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 jalview.datamodel.Alignment;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.ColumnSelection;
29 import jalview.datamodel.Sequence;
30 import jalview.datamodel.SequenceI;
31 import jalview.gui.AlignFrame;
32 import jalview.gui.JvOptionPane;
33 import jalview.gui.SequenceRenderer;
34 import jalview.schemes.JalviewColourScheme;
35 import jalview.structure.AtomSpecModel;
36 import jalview.structure.StructureCommandsI;
37 import jalview.structure.StructureMapping;
38 import jalview.structure.StructureSelectionManager;
40 import java.awt.Color;
41 import java.util.HashMap;
42 import java.util.LinkedHashMap;
45 import org.testng.annotations.BeforeClass;
46 import org.testng.annotations.Test;
48 public class JmolCommandsTest
51 @BeforeClass(alwaysRun = true)
52 public void setUpJvOptionPane()
54 JvOptionPane.setInteractiveMode(false);
55 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
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();
82 * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
84 HashMap<Integer, int[]> map = new HashMap<>();
85 for (int pos = 1; pos <= seq1.getLength(); pos++)
87 map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
89 StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
91 ssm.addStructureMapping(sm1);
92 StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
94 ssm.addStructureMapping(sm2);
96 String[] commands = new JmolCommands().colourBySequence(ssm, files,
97 seqs, sr, af.alignPanel);
98 assertEquals(commands.length, 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 StructureCommandsI testee = new JmolCommands();
132 AtomSpecModel model = new AtomSpecModel();
133 assertEquals(testee.getAtomSpec(model, false), "");
134 model.addRange(1, 2, 4, "A");
135 assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1");
136 model.addRange(1, 8, 8, "A");
137 assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1|8:A/1.1");
138 model.addRange(1, 5, 7, "B");
139 assertEquals(testee.getAtomSpec(model, false),
140 "2-4:A/1.1|8:A/1.1|5-7:B/1.1");
141 model.addRange(1, 3, 5, "A");
142 assertEquals(testee.getAtomSpec(model, false),
143 "2-5:A/1.1|8:A/1.1|5-7:B/1.1");
144 model.addRange(2, 1, 4, "B");
145 assertEquals(testee.getAtomSpec(model, false),
146 "2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1");
147 model.addRange(2, 5, 9, "C");
148 assertEquals(testee.getAtomSpec(model, false),
149 "2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1|5-9:C/2.1");
150 model.addRange(1, 8, 10, "B");
151 assertEquals(testee.getAtomSpec(model, false),
152 "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
153 model.addRange(1, 8, 9, "B");
154 assertEquals(testee.getAtomSpec(model, false),
155 "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
156 model.addRange(2, 3, 10, "C"); // subsumes 5-9
157 assertEquals(testee.getAtomSpec(model, false),
158 "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1");
159 model.addRange(5, 25, 35, " ");
160 assertEquals(testee.getAtomSpec(model, false),
161 "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");
165 @Test(groups = { "Functional" })
166 public void testColourBySequence()
168 Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
169 JmolCommands.addAtomSpecRange(map, Color.blue, 1, 2, 5, "A");
170 JmolCommands.addAtomSpecRange(map, Color.blue, 1, 7, 7, "B");
171 JmolCommands.addAtomSpecRange(map, Color.blue, 1, 9, 23, "A");
172 JmolCommands.addAtomSpecRange(map, Color.blue, 2, 1, 1, "A");
173 JmolCommands.addAtomSpecRange(map, Color.blue, 2, 4, 7, "B");
174 JmolCommands.addAtomSpecRange(map, Color.yellow, 2, 8, 8, "A");
175 JmolCommands.addAtomSpecRange(map, Color.yellow, 2, 3, 5, "A");
176 JmolCommands.addAtomSpecRange(map, Color.red, 1, 3, 5, "A");
177 JmolCommands.addAtomSpecRange(map, Color.red, 1, 6, 9, "A");
179 // Colours should appear in the Jmol command in the order in which
180 // they were added; within colour, by model, by chain, ranges in start order
181 String[] commands = new JmolCommands().colourBySequence(map);
182 assertEquals(commands.length, 1);
183 String expected = "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]; "
184 + "select 3-5:A/2.1|8:A/2.1;color[255,255,0]; "
185 + "select 3-9:A/1.1;color[255,0,0]";
186 assertEquals(commands[0], expected);
189 @Test(groups = { "Functional" })
190 public void testSuperposeStructures()
192 StructureCommandsI testee = new JmolCommands();
193 AtomSpecModel ref = new AtomSpecModel();
194 ref.addRange(1, 12, 14, "A");
195 ref.addRange(1, 18, 18, "B");
196 ref.addRange(1, 22, 23, "B");
197 AtomSpecModel toAlign = new AtomSpecModel();
198 toAlign.addRange(2, 15, 17, "B");
199 toAlign.addRange(2, 20, 21, "B");
200 toAlign.addRange(2, 22, 22, "C");
201 String command = testee.superposeStructures(ref, toAlign);
202 String refSpec = "12-14:A/1.1|18:B/1.1|22-23:B/1.1";
203 String toAlignSpec = "15-17:B/2.1|20-21:B/2.1|22:C/2.1";
204 String expected = String.format(
205 "compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS {%s}{%s} ROTATE TRANSLATE ;select %s|%s;cartoons",
206 toAlignSpec, refSpec, toAlignSpec, refSpec);
207 assertEquals(command, expected);
210 @Test(groups = "Functional")
211 public void testGetModelStartNo()
213 StructureCommandsI testee = new JmolCommands();
214 assertEquals(testee.getModelStartNo(), 1);