Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
ResidueColourSchemeTest	40	88	7	1	0.989583399%	Show methods

Class ResidueColourSchemeTest

Class ResidueColourSchemeTest	Line # 40	Total Statements 88	Complexity 7	Uncovered Elements 1	TOTAL Coverage 0.989583399%
setUp() : void   setUp() : void	4242	0.00	1.01	0.00	-1.0 -1.0 -
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4848	2.02	1.01	0.00	1.0 1.0100%
testIsApplicableTo() : void   testIsApplicableTo() : void	5555	58.058	1.01	0.00	1.0 1.0100%
isApplicableTo(AnnotatedCollectionI) : boolean   isApplicableTo(AnnotatedCollectionI) : boolean	159159	2.02	2.02	1.01	0.75 0.7575%
testIsApplicableTo_dynamicColourScheme() : void   testIsApplicableTo_dynamicColourScheme() : void	146146	7.07	1.01	0.00	1.0 1.0100%
testGetName() : void   testGetName() : void	172172	19.019	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.6145833	jalview.schemes.ResidueColourSchemeTest.testIsApplicableTojalview.schemes.ResidueColourSchemeTest.testIsApplicableTo	1PASS
	0.20833333	jalview.schemes.ResidueColourSchemeTest.testGetNamejalview.schemes.ResidueColourSchemeTest.testGetName	1PASS
	0.125	jalview.schemes.ResidueColourSchemeTest.testIsApplicableTo_dynamicColourSchemejalview.schemes.ResidueColourSchemeTest.testIsApplicableTo_dynamicColourScheme	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.schemes;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertFalse;
25		import static org.testng.AssertJUnit.assertTrue;
26
27		import jalview.datamodel.Alignment;
28		import jalview.datamodel.AlignmentAnnotation;
29		import jalview.datamodel.AlignmentI;
30		import jalview.datamodel.AnnotatedCollectionI;
31		import jalview.datamodel.Annotation;
32		import jalview.datamodel.Sequence;
33		import jalview.datamodel.SequenceI;
34		import jalview.gui.JvOptionPane;
35		import jalview.io.TCoffeeScoreFile;
36
37		import org.testng.annotations.BeforeClass;
38		import org.testng.annotations.Test;
39
		99% Uncovered Elements: 1 (96) Complexity: 7 Complexity Density: 0.08
40		public class ResidueColourSchemeTest
41		{
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
42	1	@BeforeClass(alwaysRun = true)...
43		public void setUp()
44		{
45
46		}
47
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
48	1	@BeforeClass(alwaysRun = true)...
49		public void setUpJvOptionPane()
50		{
51	1	JvOptionPane.setInteractiveMode(false);
52	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
53		}
54
		100% Uncovered Elements: 0 (58) Complexity: 1 Complexity Density: 0.02 1PASS
55	1	@Test(groups = "Functional")...
