Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
TestHtsContigDb	42	32	5	0.861111186.1%	Show methods

Class TestHtsContigDb

Class TestHtsContigDb	Line # 42	Total Statements 32	Complexity 5	TOTAL Coverage 0.861111186.1%
testGetSequenceProxy() : void   testGetSequenceProxy() : void	4444	10.010	1.01	1.0 1.0100%
testGetSequenceProxy_indexed() : void   testGetSequenceProxy_indexed() : void	7171	3.03	1.01	0.6666667 0.666666766.7%
testCreateFastaSequenceIndex() : void   testCreateFastaSequenceIndex() : void	9292	17.017	2.02	0.9411765 0.941176594.1%
testCreateIndex() : void   testCreateIndex() : void	143143	2.02	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.4722222	jalview.ext.htsjdk.TestHtsContigDb.testCreateFastaSequenceIndexjalview.ext.htsjdk.TestHtsContigDb.testCreateFastaSequenceIndex	1PASS
	0.30555555	jalview.ext.htsjdk.TestHtsContigDb.testGetSequenceProxyjalview.ext.htsjdk.TestHtsContigDb.testGetSequenceProxy	1PASS
	0.083333336	jalview.ext.htsjdk.TestHtsContigDb.testGetSequenceProxy_indexedjalview.ext.htsjdk.TestHtsContigDb.testGetSequenceProxy_indexed	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.ext.htsjdk;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertFalse;
25		import static org.testng.Assert.assertNotNull;
26		import static org.testng.Assert.assertTrue;
27		import static org.testng.Assert.fail;
28
29		import jalview.datamodel.SequenceI;
30
31		import java.io.File;
32		import java.io.IOException;
33		import java.nio.file.Files;
34		import java.nio.file.StandardCopyOption;
35
36		import org.testng.annotations.Test;
37
38		/**
39		* @author jprocter
40		*
41		*/
		86.1% Uncovered Elements: 5 (36) Complexity: 5 Complexity Density: 0.16
42		public class TestHtsContigDb
43		{
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
44	1	@Test(groups = "Functional")...
45		public final void testGetSequenceProxy() throws Exception
46		{
47	1	String pathname = "test/jalview/ext/htsjdk/pgmB.fasta";
48	1	HtsContigDb db = new HtsContigDb("ADB", new File(pathname));
49
50	1	assertTrue(db.isValid());
51	1	assertTrue(db.isIndexed()); // htsjdk opens the .fai file
52
53	1	SequenceI sq = db.getSequenceProxy("Deminut");
54	1	assertNotNull(sq);
55	1	assertEquals(sq.getLength(), 606);
56
57		/*
58		* read a sequence earlier in the file
59		*/
60	1	sq = db.getSequenceProxy("PPL_06716");
61	1	assertNotNull(sq);
62	1	assertEquals(sq.getLength(), 602);
63
64		// dict = db.getDictionary(f, truncate))
65		}
66
67		/**
68		* Trying to open a .fai file directly results in IllegalArgumentException -
69		* have to provide the unindexed file name instead
70		*/
		66.7% Uncovered Elements: 1 (3) Complexity: 1 Complexity Density: 0.33 1PASS
71	1	@Test(...
72		groups = "Functional",
73		expectedExceptions = java.lang.IllegalArgumentException.class)
74		public final void testGetSequenceProxy_indexed()
75		{
76	1	String pathname = "test/jalview/ext/htsjdk/pgmB.fasta.fai";
77	1	new HtsContigDb("ADB", new File(pathname));
78	0	fail("Expected exception opening .fai file");
79		}
80
81		/**
82		* Tests that exercise
83		* <ul>
84		* <li>opening an unindexed fasta file</li>
85		* <li>creating a .fai index</li>
86		* <li>opening the fasta file, now using the index</li>
87		* <li>error on creating index if overwrite not allowed</li>
88		* </ul>
89		*
90		* @throws IOException
91		*/
		94.1% Uncovered Elements: 1 (17) Complexity: 2 Complexity Density: 0.12 1PASS
92	1	@Test(groups = "Functional")...
93		public void testCreateFastaSequenceIndex() throws IOException
94		{
95	1	File fasta = new File("test/jalview/ext/htsjdk/pgmB.fasta");
96
97		/*
98		* create .fai with no overwrite fails if it exists
99		*/
100	1	try
101		{
102	1	HtsContigDb.createFastaSequenceIndex(fasta.toPath(), false);
103	0	fail("Expected exception");
104		} catch (IOException e)
105		{
106		// we expect an IO Exception because the pgmB.fasta.fai exists, since it
107		// was checked it in.
108		}
109
110		/*
111		* create a copy of the .fasta (as a temp file)
112		*/
113	1	File copyFasta = File.createTempFile("copyFasta", ".fasta");
114	1	copyFasta.deleteOnExit();
115	1	assertTrue(copyFasta.exists());
116	1	Files.copy(fasta.toPath(), copyFasta.toPath(),
117		StandardCopyOption.REPLACE_EXISTING);
118
119		/*
120		* open the Fasta file - not indexed, as no .fai file yet exists
121		*/
122	1	HtsContigDb db = new HtsContigDb("ADB", copyFasta);
123	1	assertTrue(db.isValid());
124	1	assertFalse(db.isIndexed());
125	1	db.close();
126
127		/*
128		* create the .fai index, re-open the .fasta file - now indexed
129		*/
130	1	HtsContigDb.createFastaSequenceIndex(copyFasta.toPath(), true);
131	1	db = new HtsContigDb("ADB", copyFasta);
132	1	assertTrue(db.isValid());
133	1	assertTrue(db.isIndexed());
134	1	db.close();
135		}
136
137		/**
138		* A convenience 'test' that may be run to create a .fai file for any given
139		* fasta file
140		*
141		* @throws IOException
142		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5 1PASS
143	0	@Test(enabled = false)...
144		public void testCreateIndex() throws IOException
145		{
146
147	0	File fasta = new File("test/jalview/io/vcf/contigs.fasta");
148	0	HtsContigDb.createFastaSequenceIndex(fasta.toPath(), true);
149		}
150		}