X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fpymol%2FPymolCommandsTest.java;h=d5dbc8604270d24afaca49236601300b73ab7b3b;hb=f1fa440f885429399436bb09ef6d0639c8acd991;hp=38031b685be12c8d5afd2a7129340eaf626ecc6b;hpb=2107a91322a1988a8a6b724c74f9d244795341e3;p=jalview.git diff --git a/test/jalview/ext/pymol/PymolCommandsTest.java b/test/jalview/ext/pymol/PymolCommandsTest.java index 38031b6..d5dbc86 100644 --- a/test/jalview/ext/pymol/PymolCommandsTest.java +++ b/test/jalview/ext/pymol/PymolCommandsTest.java @@ -21,20 +21,32 @@ package jalview.ext.pymol; 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.ext.rbvi.chimera.ChimeraCommands; import jalview.structure.AtomSpecModel; +import jalview.structure.StructureCommand; import jalview.structure.StructureCommandI; -import jalview.structure.StructureCommandsI; +import jalview.structure.StructureCommandsI.AtomSpecType; public class PymolCommandsTest { + private PymolCommands testee; + + @BeforeClass(alwaysRun = true) + public void setUp() + { + testee = new PymolCommands(); + } @Test(groups = { "Functional" }) public void testColourBySequence() @@ -53,47 +65,48 @@ public class PymolCommandsTest // Colours should appear in the Pymol command in the order in which // they were added; within colour, by model, by chain, ranges in start order - List commands = new PymolCommands() - .colourBySequence(map); + List commands = testee.colourBySequence(map); assertEquals(commands.size(), 3); - assertEquals(commands.get(0).toString(), - "color(0x0000ff,0//A/2-5+9-23/ 0//B/7/ 1//A/1/ 1//B/4-7/)"); - assertEquals(commands.get(1).toString(), "color(0xffff00,1//A/3-5+8/)"); - assertEquals( - commands.get(2).toString(), "color(0xff0000,0//A/3-9/)"); + assertEquals(commands.get(0), new StructureCommand("color", "0x0000ff", + "0//A/2-5+9-23/ 0//B/7/ 1//A/1/ 1//B/4-7/")); + assertEquals(commands.get( + 1), + new StructureCommand("color", "0xffff00", "1//A/3-5+8/")); + assertEquals(commands.get( + 2), + new StructureCommand("color", "0xff0000", "0//A/3-9/")); } @Test(groups = "Functional") public void testGetAtomSpec() { - StructureCommandsI testee = new PymolCommands(); 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/ 1//B/5-7/"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-4+8/ 1//B/5-7/"); model.addRange("1", 3, 5, "A"); - assertEquals(testee.getAtomSpec(model, false), "1//A/2-5+8/ 1//B/5-7/"); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-5+8/ 1//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/ 1//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/ 0//C/5-9/ 1//A/2-5+8/ 1//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/ 0//C/5-9/ 1//A/2-5+8/ 1//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/ 0//C/5-9/ 1//A/2-5+8/ 1//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/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/"); model.addRange("5", 25, 35, " "); - assertEquals(testee.getAtomSpec(model, false), + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/ 5///25-35/"); } @@ -101,7 +114,6 @@ public class PymolCommandsTest @Test(groups = { "Functional" }) public void testSuperposeStructures() { - StructureCommandsI testee = new PymolCommands(); AtomSpecModel ref = new AtomSpecModel(); ref.addRange("1", 12, 14, "A"); ref.addRange("1", 18, 18, "B"); @@ -111,121 +123,229 @@ public class PymolCommandsTest toAlign.addRange("2", 20, 21, "B"); toAlign.addRange("2", 22, 22, "C"); List commands = testee.superposeStructures(ref, - toAlign); - assertEquals(commands.size(), 2); - String refSpecCA = "1//A/12-14/CA 1//B/18+22-23/CA"; - String toAlignSpecCA = "2//B/15-17+20-21/CA 2//C/22/CA"; + toAlign, AtomSpecType.ALPHA); + assertEquals(commands.size(), 4); + String refSpecCA = "(1//A/12-14/CA 1//B/18+22-23/CA"; + String toAlignSpecCA = "(2//B/15-17+20-21/CA 2//C/22/CA"; String refSpec = "1//A/12-14/ 1//B/18+22-23/"; String toAlignSpec = "2//B/15-17+20-21/ 2//C/22/"; - String expected1 = String.format("super(%s,%s)", refSpecCA, - toAlignSpecCA); - String expected2 = String.format("show(cartoon,%s %s)", refSpec, - toAlignSpec); - assertEquals(commands.get(0).toString(), expected1); - assertEquals(commands.get(1).toString(), expected2); + String altLoc = " and (altloc '' or altloc 'a'))"; + // super command: separate arguments for regions to align + assertEquals(commands.get(1), + new StructureCommand("pair_fit", toAlignSpecCA+altLoc, refSpecCA+altLoc)); + // show aligned regions: one argument for combined atom specs + assertEquals(commands.get(3), new StructureCommand("show", "cartoon", + refSpec + " " + toAlignSpec)); } @Test(groups = "Functional") public void testGetAtomSpec_alphaOnly() { - StructureCommandsI testee = new PymolCommands(); 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), + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "1//A/2-4+8/CA 1//B/5-7/CA"); model.addRange("1", 3, 5, "A"); - assertEquals(testee.getAtomSpec(model, true), + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "1//A/2-5+8/CA 1//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/CA 1//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/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//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/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//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/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//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/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA"); model.addRange("5", 25, 35, " "); - assertEquals(testee.getAtomSpec(model, true), + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA 