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<Object, AtomSpecModel>();
63 ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 2, 5, "A");
64 ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 7, 7, "B");
65 ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 9, 23, "A");
66 ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 1, 1, "A");
67 ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 4, 7, "B");
68 ChimeraCommands.addAtomSpecRange(map, Color.yellow, 1, 8, 8, "A");
69 ChimeraCommands.addAtomSpecRange(map, Color.yellow, 1, 3, 5, "A");
70 ChimeraCommands.addAtomSpecRange(map, Color.red, 0, 3, 5, "A");
71 ChimeraCommands.addAtomSpecRange(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 String command = ChimeraCommands.buildColourCommands(map).get(0);
78 "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");
81 @Test(groups = { "Functional" })
82 public void testBuildSetAttributeCommands()
85 * make a map of { featureType, {featureValue, {residue range specification } } }
87 Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<String, Map<Object, AtomSpecModel>>();
88 Map<Object, AtomSpecModel> featureValues = new HashMap<Object, AtomSpecModel>();
91 * start with just one feature/value...
93 featuresMap.put("chain", featureValues);
94 ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 8, 20, "A");
96 List<String> commands = ChimeraCommands
97 .buildSetAttributeCommands(featuresMap);
98 assertEquals(1, commands.size());
101 * feature name gets a jv_ namespace prefix
102 * feature value is quoted in case it contains spaces
104 assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:8-20.A");
106 // add same feature value, overlapping range
107 ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 3, 9, "A");
108 // same feature value, contiguous range
109 ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "A");
110 commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
111 assertEquals(1, commands.size());
112 assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:3-25.A");
114 // same feature value and model, different chain
115 ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "B");
116 // same feature value and chain, different model
117 ChimeraCommands.addAtomSpecRange(featureValues, "X", 1, 26, 30, "A");
118 commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
119 assertEquals(1, commands.size());
120 assertEquals(commands.get(0),
121 "setattr r jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A");
123 // same feature, different value
124 ChimeraCommands.addAtomSpecRange(featureValues, "Y", 0, 40, 50, "A");
125 commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
126 assertEquals(2, commands.size());
127 // commands are ordered by feature type but not by value
128 // so use contains to test for the expected command:
130 .contains("setattr r jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A"));
131 assertTrue(commands.contains("setattr r jv_chain 'Y' #0:40-50.A"));
134 featureValues.clear();
135 featuresMap.put("side-chain binding!", featureValues);
136 ChimeraCommands.addAtomSpecRange(featureValues,
137 "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", 0, 7, 15,
139 // feature names are sanitised to change non-alphanumeric to underscore
140 // feature values are sanitised to encode single quote characters
141 commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
143 .contains("setattr r jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' #0:7-15.A"));
147 * Tests for the method that prefixes and sanitises a feature name so it can
148 * be used as a valid, namespaced attribute name in Chimera
150 @Test(groups = { "Functional" })
151 public void testMakeAttributeName()
153 assertEquals(ChimeraCommands.makeAttributeName(null), "jv_");
154 assertEquals(ChimeraCommands.makeAttributeName(""), "jv_");
155 assertEquals(ChimeraCommands.makeAttributeName("helix"), "jv_helix");
156 assertEquals(ChimeraCommands.makeAttributeName("Hello World 24"),
157 "jv_Hello_World_24");
159 ChimeraCommands.makeAttributeName("!this is-a_very*{odd(name"),
160 "jv__this_is_a_very__odd_name");
161 // name ending in color gets underscore appended
162 assertEquals(ChimeraCommands.makeAttributeName("helixColor"),
166 @Test(groups = { "Functional" })
167 public void testGetColourBySequenceCommands_hiddenColumns()
170 * load these sequences, coloured by Strand propensity,
171 * with columns 2-4 hidden
173 SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG");
174 SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS");
175 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
176 AlignFrame af = new AlignFrame(al, 800, 500);
177 af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
178 ColumnSelection cs = new ColumnSelection();
182 af.getViewport().setColumnSelection(cs);
183 af.hideSelColumns_actionPerformed(null);
184 SequenceRenderer sr = new SequenceRenderer(af.getViewport());
185 SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
186 String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
187 StructureSelectionManager ssm = StructureSelectionManager.getStructureSelectionManager(null);
190 * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
192 HashMap<Integer, int[]> map = new HashMap<Integer, int[]>();
193 for (int pos = 1; pos <= seq1.getLength(); pos++)
195 map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
197 StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
199 ssm.addStructureMapping(sm1);
200 StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
202 ssm.addStructureMapping(sm2);
204 StructureMappingcommandSet[] commands = ChimeraCommands
205 .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel);
206 assertEquals(1, commands.length);
207 assertEquals(1, commands[0].commands.length);
208 String theCommand = commands[0].commands[0];
209 // M colour is #82827d (see strand.html help page)
210 assertTrue(theCommand.contains("color #82827d #0:21.A|#1:21.B"));
211 // H colour is #60609f
212 assertTrue(theCommand.contains("color #60609f #0:22.A"));
213 // V colour is #ffff00
214 assertTrue(theCommand.contains("color #ffff00 #1:22.B"));
215 // hidden columns are Gray (128, 128, 128)
216 assertTrue(theCommand.contains("color #808080 #0:23-25.A|#1:23-25.B"));
217 // S and G are both coloured #4949b6
218 assertTrue(theCommand.contains("color #4949b6 #0:26-30.A|#1:26-30.B"));