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.api.AlignViewportI;
26 import jalview.bin.Cache;
27 import jalview.datamodel.Alignment;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.Sequence;
30 import jalview.datamodel.SequenceGroup;
31 import jalview.datamodel.SequenceI;
32 import jalview.gui.AlignViewport;
33 import jalview.gui.JvOptionPane;
34 import jalview.schemes.ColourSchemeI;
35 import jalview.schemes.UserColourScheme;
36 import jalview.schemes.ZappoColourScheme;
38 import java.awt.Color;
39 import java.util.ArrayList;
41 import org.testng.annotations.BeforeClass;
42 import org.testng.annotations.Test;
44 public class OverviewResColourFinderTest
47 @BeforeClass(alwaysRun = true)
48 public void setUpJvOptionPane()
50 JvOptionPane.setInteractiveMode(false);
51 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
52 Cache.loadProperties("test/jalview/io/testProps.jvprops");
55 @Test(groups = { "Functional" })
56 public void testGetResidueBoxColour_none()
58 SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
59 AlignmentI al = new Alignment(new SequenceI[] { seq });
60 final AlignViewportI av = new AlignViewport(al);
61 ResidueColourFinder rcf = new OverviewResColourFinder();
63 // gaps are grey, residues white
64 assertEquals(Color.white, rcf.getResidueColour(true,
65 av.getResidueShading(),
67 assertEquals(Color.lightGray, rcf
68 .getResidueColour(true, av.getResidueShading(), null, seq, 2,
71 // unaffected by showBoxes setting
72 assertEquals(Color.white, rcf.getResidueColour(false,
73 av.getResidueShading(), null, seq, 0, null));
74 assertEquals(Color.lightGray, rcf.getResidueColour(false,
75 av.getResidueShading(), 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 AlignViewportI 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 AlignViewportI 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;
157 assertEquals(Color.lightGray, rcf.getResidueColour(false,
158 av.getResidueShading(), null, seq, 3, null));
160 newColours[23] = Color.pink;
161 av.setGlobalColourScheme(new UserColourScheme(newColours));
163 // gap colour specified as pink
164 assertEquals(Color.pink, rcf.getResidueColour(false,
165 av.getResidueShading(), null, seq, 3, null));
169 public void testGetResidueBoxColour_group()
171 SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
172 AlignmentI al = new Alignment(new SequenceI[] { seq });
174 ColourSchemeI cs = new ZappoColourScheme();
175 ArrayList<SequenceI> seqlist = new ArrayList<>();
177 SequenceGroup sg = new SequenceGroup(seqlist, "testgroup", cs, true,
180 SequenceGroup[] groups = new SequenceGroup[1];
183 final AlignViewportI av = new AlignViewport(al);
184 ResidueColourFinder rcf = new OverviewResColourFinder();
186 // G in group specified as magenta in Zappo
187 assertEquals(Color.magenta, rcf.getResidueColour(false,
188 av.getResidueShading(), groups, seq, 7, null));
190 // Residue outside group coloured white
191 assertEquals(Color.white, rcf.getResidueColour(false,
192 av.getResidueShading(), groups, seq, 0, null));
194 // Gap outside group coloured lightgray
195 assertEquals(Color.lightGray, rcf.getResidueColour(false,
196 av.getResidueShading(), groups, seq, 2, null));
198 // use legacy colouring
199 rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
201 // G in group specified as magenta in Zappo
202 assertEquals(Color.magenta, rcf.getResidueColour(false,
203 av.getResidueShading(), groups, seq, 7, null));
205 // Residue outside group coloured lightgray
206 assertEquals(Color.lightGray, rcf.getResidueColour(false,
207 av.getResidueShading(), groups, seq, 0, null));
209 // Gap outside group coloured white
210 assertEquals(Color.white, rcf.getResidueColour(false,
211 av.getResidueShading(), groups, seq, 2, null));
214 rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
216 // G in group specified as magenta in Zappo
217 assertEquals(Color.magenta, rcf.getResidueColour(false,
218 av.getResidueShading(), groups, seq, 7, null));
220 // Residue outside group coloured white
221 assertEquals(Color.white, rcf.getResidueColour(false,
222 av.getResidueShading(), groups, seq, 0, null));
224 // Gap outside group coloured blue
225 assertEquals(Color.blue, rcf.getResidueColour(false,
226 av.getResidueShading(), groups, seq, 2, null));
230 public void testGetBoxColour()
232 SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
235 // non-legacy colouring
236 ResidueColourFinder rcf = new OverviewResColourFinder();
237 ResidueShaderI shader = new ResidueShader();
240 Color c = rcf.getBoxColour(shader, seq, 0);
241 assertEquals(Color.white, c);
244 c = rcf.getBoxColour(shader, seq, 3);
246 jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
249 // legacy colouring set explicitly via constructor
250 rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
251 shader = new ResidueShader();
253 // residues light gray
254 c = rcf.getBoxColour(shader, seq, 0);
255 assertEquals(Color.lightGray, c);
258 c = rcf.getBoxColour(shader, seq, 3);
259 assertEquals(Color.white, c);
261 // legacy colouring off
262 rcf = new OverviewResColourFinder();
263 shader = new ResidueShader();
266 c = rcf.getBoxColour(shader, seq, 0);
267 assertEquals(Color.white, c);
270 c = rcf.getBoxColour(shader, seq, 3);
271 assertEquals(OverviewResColourFinder.OVERVIEW_DEFAULT_GAP, c);
273 // non legacy colouring with colour scheme
274 rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
275 shader = new ResidueShader(new ZappoColourScheme());
278 c = rcf.getBoxColour(shader, seq, 0);
279 assertEquals(Color.pink, c);
282 c = rcf.getBoxColour(shader, seq, 3);
283 assertEquals(Color.blue, c);
285 // legacy colouring with colour scheme
286 rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
289 c = rcf.getBoxColour(shader, seq, 0);
290 assertEquals(Color.pink, c);
293 c = rcf.getBoxColour(shader, seq, 3);
294 assertEquals(Color.white, c);