Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FileFormatsTest	37	63	9	1.0100%	Show methods

Class FileFormatsTest

Class FileFormatsTest	Line # 37	Total Statements 63	Complexity 9	TOTAL Coverage 1.0100%
tearDown() : void   tearDown() : void	3939	1.01	1.01	1.0 1.0100%
setUp() : void   setUp() : void	4545	1.01	1.01	1.0 1.0100%
testIsIdentifiable() : void   testIsIdentifiable() : void	5151	11.011	1.01	1.0 1.0100%
testGetReadableFormats() : void   testGetReadableFormats() : void	7676	3.03	1.01	1.0 1.0100%
testGetWritableFormats() : void   testGetWritableFormats() : void	8484	5.05	1.01	1.0 1.0100%
testDeregisterFileFormat() : void   testDeregisterFileFormat() : void	9494	16.016	1.01	1.0 1.0100%
testForName() : void   testForName() : void	120120	7.07	1.01	1.0 1.0100%
testRegisterFileFormat() : void   testRegisterFileFormat() : void	136136	10.010	1.01	1.0 1.0100%
testGetFormats() : void   testGetFormats() : void	164164	9.09	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.2361111	jalview.io.FileFormatsTest.testDeregisterFileFormatjalview.io.FileFormatsTest.testDeregisterFileFormat	1PASS
	0.16666667	jalview.io.FileFormatsTest.testIsIdentifiablejalview.io.FileFormatsTest.testIsIdentifiable	1PASS
	0.15277778	jalview.io.FileFormatsTest.testRegisterFileFormatjalview.io.FileFormatsTest.testRegisterFileFormat	1PASS
	0.1388889	jalview.io.FileFormatsTest.testGetFormatsjalview.io.FileFormatsTest.testGetFormats	1PASS
	0.11111111	jalview.io.FileFormatsTest.testForNamejalview.io.FileFormatsTest.testForName	1PASS
	0.083333336	jalview.io.FileFormatsTest.testGetWritableFormatsjalview.io.FileFormatsTest.testGetWritableFormats	1PASS
	0.055555556	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 static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertFalse;
25		import static org.testng.Assert.assertNotEquals;
26		import static org.testng.Assert.assertNull;
27		import static org.testng.Assert.assertSame;
28		import static org.testng.Assert.assertTrue;
29
30		import java.util.Iterator;
31		import java.util.Locale;
32
33		import org.testng.annotations.AfterMethod;
34		import org.testng.annotations.BeforeMethod;
35		import org.testng.annotations.Test;
36
		100% Uncovered Elements: 0 (72) Complexity: 9 Complexity Density: 0.14
37		public class FileFormatsTest
38		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
39	7	@AfterMethod(alwaysRun = true)...
40		public void tearDown()
41		{
42	7	FileFormats.getInstance().reset();
43		}
44
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
45	7	@BeforeMethod(alwaysRun = true)...
46		public void setUp()
47		{
48	7	FileFormats.getInstance().reset();
49		}
50
		100% Uncovered Elements: 0 (11) Complexity: 1 Complexity Density: 0.09 1PASS
51	1	@Test(groups = "Functional")...
52		public void testIsIdentifiable()
53		{
54	1	FileFormats formats = FileFormats.getInstance();
55	1	assertTrue(formats.isIdentifiable(formats.forName(FileFormat.Fasta
56		.getName())));
57	1	assertTrue(formats.isIdentifiable(formats.forName(FileFormat.MMCif
58		.getName())));
59	1	assertTrue(formats.isIdentifiable(formats.forName(FileFormat.Jnet
60		.getName())));
61	1	assertTrue(formats.isIdentifiable(formats.forName(FileFormat.Jalview
62		.getName())));
63	1	assertFalse(formats.isIdentifiable(null));
64
65		/*
66		* remove and re-add a format: it is still 'identifiable'
67		*/
68	1	formats.deregisterFileFormat(FileFormat.Fasta.getName());
69	1	assertNull(formats.forName(FileFormat.Fasta.getName()));
70	1	formats.registerFileFormat(FileFormat.Fasta);
71	1	assertSame(FileFormat.Fasta,
72		formats.forName(FileFormat.Fasta.getName()));
73	1	assertTrue(formats.isIdentifiable(FileFormat.Fasta));
74		}
75
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
76	1	@Test(groups = "Functional")...
