<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
- *
+ * 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/>.
--->
-<head><title>Alignment Window Menus</title></head>
+ * 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>
+ <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, User Defined<br>
- </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
- a description of all colour schemes.</em><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>
+ </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>
+ </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>
+ </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>
+ </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