Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ResidueColourSchemeTest	40	88	7	0.00%	Show methods

Class ResidueColourSchemeTest

Class ResidueColourSchemeTest	Line # 40	Total Statements 88	Complexity 7	TOTAL Coverage 0.00%
setUp() : void   setUp() : void	4242	0.00	1.01	-1.0 -1.0 -
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4848	2.02	1.01	0.0 0.00%
testIsApplicableTo() : void   testIsApplicableTo() : void	5555	58.058	1.01	0.0 0.00%
isApplicableTo(AnnotatedCollectionI) : boolean   isApplicableTo(AnnotatedCollectionI) : boolean	160160	2.02	2.02	0.0 0.00%
testIsApplicableTo_dynamicColourScheme() : void   testIsApplicableTo_dynamicColourScheme() : void	147147	7.07	1.01	0.0 0.00%
testGetName() : void   testGetName() : void	173173	19.019	1.01	0.0 0.00%

 

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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.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
		0% Uncovered Elements: 96 (96) Complexity: 7 Complexity Density: 0.08
40		public class ResidueColourSchemeTest
41		{
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
42	0	@BeforeClass(alwaysRun = true)...
43		public void setUp()
44		{
45
46		}
47
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
48	0	@BeforeClass(alwaysRun = true)...
49		public void setUpJvOptionPane()
50		{
51	0	JvOptionPane.setInteractiveMode(false);
52	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
53		}
54
		0% Uncovered Elements: 58 (58) Complexity: 1 Complexity Density: 0.02 4-
55	0	@Test(groups = "Functional")...
56		public void testIsApplicableTo()
57		{
58	0	SequenceI pep1 = new Sequence("pep1", "APQTWLS");
59	0	SequenceI pep2 = new Sequence("pep2", "AILFQYG");
60	0	SequenceI dna1 = new Sequence("dna1", "ACTGAC");
61	0	SequenceI dna2 = new Sequence("dna2", "TCCAAG");
62	0	AlignmentI peptide = new Alignment(new SequenceI[] { pep1, pep2 });
63	0	AlignmentI nucleotide = new Alignment(new SequenceI[] { dna1, dna2 });
64
65		/*
66		* peptide-specific colour schemes
67		*/
68	0	assertTrue(new ClustalxColourScheme(peptide, null)
69		.isApplicableTo(peptide));
70	0	assertFalse(new ClustalxColourScheme(nucleotide, null)
71		.isApplicableTo(nucleotide));
72	0	assertTrue(new Blosum62ColourScheme().isApplicableTo(peptide));
73	0	assertFalse(new Blosum62ColourScheme().isApplicableTo(nucleotide));
74	0	assertTrue(new BuriedColourScheme().isApplicableTo(peptide));
75	0	assertFalse(new BuriedColourScheme().isApplicableTo(nucleotide));
76	0	assertTrue(new HelixColourScheme().isApplicableTo(peptide));
77	0	assertFalse(new HelixColourScheme().isApplicableTo(nucleotide));
78	0	assertTrue(new HydrophobicColourScheme().isApplicableTo(peptide));
79	0	assertFalse(new HydrophobicColourScheme().isApplicableTo(nucleotide));
80	0	assertTrue(new StrandColourScheme().isApplicableTo(peptide));
81	0	assertFalse(new StrandColourScheme().isApplicableTo(nucleotide));
82	0	assertTrue(new TaylorColourScheme().isApplicableTo(peptide));
83	0	assertFalse(new TaylorColourScheme().isApplicableTo(nucleotide));
84	0	assertTrue(new TurnColourScheme().isApplicableTo(peptide));
85	0	assertFalse(new TurnColourScheme().isApplicableTo(nucleotide));
86	0	assertTrue(new ZappoColourScheme().isApplicableTo(peptide));
87	0	assertFalse(new ZappoColourScheme().isApplicableTo(nucleotide));
88
89		/*
90		* nucleotide-specific colour schemes
91		*/
92	0	assertFalse(new NucleotideColourScheme().isApplicableTo(peptide));
93	0	assertTrue(new NucleotideColourScheme().isApplicableTo(nucleotide));
94	0	assertFalse(new PurinePyrimidineColourScheme().isApplicableTo(peptide));
95	0	assertTrue(
96		new PurinePyrimidineColourScheme().isApplicableTo(nucleotide));
97	0	assertFalse(new RNAInteractionColourScheme().isApplicableTo(peptide));
98	0	assertTrue(new RNAInteractionColourScheme().isApplicableTo(nucleotide));
99
100		/*
101		* indifferent
102		*/
103	0	assertTrue(new UserColourScheme().isApplicableTo(peptide));
104	0	assertTrue(new UserColourScheme().isApplicableTo(nucleotide));
105	0	assertTrue(new ScoreColourScheme(new int[] {}, new double[] {}, 0, 0d)
106		.isApplicableTo(peptide));
107	0	assertTrue(new ScoreColourScheme(new int[] {}, new double[] {}, 0, 0d)
108		.isApplicableTo(nucleotide));
109	0	ResidueColourScheme rcs = new PIDColourScheme();
110	0	assertTrue(rcs.isApplicableTo(peptide));
111	0	assertTrue(rcs.isApplicableTo(nucleotide));
