2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.renderer;
23 import static org.testng.AssertJUnit.assertEquals;
25 import jalview.bin.Cache;
26 import jalview.datamodel.Alignment;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.Sequence;
29 import jalview.datamodel.SequenceGroup;
30 import jalview.datamodel.SequenceI;
31 import jalview.gui.AlignViewport;
32 import jalview.gui.JvOptionPane;
33 import jalview.schemes.ColourSchemeI;
34 import jalview.schemes.UserColourScheme;
35 import jalview.schemes.ZappoColourScheme;
37 import java.awt.Color;
38 import java.util.ArrayList;
40 import org.testng.annotations.BeforeClass;
41 import org.testng.annotations.Test;
43 public class OverviewResColourFinderTest
46 @BeforeClass(alwaysRun = true)
47 public void setUpJvOptionPane()
49 JvOptionPane.setInteractiveMode(false);
50 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
51 Cache.loadProperties("test/jalview/io/testProps.jvprops");
54 @Test(groups = { "Functional" })
55 public void testGetResidueBoxColour_none()
57 SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
58 AlignmentI al = new Alignment(new SequenceI[] { seq });
59 final AlignViewport av = new AlignViewport(al);
60 ResidueColourFinder rcf = new OverviewResColourFinder();
62 ResidueShaderI sh = av.getResidueShading();
64 // gaps are grey, residues white
65 assertEquals(Color.white,
66 rcf.getResidueColour(true, sh, null, seq, 0, null));
67 System.out.println(rcf.getResidueColour(true, sh, null, seq, 2, null));
68 assertEquals(Color.lightGray, rcf.getResidueColour(true,
69 sh, null, seq, 2, null));
71 // unaffected by showBoxes setting
72 assertEquals(Color.white, rcf.getResidueColour(false,
73 sh, null, seq, 0, null));
74 assertEquals(Color.lightGray, rcf.getResidueColour(false,
75 sh, null, seq, 2, null));
78 @Test(groups = { "Functional" })
79 public void testGetResidueBoxColour_zappo()
81 SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
83 AlignmentI al = new Alignment(new SequenceI[] { seq });
84 final AlignViewport av = new AlignViewport(al);
85 ResidueColourFinder rcf = new OverviewResColourFinder();
86 av.setGlobalColourScheme(new ZappoColourScheme());
88 // @see ResidueProperties.zappo
89 assertEquals(Color.pink,
90 rcf.getResidueColour(true, av.getResidueShading(),
91 null, seq, 0, null)); // M
92 assertEquals(Color.green,
93 rcf.getResidueColour(true, av.getResidueShading(),
94 null, seq, 2, null)); // T
95 assertEquals(Color.magenta,
96 rcf.getResidueColour(true, av.getResidueShading(),
97 null, seq, 5, null)); // G
98 assertEquals(Color.orange,
99 rcf.getResidueColour(true, av.getResidueShading(),
100 null, seq, 12, null)); // F
102 // gap colour not specified so gaps are lightGray
103 assertEquals(Color.lightGray, rcf
104 .getResidueColour(true, av.getResidueShading(), null, seq, 3,
107 // unaffected by showBoxes setting
108 assertEquals(Color.pink, rcf.getResidueColour(false,
109 av.getResidueShading(), null, seq, 0, null)); // M
110 assertEquals(Color.green, rcf.getResidueColour(false,
111 av.getResidueShading(), null, seq, 2, null)); // T
112 assertEquals(Color.magenta, rcf.getResidueColour(false,
113 av.getResidueShading(), null, seq, 5, null)); // G
114 assertEquals(Color.orange, rcf.getResidueColour(false,
115 av.getResidueShading(), null, seq, 12, null)); // F
117 // gap colour not specified so gaps are lightGray
118 assertEquals(Color.lightGray, rcf
119 .getResidueColour(false, av.getResidueShading(), null, seq, 3,
124 @Test(groups = { "Functional" })
125 public void testGetResidueBoxColour_userdef()
127 SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
129 AlignmentI al = new Alignment(new SequenceI[] { seq });
130 final AlignViewport av = new AlignViewport(al);
131 ResidueColourFinder rcf = new OverviewResColourFinder();
133 Color[] newColours = new Color[24];
134 for (int i = 0; i < 24; i++)
136 newColours[i] = null;
139 av.setGlobalColourScheme(new UserColourScheme(newColours));
141 // gap colour not specified so gaps are lightGray
142 assertEquals(Color.lightGray, rcf
143 .getResidueColour(true, av.getResidueShading(), null, seq, 3,
146 newColours[23] = Color.pink;
147 av.setGlobalColourScheme(new UserColourScheme(newColours));
149 // gap colour specified as pink
150 assertEquals(Color.pink, rcf.getResidueColour(true,
151 av.getResidueShading(),
