X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommandsTest.java;h=f08702066ae2d906d7f6097741dfb2adea3ddfa7;hb=9dabc02511e3a334a5749a504f57f69d6c9017bd;hp=5f0e84beb92d75c863d1aee11f7c6c6743b5e890;hpb=fea6f8ed76719fd78b600adfea8891dafb8c9d12;p=jalview.git diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java index 5f0e84b..f087020 100644 --- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java +++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java @@ -23,16 +23,18 @@ package jalview.ext.rbvi.chimera; import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertTrue; -import jalview.structure.AtomSpecModel; -import jalview.structure.StructureCommandsI; - import java.awt.Color; import java.util.HashMap; import java.util.LinkedHashMap; +import java.util.List; import java.util.Map; import org.testng.annotations.Test; +import jalview.structure.AtomSpecModel; +import jalview.structure.StructureCommandI; +import jalview.structure.StructureCommandsI; + public class ChimeraCommandsTest { @@ -41,23 +43,23 @@ public class ChimeraCommandsTest { 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[] commands = new ChimeraCommands().colourBySequence(map); - assertEquals(commands.length, 1); - assertEquals( - commands[0], - "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 = new ChimeraCommands() + .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" }) @@ -73,60 +75,62 @@ public class ChimeraCommandsTest * start with just one feature/value... */ featuresMap.put("chain", featureValues); - ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 8, 20, "A"); + ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A"); ChimeraCommands commandGenerator = new ChimeraCommands(); - String[] commands = commandGenerator.setAttributes(featuresMap); - assertEquals(1, commands.length); + List commands = commandGenerator + .setAttributes(featuresMap); + assertEquals(1, commands.size()); /* * feature name gets a jv_ namespace prefix * feature value is quoted in case it contains spaces */ - assertEquals(commands[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"); + ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A"); commands = commandGenerator.setAttributes(featuresMap); - assertEquals(1, commands.length); - assertEquals(commands[0], "setattr res jv_chain 'X' #0:3-25.A"); + assertEquals(1, commands.size()); + 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"); + ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A"); commands = commandGenerator.setAttributes(featuresMap); - assertEquals(1, commands.length); + assertEquals(1, commands.size()); String expected1 = "setattr res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A"; - assertEquals(commands[0], - expected1); + assertEquals(commands.get(0).getCommand(), expected1); // same feature, different value - ChimeraCommands.addAtomSpecRange(featureValues, "Y", 0, 40, 50, "A"); + ChimeraCommands.addAtomSpecRange(featureValues, "Y", "0", 40, 50, "A"); commands = commandGenerator.setAttributes(featuresMap); - assertEquals(2, commands.length); + assertEquals(2, commands.size()); // commands are ordered by feature type but not by value // so test for the expected command in either order - assertTrue( - commands[0].equals(expected1) || commands[1].equals(expected1)); + 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( - commands[0].equals(expected2) || commands[1].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, + "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); + assertEquals(commands.size(), 1); String expected3 = "setattr res jv_side_chain_binding_ 'metal 'ion!' #0:7-15.A"; - assertTrue( - commands[0].equals(expected3) || commands[1].equals(expected3)); + assertTrue(commands.get(0).getCommand().equals(expected3)); } /** @@ -155,31 +159,30 @@ public class ChimeraCommandsTest StructureCommandsI testee = new ChimeraCommands(); AtomSpecModel model = new AtomSpecModel(); assertEquals(testee.getAtomSpec(model, false), ""); - model.addRange(1, 2, 4, "A"); + model.addRange("1", 2, 4, "A"); assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A"); - model.addRange(1, 8, 8, "A"); + model.addRange("1", 8, 8, "A"); assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A,8.A"); - model.addRange(1, 5, 7, "B"); + 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"); + 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"); + 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"); + 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"); + 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"); + 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 + 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, " "); // empty chain code - e.g. from homology - // modelling + 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."); @@ -190,20 +193,23 @@ public class ChimeraCommandsTest { StructureCommandsI testee = new ChimeraCommands(); AtomSpecModel ref = new AtomSpecModel(); - ref.addRange(1, 12, 14, "A"); - ref.addRange(1, 18, 18, "B"); - ref.addRange(1, 22, 23, "B"); + 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"); - String command = testee.superposeStructures(ref, toAlign); - String refSpec = "#1:12-14.A,18.B,22-23.B@CA|P&~@.B-Z&~@.2-9"; - String toAlignSpec = "#2:15-17.B,20-21.B,22.C@CA|P&~@.B-Z&~@.2-9"; + toAlign.addRange("2", 15, 17, "B"); + toAlign.addRange("2", 20, 21, "B"); + toAlign.addRange("2", 22, 22, "C"); + List command = testee.superposeStructures(ref, + toAlign); + // 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;~display all; chain @CA|P; ribbon %s|%s; focus", - refSpec, toAlignSpec, refSpec, toAlignSpec); - assertEquals(command, expected); + "match %s%s %s%s; ribbon %s|%s; focus", toAlignSpec, + carbonAlphas, refSpec, carbonAlphas, toAlignSpec, refSpec); + assertEquals(command.get(0).getCommand(), expected); } @Test(groups = "Functional") @@ -212,36 +218,36 @@ public class ChimeraCommandsTest StructureCommandsI testee = new ChimeraCommands(); AtomSpecModel model = new AtomSpecModel(); assertEquals(testee.getAtomSpec(model, true), ""); - model.addRange(1, 2, 4, "A"); + model.addRange("1", 2, 4, "A"); assertEquals(testee.getAtomSpec(model, true), - "#1:2-4.A@CA|P&~@.B-Z&~@.2-9"); - model.addRange(1, 8, 8, "A"); + "#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|P&~@.B-Z&~@.2-9"); - model.addRange(1, 5, 7, "B"); + "#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|P&~@.B-Z&~@.2-9"); - model.addRange(1, 3, 5, "A"); + "#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|P&~@.B-Z&~@.2-9"); - model.addRange(0, 1, 4, "B"); + "#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|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9"); - model.addRange(0, 5, 9, "C"); + "#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|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9"); - model.addRange(1, 8, 10, "B"); + "#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|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9"); - model.addRange(1, 8, 9, "B"); + "#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|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9"); - model.addRange(0, 3, 10, "C"); // subsumes 5-9 + "#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|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9"); - model.addRange(5, 25, 35, " "); // empty chain code + "#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|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9|#5:25-35.@CA|P&~@.B-Z&~@.2-9"); + "#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"); } @@ -263,28 +269,34 @@ public class ChimeraCommandsTest public void testShowBackbone() { ChimeraCommands testee = new ChimeraCommands(); - assertEquals(testee.showBackbone(), "~display all;chain @CA|P"); + 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() { ChimeraCommands testee = new ChimeraCommands(); - assertEquals(testee.openCommandFile("nowhere"), "open cmd:nowhere"); + assertEquals(testee.openCommandFile("nowhere").getCommand(), + "open cmd:nowhere"); } @Test(groups = "Functional") public void testSaveSession() { ChimeraCommands testee = new ChimeraCommands(); - assertEquals(testee.saveSession("somewhere"), "save somewhere"); + assertEquals(testee.saveSession("somewhere").getCommand(), + "save somewhere"); } @Test(groups = "Functional") public void testGetColourCommand() { ChimeraCommands testee = new ChimeraCommands(); - assertEquals(testee.getColourCommand("something", Color.MAGENTA), + assertEquals(testee.getColourCommand("something", Color.MAGENTA) + .getCommand(), "color #ff00ff something"); } @@ -293,10 +305,10 @@ public class ChimeraCommandsTest { 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), + 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"); } }