Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
JmolCommandsTest	44	46	4	0	1.0100%	Show methods

Class JmolCommandsTest

Class JmolCommandsTest	Line # 44	Total Statements 46	Complexity 4	Uncovered Elements 0	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4747	2.02	1.01	0.00	1.0 1.0100%
testGetColourBySequenceCommand_noFeatures() : void   testGetColourBySequenceCommand_noFeatures() : void	5454	9.09	1.01	0.00	1.0 1.0100%
testGetColourBySequenceCommands_hiddenColumns() : void   testGetColourBySequenceCommands_hiddenColumns() : void	7272	35.035	2.02	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.74509805	jalview.ext.jmol.JmolCommandsTest.testGetColourBySequenceCommands_hiddenColumnsjalview.ext.jmol.JmolCommandsTest.testGetColourBySequenceCommands_hiddenColumns	1PASS
	0.19607843	jalview.ext.jmol.JmolCommandsTest.testGetColourBySequenceCommand_noFeaturesjalview.ext.jmol.JmolCommandsTest.testGetColourBySequenceCommand_noFeatures	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 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.util.HashMap;
40
41		import org.testng.annotations.BeforeClass;
42		import org.testng.annotations.Test;
43
		100% Uncovered Elements: 0 (51) Complexity: 4 Complexity Density: 0.09
44		public class JmolCommandsTest
45		{
46
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
47	1	@BeforeClass(alwaysRun = true)...
48		public void setUpJvOptionPane()
49		{
50	1	JvOptionPane.setInteractiveMode(false);
51	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
52		}
53
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
54	1	@Test(groups = { "Functional" })...
55		public void testGetColourBySequenceCommand_noFeatures()
56		{
57	1	SequenceI seq1 = new Sequence("seq1", "MHRSQTRALK");
58	1	SequenceI seq2 = new Sequence("seq2", "MRLEITQSGD");
59	1	AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
60	1	AlignFrame af = new AlignFrame(al, 800, 500);
61	1	SequenceRenderer sr = new SequenceRenderer(af.getViewport());
62	1	SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
63	1	String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
64	1	StructureSelectionManager ssm = new StructureSelectionManager();
65
66		// need some mappings!
67
68	1	StructureMappingcommandSet[] commands = JmolCommands
69		.getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel);
70		}
71
		100% Uncovered Elements: 0 (37) Complexity: 2 Complexity Density: 0.06 1PASS
72	1	@Test(groups = { "Functional" })...
73		public void testGetColourBySequenceCommands_hiddenColumns()
74		{
75		/*
76		* load these sequences, coloured by Strand propensity,
77		* with columns 2-4 hidden
78		*/
79	1	SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG");
80	1	SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS");
81	1	AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
82	1	AlignFrame af = new AlignFrame(al, 800, 500);
83	1	af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
84	1	ColumnSelection cs = new ColumnSelection();
85	1	cs.addElement(2);
86	1	cs.addElement(3);
87	1	cs.addElement(4);
88	1	af.getViewport().setColumnSelection(cs);
89	1	af.hideSelColumns_actionPerformed(null);
90	1	SequenceRenderer sr = new SequenceRenderer(af.getViewport());
91	1	SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
92	1	String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
93	1	StructureSelectionManager ssm = new StructureSelectionManager();
94
95		/*
96		* map residues 1-10 to residues 21-30 (atoms 105-150) in structures
97		*/
98	1	HashMap<Integer, int[]> map = new HashMap<Integer, int[]>();
99	11	for (int pos = 1; pos <= seq1.getLength(); pos++)
100		{
101	10	map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
102		}
103	1	StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
104		"A", map, null);
105	1	ssm.addStructureMapping(sm1);
106	1	StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
107		"B", map, null);
108	1	ssm.addStructureMapping(sm2);
109
110	1	StructureMappingcommandSet[] commands = JmolCommands
111		.getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel);
112	1	assertEquals(commands.length, 2);
113	1	assertEquals(commands[0].commands.length, 1);
114
115	1	String chainACommand = commands[0].commands[0];
116		// M colour is #82827d == (130, 130, 125) (see strand.html help page)
117	1	assertTrue(chainACommand
118		.contains("select 21:A/1.1;color[130,130,125]")); // first one
119		// H colour is #60609f == (96, 96, 159)
120	1	assertTrue(chainACommand.contains(";select 22:A/1.1;color[96,96,159]"));
121		// hidden columns are Gray (128, 128, 128)
122	1	assertTrue(chainACommand
123		.contains(";select 23-25:A/1.1;color[128,128,128]"));
124		// S and G are both coloured #4949b6 == (73, 73, 182)
125	1	assertTrue(chainACommand
126		.contains(";select 26-30:A/1.1;color[73,73,182]"));
127
128	1	String chainBCommand = commands[1].commands[0];
129		// M colour is #82827d == (130, 130, 125)
130	1	assertTrue(chainBCommand
131		.contains("select 21:B/2.1;color[130,130,125]"));
132		// V colour is #ffff00 == (255, 255, 0)
133	1	assertTrue(chainBCommand
134		.contains(";select 22:B/2.1;color[255,255,0]"));
135		// hidden columns are Gray (128, 128, 128)
136	1	assertTrue(chainBCommand
137		.contains(";select 23-25:B/2.1;color[128,128,128]"));
138		// S and G are both coloured #4949b6 == (73, 73, 182)
139	1	assertTrue(chainBCommand
140		.contains(";select 26-30:B/2.1;color[73,73,182]"));
141		}
142		}