Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FileIOTester	47	29	11	1.0100%	Show methods

Class FileIOTester

Class FileIOTester	Line # 47	Total Statements 29	Complexity 11	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5050	2.02	1.01	1.0 1.0100%
setUpBeforeClass() : void   setUpBeforeClass() : void	6060	1.01	1.01	1.0 1.0100%
tearDownAfterClass() : void   tearDownAfterClass() : void	6969	0.00	1.01	-1.0 -1.0 -
assertValidFormat(FileFormatI,String,FileParse) : void   assertValidFormat(FileFormatI,String,FileParse) : void	8888	3.03	1.01	1.0 1.0100%
testStarsInFasta1() : void   testStarsInFasta1() : void	9898	3.03	1.01	1.0 1.0100%
testStarsInFasta2() : void   testStarsInFasta2() : void	108108	3.03	1.01	1.0 1.0100%
testGzipIo() : void   testGzipIo() : void	118118	3.03	1.01	1.0 1.0100%
testGziplocalFileIO() : void   testGziplocalFileIO() : void	128128	3.03	1.01	1.0 1.0100%
testIsGzipInputStream() : void   testIsGzipInputStream() : void	138138	5.05	1.01	1.0 1.0100%
testNonGzipURLIO() : void   testNonGzipURLIO() : void	161161	3.03	1.01	1.0 1.0100%
testNonGziplocalFileIO() : void   testNonGziplocalFileIO() : void	171171	3.03	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.2	jalview.io.FileIOTester.testGziplocalFileIOjalview.io.FileIOTester.testGziplocalFileIO	1PASS
	0.2	jalview.io.FileIOTester.testNonGzipURLIOjalview.io.FileIOTester.testNonGzipURLIO	1PASS
	0.2	jalview.io.FileIOTester.testStarsInFasta1jalview.io.FileIOTester.testStarsInFasta1	1PASS
	0.2	jalview.io.FileIOTester.testStarsInFasta2jalview.io.FileIOTester.testStarsInFasta2	1PASS
	0.2	jalview.io.FileIOTester.testGzipIojalview.io.FileIOTester.testGzipIo	1PASS
	0.2	jalview.io.FileIOTester.testNonGziplocalFileIOjalview.io.FileIOTester.testNonGziplocalFileIO	1PASS
	0.15	jalview.io.FileIOTester.testIsGzipInputStreamjalview.io.FileIOTester.testIsGzipInputStream	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;
22
23		import static org.testng.Assert.assertFalse;
24		import static org.testng.Assert.assertTrue;
25
26		import java.io.BufferedInputStream;
27		import java.io.ByteArrayInputStream;
28		import java.io.File;
29		import java.io.FileInputStream;
30		import java.io.IOException;
31		import java.io.InputStream;
32		import java.io.StringBufferInputStream;
33
34		import org.testng.AssertJUnit;
35		import org.testng.annotations.AfterClass;
36		import org.testng.annotations.BeforeClass;
37		import org.testng.annotations.Test;
38
39		import jalview.bin.Console;
40		import jalview.gui.JvOptionPane;
41		import jalview.util.Platform;
42
43		/**
44		* @author jimp
45		*
46		*/
		100% Uncovered Elements: 0 (40) Complexity: 11 Complexity Density: 0.38
47		public class FileIOTester
48		{
49
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
50	1	@BeforeClass(alwaysRun = true)...
51		public void setUpJvOptionPane()
52		{
53	1	JvOptionPane.setInteractiveMode(false);
54	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
55		}
56
57		/**
58		* @throws java.lang.Exception
59		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
60	1	@BeforeClass(alwaysRun = true)...
61		public static void setUpBeforeClass() throws Exception
62		{
63	1	Console.initLogger();
64		}
65
66		/**
67		* @throws java.lang.Exception
68		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
69	1	@AfterClass(alwaysRun = true)...
