Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
IdentifyFileTest	36	33	9	0.00%	Show methods

Class IdentifyFileTest

Class IdentifyFileTest	Line # 36	Total Statements 33	Complexity 9	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3939	2.02	1.01	0.0 0.00%
testIdentify(String,FileFormatI) : void   testIdentify(String,FileFormatI) : void	4646	4.04	1.01	0.0 0.00%
testIdentify_featureFile() : void   testIdentify_featureFile() : void	6262	7.07	1.01	0.0 0.00%
IdentifyFileDP() : Object[][]   IdentifyFileDP() : Object[][]	9292	1.01	1.01	0.0 0.00%
testLooksLikeFeatureData() : void   testLooksLikeFeatureData() : void	123123	8.08	1.01	0.0 0.00%
testExceptions(String,Class<? extends Exception>,FileFormatI) : void   testExceptions(String,Class<? extends Exception>,FileFormatI) : void	142142	10.010	3.03	0.0 0.00%
urlTargetsAndExceptions() : Object[][]   urlTargetsAndExceptions() : Object[][]	171171	1.01	1.01	0.0 0.00%

 

Contributing tests

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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.io;
22
23		import static org.testng.AssertJUnit.assertFalse;
24		import static org.testng.AssertJUnit.assertSame;
25		import static org.testng.AssertJUnit.assertTrue;
26
27		import java.io.FileNotFoundException;
28
29		import org.testng.Assert;
30		import org.testng.annotations.BeforeClass;
31		import org.testng.annotations.DataProvider;
32		import org.testng.annotations.Test;
33
34		import jalview.gui.JvOptionPane;
35
		0% Uncovered Elements: 42 (42) Complexity: 9 Complexity Density: 0.27
36		public class IdentifyFileTest
37		{
38
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
39	0	@BeforeClass(alwaysRun = true)...
40		public void setUpJvOptionPane()
41		{
42	0	JvOptionPane.setInteractiveMode(false);
43	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
44		}
45
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25 4-
46	0	@Test(groups = { "Functional" }, dataProvider = "identifyFiles")...
47		public void testIdentify(String data, FileFormatI expectedFileType)
48		throws FileFormatException, FileNotFoundException
49		{
50	0	DataSourceType protocol = DataSourceType.FILE;
51	0	IdentifyFile ider = new IdentifyFile();
52	0	FileFormatI actualFiletype = ider.identify(data, protocol);
53	0	Assert.assertSame(actualFiletype, expectedFileType,
54		"File identification Failed!");
55		}
56
57		/**
58		* Additional tests for Jalview features file
59		*
60		* @throws FileFormatException
61		*/
		0% Uncovered Elements: 7 (7) Complexity: 1 Complexity Density: 0.14 4-
62	0	@Test(groups = "Functional")...
63		public void testIdentify_featureFile()
64		throws FileFormatException, FileNotFoundException
65		{
66	0	IdentifyFile ider = new IdentifyFile();
67
68		/*
69		* Jalview format with features only, no feature colours
70		*/
71	0	String data = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
72		+ "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
73	0	assertSame(FileFormat.Features,
74		ider.identify(data, DataSourceType.PASTE));
75
76		/*
77		* Jalview feature colour followed by GFF format feature data
78		*/
79	0	data = "METAL\tcc9900\n" + "GFF\n"
80		+ "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\n";
81	0	assertSame(FileFormat.Features,
82		ider.identify(data, DataSourceType.PASTE));
83
84		/*
85		* Feature with '<' in the name (JAL-2098)
86		*/
87	0	data = "kD < 3\tred\n" + "Low kD\tFER_CAPAA\t-1\t39\t39\tkD < 3\n";
88	0	assertSame(FileFormat.Features,
89		ider.identify(data, DataSourceType.PASTE));
90		}
91
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
92	0	@DataProvider(name = "identifyFiles")...
93		public Object[][] IdentifyFileDP()
94		{
95	0	return new Object[][] { { "examples/example.json", FileFormat.Json },
96		{ "examples/plantfdx.fa", FileFormat.Fasta },
97		{ "examples/dna_interleaved.phy", FileFormat.Phylip },
98		{ "examples/2GIS.pdb", FileFormat.PDB },
