X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraXCommandsTest.java;h=439401a86e7f83ae48216d312a129c6eb4f2438f;hb=6e0b6fc5ebc8ebb36cada5f6df8c9e7e4a995088;hp=ddda2c08b4b03946024fd9be544cf6d47ef4da9f;hpb=fea6f8ed76719fd78b600adfea8891dafb8c9d12;p=jalview.git diff --git a/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java index ddda2c0..439401a 100644 --- a/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java +++ b/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java @@ -23,61 +23,88 @@ package jalview.ext.rbvi.chimera; import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertTrue; -import jalview.structure.AtomSpecModel; -import jalview.structure.StructureCommandsI; - 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() { - String cmd = new ChimeraXCommands().colourByCharge(); - assertEquals(cmd, + 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 testColourByChain() { - String cmd = new ChimeraXCommands().colourByChain(); - assertEquals(cmd, "rainbow chain"); + StructureCommandI cmd = testee.colourByChain(); + assertEquals(cmd.getCommand(), "rainbow chain"); } @Test(groups = { "Functional" }) public void testFocusView() { - String cmd = new ChimeraXCommands().focusView(); - assertEquals(cmd, "view"); + 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, 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 - String[] commands = new ChimeraXCommands().colourBySequence(map); - assertEquals(commands.length, 1); - assertEquals( - commands[0], - "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"); + 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" }) @@ -88,81 +115,81 @@ public class ChimeraXCommandsTest */ 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(); - String[] commands = commandGenerator.setAttributes(featuresMap); - assertEquals(commands.length, 1); + 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[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.setAttributes(featuresMap); - assertEquals(commands.length, 1); - assertEquals(commands[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.setAttributes(featuresMap); - assertEquals(commands.length, 1); + 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[0], expected1); + assertEquals(commands.get(0).getCommand(), expected1); // same feature, different value - ChimeraCommands.addAtomSpecRange(featureValues, "Y", 0, 40, 50, "A"); - commands = commandGenerator.setAttributes(featuresMap); - assertEquals(2, commands.length); + 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 test for the expected command in either order - assertTrue( - commands[0].equals(expected1) || commands[1].equals(expected1)); + 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( - commands[0].equals(expected2) || commands[1].equals(expected2)); + 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.setAttributes(featuresMap); + 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[0].equals(expected3) || commands[1].equals(expected3)); + 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"; @@ -171,41 +198,40 @@ public class ChimeraXCommandsTest * ribbon command does not */ String expected = String.format( - "align %s@CA|P toAtoms %s@CA|P; ribbon %s|%s; view", - 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() { - StructureCommandsI testee = new ChimeraXCommands(); AtomSpecModel model = new AtomSpecModel(); assertEquals(testee.getAtomSpec(model, false), ""); - model.addRange(1, 2, 4, "A"); + model.addRange("1", 2, 4, "A"); assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4"); - model.addRange(1, 8, 8, "A"); + model.addRange("1", 8, 8, "A"); assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8"); - model.addRange(1, 5, 7, "B"); + 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"); + 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"); + 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"); + 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"); + 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"); + 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 + 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, " "); + 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"); } @@ -213,89 +239,126 @@ public class ChimeraXCommandsTest @Test(groups = "Functional") public void testGetAtomSpec_alphaOnly() { - StructureCommandsI testee = new ChimeraXCommands(); 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|P"); - model.addRange(1, 8, 8, "A"); - assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8@CA|P"); - model.addRange(1, 5, 7, "B"); - assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8/B:5-7@CA|P"); - model.addRange(1, 3, 5, "A"); - assertEquals(testee.getAtomSpec(model, true), "#1/A:2-5,8/B:5-7@CA|P"); - model.addRange(0, 1, 4, "B"); + 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|P|#1/A:2-5,8/B:5-7@CA|P"); - model.addRange(0, 5, 9, "C"); + "#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|P|#1/A:2-5,8/B:5-7@CA|P"); - model.addRange(1, 8, 10, "B"); + "#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|P|#1/A:2-5,8/B:5-10@CA|P"); - model.addRange(1, 8, 9, "B"); + "#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|P|#1/A:2-5,8/B:5-10@CA|P"); - model.addRange(0, 3, 10, "C"); // subsumes 5-9 + "#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|P|#1/A:2-5,8/B:5-10@CA|P"); - model.addRange(5, 25, 35, " "); // empty chain code + "#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|P|#1/A:2-5,8/B:5-10@CA|P|#5/:25-35@CA|P"); + "#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() { - StructureCommandsI testee = new ChimeraXCommands(); assertEquals(testee.getModelStartNo(), 1); } @Test(groups = "Functional") public void testGetResidueSpec() { - ChimeraCommands testee = new ChimeraXCommands(); assertEquals(testee.getResidueSpec("ALA"), ":ALA"); } @Test(groups = "Functional") public void testShowBackbone() { - ChimeraCommands testee = new ChimeraXCommands(); - assertEquals(testee.showBackbone(), "~display all;show @CA|P pbonds"); + 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() { - ChimeraCommands testee = new ChimeraXCommands(); - assertEquals(testee.openCommandFile("nowhere"), "open nowhere"); + assertEquals(testee.openCommandFile("nowhere").getCommand(), + "open nowhere"); } @Test(groups = "Functional") public void testSaveSession() { - ChimeraCommands testee = new ChimeraXCommands(); - assertEquals(testee.saveSession("somewhere"), "save session somewhere"); + assertEquals(testee.saveSession("somewhere").getCommand(), + "save somewhere format session"); } @Test(groups = "Functional") public void testGetColourCommand() { - ChimeraCommands testee = new ChimeraXCommands(); - assertEquals(testee.getColourCommand("something", Color.MAGENTA), + assertEquals(testee.colourResidues("something", Color.MAGENTA) + .getCommand(), "color something #ff00ff"); } @Test(groups = "Functional") public void testSetAttribute() { - ChimeraCommands testee = new ChimeraXCommands(); 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("phi", "27.3", model), - "setattr #1/A:89-92|#2/B:8-9,12-20 res phi '27.3' create true"); + 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")); } }