Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
GffHelperBaseTest	36	92	3	0	1.0100%	Show methods

Class GffHelperBaseTest

Class GffHelperBaseTest	Line # 36	Total Statements 92	Complexity 3	Uncovered Elements 0	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3939	2.02	1.01	0.00	1.0 1.0100%
testParseNameValuePairs() : void   testParseNameValuePairs() : void	5050	15.015	1.01	0.00	1.0 1.0100%
testTrimMapping() : void   testTrimMapping() : void	8686	75.075	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.8	jalview.io.gff.GffHelperBaseTest.testTrimMappingjalview.io.gff.GffHelperBaseTest.testTrimMapping	1PASS
	0.16842106	jalview.io.gff.GffHelperBaseTest.testParseNameValuePairsjalview.io.gff.GffHelperBaseTest.testParseNameValuePairs	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.io.gff;
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.gui.JvOptionPane;
28
29		import java.util.Arrays;
30		import java.util.List;
31		import java.util.Map;
32
33		import org.testng.annotations.BeforeClass;
34		import org.testng.annotations.Test;
35
		100% Uncovered Elements: 0 (95) Complexity: 3 Complexity Density: 0.03
36		public class GffHelperBaseTest
37		{
38
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
39	1	@BeforeClass(alwaysRun = true)...
40		public void setUpJvOptionPane()
41		{
42	1	JvOptionPane.setInteractiveMode(false);
43	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
44		}
45
46		/**
47		* Test the method that parses lines like <br>
48		* ID=2345;Name=Something,Another thing;Notes=Hello;Notes=World
49		*/
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
50	1	@Test(groups = { "Functional" })...
51		public void testParseNameValuePairs()
52		{
53	1	assertTrue(GffHelperBase.parseNameValuePairs(null, ";", ' ', ",")
54		.isEmpty());
55	1	assertTrue(GffHelperBase.parseNameValuePairs("", ";", ' ', ",")
56		.isEmpty());
57	1	assertTrue(GffHelperBase.parseNameValuePairs("hello=world", ";", ' ',
58		",").isEmpty());
59
60	1	Map<String, List<String>> map = GffHelperBase.parseNameValuePairs(
61		"hello world", ";", ' ', ", ");
62	1	assertEquals(1, map.size());
63	1	assertEquals(1, map.get("hello").size());
64	1	assertEquals("world", map.get("hello").get(0));
65
66	1	map = GffHelperBase
67		.parseNameValuePairs(
68		"Method= manual curation ;nothing; Notes=F2 S ; Notes=Metal,Shiny; Type=",
69		";", '=', ",");
70
71		// Type is ignored as no value was supplied
72	1	assertEquals(2, map.size());
73
74	1	assertEquals(1, map.get("Method").size());
75	1	assertEquals("manual curation", map.get("Method").get(0)); // trimmed
76
77	1	assertEquals(3, map.get("Notes").size());
78	1	assertEquals("F2 S", map.get("Notes").get(0));
79	1	assertEquals("Metal", map.get("Notes").get(1));
80	1	assertEquals("Shiny", map.get("Notes").get(2));
81		}
82
83		/**
84		* Test for the method that tries to trim mappings to equivalent lengths
85		*/
		100% Uncovered Elements: 0 (75) Complexity: 1 Complexity Density: 0.01 1PASS
86	1	@Test(groups = "Functional")...
