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 java.awt.Color;
26 import java.util.ArrayList;
28 import org.testng.annotations.BeforeClass;
29 import org.testng.annotations.Test;
31 import jalview.bin.Cache;
32 import jalview.datamodel.Alignment;
33 import jalview.datamodel.AlignmentI;
34 import jalview.datamodel.Sequence;
35 import jalview.datamodel.SequenceGroup;
36 import jalview.datamodel.SequenceI;
37 import jalview.gui.AlignViewport;
38 import jalview.gui.JvOptionPane;
39 import jalview.gui.OverviewCanvas;
40 import jalview.schemes.ColourSchemeI;
41 import jalview.schemes.UserColourScheme;
42 import jalview.schemes.ZappoColourScheme;
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 AlignViewport 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(), null, seq, 0, null));
66 assertEquals(Color.lightGray, rcf.getResidueColour(true,
67 av.getResidueShading(), null, seq, 2, null));
69 // unaffected by showBoxes setting
70 assertEquals(Color.white, rcf.getResidueColour(false,
71 av.getResidueShading(), null, seq, 0, null));
72 assertEquals(Color.lightGray, rcf.getResidueColour(false,
73 av.getResidueShading(), null, seq, 2, null));
76 @Test(groups = { "Functional" })
77 public void testGetResidueBoxColour_zappo()
79 SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
81 AlignmentI al = new Alignment(new SequenceI[] { seq });
82 final AlignViewport av = new AlignViewport(al);
83 ResidueColourFinder rcf = new OverviewResColourFinder();
84 av.setGlobalColourScheme(new ZappoColourScheme());
86 // @see ResidueProperties.zappo
87 assertEquals(Color.pink, rcf.getResidueColour(true,
88 av.getResidueShading(), null, seq, 0, null)); // M
89 assertEquals(Color.green, rcf.getResidueColour(true,
90 av.getResidueShading(), null, seq, 2, null)); // T
91 assertEquals(Color.magenta, rcf.getResidueColour(true,
92 av.getResidueShading(), null, seq, 5, null)); // G
93 assertEquals(Color.orange, rcf.getResidueColour(true,
94 av.getResidueShading(), null, seq, 12, null)); // F
96 // gap colour not specified so gaps are lightGray
97 assertEquals(Color.lightGray, rcf.getResidueColour(true,
98 av.getResidueShading(), null, seq, 3, null));
100 // unaffected by showBoxes setting
101 assertEquals(Color.pink, rcf.getResidueColour(false,
102 av.getResidueShading(), null, seq, 0, null)); // M
103 assertEquals(Color.green, rcf.getResidueColour(false,
104 av.getResidueShading(), null, seq, 2, null)); // T
105 assertEquals(Color.magenta, rcf.getResidueColour(false,
106 av.getResidueShading(), null, seq, 5, null)); // G
107 assertEquals(Color.orange, rcf.getResidueColour(false,
108 av.getResidueShading(), null, seq, 12, null)); // F
110 // gap colour not specified so gaps are lightGray
111 assertEquals(Color.lightGray, rcf.getResidueColour(false,
112 av.getResidueShading(), null, seq, 3, null));
116 @Test(groups = { "Functional" })
117 public void testGetResidueBoxColour_userdef()
119 SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
121 AlignmentI al = new Alignment(new SequenceI[] { seq });
122 final AlignViewport av = new AlignViewport(al);
123 ResidueColourFinder rcf = new OverviewResColourFinder();
125 Color[] newColours = new Color[24];
126 for (int i = 0; i < 24; i++)
128 newColours[i] = null;
131 av.setGlobalColourScheme(new UserColourScheme(newColours));
133 // gap colour not specified so gaps are lightGray
134 assertEquals(Color.lightGray, rcf.getResidueColour(true,
135 av.getResidueShading(), null, seq, 3, null));
137 newColours[23] = Color.pink;
138 av.setGlobalColourScheme(new UserColourScheme(newColours));
140 // gap colour specified as pink
141 assertEquals(Color.pink, rcf.getResidueColour(true,
142 av.getResidueShading(), null, seq, 3, null));
144 // unaffected by showBoxes setting
145 // gap colour not specified so gaps are lightGray
146 newColours[23] = null;
147 assertEquals(Color.lightGray, rcf.getResidueColour(false,
148 av.getResidueShading(), null, seq, 3, null));
150 newColours[23] = Color.pink;
