-<html>\r
-\r
-<body>\r
-<p><strong>Colour schemes</strong></p>\r
-<p>Jalview allows the user to set a background colour for the whole alignment\r
- and also set the colour of defined groups within the alignment. </p>\r
-<p>To change the background colour, simply select the colour from the "Colour"\r
- menu.</p>\r
-<p>To change the colour of a group, right click on any residue within a group\r
- and use the popup menu to define the group colour. </p>\r
-<p>At the top of the "Colour" menu the tick box "Apply Background\r
- Colour to all groups". This is automatically ticked as default and means\r
- the chosen colour will be applied to all existing groups. If you wish to maintain\r
- the colour scheme for defined groups, make sure you deselect this option before\r
- changing the background colour.</p>\r
-<p> </p>\r
-<p> </p>\r
-<p> </p>\r
-<p> </p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<head>
+<title>Colour Schemes</title>
+<style type="text/css">
+<!--
+td {
+ font-family: "Courier New", Courier, mono;
+ font-style: normal;
+ font-size: medium;
+}
+-->
+</style>
+</head>
+<body>
+<p><strong>Colour schemes</strong></p>
+<p>Jalview allows the user to set a background colour for the whole
+alignment view or for each group defined on regions within it.</p>
+<p>To change the background colour, simply select the colour from
+the "Colour" menu.</p>
+<p>To change the colour of a group, right click on any residue
+within a group and use the popup menu to define the group colour.</p>
+<p>At the top of the "Colour" menu the tick box
+"Apply Background Colour to all groups". This is ticked by
+default so that a chosen colour scheme will be applied to all existing
+groups. If you wish to maintain the colour scheme for defined groups,
+make sure you deselect this option before changing the background
+colour.</p>
+<p>The <strong>"Colour→<a
+ href="../colourSchemes/textcolour.html">Colour Text...</a>"</strong> entry
+opens a dialog box to set a different text colour for light and dark
+background, and the intensity threshold for transition between them.</p>
+<p>The default colour schemes are summarised in the table below:
+<div align="center">
+<p> </p>
+<p><strong>Protein Colour Schemes</strong></p>
+<table border="1">
+ <tr>
+ <td>
+ <table border="1">
+ <tr>
+ <td nowrap></td>
+ <td>A</td>
+ <td>R</td>
+ <td>N</td>
+ <td>D</td>
+ <td>C</td>
+ <td>Q</td>
+ <td>E</td>
+ <td>G</td>
+ <td>H</td>
+ <td>I</td>
+ <td>L</td>
+ <td>K</td>
+ <td>M</td>
+ <td>F</td>
+ <td>P</td>
+ <td>S</td>
+ <td>T</td>
+ <td>W</td>
+ <td>Y</td>
+ <td>V</td>
+ <td>B</td>
+ <td>X</td>
+ <td>Z</td>
+ </tr>
+ <tr>
+ <td height="24">Clustal</td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#f01505"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#c048c0"></td>
+ <td bgcolor="#f08080"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#c048c0"></td>
+ <td bgcolor="#f09048"></td>
+ <td bgcolor="#15a4a4"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#f01505"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#ffff00"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#15a4a4"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td height="24">Zappo</td>
