-<html>\r
-<head><title>Alignment Window Menus</title></head>\r
-\r
-<body>\r
-<p><strong>Alignment Window Colour Menu</strong></p>\r
-<ul>\r
- <li><strong>Colour</strong></li>\r
-</ul>\r
-<blockquote>\r
- <ul>\r
- <li><strong>Apply Colour To All Groups<br>\r
- </strong><em>If this is selected, any changes made to the background colour\r
- will be applied to all currently defined groups.<br>\r
- </em></li>\r
- <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor,\r
- Hydrophobicity, Helix Propensity, Strand Propensity, Turn Propensity, Buried\r
- Index, Nucleotide, User Defined<br>\r
- </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for\r
- a description of all colour schemes.</em><br>\r
- </li>\r
- <li><strong>By Conservation<br>\r
- </strong><em>See <a href="../colourSchemes/conservation.html">Colouring\r
- by Conservation</a>.</em><br>\r
- </li>\r
- <li><strong>Modify Conservation Threshold<br>\r
- </strong><em>Use this to display the conservation threshold slider window.\r
- Useful if the window has been closed, or if the 'by\r
- conservation' option appears to be doing nothing!</em><br></li>\r
- <li><strong>Above Identity Threshold<br>\r
- </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage\r
- Identity</a></em><strong>.<br>\r
- </strong></li>\r
- <li><strong>Modify Identity Threshold<br>\r
- </strong><em>Use this to set the threshold value for colouring above Identity.\r
- Useful if the window has been closed. </em></li>\r
- </ul>\r
-</blockquote>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * 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>Alignment Window Menus</title></head>
+
+<body>
+<p><strong>Alignment Window Colour Menu</strong></p>
+ <ul>
+ <li><strong>Apply Colour To All Groups<br>
+ </strong><em>If this is selected, any changes made to the background colour
+ will be applied to all currently defined groups.<br>
+ </em></li>
+ <li><strong><a href="../colourSchemes/textcolour.html">Colour
+ Text ...</a></strong><em><br>
+ Opens the Colour Text dialog box to set a different text colour for light and dark background, and the intensity threshold for transition between them.
+ </em></li>
+ <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage
+ Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity,
+ Turn Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined<br>
+ </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
+ a description of all colour schemes.</em><br>
+ </li>
+ <li><strong>By Conservation<br>
+ </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
+ by Conservation</a>.</em><br>
+ </li>
+ <li><strong>Modify Conservation Threshold<br>
+ </strong><em>Use this to display the conservation threshold slider window.
+ Useful if the window has been closed, or if the 'by conservation' option
+ appears to be doing nothing!</em><br>
+ </li>
+ <li><strong>Above Identity Threshold<br>
+ </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage
+ Identity</a></em><strong>.<br>
+ </strong></li>
+ <li><strong>Modify Identity Threshold<br>
+ </strong><em>Use this to set the threshold value for colouring above Identity.
+ Useful if the window has been closed.<br>
+ </em></li>
+ <li><strong>By Annotation</strong><br>
+ <em>Colours the alignment on a per-column value from a specified annotation.
+ See <a href="../colourSchemes/annotationColouring.html">Annotation Colouring</a>.</em><br>
+ </li>
+ <li><strong>By RNA Helices</strong><br>
+ <em>Colours the helices of an RNA alignment loaded from a Stockholm file. See
+ <a href="../colourSchemes/rnahelicesColouring.html">RNA Helices
+ Colouring</a>.</em><br>
+ </li>
+ </ul>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff