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FileFormatsTest | 38 | 62 | 9 |
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 | ||
38 | public class FileFormatsTest | |
39 | { | |
40 | 7 | @AfterMethod(alwaysRun = true) |
41 | public void tearDown() | |
42 | { | |
43 | 7 | FileFormats.getInstance().reset(); |
44 | } | |
45 | ||
46 | 7 | @BeforeMethod(alwaysRun = true) |
47 | public void setUp() | |
48 | { | |
49 | 7 | FileFormats.getInstance().reset(); |
50 | } | |
51 | ||
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 | ||
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 | ||
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 | ||
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 | ||
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 | ||
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 | ||
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 | } |