Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FileFormatsTest	38	62	9	1.0100%	Show methods

Class FileFormatsTest

Class FileFormatsTest	Line # 38	Total Statements 62	Complexity 9	TOTAL Coverage 1.0100%
tearDown() : void   tearDown() : void	4040	1.01	1.01	1.0 1.0100%
setUp() : void   setUp() : void	4646	1.01	1.01	1.0 1.0100%
testIsIdentifiable() : void   testIsIdentifiable() : void	5252	11.011	1.01	1.0 1.0100%
testGetReadableFormats() : void   testGetReadableFormats() : void	7878	3.03	1.01	1.0 1.0100%
testGetWritableFormats() : void   testGetWritableFormats() : void	8686	5.05	1.01	1.0 1.0100%
testDeregisterFileFormat() : void   testDeregisterFileFormat() : void	9696	15.015	1.01	1.0 1.0100%
testForName() : void   testForName() : void	121121	7.07	1.01	1.0 1.0100%
testRegisterFileFormat() : void   testRegisterFileFormat() : void	137137	10.010	1.01	1.0 1.0100%
testGetFormats() : void   testGetFormats() : void	165165	9.09	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.22535211	jalview.io.FileFormatsTest.testDeregisterFileFormatjalview.io.FileFormatsTest.testDeregisterFileFormat	1PASS
	0.16901408	jalview.io.FileFormatsTest.testIsIdentifiablejalview.io.FileFormatsTest.testIsIdentifiable	1PASS
	0.15492958	jalview.io.FileFormatsTest.testRegisterFileFormatjalview.io.FileFormatsTest.testRegisterFileFormat	1PASS
	0.14084508	jalview.io.FileFormatsTest.testGetFormatsjalview.io.FileFormatsTest.testGetFormats	1PASS
	0.112676054	jalview.io.FileFormatsTest.testForNamejalview.io.FileFormatsTest.testForName	1PASS
	0.08450704	jalview.io.FileFormatsTest.testGetWritableFormatsjalview.io.FileFormatsTest.testGetWritableFormats	1PASS
	0.056338027	jalview.io.FileFormatsTest.testGetReadableFormatsjalview.io.FileFormatsTest.testGetReadableFormats	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 java.util.Locale;
24
25		import static org.testng.Assert.assertEquals;
26		import static org.testng.Assert.assertFalse;
27		import static org.testng.Assert.assertNotEquals;
28		import static org.testng.Assert.assertNull;
29		import static org.testng.Assert.assertSame;
30		import static org.testng.Assert.assertTrue;
31
32		import java.util.Iterator;
33
34		import org.testng.annotations.AfterMethod;
35		import org.testng.annotations.BeforeMethod;
36		import org.testng.annotations.Test;
37
		100% Uncovered Elements: 0 (71) Complexity: 9 Complexity Density: 0.15
38		public class FileFormatsTest
39		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
40	7	@AfterMethod(alwaysRun = true)...
41		public void tearDown()
42		{
43	7	FileFormats.getInstance().reset();
44		}
45
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
46	7	@BeforeMethod(alwaysRun = true)...
47		public void setUp()
48		{
49	7	FileFormats.getInstance().reset();
50		}
51
		100% Uncovered Elements: 0 (11) Complexity: 1 Complexity Density: 0.09 1PASS
52	1	@Test(groups = "Functional")...
53		public void testIsIdentifiable()
54		{
55	1	FileFormats formats = FileFormats.getInstance();
56	1	assertTrue(formats
57		.isIdentifiable(formats.forName(FileFormat.Fasta.getName())));
58	1	assertTrue(formats
59		.isIdentifiable(formats.forName(FileFormat.MMCif.getName())));
60	1	assertTrue(formats
61		.isIdentifiable(formats.forName(FileFormat.Jnet.getName())));
62	1	assertTrue(formats
63		.isIdentifiable(formats.forName(FileFormat.Jalview.getName())));
64		// GenBank/ENA
65	1	assertFalse(formats.isIdentifiable(null));
66
67		/*
68		* remove and re-add a format: it is still 'identifiable'
69		*/
70	1	formats.deregisterFileFormat(FileFormat.Fasta.getName());
71	1	assertNull(formats.forName(FileFormat.Fasta.getName()));
72	1	formats.registerFileFormat(FileFormat.Fasta);
73	1	assertSame(FileFormat.Fasta,
74		formats.forName(FileFormat.Fasta.getName()));
75	1	assertTrue(formats.isIdentifiable(FileFormat.Fasta));
76		}
77
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
78	1	@Test(groups = "Functional")...
