1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.ext.jmol

File JmolCommandsTest.java

 

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Class
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Actions
JmolCommandsTest 49 110 15
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Contributing tests

This file is covered by 13 tests. .

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.ext.jmol;
22   
23    import static org.testng.Assert.assertEquals;
24    import static org.testng.Assert.assertTrue;
25   
26    import java.awt.Color;
27    import java.util.HashMap;
28    import java.util.LinkedHashMap;
29    import java.util.List;
30    import java.util.Map;
31   
32    import org.testng.annotations.BeforeClass;
33    import org.testng.annotations.Test;
34   
35    import jalview.datamodel.Alignment;
36    import jalview.datamodel.AlignmentI;
37    import jalview.datamodel.ColumnSelection;
38    import jalview.datamodel.Sequence;
39    import jalview.datamodel.SequenceI;
40    import jalview.gui.AlignFrame;
41    import jalview.gui.SequenceRenderer;
42    import jalview.schemes.JalviewColourScheme;
43    import jalview.structure.AtomSpecModel;
44    import jalview.structure.StructureCommandI;
45    import jalview.structure.StructureCommandsI.AtomSpecType;
46    import jalview.structure.StructureMapping;
47    import jalview.structure.StructureSelectionManager;
48   
 
49    public class JmolCommandsTest
50    {
51    private JmolCommands testee;
52   
 
53  1 toggle @BeforeClass(alwaysRun = true)
54    public void setUp()
55    {
56  1 testee = new JmolCommands();
57    }
58   
 
59  1 toggle @Test(groups = { "Functional" })
60    public void testGetColourBySequenceCommands_hiddenColumns()
61    {
62    /*
63    * load these sequences, coloured by Strand propensity,
64    * with columns 2-4 hidden
65    */
66  1 SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG");
67  1 SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS");
68  1 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
69  1 AlignFrame af = new AlignFrame(al, 800, 500);
70  1 af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
71  1 ColumnSelection cs = new ColumnSelection();
72  1 cs.addElement(2);
73  1 cs.addElement(3);
74  1 cs.addElement(4);
75  1 af.getViewport().setColumnSelection(cs);
76  1 af.hideSelColumns_actionPerformed(null);
77  1 SequenceRenderer sr = new SequenceRenderer(af.getViewport());
78  1 SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
79  1 String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
80  1 StructureSelectionManager ssm = new StructureSelectionManager();
81   
82    /*
83    * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
84    */
85  1 HashMap<Integer, int[]> map = new HashMap<>();
86  11 for (int pos = 1; pos <= seq1.getLength(); pos++)
87    {
88  10 map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
89    }
90  1 StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
91    "A", map, null);
92  1 ssm.addStructureMapping(sm1);
93  1 StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
94    "B", map, null);
95  1 ssm.addStructureMapping(sm2);
96   
97  1 String[] commands = testee.colourBySequence(ssm, files, seqs, sr,
98    af.alignPanel);
99  1 assertEquals(commands.length, 2);
100   
101  1 String chainACommand = commands[0];
102    // M colour is #82827d == (130, 130, 125) (see strand.html help page)
103  1 assertTrue(
104    chainACommand.contains("select 21:A/1.1;color[130,130,125]")); // first
105    // one
106    // H colour is #60609f == (96, 96, 159)
107  1 assertTrue(chainACommand.contains(";select 22:A/1.1;color[96,96,159]"));
108    // hidden columns are Gray (128, 128, 128)
109  1 assertTrue(chainACommand
110    .contains(";select 23-25:A/1.1;color[128,128,128]"));
111    // S and G are both coloured #4949b6 == (73, 73, 182)
112  1 assertTrue(
113    chainACommand.contains(";select 26-30:A/1.1;color[73,73,182]"));
114   
115  1 String chainBCommand = commands[1];
116    // M colour is #82827d == (130, 130, 125)
117  1 assertTrue(
118    chainBCommand.contains("select 21:B/2.1;color[130,130,125]"));
119    // V colour is #ffff00 == (255, 255, 0)
120  1 assertTrue(chainBCommand.contains(";select 22:B/2.1;color[255,255,0]"));
121    // hidden columns are Gray (128, 128, 128)
122  1 assertTrue(chainBCommand
123    .contains(";select 23-25:B/2.1;color[128,128,128]"));
124    // S and G are both coloured #4949b6 == (73, 73, 182)
125  1 assertTrue(
126    chainBCommand.contains(";select 26-30:B/2.1;color[73,73,182]"));
127    }
128   
 
