X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2FannotationColouring.html;h=6f2f59db7452747bb15ab7dc8d59f2d6fe1472bb;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=ec01fa9687cab13e1dde3e4b1e723219875c1820;hpb=b66118c2f1447ade32ba9791150fc055a9137bfc;p=jalview.git
diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html
index ec01fa9..6f2f59d 100755
--- a/help/html/colourSchemes/annotationColouring.html
+++ b/help/html/colourSchemes/annotationColouring.html
@@ -1,30 +1,61 @@
-
-
-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.
-
-
-
-
+
+
+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.
+
+
+
+