Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JmolCommandsTest	49	110	15	1.0100%	Show methods

Class JmolCommandsTest

Class JmolCommandsTest	Line # 49	Total Statements 110	Complexity 15	TOTAL Coverage 1.0100%
setUp() : void   setUp() : void	5353	1.01	1.01	1.0 1.0100%
testGetColourBySequenceCommands_hiddenColumns() : void   testGetColourBySequenceCommands_hiddenColumns() : void	5959	34.034	2.02	1.0 1.0100%
testGetAtomSpec() : void   testGetAtomSpec() : void	129129	22.022	1.01	1.0 1.0100%
testColourBySequence() : void   testColourBySequence() : void	167167	16.016	1.01	1.0 1.0100%
testSuperposeStructures() : void   testSuperposeStructures() : void	192192	14.014	1.01	1.0 1.0100%
testGetModelStartNo() : void   testGetModelStartNo() : void	215215	1.01	1.01	1.0 1.0100%
testColourByChain() : void   testColourByChain() : void	221221	2.02	1.01	1.0 1.0100%
testColourByCharge() : void   testColourByCharge() : void	228228	3.03	1.01	1.0 1.0100%
testSetBackgroundColour() : void   testSetBackgroundColour() : void	238238	2.02	1.01	1.0 1.0100%
testFocusView() : void   testFocusView() : void	245245	2.02	1.01	1.0 1.0100%
testSaveSession() : void   testSaveSession() : void	252252	2.02	1.01	1.0 1.0100%
testShowBackbone() : void   testShowBackbone() : void	259259	3.03	1.01	1.0 1.0100%
testLoadFile() : void   testLoadFile() : void	268268	4.04	1.01	1.0 1.0100%
testOpenSession() : void   testOpenSession() : void	279279	4.04	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.2936508	jalview.ext.jmol.JmolCommandsTest.testGetColourBySequenceCommands_hiddenColumnsjalview.ext.jmol.JmolCommandsTest.testGetColourBySequenceCommands_hiddenColumns	1PASS
	0.18253969	jalview.ext.jmol.JmolCommandsTest.testGetAtomSpecjalview.ext.jmol.JmolCommandsTest.testGetAtomSpec	1PASS
	0.13492064	jalview.ext.jmol.JmolCommandsTest.testColourBySequencejalview.ext.jmol.JmolCommandsTest.testColourBySequence	1PASS
	0.11904762	jalview.ext.jmol.JmolCommandsTest.testSuperposeStructuresjalview.ext.jmol.JmolCommandsTest.testSuperposeStructures	1PASS
	0.03968254	jalview.ext.jmol.JmolCommandsTest.testOpenSessionjalview.ext.jmol.JmolCommandsTest.testOpenSession	1PASS
	0.03968254	jalview.ext.jmol.JmolCommandsTest.testLoadFilejalview.ext.jmol.JmolCommandsTest.testLoadFile	1PASS
	0.031746034	jalview.ext.jmol.JmolCommandsTest.testShowBackbonejalview.ext.jmol.JmolCommandsTest.testShowBackbone	1PASS
	0.031746034	jalview.ext.jmol.JmolCommandsTest.testColourByChargejalview.ext.jmol.JmolCommandsTest.testColourByCharge	1PASS
	0.023809524	jalview.ext.jmol.JmolCommandsTest.testSetBackgroundColourjalview.ext.jmol.JmolCommandsTest.testSetBackgroundColour	1PASS
	0.023809524	jalview.ext.jmol.JmolCommandsTest.testSaveSessionjalview.ext.jmol.JmolCommandsTest.testSaveSession	1PASS
	0.023809524	jalview.ext.jmol.JmolCommandsTest.testColourByChainjalview.ext.jmol.JmolCommandsTest.testColourByChain	1PASS
	0.023809524	jalview.ext.jmol.JmolCommandsTest.testFocusViewjalview.ext.jmol.JmolCommandsTest.testFocusView	1PASS
	0.015873017	jalview.ext.jmol.JmolCommandsTest.testGetModelStartNojalview.ext.jmol.JmolCommandsTest.testGetModelStartNo	1PASS

 

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.StructureCommandsI.AtomSpecType;
46		import jalview.structure.StructureMapping;
47		import jalview.structure.StructureSelectionManager;
48
		100% Uncovered Elements: 0 (126) Complexity: 15 Complexity Density: 0.14
49		public class JmolCommandsTest
50		{
51		private JmolCommands testee;
52
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
53	1	@BeforeClass(alwaysRun = true)...
54		public void setUp()
55		{
56	1	testee = new JmolCommands();
57		}
58
		100% Uncovered Elements: 0 (36) Complexity: 2 Complexity Density: 0.06 1PASS
59	1	@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
		100% Uncovered Elements: 0 (22) Complexity: 1 Complexity Density: 0.05 1PASS
129	1	@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
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.06 1PASS
167	1	@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
		100% Uncovered Elements: 0 (14) Complexity: 1 Complexity Density: 0.07 1PASS
192	1	@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
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1 1PASS
215	1	@Test(groups = "Functional")...
216		public void testGetModelStartNo()
217		{
218	1	assertEquals(testee.getModelStartNo(), 1);
219		}
220
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5 1PASS
221	1	@Test(groups = "Functional")...
222		public void testColourByChain()
223		{
224	1	StructureCommandI cmd = testee.colourByChain();
225	1	assertEquals(cmd.getCommand(), "select *;color chain");
226		}
227
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
228	1	@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
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5 1PASS
238	1	@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
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5 1PASS
245	1	@Test(groups = "Functional")...
246		public void testFocusView()
247		{
248	1	StructureCommandI cmd = testee.focusView();
249	1	assertEquals(cmd.getCommand(), "zoom 0");
250		}
251
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5 1PASS
252	1	@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
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
259	1	@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
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25 1PASS
268	1	@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
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25 1PASS
279	1	@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		}