help/html/colourSchemes/index.html

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   2 # Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
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  20  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
  21  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  22  *
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  25  * Jalview is free software: you can redistribute it and/or
  26  * modify it under the terms of the GNU General Public License
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  29  * Jalview is distributed in the hope that it will be useful, but
  30  * WITHOUT ANY WARRANTY; without even the implied warranty
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  35 -->
  36 <head>
  37 <title>Colour Schemes</title>
  38 <style type="text/css">
  39 <!--
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  42         font-style: normal;
  43         font-size: medium;
  44 }
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  46 </style>
  47 </head>
  48 <body>
  49 <p><strong>Colour schemes</strong></p>
  50 <p>Jalview allows the user to set a background colour for the whole
  51 alignment view or for each group defined on regions within it.</p>
  52 <p>To change the background colour, simply select the colour from
  53 the &quot;Colour&quot; menu.</p>
  54 <p>To change the colour of a group, right click on any residue
  55 within a group and use the popup menu to define the group colour.</p>
  56 <p>At the top of the &quot;Colour&quot; menu the tick box
  57 &quot;Apply Background Colour to all groups&quot;. This is ticked by
  58 default so that a chosen colour scheme will be applied to all existing
  59 groups. If you wish to maintain the colour scheme for defined groups,
  60 make sure you deselect this option before changing the background
  61 colour.</p>
  62 <p>The <strong>&quot;Colour&#8594;<a
  63         href="../colourSchemes/textcolour.html">Colour Text...</a>&quot;</strong> entry
  64 opens a dialog box to set a different text colour for light and dark
  65 background, and the intensity threshold for transition between them.</p>
  66 <p>The default colour schemes are summarised in the table below:
  67 <div align="center">
  68 <p>&nbsp;</p>
  69 <table border="1">
  70         <tr>
  71                 <td>
  72                 <table border="1">
  73                         <tr>
  74                                 <td nowrap></td>
  75                                 <td>A</td>
  76                                 <td>R</td>
  77                                 <td>N</td>
  78                                 <td>D</td>
  79                                 <td>C</td>
  80                                 <td>Q</td>
  81                                 <td>E</td>
  82                                 <td>G</td>
  83                                 <td>H</td>
  84                                 <td>I</td>
  85                                 <td>L</td>
  86                                 <td>K</td>
  87                                 <td>M</td>
  88                                 <td>F</td>
  89                                 <td>P</td>
  90                                 <td>S</td>
  91                                 <td>T</td>
  92                                 <td>W</td>
  93                                 <td>Y</td>
  94                                 <td>V</td>
  95                                 <td>B</td>
  96                                 <td>X</td>
  97                                 <td>Z</td>
  98                         </tr>
  99                         <tr>
 100                                 <td height="24">Clustal</td>
 101                                 <td bgcolor="#80a0f0"></td>
 102                                 <td bgcolor="#f01505"></td>
 103                                 <td bgcolor="#00ff00"></td>
 104                                 <td bgcolor="#c048c0"></td>
 105                                 <td bgcolor="#f08080"></td>
 106                                 <td bgcolor="#00ff00"></td>
 107                                 <td bgcolor="#c048c0"></td>
 108                                 <td bgcolor="#f09048"></td>
 109                                 <td bgcolor="#15a4a4"></td>
 110                                 <td bgcolor="#80a0f0"></td>
 111                                 <td bgcolor="#80a0f0"></td>
 112                                 <td bgcolor="#f01505"></td>
 113                                 <td bgcolor="#80a0f0"></td>
 114                                 <td bgcolor="#80a0f0"></td>
 115                                 <td bgcolor="#ffff00"></td>
 116                                 <td bgcolor="#00ff00"></td>
 117                                 <td bgcolor="#00ff00"></td>
 118                                 <td bgcolor="#80a0f0"></td>
 119                                 <td bgcolor="#15a4a4"></td>
 120                                 <td bgcolor="#80a0f0"></td>
 121                                 <td></td>
 122                                 <td></td>
 123                                 <td></td>
 124                         </tr>
 125                         <tr>
 126                                 <td height="24">Zappo</td>
 127                                 <td bgcolor="#ffafaf"></td>
 128                                 <td bgcolor="#6464ff"></td>
 129                                 <td bgcolor="#00ff00"></td>
 130                                 <td bgcolor="#ff0000"></td>
