X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommandsTest.java;h=d71b5fd640673c4b9208ced07ec369d1e3475bd0;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=f08702066ae2d906d7f6097741dfb2adea3ddfa7;hpb=9dabc02511e3a334a5749a504f57f69d6c9017bd;p=jalview.git diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java index f087020..d71b5fd 100644 --- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java +++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java @@ -29,14 +29,23 @@ 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 ChimeraCommandsTest { + private ChimeraCommands testee; + + @BeforeClass(alwaysRun = true) + public void setUp() + { + testee = new ChimeraCommands(); + } @Test(groups = { "Functional" }) public void testColourBySequence() @@ -55,8 +64,7 @@ public class ChimeraCommandsTest // 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 ChimeraCommands() - .colourBySequence(map); + List commands = testee.colourBySequence(map); assertEquals(commands.size(), 1); assertEquals(commands.get(0).getCommand(), "color #0000ff #0:2-5.A,9-23.A,7.B|#1:1.A,4-7.B;color #ffff00 #1:3-5.A,8.A;color #ff0000 #0:3-9.A"); @@ -70,16 +78,14 @@ public class ChimeraCommandsTest */ 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"); - - ChimeraCommands commandGenerator = new ChimeraCommands(); - List commands = commandGenerator - .setAttributes(featuresMap); + + List commands = testee.setAttributes(featuresMap); assertEquals(1, commands.size()); /* @@ -93,7 +99,7 @@ public class ChimeraCommandsTest 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(1, commands.size()); assertEquals(commands.get(0).getCommand(), "setattr res jv_chain 'X' #0:3-25.A"); @@ -102,14 +108,14 @@ public class ChimeraCommandsTest 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(1, commands.size()); String expected1 = "setattr res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A"; 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 @@ -123,11 +129,10 @@ public class ChimeraCommandsTest 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 res jv_side_chain_binding_ 'metal 'ion!' #0:7-15.A"; assertTrue(commands.get(0).getCommand().equals(expected3)); @@ -135,55 +140,56 @@ public class ChimeraCommandsTest /** * Tests for the method that prefixes and sanitises a feature name so it can - * be used as a valid, namespaced attribute name in Chimera + * be used as a valid, namespaced attribute name in Chimera or PyMol */ @Test(groups = { "Functional" }) public void testMakeAttributeName() { - assertEquals(ChimeraCommands.makeAttributeName(null), "jv_"); - assertEquals(ChimeraCommands.makeAttributeName(""), "jv_"); - assertEquals(ChimeraCommands.makeAttributeName("helix"), "jv_helix"); - assertEquals(ChimeraCommands.makeAttributeName("Hello World 24"), + assertEquals(testee.makeAttributeName(null), "jv_"); + assertEquals(testee.makeAttributeName(""), "jv_"); + assertEquals(testee.makeAttributeName("helix"), "jv_helix"); + assertEquals(testee.makeAttributeName("Hello World 24"), "jv_Hello_World_24"); - assertEquals( - ChimeraCommands.makeAttributeName("!this is-a_very*{odd(name"), + assertEquals(testee.makeAttributeName("!this is-a_very*{odd(name"), "jv__this_is_a_very__odd_name"); // name ending in color gets underscore appended - assertEquals(ChimeraCommands.makeAttributeName("helixColor"), - "jv_helixColor_"); + assertEquals(testee.makeAttributeName("helixColor"), "jv_helixColor_"); } @Test(groups = "Functional") public void testGetAtomSpec() { - StructureCommandsI testee = new ChimeraCommands(); 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), "#1:2-4.A"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), + "#1:2-4.A"); model.addRange("1", 8, 8, "A"); - assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A,8.A"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), + "#1:2-4.A,8.A"); model.addRange("1", 5, 7, "B"); - assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A,8.A,5-7.B"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), + "#1:2-4.A,8.A,5-7.B"); model.addRange("1", 