X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpreferences.html;h=b29b66bf1dc60d890736470108b7337c49969816;hb=b1e2aea95b3839a1a53f809c579666075cd3d348;hp=acd7ba698dac33958efe7f0a1296b9bb76786271;hpb=1aa769198666becd30648eed7f9037e9d0502ce9;p=jalview.git diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index acd7ba6..b29b66b 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -41,6 +41,9 @@ Preferences tab allows you to configure default colourschemes for a new alignment window. +
+ "Overview" + Preferences tab +
++ Use legacy gap colouring (gaps are white) - when enabled, + Jalview's overview shows gaps as white, and sequences with no + colourscheme applied as grey. +
++ Show Hidden regions when opening overview - default setting + for inclusion of hidden regions. +
++ Gap Colour - When legacy gap colouring is not enabled, this + configures the default colour for gaps in the overview. +
++ Hidden Colour - colour used to highlight regions in the + overview that are hidden in the alignment. +
++ Gap Colour - The default colour scheme for a new alignment + window. If the chosen option is "User Defined" then the + last User Defined Colour loaded or saved via the User Defined + Colours panel will be loaded. +
"Structure" Preferences tab added in Jalview 2.8.2