Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ColourSchemePropertyTest	36	89	2	0.00%	Show methods

Class ColourSchemePropertyTest

Class ColourSchemePropertyTest	Line # 36	Total Statements 89	Complexity 2	TOTAL Coverage 0.00%
testGetColourName() : void   testGetColourName() : void	3838	41.041	1.01	0.0 0.00%
testGetColourScheme() : void   testGetColourScheme() : void	9393	48.048	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.Assert.assertEquals;
24		import static org.testng.Assert.assertNull;
25		import static org.testng.Assert.assertTrue;
26
27		import jalview.datamodel.Alignment;
28		import jalview.datamodel.AlignmentI;
29		import jalview.datamodel.Sequence;
30		import jalview.datamodel.SequenceI;
31
32		import java.awt.Color;
33
34		import org.testng.annotations.Test;
35
		0% Uncovered Elements: 91 (91) Complexity: 2 Complexity Density: 0.02
36		public class ColourSchemePropertyTest
37		{
		0% Uncovered Elements: 41 (41) Complexity: 1 Complexity Density: 0.02 4-
38	0	@Test(groups = "Functional")...
39		public void testGetColourName()
40		{
41	0	SequenceI seq = new Sequence("Seq1", "abcd");
42	0	AlignmentI al = new Alignment(new SequenceI[] { seq });
43	0	ColourSchemeI cs = new ClustalxColourScheme(al, null);
44	0	assertEquals(ColourSchemeProperty.getColourName(cs), "Clustal");
45	0	cs = new Blosum62ColourScheme();
46	0	assertEquals(ColourSchemeProperty.getColourName(cs), "Blosum62");
47	0	cs = new PIDColourScheme();
48	0	assertEquals(ColourSchemeProperty.getColourName(cs), "% Identity");
49	0	cs = new HydrophobicColourScheme();
50	0	assertEquals(ColourSchemeProperty.getColourName(cs), "Hydrophobic");
51	0	cs = new ZappoColourScheme();
52	0	assertEquals(ColourSchemeProperty.getColourName(cs), "Zappo");
53	0	cs = new TaylorColourScheme();
54	0	assertEquals(ColourSchemeProperty.getColourName(cs), "Taylor");
55	0	cs = new HelixColourScheme();
56	0	assertEquals(ColourSchemeProperty.getColourName(cs),
57		"Helix Propensity");
58	0	cs = new StrandColourScheme();
59	0	assertEquals(ColourSchemeProperty.getColourName(cs),
60		"Strand Propensity");
61	0	cs = new TurnColourScheme();
62	0	assertEquals(ColourSchemeProperty.getColourName(cs), "Turn Propensity");
63	0	cs = new BuriedColourScheme();
64	0	assertEquals(ColourSchemeProperty.getColourName(cs), "Buried Index");
65	0	cs = new NucleotideColourScheme();
66	0	assertEquals(ColourSchemeProperty.getColourName(cs), "Nucleotide");
67	0	cs = new PurinePyrimidineColourScheme();
68	0	assertEquals(ColourSchemeProperty.getColourName(cs),
69		"Purine/Pyrimidine");
70	0	cs = new TCoffeeColourScheme(al);
71	0	assertEquals(ColourSchemeProperty.getColourName(cs), "T-Coffee Scores");
72	0	cs = new RNAHelicesColour(al);
73	0	assertEquals(ColourSchemeProperty.getColourName(cs), "RNA Helices");
74	0	cs = new RNAInteractionColourScheme();
75	0	assertEquals(ColourSchemeProperty.getColourName(cs),
76		"RNA Interaction type");
77	0	cs = new UserColourScheme();
78	0	assertEquals(ColourSchemeProperty.getColourName(cs), "User Defined");
79
80		/*
81		* UserColourScheme may have a bespoke name
82		*/
83	0	((UserColourScheme) cs).setName("stripy");
84	0	assertEquals(ColourSchemeProperty.getColourName(cs), "stripy");
85	0	((UserColourScheme) cs).setName("");
86	0	assertEquals(ColourSchemeProperty.getColourName(cs), "User Defined");
87	0	((UserColourScheme) cs).setName(null);
88	0	assertEquals(ColourSchemeProperty.getColourName(cs), "User Defined");
89
90	0	assertEquals(ColourSchemeProperty.getColourName(null), "None");
91		}
92
		0% Uncovered Elements: 48 (48) Complexity: 1 Complexity Density: 0.02 4-
93	0	@Test(groups = "Functional")...
