Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
FileIOTester	37	23	10	0	1.0100%	Show methods

Class FileIOTester

Class FileIOTester	Line # 37	Total Statements 23	Complexity 10	Uncovered Elements 0	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4040	2.02	1.01	0.00	1.0 1.0100%
setUpBeforeClass() : void   setUpBeforeClass() : void	5050	0.00	1.01	0.00	-1.0 -1.0 -
tearDownAfterClass() : void   tearDownAfterClass() : void	5858	0.00	1.01	0.00	-1.0 -1.0 -
assertValidFormat(FileFormatI,String,FileParse) : void   assertValidFormat(FileFormatI,String,FileParse) : void	7777	3.03	1.01	0.00	1.0 1.0100%
testStarsInFasta1() : void   testStarsInFasta1() : void	8787	3.03	1.01	0.00	1.0 1.0100%
testStarsInFasta2() : void   testStarsInFasta2() : void	9696	3.03	1.01	0.00	1.0 1.0100%
testGzipIo() : void   testGzipIo() : void	105105	3.03	1.01	0.00	1.0 1.0100%
testGziplocalFileIO() : void   testGziplocalFileIO() : void	114114	3.03	1.01	0.00	1.0 1.0100%
testNonGzipURLIO() : void   testNonGzipURLIO() : void	123123	3.03	1.01	0.00	1.0 1.0100%
testNonGziplocalFileIO() : void   testNonGziplocalFileIO() : void	132132	3.03	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.24242425	jalview.io.FileIOTester.testNonGzipURLIOjalview.io.FileIOTester.testNonGzipURLIO	1PASS
	0.24242425	jalview.io.FileIOTester.testGziplocalFileIOjalview.io.FileIOTester.testGziplocalFileIO	1PASS
	0.24242425	jalview.io.FileIOTester.testGzipIojalview.io.FileIOTester.testGzipIo	1PASS
	0.24242425	jalview.io.FileIOTester.testNonGziplocalFileIOjalview.io.FileIOTester.testNonGziplocalFileIO	1PASS
	0.24242425	jalview.io.FileIOTester.testStarsInFasta1jalview.io.FileIOTester.testStarsInFasta1	1PASS
	0.24242425	jalview.io.FileIOTester.testStarsInFasta2jalview.io.FileIOTester.testStarsInFasta2	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 jalview.gui.JvOptionPane;
24
25		import java.io.File;
26		import java.io.IOException;
27
28		import org.testng.AssertJUnit;
29		import org.testng.annotations.AfterClass;
30		import org.testng.annotations.BeforeClass;
31		import org.testng.annotations.Test;
32
33		/**
34		* @author jimp
35		*
36		*/
		100% Uncovered Elements: 0 (33) Complexity: 10 Complexity Density: 0.43
37		public class FileIOTester
38		{
39
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
40	1	@BeforeClass(alwaysRun = true)...
41		public void setUpJvOptionPane()
42		{
43	1	JvOptionPane.setInteractiveMode(false);
44	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
45		}
46
47		/**
48		* @throws java.lang.Exception
49		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
50	1	@BeforeClass(alwaysRun = true)...
51		public static void setUpBeforeClass() throws Exception
52		{
53		}
54
55		/**
56		* @throws java.lang.Exception
57		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
58	1	@AfterClass(alwaysRun = true)...
59		public static void tearDownAfterClass() throws Exception
60		{
61		}
62
63		// TODO: make a better/more comprehensive test harness for identify/io
64
65		final static File ALIGN_FILE = new File(
66		"test/jalview/io/test_gz_fasta.gz");
67
68		final static File NOTGZALIGN_FILE = new File(
69		"test/jalview/io/test_gz_fasta_notgz.gz");
70
71		final static File STARS_FA_FILE1 = new File(
72		"test/jalview/io/test_fasta_stars.fa");
73
74		final static File STARS_FA_FILE2 = new File(
75		"test/jalview/io/test_fasta_stars2.fa");
76
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
77	6	private void assertValidFormat(FileFormatI fmt, String src, FileParse fp)...
78		throws FileFormatException
79		{
80	6	AssertJUnit.assertTrue("Couldn't resolve " + src + " as a valid file",
81		fp.isValid());
82	6	FileFormatI type = new IdentifyFile().identify(fp);
83	6	AssertJUnit.assertSame("Data from '" + src + "' Expected to be '" + fmt
84		+ "' identified as '" + type + "'", type, fmt);
85		}
86
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
87	1	@Test(groups = { "Functional" })...
88		public void testStarsInFasta1() throws IOException
89		{
90	1	String uri;
91	1	FileParse fp = new FileParse(uri = STARS_FA_FILE1.getAbsoluteFile()
92		.toString(), DataSourceType.FILE);
93	1	assertValidFormat(FileFormat.Fasta, uri, fp);
94		}
95
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
96	1	@Test(groups = { "Functional" })...
97		public void testStarsInFasta2() throws IOException
98		{
99	1	String uri;
100	1	FileParse fp = new FileParse(uri = STARS_FA_FILE2.getAbsoluteFile()
101		.toString(), DataSourceType.FILE);
102	1	assertValidFormat(FileFormat.Fasta, uri, fp);
103		}
104
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
105	1	@Test(groups = { "Functional" })...
106		public void testGzipIo() throws IOException
107		{
108	1	String uri;
109	1	FileParse fp = new FileParse(uri = ALIGN_FILE.getAbsoluteFile().toURI()
110		.toString(), DataSourceType.URL);
111	1	assertValidFormat(FileFormat.Fasta, uri, fp);
112		}
113
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
114	1	@Test(groups = { "Functional" })...
115		public void testGziplocalFileIO() throws IOException
116		{
117	1	String filepath;
118	1	FileParse fp = new FileParse(filepath = ALIGN_FILE.getAbsoluteFile()
119		.toString(), DataSourceType.FILE);
120	1	assertValidFormat(FileFormat.Fasta, filepath, fp);
121		}
122
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
123	1	@Test(groups = { "Functional" })...
124		public void testNonGzipURLIO() throws IOException
125		{
126	1	String uri;
127	1	FileParse fp = new FileParse(uri = NOTGZALIGN_FILE.getAbsoluteFile()
128		.toURI().toString(), DataSourceType.URL);
129	1	assertValidFormat(FileFormat.Fasta, uri, fp);
130		}
131
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
132	1	@Test(groups = { "Functional" })...
133		public void testNonGziplocalFileIO() throws IOException
134		{
135	1	String filepath;
136	1	FileParse fp = new FileParse(filepath = NOTGZALIGN_FILE
137		.getAbsoluteFile().toString(), DataSourceType.FILE);
138	1	assertValidFormat(FileFormat.Fasta, filepath, fp);
139		}
140		}