 131                                 <td bgcolor="#ffff00"></td>
 132                                 <td bgcolor="#00ff00"></td>
 133                                 <td bgcolor="#ff0000"></td>
 134                                 <td bgcolor="#ff00ff"></td>
 135                                 <td bgcolor="#6464ff"></td>
 136                                 <td bgcolor="#ffafaf"></td>
 137                                 <td bgcolor="#ffafaf"></td>
 138                                 <td bgcolor="#6464ff"></td>
 139                                 <td bgcolor="#ffafaf"></td>
 140                                 <td bgcolor="#ffc800"></td>
 141                                 <td bgcolor="#ff00ff"></td>
 142                                 <td bgcolor="#00ff00"></td>
 143                                 <td bgcolor="#00ff00"></td>
 144                                 <td bgcolor="#ffc800"></td>
 145                                 <td bgcolor="#ffc800"></td>
 146                                 <td bgcolor="#ffafaf"></td>
 147                                 <td></td>
 148                                 <td></td>
 149                                 <td></td>
 150                         </tr>
 151                         <tr>
 152                                 <td>Taylor</td>
 153                                 <td bgcolor="#ccff00"></td>
 154                                 <td bgcolor="#0000ff"></td>
 155                                 <td bgcolor="#cc00ff"></td>
 156                                 <td bgcolor="#ff0000"></td>
 157                                 <td bgcolor="#ffff00"></td>
 158                                 <td bgcolor="#ff00cc"></td>
 159                                 <td bgcolor="#ff0066"></td>
 160                                 <td bgcolor="#ff9900"></td>
 161                                 <td bgcolor="#0066ff"></td>
 162                                 <td bgcolor="#66ff00"></td>
 163                                 <td bgcolor="#33ff00"></td>
 164                                 <td bgcolor="#6600ff"></td>
 165                                 <td bgcolor="#00ff00"></td>
 166                                 <td bgcolor="#00ff66"></td>
 167                                 <td bgcolor="#ffcc00"></td>
 168                                 <td bgcolor="#ff3300"></td>
 169                                 <td bgcolor="#ff6600"></td>
 170                                 <td bgcolor="#00ccff"></td>
 171                                 <td bgcolor="#00ffcc"></td>
 172                                 <td bgcolor="#99ff00"></td>
 173                                 <td></td>
 174                                 <td></td>
 175                                 <td></td>
 176                         </tr>
 177                         <tr>
 178                                 <td>Hydrophobicity</td>
 179                                 <td bgcolor="#ad0052"></td>
 180                                 <td bgcolor="#0000ff"></td>
 181                                 <td bgcolor="#0c00f3"></td>
 182                                 <td bgcolor="#0c00f3"></td>
 183                                 <td bgcolor="#c2003d"></td>
 184                                 <td bgcolor="#0c00f3"></td>
 185                                 <td bgcolor="#0c00f3"></td>
 186                                 <td bgcolor="#6a0095"></td>
 187                                 <td bgcolor="#1500ea"></td>
 188                                 <td bgcolor="#ff0000"></td>
 189                                 <td bgcolor="#ea0015"></td>
 190                                 <td bgcolor="#0000ff"></td>
 191                                 <td bgcolor="#b0004f"></td>
 192                                 <td bgcolor="#cb0034"></td>
 193                                 <td bgcolor="#4600b9"></td>
 194                                 <td bgcolor="#5e00a1"></td>
 195                                 <td bgcolor="#61009e"></td>
 196                                 <td bgcolor="#5b00a4"></td>
 197                                 <td bgcolor="#4f00b0"></td>
 198                                 <td bgcolor="#f60009"></td>
 199                                 <td bgcolor="#0c00f3"></td>
 200                                 <td bgcolor="#680097"></td>
 201                                 <td bgcolor="#0c00f3"></td>
 202                         </tr>
 203                         <tr>
 204                                 <td>Helix Propensity</td>
 205                                 <td bgcolor="#e718e7"></td>
 206                                 <td bgcolor="#6f906f"></td>
 207                                 <td bgcolor="#1be41b"></td>
 208                                 <td bgcolor="#778877"></td>
 209                                 <td bgcolor="#23dc23"></td>
 210                                 <td bgcolor="#926d92"></td>
 211                                 <td bgcolor="#ff00ff"></td>
 212                                 <td bgcolor="#00ff00"></td>
 213                                 <td bgcolor="#758a75"></td>
 214                                 <td bgcolor="#8a758a"></td>
 215                                 <td bgcolor="#ae51ae"></td>
 216                                 <td bgcolor="#a05fa0"></td>
 217                                 <td bgcolor="#ef10ef"></td>
 218                                 <td bgcolor="#986798"></td>
 219                                 <td bgcolor="#00ff00"></td>
 220                                 <td bgcolor="#36c936"></td>
