X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2FannotationColouring.html;h=75d9f556ac3fe6af7de7c93e415db391894f3785;hb=b12de4788f39931038a17ef1627e8cf77a6d84d2;hp=ec01fa9687cab13e1dde3e4b1e723219875c1820;hpb=b66118c2f1447ade32ba9791150fc055a9137bfc;p=jalview.git
diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html
index ec01fa9..75d9f55 100755
--- a/help/html/colourSchemes/annotationColouring.html
+++ b/help/html/colourSchemes/annotationColouring.html
@@ -1,30 +1,90 @@
-
-
-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 Per-sequence
+ only tick box is not greyed out, then ticking it will limit the
+ available annotation rows to just those that are sequence associated
+ (e.g. T-COFFEE scores and protein disorder
+ predictions), which will colour each sequence according to its own
+ per-residue scores.
+ Per-sequence associated annotation colouring was introduced
+ in Jalview 2.8
+
+ - 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.
+
Please Note: If no colour scheme was
+ applied previously, then the colours for lines and labels at each
+ position in the annotation row will be used, for secondary structure
+ symbols and graphs, this may be black by default, so your alignment
+ will be coloured black.
+
+ - 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.
+
+ - 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.).
+ Default min and max colours were introduced in Jalview 2.7
+
+
+
+ - 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.
+
+
+ 
+
+
+