3, 5, "A"); - assertEquals(testee.getAtomSpec(model, false), "#1:2-5.A,8.A,5-7.B"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), + "#1:2-5.A,8.A,5-7.B"); model.addRange("0", 1, 4, "B"); - assertEquals(testee.getAtomSpec(model, false), + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#0:1-4.B|#1:2-5.A,8.A,5-7.B"); model.addRange("0", 5, 9, "C"); - assertEquals(testee.getAtomSpec(model, false), + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-7.B"); model.addRange("1", 8, 10, "B"); - assertEquals(testee.getAtomSpec(model, false), + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B"); model.addRange("1", 8, 9, "B"); - assertEquals(testee.getAtomSpec(model, false), + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B"); model.addRange("0", 3, 10, "C"); // subsumes 5-9 - assertEquals(testee.getAtomSpec(model, false), + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B"); model.addRange("5", 25, 35, " "); - assertEquals(testee.getAtomSpec(model, false), + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B|#5:25-35."); } @@ -191,7 +197,6 @@ public class ChimeraCommandsTest @Test(groups = { "Functional" }) public void testSuperposeStructures() { - StructureCommandsI testee = new ChimeraCommands(); AtomSpecModel ref = new AtomSpecModel(); ref.addRange("1", 12, 14, "A"); ref.addRange("1", 18, 18, "B"); @@ -201,74 +206,70 @@ public class ChimeraCommandsTest toAlign.addRange("2", 20, 21, "B"); toAlign.addRange("2", 22, 22, "C"); List command = testee.superposeStructures(ref, - toAlign); + toAlign, AtomSpecType.ALPHA); // qualifier to restrict match to CA and no altlocs String carbonAlphas = "@CA&~@.B-Z&~@.2-9"; String refSpec = "#1:12-14.A,18.B,22-23.B"; String toAlignSpec = "#2:15-17.B,20-21.B,22.C"; - String expected = String.format( - "match %s%s %s%s; ribbon %s|%s; focus", toAlignSpec, - carbonAlphas, refSpec, carbonAlphas, toAlignSpec, refSpec); + String expected = String.format("match %s%s %s%s; ribbon %s|%s; focus", + toAlignSpec, carbonAlphas, refSpec, carbonAlphas, toAlignSpec, + refSpec); assertEquals(command.get(0).getCommand(), expected); } @Test(groups = "Functional") public void testGetAtomSpec_alphaOnly() { - StructureCommandsI testee = new ChimeraCommands(); 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), + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1:2-4.A@CA&~@.B-Z&~@.2-9"); model.addRange("1", 8, 8, "A"); - assertEquals(testee.getAtomSpec(model, true), + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1:2-4.A,8.A@CA&~@.B-Z&~@.2-9"); model.addRange("1", 5, 7, "B"); - assertEquals(testee.getAtomSpec(model, true), + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1:2-4.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9"); model.addRange("1", 3, 5, "A"); - assertEquals(testee.getAtomSpec(model, true), + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9"); model.addRange("0", 1, 4, "B"); - assertEquals(testee.getAtomSpec(model, true), + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#0:1-4.B@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9"); model.addRange("0", 5, 9, "C"); - assertEquals(testee.getAtomSpec(model, true), + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9"); model.addRange("1", 8, 10, "B"); - assertEquals(testee.getAtomSpec(model, true), + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9"); model.addRange("1", 8, 9, "B"); - assertEquals(testee.getAtomSpec(model, true), + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9"); model.addRange("0", 3, 10, "C"); // subsumes 5-9 - assertEquals(testee.getAtomSpec(model, true), + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#0:1-4.B,3-10.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9"); model.addRange("5", 25, 35, " "); // empty chain code - assertEquals(testee.getAtomSpec(model, true), + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#0:1-4.B,3-10.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9|#5:25-35.