3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
4 * Copyright (C) 2014 The Jalview Authors
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/>.
18 * The Jalview Authors are detailed in the 'AUTHORS' file.
20 <head><title>Alignment Window Menus</title></head>
23 <p><strong>Alignment Window Colour Menu</strong></p>
25 <li><strong>Apply Colour To All Groups<br>
26 </strong><em>If this is selected, any changes made to the background colour
27 will be applied to all currently defined groups.<br>
29 <li><strong><a href="../colourSchemes/textcolour.html">Colour
30 Text ...</a></strong><em><br>
31 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.
33 <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage
34 Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity,
35 Turn Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined<br>
36 </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
37 a description of all colour schemes.</em><br>
39 <li><strong>By Conservation<br>
40 </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
41 by Conservation</a>.</em><br>
43 <li><strong>Modify Conservation Threshold<br>
44 </strong><em>Use this to display the conservation threshold slider window.
45 Useful if the window has been closed, or if the 'by conservation' option
46 appears to be doing nothing!</em><br>
48 <li><strong>Above Identity Threshold<br>
49 </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage
50 Identity</a></em><strong>.<br>
52 <li><strong>Modify Identity Threshold<br>
53 </strong><em>Use this to set the threshold value for colouring above Identity.
54 Useful if the window has been closed.<br>
56 <li><strong>By Annotation</strong><br>
57 <em>Colours the alignment on a per-column value from a specified annotation.
58 See <a href="../colourSchemes/annotationColouring.html">Annotation Colouring</a>.</em><br>
60 <li><strong>By RNA Helices</strong><br>
61 <em>Colours the helices of an RNA alignment loaded from a Stockholm file. See
62 <a href="../colourSchemes/rnahelicesColouring.html">RNA Helices
63 Colouring</a>.</em><br>