2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ext.jmol;
23 import static org.testng.Assert.assertEquals;
24 import static org.testng.Assert.assertTrue;
26 import java.awt.Color;
27 import java.util.HashMap;
28 import java.util.LinkedHashMap;
29 import java.util.List;
32 import org.testng.annotations.BeforeClass;
33 import org.testng.annotations.Test;
34 import jalview.datamodel.Alignment;
35 import jalview.datamodel.AlignmentI;
36 import jalview.datamodel.ColumnSelection;
37 import jalview.datamodel.Sequence;
38 import jalview.datamodel.SequenceI;
39 import jalview.gui.AlignFrame;
40 import jalview.gui.SequenceRenderer;
41 import jalview.schemes.JalviewColourScheme;
42 import jalview.structure.AtomSpecModel;
43 import jalview.structure.StructureCommandI;
44 import jalview.structure.StructureMapping;
45 import jalview.structure.StructureSelectionManager;
48 public class JmolCommandsTest
50 private JmolCommands testee;
52 @BeforeClass(alwaysRun = true)
55 testee = new JmolCommands();
58 @Test(groups = { "Functional" })
59 public void testGetColourBySequenceCommands_hiddenColumns()
62 * load these sequences, coloured by Strand propensity,
63 * with columns 2-4 hidden
65 SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG");
66 SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS");
67 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
68 AlignFrame af = new AlignFrame(al, 800, 500);
69 af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
70 ColumnSelection cs = new ColumnSelection();
74 af.getViewport().setColumnSelection(cs);
75 af.hideSelColumns_actionPerformed(null);
76 SequenceRenderer sr = new SequenceRenderer(af.getViewport());
77 SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
78 String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
79 StructureSelectionManager ssm = new StructureSelectionManager();
81 * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
83 HashMap<Integer, int[]> map = new HashMap<>();
84 for (int pos = 1; pos <= seq1.getLength(); pos++)
86 map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
88 StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
90 ssm.addStructureMapping(sm1);
91 StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
93 ssm.addStructureMapping(sm2);
94 String[] commands = testee.colourBySequence(ssm,
96 seqs, sr, af.alignPanel);
97 assertEquals(commands.length, 2);
98 assertEquals(commands[0].commands.length, 1); // from 2.12 merge from 2.11.2
100 String chainACommand = commands[0];
101 // M colour is #82827d == (130, 130, 125) (see strand.html help page)
103 chainACommand.contains("select 21:A/1.1;color[130,130,125]")); // first
105 // H colour is #60609f == (96, 96, 159)
106 assertTrue(chainACommand.contains(";select 22:A/1.1;color[96,96,159]"));
107 // hidden columns are Gray (128, 128, 128)
108 assertTrue(chainACommand
109 .contains(";select 23-25:A/1.1;color[128,128,128]"));
110 // S and G are both coloured #4949b6 == (73, 73, 182)
112 chainACommand.contains(";select 26-30:A/1.1;color[73,73,182]"));
114 String chainBCommand = commands[1];
115 // M colour is #82827d == (130, 130, 125)
117 chainBCommand.contains("select 21:B/2.1;color[130,130,125]"));
118 // V colour is #ffff00 == (255, 255, 0)
119 assertTrue(chainBCommand.contains(";select 22:B/2.1;color[255,255,0]"));
120 // hidden columns are Gray (128, 128, 128)
121 assertTrue(chainBCommand
122 .contains(";select 23-25:B/2.1;color[128,128,128]"));
123 // S and G are both coloured #4949b6 == (73, 73, 182)
125 chainBCommand.contains(";select 26-30:B/2.1;color[73,73,182]"));
128 @Test(groups = "Functional")
129 public void testGetAtomSpec()
131 AtomSpecModel model = new AtomSpecModel();
132 assertEquals(testee.getAtomSpec(model, false), "");
133 model.addRange("1", 2, 4, "A");
134 assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1");
135 model.addRange("1", 8, 8, "A");
136 assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1|8:A/1.1");
137 model.addRange("1", 5, 7, "B");
138 assertEquals(testee.getAtomSpec(model, false),
139 "2-4:A/1.1|8:A/1.1|5-7:B/1.1");
140 model.addRange("1", 3, 5, "A");
141 assertEquals(testee.getAtomSpec(model, false),
142 "2-5:A/1.1|8:A/1.1|5-7:B/1.1");
143 model.addRange("2", 1, 4, "B");
144 assertEquals(testee.getAtomSpec(model, false),
145 "2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1");
146 model.addRange("2", 5, 9, "C");
147 assertEquals(testee.getAtomSpec(model, false),
148 "2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1|5-9:C/2.1");
149 model.addRange("1", 8, 10, "B");
150 assertEquals(testee.getAtomSpec(model, false),
151 "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
152 model.addRange("1", 8, 9, "B");
153 assertEquals(testee.getAtomSpec(model, false),
