Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignedCodonIteratorTest	41	86	7	0.00%	Show methods

Class AlignedCodonIteratorTest

Class AlignedCodonIteratorTest	Line # 41	Total Statements 86	Complexity 7	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4444	2.02	1.01	0.0 0.00%
testNext() : void   testNext() : void	5454	17.017	1.01	0.0 0.00%
testNext_unmappedPeptide() : void   testNext_unmappedPeptide() : void	8282	17.017	1.01	0.0 0.00%
testNext_incompleteCodon() : void   testNext_incompleteCodon() : void	110110	13.013	2.02	0.0 0.00%
testAnother() : void   testAnother() : void	139139	20.020	1.01	0.0 0.00%
testNext_withOffset() : void   testNext_withOffset() : void	169169	17.017	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.datamodel;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertFalse;
25
26		import jalview.gui.JvOptionPane;
27		import jalview.util.MapList;
28
29		import java.util.Iterator;
30
31		import org.testng.Assert;
32		import org.testng.annotations.BeforeClass;
33		import org.testng.annotations.Test;
34
35		/**
36		* Unit tests for Mapping$AlignedCodonIterator
37		*
38		* @author gmcarstairs
39		*
40		*/
		0% Uncovered Elements: 92 (92) Complexity: 7 Complexity Density: 0.08
41		public class AlignedCodonIteratorTest
42		{
43
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
44	0	@BeforeClass(alwaysRun = true)...
45		public void setUpJvOptionPane()
46		{
47	0	JvOptionPane.setInteractiveMode(false);
48	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
49		}
50
51		/**
52		* Test normal case for iterating over aligned codons.
53		*/
		0% Uncovered Elements: 17 (17) Complexity: 1 Complexity Density: 0.06 4-
54	0	@Test(groups = { "Functional" })...
55		public void testNext()
56		{
57	0	SequenceI from = new Sequence("Seq1", "-CgC-C-cCtAG-AtG-Gc");
58	0	from.createDatasetSequence();
59	0	SequenceI to = new Sequence("Seq1", "-PQ-R-");
60	0	to.createDatasetSequence();
61	0	MapList map = new MapList(new int[] { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 },
62		new int[]
63		{ 1, 3 }, 3, 1);
64	0	Mapping m = new Mapping(to.getDatasetSequence(), map);
65
66	0	Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
67	0	AlignedCodon codon = codons.next();
68	0	assertEquals("[1, 3, 5]", codon.toString());
69	0	assertEquals("P", codon.product);
70	0	codon = codons.next();
71	0	assertEquals("[8, 10, 11]", codon.toString());
72	0	assertEquals("Q", codon.product);
73	0	codon = codons.next();
74	0	assertEquals("[13, 15, 17]", codon.toString());
75	0	assertEquals("R", codon.product);
76	0	assertFalse(codons.hasNext());
77		}
78
79		/**
80		* Test weird case where the mapping skips over a peptide.
81		*/
		0% Uncovered Elements: 17 (17) Complexity: 1 Complexity Density: 0.06 4-
82	0	@Test(groups = { "Functional" })...
83		public void testNext_unmappedPeptide()
84		{
85	0	SequenceI from = new Sequence("Seq1", "-CgC-C-cCtAG-AtG-Gc");
86	0	from.createDatasetSequence();
87	0	SequenceI to = new Sequence("Seq1", "-PQ-TR-");
88	0	to.createDatasetSequence();
89	0	MapList map = new MapList(new int[] { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 },
90		new int[]
91		{ 1, 2, 4, 4 }, 3, 1);
92	0	Mapping m = new Mapping(to.getDatasetSequence(), map);
93
94	0	Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
95	0	AlignedCodon codon = codons.next();
96	0	assertEquals("[1, 3, 5]", codon.toString());
97	0	assertEquals("P", codon.product);
98	0	codon = codons.next();
99	0	assertEquals("[8, 10, 11]", codon.toString());
100	0	assertEquals("Q", codon.product);
101	0	codon = codons.next();
102	0	assertEquals("[13, 15, 17]", codon.toString());
103	0	assertEquals("R", codon.product);
104	0	assertFalse(codons.hasNext());
105		}
106
107		/**
108		* Test for exception thrown for an incomplete codon.
