X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Ffeaturesettings.html;h=9335d93e7ac4b06352f1f1297c763eebec17d524;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=7c4840d781bc27437736100c6a8c828bc8ddc4a7;hpb=8e068512cd4573dc4388dfca63072c95f294ef84;p=jalview.git diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html index 7c4840d..9335d93 100755 --- a/help/html/features/featuresettings.html +++ b/help/html/features/featuresettings.html @@ -1,4 +1,22 @@ +
The top section of the dialog box lists all the sequence feature groups, along with a tickbox for each that controls whether its features are displayed. The table in the middle lists all the features in the -currently selected groups, along with their display colour and whether +currently selected groups, along with their display style and whether they are currently being displayed (only the ticked features and groups -are displayed). You can change the colour used -for a feature in the associated alignment by clicking on its colour box.
-Feature settings pop-up menu
+are displayed). You can change the colour or
+shading style used for a feature in the associated alignment by clicking
+on its colour box.
+ Selecting alignment columns by feature
+ Double-click a feature to add all the columns where
+ that feature is found to the current column selection. Shift+Double-click
+ will add all the columns where that feature is not
+ found. You can also find these options in the feature's pop-up menu
+ (see below).
+ Select columns by feature was added in Jalview 2.8.1
+
Feature settings pop-up menu
Right-click on a feature to open a pop-up menu that
allows you to sort the alignment or current selection using that feature
-type (see below), or create a feature colourscheme based on either the
+type (see below), or toggle the type of colouring used for the feature.
+Features may be highlighted with either a single colour or a feature colourscheme based on either the
scores associated with that feature or from the feature's description
(e.g. to distinguish different names associated with a DOMAIN feature).
Ordering alignment by features
-The 'Order by Score' and 'Order by Density' buttons will order the
+The 'Seq Sort by Score' and 'Seq Sort by Density' buttons will sort the
alignment based on the average score or total number of currently active
-features and groups on each sequence.
-Feature sorting and colour feature by score and description was
-introduced in jalview 2.4.1
Transparency and Feature Ordering
It is important to realise that sequence features are often not