5///25-35/CA"); } @Test(groups = "Functional") public void testGetModelStartNo() { - StructureCommandsI testee = new PymolCommands(); assertEquals(testee.getModelStartNo(), 0); } @Test(groups = "Functional") public void testGetResidueSpec() { - PymolCommands testee = new PymolCommands(); assertEquals(testee.getResidueSpec("ALA"), "resn ALA"); } @Test(groups = "Functional") public void testShowBackbone() { - PymolCommands testee = new PymolCommands(); List cmds = testee.showBackbone(); assertEquals(cmds.size(), 2); - assertEquals(cmds.get(0).toString(), "hide(everything)"); - assertEquals(cmds.get(1).toString(), "show(ribbon)"); + assertEquals(cmds.get(0), new StructureCommand("hide", "everything")); + assertEquals(cmds.get(1), new StructureCommand("show", "ribbon")); } @Test(groups = "Functional") public void testColourByCharge() { - PymolCommands testee = new PymolCommands(); List cmds = testee.colourByCharge(); assertEquals(cmds.size(), 4); - assertEquals(cmds.get(0).toString(), "color(white,*)"); - assertEquals(cmds.get(1).toString(), "color(red,resn ASP resn GLU)"); - assertEquals(cmds.get(2).toString(), "color(blue,resn LYS resn ARG)"); - assertEquals(cmds.get(3).toString(), "color(yellow,resn CYS)"); + assertEquals(cmds.get(0), new StructureCommand("color", "white", "*")); + assertEquals(cmds.get(1), + new StructureCommand("color", "red", "resn ASP resn GLU")); + assertEquals(cmds.get(2), + new StructureCommand("color", "blue", "resn LYS resn ARG")); + assertEquals(cmds.get(3), + new StructureCommand("color", "yellow", "resn CYS")); } @Test(groups = "Functional") public void testOpenCommandFile() { - PymolCommands testee = new PymolCommands(); - assertEquals(testee.openCommandFile("commands.pml").toString(), - "run(commands.pml)"); + assertEquals(testee.openCommandFile("commands.pml"), + new StructureCommand("run", "commands.pml")); } @Test(groups = "Functional") public void testSaveSession() { - PymolCommands testee = new PymolCommands(); - assertEquals(testee.saveSession("somewhere.pse").toString(), - "save(somewhere.pse)"); + assertEquals(testee.saveSession("somewhere.pse"), + new StructureCommand("save", "somewhere.pse")); + } + + @Test(groups = "Functional") + public void testOpenSession() + { + assertEquals(testee.openSession("/some/path"), + new StructureCommand("load", "/some/path", "", "0", "pse")); } @Test(groups = "Functional") public void testColourByChain() { - PymolCommands testee = new PymolCommands(); - assertEquals(testee.colourByChain().toString(), "spectrum(chain)"); + assertEquals(testee.colourByChain(), + new StructureCommand("spectrum", "chain")); + } + + @Test(groups = "Functional") + public void testColourResidues() + { + assertEquals(testee.colourResidues("something", + Color.MAGENTA), + new StructureCommand("color", "0xff00ff", "something")); + } + + @Test(groups = "Functional") + public void testLoadFile() + { + assertEquals(testee.loadFile("/some/path"), + new StructureCommand("load", "/some/path")); + } + + @Test(groups = "Functional") + public void testSetBackgroundColour() + { + assertEquals(testee.setBackgroundColour( + Color.PINK), + new StructureCommand("bg_color", "0xffafaf")); + } + + @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), + new StructureCommand("iterate", "1//A/89-92/ 2//B/8-9+12-20/", + "p.jv_kd='27.3'")); + } + + @Test(groups = { "Functional" }) + 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"); + + List commands = testee.setAttributes(featuresMap); + assertEquals(commands.size(), 1); + + /* + * feature name gets a jv_ namespace prefix + */ + assertEquals(commands.get(0), new StructureCommand("iterate", + "0//A/8-20/", "p.jv_chain='X'")); + + // add same feature value, overlapping range + ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 3, 9, "A"); + // same feature value, contiguous range + ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A"); + commands = testee.setAttributes(featuresMap); + assertEquals(commands.size(), 1); + assertEquals(commands.get(0), new StructureCommand("iterate", + "0//A/3-25/", "p.jv_chain='X'")); + + // same feature value and model, different chain + ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "B"); + // same feature value and chain, different model + ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A"); + commands = testee.setAttributes(featuresMap); + assertEquals(commands.size(), 1); + StructureCommand expected1 = new StructureCommand("iterate", + "0//A/3-25/ 0//B/21-25/ 1//A/26-30/", "p.jv_chain='X'"); + assertEquals(commands.get(0), expected1); + + // same feature, different value + 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 + StructureCommandI cmd1 = commands.get(0); + StructureCommandI cmd2 = commands.get(1); + StructureCommand expected2 = new StructureCommand("iterate", + "0//A/40-50/", "p.jv_chain='Y'"); + 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"); + // feature names are sanitised to change non-alphanumeric to underscore + // feature values are sanitised to encode single quote characters + commands = testee.setAttributes(featuresMap); + assertEquals(commands.size(), 1); + StructureCommandI expected3 = new StructureCommand("iterate", + "0//A/7-15/", + "p.jv_side_chain_binding_='metal 'ion!'"); + assertEquals(commands.get(0), expected3); } @Test(groups = "Functional") - public void testGetColourCommand() + public void testCloseViewer() { - PymolCommands testee = new PymolCommands(); - assertEquals( - testee.colourResidues("something", Color.MAGENTA).toString(), - "color(0xff00ff,something)"); + assertEquals(testee.closeViewer(), new StructureCommand("quit")); } }