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.rbvi.chimera;
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.SequenceRenderer;
33 import jalview.schemes.JalviewColourScheme;
34 import jalview.structure.AtomSpecModel;
35 import jalview.structure.StructureCommandsI;
36 import jalview.structure.StructureMapping;
37 import jalview.structure.StructureSelectionManager;
39 import java.awt.Color;
40 import java.util.HashMap;
41 import java.util.LinkedHashMap;
42 import java.util.List;
45 import org.testng.annotations.Test;
47 public class ChimeraXCommandsTest
50 @Test(groups = { "Functional" })
51 public void testBuildColourCommands()
54 Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
55 ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 2, 5, "A");
56 ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 7, 7, "B");
57 ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 9, 23, "A");
58 ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 1, 1, "A");
59 ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 4, 7, "B");
60 ChimeraCommands.addAtomSpecRange(map, Color.yellow, 1, 8, 8, "A");
61 ChimeraCommands.addAtomSpecRange(map, Color.yellow, 1, 3, 5, "A");
62 ChimeraCommands.addAtomSpecRange(map, Color.red, 0, 3, 5, "A");
63 ChimeraCommands.addAtomSpecRange(map, Color.red, 0, 6, 9, "A");
65 // Colours should appear in the Chimera command in the order in which
66 // they were added; within colour, by model, by chain, ranges in start order
67 String command = new ChimeraXCommands().buildColourCommands(map).get(0);
70 "color #0/A:2-5,9-23/B:7|#1/A:1/B:4-7 #0000ff; color #1/A:3-5,8 #ffff00; color #0/A:3-9 #ff0000");
73 @Test(groups = { "Functional" })
74 public void testBuildSetAttributeCommands()
77 * make a map of { featureType, {featureValue, {residue range specification } } }
79 Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
80 Map<Object, AtomSpecModel> featureValues = new HashMap<>();
83 * start with just one feature/value...
85 featuresMap.put("chain", featureValues);
86 ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 8, 20, "A");
88 ChimeraXCommands commandGenerator = new ChimeraXCommands();
89 List<String> commands = commandGenerator
90 .buildSetAttributeCommands(featuresMap);
91 assertEquals(1, commands.size());
94 * feature name gets a jv_ namespace prefix
95 * feature value is quoted in case it contains spaces
97 assertEquals(commands.get(0),
98 "setattr #0/A:8-20 res jv_chain 'X' create true");
100 // add same feature value, overlapping range
101 ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 3, 9, "A");
102 // same feature value, contiguous range
103 ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "A");
104 commands = commandGenerator.buildSetAttributeCommands(featuresMap);
105 assertEquals(1, commands.size());
106 assertEquals(commands.get(0),
107 "setattr #0/A:3-25 res jv_chain 'X' create true");
109 // same feature value and model, different chain
110 ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "B");
111 // same feature value and chain, different model
112 ChimeraCommands.addAtomSpecRange(featureValues, "X", 1, 26, 30, "A");
113 commands = commandGenerator.buildSetAttributeCommands(featuresMap);
114 assertEquals(1, commands.size());
115 assertEquals(commands.get(0),
116 "setattr #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true");
118 // same feature, different value
119 ChimeraCommands.addAtomSpecRange(featureValues, "Y", 0, 40, 50, "A");
120 commands = commandGenerator.buildSetAttributeCommands(featuresMap);
121 assertEquals(2, commands.size());
122 // commands are ordered by feature type but not by value
123 // so use contains to test for the expected command:
126 "setattr #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true"));
128 .contains("setattr #0/A:40-50 res jv_chain 'Y' create true"));
131 featureValues.clear();
132 featuresMap.put("side-chain binding!", featureValues);
133 ChimeraCommands.addAtomSpecRange(featureValues,
134 "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", 0, 7, 15,
136 // feature names are sanitised to change non-alphanumeric to underscore
137 // feature values are sanitised to encode single quote characters
138 commands = commandGenerator.buildSetAttributeCommands(featuresMap);
139 assertTrue(commands.contains(
140 "setattr #0/A:7-15 res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' create true"));
143 @Test(groups = { "Functional" })
144 public void testColourBySequence_hiddenColumns()
147 * load these sequences, coloured by Strand propensity,
148 * with columns 2-4 hidden
150 SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG");
151 SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS");
152 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
153 AlignFrame af = new AlignFrame(al, 800, 500);
154 af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
155 ColumnSelection cs = new ColumnSelection();
159 af.getViewport().setColumnSelection(cs);
160 af.hideSelColumns_actionPerformed(null);
161 SequenceRenderer sr = new SequenceRenderer(af.getViewport());
162 SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
163 String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
164 StructureSelectionManager ssm = new StructureSelectionManager();
167 * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
169 HashMap<Integer, int[]> map = new HashMap<>();
170 for (int pos = 1; pos <= seq1.getLength(); pos++)
172 map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
174 StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
176 ssm.addStructureMapping(sm1);
177 StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
179 ssm.addStructureMapping(sm2);
181 String[] commands = new ChimeraXCommands()
182 .colourBySequence(ssm, files, seqs, sr, af.alignPanel);
183 assertEquals(1, commands.length);
184 String theCommand = commands[0];
185 // M colour is #82827d (see strand.html help page)
186 assertTrue(theCommand.contains("color #0/A:21|#1/B:21 #82827d"));// #0:21.A|#1:21.B"));
187 // H colour is #60609f
188 assertTrue(theCommand.contains("color #0/A:22 #60609f"));
189 // V colour is #ffff00
190 assertTrue(theCommand.contains("color #1/B:22 #ffff00"));
191 // hidden columns are Gray (128, 128, 128)
192 assertTrue(theCommand.contains("color #0/A:23-25|#1/B:23-25"));
193 // S and G are both coloured #4949b6
194 assertTrue(theCommand.contains("color #0/A:26-30|#1/B:26-30"));
197 @Test(groups = { "Functional" })
198 public void testSuperposeStructures()
200 StructureCommandsI testee = new ChimeraXCommands();
201 AtomSpecModel ref = new AtomSpecModel();
202 ref.addRange(1, 12, 14, "A");
203 ref.addRange(1, 18, 18, "B");
204 ref.addRange(1, 22, 23, "B");
205 AtomSpecModel toAlign = new AtomSpecModel();
206 toAlign.addRange(2, 15, 17, "B");
207 toAlign.addRange(2, 20, 21, "B");
208 toAlign.addRange(2, 22, 22, "C");
209 String command = testee.superposeStructures(ref, toAlign);
210 String refSpec = "#1/A:12-14/B:18,22-23";
211 String toAlignSpec = "#2/B:15-17,20-21/C:22";
212 String expected = String.format(
213 "align %s %s;~display all; chain @CA|P; ribbon %s|%s; focus",
214 refSpec, toAlignSpec, refSpec, toAlignSpec);
215 assertEquals(command, expected);