Alignment Window Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwcolour.html;h=2ad79d591cea6b658056894c280d5dfe08843d8f;hb=8d0d8f010041eb2089bfe0bf7e5ad481ceae56d5;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/menus/alwcolour.html b/help/html/menus/alwcolour.html index e18e273..2ad79d5 100755 --- a/help/html/menus/alwcolour.html +++ b/help/html/menus/alwcolour.html @@ -1,18 +1,69 @@ + * 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.
+

+ +