79		public void testGetReadableFormats()
80		{
81	1	String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";
82	1	FileFormats formats = FileFormats.getInstance();
83	1	assertEquals(formats.getReadableFormats().toString(), expected);
84		}
85
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2 1PASS
86	1	@Test(groups = "Functional")...
87		public void testGetWritableFormats()
88		{
89	1	String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
90	1	FileFormats formats = FileFormats.getInstance();
91	1	assertEquals(formats.getWritableFormats(true).toString(), expected);
92	1	expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Jalview]";
93	1	assertEquals(formats.getWritableFormats(false).toString(), expected);
94		}
95
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
96	1	@Test(groups = "Functional")...
97		public void testDeregisterFileFormat()
98		{
99	1	String writable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
100	1	String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";
101	1	FileFormats formats = FileFormats.getInstance();
102	1	assertEquals(formats.getWritableFormats(true).toString(), writable);
103	1	assertEquals(formats.getReadableFormats().toString(), readable);
104
105	1	formats.deregisterFileFormat(FileFormat.Fasta.getName());
106	1	writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
107	1	readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";
108	1	assertEquals(formats.getWritableFormats(true).toString(), writable);
109	1	assertEquals(formats.getReadableFormats().toString(), readable);
110
111		/*
112		* re-register the format: it gets added to the end of the list
113		*/
114	1	formats.registerFileFormat(FileFormat.Fasta);
115	1	writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Fasta]";
116	1	readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview, Fasta]";
117	1	assertEquals(formats.getWritableFormats(true).toString(), writable);
118	1	assertEquals(formats.getReadableFormats().toString(), readable);
119		}
120
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
121	1	@Test(groups = "Functional")...
122		public void testForName()
123		{
124	1	FileFormats formats = FileFormats.getInstance();
125	1	for (FileFormatI ff : FileFormat.values())
126		{
127	22	assertSame(ff, formats.forName(ff.getName()));
128	22	assertSame(ff,
129		formats.forName(ff.getName().toUpperCase(Locale.ROOT)));
130	22	assertSame(ff,
131		formats.forName(ff.getName().toLowerCase(Locale.ROOT)));
132		}
133	1	assertNull(formats.forName(null));
134	1	assertNull(formats.forName("rubbish"));
135		}
136
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
137	1	@Test(groups = "Functional")...
138		public void testRegisterFileFormat()
139		{
140	1	FileFormats formats = FileFormats.getInstance();
141	1	assertSame(FileFormat.MMCif,
142		formats.forName(FileFormat.MMCif.getName()));
143	1	assertTrue(formats.isIdentifiable(FileFormat.MMCif));
144
145		/*
146		* deregister mmCIF format
147		*/
148	1	formats.deregisterFileFormat(FileFormat.MMCif.getName());
149	1	assertNull(formats.forName(FileFormat.MMCif.getName()));
150
151		/*
152		* re-register mmCIF format
153		* it is reinstated (still 'identifiable')
154		*/
155	1	formats.registerFileFormat(FileFormat.MMCif);
156	1	assertSame(FileFormat.MMCif,
157		formats.forName(FileFormat.MMCif.getName()));
158	1	assertTrue(formats.isIdentifiable(FileFormat.MMCif));
159		// repeating does nothing
160	1	formats.registerFileFormat(FileFormat.MMCif);
161	1	assertSame(FileFormat.MMCif,
162		formats.forName(FileFormat.MMCif.getName()));
163		}
164
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
165	1	@Test(groups = "Functional")...
166		public void testGetFormats()
167		{
168		/*
169		* verify the list of file formats registered matches the enum values
170		*/
171	1	FileFormats instance = FileFormats.getInstance();
172	1	Iterator<FileFormatI> formats = instance.getFormats().iterator();
173	1	FileFormatI[] builtIn = FileFormat.values();
174
175	1	for (FileFormatI ff : builtIn)
176		{
177	22	assertSame(ff, formats.next());
178		}
179	1	assertFalse(formats.hasNext());
180
181		/*
182		* remove the first format, check it is no longer in
183		* the list of formats
184		*/
185	1	String firstFormatName = instance.getFormats().iterator().next()
186		.getName();
187	1	instance.deregisterFileFormat(firstFormatName);
188	1	assertNotEquals(instance.getFormats().iterator().next().getName(),
189		firstFormatName);
190		}
191		}