3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 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 along with Jalview. If not, see <http://www.gnu.org/licenses/>.
22 <p><strong>Colour schemes</strong></p>
23 <p>Jalview allows the user to set a background colour for the whole
24 alignment view or for each group defined on regions within it.</p>
25 <p>To change the background colour, simply select the colour from
26 the "Colour" menu.</p>
27 <p>To change the colour of a group, right click on any residue
28 within a group and use the popup menu to define the group colour.</p>
29 <p>At the top of the "Colour" menu the tick box
30 "Apply Background Colour to all groups". This is ticked by
31 default so that a chosen colour scheme will be applied to all existing
32 groups. If you wish to maintain the colour scheme for defined groups,
33 make sure you deselect this option before changing the background
35 <p>The <strong>"Colour→<a
36 href="../colourSchemes/textcolour.html">Colour Text...</a>"</strong> entry
37 opens a dialog box to set a different text colour for light and dark
38 background, and the intensity threshold for transition between them.</p>
39 <p>The default colour schemes are summarised in the table below:
73 <td height="24">Clustal</td>
74 <td bgcolor="#80a0f0"></td>
75 <td bgcolor="#f01505"></td>
76 <td bgcolor="#00ff00"></td>
77 <td bgcolor="#c048c0"></td>
78 <td bgcolor="#f08080"></td>
79 <td bgcolor="#00ff00"></td>
80 <td bgcolor="#c048c0"></td>
81 <td bgcolor="#f09048"></td>
82 <td bgcolor="#15a4a4"></td>
83 <td bgcolor="#80a0f0"></td>
84 <td bgcolor="#80a0f0"></td>
85 <td bgcolor="#f01505"></td>
86 <td bgcolor="#80a0f0"></td>
87 <td bgcolor="#80a0f0"></td>
88 <td bgcolor="#ffff00"></td>
89 <td bgcolor="#00ff00"></td>
90 <td bgcolor="#00ff00"></td>
91 <td bgcolor="#80a0f0"></td>
92 <td bgcolor="#15a4a4"></td>
93 <td bgcolor="#80a0f0"></td>
99 <td height="24">Zappo</td>
100 <td bgcolor="#ffafaf"></td>
101 <td bgcolor="#6464ff"></td>
102 <td bgcolor="#00ff00"></td>
103 <td bgcolor="#ff0000"></td>
104 <td bgcolor="#ffff00"></td>
105 <td bgcolor="#00ff00"></td>
106 <td bgcolor="#ff0000"></td>
107 <td bgcolor="#ff00ff"></td>
108 <td bgcolor="#6464ff"></td>
109 <td bgcolor="#ffafaf"></td>
110 <td bgcolor="#ffafaf"></td>
111 <td bgcolor="#6464ff"></td>
112 <td bgcolor="#ffafaf"></td>
113 <td bgcolor="#ffc800"></td>
114 <td bgcolor="#ff00ff"></td>
115 <td bgcolor="#00ff00"></td>
116 <td bgcolor="#00ff00"></td>
117 <td bgcolor="#ffc800"></td>
118 <td bgcolor="#ffc800"></td>
119 <td bgcolor="#ffafaf"></td>
126 <td bgcolor="#ccff00"></td>
127 <td bgcolor="#0000ff"></td>
128 <td bgcolor="#cc00ff"></td>
129 <td bgcolor="#ff0000"></td>
130 <td bgcolor="#ffff00"></td>
131 <td bgcolor="#ff00cc"></td>
132 <td bgcolor="#ff0066"></td>
133 <td bgcolor="#ff9900"></td>
134 <td bgcolor="#0066ff"></td>
135 <td bgcolor="#66ff00"></td>
136 <td bgcolor="#33ff00"></td>
137 <td bgcolor="#6600ff"></td>
138 <td bgcolor="#00ff00"></td>
139 <td bgcolor="#00ff66"></td>
140 <td bgcolor="#ffcc00"></td>
141 <td bgcolor="#ff3300"></td>
142 <td bgcolor="#ff6600"></td>
143 <td bgcolor="#00ccff"></td>
144 <td bgcolor="#00ffcc"></td>
145 <td bgcolor="#99ff00"></td>
151 <td>Hydrophobicity</td>
152 <td bgcolor="#ad0052"></td>
153 <td bgcolor="#0000ff"></td>
154 <td bgcolor="#0c00f3"></td>
155 <td bgcolor="#0c00f3"></td>
156 <td bgcolor="#c2003d"></td>
157 <td bgcolor="#0c00f3"></td>
158 <td bgcolor="#0c00f3"></td>
159 <td bgcolor="#6a0095"></td>
160 <td bgcolor="#1500ea"></td>