56		public void testIsApplicableTo()
57		{
58	1	SequenceI pep1 = new Sequence("pep1", "APQTWLS");
59	1	SequenceI pep2 = new Sequence("pep2", "AILFQYG");
60	1	SequenceI dna1 = new Sequence("dna1", "ACTGAC");
61	1	SequenceI dna2 = new Sequence("dna2", "TCCAAG");
62	1	AlignmentI peptide = new Alignment(new SequenceI[] { pep1, pep2 });
63	1	AlignmentI nucleotide = new Alignment(new SequenceI[] { dna1, dna2 });
64
65		/*
66		* peptide-specific colour schemes
67		*/
68	1	assertTrue(new ClustalxColourScheme(peptide, null)
69		.isApplicableTo(peptide));
70	1	assertFalse(new ClustalxColourScheme(nucleotide, null)
71		.isApplicableTo(nucleotide));
72	1	assertTrue(new Blosum62ColourScheme().isApplicableTo(peptide));
73	1	assertFalse(new Blosum62ColourScheme().isApplicableTo(nucleotide));
74	1	assertTrue(new BuriedColourScheme().isApplicableTo(peptide));
75	1	assertFalse(new BuriedColourScheme().isApplicableTo(nucleotide));
76	1	assertTrue(new HelixColourScheme().isApplicableTo(peptide));
77	1	assertFalse(new HelixColourScheme().isApplicableTo(nucleotide));
78	1	assertTrue(new HydrophobicColourScheme().isApplicableTo(peptide));
79	1	assertFalse(new HydrophobicColourScheme().isApplicableTo(nucleotide));
80	1	assertTrue(new StrandColourScheme().isApplicableTo(peptide));
81	1	assertFalse(new StrandColourScheme().isApplicableTo(nucleotide));
82	1	assertTrue(new TaylorColourScheme().isApplicableTo(peptide));
83	1	assertFalse(new TaylorColourScheme().isApplicableTo(nucleotide));
84	1	assertTrue(new TurnColourScheme().isApplicableTo(peptide));
85	1	assertFalse(new TurnColourScheme().isApplicableTo(nucleotide));
86	1	assertTrue(new ZappoColourScheme().isApplicableTo(peptide));
87	1	assertFalse(new ZappoColourScheme().isApplicableTo(nucleotide));
88
89		/*
90		* nucleotide-specific colour schemes
91		*/
92	1	assertFalse(new NucleotideColourScheme().isApplicableTo(peptide));
93	1	assertTrue(new NucleotideColourScheme().isApplicableTo(nucleotide));
94	1	assertFalse(new PurinePyrimidineColourScheme().isApplicableTo(peptide));
95	1	assertTrue(new PurinePyrimidineColourScheme()
96		.isApplicableTo(nucleotide));
97	1	assertFalse(new RNAInteractionColourScheme().isApplicableTo(peptide));
98	1	assertTrue(new RNAInteractionColourScheme().isApplicableTo(nucleotide));
99
100		/*
101		* indifferent
102		*/
103	1	assertTrue(new UserColourScheme().isApplicableTo(peptide));
104	1	assertTrue(new UserColourScheme().isApplicableTo(nucleotide));
105	1	assertTrue(new ScoreColourScheme(new int[] {}, new double[] {}, 0, 0d)
106		.isApplicableTo(peptide));
107	1	assertTrue(new ScoreColourScheme(new int[] {}, new double[] {}, 0, 0d)
108		.isApplicableTo(nucleotide));
109	1	ResidueColourScheme rcs = new PIDColourScheme();
110	1	assertTrue(rcs.isApplicableTo(peptide));
111	1	assertTrue(rcs.isApplicableTo(nucleotide));
112	1	assertTrue(new PIDColourScheme().isApplicableTo(peptide));
113	1	assertTrue(new PIDColourScheme().isApplicableTo(nucleotide));
114	1	assertTrue(new FollowerColourScheme().isApplicableTo(peptide));
115	1	assertTrue(new FollowerColourScheme().isApplicableTo(nucleotide));
116
117		/*
118		* TCoffee colour requires the presence of TCoffee score annotation
119		*/
120	1	assertFalse(new TCoffeeColourScheme(peptide).isApplicableTo(peptide));
121	1	assertFalse(new TCoffeeColourScheme(nucleotide)
122		.isApplicableTo(nucleotide));
123	1	AlignmentAnnotation aa = new AlignmentAnnotation("T-COFFEE", "", null);
124	1	aa.setCalcId(TCoffeeScoreFile.TCOFFEE_SCORE);
125	1	peptide.addAnnotation(aa);
126	1	aa = new AlignmentAnnotation("T-COFFEE", "", null);
127	1	aa.setCalcId(TCoffeeScoreFile.TCOFFEE_SCORE);
128	1	nucleotide.addAnnotation(aa);
129	1	assertTrue(new TCoffeeColourScheme(peptide).isApplicableTo(peptide));
130	1	assertTrue(new TCoffeeColourScheme(nucleotide)
131		.isApplicableTo(nucleotide));
132
133		/*
134		* RNAHelices requires the presence of rna secondary structure
135		*/
136	1	assertFalse(new RNAHelicesColour(peptide).isApplicableTo(peptide));
137	1	assertFalse(new RNAHelicesColour(nucleotide).isApplicableTo(nucleotide));
138		// add secondary structure (small but perfectly formed)
139	1	Annotation[] ss = new Annotation[2];
140	1	ss[0] = new Annotation("", "", '{', 0f);
141	1	ss[1] = new Annotation("", "", '}', 0f);
142	1	nucleotide.addAnnotation(new AlignmentAnnotation("SS", "", ss));
143	1	assertTrue(new RNAHelicesColour(nucleotide).isApplicableTo(nucleotide));
144		}
145
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
146	1	@Test(groups = "Functional")...