112	0	assertTrue(new PIDColourScheme().isApplicableTo(peptide));
113	0	assertTrue(new PIDColourScheme().isApplicableTo(nucleotide));
114	0	assertTrue(new FollowerColourScheme().isApplicableTo(peptide));
115	0	assertTrue(new FollowerColourScheme().isApplicableTo(nucleotide));
116
117		/*
118		* TCoffee colour requires the presence of TCoffee score annotation
119		*/
120	0	assertFalse(new TCoffeeColourScheme(peptide).isApplicableTo(peptide));
121	0	assertFalse(
122		new TCoffeeColourScheme(nucleotide).isApplicableTo(nucleotide));
123	0	AlignmentAnnotation aa = new AlignmentAnnotation("T-COFFEE", "", null);
124	0	aa.setCalcId(TCoffeeScoreFile.TCOFFEE_SCORE);
125	0	peptide.addAnnotation(aa);
126	0	aa = new AlignmentAnnotation("T-COFFEE", "", null);
127	0	aa.setCalcId(TCoffeeScoreFile.TCOFFEE_SCORE);
128	0	nucleotide.addAnnotation(aa);
129	0	assertTrue(new TCoffeeColourScheme(peptide).isApplicableTo(peptide));
130	0	assertTrue(
131		new TCoffeeColourScheme(nucleotide).isApplicableTo(nucleotide));
132
133		/*
134		* RNAHelices requires the presence of rna secondary structure
135		*/
136	0	assertFalse(new RNAHelicesColour(peptide).isApplicableTo(peptide));
137	0	assertFalse(
138		new RNAHelicesColour(nucleotide).isApplicableTo(nucleotide));
139		// add secondary structure (small but perfectly formed)
140	0	Annotation[] ss = new Annotation[2];
141	0	ss[0] = new Annotation("", "", '{', 0f);
142	0	ss[1] = new Annotation("", "", '}', 0f);
143	0	nucleotide.addAnnotation(new AlignmentAnnotation("SS", "", ss));
144	0	assertTrue(new RNAHelicesColour(nucleotide).isApplicableTo(nucleotide));
145		}
146
		0% Uncovered Elements: 7 (7) Complexity: 1 Complexity Density: 0.14 4-
147	0	@Test(groups = "Functional")...
148		public void testIsApplicableTo_dynamicColourScheme()
149		{
150	0	SequenceI pep1 = new Sequence("pep1", "APQTWLS");
151	0	SequenceI pep2 = new Sequence("pep2", "AILFQYG");
152	0	AlignmentI peptide = new Alignment(new SequenceI[] { pep1, pep2 });
153
154		/*
155		* demonstrate that we can 'plug in' a colour scheme with specified
156		* criteria for applicability; here, that there are more than 2 sequences
157		*/
158	0	ColourSchemeI cs = new UserColourScheme()
159		{
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
160	0	@Override...
161		public boolean isApplicableTo(AnnotatedCollectionI ac)
162		{
163	0	AlignmentI al = ac.getContext() == null ? (AlignmentI) ac
164		: (AlignmentI) ac.getContext();
165	0	return al.getSequences().size() > 2;
166		}
167		};
168	0	assertFalse(cs.isApplicableTo(peptide));
169	0	peptide.addSequence(pep1);
170	0	assertTrue(cs.isApplicableTo(peptide));
171		}
172
		0% Uncovered Elements: 19 (19) Complexity: 1 Complexity Density: 0.05 4-
173	0	@Test(groups = "Functional")...
174		public void testGetName()
175		{
176	0	SequenceI pep1 = new Sequence("pep1", "APQTWLS");
177	0	AlignmentI peptide = new Alignment(new SequenceI[] { pep1 });
178
179	0	assertEquals("Blosum62", new Blosum62ColourScheme().getSchemeName());
180	0	assertEquals("Buried Index", new BuriedColourScheme().getSchemeName());
181	0	assertEquals("Helix Propensity",
182		new HelixColourScheme().getSchemeName());
183	0	assertEquals("Hydrophobic",
184		new HydrophobicColourScheme().getSchemeName());
185	0	assertEquals("Strand Propensity",
186		new StrandColourScheme().getSchemeName());
187	0	assertEquals("Taylor", new TaylorColourScheme().getSchemeName());
188	0	assertEquals("Turn Propensity", new TurnColourScheme().getSchemeName());
189	0	assertEquals("Zappo", new ZappoColourScheme().getSchemeName());
190	0	assertEquals("Nucleotide",
191		new NucleotideColourScheme().getSchemeName());
192	0	assertEquals("Purine/Pyrimidine",
193		new PurinePyrimidineColourScheme().getSchemeName());
194	0	assertEquals("RNA Interaction type",
195		new RNAInteractionColourScheme().getSchemeName());
196	0	assertEquals("User Defined", new UserColourScheme().getSchemeName());
197	0	assertEquals("Score",
198		new ScoreColourScheme(new int[] {}, new double[] {}, 0, 0d)
199		.getSchemeName());
200	0	assertEquals("% Identity", new PIDColourScheme().getSchemeName());
201	0	assertEquals("Follower", new FollowerColourScheme().getSchemeName());
202	0	assertEquals("T-Coffee Scores",
203		new TCoffeeColourScheme(peptide).getSchemeName());
204	0	assertEquals("RNA Helices",
205		new RNAHelicesColour(peptide).getSchemeName());
206		}
207		}