X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwcolour.html;h=41c8a1587a4cb90b5543a4948a3c07e9f6751d70;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=4d2816342a4c636f61101dc08371645423fbc8f3;hpb=f902741a45fba3856958b893e37c74344d397a60;p=jalview.git
diff --git a/help/html/menus/alwcolour.html b/help/html/menus/alwcolour.html
index 4d281634..41c8a15 100755
--- a/help/html/menus/alwcolour.html
+++ b/help/html/menus/alwcolour.html
@@ -1,39 +1,67 @@
-
-Alignment Window Menus
-
-
-Alignment Window Colour Menu
-
-
-
- - Apply Colour To All Groups
- If this is selected, any changes made to the background colour
- will be applied to all currently defined groups.
-
- - Colour Scheme options: None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor,
- Hydrophobicity, Helix Propensity, Strand Propensity, Turn Propensity, Buried
- Index, Nucleotide, User Defined
- See colours for
- a description of all colour schemes.
-
- - By Conservation
- See Colouring
- by Conservation.
-
- - Modify Conservation Threshold
- Use this to display the conservation threshold slider window.
- Useful if the window has been closed, or if the 'by
- conservation' option appears to be doing nothing!
- - Above Identity Threshold
- See Above Percentage
- Identity.
-
- - Modify Identity Threshold
- Use this to set the threshold value for colouring above Identity.
- Useful if the window has been closed.
-
-
-
-
+
+
+Alignment Window Menus
+
+
+Alignment Window Colour Menu
+
+ - Apply Colour To All Groups
+ If this is selected, any changes made to the background colour
+ will be applied to all currently defined groups.
+
+ - Colour
+ Text ...
+ Opens the Colour Text dialog box to set a different text colour for light and dark background, and the intensity threshold for transition between them.
+
+ - Colour Scheme options: None, ClustalX, Blosum62 Score, Percentage
+ Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity,
+ Turn Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined
+ See colours for
+ a description of all colour schemes.
+
+ - By Conservation
+ See Colouring
+ by Conservation.
+
+ - Modify Conservation Threshold
+ Use this to display the conservation threshold slider window.
+ Useful if the window has been closed, or if the 'by conservation' option
+ appears to be doing nothing!
+
+ - Above Identity Threshold
+ See Above Percentage
+ Identity.
+
+ - Modify Identity Threshold
+ Use this to set the threshold value for colouring above Identity.
+ Useful if the window has been closed.
+
+ - By Annotation
+ Colours the alignment on a per-column value from a specified annotation.
+ See Annotation Colouring.
+
+ - By RNA Helices
+ Colours the helices of an RNA alignment loaded from a Stockholm file. See
+ RNA Helices
+ Colouring.
+
+
+
+