X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommandsTest.java;h=23e42ca8415111d50ab4ecba7259d0b14c55e6c2;hb=1d9a10caca0850531fffbbc16ae9af72df65990a;hp=6a02576840a31de0950bdc2f2f2084268fbb54ad;hpb=2ab7b9b152018bb808693218ad88dc3778166492;p=jalview.git diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java index 6a02576..23e42ca 100644 --- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java +++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java @@ -23,193 +23,375 @@ 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.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; +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 testBuildColourCommands() + 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"); + 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 ChimeraCommands().buildColourCommands(map).get(0); - assertEquals( - command, - "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"); + 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"); } @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"); - - List commands = ChimeraCommands - .buildSetAttributeCommands(featuresMap, false); + ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A"); + + List commands = testee.setAttributes(featuresMap); assertEquals(1, commands.size()); /* * feature name gets a jv_ namespace prefix * feature value is quoted in case it contains spaces */ - assertEquals(commands.get(0), "setattr res jv_chain 'X' #0:8-20.A"); + assertEquals(commands.get(0).getCommand(), + "setattr res jv_chain 'X' #0:8-20.A"); // 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 = ChimeraCommands.buildSetAttributeCommands(featuresMap, - false); + ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A"); + commands = testee.setAttributes(featuresMap); assertEquals(1, commands.size()); - assertEquals(commands.get(0), "setattr res jv_chain 'X' #0:3-25.A"); + assertEquals(commands.get(0).getCommand(), + "setattr res jv_chain 'X' #0:3-25.A"); // 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 = ChimeraCommands.buildSetAttributeCommands(featuresMap, - false); + ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A"); + commands = testee.setAttributes(featuresMap); assertEquals(1, commands.size()); - assertEquals(commands.get(0), - "setattr res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A"); + 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 = ChimeraCommands.buildSetAttributeCommands(featuresMap, - false); + 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 res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A")); - assertTrue(commands.contains("setattr res jv_chain 'Y' #0:40-50.A")); + // 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 res jv_chain 'Y' #0:40-50.A"; + 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 = ChimeraCommands.buildSetAttributeCommands(featuresMap, - false); - assertTrue(commands - .contains( - "setattr res jv_side_chain_binding_ 'metal 'ion!' #0:7-15.A")); + 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)); } /** * 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() + { + AtomSpecModel model = new AtomSpecModel(); + assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), ""); + model.addRange("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, AtomSpecType.RESIDUE_ONLY), "#1:2-4.A,8.A"); + model.addRange("1", 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, AtomSpecType.RESIDUE_ONLY), "#1:2-5.A,8.A,5-7.B"); + model.addRange("0", 1, 4, "B"); + 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, 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, 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, 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, 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, AtomSpecType.RESIDUE_ONLY), + "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B|#5:25-35."); + } @Test(groups = { "Functional" }) - public void testGetColourBySequenceCommands_hiddenColumns() + public void testSuperposeStructures() { - /* - * 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(); + AtomSpecModel ref = new AtomSpecModel(); + 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"); + List command = testee.superposeStructures(ref, + 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); + assertEquals(command.get(0).getCommand(), expected); + } - /* - * 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 ChimeraCommands() - .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 #82827d #0:21.A|#1:21.B")); - // H colour is #60609f - assertTrue(theCommand.contains("color #60609f #0:22.A")); - // V colour is #ffff00 - assertTrue(theCommand.contains("color #ffff00 #1:22.B")); - // hidden columns are Gray (128, 128, 128) - assertTrue(theCommand.contains("color #808080 #0:23-25.A|#1:23-25.B")); - // S and G are both coloured #4949b6 - assertTrue(theCommand.contains("color #4949b6 #0:26-30.A|#1:26-30.B")); + @Test(groups = "Functional") + public void testGetAtomSpec_alphaOnly() + { + AtomSpecModel model = new AtomSpecModel(); + assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), ""); + model.addRange("1", 2, 4, "A"); + 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, AtomSpecType.ALPHA), + "#1:2-4.A,8.A@CA&~@.B-Z&~@.2-9"); + model.addRange("1", 5, 7, "B"); + 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, 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, 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, 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, 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, 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, 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, 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() + { + assertEquals(testee.getModelStartNo(), 0); + } + + @Test(groups = "Functional") + public void testGetResidueSpec() + { + assertEquals(testee.getResidueSpec("ALA"), "::ALA"); + } + + @Test(groups = "Functional") + public void testShowBackbone() + { + List cmds = testee.showBackbone(); + assertEquals(cmds.size(), 1); + assertEquals(cmds.get(0).getCommand(), + "~display all;~ribbon;chain @CA|P"); + } + + @Test(groups = "Functional") + public void testOpenCommandFile() + { + assertEquals(testee.openCommandFile("nowhere").getCommand(), + "open cmd:nowhere"); + } + + @Test(groups = "Functional") + public void testSaveSession() + { + 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() + { + 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() + { + 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 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")); } }