Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FileIOTester	46	29	11	1.0100%	Show methods

Class FileIOTester

Class FileIOTester	Line # 46	Total Statements 29	Complexity 11	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4949	2.02	1.01	1.0 1.0100%
setUpBeforeClass() : void   setUpBeforeClass() : void	5959	1.01	1.01	1.0 1.0100%
tearDownAfterClass() : void   tearDownAfterClass() : void	6868	0.00	1.01	-1.0 -1.0 -
assertValidFormat(FileFormatI,String,FileParse) : void   assertValidFormat(FileFormatI,String,FileParse) : void	8787	3.03	1.01	1.0 1.0100%
testStarsInFasta1() : void   testStarsInFasta1() : void	9797	3.03	1.01	1.0 1.0100%
testStarsInFasta2() : void   testStarsInFasta2() : void	107107	3.03	1.01	1.0 1.0100%
testGzipIo() : void   testGzipIo() : void	117117	3.03	1.01	1.0 1.0100%
testGziplocalFileIO() : void   testGziplocalFileIO() : void	127127	3.03	1.01	1.0 1.0100%
testIsGzipInputStream() : void   testIsGzipInputStream() : void	137137	5.05	1.01	1.0 1.0100%
testNonGzipURLIO() : void   testNonGzipURLIO() : void	160160	3.03	1.01	1.0 1.0100%
testNonGziplocalFileIO() : void   testNonGziplocalFileIO() : void	170170	3.03	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

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