@CA&~@.B-Z&~@.2-9"); - + } @Test(groups = "Functional") public void testGetModelStartNo() { - StructureCommandsI testee = new ChimeraCommands(); assertEquals(testee.getModelStartNo(), 0); } @Test(groups = "Functional") public void testGetResidueSpec() { - ChimeraCommands testee = new ChimeraCommands(); assertEquals(testee.getResidueSpec("ALA"), "::ALA"); } @Test(groups = "Functional") public void testShowBackbone() { - ChimeraCommands testee = new ChimeraCommands(); List cmds = testee.showBackbone(); assertEquals(cmds.size(), 1); assertEquals(cmds.get(0).getCommand(), @@ -278,7 +279,6 @@ public class ChimeraCommandsTest @Test(groups = "Functional") public void testOpenCommandFile() { - ChimeraCommands testee = new ChimeraCommands(); assertEquals(testee.openCommandFile("nowhere").getCommand(), "open cmd:nowhere"); } @@ -286,29 +286,116 @@ public class ChimeraCommandsTest @Test(groups = "Functional") public void testSaveSession() { - ChimeraCommands testee = new ChimeraCommands(); assertEquals(testee.saveSession("somewhere").getCommand(), "save somewhere"); } @Test(groups = "Functional") + public void testColourByChain() + { + assertEquals(testee.colourByChain().getCommand(), "rainbow chain"); + } + + @Test(groups = { "Functional" }) + public void testSetBackgroundColour() + { + StructureCommandI cmd = testee.setBackgroundColour(Color.PINK); + assertEquals(cmd.getCommand(), "set bgColor #ffafaf"); + } + + @Test(groups = { "Functional" }) + public void testLoadFile() + { + StructureCommandI cmd = testee.loadFile("/some/filepath"); + assertEquals(cmd.getCommand(), "open /some/filepath"); + } + + @Test(groups = { "Functional" }) + public void testOpenSession() + { + StructureCommandI cmd = testee.openSession("/some/filepath"); + assertEquals(cmd.getCommand(), "open chimera:/some/filepath"); + } + + @Test(groups = "Functional") + public void testColourByCharge() + { + List cmds = testee.colourByCharge(); + assertEquals(cmds.size(), 1); + assertEquals(cmds.get(0).getCommand(), + "color white;color red ::ASP,GLU;color blue ::LYS,ARG;color yellow ::CYS"); + } + + @Test(groups = "Functional") public void testGetColourCommand() { - ChimeraCommands testee = new ChimeraCommands(); - assertEquals(testee.getColourCommand("something", Color.MAGENTA) - .getCommand(), + assertEquals( + testee.colourResidues("something", Color.MAGENTA).getCommand(), "color #ff00ff something"); } @Test(groups = "Functional") + public void testFocusView() + { + assertEquals(testee.focusView().getCommand(), "focus"); + } + + @Test(groups = "Functional") public void testSetAttribute() { - ChimeraCommands testee = new ChimeraCommands(); 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 res phi '27.3' #1:89-92.A|#2:8-9.B,12-20.B"); + assertEquals(testee.setAttribute("jv_kd", "27.3", model).getCommand(), + "setattr res jv_kd '27.3' #1:89-92.A|#2:8-9.B,12-20.B"); + } + + @Test(groups = "Functional") + public void testCloseViewer() + { + assertEquals(testee.closeViewer(), new StructureCommand("stop really")); + } + + @Test(groups = "Functional") + public void testGetSelectedResidues() + { + assertEquals(testee.getSelectedResidues(), + new StructureCommand("list selection level residue")); + } + + @Test(groups = "Functional") + public void testListResidueAttributes() + { + assertEquals(testee.listResidueAttributes(), + new StructureCommand("list resattr")); + } + + @Test(groups = "Functional") + public void testGetResidueAttributes() + { + assertEquals(testee.getResidueAttributes("binding site"), + new StructureCommand("list residues attr 'binding site'")); + } + + @Test(groups = "Functional") + public void testStartNotifications() + { + List cmds = testee.startNotifications("to here"); + assertEquals(cmds.size(), 2); + assertEquals(cmds.get(0), + new StructureCommand("listen start models url to here")); + assertEquals(cmds.get(1), new StructureCommand( + "listen start select 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("listen stop models")); + assertEquals(cmds.get(1), + new StructureCommand("listen stop selection")); } }