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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+
+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.
+
+
+
+