X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommandsTest.java;h=f08702066ae2d906d7f6097741dfb2adea3ddfa7;hb=9dabc02511e3a334a5749a504f57f69d6c9017bd;hp=e8b6b194056923dd77c2921ab2df1af86e81eef4;hpb=c93b9ad2ebfab4cad4608a8890132918589576be;p=jalview.git diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java index e8b6b19..f087020 100644 --- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java +++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java @@ -1,92 +1,314 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ 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.Test; +import jalview.structure.AtomSpecModel; +import jalview.structure.StructureCommandI; +import jalview.structure.StructureCommandsI; + public class ChimeraCommandsTest { - @Test - public void testAddColourRange() + + @Test(groups = { "Functional" }) + 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()); - - // 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()); - - // 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()); - - // 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))); - - posList = map.get(Color.pink).get(1).get("B"); - assertEquals(1, posList.size()); - assertTrue(Arrays.equals(new int[] - { 5, 7 }, posList.get(0))); - - posList = map.get(Color.red).get(0).get("B"); - assertEquals(1, posList.size()); - assertTrue(Arrays.equals(new int[] - { 1, 4 }, posList.get(0))); - - posList = map.get(Color.red).get(1).get("A"); - assertEquals(1, posList.size()); - assertTrue(Arrays.equals(new int[] - { 3, 5 }, posList.get(0))); - - posList = map.get(Color.orange).get(0).get("C"); - assertEquals(1, posList.size()); - assertTrue(Arrays.equals(new int[] - { 5, 9 }, posList.get(0))); + + 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 = 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 - public void testBuildColourCommands() + @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"); + + ChimeraCommands commandGenerator = new ChimeraCommands(); + List commands = commandGenerator + .setAttributes(featuresMap); + assertEquals(1, commands.size()); - 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"); + /* + * 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"); - // 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); + // 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 = commandGenerator.setAttributes(featuresMap); + 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"); + // same feature value and chain, different model + ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A"); + commands = commandGenerator.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); + 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)); + + 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 = commandGenerator.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 + */ + @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"), + "jv_Hello_World_24"); 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); + ChimeraCommands.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_"); + } + + @Test(groups = "Functional") + public void testGetAtomSpec() + { + StructureCommandsI testee = new ChimeraCommands(); + 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."); + + } + + @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"); + 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); + // 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() + { + StructureCommandsI testee = new ChimeraCommands(); + 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() + { + 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(), + "~display all;~ribbon;chain @CA|P"); + } + + @Test(groups = "Functional") + public void testOpenCommandFile() + { + ChimeraCommands testee = new ChimeraCommands(); + assertEquals(testee.openCommandFile("nowhere").getCommand(), + "open cmd:nowhere"); + } + + @Test(groups = "Functional") + public void testSaveSession() + { + ChimeraCommands testee = new ChimeraCommands(); + assertEquals(testee.saveSession("somewhere").getCommand(), + "save somewhere"); + } + + @Test(groups = "Functional") + public void testGetColourCommand() + { + ChimeraCommands testee = new ChimeraCommands(); + assertEquals(testee.getColourCommand("something", Color.MAGENTA) + .getCommand(), + "color #ff00ff something"); + } + + @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"); } }