X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommandsTest.java;h=a5933d280595e1aef7ff0c30cfb977a4d22e7ba5;hb=7af7ccb2d58a22ffabe1f3129d9f33348efb2534;hp=317d15e33fe5d6d142b4e68bb6414902d6a62785;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java index 317d15e..a5933d2 100644 --- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java +++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,87 +20,377 @@ */ package jalview.ext.rbvi.chimera; -import static org.testng.AssertJUnit.assertEquals; -import static org.testng.AssertJUnit.assertTrue; +import static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertTrue; import java.awt.Color; -import java.util.Arrays; +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 ChimeraCommandsTest { + private ChimeraCommands testee; + + @BeforeClass(alwaysRun = true) + public void setUp() + { + testee = new ChimeraCommands(); + } + @Test(groups = { "Functional" }) - public void testAddColourRange() + public void testColourBySequence() { - Map>>> map = new LinkedHashMap>>>(); - ChimeraCommands.addColourRange(map, Color.pink, 1, 2, 4, "A"); - ChimeraCommands.addColourRange(map, Color.pink, 1, 8, 8, "A"); - ChimeraCommands.addColourRange(map, Color.pink, 1, 5, 7, "B"); - ChimeraCommands.addColourRange(map, Color.red, 1, 3, 5, "A"); - ChimeraCommands.addColourRange(map, Color.red, 0, 1, 4, "B"); - ChimeraCommands.addColourRange(map, Color.orange, 0, 5, 9, "C"); - // three colours mapped - assertEquals(3, map.keySet().size()); + 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"); + + // 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 #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 testSetAttributes() + { + /* + * make a map of { featureType, {featureValue, {residue range specification } } } + */ + Map> featuresMap = new LinkedHashMap<>(); + Map featureValues = new HashMap<>(); - // Red has two models, Pink and Orange one each - assertEquals(2, map.get(Color.red).keySet().size()); - assertEquals(1, map.get(Color.orange).keySet().size()); - assertEquals(1, map.get(Color.pink).keySet().size()); + /* + * start with just one feature/value... + */ + featuresMap.put("chain", featureValues); + ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A"); - // pink model 1 has two chains, red.0 / red.1 / orange.0 one each - assertEquals(2, map.get(Color.pink).get(1).keySet().size()); - assertEquals(1, map.get(Color.red).get(0).keySet().size()); - assertEquals(1, map.get(Color.red).get(1).keySet().size()); - assertEquals(1, map.get(Color.orange).get(0).keySet().size()); + List commands = testee.setAttributes(featuresMap); + assertEquals(1, commands.size()); - // inspect positions - List posList = map.get(Color.pink).get(1).get("A"); - assertEquals(2, posList.size()); - assertTrue(Arrays.equals(new int[] { 2, 4 }, posList.get(0))); - assertTrue(Arrays.equals(new int[] { 8, 8 }, posList.get(1))); + /* + * feature name gets a jv_ namespace prefix + * feature value is quoted in case it contains spaces + */ + assertEquals(commands.get(0).getCommand(), + "setattr res jv_chain 'X' #0:8-20.A"); - posList = map.get(Color.pink).get(1).get("B"); - assertEquals(1, posList.size()); - assertTrue(Arrays.equals(new int[] { 5, 7 }, posList.get(0))); + // 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(1, commands.size()); + assertEquals(commands.get(0).getCommand(), + "setattr res jv_chain 'X' #0:3-25.A"); - posList = map.get(Color.red).get(0).get("B"); - assertEquals(1, posList.size()); - assertTrue(Arrays.equals(new int[] { 1, 4 }, posList.get(0))); + // 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(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); - posList = map.get(Color.red).get(1).get("A"); - assertEquals(1, posList.size()); - assertTrue(Arrays.equals(new int[] { 3, 5 }, posList.get(0))); + // 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 + 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)); - posList = map.get(Color.orange).get(0).get("C"); - assertEquals(1, posList.size()); - assertTrue(Arrays.equals(new int[] { 5, 9 }, posList.get(0))); + 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); + 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 or PyMol + */ @Test(groups = { "Functional" }) - public void testBuildColourCommands() + public void testMakeAttributeName() { + 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(testee.makeAttributeName( + "!this is-a_very*{odd(name"), + "jv__this_is_a_very__odd_name"); + // name ending in color gets underscore appended + assertEquals(testee.makeAttributeName("helixColor"), "jv_helixColor_"); + } - Map>>> map = new LinkedHashMap>>>(); - ChimeraCommands.addColourRange(map, Color.blue, 0, 2, 5, "A"); - ChimeraCommands.addColourRange(map, Color.blue, 0, 7, 7, "B"); - ChimeraCommands.addColourRange(map, Color.blue, 0, 9, 23, "A"); - ChimeraCommands.addColourRange(map, Color.blue, 1, 1, 1, "A"); - ChimeraCommands.addColourRange(map, Color.blue, 1, 4, 7, "B"); - ChimeraCommands.addColourRange(map, Color.yellow, 1, 8, 8, "A"); - ChimeraCommands.addColourRange(map, Color.yellow, 1, 3, 5, "A"); - ChimeraCommands.addColourRange(map, Color.red, 0, 3, 5, "A"); + @Test(groups = "Functional") + public void testGetAtomSpec() + { + AtomSpecModel model = new AtomSpecModel(); + assertEquals(testee.getAtomSpec(model, false), ""); + model.addRange("1", 2, 4, "A"); + assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A"); + model.addRange("1", 8, 8, "A"); + assertEquals(testee.getAtomSpec(model, false), "#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"); + model.addRange("1", 3, 5, "A"); + assertEquals(testee.getAtomSpec(model, false), "#1:2-5.A,8.A,5-7.B"); + model.addRange("0", 1, 4, "B"); + assertEquals(testee.getAtomSpec(model, false), + "#0:1-4.B|#1:2-5.A,8.A,5-7.B"); + model.addRange("0", 5, 9, "C"); + assertEquals(testee.getAtomSpec(model, false), + "#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), + "#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), + "#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), + "#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), + "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B|#5:25-35."); - // Colours should appear in the Chimera command in the order in which - // they were added; within colour, by model, by chain, and positions as - // added - String command = ChimeraCommands.buildColourCommands(map).get(0); - assertEquals( - "color #0000ff #0:2-5.A,9-23.A,7.B|#1:1.A,4-7.B; color #ffff00 #1:8.A,3-5.A; color #ff0000 #0:3-5.A", - command); + } + + @Test(groups = { "Functional" }) + public void testSuperposeStructures() + { + 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, false); + // 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); + } + + @Test(groups = "Functional") + public void testGetAtomSpec_alphaOnly() + { + AtomSpecModel model = new AtomSpecModel(); + assertEquals(testee.getAtomSpec(model, true), ""); + model.addRange("1", 2, 4, "A"); + assertEquals(testee.getAtomSpec(model, true), + "#1:2-4.A@CA&~@.B-Z&~@.2-9"); + model.addRange("1", 8, 8, "A"); + assertEquals(testee.getAtomSpec(model, true), + "#1:2-4.A,8.A@CA&~@.B-Z&~@.2-9"); + model.addRange("1", 5, 7, "B"); + assertEquals(testee.getAtomSpec(model, true), + "#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), + "#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), + "#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), + "#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), + "#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), + "#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), + "#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), + "#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")); } }