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ColourSchemesTest | 49 | 65 | 9 | ||
ColourSchemesTest.Stripy | 55 | 9 | 6 | ||
ColourSchemesTest.MyClustal | 113 | 22 | 13 |
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.schemes; | |
22 | ||
23 | import static org.testng.Assert.assertEquals; | |
24 | import static org.testng.Assert.assertFalse; | |
25 | import static org.testng.Assert.assertSame; | |
26 | import static org.testng.Assert.assertTrue; | |
27 | ||
28 | import java.awt.Color; | |
29 | import java.util.Iterator; | |
30 | import java.util.Map; | |
31 | ||
32 | import org.testng.annotations.AfterClass; | |
33 | import org.testng.annotations.BeforeClass; | |
34 | import org.testng.annotations.Test; | |
35 | ||
36 | import jalview.api.AlignViewportI; | |
37 | import jalview.bin.Cache; | |
38 | import jalview.bin.Jalview; | |
39 | import jalview.datamodel.AnnotatedCollectionI; | |
40 | import jalview.datamodel.SequenceCollectionI; | |
41 | import jalview.datamodel.SequenceI; | |
42 | import jalview.gui.AlignFrame; | |
43 | import jalview.gui.Desktop; | |
44 | import jalview.gui.SequenceRenderer; | |
45 | import jalview.io.DataSourceType; | |
46 | import jalview.io.FileLoader; | |
47 | import jalview.schemes.ClustalxColourScheme.ClustalColour; | |
48 | ||
49 | public class ColourSchemesTest | |
50 | { | |
51 | /* | |
52 | * a colour scheme that alternates Taylor and Zappo | |
53 | * colouring by column | |
54 | */ | |
55 | class Stripy extends ResidueColourScheme | |
56 | { | |
57 | private ResidueColourScheme odd; | |
58 | ||
59 | private ResidueColourScheme even; | |
60 | ||
61 | 1 | private Stripy() |
62 | { | |
63 | } | |
64 | ||
65 | /** | |
66 | * constructor given colours for odd and even columns | |
67 | * | |
68 | * @param odd | |
69 | * @param even | |
70 | */ | |
71 | 1 | private Stripy(ColourSchemeI cs1, ColourSchemeI cs2) |
72 | { | |
73 | 1 | odd = (ResidueColourScheme) cs1; |
74 | 1 | even = (ResidueColourScheme) cs2; |
75 | } | |
76 | ||
77 | 1 | @Override |
78 | public ColourSchemeI getInstance(AlignViewportI view, | |
79 | AnnotatedCollectionI sg) | |
80 | { | |
81 | 1 | final ColourSchemeI cs1 = ColourSchemes.getInstance().getColourScheme( |
82 | JalviewColourScheme.Taylor.toString(), | |
83 | (AnnotatedCollectionI) null); | |
84 | 1 | final ColourSchemeI cs2 = ColourSchemes.getInstance().getColourScheme( |
85 | JalviewColourScheme.Zappo.toString(), | |
86 | (AnnotatedCollectionI) null); | |
87 | 1 | return new Stripy(cs1, cs2); |
88 | } | |
89 | ||
90 | 3 | @Override |
91 | public Color findColour(char c, int j, SequenceI seq) | |
92 | { | |
93 | 3 | if (j % 2 == 1) |
94 | { | |
95 | 1 | return odd.findColour(c, j, seq); |
96 | } | |
97 | else | |
98 | { | |
99 | 2 | return even.findColour(c, j, seq); |
100 | } | |
101 | } | |
102 | ||
103 | 163 | @Override |
104 | public String getSchemeName() | |
105 | { | |
106 | 163 | return "stripy"; |
107 | } | |
108 | }; | |
109 | ||
110 | /* | |
111 | * a colour scheme that is Clustal but using AWT colour equivalents | |
112 | */ | |
113 | class MyClustal extends ResidueColourScheme | |
114 | { | |
115 | ClustalxColourScheme delegate; | |
116 | ||
117 | 1 | private MyClustal() |
118 | { | |
119 | } | |
120 | ||
121 | 1 | private MyClustal(AnnotatedCollectionI sg, |
122 | Map<SequenceI, SequenceCollectionI> hiddenRepSequences) | |
123 | { | |
124 | 1 | delegate = new ClustalxColourScheme(sg, hiddenRepSequences); |
125 | } | |
126 | ||
127 | 3 | @Override |
128 | public Color findColour(char c, int j, SequenceI seq) | |
129 | { | |
130 | 3 | Color col = delegate.findColour(c, j, seq); |
131 | 3 | Color result = col; |
132 | 3 | if (col.equals(ClustalColour.BLUE.colour)) |
133 | { | |