+ <td bgcolor="#ffafaf"></td>
+ <td bgcolor="#6464ff"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#ffff00"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#ff00ff"></td>
+ <td bgcolor="#6464ff"></td>
+ <td bgcolor="#ffafaf"></td>
+ <td bgcolor="#ffafaf"></td>
+ <td bgcolor="#6464ff"></td>
+ <td bgcolor="#ffafaf"></td>
+ <td bgcolor="#ffc800"></td>
+ <td bgcolor="#ff00ff"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#ffc800"></td>
+ <td bgcolor="#ffc800"></td>
+ <td bgcolor="#ffafaf"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td>Taylor</td>
+ <td bgcolor="#ccff00"></td>
+ <td bgcolor="#0000ff"></td>
+ <td bgcolor="#cc00ff"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#ffff00"></td>
+ <td bgcolor="#ff00cc"></td>
+ <td bgcolor="#ff0066"></td>
+ <td bgcolor="#ff9900"></td>
+ <td bgcolor="#0066ff"></td>
+ <td bgcolor="#66ff00"></td>
+ <td bgcolor="#33ff00"></td>
+ <td bgcolor="#6600ff"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#00ff66"></td>
+ <td bgcolor="#ffcc00"></td>
+ <td bgcolor="#ff3300"></td>
+ <td bgcolor="#ff6600"></td>
+ <td bgcolor="#00ccff"></td>
+ <td bgcolor="#00ffcc"></td>
+ <td bgcolor="#99ff00"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td>Hydrophobicity</td>
+ <td bgcolor="#ad0052"></td>
+ <td bgcolor="#0000ff"></td>
+ <td bgcolor="#0c00f3"></td>
+ <td bgcolor="#0c00f3"></td>
+ <td bgcolor="#c2003d"></td>
+ <td bgcolor="#0c00f3"></td>
+ <td bgcolor="#0c00f3"></td>
+ <td bgcolor="#6a0095"></td>
+ <td bgcolor="#1500ea"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#ea0015"></td>
+ <td bgcolor="#0000ff"></td>
+ <td bgcolor="#b0004f"></td>
+ <td bgcolor="#cb0034"></td>
+ <td bgcolor="#4600b9"></td>
+ <td bgcolor="#5e00a1"></td>
+ <td bgcolor="#61009e"></td>
+ <td bgcolor="#5b00a4"></td>
+ <td bgcolor="#4f00b0"></td>
+ <td bgcolor="#f60009"></td>
+ <td bgcolor="#0c00f3"></td>
+ <td bgcolor="#680097"></td>
+ <td bgcolor="#0c00f3"></td>
+ </tr>
+ <tr>
+ <td>Helix Propensity</td>
+ <td bgcolor="#e718e7"></td>
+ <td bgcolor="#6f906f"></td>
+ <td bgcolor="#1be41b"></td>
+ <td bgcolor="#778877"></td>
+ <td bgcolor="#23dc23"></td>
+ <td bgcolor="#926d92"></td>
+ <td bgcolor="#ff00ff"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#758a75"></td>
+ <td bgcolor="#8a758a"></td>
+ <td bgcolor="#ae51ae"></td>
+ <td bgcolor="#a05fa0"></td>
+ <td bgcolor="#ef10ef"></td>
+ <td bgcolor="#986798"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#36c936"></td>
+ <td bgcolor="#47b847"></td>
+ <td bgcolor="#8a758a"></td>
+ <td bgcolor="#21de21"></td>
+ <td bgcolor="#857a85"></td>
+ <td bgcolor="#49b649"></td>
+ <td bgcolor="#758a75"></td>
+ <td bgcolor="#c936c9"></td>
+ </tr>
+ <tr>
+ <td nowrap>Strand Propensity</td>
+ <td bgcolor="#5858a7"></td>
+ <td bgcolor="#6b6b94"></td>
+ <td bgcolor="#64649b"></td>
+ <td bgcolor="#2121de"></td>
+ <td bgcolor="#9d9d62"></td>
+ <td bgcolor="#8c8c73"></td>
+ <td bgcolor="#0000ff"></td>
+ <td bgcolor="#4949b6"></td>
+ <td bgcolor="#60609f"></td>
+ <td bgcolor="#ecec13"></td>
+ <td bgcolor="#b2b24d"></td>
+ <td bgcolor="#4747b8"></td>
+ <td bgcolor="#82827d"></td>
+ <td bgcolor="#c2c23d"></td>
+ <td bgcolor="#2323dc"></td>
+ <td bgcolor="#4949b6"></td>