129  1 toggle @Test(groups = "Functional")
130    public void testGetAtomSpec()
131    {
132  1 AtomSpecModel model = new AtomSpecModel();
133  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
134  1 model.addRange("1", 2, 4, "A");
135  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
136    "2-4:A/1.1");
137  1 model.addRange("1", 8, 8, "A");
138  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
139    "2-4:A/1.1|8:A/1.1");
140  1 model.addRange("1", 5, 7, "B");
141  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
142    "2-4:A/1.1|8:A/1.1|5-7:B/1.1");
143  1 model.addRange("1", 3, 5, "A");
144  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
145    "2-5:A/1.1|8:A/1.1|5-7:B/1.1");
146  1 model.addRange("2", 1, 4, "B");
147  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
148    "2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1");
149  1 model.addRange("2", 5, 9, "C");
150  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
151    "2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1|5-9:C/2.1");
152  1 model.addRange("1", 8, 10, "B");
153  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
154    "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
155  1 model.addRange("1", 8, 9, "B");
156  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
157    "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
158  1 model.addRange("2", 3, 10, "C"); // subsumes 5-9
159  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
160    "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1");
161  1 model.addRange("5", 25, 35, " ");
162  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
163    "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");
164   
165    }
166   
 
167  1 toggle @Test(groups = { "Functional" })
168    public void testColourBySequence()
169    {
170  1 Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
171  1 JmolCommands.addAtomSpecRange(map, Color.blue, "1", 2, 5, "A");
172  1 JmolCommands.addAtomSpecRange(map, Color.blue, "1", 7, 7, "B");
173  1 JmolCommands.addAtomSpecRange(map, Color.blue, "1", 9, 23, "A");
174  1 JmolCommands.addAtomSpecRange(map, Color.blue, "2", 1, 1, "A");
175  1 JmolCommands.addAtomSpecRange(map, Color.blue, "2", 4, 7, "B");
176  1 JmolCommands.addAtomSpecRange(map, Color.yellow, "2", 8, 8, "A");
177  1 JmolCommands.addAtomSpecRange(map, Color.yellow, "2", 3, 5, "A");
178  1 JmolCommands.addAtomSpecRange(map, Color.red, "1", 3, 5, "A");
179  1 JmolCommands.addAtomSpecRange(map, Color.red, "1", 6, 9, "A");
180   
181    // Colours should appear in the Jmol command in the order in which
182    // they were added; within colour, by model, by chain, ranges in start order
183  1 List<StructureCommandI> commands = testee.colourBySequence(map);
184  1 assertEquals(commands.size(), 1);
185  1 String expected1 = "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]";
186  1 String expected2 = "select 3-5:A/2.1|8:A/2.1;color[255,255,0]";
187  1 String expected3 = "select 3-9:A/1.1;color[255,0,0]";
188  1 assertEquals(commands.get(0).getCommand(),
189    expected1 + ";" + expected2 + ";" + expected3);
190    }
191   
 
