X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2FcolourSchemes%2FannotationColouring.html;h=6f2f59db7452747bb15ab7dc8d59f2d6fe1472bb;hb=2d6be9a94eb65474a7272d3766881521ed35a760;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git
diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html
index e18e273..6f2f59d 100755
--- a/help/html/colourSchemes/annotationColouring.html
+++ b/help/html/colourSchemes/annotationColouring.html
@@ -1,7 +1,7 @@
+Annotation Colouring
+
+
+ Annotation Colouring
+Jalview allows the columns of an alignment to be coloured using any
+ numerical annotation rows 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.
+
+ - New in Jalview 2.7: Press the "Defaults"
+ button to reset the minimum and maximum colours to their default
+ settings (these are configured in the applet's parameters or the application's user
+ preferences.)
+
+
+
+ - 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.
+
+ - Select the "Threshold is Min/Max" checkbox to
+ assign colours using the thresholded range's minimum and maximum
+ values, otherwise the scale will be defined by the range of values in
+ the annotation row.
+
+
+
+