X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fjmol%2FJmolCommandsTest.java;h=1ade00ee5be3cbaa240f044f00486a4e94446849;hb=c38d37887ae51d63942ac4321f6769308188ed6b;hp=439e188410d7df4c336f766c663bb8db8d3e5e4f;hpb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;p=jalview.git diff --git a/test/jalview/ext/jmol/JmolCommandsTest.java b/test/jalview/ext/jmol/JmolCommandsTest.java index 439e188..1ade00e 100644 --- a/test/jalview/ext/jmol/JmolCommandsTest.java +++ b/test/jalview/ext/jmol/JmolCommandsTest.java @@ -20,19 +20,33 @@ */ package jalview.ext.jmol; +import static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertTrue; + +import java.awt.Color; +import java.util.HashMap; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; + +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.gui.JvOptionPane; import jalview.gui.SequenceRenderer; -import jalview.structure.StructureMappingcommandSet; +import jalview.schemes.JalviewColourScheme; +import jalview.structure.AtomSpecModel; +import jalview.structure.StructureCommandI; +import jalview.structure.StructureCommandsI; +import jalview.structure.StructureMapping; import jalview.structure.StructureSelectionManager; -import org.testng.annotations.BeforeClass; -import org.testng.annotations.Test; - public class JmolCommandsTest { @@ -44,20 +58,165 @@ public class JmolCommandsTest } @Test(groups = { "Functional" }) - public void testGetColourBySequenceCommand_noFeatures() + public void testGetColourBySequenceCommands_hiddenColumns() { - SequenceI seq1 = new Sequence("seq1", "MHRSQTRALK"); - SequenceI seq2 = new Sequence("seq2", "MRLEITQSGD"); + /* + * 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 SequenceRenderer(af.getViewport()); SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } }; String[] files = new String[] { "seq1.pdb", "seq2.pdb" }; StructureSelectionManager ssm = new StructureSelectionManager(); - // need some mappings! + /* + * 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); + + String[] commands = new JmolCommands().colourBySequence(ssm, files, + seqs, sr, af.alignPanel); + assertEquals(commands.length, 2); + + String chainACommand = commands[0]; + // M colour is #82827d == (130, 130, 125) (see strand.html help page) + assertTrue( + chainACommand.contains("select 21:A/1.1;color[130,130,125]")); // first + // one + // H colour is #60609f == (96, 96, 159) + assertTrue(chainACommand.contains(";select 22:A/1.1;color[96,96,159]")); + // hidden columns are Gray (128, 128, 128) + assertTrue(chainACommand + .contains(";select 23-25:A/1.1;color[128,128,128]")); + // S and G are both coloured #4949b6 == (73, 73, 182) + assertTrue( + chainACommand.contains(";select 26-30:A/1.1;color[73,73,182]")); - StructureMappingcommandSet[] commands = JmolCommands - .getColourBySequenceCommand(ssm, files, seqs, sr, null, al); + String chainBCommand = commands[1]; + // M colour is #82827d == (130, 130, 125) + assertTrue( + chainBCommand.contains("select 21:B/2.1;color[130,130,125]")); + // V colour is #ffff00 == (255, 255, 0) + assertTrue(chainBCommand.contains(";select 22:B/2.1;color[255,255,0]")); + // hidden columns are Gray (128, 128, 128) + assertTrue(chainBCommand + .contains(";select 23-25:B/2.1;color[128,128,128]")); + // S and G are both coloured #4949b6 == (73, 73, 182) + assertTrue( + chainBCommand.contains(";select 26-30:B/2.1;color[73,73,182]")); + } + + @Test(groups = "Functional") + public void testGetAtomSpec() + { + StructureCommandsI testee = new JmolCommands(); + AtomSpecModel model = new AtomSpecModel(); + assertEquals(testee.getAtomSpec(model, false), ""); + model.addRange("1", 2, 