Show Annotations - If this is selected the new window will display an annotation panel below the sequences. This annotation - panel may have several rows describing the whole alignment. The 3 - standard annotations Conservation, Quality and Consensus - for the alignment may be shown or hidden by default using the - checkboxes below. + panel may have several rows describing the whole alignment. The 4 + standard annotations Conservation, Quality, + Occupancy and Consensus for the alignment may + be shown or hidden by default using the checkboxes adjacent and + below.
Show group: Conservation and Consensus controls the display @@ -180,6 +184,33 @@ by Annotation... is selected from the alignment window's colours menu.
++ "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 @@ -260,7 +291,11 @@ The Custom only button limits the entries in the table to just those you have configured yourself via the Edit Links buttons. Press Show all to clear any filters. -
+
+The links table is prepoulated with persistent URLs for many common + bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from + the identifiers.org website, and the names and URLs are not + user editable. Read more about configuring URL links.