70		public static void tearDownAfterClass() throws Exception
71		{
72		}
73
74		// TODO: make a better/more comprehensive test harness for identify/io
75
76		final static File ALIGN_FILE = new File(
77		"test/jalview/io/test_gz_fasta.gz");
78
79		final static File NOTGZALIGN_FILE = new File(
80		"test/jalview/io/test_gz_fasta_notgz.gz");
81
82		final static File STARS_FA_FILE1 = new File(
83		"test/jalview/io/test_fasta_stars.fa");
84
85		final static File STARS_FA_FILE2 = new File(
86		"test/jalview/io/test_fasta_stars2.fa");
87
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
88	6	private void assertValidFormat(FileFormatI fmt, String src, FileParse fp)...
89		throws FileFormatException
90		{
91	6	AssertJUnit.assertTrue("Couldn't resolve " + src + " as a valid file",
92		fp.isValid());
93	6	FileFormatI type = new IdentifyFile().identify(fp);
94	6	AssertJUnit.assertSame("Data from '" + src + "' Expected to be '" + fmt
95		+ "' identified as '" + type + "'", type, fmt);
96		}
97
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
98	1	@Test(groups = { "Functional" })...
99		public void testStarsInFasta1() throws IOException
100		{
101	1	String uri;
102	1	FileParse fp = new FileParse(
103		uri = STARS_FA_FILE1.getAbsoluteFile().toString(),
104		DataSourceType.FILE);
105	1	assertValidFormat(FileFormat.Fasta, uri, fp);
106		}
107
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
108	1	@Test(groups = { "Functional" })...
109		public void testStarsInFasta2() throws IOException
110		{
111	1	String uri;
112	1	FileParse fp = new FileParse(
113		uri = STARS_FA_FILE2.getAbsoluteFile().toString(),
114		DataSourceType.FILE);
115	1	assertValidFormat(FileFormat.Fasta, uri, fp);
116		}
117
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
118	1	@Test(groups = { "Functional" })...
119		public void testGzipIo() throws IOException
120		{
121	1	String uri;
122	1	FileParse fp = new FileParse(
123		uri = ALIGN_FILE.getAbsoluteFile().toURI().toString(),
124		DataSourceType.URL);
125	1	assertValidFormat(FileFormat.Fasta, uri, fp);
126		}
127
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
128	1	@Test(groups = { "Functional" })...
129		public void testGziplocalFileIO() throws IOException
130		{
131	1	String filepath;
132	1	FileParse fp = new FileParse(
133		filepath = ALIGN_FILE.getAbsoluteFile().toString(),
134		DataSourceType.FILE);
135	1	assertValidFormat(FileFormat.Fasta, filepath, fp);
136		}
137
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2 1PASS
138	1	@Test(groups = { "Functional" })...
139		public void testIsGzipInputStream() throws IOException
140		{
141	1	InputStream is = new FileInputStream(ALIGN_FILE);
142
143		/*
144		* first try fails - FileInputStream does not support mark/reset
145		*/
146	1	assertFalse(Platform.isGzipStream(is));
147
148		/*
149		* wrap in a BufferedInputStream and try again
150		*/
151	1	is = new BufferedInputStream(is, 16);
152	1	assertTrue(Platform.isGzipStream(is));
153
154		/*
155		* check recognition of non-gzipped input
156		*/
157	1	assertFalse(Platform.isGzipStream(new BufferedInputStream(
158		new ByteArrayInputStream("NOT A GZIP".getBytes()))));
159		}
160
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
161	1	@Test(groups = { "Functional" })...
162		public void testNonGzipURLIO() throws IOException
163		{
164	1	String uri;
165	1	FileParse fp = new FileParse(
166		uri = NOTGZALIGN_FILE.getAbsoluteFile().toURI().toString(),
167		DataSourceType.URL);
168	1	assertValidFormat(FileFormat.Fasta, uri, fp);
169		}
170
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
171	1	@Test(groups = { "Functional" })...
172		public void testNonGziplocalFileIO() throws IOException
173		{
174	1	String filepath;
175	1	FileParse fp = new FileParse(
176		filepath = NOTGZALIGN_FILE.getAbsoluteFile().toString(),
177		DataSourceType.FILE);
178	1	assertValidFormat(FileFormat.Fasta, filepath, fp);
179		}
180		}