+ <td bgcolor="#9d9d62"></td>
+ <td bgcolor="#c0c03f"></td>
+ <td bgcolor="#d3d32c"></td>
+ <td bgcolor="#ffff00"></td>
+ <td bgcolor="#4343bc"></td>
+ <td bgcolor="#797986"></td>
+ <td bgcolor="#4747b8"></td>
+ </tr>
+ <tr>
+ <td>Turn Propensity</td>
+ <td bgcolor="#2cd3d3"></td>
+ <td bgcolor="#708f8f"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#e81717"></td>
+ <td bgcolor="#a85757"></td>
+ <td bgcolor="#3fc0c0"></td>
+ <td bgcolor="#778888"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#708f8f"></td>
+ <td bgcolor="#00ffff"></td>
+ <td bgcolor="#1ce3e3"></td>
+ <td bgcolor="#7e8181"></td>
+ <td bgcolor="#1ee1e1"></td>
+ <td bgcolor="#1ee1e1"></td>
+ <td bgcolor="#f60909"></td>
+ <td bgcolor="#e11e1e"></td>
+ <td bgcolor="#738c8c"></td>
+ <td bgcolor="#738c8c"></td>
+ <td bgcolor="#9d6262"></td>
+ <td bgcolor="#07f8f8"></td>
+ <td bgcolor="#f30c0c"></td>
+ <td bgcolor="#7c8383"></td>
+ <td bgcolor="#5ba4a4"></td>
+ </tr>
+ <tr>
+ <td>Buried Index</td>
+ <td bgcolor="#00a35c"></td>
+ <td bgcolor="#00fc03"></td>
+ <td bgcolor="#00eb14"></td>
+ <td bgcolor="#00eb14"></td>
+ <td bgcolor="#0000ff"></td>
+ <td bgcolor="#00f10e"></td>
+ <td bgcolor="#00f10e"></td>
+ <td bgcolor="#009d62"></td>
+ <td bgcolor="#00d52a"></td>
+ <td bgcolor="#0054ab"></td>
+ <td bgcolor="#007b84"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#009768"></td>
+ <td bgcolor="#008778"></td>
+ <td bgcolor="#00e01f"></td>
+ <td bgcolor="#00d52a"></td>
+ <td bgcolor="#00db24"></td>
+ <td bgcolor="#00a857"></td>
+ <td bgcolor="#00e619"></td>
+ <td bgcolor="#005fa0"></td>
+ <td bgcolor="#00eb14"></td>
+ <td bgcolor="#00b649"></td>
+ <td bgcolor="#00f10e"></td>
+ </tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<p> </p>
+<p><strong>Nucleotide Colour Schemes</strong></p>
+<table border="1">
+ <tr>
+ <td>
+ <table border="1">
+ <tr>
+ <td nowrap></td>
+ <td>A</td> <!--Adenine-->
+ <td>C</td> <!--Cytosine-->
+ <td>G</td> <!--Guanine-->
+ <td>T</td> <!--Thymine-->
+ <td>U</td> <!--Uracil-->
+ <td>I</td> <!--Inosine-->
+ <td>X</td> <!--Xanthine-->
+ <td>R</td> <!--Unknown Purine-->
+ <td>Y</td> <!--Unknown Pyrimidine-->
+ <td>N</td> <!--Unknown-->
+ <td>W</td> <!--Weak nucleotide (A or T)-->
+ <td>S</td> <!--Strong nucleotide (G or C)-->
+ <td>M</td> <!--Amino (A or C)-->
+ <td>K</td> <!--Keto (G or T)-->
+ <td>B</td> <!--Not A (G or C or T)-->
+ <td>H</td> <!--Not G (A or C or T)-->
+ <td>D</td> <!--Not C (A or G or T)-->
+ <td>V</td> <!--Not T (A or G or C-->
+ </tr>
+ <tr>
+ <td height="24">Nucleotide</td>
+ <td bgcolor="#64F73F"></td>
+ <td bgcolor="#FFB340"></td>
+ <td bgcolor="#EB413C"></td>
+ <td bgcolor="#3C88EE"></td>
+ <td bgcolor="#3C88EE"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td height="24">Purine/Pyrimidine</td>
+ <td bgcolor="#FF83FA"></td>
+ <td bgcolor="#40E0D0"></td>
+ <td bgcolor="#FF83FA"></td>
+ <td bgcolor="#40E0D0"></td>
+ <td bgcolor="#40E0D0"></td>
+ <td></td>
+ <td></td>
+ <td bgcolor="#FF83FA"></td>
+ <td bgcolor="#40E0D0"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ </table>
+ </td>
+ </tr>
+</table>
+
+
+</div>
+<p align="center"> </p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff