Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
ChimeraCommandsTest	48	79	6	0	1.0100%	Show methods

Class ChimeraCommandsTest

Class ChimeraCommandsTest	Line # 48	Total Statements 79	Complexity 6	Uncovered Elements 0	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5151	2.02	1.01	0.00	1.0 1.0100%
testBuildColourCommands() : void   testBuildColourCommands() : void	5858	12.012	1.01	0.00	1.0 1.0100%
testBuildSetAttributeCommands() : void   testBuildSetAttributeCommands() : void	8181	28.028	1.01	0.00	1.0 1.0100%
testMakeAttributeName() : void   testMakeAttributeName() : void	150150	6.06	1.01	0.00	1.0 1.0100%
testGetColourBySequenceCommands_hiddenColumns() : void   testGetColourBySequenceCommands_hiddenColumns() : void	166166	31.031	2.02	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.39534885	jalview.ext.rbvi.chimera.ChimeraCommandsTest.testGetColourBySequenceCommands_hiddenColumnsjalview.ext.rbvi.chimera.ChimeraCommandsTest.testGetColourBySequenceCommands_hiddenColumns	1PASS
	0.3372093	jalview.ext.rbvi.chimera.ChimeraCommandsTest.testBuildSetAttributeCommandsjalview.ext.rbvi.chimera.ChimeraCommandsTest.testBuildSetAttributeCommands	1PASS
	0.15116279	jalview.ext.rbvi.chimera.ChimeraCommandsTest.testBuildColourCommandsjalview.ext.rbvi.chimera.ChimeraCommandsTest.testBuildColourCommands	1PASS
	0.08139535	jalview.ext.rbvi.chimera.ChimeraCommandsTest.testMakeAttributeNamejalview.ext.rbvi.chimera.ChimeraCommandsTest.testMakeAttributeName	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.rbvi.chimera;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertTrue;
25
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;
38
39		import java.awt.Color;
40		import java.util.HashMap;
41		import java.util.LinkedHashMap;
42		import java.util.List;
43		import java.util.Map;
44
45		import org.testng.annotations.BeforeClass;
46		import org.testng.annotations.Test;
47
		100% Uncovered Elements: 0 (86) Complexity: 6 Complexity Density: 0.08
48		public class ChimeraCommandsTest
49		{
50
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
51	1	@BeforeClass(alwaysRun = true)...
52		public void setUpJvOptionPane()
53		{
54	1	JvOptionPane.setInteractiveMode(false);
55	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
56		}
57
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
58	1	@Test(groups = { "Functional" })...
59		public void testBuildColourCommands()
60		{
61
62	1	Map<Object, AtomSpecModel> map = new LinkedHashMap<Object, AtomSpecModel>();
63	1	ChimeraCommands.addColourRange(map, Color.blue, 0, 2, 5, "A");
64	1	ChimeraCommands.addColourRange(map, Color.blue, 0, 7, 7, "B");
65	1	ChimeraCommands.addColourRange(map, Color.blue, 0, 9, 23, "A");
66	1	ChimeraCommands.addColourRange(map, Color.blue, 1, 1, 1, "A");
67	1	ChimeraCommands.addColourRange(map, Color.blue, 1, 4, 7, "B");
68	1	ChimeraCommands.addColourRange(map, Color.yellow, 1, 8, 8, "A");
69	1	ChimeraCommands.addColourRange(map, Color.yellow, 1, 3, 5, "A");
70	1	ChimeraCommands.addColourRange(map, Color.red, 0, 3, 5, "A");
71	1	ChimeraCommands.addColourRange(map, Color.red, 0, 6, 9, "A");
72
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	1	String command = ChimeraCommands.buildColourCommands(map).get(0);
76	1	assertEquals(
77		command,
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");
79		}
80
		100% Uncovered Elements: 0 (28) Complexity: 1 Complexity Density: 0.04 1PASS
81	1	@Test(groups = { "Functional" })...
82		public void testBuildSetAttributeCommands()
83		{
84		/*
85		* make a map of { featureType, {featureValue, {residue range specification } } }
86		*/
87	1	Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<String, Map<Object, AtomSpecModel>>();
88	1	Map<Object, AtomSpecModel> featureValues = new HashMap<Object, AtomSpecModel>();
89
90		/*
91		* start with just one feature/value...
