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.JvOptionPane;
33 import jalview.gui.SequenceRenderer;
34 import jalview.schemes.JalviewColourScheme;
35 import jalview.structure.StructureMapping;
36 import jalview.structure.StructureMappingcommandSet;
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.BeforeClass;
46 import org.testng.annotations.Test;
48 public class ChimeraCommandsTest
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 testBuildColourCommands()
62 Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
63 ChimeraCommands.addColourRange(map, Color.blue, 0, 2, 5, "A");
64 ChimeraCommands.addColourRange(map, Color.blue, 0, 7, 7, "B");
65 ChimeraCommands.addColourRange(map, Color.blue, 0, 9, 23, "A");
66 ChimeraCommands.addColourRange(map, Color.blue, 1, 1, 1, "A");
67 ChimeraCommands.addColourRange(map, Color.blue, 1, 4, 7, "B");
68 ChimeraCommands.addColourRange(map, Color.yellow, 1, 8, 8, "A");
69 ChimeraCommands.addColourRange(map, Color.yellow, 1, 3, 5, "A");
70 ChimeraCommands.addColourRange(map, Color.red, 0, 3, 5, "A");
71 ChimeraCommands.addColourRange(map, Color.red, 0, 6, 9, "A");
73 // Colours should appear in the Chimera command in the order in which
74 // they were added; within colour, by model, by chain, ranges in start order
75 // all prefixed with #808080 to colour hidden regions (if shown) gray
76 String command = ChimeraCommands.buildColourCommands(map).get(0);
79 "color #808080; 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");
82 @Test(groups = { "Functional" })
83 public void testBuildSetAttributeCommands()
86 * make a map of { featureType, {featureValue, {residue range specification } } }
88 Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
89 Map<Object, AtomSpecModel> featureValues = new HashMap<>();
92 * start with just one feature/value...
94 featuresMap.put("chain", featureValues);
95 ChimeraCommands.addColourRange(featureValues, "X", 0, 8, 20, "A");
97 List<String> commands = ChimeraCommands
98 .buildSetAttributeCommands(featuresMap);
99 assertEquals(1, commands.size());
102 * feature name gets a jv_ namespace prefix
103 * feature value is quoted in case it contains spaces
105 assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:8-20.A");
107 // add same feature value, overlapping range
108 ChimeraCommands.addColourRange(featureValues, "X", 0, 3, 9, "A");
109 // same feature value, contiguous range
110 ChimeraCommands.addColourRange(featureValues, "X", 0, 21, 25, "A");
111 commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
112 assertEquals(1, commands.size());
113 assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:3-25.A");
115 // same feature value and model, different chain
116 ChimeraCommands.addColourRange(featureValues, "X", 0, 21, 25, "B");
117 // same feature value and chain, different model
118 ChimeraCommands.addColourRange(featureValues, "X", 1, 26, 30, "A");
119 commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
120 assertEquals(1, commands.size());
121 assertEquals(commands.get(0),
122 "setattr r jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A");
124 // same feature, different value
125 ChimeraCommands.addColourRange(featureValues, "Y", 0, 40, 50, "A");
126 commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
127 assertEquals(2, commands.size());
128 // commands are ordered by feature type but not by value
129 // so use contains to test for the expected command:
131 .contains("setattr r jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A"));
132 assertTrue(commands.contains("setattr r jv_chain 'Y' #0:40-50.A"));
135 featureValues.clear();
136 featuresMap.put("side-chain binding!", featureValues);
137 ChimeraCommands.addColourRange(featureValues,
138 "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", 0, 7, 15,
140 // feature names are sanitised to change non-alphanumeric to underscore
141 // feature values are sanitised to encode single quote characters
142 commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
144 .contains("setattr r jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' #0:7-15.A"));
148 * Tests for the method that prefixes and sanitises a feature name so it can
149 * be used as a valid, namespaced attribute name in Chimera
151 @Test(groups = { "Functional" })
152 public void testMakeAttributeName()
154 assertEquals(ChimeraCommands.makeAttributeName(null), "jv_");
155 assertEquals(ChimeraCommands.makeAttributeName(""), "jv_");
156 assertEquals(ChimeraCommands.makeAttributeName("helix"), "jv_helix");
157 assertEquals(ChimeraCommands.makeAttributeName("Hello World 24"),
158 "jv_Hello_World_24");
160 ChimeraCommands.makeAttributeName("!this is-a_very*{odd(name"),
161 "jv__this_is_a_very__odd_name");
162 // name ending in color gets underscore appended
163 assertEquals(ChimeraCommands.makeAttributeName("helixColor"),
167 @Test(groups = { "Functional" })
168 public void testGetColourBySequenceCommands_hiddenColumns()
171 * load these sequences, coloured by Strand propensity,
172 * with columns 2-4 hidden
174 SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG");
175 SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS");
176 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
177 AlignFrame af = new AlignFrame(al, 800, 500);
178 af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
179 ColumnSelection cs = new ColumnSelection();
183 af.getViewport().setColumnSelection(cs);
184 af.hideSelColumns_actionPerformed(null);
185 SequenceRenderer sr = new SequenceRenderer(af.getViewport());
186 SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
187 String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
188 StructureSelectionManager ssm = new StructureSelectionManager();
191 * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
193 HashMap<Integer, int[]> map = new HashMap<>();
194 for (int pos = 1; pos <= seq1.getLength(); pos++)
196 map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
198 StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
200 ssm.addStructureMapping(sm1);
201 StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
203 ssm.addStructureMapping(sm2);
205 StructureMappingcommandSet[] commands = ChimeraCommands
206 .getColourBySequenceCommand(ssm, files, seqs, sr, false,
208 assertEquals(1, commands.length);
209 assertEquals(1, commands[0].commands.length);
210 String theCommand = commands[0].commands[0];
211 // M colour is #82827d (see strand.html help page)
212 assertTrue(theCommand.contains("color #82827d #0:21.A|#1:21.B"));
213 // H colour is #60609f
214 assertTrue(theCommand.contains("color #60609f #0:22.A"));
215 // V colour is #ffff00
216 assertTrue(theCommand.contains("color #ffff00 #1:22.B"));
217 // hidden columns are Gray (128, 128, 128)
218 assertTrue(theCommand.contains("color #808080 #0:23-25.A|#1:23-25.B"));
219 // S and G are both coloured #4949b6
220 assertTrue(theCommand.contains("color #4949b6 #0:26-30.A|#1:26-30.B"));