77		public void testGetReadableFormats()
78		{
79	1	String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, A3M (HHSuite), HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3, BSML]";
80	1	FileFormats formats = FileFormats.getInstance();
81	1	assertEquals(formats.getReadableFormats().toString(), expected);
82		}
83
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2 1PASS
84	1	@Test(groups = "Functional")...
85		public void testGetWritableFormats()
86		{
87	1	String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3]";
88	1	FileFormats formats = FileFormats.getInstance();
89	1	assertEquals(formats.getWritableFormats(true).toString(), expected);
90	1	expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Jalview, HMMER3]";
91	1	assertEquals(formats.getWritableFormats(false).toString(), expected);
92		}
93
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.06 1PASS
94	1	@Test(groups = "Functional")...
95		public void testDeregisterFileFormat()
96		{
97	1	String writable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3]";
98	1	String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, A3M (HHSuite), HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3, BSML]";
99	1	FileFormats formats = FileFormats.getInstance();
100	1	System.out.println(formats.getReadableFormats().toString());
101	1	assertEquals(formats.getWritableFormats(true).toString(), writable);
102	1	assertEquals(formats.getReadableFormats().toString(), readable);
103
104	1	formats.deregisterFileFormat(FileFormat.Fasta.getName());
105	1	writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3]";
106	1	readable = "[PFAM, Stockholm, PIR, BLC, AMSA, A3M (HHSuite), HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3, BSML]";
107	1	assertEquals(formats.getWritableFormats(true).toString(), writable);
108	1	assertEquals(formats.getReadableFormats().toString(), readable);
109
110		/*
111		* re-register the format: it gets added to the end of the list
112		*/
113	1	formats.registerFileFormat(FileFormat.Fasta);
114	1	writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3, Fasta]";
115	1	readable = "[PFAM, Stockholm, PIR, BLC, AMSA, A3M (HHSuite), HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3, BSML, Fasta]";
116	1	assertEquals(formats.getWritableFormats(true).toString(), writable);
117	1	assertEquals(formats.getReadableFormats().toString(), readable);
118		}
119
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
120	1	@Test(groups = "Functional")...
121		public void testForName()
122		{
123	1	FileFormats formats = FileFormats.getInstance();
124	1	for (FileFormatI ff : FileFormat.values())
125		{
126	26	assertSame(ff, formats.forName(ff.getName()));
127	26	assertSame(ff,
128		formats.forName(ff.getName().toUpperCase(Locale.ROOT)));
129	26	assertSame(ff,
130		formats.forName(ff.getName().toLowerCase(Locale.ROOT)));
131		}
132	1	assertNull(formats.forName(null));
133	1	assertNull(formats.forName("rubbish"));
134		}
135
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
136	1	@Test(groups = "Functional")...
137		public void testRegisterFileFormat()
138		{
139	1	FileFormats formats = FileFormats.getInstance();
140	1	assertSame(FileFormat.MMCif,
141		formats.forName(FileFormat.MMCif.getName()));
142	1	assertTrue(formats.isIdentifiable(FileFormat.MMCif));
143
144		/*
145		* deregister mmCIF format
146		*/
147	1	formats.deregisterFileFormat(FileFormat.MMCif.getName());
148	1	assertNull(formats.forName(FileFormat.MMCif.getName()));
149
150		/*
151		* re-register mmCIF format
152		* it is reinstated (still 'identifiable')
153		*/
154	1	formats.registerFileFormat(FileFormat.MMCif);
155	1	assertSame(FileFormat.MMCif,
156		formats.forName(FileFormat.MMCif.getName()));
157	1	assertTrue(formats.isIdentifiable(FileFormat.MMCif));
158		// repeating does nothing
159	1	formats.registerFileFormat(FileFormat.MMCif);
160	1	assertSame(FileFormat.MMCif,
161		formats.forName(FileFormat.MMCif.getName()));
162		}
163
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
164	1	@Test(groups = "Functional")...
165		public void testGetFormats()
166		{
167		/*
168		* verify the list of file formats registered matches the enum values
169		*/
170	1	FileFormats instance = FileFormats.getInstance();
171	1	Iterator<FileFormatI> formats = instance.getFormats()
172		.iterator();
173	1	FileFormatI[] builtIn = FileFormat.values();
174
175	1	for (FileFormatI ff : builtIn)
176		{
177	26	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		}