99		{ "examples/RF00031_folded.stk", FileFormat.Stockholm },
100		{ "examples/testdata/test.rnaml", FileFormat.Rnaml },
101		{ "examples/testdata/test.aln", FileFormat.Clustal },
102		{ "examples/testdata/test.pfam", FileFormat.Pfam },
103		{ "examples/testdata/test.msf", FileFormat.MSF },
104		{ "examples/testdata/test.pir", FileFormat.PIR },
105		{ "examples/testdata/test.html", FileFormat.Html },
106		{ "examples/testdata/test.pileup", FileFormat.Pileup },
107		{ "examples/testdata/test.blc", FileFormat.BLC },
108		{ "test/jalview/io/J03321.embl.txt", FileFormat.Embl },
109		{ "test/jalview/io/J03321.gb", FileFormat.GenBank },
110		{ "examples/exampleFeatures.txt", FileFormat.Features },
111		{ "examples/testdata/simpleGff3.gff", FileFormat.Features },
112		{ "examples/testdata/test.jvp", FileFormat.Jalview },
113		{ "examples/testdata/test.cif", FileFormat.MMCif },
114		{ "examples/testdata/cullpdb_pc25_res3.0_R0.3_d150729_chains9361.fasta.15316",
115		FileFormat.Fasta },
116		{ "resources/scoreModel/pam250.scm", FileFormat.ScoreMatrix },
117		{ "resources/scoreModel/blosum80.scm", FileFormat.ScoreMatrix }
118		// { "examples/testdata/test.amsa", "AMSA" },
119		// { "examples/test.jnet", "JnetFile" },
120		};
121		}
122
		0% Uncovered Elements: 8 (8) Complexity: 1 Complexity Density: 0.12 4-
123	0	@Test(groups = "Functional")...
124		public void testLooksLikeFeatureData()
125		{
126	0	IdentifyFile id = new IdentifyFile();
127	0	assertFalse(id.looksLikeFeatureData(null));
128	0	assertFalse(id.looksLikeFeatureData(""));
129		// too few columns:
130	0	assertFalse(id.looksLikeFeatureData("1 \t 2 \t 3 \t 4 \t 5"));
131		// GFF format:
132	0	assertTrue(
133		id.looksLikeFeatureData("Seq1\tlocal\tHelix\t2456\t2462\tss"));
134		// Jalview format:
135	0	assertTrue(id.looksLikeFeatureData("Helix\tSeq1\t-1\t2456\t2462\tss"));
136		// non-numeric start column:
137	0	assertFalse(id.looksLikeFeatureData("Helix\tSeq1\t-1\t.\t2462\tss"));
138		// non-numeric start column:
139	0	assertFalse(id.looksLikeFeatureData("Helix\tSeq1\t-1\t2456\t.\tss"));
140		}
141
		0% Uncovered Elements: 12 (12) Complexity: 3 Complexity Density: 0.3 4-
142	0	@Test(groups = "Network", dataProvider = "urlTargetsAndExceptions")...
143		public void testExceptions(String url,
144		Class<? extends Exception> expectedExceptionClass,
145		FileFormatI expectedFormat)
146		{
147	0	Class<? extends Exception> actualExceptionClass = null;
148	0	FileFormatI actualFormat = null;
149	0	try
150		{
151	0	actualFormat = new IdentifyFile().identify(url, DataSourceType.URL);
152		} catch (FileFormatException | FileNotFoundException e)
153		{
154	0	Assert.assertNull(expectedFormat,
155		"Exception occurred when expecting an identifiable format.");
156	0	Assert.assertNotNull(expectedExceptionClass,
157		"An unexpected exception occurred: '" + e.getMessage() + "'");
158	0	Assert.assertEquals(e.getClass(), expectedExceptionClass,
159		"Got the wrong kind of exception.");
160	0	actualExceptionClass = e.getClass();
161		}
162
163	0	if (expectedExceptionClass != null)
164		{
165	0	Assert.assertEquals(actualExceptionClass, expectedExceptionClass,
166		"Expected an exception but got the wrong one.");
167		}
168
169		}
170
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
171	0	@DataProvider(name = "urlTargetsAndExceptions")...
172		public Object[][] urlTargetsAndExceptions()
173		{
174		/*
175		String targetUrl,
176		String finalUrl,
177		String foundInFirstLine,
178		*/
179	0	return new Object[][] {
180		//
181		/*
182		{ "http://jalview.org/examples/uniref50.fa", null,
183		FileFormat.Fasta },
184		{ "https://www.jalview.org/examples/NOFILE.fa",
185		FileNotFoundException.class, null },
186		{ "https://NOSERVER.jalview.org/", FileNotFoundException.class,
187		null },
188		*/
189		{ "https://www.jalview.org/schools/Jalview_Schools_Workbook_200.jpg",
190		FileFormatException.class, null },
191		/*
192		*/
193		//
194		};
195		}
196
197		}