X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2FcolourSchemes%2FannotationColouring.html;h=e8c87e1326e7eb47c246e39ca3539350692cfcd6;hb=e66322bfd895b80f19ae39ec0367a6c1cd4a93a3;hp=e891a9f8ace0caf05f23ac47a869dc54dace67da;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html
index e891a9f..e8c87e1 100755
--- a/help/html/colourSchemes/annotationColouring.html
+++ b/help/html/colourSchemes/annotationColouring.html
@@ -1,6 +1,6 @@
+-->
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.
+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.
- - Select whether to colour the alignment above or below an adjustable threshold
+
- 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.
-
-
+ 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.
+
+