152 null, seq, 3, null));
154 // unaffected by showBoxes setting
155 // gap colour not specified so gaps are lightGray
156 newColours[23] = null;
158 assertEquals(Color.lightGray, rcf.getResidueColour(false,
159 av.getResidueShading(), null, seq, 3, null));
161 newColours[23] = Color.pink;
162 av.setGlobalColourScheme(new UserColourScheme(newColours));
164 // gap colour specified as pink
165 assertEquals(Color.pink, rcf.getResidueColour(false,
166 av.getResidueShading(), null, seq, 3, null));
169 @Test(groups = "Functional")
170 public void testGetResidueBoxColour_group()
172 SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
173 AlignmentI al = new Alignment(new SequenceI[] { seq });
175 ColourSchemeI cs = new ZappoColourScheme();
176 ArrayList<SequenceI> seqlist = new ArrayList<>();
178 SequenceGroup sg = new SequenceGroup(seqlist, "testgroup", cs, true,
181 SequenceGroup[] groups = new SequenceGroup[1];
184 final AlignViewport av = new AlignViewport(al);
185 ResidueColourFinder rcf = new OverviewResColourFinder();
187 // G in group specified as magenta in Zappo
188 assertEquals(Color.magenta, rcf.getResidueColour(false,
189 av.getResidueShading(), groups, seq, 7, null));
191 // Residue outside group coloured white
192 assertEquals(Color.white, rcf.getResidueColour(false,
193 av.getResidueShading(), groups, seq, 0, null));
195 // Gap outside group coloured lightgray
196 assertEquals(Color.lightGray, rcf.getResidueColour(false,
197 av.getResidueShading(), groups, seq, 2, null));
199 // use legacy colouring
200 rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
202 // G in group specified as magenta in Zappo
203 assertEquals(Color.magenta, rcf.getResidueColour(false,
204 av.getResidueShading(), groups, seq, 7, null));
206 // Residue outside group coloured lightgray
207 assertEquals(Color.lightGray, rcf.getResidueColour(false,
208 av.getResidueShading(), groups, seq, 0, null));
210 // Gap outside group coloured white
211 assertEquals(Color.white, rcf.getResidueColour(false,
212 av.getResidueShading(), groups, seq, 2, null));
215 rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
217 // G in group specified as magenta in Zappo
218 assertEquals(Color.magenta, rcf.getResidueColour(false,
219 av.getResidueShading(), groups, seq, 7, null));
221 // Residue outside group coloured white
222 assertEquals(Color.white, rcf.getResidueColour(false,
223 av.getResidueShading(), groups, seq, 0, null));
225 // Gap outside group coloured blue
226 assertEquals(Color.blue, rcf.getResidueColour(false,
227 av.getResidueShading(), groups, seq, 2, null));
230 @Test(groups = "Functional")
231 public void testGetBoxColour()
233 SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
235 AlignmentI al = new Alignment(new SequenceI[] { seq });
236 final AlignViewport av = new AlignViewport(al);
238 // non-legacy colouring
239 ResidueColourFinder rcf = new OverviewResColourFinder();
240 ResidueShaderI shader = new ResidueShader();
243 Color c = rcf.getBoxColour(shader, seq, 0);
244 assertEquals(Color.white, c);
247 c = rcf.getBoxColour(shader, seq, 3);
249 jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
252 // legacy colouring set explicitly via constructor
253 rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
254 shader = new ResidueShader();
256 // residues light gray
257 c = rcf.getBoxColour(shader, seq, 0);
258 assertEquals(Color.lightGray, c);
261 c = rcf.getBoxColour(shader, seq, 3);
262 assertEquals(Color.white, c);
264 // legacy colouring off
265 rcf = new OverviewResColourFinder();
266 shader = new ResidueShader();
269 c = rcf.getBoxColour(shader, seq, 0);
270 assertEquals(Color.white, c);
273 c = rcf.getBoxColour(shader, seq, 3);
275 jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
278 // non legacy colouring with colour scheme
279 rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
280 shader = new ResidueShader(new ZappoColourScheme());
283 c = rcf.getBoxColour(shader, seq, 0);
284 assertEquals(Color.pink, c);
287 c = rcf.getBoxColour(shader, seq, 3);
288 assertEquals(Color.blue, c);
290 // legacy colouring with colour scheme
291 rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
294 c = rcf.getBoxColour(shader, seq, 0);
295 assertEquals(Color.pink, c);
298 c = rcf.getBoxColour(shader, seq, 3);
299 assertEquals(Color.white, c);