X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraXCommandsTest.java;h=439401a86e7f83ae48216d312a129c6eb4f2438f;hb=refs%2Ftags%2FDevelop-2_11_2_0-d20210205;hp=a9eaca3695437445ba75c908ebe2b6e928f541fc;hpb=9c1a9d682a2664d525bfd0f38bae861292dc3921;p=jalview.git diff --git a/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java index a9eaca3..439401a 100644 --- a/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java +++ b/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java @@ -23,195 +23,342 @@ package jalview.ext.rbvi.chimera; import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertTrue; -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.SequenceRenderer; -import jalview.schemes.JalviewColourScheme; -import jalview.structure.AtomSpecModel; -import jalview.structure.StructureCommandsI; -import jalview.structure.StructureMapping; -import jalview.structure.StructureSelectionManager; - 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.structure.AtomSpecModel; +import jalview.structure.StructureCommand; +import jalview.structure.StructureCommandI; + public class ChimeraXCommandsTest { + private ChimeraXCommands testee; + + @BeforeClass(alwaysRun = true) + public void setUp() + { + testee = new ChimeraXCommands(); + } + + @Test(groups = { "Functional" }) + public void testColourByCharge() + { + List cmd = testee.colourByCharge(); + assertEquals(cmd.size(), 1); + assertEquals(cmd.get(0).getCommand(), + "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow"); + } @Test(groups = { "Functional" }) - public void testBuildColourCommands() + public void testColourByChain() { + StructureCommandI cmd = testee.colourByChain(); + assertEquals(cmd.getCommand(), "rainbow chain"); + } + + @Test(groups = { "Functional" }) + public void testFocusView() + { + StructureCommandI cmd = testee.focusView(); + assertEquals(cmd.getCommand(), "view"); + } + @Test(groups = { "Functional" }) + public void testSetBackgroundColour() + { + StructureCommandI cmd = testee.setBackgroundColour(Color.PINK); + assertEquals(cmd.getCommand(), "set bgColor #ffafaf"); + } + + @Test(groups = { "Functional" }) + public void testOpenSession() + { + StructureCommandI cmd = testee.openSession("/some/filepath"); + assertEquals(cmd.getCommand(), "open /some/filepath format session"); + } + + @Test(groups = { "Functional" }) + public void testColourBySequence() + { Map map = new LinkedHashMap<>(); - ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 2, 5, "A"); - ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 7, 7, "B"); - ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 9, 23, "A"); - ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 1, 1, "A"); - ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 4, 7, "B"); - ChimeraCommands.addAtomSpecRange(map, Color.yellow, 1, 8, 8, "A"); - ChimeraCommands.addAtomSpecRange(map, Color.yellow, 1, 3, 5, "A"); - ChimeraCommands.addAtomSpecRange(map, Color.red, 0, 3, 5, "A"); - ChimeraCommands.addAtomSpecRange(map, Color.red, 0, 6, 9, "A"); - - // Colours should appear in the Chimera command in the order in which - // they were added; within colour, by model, by chain, ranges in start order - String command = new ChimeraXCommands().buildColourCommands(map).get(0); - assertEquals( - command, - "color #0/A:2-5,9-23/B:7|#1/A:1/B:4-7 #0000ff; color #1/A:3-5,8 #ffff00; color #0/A:3-9 #ff0000"); + ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 2, 5, "A"); + ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 7, 7, "B"); + ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 9, 23, "A"); + ChimeraCommands.addAtomSpecRange(map, Color.blue, "2", 1, 1, "A"); + ChimeraCommands.addAtomSpecRange(map, Color.blue, "2", 4, 7, "B"); + ChimeraCommands.addAtomSpecRange(map, Color.yellow, "2", 8, 8, "A"); + ChimeraCommands.addAtomSpecRange(map, Color.yellow, "2", 3, 5, "A"); + ChimeraCommands.addAtomSpecRange(map, Color.red, "1", 3, 5, "A"); + ChimeraCommands.addAtomSpecRange(map, Color.red, "1", 6, 