git://source.jalview.org / jalview.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
JAL-1683 replace year/version strings with tokens in source
[jalview.git] / help / html / colourSchemes / annotationColouring.html
diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html
index 75d9f55..3b23a48 100755 (executable)
--- a/help/html/colourSchemes/annotationColouring.html
+++ b/help/html/colourSchemes/annotationColouring.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -58,6 +58,12 @@
                                symbols and graphs, this may be black by default, so your alignment
                                will be coloured black.</em>
                </li>
+               <li><em>Secondary structure annotation colouring</em><br />By
+                       default, Jalview will employ the helix or sheet colours to shade
+                       sequences and columns by available secondary structure annotation
+                       tracks. In the case of RNA, each structure is processed to identify
+                       distinct RNA helices and rendered in the same way as the <a
+                       href="rnahelicesColouring.html">RNA Helices shading scheme</a>. <em>Structure based sequence shading was added in Jalview 2.8.2</em></li>
                <li>The colour scheme can display a colour gradient from a colour
                        representing the minimum value in the selected annotation to a colour
                        representing the maximum value in the selected annotation. Use the