X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2FannotationColouring.html;h=9275a091077e2153fd7f0a707729e869882ee136;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hb=c53aeee9a688f68d64106a968876e542f701fbc6;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5
diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html
index e18e273..9275a09 100755
--- a/help/html/colourSchemes/annotationColouring.html
+++ b/help/html/colourSchemes/annotationColouring.html
@@ -16,3 +16,31 @@
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
-->
+Annotation Colouring
+
+
+ Annotation Colouring
+Jalview 2.08 allows an alignment to be coloured on a per-column basis based
+ on any numerical annotation added to that alignment.
+Select "Colour" → "..
+ by Annotation" to bring up the Colour by Annotation settings window.
+
+
+ - Select which annotation to base the colouring scheme on using the top left
+ selection box.
+ - If the "Use Original Colours" box is selected, the colouring
+ scheme will use the colouring scheme present on the alignment before the Annotation
+ Colour Settings window was displayed.
+ - 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 "Min Colour" and
+ "Max Colour" to set the colour gradient range.
+ - Select whether to colour the alignment above or below an adjustable threshold
+ with the selection box center left of the window.
+ - Change the threshold value with the slider, or enter the exact value in
+ the text box.
+
+
+
+