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Coverage Report

  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.ext.jmol

File JmolCommandsTest.java

 

Code metrics

2
110
14
1
286
219
15
0.14
7.86
14
1.07

Classes

Class Line # Actions
JmolCommandsTest 48 110 15
1.0100%
 

Contributing tests

This file is covered by 13 tests. .

Source view

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.StructureMapping;
46    import jalview.structure.StructureSelectionManager;
47   
 
48    public class JmolCommandsTest
49    {
50    private JmolCommands testee;
51   
 
52  1 toggle @BeforeClass(alwaysRun = true)
53    public void setUp()
54    {
55  1 testee = new JmolCommands();
56    }
57   
 
58  1 toggle @Test(groups = { "Functional" })
59    public void testGetColourBySequenceCommands_hiddenColumns()
60    {
61    /*
62    * load these sequences, coloured by Strand propensity,
63    * with columns 2-4 hidden
64    */
65  1 SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG");
66  1 SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS");
67  1 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
68  1 AlignFrame af = new AlignFrame(al, 800, 500);
69  1 af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
70  1 ColumnSelection cs = new ColumnSelection();
71  1 cs.addElement(2);
72  1 cs.addElement(3);
73  1 cs.addElement(4);
74  1 af.getViewport().setColumnSelection(cs);
75  1 af.hideSelColumns_actionPerformed(null);
76  1 SequenceRenderer sr = new SequenceRenderer(af.getViewport());
77  1 SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
78  1 String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
79  1 StructureSelectionManager ssm = new StructureSelectionManager();
80   
81    /*
82    * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
83    */
84  1 HashMap<Integer, int[]> map = new HashMap<>();
85  11 for (int pos = 1; pos <= seq1.getLength(); pos++)
86    {
87  10 map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
88    }
89  1 StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
90    "A", map, null);
91  1 ssm.addStructureMapping(sm1);
92  1 StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
93    "B", map, null);
94  1 ssm.addStructureMapping(sm2);
95   
96  1 String[] commands = testee.colourBySequence(ssm,
97    files,
98    seqs, sr, 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, false), "");
134  1 model.addRange("1", 2, 4, "A");
135  1 assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1");
136  1 model.addRange("1", 8, 8, "A");
137  1 assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1|8:A/1.1");
138  1 model.addRange("1", 5, 7, "B");
139  1 assertEquals(testee.getAtomSpec(model, false),
140    "2-4:A/1.1|8:A/1.1|5-7:B/1.1");
141  1 model.addRange("1", 3, 5, "A");
142  1 assertEquals(testee.getAtomSpec(model, false),
143    "2-5:A/1.1|8:A/1.1|5-7:B/1.1");
144  1 model.addRange("2", 1, 4, "B");
145  1 assertEquals(testee.getAtomSpec(model, false),
146    "2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1");
147  1 model.addRange("2", 5, 9, "C");
148  1 assertEquals(testee.getAtomSpec(model, false),
149    "2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1|5-9:C/2.1");
150  1 model.addRange("1", 8, 10, "B");
151  1 assertEquals(testee.getAtomSpec(model, false),
152    "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
153  1 model.addRange("1", 8, 9, "B");
154  1 assertEquals(testee.getAtomSpec(model, false),
155    "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
156  1 model.addRange("2", 3, 10, "C"); // subsumes 5-9
157  1 assertEquals(testee.getAtomSpec(model, false),
158    "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1");
159  1 model.addRange("5", 25, 35, " ");
160  1 assertEquals(testee.getAtomSpec(model, false),
161    "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");
162   
163    }
164   
 
165  1 toggle @Test(groups = { "Functional" })
166    public void testColourBySequence()
167    {
168  1 Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
169  1 JmolCommands.addAtomSpecRange(map, Color.blue, "1", 2, 5, "A");
170  1 JmolCommands.addAtomSpecRange(map, Color.blue, "1", 7, 7, "B");
171  1 JmolCommands.addAtomSpecRange(map, Color.blue, "1", 9, 23, "A");
172  1 JmolCommands.addAtomSpecRange(map, Color.blue, "2", 1, 1, "A");
173  1 JmolCommands.addAtomSpecRange(map, Color.blue, "2", 4, 7, "B");
174  1 JmolCommands.addAtomSpecRange(map, Color.yellow, "2", 8, 8, "A");
175  1 JmolCommands.addAtomSpecRange(map, Color.yellow, "2", 3, 5, "A");
176  1 JmolCommands.addAtomSpecRange(map, Color.red, "1", 3, 5, "A");
177  1 JmolCommands.addAtomSpecRange(map, Color.red, "1", 6, 9, "A");
178   
179    // Colours should appear in the Jmol command in the order in which
180    // they were added; within colour, by model, by chain, ranges in start order
181  1 List<StructureCommandI> commands = testee.colourBySequence(map);
182  1 assertEquals(commands.size(), 1);
183  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]";
184  1 String expected2 = "select 3-5:A/2.1|8:A/2.1;color[255,255,0]";
185  1 String expected3 = "select 3-9:A/1.1;color[255,0,0]";
186  1 assertEquals(commands.get(0).getCommand(),
187    expected1 + ";" + expected2 + ";" + expected3);
188    }
189   
 
190  1 toggle @Test(groups = { "Functional" })
191    public void testSuperposeStructures()
192    {
193  1 AtomSpecModel ref = new AtomSpecModel();
194  1 ref.addRange("1", 12, 14, "A");
195  1 ref.addRange("1", 18, 18, "B");
196  1 ref.addRange("1", 22, 23, "B");
197  1 AtomSpecModel toAlign = new AtomSpecModel();
198  1 toAlign.addRange("2", 15, 17, "B");
199  1 toAlign.addRange("2", 20, 21, "B");
200  1 toAlign.addRange("2", 22, 22, "C");
201  1 List<StructureCommandI> command = testee.superposeStructures(ref,
202    toAlign);
203  1 assertEquals(command.size(), 1);
204  1 String refSpec = "12-14:A/1.1|18:B/1.1|22-23:B/1.1";
205  1 String toAlignSpec = "15-17:B/2.1|20-21:B/2.1|22:C/2.1";
206  1 String expected = String.format(
207    "compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS {%s}{%s} ROTATE TRANSLATE ;select %s|%s;cartoons",
208    toAlignSpec, refSpec, toAlignSpec, refSpec);
209  1 assertEquals(command.get(0).getCommand(), expected);
210    }
211   
 
212  1 toggle @Test(groups = "Functional")
213    public void testGetModelStartNo()
214    {
215  1 assertEquals(testee.getModelStartNo(), 1);
216    }
217   
 
218  1 toggle @Test(groups = "Functional")
219    public void testColourByChain()
220    {
221  1 StructureCommandI cmd = testee.colourByChain();
222  1 assertEquals(cmd.getCommand(), "select *;color chain");
223    }
224   
 
225  1 toggle @Test(groups = "Functional")
226    public void testColourByCharge()
227    {
228  1 List<StructureCommandI> cmds = testee.colourByCharge();
229  1 assertEquals(cmds.size(), 1);
230  1 assertEquals(cmds.get(0).getCommand(),
231    "select *;color white;select ASP,GLU;color red;"
232    + "select LYS,ARG;color blue;select CYS;color yellow");
233    }
234   
 
235  1 toggle @Test(groups = "Functional")
236    public void testSetBackgroundColour()
237    {
238  1 StructureCommandI cmd = testee.setBackgroundColour(Color.PINK);
239  1 assertEquals(cmd.getCommand(), "background [255,175,175]");
240    }
241   
 
242  1 toggle @Test(groups = "Functional")
243    public void testFocusView()
244    {
245  1 StructureCommandI cmd = testee.focusView();
246  1 assertEquals(cmd.getCommand(), "zoom 0");
247    }
248   
 
249  1 toggle @Test(groups = "Functional")
250    public void testSaveSession()
251    {
252  1 StructureCommandI cmd = testee.saveSession("/some/filepath");
253  1 assertEquals(cmd.getCommand(), "write STATE \"/some/filepath\"");
254    }
255   
 
256  1 toggle @Test(groups = "Functional")
257    public void testShowBackbone()
258    {
259  1 List<StructureCommandI> cmds = testee.showBackbone();
260  1 assertEquals(cmds.size(), 1);
261  1 assertEquals(cmds.get(0).getCommand(),
262    "select *; cartoons off; backbone");
263    }
264   
 
265  1 toggle @Test(groups = "Functional")
266    public void testLoadFile()
267    {
268  1 StructureCommandI cmd = testee.loadFile("/some/filepath");
269  1 assertEquals(cmd.getCommand(), "load FILES \"/some/filepath\"");
270   
271    // single backslash gets escaped to double
272  1 cmd = testee.loadFile("\\some\\filepath");
273  1 assertEquals(cmd.getCommand(), "load FILES \"\\\\some\\\\filepath\"");
274    }
275   
 
276  1 toggle @Test(groups = "Functional")
277    public void testOpenSession()
278    {
279  1 StructureCommandI cmd = testee.openSession("/some/filepath");
280  1 assertEquals(cmd.getCommand(), "load FILES \"/some/filepath\"");
281   
282    // single backslash gets escaped to double
283  1 cmd = testee.openSession("\\some\\filepath");
284  1 assertEquals(cmd.getCommand(), "load FILES \"\\\\some\\\\filepath\"");
285    }
286    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.