192  1 toggle @Test(groups = { "Functional" })
193    public void testSuperposeStructures()
194    {
195  1 AtomSpecModel ref = new AtomSpecModel();
196  1 ref.addRange("1", 12, 14, "A");
197  1 ref.addRange("1", 18, 18, "B");
198  1 ref.addRange("1", 22, 23, "B");
199  1 AtomSpecModel toAlign = new AtomSpecModel();
200  1 toAlign.addRange("2", 15, 17, "B");
201  1 toAlign.addRange("2", 20, 21, "B");
202  1 toAlign.addRange("2", 22, 22, "C");
203  1 List<StructureCommandI> command = testee.superposeStructures(ref,
204    toAlign, AtomSpecType.ALPHA); // doesn't matter for Jmol whether nuc
205    // or protein
206  1 assertEquals(command.size(), 1);
207  1 String refSpec = "12-14:A/1.1|18:B/1.1|22-23:B/1.1";
208  1 String toAlignSpec = "15-17:B/2.1|20-21:B/2.1|22:C/2.1";
209  1 String expected = String.format(
210    "compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS {%s}{%s} ROTATE TRANSLATE ;select %s|%s;cartoons",
211    toAlignSpec, refSpec, toAlignSpec, refSpec);
212  1 assertEquals(command.get(0).getCommand(), expected);
213    }
214   
 
215  1 toggle @Test(groups = "Functional")
216    public void testGetModelStartNo()
217    {
218  1 assertEquals(testee.getModelStartNo(), 1);
219    }
220   
 
221  1 toggle @Test(groups = "Functional")
222    public void testColourByChain()
223    {
224  1 StructureCommandI cmd = testee.colourByChain();
225  1 assertEquals(cmd.getCommand(), "select *;color chain");
226    }
227   
 
228  1 toggle @Test(groups = "Functional")
229    public void testColourByCharge()
230    {
231  1 List<StructureCommandI> cmds = testee.colourByCharge();
232  1 assertEquals(cmds.size(), 1);
233  1 assertEquals(cmds.get(0).getCommand(),
234    "select *;color white;select ASP,GLU;color red;"
235    + "select LYS,ARG;color blue;select CYS;color yellow");
236    }
237   
 
238  1 toggle @Test(groups = "Functional")
239    public void testSetBackgroundColour()
240    {
241  1 StructureCommandI cmd = testee.setBackgroundColour(Color.PINK);
242  1 assertEquals(cmd.getCommand(), "background [255,175,175]");
243    }
244   
 
245  1 toggle @Test(groups = "Functional")
246    public void testFocusView()
247    {
248  1 StructureCommandI cmd = testee.focusView();
249  1 assertEquals(cmd.getCommand(), "zoom 0");
250    }
251   
 
252  1 toggle @Test(groups = "Functional")
253    public void testSaveSession()
254    {
255  1 StructureCommandI cmd = testee.saveSession("/some/filepath");
256  1 assertEquals(cmd.getCommand(), "write STATE \"/some/filepath\"");
257    }
258   
 
259  1 toggle @Test(groups = "Functional")
260    public void testShowBackbone()
261    {
262  1 List<StructureCommandI> cmds = testee.showBackbone();
263  1 assertEquals(cmds.size(), 1);
264  1 assertEquals(cmds.get(0).getCommand(),
265    "select *; cartoons off; backbone");
266    }
267   
 
268  1 toggle @Test(groups = "Functional")
269    public void testLoadFile()
270    {
271  1 StructureCommandI cmd = testee.loadFile("/some/filepath");
272  1 assertEquals(cmd.getCommand(), "load FILES \"/some/filepath\"");
273   
274    // single backslash gets escaped to double
275  1 cmd = testee.loadFile("\\some\\filepath");
276  1 assertEquals(cmd.getCommand(), "load FILES \"\\\\some\\\\filepath\"");
277    }
278   
 
279  1 toggle @Test(groups = "Functional")
280    public void testOpenSession()
281    {
282  1 StructureCommandI cmd = testee.openSession("/some/filepath");
283  1 assertEquals(cmd.getCommand(), "load FILES \"/some/filepath\"");
284   
285    // single backslash gets escaped to double
286  1 cmd = testee.openSession("\\some\\filepath");
287  1 assertEquals(cmd.getCommand(), "load FILES \"\\\\some\\\\filepath\"");
288    }
289    }