Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ClustalxColourSchemeTest	34	31	3	0.8823529588.2%	Show methods

Class ClustalxColourSchemeTest

Class ClustalxColourSchemeTest	Line # 34	Total Statements 31	Complexity 3	TOTAL Coverage 0.8823529588.2%
testFindColour() : void   testFindColour() : void	5050	16.016	1.01	1.0 1.0100%
testFindColour_ignoreGaps() : void   testFindColour_ignoreGaps() : void	115115	12.012	1.01	1.0 1.0100%
testDocString() : void   testDocString() : void	155155	3.03	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.5	jalview.schemes.ClustalxColourSchemeTest.testFindColourjalview.schemes.ClustalxColourSchemeTest.testFindColour	1PASS
	0.38235295	jalview.schemes.ClustalxColourSchemeTest.testFindColour_ignoreGapsjalview.schemes.ClustalxColourSchemeTest.testFindColour_ignoreGaps	1PASS

 

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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.schemes;
22
23		import static org.testng.Assert.assertEquals;
24
25		import jalview.datamodel.AlignmentI;
26		import jalview.gui.AlignFrame;
27		import jalview.io.DataSourceType;
28		import jalview.io.FileLoader;
29
30		import java.awt.Color;
31
32		import org.testng.annotations.Test;
33
		88.2% Uncovered Elements: 4 (34) Complexity: 3 Complexity Density: 0.1
34		public class ClustalxColourSchemeTest
35		{
36		// @formatter:off
37		private static final String FASTA =
38		">seq1\nAAANNNRQ\n" +
39		">seq2\nAAANNNRQ\n" +
40		">seq3\nAAANNNRQ\n" +
41		">seq4\nAAANNNRQ\n" +
42		">seq5\nAAANYYKQ\n" +
43		">seq6\nAAANYYKQ\n" +
44		">seq7\nAVKWYYKQ\n" +
45		">seq8\nKKKWYYQQ\n" +
46		">seq9\nKKKWWYQQ\n" +
47		">seq0\nKKKWWWQW\n";
48		// @formatter:on
49
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.06 1PASS
50	1	@Test(groups = "Functional")...
51		public void testFindColour()
52		{
53	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(FASTA,
54		DataSourceType.PASTE);
55	1	AlignmentI al = af.getViewport().getAlignment();
56	1	ClustalxColourScheme cs = new ClustalxColourScheme(al, null);
57
58		/*
59		* column 1 is 70% A which is above Clustalx threshold of 60%
60		*/
61	1	Color clustalBlue = new Color(0.5f, 0.7f, 0.9f);
62	1	assertEquals(cs.findColour('A', 0, al.getSequenceAt(0)), clustalBlue);
63
64		/*
65		* column 2 is 70% A or V which is above Clustalx threshold for group
66		*/
67	1	assertEquals(cs.findColour('A', 0, al.getSequenceAt(1)), clustalBlue);
68
69		/*
70		* column 3 is 60% A which is not above Clustalx threshold
71		* the Ks in the other rows are not in the same Clustalx group
72		*/
73	1	assertEquals(cs.findColour('A', 2, al.getSequenceAt(1)), Color.white);
74
75		/*
76		* column 4 is 60% N which is above Clustalx threshold of 50%
77		*/
78	1	Color clustalGreen = new Color(0.1f, 0.8f, 0.1f);
79	1	assertEquals(cs.findColour('N', 3, al.getSequenceAt(1)), clustalGreen);
80
81		/*
82		* column 5 is 40% N and 40% Y which fails to pass the threshold of
83		* 50% N or 85% either
84		*/
85	1	assertEquals(cs.findColour('N', 4, al.getSequenceAt(1)), Color.white);
86
87		/*
88		* column 6 is 40% N and 50% Y which fails to pass the threshold of
89		* 85% for either
90		*/
91	1	assertEquals(cs.findColour('N', 5, al.getSequenceAt(1)), Color.white);
92
93		/*
94		* column 7 is 40% R and 30% K which combine to make > 60%
95		*/
96	1	Color clustalRed = new Color(0.9f, 0.2f, 0.1f);
97	1	assertEquals(cs.findColour('R', 6, al.getSequenceAt(1)), clustalRed);
98	1	assertEquals(cs.findColour('K', 6, al.getSequenceAt(7)), clustalRed);
99
100		/*
101		* column 8 is >85% Q which qualifies K and R to be red
102		*/
103	1	assertEquals(cs.findColour('R', 7, al.getSequenceAt(1)), clustalRed);
104	1	assertEquals(cs.findColour('K', 7, al.getSequenceAt(1)), clustalRed);
105
106		// TODO more test cases; check if help documentation matches implementation
107		}
108
109		// @formatter:on
110
111		/**
112		* Test for colour calculation when the consensus percentage ignores gapped
113		* sequences
114		*/
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
115	1	@Test(groups = "Functional")...
116		public void testFindColour_ignoreGaps()
117		{
118		/*
119		* CCC
120		* CCC
121		* -CC
122		* first column is 66% C (blue) including gaps
123		* or 100% C ignoring gaps
124		*/
125	1	String fasta = ">seq1\nCCC\n>seq2\nccc\n>seq3\n-CC\n";
126	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
127		DataSourceType.PASTE);
128	1	AlignmentI al = af.getViewport().getAlignment();
129	1	ClustalxColourScheme cs = new ClustalxColourScheme(al, null);
130
131		/*
132		* column 1 is 66% C which is above Clustalx threshold of 60%
133		*/
134	1	Color clustalBlue = ClustalxColourScheme.ClustalColour.BLUE.colour;
135	1	assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalBlue);
136
137		/*
138		* set directly to ignore gaps
139		*/
140	1	cs.setIncludeGaps(false);
141	1	Color clustalPink = ClustalxColourScheme.ClustalColour.PINK.colour;
142	1	assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalPink);
143
144		/*
145		* set ignore gaps on the viewport...
146		*/
147	1	cs.setIncludeGaps(true);
148	1	assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalBlue);
149	1	af.getViewport().setIgnoreGapsConsensus(true, af.alignPanel);
150		// next test fails: colour scheme does not read ignore gaps flag from
151		// viewport
152		// assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalPink);
153		}
154
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33 1PASS
155	0	@Test...
156		public void testDocString()
157		{
158		/* verify we have some sort of useful output */
159	0	ClustalxColourScheme x = new ClustalxColourScheme();
160	0	String out = x.toRuleRep();
161	0	System.out.print(out);
162		}
163		}