92		*/
93	1	featuresMap.put("chain", featureValues);
94	1	ChimeraCommands.addColourRange(featureValues, "X", 0, 8, 20, "A");
95
96	1	List<String> commands = ChimeraCommands
97		.buildSetAttributeCommands(featuresMap);
98	1	assertEquals(1, commands.size());
99
100		/*
101		* feature name gets a jv_ namespace prefix
102		* feature value is quoted in case it contains spaces
103		*/
104	1	assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:8-20.A");
105
106		// add same feature value, overlapping range
107	1	ChimeraCommands.addColourRange(featureValues, "X", 0, 3, 9, "A");
108		// same feature value, contiguous range
109	1	ChimeraCommands.addColourRange(featureValues, "X", 0, 21, 25, "A");
110	1	commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
111	1	assertEquals(1, commands.size());
112	1	assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:3-25.A");
113
114		// same feature value and model, different chain
115	1	ChimeraCommands.addColourRange(featureValues, "X", 0, 21, 25, "B");
116		// same feature value and chain, different model
117	1	ChimeraCommands.addColourRange(featureValues, "X", 1, 26, 30, "A");
118	1	commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
119	1	assertEquals(1, commands.size());
120	1	assertEquals(commands.get(0),
121		"setattr r jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A");
122
123		// same feature, different value
124	1	ChimeraCommands.addColourRange(featureValues, "Y", 0, 40, 50, "A");
125	1	commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
126	1	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:
129	1	assertTrue(commands
130		.contains("setattr r jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A"));
131	1	assertTrue(commands.contains("setattr r jv_chain 'Y' #0:40-50.A"));
132
133	1	featuresMap.clear();
134	1	featureValues.clear();
135	1	featuresMap.put("side-chain binding!", featureValues);
136	1	ChimeraCommands.addColourRange(featureValues,
137		"<html>metal <a href=\"http:a.b.c/x\"> 'ion!", 0, 7, 15,
138		"A");
139		// feature names are sanitised to change non-alphanumeric to underscore
140		// feature values are sanitised to encode single quote characters
141	1	commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
142	1	assertTrue(commands
143		.contains("setattr r jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> &#39;ion!' #0:7-15.A"));
144		}
145
146		/**
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
149		*/
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17 1PASS
150	1	@Test(groups = { "Functional" })...
151		public void testMakeAttributeName()
152		{
153	1	assertEquals(ChimeraCommands.makeAttributeName(null), "jv_");
154	1	assertEquals(ChimeraCommands.makeAttributeName(""), "jv_");
155	1	assertEquals(ChimeraCommands.makeAttributeName("helix"), "jv_helix");
156	1	assertEquals(ChimeraCommands.makeAttributeName("Hello World 24"),
157		"jv_Hello_World_24");
158	1	assertEquals(
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	1	assertEquals(ChimeraCommands.makeAttributeName("helixColor"),
163		"jv_helixColor_");
164		}
165
		100% Uncovered Elements: 0 (33) Complexity: 2 Complexity Density: 0.06 1PASS
166	1	@Test(groups = { "Functional" })...
167		public void testGetColourBySequenceCommands_hiddenColumns()
168		{
169		/*
170		* load these sequences, coloured by Strand propensity,
171		* with columns 2-4 hidden
172		*/
173	1	SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG");
174	1	SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS");
175	1	AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
176	1	AlignFrame af = new AlignFrame(al, 800, 500);
177	1	af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
178	1	ColumnSelection cs = new ColumnSelection();
179	1	cs.addElement(2);
180	1	cs.addElement(3);
181	1	cs.addElement(4);
182	1	af.getViewport().setColumnSelection(cs);
183	1	af.hideSelColumns_actionPerformed(null);
184	1	SequenceRenderer sr = new SequenceRenderer(af.getViewport());
185	1	SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
186	1	String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
187	1	StructureSelectionManager ssm = new StructureSelectionManager();
188
189		/*
190		* map residues 1-10 to residues 21-30 (atoms 105-150) in structures
191		*/
192	1	HashMap<Integer, int[]> map = new HashMap<Integer, int[]>();
193	11	for (int pos = 1; pos <= seq1.getLength(); pos++)
194		{
195	10	map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
196		}
197	1	StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
198		"A", map, null);
199	1	ssm.addStructureMapping(sm1);
200	1	StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
201		"B", map, null);
202	1	ssm.addStructureMapping(sm2);
203
204	1	StructureMappingcommandSet[] commands = ChimeraCommands
205		.getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel);
206	1	assertEquals(1, commands.length);
207	1	assertEquals(1, commands[0].commands.length);
208	1	String theCommand = commands[0].commands[0];
209		// M colour is #82827d (see strand.html help page)
210	1	assertTrue(theCommand.contains("color #82827d #0:21.A|#1:21.B"));
211		// H colour is #60609f
212	1	assertTrue(theCommand.contains("color #60609f #0:22.A"));
213		// V colour is #ffff00
214	1	assertTrue(theCommand.contains("color #ffff00 #1:22.B"));
215		// hidden columns are Gray (128, 128, 128)
216	1	assertTrue(theCommand.contains("color #808080 #0:23-25.A|#1:23-25.B"));
217		// S and G are both coloured #4949b6
218	1	assertTrue(theCommand.contains("color #4949b6 #0:26-30.A|#1:26-30.B"));
219		}
220		}