9, "A"); + + /* + * Colours should appear in the Chimera command in the order in which + * they were added; within colour, by model, by chain, ranges in start order + */ + List commands = testee.colourBySequence(map); + assertEquals(commands.size(), 1); + assertEquals(commands.get(0).getCommand(), + "color #1/A:2-5,9-23/B:7|#2/A:1/B:4-7 #0000ff;color #2/A:3-5,8 #ffff00;color #1/A:3-9 #ff0000"); } @Test(groups = { "Functional" }) - public void testBuildSetAttributeCommands() + public void testSetAttributes() { /* * make a map of { featureType, {featureValue, {residue range specification } } } */ Map> featuresMap = new LinkedHashMap<>(); Map featureValues = new HashMap<>(); - + /* * start with just one feature/value... */ featuresMap.put("chain", featureValues); - ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 8, 20, "A"); - - ChimeraXCommands commandGenerator = new ChimeraXCommands(); - List commands = commandGenerator - .buildSetAttributeCommands(featuresMap); - assertEquals(1, commands.size()); + ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A"); + + List commands = testee.setAttributes(featuresMap); + assertEquals(commands.size(), 1); /* * feature name gets a jv_ namespace prefix * feature value is quoted in case it contains spaces */ - assertEquals(commands.get(0), + assertEquals(commands.get(0).getCommand(), "setattr #0/A:8-20 res jv_chain 'X' create true"); // add same feature value, overlapping range - ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 3, 9, "A"); + ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 3, 9, "A"); // same feature value, contiguous range - ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "A"); - commands = commandGenerator.buildSetAttributeCommands(featuresMap); - assertEquals(1, commands.size()); - assertEquals(commands.get(0), + ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A"); + commands = testee.setAttributes(featuresMap); + assertEquals(commands.size(), 1); + assertEquals(commands.get(0).getCommand(), "setattr #0/A:3-25 res jv_chain 'X' create true"); // same feature value and model, different chain - ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "B"); + ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "B"); // same feature value and chain, different model - ChimeraCommands.addAtomSpecRange(featureValues, "X", 1, 26, 30, "A"); - commands = commandGenerator.buildSetAttributeCommands(featuresMap); - assertEquals(1, commands.size()); - assertEquals(commands.get(0), - "setattr #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true"); + ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A"); + commands = testee.setAttributes(featuresMap); + assertEquals(commands.size(), 1); + String expected1 = "setattr #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true"; + assertEquals(commands.get(0).getCommand(), expected1); // same feature, different value - ChimeraCommands.addAtomSpecRange(featureValues, "Y", 0, 40, 50, "A"); - commands = commandGenerator.buildSetAttributeCommands(featuresMap); + ChimeraCommands.addAtomSpecRange(featureValues, "Y", "0", 40, 50, "A"); + commands = testee.setAttributes(featuresMap); assertEquals(2, commands.size()); // commands are ordered by feature type but not by value - // so use contains to test for the expected command: - assertTrue(commands - .contains( - "setattr #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true")); - assertTrue(commands - .contains("setattr #0/A:40-50 res jv_chain 'Y' create true")); + // so test for the expected command in either order + String cmd1 = commands.get(0).getCommand(); + String cmd2 = commands.get(1).getCommand(); + assertTrue(cmd1.equals(expected1) || cmd2.equals(expected1)); + String expected2 = "setattr #0/A:40-50 res jv_chain 'Y' create true"; + assertTrue(cmd1.equals(expected2) || cmd2.equals(expected2)); featuresMap.clear(); featureValues.clear(); featuresMap.put("side-chain binding!", featureValues); ChimeraCommands.addAtomSpecRange(featureValues, - "metal 'ion!", 0, 7, 15, - "A"); + "metal 