154 "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
155 model.addRange("2", 3, 10, "C"); // subsumes 5-9
156 assertEquals(testee.getAtomSpec(model, false),
157 "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1");
158 model.addRange("5", 25, 35, " ");
159 assertEquals(testee.getAtomSpec(model, false),
160 "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1|25-35:/5.1");
164 @Test(groups = { "Functional" })
165 public void testColourBySequence()
167 Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
168 JmolCommands.addAtomSpecRange(map, Color.blue, "1", 2, 5, "A");
169 JmolCommands.addAtomSpecRange(map, Color.blue, "1", 7, 7, "B");
170 JmolCommands.addAtomSpecRange(map, Color.blue, "1", 9, 23, "A");
171 JmolCommands.addAtomSpecRange(map, Color.blue, "2", 1, 1, "A");
172 JmolCommands.addAtomSpecRange(map, Color.blue, "2", 4, 7, "B");
173 JmolCommands.addAtomSpecRange(map, Color.yellow, "2", 8, 8, "A");
174 JmolCommands.addAtomSpecRange(map, Color.yellow, "2", 3, 5, "A");
175 JmolCommands.addAtomSpecRange(map, Color.red, "1", 3, 5, "A");
176 JmolCommands.addAtomSpecRange(map, Color.red, "1", 6, 9, "A");
178 // Colours should appear in the Jmol command in the order in which
179 // they were added; within colour, by model, by chain, ranges in start order
180 List<StructureCommandI> commands = testee.colourBySequence(map);
181 assertEquals(commands.size(), 1);
182 String expected1 = "select 2-5:A/1.1|9-23:A/1.1|7:B/1.1|1:A/2.1|4-7:B/2.1;color[0,0,255]";
183 String expected2 = "select 3-5:A/2.1|8:A/2.1;color[255,255,0]";
184 String expected3 = "select 3-9:A/1.1;color[255,0,0]";
185 assertEquals(commands.get(0).getCommand(),
186 expected1 + ";" + expected2 + ";" + expected3);
189 @Test(groups = { "Functional" })
190 public void testSuperposeStructures()
192 AtomSpecModel ref = new AtomSpecModel();
193 ref.addRange("1", 12, 14, "A");
194 ref.addRange("1", 18, 18, "B");
195 ref.addRange("1", 22, 23, "B");
196 AtomSpecModel toAlign = new AtomSpecModel();
197 toAlign.addRange("2", 15, 17, "B");
198 toAlign.addRange("2", 20, 21, "B");
199 toAlign.addRange("2", 22, 22, "C");
200 List<StructureCommandI> command = testee.superposeStructures(ref,
202 assertEquals(command.size(), 1);
203 String refSpec = "12-14:A/1.1|18:B/1.1|22-23:B/1.1";
204 String toAlignSpec = "15-17:B/2.1|20-21:B/2.1|22:C/2.1";
205 String expected = String.format(
206 "compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS {%s}{%s} ROTATE TRANSLATE ;select %s|%s;cartoons",
207 toAlignSpec, refSpec, toAlignSpec, refSpec);
208 assertEquals(command.get(0).getCommand(), expected);
211 @Test(groups = "Functional")
212 public void testGetModelStartNo()
214 assertEquals(testee.getModelStartNo(), 1);
217 @Test(groups = "Functional")
218 public void testColourByChain()
220 StructureCommandI cmd = testee.colourByChain();
221 assertEquals(cmd.getCommand(), "select *;color chain");
224 @Test(groups = "Functional")
225 public void testColourByCharge()
227 List<StructureCommandI> cmds = testee.colourByCharge();
228 assertEquals(cmds.size(), 1);
229 assertEquals(cmds.get(0).getCommand(),
230 "select *;color white;select ASP,GLU;color red;"
231 + "select LYS,ARG;color blue;select CYS;color yellow");
234 @Test(groups = "Functional")
235 public void testSetBackgroundColour()
237 StructureCommandI cmd = testee.setBackgroundColour(Color.PINK);
238 assertEquals(cmd.getCommand(), "background [255,175,175]");
241 @Test(groups = "Functional")
242 public void testFocusView()
244 StructureCommandI cmd = testee.focusView();
245 assertEquals(cmd.getCommand(), "zoom 0");
248 @Test(groups = "Functional")
249 public void testSaveSession()
251 StructureCommandI cmd = testee.saveSession("/some/filepath");
252 assertEquals(cmd.getCommand(), "write STATE \"/some/filepath\"");
255 @Test(groups = "Functional")
256 public void testShowBackbone()
258 List<StructureCommandI> cmds = testee.showBackbone();
259 assertEquals(cmds.size(), 1);
260 assertEquals(cmds.get(0).getCommand(),
261 "select *; cartoons off; backbone");
264 @Test(groups = "Functional")
265 public void testLoadFile()
267 StructureCommandI cmd = testee.loadFile("/some/filepath");
268 assertEquals(cmd.getCommand(), "load FILES \"/some/filepath\"");
270 // single backslash gets escaped to double
271 cmd = testee.loadFile("\\some\\filepath");
272 assertEquals(cmd.getCommand(), "load FILES \"\\\\some\\\\filepath\"");
275 @Test(groups = "Functional")
276 public void testOpenSession()
278 StructureCommandI cmd = testee.openSession("/some/filepath");
279 assertEquals(cmd.getCommand(), "load FILES \"/some/filepath\"");
281 // single backslash gets escaped to double
282 cmd = testee.openSession("\\some\\filepath");
283 assertEquals(cmd.getCommand(), "load FILES \"\\\\some\\\\filepath\"");