134 | 1 | result = Color.blue; |
135 | } | |
136 | 2 | else if (col.equals(ClustalColour.CYAN.colour)) |
137 | { | |
138 | 0 | result = Color.cyan; |
139 | } | |
140 | 2 | else if (col.equals(ClustalColour.GREEN.colour)) |
141 | { | |
142 | 0 | result = Color.green; |
143 | } | |
144 | 2 | else if (col.equals(ClustalColour.MAGENTA.colour)) |
145 | { | |
146 | 1 | result = Color.magenta; |
147 | } | |
148 | 1 | else if (col.equals(ClustalColour.ORANGE.colour)) |
149 | { | |
150 | 1 | result = Color.orange; |
151 | } | |
152 | 0 | else if (col.equals(ClustalColour.PINK.colour)) |
153 | { | |
154 | 0 | result = Color.pink; |
155 | } | |
156 | 0 | else if (col.equals(ClustalColour.RED.colour)) |
157 | { | |
158 | 0 | result = Color.red; |
159 | } | |
160 | 0 | else if (col.equals(ClustalColour.YELLOW.colour)) |
161 | { | |
162 | 0 | result = Color.yellow; |
163 | } | |
164 | 3 | return result; |
165 | } | |
166 | ||
167 | 1 | @Override |
168 | public ColourSchemeI getInstance(AlignViewportI view, | |
169 | AnnotatedCollectionI sg) | |
170 | { | |
171 | 1 | return new MyClustal(sg, view.getHiddenRepSequences()); |
172 | } | |
173 | ||
174 | 163 | @Override |
175 | public String getSchemeName() | |
176 | { | |
177 | 163 | return "MyClustal"; |
178 | } | |
179 | ||
180 | } | |
181 | ||
182 | 1 | @BeforeClass(alwaysRun = true) |
183 | public static void setUpBeforeClass() throws Exception | |
184 | { | |
185 | /* | |
186 | * use read-only test properties file | |
187 | */ | |
188 | 1 | Cache.loadProperties("test/jalview/io/testProps.jvprops"); |
189 | 1 | Jalview.main(new String[] { "--nonews" }); |
190 | } | |
191 | ||
192 | 1 | @AfterClass(alwaysRun = true) |
193 | public static void tearDownAfterClass() throws Exception | |
194 | { | |
195 | 1 | if (Desktop.instance != null) |
196 | 1 | Desktop.instance.closeAll_actionPerformed(null); |
197 | } | |
198 | ||
199 | 1 | @Test(groups = "Functional") |
200 | public void testGetColourSchemes() | |
201 | { | |
202 | /* | |
203 | * this just verifies that built-in colour schemes are loaded into ColourSchemes | |
204 | * in the order in which they are declared in the JalviewColourScheme enum | |
205 | * (this also determines their order in Colour menus) | |
206 | */ | |
207 | 1 | Iterator<ColourSchemeI> schemes = ColourSchemes.getInstance() |
208 | .getColourSchemes().iterator(); | |
209 | 1 | JalviewColourScheme[] jalviewSchemes = JalviewColourScheme.values(); |
210 | 1 | int i = 0; |
211 | 21 | while (schemes.hasNext() && i < jalviewSchemes.length) |
212 | { | |
213 | 20 | assertTrue(schemes.next().getSchemeName() |
214 | .equals(jalviewSchemes[i].toString())); | |
215 | 20 | i++; |
216 | } | |
217 | } | |
218 | ||
219 | 1 | @Test(groups = "Functional") |
220 | public void testGetColourScheme() | |
221 | { | |
222 | 1 | AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( |
223 | ">seq1\nAGLRTWQU", DataSourceType.PASTE); | |
224 | 1 | ColourSchemes schemes = ColourSchemes.getInstance(); |
225 | ||
226 | 1 | AnnotatedCollectionI al = af.getViewport().getAlignment(); |
227 | ||
228 | 1 | for (JalviewColourScheme cs : JalviewColourScheme.values()) |
229 | { | |
230 | 20 | ColourSchemeI registered = schemes.getColourScheme(cs.toString(), al); |
231 | 20 | assertSame(registered.getClass(), cs.getSchemeClass()); |
232 | } | |
233 | 1 | af.closeMenuItem_actionPerformed(true); |
234 | } | |
235 | ||
236 | 1 | @Test(groups = "Functional") |
237 | public void testRegisterColourScheme() | |
238 | { | |
239 | 1 | ColourSchemes.getInstance().registerColourScheme(new Stripy()); |
240 | 1 | ColourSchemes.getInstance().registerColourScheme(new MyClustal()); |
241 | 1 | AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( |