109		*/
		0% Uncovered Elements: 13 (13) Complexity: 2 Complexity Density: 0.15 4-
110	0	@Test(groups = { "Functional" })...
111		public void testNext_incompleteCodon()
112		{
113	0	SequenceI from = new Sequence("Seq1", "-CgC-C-cCgTt");
114	0	from.createDatasetSequence();
115	0	SequenceI to = new Sequence("Seq1", "-PQ-R-");
116	0	to.createDatasetSequence();
117	0	MapList map = new MapList(new int[] { 1, 1, 3, 4, 6, 6, 8, 8 },
118		new int[]
119		{ 1, 3 }, 3, 1);
120	0	Mapping m = new Mapping(to.getDatasetSequence(), map);
121
122	0	Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
123	0	AlignedCodon codon = codons.next();
124	0	assertEquals("[1, 3, 5]", codon.toString());
125	0	assertEquals("P", codon.product);
126	0	try
127		{
128	0	codon = codons.next();
129	0	Assert.fail("expected exception");
130		} catch (IncompleteCodonException e)
131		{
132		// expected
133		}
134		}
135
136		/**
137		* Test normal case for iterating over aligned codons.
138		*/
		0% Uncovered Elements: 20 (20) Complexity: 1 Complexity Density: 0.05 4-
139	0	@Test(groups = { "Functional" })...
140		public void testAnother()
141		{
142	0	SequenceI from = new Sequence("Seq1", "TGCCATTACCAG-");
143	0	from.createDatasetSequence();
144	0	SequenceI to = new Sequence("Seq1", "CHYQ");
145	0	to.createDatasetSequence();
146	0	MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3,
147		1);
148	0	Mapping m = new Mapping(to.getDatasetSequence(), map);
149
150	0	Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
151	0	AlignedCodon codon = codons.next();
152	0	assertEquals("[0, 1, 2]", codon.toString());
153	0	assertEquals("C", codon.product);
154	0	codon = codons.next();
155	0	assertEquals("[3, 4, 5]", codon.toString());
156	0	assertEquals("H", codon.product);
157	0	codon = codons.next();
158	0	assertEquals("[6, 7, 8]", codon.toString());
159	0	assertEquals("Y", codon.product);
160	0	codon = codons.next();
161	0	assertEquals("[9, 10, 11]", codon.toString());
162	0	assertEquals("Q", codon.product);
163	0	assertFalse(codons.hasNext());
164		}
165
166		/**
167		* Test for a case with sequence (and mappings) not starting at 1
168		*/
		0% Uncovered Elements: 17 (17) Complexity: 1 Complexity Density: 0.06 4-
169	0	@Test(groups = { "Functional" })...
170		public void testNext_withOffset()
171		{
172	0	SequenceI from = new Sequence("Seq1", "-CgC-C-cCtAG-AtG-Gc", 7, 20);
173	0	from.createDatasetSequence();
174	0	SequenceI to = new Sequence("Seq1/10-12", "-PQ-R-");
175	0	to.createDatasetSequence();
176	0	MapList map = new MapList(
177		new int[]
178		{ 7, 7, 9, 10, 12, 12, 14, 16, 18, 19 }, new int[] { 10, 12 },
179		3, 1);
180	0	Mapping m = new Mapping(to.getDatasetSequence(), map);
181
182	0	Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
183	0	AlignedCodon codon = codons.next();
184	0	assertEquals("[1, 3, 5]", codon.toString());
185	0	assertEquals("P", codon.product);
186	0	codon = codons.next();
187	0	assertEquals("[8, 10, 11]", codon.toString());
188	0	assertEquals("Q", codon.product);
189	0	codon = codons.next();
190	0	assertEquals("[13, 15, 17]", codon.toString());
191	0	assertEquals("R", codon.product);
192	0	assertFalse(codons.hasNext());
193		}
194		}