X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraXCommandsTest.java;h=03bfbcd19c783cccecaa31de874d956188c54feb;hb=1140532d01b32b648e7e5b17ea717ae790625f8f;hp=044a1d9820678c4b9ba23ef1c601b2c455cabced;hpb=9dabc02511e3a334a5749a504f57f69d6c9017bd;p=jalview.git diff --git a/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java index 044a1d9..03bfbcd 100644 --- a/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java +++ b/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java @@ -29,18 +29,28 @@ 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; -import jalview.structure.StructureCommandsI; +import jalview.structure.StructureCommandsI.AtomSpecType; public class ChimeraXCommandsTest { + private ChimeraXCommands testee; + + @BeforeClass(alwaysRun = true) + public void setUp() + { + testee = new ChimeraXCommands(); + } + @Test(groups = { "Functional" }) public void testColourByCharge() { - List cmd = new ChimeraXCommands().colourByCharge(); + 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"); @@ -49,18 +59,32 @@ public class ChimeraXCommandsTest @Test(groups = { "Functional" }) public void testColourByChain() { - StructureCommandI cmd = new ChimeraXCommands().colourByChain(); + StructureCommandI cmd = testee.colourByChain(); assertEquals(cmd.getCommand(), "rainbow chain"); } @Test(groups = { "Functional" }) public void testFocusView() { - StructureCommandI cmd = new ChimeraXCommands().focusView(); + 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<>(); @@ -78,8 +102,7 @@ public class ChimeraXCommandsTest * 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 = new ChimeraXCommands() - .colourBySequence(map); + 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"); @@ -93,16 +116,14 @@ 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(); - List commands = commandGenerator - .setAttributes(featuresMap); + + List commands = testee.setAttributes(featuresMap); assertEquals(commands.size(), 1); /* @@ -116,7 +137,7 @@ public class ChimeraXCommandsTest 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); + commands = testee.setAttributes(featuresMap); assertEquals(commands.size(), 1); assertEquals(commands.get(0).getCommand(), "setattr #0/A:3-25 res jv_chain 'X' create true"); @@ -125,34 +146,31 @@ public class ChimeraXCommandsTest 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); + 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.setAttributes(featuresMap); + 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 String cmd1 = commands.get(0).getCommand(); String cmd2 = commands.get(1).getCommand(); - assertTrue( - cmd1.equals(expected1) || cmd2.equals(expected1)); + 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)); + 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.get(0).getCommand().equals(expected3)); @@ -161,7 +179,6 @@ public class ChimeraXCommandsTest @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"); @@ -171,7 +188,7 @@ public class ChimeraXCommandsTest toAlign.addRange("2", 20, 21, "B"); toAlign.addRange("2", 22, 22, "C"); List command = testee.superposeStructures(ref, - toAlign); + toAlign, AtomSpecType.ALPHA); assertEquals(command.size(), 1); String cmd = command.get(0).getCommand(); String refSpec = "#1/A:12-14/B:18,22-23"; @@ -182,97 +199,100 @@ public class ChimeraXCommandsTest * ribbon command does not */ String expected = String.format( - "align %s@CA toAtoms %s@CA; ribbon %s|%s; view", - toAlignSpec, refSpec, toAlignSpec, refSpec); + "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), ""); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), ""); model.addRange("1", 2, 4, "A"); - assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), + "#1/A:2-4"); model.addRange("1", 8, 8, "A"); - assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), + "#1/A:2-4,8"); model.addRange("1", 5, 7, "B"); - assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8/B:5-7"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), + "#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"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), + "#1/A:2-5,8/B:5-7"); model.addRange("0", 1, 4, "B"); - assertEquals(testee.getAtomSpec(model, false), + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#0/B:1-4|#1/A:2-5,8/B:5-7"); model.addRange("0", 5, 9, "C"); - assertEquals(testee.getAtomSpec(model, false), + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#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), + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#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), + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#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), + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#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), + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#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() { - StructureCommandsI testee = new ChimeraXCommands(); AtomSpecModel model = new AtomSpecModel(); - assertEquals(testee.getAtomSpec(model, true), ""); + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), ""); model.addRange("1", 2, 4, "A"); - assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4@CA"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), + "#1/A:2-4@CA"); model.addRange("1", 8, 8, "A"); - assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8@CA"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), + "#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"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), + "#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"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), + "#1/A:2-5,8/B:5-7@CA"); model.addRange("0", 1, 4, "B"); - assertEquals(testee.getAtomSpec(model, true), + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#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), + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#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), + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#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), + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#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), + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#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), + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#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(); List showBackbone = testee.showBackbone(); assertEquals(showBackbone.size(), 1); assertEquals(showBackbone.get(0).getCommand(), @@ -282,7 +302,6 @@ public class ChimeraXCommandsTest @Test(groups = "Functional") public void testOpenCommandFile() { - ChimeraCommands testee = new ChimeraXCommands(); assertEquals(testee.openCommandFile("nowhere").getCommand(), "open nowhere"); } @@ -290,29 +309,68 @@ public class ChimeraXCommandsTest @Test(groups = "Functional") public void testSaveSession() { - ChimeraCommands testee = new ChimeraXCommands(); assertEquals(testee.saveSession("somewhere").getCommand(), - "save session somewhere"); + "save somewhere format session"); } @Test(groups = "Functional") public void testGetColourCommand() { - ChimeraCommands testee = new ChimeraXCommands(); - assertEquals(testee.getColourCommand("something", Color.MAGENTA) - .getCommand(), + 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).getCommand(), - "setattr #1/A:89-92|#2/B:8-9,12-20 res phi '27.3' create true"); + 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")); } }