147		public void testIsApplicableTo_dynamicColourScheme()
148		{
149	1	SequenceI pep1 = new Sequence("pep1", "APQTWLS");
150	1	SequenceI pep2 = new Sequence("pep2", "AILFQYG");
151	1	AlignmentI peptide = new Alignment(new SequenceI[] { pep1, pep2 });
152
153		/*
154		* demonstrate that we can 'plug in' a colour scheme with specified
155		* criteria for applicability; here, that there are more than 2 sequences
156		*/
157	1	ColourSchemeI cs = new UserColourScheme()
158		{
		75% Uncovered Elements: 1 (4) Complexity: 2 Complexity Density: 1
159	2	@Override...
160		public boolean isApplicableTo(AnnotatedCollectionI ac)
161		{
162	2	AlignmentI al = ac.getContext() == null ? (AlignmentI) ac
163		: (AlignmentI) ac.getContext();
164	2	return al.getSequences().size() > 2;
165		}
166		};
167	1	assertFalse(cs.isApplicableTo(peptide));
168	1	peptide.addSequence(pep1);
169	1	assertTrue(cs.isApplicableTo(peptide));
170		}
171
		100% Uncovered Elements: 0 (19) Complexity: 1 Complexity Density: 0.05 1PASS
172	1	@Test(groups = "Functional")...
173		public void testGetName()
174		{
175	1	SequenceI pep1 = new Sequence("pep1", "APQTWLS");
176	1	AlignmentI peptide = new Alignment(new SequenceI[] { pep1 });
177
178	1	assertEquals("Blosum62", new Blosum62ColourScheme().getSchemeName());
179	1	assertEquals("Buried Index", new BuriedColourScheme().getSchemeName());
180	1	assertEquals("Helix Propensity", new HelixColourScheme().getSchemeName());
181	1	assertEquals("Hydrophobic", new HydrophobicColourScheme().getSchemeName());
182	1	assertEquals("Strand Propensity", new StrandColourScheme().getSchemeName());
183	1	assertEquals("Taylor", new TaylorColourScheme().getSchemeName());
184	1	assertEquals("Turn Propensity", new TurnColourScheme().getSchemeName());
185	1	assertEquals("Zappo", new ZappoColourScheme().getSchemeName());
186	1	assertEquals("Nucleotide", new NucleotideColourScheme().getSchemeName());
187	1	assertEquals("Purine/Pyrimidine",
188		new PurinePyrimidineColourScheme().getSchemeName());
189	1	assertEquals("RNA Interaction type",
190		new RNAInteractionColourScheme().getSchemeName());
191	1	assertEquals("User Defined", new UserColourScheme().getSchemeName());
192	1	assertEquals("Score", new ScoreColourScheme(new int[] {},
193		new double[] {}, 0, 0d).getSchemeName());
194	1	assertEquals("% Identity", new PIDColourScheme().getSchemeName());
195	1	assertEquals("Follower", new FollowerColourScheme().getSchemeName());
196	1	assertEquals("T-Coffee Scores",
197		new TCoffeeColourScheme(peptide).getSchemeName());
198	1	assertEquals("RNA Helices",
199		new RNAHelicesColour(peptide).getSchemeName());
200		}
201		}