87		public void testTrimMapping()
88		{
89	1	int[] from = { 1, 12 };
90	1	int[] to = { 20, 31 };
91	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
92	1	assertEquals("[1, 12]", Arrays.toString(from)); // unchanged
93	1	assertEquals("[20, 31]", Arrays.toString(to)); // unchanged
94
95		// from too long:
96	1	from = new int[] { 1, 13 };
97	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
98	1	assertEquals("[1, 12]", Arrays.toString(from)); // trimmed
99	1	assertEquals("[20, 31]", Arrays.toString(to)); // unchanged
100
101		// to too long:
102	1	to = new int[] { 20, 33 };
103	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
104	1	assertEquals("[1, 12]", Arrays.toString(from)); // unchanged
105	1	assertEquals("[20, 31]", Arrays.toString(to)); // trimmed
106
107		// from reversed:
108	1	from = new int[] { 12, 1 };
109	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
110	1	assertEquals("[12, 1]", Arrays.toString(from)); // unchanged
111	1	assertEquals("[20, 31]", Arrays.toString(to)); // unchanged
112
113		// to reversed:
114	1	to = new int[] { 31, 20 };
115	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
116	1	assertEquals("[12, 1]", Arrays.toString(from)); // unchanged
117	1	assertEquals("[31, 20]", Arrays.toString(to)); // unchanged
118
119		// from reversed and too long:
120	1	from = new int[] { 14, 1 };
121	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
122	1	assertEquals("[14, 3]", Arrays.toString(from)); // end trimmed
123	1	assertEquals("[31, 20]", Arrays.toString(to)); // unchanged
124
125		// to reversed and too long:
126	1	to = new int[] { 31, 10 };
127	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
128	1	assertEquals("[14, 3]", Arrays.toString(from)); // unchanged
129	1	assertEquals("[31, 20]", Arrays.toString(to)); // end trimmed
130
131		// cdna to peptide (matching)
132	1	from = new int[] { 1, 18 };
133	1	to = new int[] { 4, 9 };
134	1	assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
135	1	assertEquals("[1, 18]", Arrays.toString(from)); // unchanged
136	1	assertEquals("[4, 9]", Arrays.toString(to)); // unchanged
137
138		// overlong cdna to peptide
139	1	from = new int[] { 1, 20 };
140	1	assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
141	1	assertEquals("[1, 18]", Arrays.toString(from)); // end trimmed
142	1	assertEquals("[4, 9]", Arrays.toString(to)); // unchanged
143
144		// overlong cdna (reversed) to peptide
145	1	from = new int[] { 20, 1 };
146	1	assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
147	1	assertEquals("[20, 3]", Arrays.toString(from)); // end trimmed
148	1	assertEquals("[4, 9]", Arrays.toString(to)); // unchanged
149
150		// overlong cdna (reversed) to peptide (reversed)
151	1	from = new int[] { 20, 1 };
152	1	to = new int[] { 9, 4 };
153	1	assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
154	1	assertEquals("[20, 3]", Arrays.toString(from)); // end trimmed
155	1	assertEquals("[9, 4]", Arrays.toString(to)); // unchanged
156
157		// peptide to cdna (matching)
158	1	from = new int[] { 4, 9 };
159	1	to = new int[] { 1, 18 };
160	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
161	1	assertEquals("[4, 9]", Arrays.toString(from)); // unchanged
162	1	assertEquals("[1, 18]", Arrays.toString(to)); // unchanged
163
164		// peptide to overlong cdna
165	1	to = new int[] { 1, 20 };
166	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
167	1	assertEquals("[4, 9]", Arrays.toString(from)); // unchanged
168	1	assertEquals("[1, 18]", Arrays.toString(to)); // end trimmed
169
170		// peptide to overlong cdna (reversed)
171	1	to = new int[] { 20, 1 };
172	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
173	1	assertEquals("[4, 9]", Arrays.toString(from)); // unchanged
174	1	assertEquals("[20, 3]", Arrays.toString(to)); // end trimmed
175
176		// peptide (reversed) to overlong cdna (reversed)
177	1	from = new int[] { 9, 4 };
178	1	to = new int[] { 20, 1 };
179	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
180	1	assertEquals("[9, 4]", Arrays.toString(from)); // unchanged
181	1	assertEquals("[20, 3]", Arrays.toString(to)); // end trimmed
182
183		// overlong peptide to word-length cdna
184	1	from = new int[] { 4, 10 };
185	1	to = new int[] { 1, 18 };
186	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
187	1	assertEquals("[4, 9]", Arrays.toString(from)); // end trimmed
188	1	assertEquals("[1, 18]", Arrays.toString(to)); // unchanged
189
190		// overlong peptide to non-word-length cdna
191	1	from = new int[] { 4, 10 };
192	1	to = new int[] { 1, 19 };
193	1	assertFalse(GffHelperBase.trimMapping(from, to, 1, 3));
194	1	assertEquals("[4, 10]", Arrays.toString(from)); // unchanged
195	1	assertEquals("[1, 19]", Arrays.toString(to)); // unchanged
196
197		}
198		}