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,
192 // G in group specified as magenta in Zappo
193 assertEquals(Color.magenta, rcf.getResidueColour(false,
194 av.getResidueShading(), groups, seq, 7, null));
196 // Residue outside group coloured lightgray
197 assertEquals(Color.lightGray, rcf.getResidueColour(false,
198 av.getResidueShading(), groups, seq, 0, null));
200 // Gap outside group coloured white
201 assertEquals(Color.white, rcf.getResidueColour(false,
202 av.getResidueShading(), groups, seq, 2, null));
205 rcf = new OverviewResColourFinder(Color.blue, Color.white, Color.red);
207 // G in group specified as magenta in Zappo
208 assertEquals(Color.magenta, rcf.getResidueColour(false,
209 av.getResidueShading(), groups, seq, 7, null));
211 // Residue outside group coloured white
212 assertEquals(Color.white, rcf.getResidueColour(false,
213 av.getResidueShading(), groups, seq, 0, null));
215 // Gap outside group coloured blue
216 assertEquals(Color.blue, rcf.getResidueColour(false,
217 av.getResidueShading(), groups, seq, 2, null));
221 public void testGetBoxColour()
223 SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
225 AlignmentI al = new Alignment(new SequenceI[] { seq });
226 final AlignViewport av = new AlignViewport(al);
228 // non-legacy colouring
229 ResidueColourFinder rcf = new OverviewResColourFinder();
230 ResidueShaderI shader = new ResidueShader();
233 Color c = rcf.getBoxColour(shader, seq, 0);
234 assertEquals(Color.white, c);
237 c = rcf.getBoxColour(shader, seq, 3);
238 assertEquals(OverviewCanvas.OVERVIEW_DEFAULT_GAP, c);
240 // legacy colouring set explicitly via constructor
241 rcf = new OverviewResColourFinder(Color.white, Color.lightGray,
243 shader = new ResidueShader();
245 // residues light gray
246 c = rcf.getBoxColour(shader, seq, 0);
247 assertEquals(Color.lightGray, c);
250 c = rcf.getBoxColour(shader, seq, 3);
251 assertEquals(Color.white, c);
253 // legacy colouring off
254 rcf = new OverviewResColourFinder();
255 shader = new ResidueShader();
258 c = rcf.getBoxColour(shader, seq, 0);
259 assertEquals(Color.white, c);
262 c = rcf.getBoxColour(shader, seq, 3);
263 assertEquals(OverviewCanvas.OVERVIEW_DEFAULT_GAP, c);
265 // non legacy colouring with colour scheme
266 rcf = new OverviewResColourFinder(Color.blue, Color.white, Color.red);
267 shader = new ResidueShader(new ZappoColourScheme());
270 c = rcf.getBoxColour(shader, seq, 0);
271 assertEquals(Color.pink, c);
274 c = rcf.getBoxColour(shader, seq, 3);
275 assertEquals(Color.blue, c);
277 // legacy colouring with colour scheme
278 rcf = new OverviewResColourFinder(Color.white, Color.lightGray,
282 c = rcf.getBoxColour(shader, seq, 0);
283 assertEquals(Color.pink, c);
286 c = rcf.getBoxColour(shader, seq, 3);
287 assertEquals(Color.white, c);