X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpreferences.html;h=52e88dbb8ef7f97fcab90aa93192c5187318cce5;hb=b8f4de5dd53eef24e68caf6aa2dad022f6337293;hp=acd7ba698dac33958efe7f0a1296b9bb76786271;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index acd7ba6..52e88db 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 @@ -337,7 +363,7 @@ and PDB file association (if available). The Jalview id/start-end option is ignored if Modeller output is selected.
- e"Editinge" Preferences tab + "Editing" Preferences tab
There are currently three options available which can be selected / deselected.