94		public void testGetColourScheme()
95		{
96	0	SequenceI seq = new Sequence("Seq1", "abcd");
97	0	AlignmentI al = new Alignment(new SequenceI[] { seq });
98		// the strings here correspond to JalviewColourScheme.toString() values
99	0	ColourSchemeI cs = ColourSchemeProperty.getColourScheme(null, al,
100		"Clustal");
101	0	assertTrue(cs instanceof ClustalxColourScheme);
102		// not case-sensitive
103	0	cs = ColourSchemeProperty.getColourScheme(null, al, "CLUSTAL");
104	0	assertTrue(cs instanceof ClustalxColourScheme);
105	0	cs = ColourSchemeProperty.getColourScheme(null, al, "clustal");
106	0	assertTrue(cs instanceof ClustalxColourScheme);
107	0	cs = ColourSchemeProperty.getColourScheme(null, al, "Blosum62");
108	0	assertTrue(cs instanceof Blosum62ColourScheme);
109	0	cs = ColourSchemeProperty.getColourScheme(null, al, "% Identity");
110	0	assertTrue(cs instanceof PIDColourScheme);
111	0	cs = ColourSchemeProperty.getColourScheme(null, al, "Zappo");
112	0	assertTrue(cs instanceof ZappoColourScheme);
113	0	cs = ColourSchemeProperty.getColourScheme(null, al, "Taylor");
114	0	assertTrue(cs instanceof TaylorColourScheme);
115	0	cs = ColourSchemeProperty.getColourScheme(null, al, "Hydrophobic");
116	0	assertTrue(cs instanceof HydrophobicColourScheme);
117	0	cs = ColourSchemeProperty.getColourScheme(null, al, "Helix Propensity");
118	0	assertTrue(cs instanceof HelixColourScheme);
119	0	cs = ColourSchemeProperty.getColourScheme(null, al,
120		"Strand Propensity");
121	0	assertTrue(cs instanceof StrandColourScheme);
122	0	cs = ColourSchemeProperty.getColourScheme(null, al, "Turn Propensity");
123	0	assertTrue(cs instanceof TurnColourScheme);
124	0	cs = ColourSchemeProperty.getColourScheme(null, al, "Buried Index");
125	0	assertTrue(cs instanceof BuriedColourScheme);
126	0	cs = ColourSchemeProperty.getColourScheme(null, al, "Nucleotide");
127	0	assertTrue(cs instanceof NucleotideColourScheme);
128	0	cs = ColourSchemeProperty.getColourScheme(null, al,
129		"Purine/Pyrimidine");
130	0	assertTrue(cs instanceof PurinePyrimidineColourScheme);
131	0	cs = ColourSchemeProperty.getColourScheme(null, al, "T-Coffee Scores");
132	0	assertTrue(cs instanceof TCoffeeColourScheme);
133	0	cs = ColourSchemeProperty.getColourScheme(null, al, "RNA Helices");
134	0	assertTrue(cs instanceof RNAHelicesColour);
135		// 'None' is a special value
136	0	assertNull(ColourSchemeProperty.getColourScheme(null, al, "None"));
137	0	assertNull(ColourSchemeProperty.getColourScheme(null, al, "none"));
138		// default is to convert the name into a fixed colour
139	0	cs = ColourSchemeProperty.getColourScheme(null, al, "elephants");
140	0	assertTrue(cs instanceof UserColourScheme);
141
142		/*
143		* explicit aa colours
144		*/
145	0	UserColourScheme ucs = (UserColourScheme) ColourSchemeProperty
146		.getColourScheme(null, al,
147		"R,G=red;C=blue;c=green;Q=10,20,30;S,T=11ffdd");
148	0	assertEquals(ucs.findColour('H'), Color.white);
149	0	assertEquals(ucs.findColour('R'), Color.red);
150	0	assertEquals(ucs.findColour('r'), Color.red);
151	0	assertEquals(ucs.findColour('G'), Color.red);
152	0	assertEquals(ucs.findColour('C'), Color.blue);
153	0	assertEquals(ucs.findColour('c'), Color.green);
154	0	assertEquals(ucs.findColour('Q'), new Color(10, 20, 30));
155	0	assertEquals(ucs.findColour('S'), new Color(0x11ffdd));
156	0	assertEquals(ucs.findColour('T'), new Color(0x11ffdd));
157		}
158		}