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.SequenceI;
30 import jalview.gui.AlignViewport;
31 import jalview.gui.JvOptionPane;
32 import jalview.gui.Preferences;
33 import jalview.schemes.UserColourScheme;
34 import jalview.schemes.ZappoColourScheme;
36 import java.awt.Color;
38 import org.testng.annotations.BeforeClass;
39 import org.testng.annotations.Test;
41 public class OverviewResColourFinderTest
44 @BeforeClass(alwaysRun = true)
45 public void setUpJvOptionPane()
47 JvOptionPane.setInteractiveMode(false);
48 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
51 @Test(groups = { "Functional" })
52 public void testGetResidueBoxColour_none()
54 SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
55 AlignmentI al = new Alignment(new SequenceI[] { seq });
56 final AlignViewport av = new AlignViewport(al);
57 ResidueColourFinder rcf = new OverviewResColourFinder();
59 // gaps are grey, residues white
60 assertEquals(Color.white, rcf.getResidueColour(true,
61 av.getResidueShading(),
63 assertEquals(Color.lightGray, rcf
64 .getResidueColour(true, av.getResidueShading(), null, seq, 2,
67 // unaffected by showBoxes setting
68 assertEquals(Color.white, rcf.getResidueColour(false,
69 av.getResidueShading(), null, seq, 0, null));
70 assertEquals(Color.lightGray, rcf.getResidueColour(false,
71 av.getResidueShading(), null, seq, 2, null));
74 @Test(groups = { "Functional" })
75 public void testGetResidueBoxColour_zappo()
77 SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
79 AlignmentI al = new Alignment(new SequenceI[] { seq });
80 final AlignViewport av = new AlignViewport(al);
81 ResidueColourFinder rcf = new OverviewResColourFinder();
82 av.setGlobalColourScheme(new ZappoColourScheme());
84 // @see ResidueProperties.zappo
85 assertEquals(Color.pink,
86 rcf.getResidueColour(true, av.getResidueShading(),
87 null, seq, 0, null)); // M
88 assertEquals(Color.green,
89 rcf.getResidueColour(true, av.getResidueShading(),
90 null, seq, 2, null)); // T
91 assertEquals(Color.magenta,
92 rcf.getResidueColour(true, av.getResidueShading(),
93 null, seq, 5, null)); // G
94 assertEquals(Color.orange,
95 rcf.getResidueColour(true, av.getResidueShading(),
96 null, seq, 12, null)); // F
98 // gap colour not specified so gaps are lightGray
99 assertEquals(Color.lightGray, rcf
100 .getResidueColour(true, av.getResidueShading(), null, seq, 3,
103 // unaffected by showBoxes setting
104 assertEquals(Color.pink, rcf.getResidueColour(false,
105 av.getResidueShading(), null, seq, 0, null)); // M
106 assertEquals(Color.green, rcf.getResidueColour(false,
107 av.getResidueShading(), null, seq, 2, null)); // T
108 assertEquals(Color.magenta, rcf.getResidueColour(false,
109 av.getResidueShading(), null, seq, 5, null)); // G
110 assertEquals(Color.orange, rcf.getResidueColour(false,
111 av.getResidueShading(), null, seq, 12, null)); // F
113 // gap colour not specified so gaps are lightGray
114 assertEquals(Color.lightGray, rcf
115 .getResidueColour(false, av.getResidueShading(), null, seq, 3,
120 @Test(groups = { "Functional" })
121 public void testGetResidueBoxColour_userdef()
123 SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
125 AlignmentI al = new Alignment(new SequenceI[] { seq });
126 final AlignViewport av = new AlignViewport(al);
127 ResidueColourFinder rcf = new OverviewResColourFinder();
129 Color[] newColours = new Color[24];
130 for (int i = 0; i < 24; i++)
132 newColours[i] = null;
135 av.setGlobalColourScheme(new UserColourScheme(newColours));
137 // gap colour not specified so gaps are lightGray
138 assertEquals(Color.lightGray, rcf
139 .getResidueColour(true, av.getResidueShading(), null, seq, 3,
142 newColours[23] = Color.pink;
143 av.setGlobalColourScheme(new UserColourScheme(newColours));
145 // gap colour specified as pink
146 assertEquals(Color.pink, rcf.getResidueColour(true,
147 av.getResidueShading(),
148 null, seq, 3, null));
150 // unaffected by showBoxes setting
151 // gap colour not specified so gaps are lightGray
152 newColours[23] = null;
153 assertEquals(Color.lightGray, rcf.getResidueColour(false,
154 av.getResidueShading(), null, seq, 3, null));
156 newColours[23] = Color.pink;
157 av.setGlobalColourScheme(new UserColourScheme(newColours));
159 // gap colour specified as pink
160 assertEquals(Color.pink, rcf.getResidueColour(false,
161 av.getResidueShading(), null, seq, 3, null));
165 public void testGetBoxColour()
167 Cache.loadProperties("test/jalview/io/testProps.jvprops");
169 SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
171 AlignmentI al = new Alignment(new SequenceI[] { seq });
172 final AlignViewport av = new AlignViewport(al);
174 // non-legacy colouring
175 ResidueColourFinder rcf = new OverviewResColourFinder();
176 ResidueShaderI shader = new ResidueShader();
179 Color c = rcf.getBoxColour(shader, seq, 0);
180 assertEquals(Color.white, c);
183 c = rcf.getBoxColour(shader, seq, 3);
184 assertEquals(Preferences.OVERVIEW_DEFAULT_GAP, c);
186 // legacy colouring set explicitly via constructor
187 rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
188 shader = new ResidueShader();
190 // residues light gray
191 c = rcf.getBoxColour(shader, seq, 0);
192 assertEquals(Color.lightGray, c);
195 c = rcf.getBoxColour(shader, seq, 3);
196 assertEquals(Color.white, c);
198 // legacy colouring off
199 rcf = new OverviewResColourFinder();
200 shader = new ResidueShader();
203 c = rcf.getBoxColour(shader, seq, 0);
204 assertEquals(Color.white, c);
207 c = rcf.getBoxColour(shader, seq, 3);
208 assertEquals(Preferences.OVERVIEW_DEFAULT_GAP, c);
210 // non legacy colouring with colour scheme
211 rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
212 shader = new ResidueShader(new ZappoColourScheme());
215 c = rcf.getBoxColour(shader, seq, 0);
216 assertEquals(Color.pink, c);
219 c = rcf.getBoxColour(shader, seq, 3);
220 assertEquals(Color.blue, c);
222 // legacy colouring with colour scheme
223 rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
226 c = rcf.getBoxColour(shader, seq, 0);
227 assertEquals(Color.pink, c);
230 c = rcf.getBoxColour(shader, seq, 3);
231 assertEquals(Color.white, c);