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.StructureMapping;
35 import jalview.structure.StructureSelectionManager;
37 import java.awt.Color;
38 import java.util.HashMap;
39 import java.util.LinkedHashMap;
40 import java.util.List;
43 import org.testng.annotations.Test;
45 public class ChimeraCommandsTest
48 @Test(groups = { "Functional" })
49 public void testBuildColourCommands()
52 Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
53 ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 2, 5, "A");
54 ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 7, 7, "B");
55 ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 9, 23, "A");
56 ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 1, 1, "A");
57 ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 4, 7, "B");
58 ChimeraCommands.addAtomSpecRange(map, Color.yellow, 1, 8, 8, "A");
59 ChimeraCommands.addAtomSpecRange(map, Color.yellow, 1, 3, 5, "A");
60 ChimeraCommands.addAtomSpecRange(map, Color.red, 0, 3, 5, "A");
61 ChimeraCommands.addAtomSpecRange(map, Color.red, 0, 6, 9, "A");
63 // Colours should appear in the Chimera command in the order in which
64 // they were added; within colour, by model, by chain, ranges in start order
65 String command = new ChimeraCommands().buildColourCommands(map).get(0);
68 "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");
71 @Test(groups = { "Functional" })
72 public void testBuildSetAttributeCommands()
75 * make a map of { featureType, {featureValue, {residue range specification } } }
77 Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
78 Map<Object, AtomSpecModel> featureValues = new HashMap<>();
81 * start with just one feature/value...
83 featuresMap.put("chain", featureValues);
84 ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 8, 20, "A");
86 ChimeraCommands commandGenerator = new ChimeraCommands();
87 List<String> commands = commandGenerator
88 .buildSetAttributeCommands(featuresMap);
89 assertEquals(1, commands.size());
92 * feature name gets a jv_ namespace prefix
93 * feature value is quoted in case it contains spaces
95 assertEquals(commands.get(0), "setattr res jv_chain 'X' #0:8-20.A");
97 // add same feature value, overlapping range
98 ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 3, 9, "A");
99 // same feature value, contiguous range
100 ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "A");
101 commands = commandGenerator.buildSetAttributeCommands(featuresMap);
102 assertEquals(1, commands.size());
103 assertEquals(commands.get(0), "setattr res jv_chain 'X' #0:3-25.A");
105 // same feature value and model, different chain
106 ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "B");
107 // same feature value and chain, different model
108 ChimeraCommands.addAtomSpecRange(featureValues, "X", 1, 26, 30, "A");
109 commands = commandGenerator.buildSetAttributeCommands(featuresMap);
110 assertEquals(1, commands.size());
111 assertEquals(commands.get(0),
112 "setattr res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A");
114 // same feature, different value
115 ChimeraCommands.addAtomSpecRange(featureValues, "Y", 0, 40, 50, "A");
116 commands = commandGenerator.buildSetAttributeCommands(featuresMap);
117 assertEquals(2, commands.size());
118 // commands are ordered by feature type but not by value
119 // so use contains to test for the expected command:
122 "setattr res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A"));
123 assertTrue(commands.contains("setattr res jv_chain 'Y' #0:40-50.A"));
126 featureValues.clear();
127 featuresMap.put("side-chain binding!", featureValues);
128 ChimeraCommands.addAtomSpecRange(featureValues,
129 "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", 0, 7, 15,
131 // feature names are sanitised to change non-alphanumeric to underscore
132 // feature values are sanitised to encode single quote characters
133 commands = commandGenerator.buildSetAttributeCommands(featuresMap);
136 "setattr res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' #0:7-15.A"));
140 * Tests for the method that prefixes and sanitises a feature name so it can
141 * be used as a valid, namespaced attribute name in Chimera
143 @Test(groups = { "Functional" })
144 public void testMakeAttributeName()
146 assertEquals(ChimeraCommands.makeAttributeName(null), "jv_");
147 assertEquals(ChimeraCommands.makeAttributeName(""), "jv_");
148 assertEquals(ChimeraCommands.makeAttributeName("helix"), "jv_helix");
149 assertEquals(ChimeraCommands.makeAttributeName("Hello World 24"),
150 "jv_Hello_World_24");
152 ChimeraCommands.makeAttributeName("!this is-a_very*{odd(name"),
153 "jv__this_is_a_very__odd_name");
154 // name ending in color gets underscore appended
155 assertEquals(ChimeraCommands.makeAttributeName("helixColor"),
159 @Test(groups = { "Functional" })
160 public void testColourBySequence_hiddenColumns()
163 * load these sequences, coloured by Strand propensity,
164 * with columns 2-4 hidden
166 SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG");
167 SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS");
168 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
169 AlignFrame af = new AlignFrame(al, 800, 500);
170 af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
171 ColumnSelection cs = new ColumnSelection();
175 af.getViewport().setColumnSelection(cs);
176 af.hideSelColumns_actionPerformed(null);
177 SequenceRenderer sr = new SequenceRenderer(af.getViewport());
178 SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
179 String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
180 StructureSelectionManager ssm = new StructureSelectionManager();
183 * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
185 HashMap<Integer, int[]> map = new HashMap<>();
186 for (int pos = 1; pos <= seq1.getLength(); pos++)
188 map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
190 StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
192 ssm.addStructureMapping(sm1);
193 StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
195 ssm.addStructureMapping(sm2);
197 String[] commands = new ChimeraCommands()
198 .colourBySequence(ssm, files, seqs, sr, af.alignPanel);
199 assertEquals(1, commands.length);
200 String theCommand = commands[0];
201 // M colour is #82827d (see strand.html help page)
202 assertTrue(theCommand.contains("color #82827d #0:21.A|#1:21.B"));
203 // H colour is #60609f
204 assertTrue(theCommand.contains("color #60609f #0:22.A"));
205 // V colour is #ffff00
206 assertTrue(theCommand.contains("color #ffff00 #1:22.B"));
207 // hidden columns are Gray (128, 128, 128)
208 assertTrue(theCommand.contains("color #808080 #0:23-25.A|#1:23-25.B"));
209 // S and G are both coloured #4949b6
210 assertTrue(theCommand.contains("color #4949b6 #0:26-30.A|#1:26-30.B"));