'ion!", "0", 7, 15, "A"); // feature names are sanitised to change non-alphanumeric to underscore // feature values are sanitised to encode single quote characters - commands = commandGenerator.buildSetAttributeCommands(featuresMap); - assertTrue(commands.contains( - "setattr #0/A:7-15 res jv_side_chain_binding_ 'metal 'ion!' create true")); - } - - @Test(groups = { "Functional" }) - public void testColourBySequence_hiddenColumns() - { - /* - * 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(); - - /* - * 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 ChimeraXCommands() - .colourBySequence(ssm, files, seqs, sr, af.alignPanel); - assertEquals(1, commands.length); - String theCommand = commands[0]; - // M colour is #82827d (see strand.html help page) - assertTrue(theCommand.contains("color #0/A:21|#1/B:21 #82827d"));// #0:21.A|#1:21.B")); - // H colour is #60609f - assertTrue(theCommand.contains("color #0/A:22 #60609f")); - // V colour is #ffff00 - assertTrue(theCommand.contains("color #1/B:22 #ffff00")); - // hidden columns are Gray (128, 128, 128) - assertTrue(theCommand.contains("color #0/A:23-25|#1/B:23-25")); - // S and G are both coloured #4949b6 - assertTrue(theCommand.contains("color #0/A:26-30|#1/B:26-30")); + commands = testee.setAttributes(featuresMap); + assertEquals(commands.size(), 1); + String expected3 = "setattr #0/A:7-15 res jv_side_chain_binding_ 'metal 'ion!' create true"; + assertTrue(commands.get(0).getCommand().equals(expected3)); } @Test(groups = { "Functional" }) public void testSuperposeStructures() { - StructureCommandsI testee = new ChimeraXCommands(); AtomSpecModel ref = new AtomSpecModel(); - ref.addRange(1, 12, 14, "A"); - ref.addRange(1, 18, 18, "B"); - ref.addRange(1, 22, 23, "B"); + 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"); - String command = testee.superposeStructures(ref, toAlign); + 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 cmd = command.get(0).getCommand(); String refSpec = "#1/A:12-14/B:18,22-23"; String toAlignSpec = "#2/B:15-17,20-21/C:22"; + + /* + * superposition arguments include AlphaCarbon restriction, + * ribbon command does not + */ String expected = String.format( - "align %s %s;~display all; chain @CA|P; ribbon %s|%s; focus", - refSpec, toAlignSpec, refSpec, toAlignSpec); - assertEquals(command, expected); + "align %s@CA toAtoms %s@CA; ribbon %s|%s; view", toAlignSpec, + refSpec, toAlignSpec, refSpec); + assertEquals(cmd, expected); + } + + @Test(groups = "Functional") + public void testGetAtomSpec() + { + AtomSpecModel model = new AtomSpecModel(); + assertEquals(testee.getAtomSpec(model, false), ""); + model.addRange("1", 2, 4, "A"); + assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4"); + model.addRange("1", 8, 8, "A"); + assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8"); + model.addRange("1", 5, 7, "B"); + assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8/B:5-7"); + model.addRange("1", 3, 5, "A"); + assertEquals(testee.getAtomSpec(model, false), "#1/A:2-5,8/B:5-7"); + model.addRange("0", 1, 4, "B"); + assertEquals(testee.getAtomSpec(model, false), + "#0/B:1-4|#1/A:2-5,8/B:5-7"); + model.addRange("0", 5, 9, "C"); + assertEquals(testee.getAtomSpec(model, false), + "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-7"); + model.addRange("1", 8, 10, "B"); + assertEquals(testee.getAtomSpec(model, false), + "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10"); + model.addRange("1", 8, 9, "B"); + assertEquals(testee.getAtomSpec(model, false), + "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10"); + model.addRange("0", 3, 10, "C"); // subsumes 5-9 + assertEquals(testee.getAtomSpec(model, false), + "#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10"); + model.addRange("5", 25, 35, " "); + assertEquals(testee.getAtomSpec(model, false), + "#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10|#5/:25-35"); + } + + @Test(groups = "Functional") + public void testGetAtomSpec_alphaOnly() + { + AtomSpecModel model = new AtomSpecModel(); + assertEquals(testee.getAtomSpec(model, true), ""); + model.addRange("1", 2, 4, "A"); + assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4@CA"); + model.addRange("1", 8, 8, "A"); + assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8@CA"); + model.addRange("1", 5, 7, "B"); + assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8/B:5-7@CA"); + model.addRange("1", 3, 5, "A"); + assertEquals(testee.getAtomSpec(model, true), "#1/A:2-5,8/B:5-7@CA"); + model.addRange("0", 1, 4, "B"); + assertEquals(testee.getAtomSpec(model, true), + "#0/B:1-4@CA|#1/A:2-5,8/B:5-7@CA"); + model.addRange("0", 5, 9, "C"); + assertEquals(testee.getAtomSpec(model, true), + "#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-7@CA"); + model.addRange("1", 8, 10, "B"); + assertEquals(testee.getAtomSpec(model, true), + "#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA"); + model.addRange("1", 8, 9, "B"); + assertEquals(testee.getAtomSpec(model, true), + "#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA"); + model.addRange("0", 3, 10, "C"); // subsumes 5-9 + assertEquals(testee.getAtomSpec(model, true), + "#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA"); + model.addRange("5", 25, 35, " "); // empty chain code + assertEquals(testee.getAtomSpec(model, true), + "#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA|#5/:25-35@CA"); + } + + @Test(groups = "Functional") + public void testGetModelStartNo() + { + assertEquals(testee.getModelStartNo(), 1); + } + + @Test(groups = "Functional") + public void testGetResidueSpec() + { + assertEquals(testee.getResidueSpec("ALA"), ":ALA"); + } + + @Test(groups = "Functional") + public void testShowBackbone() + { + List showBackbone = testee.showBackbone(); + assertEquals(showBackbone.size(), 1); + assertEquals(showBackbone.get(0).getCommand(), + "~display all;~ribbon;show @CA|P atoms"); + } + + @Test(groups = "Functional") + public void testOpenCommandFile() + { + assertEquals(testee.openCommandFile("nowhere").getCommand(), + "open nowhere"); + } + + @Test(groups = "Functional") + public void testSaveSession() + { + assertEquals(testee.saveSession("somewhere").getCommand(), + "save somewhere format session"); + } + + @Test(groups = "Functional") + public void testGetColourCommand() + { + assertEquals(testee.colourResidues("something", Color.MAGENTA) + .getCommand(), + "color something #ff00ff"); + } + + @Test(groups = "Functional") + public void testSetAttribute() + { + AtomSpecModel model = new AtomSpecModel(); + model.addRange("1", 89, 92, "A"); + model.addRange("2", 12, 20, "B"); + model.addRange("2", 8, 9, "B"); + assertEquals(testee.setAttribute("jv_kd", "27.3", model) + .getCommand(), + "setattr #1/A:89-92|#2/B:8-9,12-20 res jv_kd '27.3' create true"); + } + + @Test(groups = "Functional") + public void testCloseViewer() + { + assertEquals(testee.closeViewer(), new StructureCommand("exit")); + } + + @Test(groups = "Functional") + public void testGetSelectedResidues() + { + assertEquals(testee.getSelectedResidues(), + new StructureCommand("info selection level residue")); + } + + @Test(groups = "Functional") + public void testStartNotifications() + { + List cmds = testee.startNotifications("to here"); + assertEquals(cmds.size(), 2); + assertEquals(cmds.get(0), new StructureCommand("info notify start models jalview prefix ModelChanged url to here")); + assertEquals(cmds.get(1), new StructureCommand("info notify start selection jalview prefix SelectionChanged url to here")); + } + + @Test(groups = "Functional") + public void testStopNotifications() + { + List cmds = testee.stopNotifications(); + assertEquals(cmds.size(), 2); + assertEquals(cmds.get(0), new StructureCommand("info notify stop models jalview")); + assertEquals(cmds.get(1), new StructureCommand("info notify stop selection jalview")); + } + + @Test(groups = "Functional") + public void testListResidueAttributes() + { + assertEquals(testee.listResidueAttributes(), + new StructureCommand("info resattr")); } }