242 | "examples/uniref50.fa", DataSourceType.FILE); | |
243 | /* | |
244 | * set a breakpoint here to see and play with the newly registered | |
245 | * colour schemes in the AlignFrame colour menu | |
246 | */ | |
247 | 1 | SequenceRenderer sr = new SequenceRenderer(af.getViewport()); |
248 | 1 | SequenceI seq = af.getViewport().getAlignment().findName("FER_CAPAA"); |
249 | ||
250 | /* | |
251 | * set and check Taylor colours | |
252 | */ | |
253 | 1 | af.changeColour_actionPerformed(JalviewColourScheme.Taylor.toString()); |
254 | 1 | Color taylor1 = sr.getResidueColour(seq, 88, null); // E 255,0,102 |
255 | 1 | Color taylor2 = sr.getResidueColour(seq, 89, null); // A 204,255,0 |
256 | 1 | Color taylor3 = sr.getResidueColour(seq, 90, null); // G 255,153,0 |
257 | 1 | assertEquals(taylor1, new Color(255, 0, 102)); |
258 | 1 | assertEquals(taylor2, new Color(204, 255, 0)); |
259 | 1 | assertEquals(taylor3, new Color(255, 153, 0)); |
260 | ||
261 | /* | |
262 | * set and check Zappo colours | |
263 | */ | |
264 | 1 | af.changeColour_actionPerformed(JalviewColourScheme.Zappo.toString()); |
265 | 1 | Color zappo1 = sr.getResidueColour(seq, 88, null); // E red |
266 | 1 | Color zappo2 = sr.getResidueColour(seq, 89, null); // A pink |
267 | 1 | Color zappo3 = sr.getResidueColour(seq, 90, null); // G magenta |
268 | 1 | assertEquals(zappo1, Color.red); |
269 | 1 | assertEquals(zappo2, Color.pink); |
270 | 1 | assertEquals(zappo3, Color.magenta); |
271 | ||
272 | /* | |
273 | * set 'stripy' colours - odd columns are Taylor and even are Zappo | |
274 | */ | |
275 | 1 | af.changeColour_actionPerformed("stripy"); |
276 | 1 | Color stripy1 = sr.getResidueColour(seq, 88, null); |
277 | 1 | Color stripy2 = sr.getResidueColour(seq, 89, null); |
278 | 1 | Color stripy3 = sr.getResidueColour(seq, 90, null); |
279 | 1 | assertEquals(stripy1, zappo1); |
280 | 1 | assertEquals(stripy2, taylor2); |
281 | 1 | assertEquals(stripy3, zappo3); |
282 | ||
283 | /* | |
284 | * set and check Clustal colours | |
285 | */ | |
286 | 1 | af.changeColour_actionPerformed(JalviewColourScheme.Clustal.toString()); |
287 | 1 | Color clustal1 = sr.getResidueColour(seq, 88, null); |
288 | 1 | Color clustal2 = sr.getResidueColour(seq, 89, null); |
289 | 1 | Color clustal3 = sr.getResidueColour(seq, 90, null); |
290 | 1 | assertEquals(clustal1, ClustalColour.MAGENTA.colour); |
291 | 1 | assertEquals(clustal2, ClustalColour.BLUE.colour); |
292 | 1 | assertEquals(clustal3, ClustalColour.ORANGE.colour); |
293 | ||
294 | /* | |
295 | * set 'MyClustal' colours - uses AWT colour equivalents | |
296 | */ | |
297 | 1 | af.changeColour_actionPerformed("MyClustal"); |
298 | 1 | Color myclustal1 = sr.getResidueColour(seq, 88, null); |
299 | 1 | Color myclustal2 = sr.getResidueColour(seq, 89, null); |
300 | 1 | Color myclustal3 = sr.getResidueColour(seq, 90, null); |
301 | 1 | assertEquals(myclustal1, Color.MAGENTA); |
302 | 1 | assertEquals(myclustal2, Color.BLUE); |
303 | 1 | assertEquals(myclustal3, Color.ORANGE); |
304 | } | |
305 | ||
306 | /** | |
307 | * Tests for check if scheme name exists. Built-in scheme names are the | |
308 | * toString() values of enum JalviewColourScheme. | |
309 | */ | |
310 | 1 | @Test(groups = "Functional") |
311 | public void testNameExists() | |
312 | { | |
313 | 1 | ColourSchemes cs = ColourSchemes.getInstance(); |
314 | 1 | assertFalse(cs.nameExists(null)); |
315 | 1 | assertFalse(cs.nameExists("")); |
316 | 1 | assertTrue(cs.nameExists("Clustal")); |
317 | 1 | assertTrue(cs.nameExists("CLUSTAL")); |
318 | 1 | assertFalse(cs.nameExists("CLUSTAL ")); |
319 | 1 | assertTrue(cs.nameExists("% Identity")); |
320 | 1 | assertFalse(cs.nameExists("PID")); |
321 | } | |
322 | } |