151 av.setGlobalColourScheme(new UserColourScheme(newColours));
153 // gap colour specified as pink
154 assertEquals(Color.pink, rcf.getResidueColour(false,
155 av.getResidueShading(), null, seq, 3, null));
159 public void testGetResidueBoxColour_group()
161 SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
162 AlignmentI al = new Alignment(new SequenceI[] { seq });
164 ColourSchemeI cs = new ZappoColourScheme();
165 ArrayList<SequenceI> seqlist = new ArrayList<>();
167 SequenceGroup sg = new SequenceGroup(seqlist, "testgroup", cs, true,
170 SequenceGroup[] groups = new SequenceGroup[1];
173 final AlignViewport av = new AlignViewport(al);
174 ResidueColourFinder rcf = new OverviewResColourFinder();
176 // G in group specified as magenta in Zappo
177 assertEquals(Color.magenta, rcf.getResidueColour(false,
178 av.getResidueShading(), groups, seq, 7, null));
180 // Residue outside group coloured white
181 assertEquals(Color.white, rcf.getResidueColour(false,
182 av.getResidueShading(), groups, seq, 0, null));
184 // Gap outside group coloured lightgray
185 assertEquals(Color.lightGray, rcf.getResidueColour(false,
186 av.getResidueShading(), groups, seq, 2, null));
188 // use legacy colouring
189 rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red);
191 // G in group specified as magenta in Zappo
192 assertEquals(Color.magenta, rcf.getResidueColour(false,
193 av.getResidueShading(), groups, seq, 7, null));
195 // Residue outside group coloured lightgray
196 assertEquals(Color.lightGray, rcf.getResidueColour(false,
197 av.getResidueShading(), groups, seq, 0, null));
199 // Gap outside group coloured white
200 assertEquals(Color.white, rcf.getResidueColour(false,
201 av.getResidueShading(), groups, seq, 2, null));
204 rcf = new OverviewResColourFinder(Color.blue, Color.white, Color.red);
206 // G in group specified as magenta in Zappo
207 assertEquals(Color.magenta, rcf.getResidueColour(false,
208 av.getResidueShading(), groups, seq, 7, null));
210 // Residue outside group coloured white
211 assertEquals(Color.white, rcf.getResidueColour(false,
212 av.getResidueShading(), groups, seq, 0, null));
214 // Gap outside group coloured blue
215 assertEquals(Color.blue, rcf.getResidueColour(false,
216 av.getResidueShading(), groups, seq, 2, null));
220 public void testGetBoxColour()
222 SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
224 AlignmentI al = new Alignment(new SequenceI[] { seq });
225 final AlignViewport av = new AlignViewport(al);
227 // non-legacy colouring
228 ResidueColourFinder rcf = new OverviewResColourFinder();
229 ResidueShaderI shader = new ResidueShader();
232 Color c = rcf.getBoxColour(shader, seq, 0);
233 assertEquals(Color.white, c);
236 c = rcf.getBoxColour(shader, seq, 3);
237 assertEquals(OverviewCanvas.OVERVIEW_DEFAULT_GAP, c);
239 // legacy colouring set explicitly via constructor
240 rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red);
241 shader = new ResidueShader();
243 // residues light gray
244 c = rcf.getBoxColour(shader, seq, 0);
245 assertEquals(Color.lightGray, c);
248 c = rcf.getBoxColour(shader, seq, 3);
249 assertEquals(Color.white, c);
251 // legacy colouring off
252 rcf = new OverviewResColourFinder();
253 shader = new ResidueShader();
256 c = rcf.getBoxColour(shader, seq, 0);
257 assertEquals(Color.white, c);
260 c = rcf.getBoxColour(shader, seq, 3);
261 assertEquals(OverviewCanvas.OVERVIEW_DEFAULT_GAP, c);
263 // non legacy colouring with colour scheme
264 rcf = new OverviewResColourFinder(Color.blue, Color.white, Color.red);
265 shader = new ResidueShader(new ZappoColourScheme());
268 c = rcf.getBoxColour(shader, seq, 0);
269 assertEquals(Color.pink, c);
272 c = rcf.getBoxColour(shader, seq, 3);
273 assertEquals(Color.blue, c);
275 // legacy colouring with colour scheme
276 rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red);
279 c = rcf.getBoxColour(shader, seq, 0);
280 assertEquals(Color.pink, c);
283 c = rcf.getBoxColour(shader, seq, 3);
284 assertEquals(Color.white, c);