X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpreferences.html;h=cbbca28befeba1ab3edfdde1a93299bd26579247;hb=7692386ccfe778075dd83a753d30a7a27fe507be;hp=fb2183641dc866450d6945ee5349b577db00f18c;hpb=3c2ee3e1b9c507c7dfa550bc8546a43ff305f85a;p=jalview.git diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index fb21836..cbbca28 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. +
Show group: Conservation and Consensus controls the display @@ -180,6 +182,33 @@ 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 +289,11 @@ 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.
@@ -332,7 +365,7 @@ and PDB file association (if available). The Jalview id/start-end option is ignored if Modeller output is selected.- Editing Preferences tab + "Editing" Preferences tab
There are currently three options available which can be selected / deselected.
@@ -352,7 +385,13 @@ Sort with New Tree - When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment. --
+ +
If you have installed HMMER tools (available from hmmer.org), + then you should specify on this screen the location of the installation (the path to the folder + containing binary executable programs). Double-click in the input field to open a file browser.
+When this path is configured, the HMMER menu will be + enabled in the Alignment window.