 221                                 <td bgcolor="#47b847"></td>
 222                                 <td bgcolor="#8a758a"></td>
 223                                 <td bgcolor="#21de21"></td>
 224                                 <td bgcolor="#857a85"></td>
 225                                 <td bgcolor="#49b649"></td>
 226                                 <td bgcolor="#758a75"></td>
 227                                 <td bgcolor="#c936c9"></td>
 228                         </tr>
 229                         <tr>
 230                                 <td nowrap>Strand Propensity</td>
 231                                 <td bgcolor="#5858a7"></td>
 232                                 <td bgcolor="#6b6b94"></td>
 233                                 <td bgcolor="#64649b"></td>
 234                                 <td bgcolor="#2121de"></td>
 235                                 <td bgcolor="#9d9d62"></td>
 236                                 <td bgcolor="#8c8c73"></td>
 237                                 <td bgcolor="#0000ff"></td>
 238                                 <td bgcolor="#4949b6"></td>
 239                                 <td bgcolor="#60609f"></td>
 240                                 <td bgcolor="#ecec13"></td>
 241                                 <td bgcolor="#b2b24d"></td>
 242                                 <td bgcolor="#4747b8"></td>
 243                                 <td bgcolor="#82827d"></td>
 244                                 <td bgcolor="#c2c23d"></td>
 245                                 <td bgcolor="#2323dc"></td>
 246                                 <td bgcolor="#4949b6"></td>
 247                                 <td bgcolor="#9d9d62"></td>
 248                                 <td bgcolor="#c0c03f"></td>
 249                                 <td bgcolor="#d3d32c"></td>
 250                                 <td bgcolor="#ffff00"></td>
 251                                 <td bgcolor="#4343bc"></td>
 252                                 <td bgcolor="#797986"></td>
 253                                 <td bgcolor="#4747b8"></td>
 254                         </tr>
 255                         <tr>
 256                                 <td>Turn Propensity</td>
 257                                 <td bgcolor="#2cd3d3"></td>
 258                                 <td bgcolor="#708f8f"></td>
 259                                 <td bgcolor="#ff0000"></td>
 260                                 <td bgcolor="#e81717"></td>
 261                                 <td bgcolor="#a85757"></td>
 262                                 <td bgcolor="#3fc0c0"></td>
 263                                 <td bgcolor="#778888"></td>
 264                                 <td bgcolor="#ff0000"></td>
 265                                 <td bgcolor="#708f8f"></td>
 266                                 <td bgcolor="#00ffff"></td>
 267                                 <td bgcolor="#1ce3e3"></td>
 268                                 <td bgcolor="#7e8181"></td>
 269                                 <td bgcolor="#1ee1e1"></td>
 270                                 <td bgcolor="#1ee1e1"></td>
 271                                 <td bgcolor="#f60909"></td>
 272                                 <td bgcolor="#e11e1e"></td>
 273                                 <td bgcolor="#738c8c"></td>
 274                                 <td bgcolor="#738c8c"></td>
 275                                 <td bgcolor="#9d6262"></td>
 276                                 <td bgcolor="#07f8f8"></td>
 277                                 <td bgcolor="#f30c0c"></td>
 278                                 <td bgcolor="#7c8383"></td>
 279                                 <td bgcolor="#5ba4a4"></td>
 280                         </tr>
 281                         <tr>
 282                                 <td>Buried Index</td>
 283                                 <td bgcolor="#00a35c"></td>
 284                                 <td bgcolor="#00fc03"></td>
 285                                 <td bgcolor="#00eb14"></td>
 286                                 <td bgcolor="#00eb14"></td>
 287                                 <td bgcolor="#0000ff"></td>
 288                                 <td bgcolor="#00f10e"></td>
 289                                 <td bgcolor="#00f10e"></td>
 290                                 <td bgcolor="#009d62"></td>
 291                                 <td bgcolor="#00d52a"></td>
 292                                 <td bgcolor="#0054ab"></td>
 293                                 <td bgcolor="#007b84"></td>
 294                                 <td bgcolor="#00ff00"></td>
 295                                 <td bgcolor="#009768"></td>
 296                                 <td bgcolor="#008778"></td>
 297                                 <td bgcolor="#00e01f"></td>
 298                                 <td bgcolor="#00d52a"></td>
 299                                 <td bgcolor="#00db24"></td>
 300                                 <td bgcolor="#00a857"></td>
 301                                 <td bgcolor="#00e619"></td>
 302                                 <td bgcolor="#005fa0"></td>
 303                                 <td bgcolor="#00eb14"></td>
 304                                 <td bgcolor="#00b649"></td>
 305                                 <td bgcolor="#00f10e"></td>
 306                         </tr>
 307                 </table>
 308                 </td>
 309         </tr>
 310 </table>
 311 </div>
 312 <p align="center">&nbsp;</p>
 313 </body>
 314 </html>