161 <td bgcolor="#ff0000"></td>
162 <td bgcolor="#ea0015"></td>
163 <td bgcolor="#0000ff"></td>
164 <td bgcolor="#b0004f"></td>
165 <td bgcolor="#cb0034"></td>
166 <td bgcolor="#4600b9"></td>
167 <td bgcolor="#5e00a1"></td>
168 <td bgcolor="#61009e"></td>
169 <td bgcolor="#5b00a4"></td>
170 <td bgcolor="#4f00b0"></td>
171 <td bgcolor="#f60009"></td>
172 <td bgcolor="#0c00f3"></td>
173 <td bgcolor="#680097"></td>
174 <td bgcolor="#0c00f3"></td>
177 <td>Helix Propensity</td>
178 <td bgcolor="#e718e7"></td>
179 <td bgcolor="#6f906f"></td>
180 <td bgcolor="#1be41b"></td>
181 <td bgcolor="#778877"></td>
182 <td bgcolor="#23dc23"></td>
183 <td bgcolor="#926d92"></td>
184 <td bgcolor="#ff00ff"></td>
185 <td bgcolor="#00ff00"></td>
186 <td bgcolor="#758a75"></td>
187 <td bgcolor="#8a758a"></td>
188 <td bgcolor="#ae51ae"></td>
189 <td bgcolor="#a05fa0"></td>
190 <td bgcolor="#ef10ef"></td>
191 <td bgcolor="#986798"></td>
192 <td bgcolor="#00ff00"></td>
193 <td bgcolor="#36c936"></td>
194 <td bgcolor="#47b847"></td>
195 <td bgcolor="#8a758a"></td>
196 <td bgcolor="#21de21"></td>
197 <td bgcolor="#857a85"></td>
198 <td bgcolor="#49b649"></td>
199 <td bgcolor="#758a75"></td>
200 <td bgcolor="#c936c9"></td>
203 <td nowrap>Strand Propensity</td>
204 <td bgcolor="#5858a7"></td>
205 <td bgcolor="#6b6b94"></td>
206 <td bgcolor="#64649b"></td>
207 <td bgcolor="#2121de"></td>
208 <td bgcolor="#9d9d62"></td>
209 <td bgcolor="#8c8c73"></td>
210 <td bgcolor="#0000ff"></td>
211 <td bgcolor="#4949b6"></td>
212 <td bgcolor="#60609f"></td>
213 <td bgcolor="#ecec13"></td>
214 <td bgcolor="#b2b24d"></td>
215 <td bgcolor="#4747b8"></td>
216 <td bgcolor="#82827d"></td>
217 <td bgcolor="#c2c23d"></td>
218 <td bgcolor="#2323dc"></td>
219 <td bgcolor="#4949b6"></td>
220 <td bgcolor="#9d9d62"></td>
221 <td bgcolor="#c0c03f"></td>
222 <td bgcolor="#d3d32c"></td>
223 <td bgcolor="#ffff00"></td>
224 <td bgcolor="#4343bc"></td>
225 <td bgcolor="#797986"></td>
226 <td bgcolor="#4747b8"></td>
229 <td>Turn Propensity</td>
230 <td bgcolor="#2cd3d3"></td>
231 <td bgcolor="#708f8f"></td>
232 <td bgcolor="#ff0000"></td>
233 <td bgcolor="#e81717"></td>
234 <td bgcolor="#a85757"></td>
235 <td bgcolor="#3fc0c0"></td>
236 <td bgcolor="#778888"></td>
237 <td bgcolor="#ff0000"></td>
238 <td bgcolor="#708f8f"></td>
239 <td bgcolor="#00ffff"></td>
240 <td bgcolor="#1ce3e3"></td>
241 <td bgcolor="#7e8181"></td>
242 <td bgcolor="#1ee1e1"></td>
243 <td bgcolor="#1ee1e1"></td>
244 <td bgcolor="#f60909"></td>
245 <td bgcolor="#e11e1e"></td>
246 <td bgcolor="#738c8c"></td>
247 <td bgcolor="#738c8c"></td>
248 <td bgcolor="#9d6262"></td>
249 <td bgcolor="#07f8f8"></td>
250 <td bgcolor="#f30c0c"></td>
251 <td bgcolor="#7c8383"></td>
252 <td bgcolor="#5ba4a4"></td>
255 <td>Buried Index</td>
256 <td bgcolor="#00a35c"></td>
257 <td bgcolor="#00fc03"></td>
258 <td bgcolor="#00eb14"></td>
259 <td bgcolor="#00eb14"></td>
260 <td bgcolor="#0000ff"></td>
261 <td bgcolor="#00f10e"></td>
262 <td bgcolor="#00f10e"></td>
263 <td bgcolor="#009d62"></td>
264 <td bgcolor="#00d52a"></td>
265 <td bgcolor="#0054ab"></td>
266 <td bgcolor="#007b84"></td>
267 <td bgcolor="#00ff00"></td>
268 <td bgcolor="#009768"></td>
269 <td bgcolor="#008778"></td>
270 <td bgcolor="#00e01f"></td>
271 <td bgcolor="#00d52a"></td>
272 <td bgcolor="#00db24"></td>
273 <td bgcolor="#00a857"></td>
274 <td bgcolor="#00e619"></td>
275 <td bgcolor="#005fa0"></td>
276 <td bgcolor="#00eb14"></td>
277 <td bgcolor="#00b649"></td>
278 <td bgcolor="#00f10e"></td>
285 <p align="center"> </p>