Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PIDColourSchemeTest	35	27	4	0.967741996.8%	Show methods

Class PIDColourSchemeTest

Class PIDColourSchemeTest	Line # 35	Total Statements 27	Complexity 4	TOTAL Coverage 0.967741996.8%
testFindColour() : void   testFindColour() : void	5858	13.013	1.01	1.0 1.0100%
testFindColour_ignoreGaps() : void   testFindColour_ignoreGaps() : void	8787	14.014	3.03	0.9375 0.937593.8%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.516129	jalview.schemes.PIDColourSchemeTest.testFindColour_ignoreGapsjalview.schemes.PIDColourSchemeTest.testFindColour_ignoreGaps	1PASS
	0.4516129	jalview.schemes.PIDColourSchemeTest.testFindColourjalview.schemes.PIDColourSchemeTest.testFindColour	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 java.awt.Color;
26
27		import org.testng.annotations.Test;
28
29		import jalview.datamodel.SequenceI;
30		import jalview.gui.AlignFrame;
31		import jalview.gui.AlignViewport;
32		import jalview.io.DataSourceType;
33		import jalview.io.FileLoader;
34
		96.8% Uncovered Elements: 1 (31) Complexity: 4 Complexity Density: 0.15
35		public class PIDColourSchemeTest
36		{
37		static final Color white = Color.white;
38
39		static final Color over40 = new Color(204, 204, 255);
40
41		static final Color over60 = new Color(153, 153, 255);
42
43		static final Color over80 = new Color(100, 100, 255);
44
45		/**
46		* Test findColour for cases:
47		* <ul>
48		* <li>gap: white</li>
49		* <li>no match to consensus: white</li>
50		* <li>match consensus with pid > 80%: 100,100,255</li>
51		* <li>match consensus with pid > 60%: 153, 153, 255</li>
52		* <li>match consensus with pid > 40%: 204, 204, 255</li>
53		* <li>match consensus with pid <= 40%: white</li>
54		* <li>joint consensus matching</li>
55		* <li>case insensitive matching</li>
56		* <ul>
57		*/
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
58	1	@Test(groups = "Functional")...
59		public void testFindColour()
60		{
61	1	ColourSchemeI scheme = new PIDColourScheme();
62
63		/*
64		* doesn't use column or sequence
65		* we assume consensus residue is computed as upper case
66		*/
67	1	assertEquals(scheme.findColour('A', 0, null, "A", 0f), white);
68	1	assertEquals(scheme.findColour('A', 0, null, "A", 40f), white);
69	1	assertEquals(scheme.findColour('A', 0, null, "A", 40.1f), over40);
70	1	assertEquals(scheme.findColour('A', 0, null, "A", 60f), over40);
71	1	assertEquals(scheme.findColour('A', 0, null, "A", 60.1f), over60);
72	1	assertEquals(scheme.findColour('A', 0, null, "A", 80f), over60);
73	1	assertEquals(scheme.findColour('A', 0, null, "A", 80.1f), over80);
74	1	assertEquals(scheme.findColour('A', 0, null, "A", 100f), over80);
75	1	assertEquals(scheme.findColour('A', 0, null, "KFV", 100f), white);
76
77	1	assertEquals(scheme.findColour('a', 0, null, "A", 80f), over60);
78	1	assertEquals(scheme.findColour('A', 0, null, "AC", 80f), over60);
79	1	assertEquals(scheme.findColour('A', 0, null, "KCA", 80f), over60);
80		}
81
82		/**
83		* Test that changing the 'ignore gaps in consensus' in the viewport (an
84		* option on the annotation label popup menu) results in a change to the
85		* colouring
86		*/
		93.8% Uncovered Elements: 1 (16) Complexity: 3 Complexity Density: 0.21 1PASS
87	1	@Test(groups = "Functional")...
88		public void testFindColour_ignoreGaps()
89		{
90		/*
91		* AAAAA
92		* AAAAA
93		* -CCCC
94		* FFFFF
95		*
96		* first column consensus is A
97		* first column PID is 50%, or 67% ignoring gaps
98		*/
99	1	String seqs = ">seq1\nAAAAA\n>seq2\nAAAAA\n>seq3\n-CCCC\n>seq4\nFFFFF\n";
100
101		/*
102		* load data and wait for consensus to be computed
103		*/
104	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqs,
105		DataSourceType.PASTE);
106	1	AlignViewport viewport = af.getViewport();
107	1	viewport.setIgnoreGapsConsensus(false, af.alignPanel);
108	1	do
109		{
110	1	try
111		{
112	1	Thread.sleep(50);
113		} catch (InterruptedException x)
114		{
115		}
116	1	} while (af.getViewport().getCalcManager().isWorking());
117	1	af.changeColour_actionPerformed(JalviewColourScheme.PID.toString());
118
119	1	SequenceI seq = viewport.getAlignment().getSequenceAt(0);
120
121		/*
122		* including gaps, A should be coloured for 50% consensus
123		*/
124	1	Color c = viewport.getResidueShading().findColour('A', 0, seq);
125	1	assertEquals(c, over40);
126
127		/*
128		* now choose to ignore gaps; colour should be for 67%
129		*/
130	1	viewport.setIgnoreGapsConsensus(true, af.alignPanel);
131	1	c = viewport.getResidueShading().findColour('A', 0, seq);
132	1	assertEquals(c, over60);
133		}
134		}