4, "A"); + assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1"); + model.addRange("1", 8, 8, "A"); + assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1|8:A/1.1"); + model.addRange("1", 5, 7, "B"); + assertEquals(testee.getAtomSpec(model, false), + "2-4:A/1.1|8:A/1.1|5-7:B/1.1"); + model.addRange("1", 3, 5, "A"); + assertEquals(testee.getAtomSpec(model, false), + "2-5:A/1.1|8:A/1.1|5-7:B/1.1"); + model.addRange("2", 1, 4, "B"); + assertEquals(testee.getAtomSpec(model, false), + "2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1"); + model.addRange("2", 5, 9, "C"); + assertEquals(testee.getAtomSpec(model, false), + "2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1|5-9:C/2.1"); + model.addRange("1", 8, 10, "B"); + assertEquals(testee.getAtomSpec(model, false), + "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1"); + model.addRange("1", 8, 9, "B"); + assertEquals(testee.getAtomSpec(model, false), + "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1"); + model.addRange("2", 3, 10, "C"); // subsumes 5-9 + assertEquals(testee.getAtomSpec(model, false), + "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1"); + model.addRange("5", 25, 35, " "); + assertEquals(testee.getAtomSpec(model, false), + "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1|25-35:/5.1"); + + } + + @Test(groups = { "Functional" }) + public void testColourBySequence() + { + Map map = new LinkedHashMap<>(); + JmolCommands.addAtomSpecRange(map, Color.blue, "1", 2, 5, "A"); + JmolCommands.addAtomSpecRange(map, Color.blue, "1", 7, 7, "B"); + JmolCommands.addAtomSpecRange(map, Color.blue, "1", 9, 23, "A"); + JmolCommands.addAtomSpecRange(map, Color.blue, "2", 1, 1, "A"); + JmolCommands.addAtomSpecRange(map, Color.blue, "2", 4, 7, "B"); + JmolCommands.addAtomSpecRange(map, Color.yellow, "2", 8, 8, "A"); + JmolCommands.addAtomSpecRange(map, Color.yellow, "2", 3, 5, "A"); + JmolCommands.addAtomSpecRange(map, Color.red, "1", 3, 5, "A"); + JmolCommands.addAtomSpecRange(map, Color.red, "1", 6, 9, "A"); + + // Colours should appear in the Jmol command in the order in which + // they were added; within colour, by model, by chain, ranges in start order + List commands = new JmolCommands() + .colourBySequence(map); + assertEquals(commands.size(), 1); + String expected1 = "select 2-5:A/1.1|9-23:A/1.1|7:B/1.1|1:A/2.1|4-7:B/2.1;color[0,0,255]"; + String expected2 = "select 3-5:A/2.1|8:A/2.1;color[255,255,0]"; + String expected3 = "select 3-9:A/1.1;color[255,0,0]"; + assertEquals(commands.get(0).getCommand(), + expected1 + ";" + expected2 + ";" + expected3); + } + + @Test(groups = { "Functional" }) + public void testSuperposeStructures() + { + StructureCommandsI testee = new JmolCommands(); + AtomSpecModel ref = new AtomSpecModel(); + ref.addRange("1", 12, 14, "A"); + ref.addRange("1", 18, 18, "B"); + ref.addRange("1", 22, 23, "B"); + AtomSpecModel toAlign = new AtomSpecModel(); + toAlign.addRange("2", 15, 17, "B"); + toAlign.addRange("2", 20, 21, "B"); + toAlign.addRange("2", 22, 22, "C"); + List command = testee.superposeStructures(ref, + toAlign); + assertEquals(command.size(), 1); + String refSpec = "12-14:A/1.1|18:B/1.1|22-23:B/1.1"; + String toAlignSpec = "15-17:B/2.1|20-21:B/2.1|22:C/2.1"; + String expected = String.format( + "compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS {%s}{%s} ROTATE TRANSLATE ;select %s|%s;cartoons", + toAlignSpec, refSpec, toAlignSpec, refSpec); + assertEquals(command.get(0).getCommand(), expected); + } + + @Test(groups = "Functional") + public void testGetModelStartNo() + { + StructureCommandsI testee = new JmolCommands(); + assertEquals(testee.getModelStartNo(), 1); } }