|#1:2-97.B");
-
- /*
- * now with a chain hidden
- */
- chainsToHide.add("4ZHO:C");
- cmd = testee.buildShowStructuresCommand(av, false);
- String expected = "~display; ~ribbon; ribbon #0:1-50.A,60-97.A|#1:2-97.B; ~ribbon #1:.C";
- assertEquals(cmd.getCommand(), expected);
-
- /*
- * hide columns in the mapped region - should not change the command (yet)
- */
- int fromCol = seq1.findIndex(60); // structure residue 10
- int toCol = seq1.findIndex(70); // structure residue 20
- av.hideColumns(fromCol - 1, toCol - 1);
- cmd = testee.buildShowStructuresCommand(av, false);
- assertEquals(cmd.getCommand(), expected);
-
- /*
- * select 'hide hidden columns'
- * command should now exclude these in both mapped sequences
- */
- testee.setHideHiddenRegions(true);
- cmd = testee.buildShowStructuresCommand(av, false);
- expected = "~display; ~ribbon; ribbon #0:1-9.A,21-50.A,60-97.A|#1:2-10.B,22-97.B; ~ribbon #1:.C";
- assertEquals(cmd.getCommand(), expected);
-
- /*
- * deselect 'show alignment only'
- * hide hidden columns is now ignored
- */
- testee.setShowAlignmentOnly(false);
- cmd = testee.buildShowStructuresCommand(av, false);
- assertEquals(cmd.getCommand(), "~display; ribbon; ~ribbon #1:.C");
- }
-}
git://source.jalview.org / jalview.git / blobdiff